"." , user_incar_settings = { "LWAVE" : True , "EDIFF" : 1e-6 },
ediff_per_atom = False )
settings . extend ([
- { "dict" : "INCAR" ,
+ { "dict" : "INCAR" ,
"action" : { "_set" : dict ( vis . incar )}},
{ 'dict' : 'KPOINTS' ,
'action' : { '_set' : vis . kpoints . as_dict ()}}])
@@ -197,8 +197,7 @@ Source code for custodian.cli.run_vasp
"LDAUU" : [ u * f for u in ldauu ]}}})
copy_magmom = True
ramps += 1
- elif job_type . startswith ( "quick_relax" ) or job_type . startswith ( \
- "quickrelax" ):
+ elif job_type . startswith ( "quick_relax" ) or job_type . startswith ( "quickrelax" ):
kpoints = vinput [ "KPOINTS" ]
incar = vinput [ "INCAR" ]
structure = vinput [ "POSCAR" ] . structure
@@ -214,7 +213,7 @@ Source code for custodian.cli.run_vasp
"action" : { "_set" : kpoints . as_dict ()}})
# lattice vectors with length < 9 will get >1 KPOINT
low_kpoints = Kpoints . gamma_automatic (
- [ max ( int ( 18 / l ), 1 ) for l in structure . lattice . abc ])
+ [ max ( int ( 18 / l ), 1 ) for l in structure . lattice . abc ])
settings . extend ([
{ "dict" : "INCAR" ,
"action" : { "_set" : { "ISMEAR" : 0 }}},
@@ -284,7 +283,6 @@ Source code for custodian.cli.run_vasp
help = "Set to true to turn off auto_npar. Useful for certain machines "
"and calculations where you want absolute control." )
-
parser . add_argument (
"-z" , "--gzip" , dest = "gzip" , action = "store_true" ,
help = "Add this option to gzip the final output. Do not gzip if you "
@@ -310,7 +308,7 @@ Source code for custodian.cli.run_vasp
)
parser . add_argument (
- "-me" , "--max-errors" , dest = "max_errors" , nargs = "?" ,
+ "-me" , "--max-errors" , dest = "max_errors" , nargs = "?" ,
default = 10 , type = int ,
help = "Maximum number of errors to allow before quitting" )
diff --git a/docs/_modules/custodian/custodian.html b/docs/_modules/custodian/custodian.html
index 0aa53828..3dfae35e 100644
--- a/docs/_modules/custodian/custodian.html
+++ b/docs/_modules/custodian/custodian.html
@@ -4,7 +4,7 @@
custodian.custodian — custodian 2019.8.23 documentation
+ custodian.custodian — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »Source code for custodian.custodian
from abc import ABCMeta , abstractmethod
from itertools import islice
import warnings
-from pprint import pformat
from ast import literal_eval
-import six
-
from .utils import get_execution_host_info
from monty.tempfile import ScratchDir
@@ -88,7 +85,6 @@ Source code for custodian.custodian
__email__ = "ongsp@ucsd.edu"
__date__ = "Sep 17 2014"
-
logger = logging . getLogger ( __name__ )
if "SENTRY_DSN" in os . environ :
@@ -98,17 +94,17 @@ Source code for custodian.custodian
# will not be used.
import sentry_sdk
+
sentry_sdk . init ( dsn = os . environ [ "SENTRY_DSN" ])
-
+
with sentry_sdk . configure_scope () as scope :
-
+
from getpass import getuser
+
try :
scope . user = { "username" : getuser ()}
- except :
+ except Exception :
pass
-
-
# Sentry.io is a service to aggregate logs remotely, this is useful
# for Custodian to get statistics on which errors are most common.
@@ -128,17 +124,20 @@ Source code for custodian.custodian
if SENTRY_DSN :
import sentry_sdk
+
sentry_sdk . init ( dsn = SENTRY_DSN )
-
+
with sentry_sdk . configure_scope () as scope :
-
+
from getpass import getuser
+
try :
scope . user = { "username" : getuser ()}
- except :
+ except Exception :
pass
-
+
import socket
+
scope . set_tag ( "hostname" , socket . gethostname ())
@@ -293,7 +292,7 @@ Source code for custodian.custodian
try :
Custodian . _delete_checkpoints ( cwd )
n = os . path . join ( cwd , "custodian.chk. {} .tar.gz" . format ( index ))
- with tarfile . open ( n , mode = "w:gz" , compresslevel = 3 ) as f :
+ with tarfile . open ( n , mode = "w:gz" , compresslevel = 3 ) as f :
f . add ( cwd , arcname = '.' )
logger . info ( "Checkpoint written to {} " . format ( n ))
except Exception as ex :
@@ -713,7 +712,7 @@ Source code for custodian.custodian
self . run_log [ - 1 ][ "max_errors_per_handler" ] = True
raise MaxCorrectionsPerHandlerError ( msg , True , h . max_num_corrections , h )
else :
- logger . warning ( msg + " Correction not applied." )
+ logger . warning ( msg + " Correction not applied." )
continue
if terminate_func is not None and h . is_terminating :
logger . info ( "Terminating job" )
@@ -744,7 +743,7 @@ Source code for custodian.custodian
return len ( corrections ) > 0 [docs] class Job ( six . with_metaclass ( ABCMeta , MSONable )):
+
[docs] class Job ( MSONable ):
"""
Abstract base class defining the interface for a Job.
"""
@@ -827,7 +826,7 @@
Source code for custodian.custodian
fixed maximum number of times on a single job (i.e. the counter is reset
at the beginning of each job). If the maximum number is reached the code
will either raise a MaxCorrectionsPerHandlerError (raise_on_max==True) or stops
- considering the correction (raise_on_max==False). If max_num_corrections
+ considering the correction (raise_on_max==False). If max_num_corrections
is None this option is not considered. These options can be overridden
as class attributes of the subclass or as customizable options setting
an instance attribute from __init__.
@@ -885,7 +884,7 @@ Source code for custodian.custodian
self . _num_applied_corrections = value [docs] class Validator ( six . with_metaclass ( ABCMeta , MSONable )):
+
[docs] class Validator ( MSONable ):
"""
Abstract base class defining the interface for a Validator. A Validator
differs from an ErrorHandler in that it does not correct a run and is run
diff --git a/docs/_modules/custodian/feff/handlers.html b/docs/_modules/custodian/feff/handlers.html
index 41572ad8..34efe487 100644
--- a/docs/_modules/custodian/feff/handlers.html
+++ b/docs/_modules/custodian/feff/handlers.html
@@ -4,7 +4,7 @@
-
custodian.feff.handlers — custodian 2019.8.23 documentation
+
custodian.feff.handlers — custodian 2019.8.24 documentation
@@ -37,7 +37,7 @@
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »
@@ -118,8 +118,8 @@
Source code for custodian.feff.handlers
nmix = scf_values [ 4 ]
actions = []
- #Add RESTART card to PARAMETERS
- if not "RESTART" in feff_input . tags :
+ # Add RESTART card to PARAMETERS
+ if "RESTART" not in feff_input . tags :
actions . append ({ "dict" : "PARAMETERS" ,
"action" : { "_set" : { "RESTART" : []}}})
diff --git a/docs/_modules/custodian/feff/interpreter.html b/docs/_modules/custodian/feff/interpreter.html
index 2717bfb8..427fe659 100644
--- a/docs/_modules/custodian/feff/interpreter.html
+++ b/docs/_modules/custodian/feff/interpreter.html
@@ -4,7 +4,7 @@
custodian.feff.interpreter — custodian 2019.8.23 documentation
+ custodian.feff.interpreter — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »
@@ -55,7 +55,6 @@
Source code for custodian.feff.interpreter
from custodian.ansible.actions import FileActions , DictActions
from custodian.ansible.interpreter import Modder
from pymatgen.io.feff.sets import FEFFDictSet
-import six
import os
@@ -107,7 +106,7 @@ Source code for custodian.feff.interpreter
feff_input = " \n\n " . join ( str ( feff [ k ]) for k in
[ "HEADER" , "PARAMETERS" , "POTENTIALS" , "ATOMS" ]
if k in feff )
- for k , v in six . iteritems ( feff ):
+ for k , v in feff . items ():
with open ( os . path . join ( '.' , k ), "w" ) as f :
f . write ( str ( v ))
diff --git a/docs/_modules/custodian/feff/jobs.html b/docs/_modules/custodian/feff/jobs.html
index a2790500..c04b5d8e 100644
--- a/docs/_modules/custodian/feff/jobs.html
+++ b/docs/_modules/custodian/feff/jobs.html
@@ -4,7 +4,7 @@
custodian.feff.jobs — custodian 2019.8.23 documentation
+ custodian.feff.jobs — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »custodian.nwchem.handlers — custodian 2019.8.23 documentation
+ custodian.nwchem.handlers — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »
@@ -57,7 +57,6 @@
Source code for custodian.nwchem.handlers
for B3LYP DFT jobs.
"""
-
__author__ = "Shyue Ping Ong"
__version__ = "0.1"
__maintainer__ = "Shyue Ping Ong"
@@ -65,7 +64,6 @@ Source code for custodian.nwchem.handlers
__status__ = "Beta"
__date__ = "5/20/13"
-
from custodian.custodian import ErrorHandler
from custodian.utils import backup
from pymatgen.io.nwchem import NwOutput , NwInput
@@ -132,7 +130,7 @@ Source code for custodian.nwchem.handlers
t . theory_directives [ "cgmin" ] = ""
for t in nwi . tasks :
if t . operation . startswith ( "freq" ):
- #You cannot calculate hessian with cgmin.
+ # You cannot calculate hessian with cgmin.
t . theory_directives [ "nocgmin" ] = ""
action = { "_set" : { "tasks" : [ t . as_dict () for t in nwi . tasks ]}}
actions . append ( action )
diff --git a/docs/_modules/custodian/nwchem/jobs.html b/docs/_modules/custodian/nwchem/jobs.html
index 0a597352..f5cf4d15 100644
--- a/docs/_modules/custodian/nwchem/jobs.html
+++ b/docs/_modules/custodian/nwchem/jobs.html
@@ -4,7 +4,7 @@
custodian.nwchem.jobs — custodian 2019.8.23 documentation
+ custodian.nwchem.jobs — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »custodian.qchem.handlers — custodian 2019.8.23 documentation
+ custodian.qchem.handlers — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »Source code for custodian.qchem.handlers
# Checks output file for errors.
self . outdata = QCOutput ( self . output_file ) . data
self . errors = self . outdata . get ( "errors" )
+ self . warnings = self . outdata . get ( "warnings" )
# If we aren't out of optimization cycles, but we were in the past, reset the history
if "out_of_opt_cycles" not in self . errors and len ( self . opt_error_history ) > 0 :
self . opt_error_history = []
@@ -127,12 +128,18 @@ Source code for custodian.qchem.handlers
self . scf_max_cycles ):
self . qcinp . rem [ "max_scf_cycles" ] = self . scf_max_cycles
actions . append ({ "max_scf_cycles" : self . scf_max_cycles })
+ elif self . qcinp . rem . get ( "thresh" , "10" ) != "14" :
+ self . qcinp . rem [ "thresh" ] = "14"
+ actions . append ({ "thresh" : "14" })
elif self . qcinp . rem . get ( "scf_algorithm" , "diis" ) . lower () == "diis" :
- self . qcinp . rem [ "scf_algorithm" ] = "gdm"
- actions . append ({ "scf_algorithm" : "gdm" })
- elif self . qcinp . rem . get ( "scf_algorithm" , "gdm" ) . lower () == "gdm" :
self . qcinp . rem [ "scf_algorithm" ] = "diis_gdm"
actions . append ({ "scf_algorithm" : "diis_gdm" })
+ elif self . qcinp . rem . get ( "scf_algorithm" , "diis" ) . lower () == "diis_gdm" :
+ self . qcinp . rem [ "scf_algorithm" ] = "gdm"
+ actions . append ({ "scf_algorithm" : "gdm" })
+ elif self . qcinp . rem . get ( "scf_guess_always" , "none" ) . lower () != "true" :
+ self . qcinp . rem [ "scf_guess_always" ] = True
+ actions . append ({ "scf_guess_always" : True })
else :
print (
"More advanced changes may impact the SCF result. Use the SCF error handler"
@@ -149,8 +156,16 @@ Source code for custodian.qchem.handlers
self . qcinp . molecule = self . outdata . get (
"molecule_from_last_geometry" )
actions . append ({ "molecule" : "molecule_from_last_geometry" })
- # If already at geom_max_cycles, often can just get convergence by restarting
- # from the geometry of the last cycle. But we'll also save any structural
+ elif self . qcinp . rem . get ( "thresh" , "10" ) != "14" :
+ self . qcinp . rem [ "thresh" ] = "14"
+ actions . append ({ "thresh" : "14" })
+ # Will need to try and implement this dmax handler below when I have more time
+ # to fix the tests and the general handling procedure.
+ # elif self.qcinp.rem.get("geom_opt_dmax",300) != 150:
+ # self.qcinp.rem["geom_opt_dmax"] = 150
+ # actions.append({"geom_opt_dmax": "150"})
+ # If already at geom_max_cycles, thresh 14, and dmax 150, often can just get convergence
+ # by restarting from the geometry of the last cycle. But we'll also save any structural
# changes that happened along the way.
else :
self . opt_error_history += [ self . outdata [ "structure_change" ]]
@@ -169,27 +184,30 @@ Source code for custodian.qchem.handlers
self . qcinp . molecule = self . outdata . get (
"molecule_from_last_geometry" )
actions . append ({ "molecule" : "molecule_from_last_geometry" })
- elif self . qcinp . rem . get ( "scf_algorithm" , "diis" ) . lower () == "diis" :
- self . qcinp . rem [ "scf_algorithm" ] = "rca_diis"
- actions . append ({ "scf_algorithm" : "rca_diis" })
- if self . qcinp . rem . get ( "gen_scfman" ):
- self . qcinp . rem [ "gen_scfman" ] = False
- actions . append ({ "gen_scfman" : False })
+ elif self . qcinp . rem . get ( "thresh" , "10" ) != "14" :
+ self . qcinp . rem [ "thresh" ] = "14"
+ actions . append ({ "thresh" : "14" })
else :
print (
"Use a different initial guess? Perhaps a different basis?"
)
- elif "linear_dependent_basis" in self . errors :
- # DIIS -> RCA_DIIS. If already RCA_DIIS, change basis?
- if self . qcinp . rem . get ( "scf_algorithm" , "diis" ) . lower () == "diis" :
- self . qcinp . rem [ "scf_algorithm" ] = "rca_diis"
- actions . append ({ "scf_algorithm" : "rca_diis" })
- if self . qcinp . rem . get ( "gen_scfman" ):
- self . qcinp . rem [ "gen_scfman" ] = False
- actions . append ({ "gen_scfman" : False })
+ elif "premature_end_FileMan_error" in self . errors :
+ if self . qcinp . rem . get ( "thresh" , "10" ) != "14" :
+ self . qcinp . rem [ "thresh" ] = "14"
+ actions . append ({ "thresh" : "14" })
+ elif self . qcinp . rem . get ( "scf_guess_always" , "none" ) . lower () != "true" :
+ self . qcinp . rem [ "scf_guess_always" ] = True
+ actions . append ({ "scf_guess_always" : True })
+ else :
+ print ( "We're in a bad spot if we get a FileMan error while always generating a new SCF guess..." )
+
+ elif "hessian_eigenvalue_error" in self . errors :
+ if self . qcinp . rem . get ( "thresh" , "10" ) != "14" :
+ self . qcinp . rem [ "thresh" ] = "14"
+ actions . append ({ "thresh" : "14" })
else :
- print ( "Perhaps use a better basis?" )
+ print ( "Not sure how to fix hessian_eigenvalue_error if thresh is already 14!" )
elif "failed_to_transform_coords" in self . errors :
# Check for symmetry flag in rem. If not False, set to False and rerun.
@@ -211,34 +229,45 @@ Source code for custodian.qchem.handlers
elif "failed_to_read_input" in self . errors :
# Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
- actions . append ({ "rerun job as-is" })
-
- elif "IO_error" in self . errors :
- # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
- actions . append ({ "rerun job as-is" })
+ actions . append ({ "rerun_job_no_changes" : True })
elif "read_molecule_error" in self . errors :
# Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
- actions . append ({ "rerun job as-is" })
+ actions . append ({ "rerun_job_no_changes" : True })
elif "never_called_qchem" in self . errors :
# Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
- actions . append ({ "rerun job as-is" })
+ actions . append ({ "rerun_job_no_changes" : True })
+
+ elif "licensing_error" in self . errors :
+ # Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
+ actions . append ({ "rerun_job_no_changes" : True })
elif "unknown_error" in self . errors :
- print ( "Examine error message by hand." )
- return { "errors" : self . errors , "actions" : None }
+ if self . qcinp . rem . get ( "scf_guess" , "none" ) . lower () == "read" :
+ del self . qcinp . rem [ "scf_guess" ]
+ actions . append ({ "scf_guess" : "deleted" })
+ elif self . qcinp . rem . get ( "thresh" , "10" ) != "14" :
+ self . qcinp . rem [ "thresh" ] = "14"
+ actions . append ({ "thresh" : "14" })
+ else :
+ print ( "Unknown error. Examine output and log files by hand." )
+ return { "errors" : self . errors , "actions" : None }
else :
# You should never get here. If correct is being called then errors should have at least one entry,
# in which case it should have been caught by the if/elifs above.
- print (
- "If you get this message, something has gone terribly wrong!" )
+ print ( "Errors:" , self . errors )
+ print ( "Must have gotten an error which is correctly parsed but not included in the handler. FIX!!!" )
return { "errors" : self . errors , "actions" : None }
+ if { "molecule" : "molecule_from_last_geometry" } in actions and \
+ str ( self . qcinp . rem . get ( "geom_opt_hessian" )) . lower () == "read" :
+ del self . qcinp . rem [ "geom_opt_hessian" ]
+ actions . append ({ "geom_opt_hessian" : "deleted" })
os . rename ( self . input_file , self . input_file + ".last" )
self . qcinp . write_file ( self . input_file )
- return { "errors" : self . errors , "actions" : actions } return { "errors" : self . errors , "warnings" : self . warnings , "actions" : actions } [docs] class QChemSCFErrorHandler ( ErrorHandler ):
diff --git a/docs/_modules/custodian/qchem/jobs.html b/docs/_modules/custodian/qchem/jobs.html
index 81f8756a..dafdeae4 100644
--- a/docs/_modules/custodian/qchem/jobs.html
+++ b/docs/_modules/custodian/qchem/jobs.html
@@ -4,7 +4,7 @@
-
custodian.qchem.jobs — custodian 2019.8.23 documentation
+
custodian.qchem.jobs — custodian 2019.8.24 documentation
@@ -37,7 +37,7 @@
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »Source code for custodian.qchem.jobs
import shutil
import copy
import subprocess
+import random
import numpy as np
from pymatgen.core import Molecule
from pymatgen.io.qchem.inputs import QCInput
-from pymatgen.io.qchem.outputs import QCOutput
+from pymatgen.io.qchem.outputs import QCOutput , check_for_structure_changes
from pymatgen.analysis.graphs import MoleculeGraph
from pymatgen.analysis.local_env import OpenBabelNN
from custodian.custodian import Job
-
__author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath"
__copyright__ = "Copyright 2018, The Materials Project"
__version__ = "0.1"
@@ -92,9 +92,9 @@ Source code for custodian.qchem.jobs
output_file = "mol.qout" ,
qclog_file = "mol.qclog" ,
suffix = "" ,
- scratch_dir = "/dev/shm/qcscratch/" ,
+ scratch_dir = os . getcwd (),
save_scratch = False ,
- save_name = "default_save_name" ,
+ save_name = "saved_scratch" ,
backup = True ):
"""
Args:
@@ -106,11 +106,11 @@ Source code for custodian.qchem.jobs
qclog_file (str): Name of the file to redirect the standard output
to. None means not to record the standard output.
suffix (str): String to append to the file in postprocess.
- scratch_dir (str): QCSCRATCH directory. Defaults to "/dev/shm/qcscratch/".
- save_scratch (bool): Whether to save scratch directory contents.
+ scratch_dir (str): QCSCRATCH directory. Defaults to current directory.
+ save_scratch (bool): Whether to save basic scratch directory contents.
Defaults to False.
save_name (str): Name of the saved scratch directory. Defaults to
- to "default_save_name".
+ to "saved_scratch".
backup (bool): Whether to backup the initial input file. If True, the
input will be copied with a ".orig" appended. Defaults to True.
"""
@@ -128,40 +128,27 @@ Source code for custodian.qchem.jobs
@property
def current_command ( self ):
- multimode_index = 0
+ multi = { "openmp" : "-nt" , "mpi" : "-np" }
+ if self . multimode not in multi :
+ raise RuntimeError ( "ERROR: Multimode should only be set to openmp or mpi" )
+ command = [ multi [ self . multimode ], str ( self . max_cores ), self . input_file , self . output_file ]
if self . save_scratch :
- command = [
- "-save" , "" ,
- str ( self . max_cores ), self . input_file , self . output_file ,
- self . save_name
- ]
- multimode_index = 1
- else :
- command = [
- "" , str ( self . max_cores ), self . input_file , self . output_file
- ]
- if self . multimode == 'openmp' :
- command [ multimode_index ] = "-nt"
- elif self . multimode == 'mpi' :
- command [ multimode_index ] = "-np"
- else :
- print ( "ERROR: Multimode should only be set to openmp or mpi" )
+ command . append ( self . save_name )
command = self . qchem_command + command
- return command
+ com_str = ""
+ for part in command :
+ com_str = com_str + " " + part
+ return com_str
[docs] def setup ( self ):
if self . backup :
shutil . copy ( self . input_file , " {} .orig" . format ( self . input_file ))
-
os . putenv ( "QCSCRATCH" , self . scratch_dir )
+
os . environ [ "QCSCRATCH" ] = self . scratch_dir
if self . multimode == 'openmp' :
-
os . putenv ( 'QCTHREADS' , str ( self . max_cores ))
-
os . putenv ( 'OMP_NUM_THREADS' , str ( self . max_cores )) os . environ [ 'QCTHREADS' ] = str ( self . max_cores )
+ os . environ [ 'OMP_NUM_THREADS' ] = str ( self . max_cores ) [docs] def postprocess ( self ):
-
if self . save_scratch :
-
shutil . copytree (
-
os . path . join ( self . scratch_dir , self . save_name ),
-
os . path . join ( os . path . dirname ( self . input_file ), self . save_name ))
if self . suffix != "" :
shutil . move ( self . input_file , self . input_file + self . suffix )
shutil . move ( self . output_file , self . output_file + self . suffix )
@@ -174,8 +161,12 @@
Source code for custodian.qchem.jobs
Returns:
(subprocess.Popen) Used for monitoring.
"""
+ myrand = str ( random . randint ( 1 , 1000000000 ))
+ mydir = os . path . join ( "/tmp" , "qchem" + myrand )
+ os . mkdir ( mydir )
+ os . environ [ "QCLOCALSCR" ] = mydir
qclog = open ( self . qclog_file , 'w' )
- p = subprocess . Popen ( self . current_command , stdout = qclog )
+ p = subprocess . Popen ( self . current_command , stdout = qclog , shell = True )
return p [docs] @classmethod
@@ -188,6 +179,7 @@
Source code for custodian.qchem.jobs
max_iterations = 10 ,
max_molecule_perturb_scale = 0.3 ,
check_connectivity = True ,
+ linked = True ,
** QCJob_kwargs ):
"""
Optimize a structure and calculate vibrational frequencies to check if the
@@ -209,121 +201,272 @@ Source code for custodian.qchem.jobs
**QCJob_kwargs: Passthrough kwargs to QCJob. See
:class:`custodian.qchem.jobs.QCJob`.
"""
-
- min_molecule_perturb_scale = 0.1
- scale_grid = 10
- perturb_scale_grid = (
- max_molecule_perturb_scale - min_molecule_perturb_scale
- ) / scale_grid
-
if not os . path . exists ( input_file ):
raise AssertionError ( 'Input file must be present!' )
- orig_opt_input = QCInput . from_file ( input_file )
- orig_opt_rem = copy . deepcopy ( orig_opt_input . rem )
- orig_freq_rem = copy . deepcopy ( orig_opt_input . rem )
- orig_freq_rem [ "job_type" ] = "freq"
- first = True
- reversed_direction = False
- num_neg_freqs = []
-
- for ii in range ( max_iterations ):
- yield ( QCJob (
- qchem_command = qchem_command ,
- multimode = multimode ,
- input_file = input_file ,
- output_file = output_file ,
- qclog_file = qclog_file ,
- suffix = ".opt_" + str ( ii ),
- backup = first ,
- ** QCJob_kwargs ))
- first = False
- opt_outdata = QCOutput ( output_file + ".opt_" + str ( ii )) . data
- if opt_outdata [ "structure_change" ] == "unconnected_fragments" and not opt_outdata [ "completion" ]:
- print ( "Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..." )
- break
- else :
- freq_QCInput = QCInput (
- molecule = opt_outdata . get ( "molecule_from_optimized_geometry" ),
- rem = orig_freq_rem ,
- opt = orig_opt_input . opt ,
- pcm = orig_opt_input . pcm ,
- solvent = orig_opt_input . solvent )
- freq_QCInput . write_file ( input_file )
+
+ if linked :
+
+ energy_diff_cutoff = 0.0000001
+
+ orig_input = QCInput . from_file ( input_file )
+ freq_rem = copy . deepcopy ( orig_input . rem )
+ freq_rem [ "job_type" ] = "freq"
+ opt_rem = copy . deepcopy ( orig_input . rem )
+ opt_rem [ "geom_opt_hessian" ] = "read"
+ opt_rem [ "scf_guess_always" ] = True
+ first = True
+ energy_history = []
+
+ for ii in range ( max_iterations ):
yield ( QCJob (
qchem_command = qchem_command ,
multimode = multimode ,
input_file = input_file ,
output_file = output_file ,
qclog_file = qclog_file ,
- suffix = ".freq_" + str ( ii ),
+ suffix = ".opt_" + str ( ii ),
+ scratch_dir = os . getcwd (),
+ save_scratch = True ,
+ save_name = "chain_scratch" ,
backup = first ,
** QCJob_kwargs ))
- outdata = QCOutput ( output_file + ".freq_" + str ( ii )) . data
- errors = outdata . get ( "errors" )
- if len ( errors ) != 0 :
- raise AssertionError ( 'No errors should be encountered while flattening frequencies!' )
- if outdata . get ( 'frequencies' )[ 0 ] > 0.0 :
- print ( "All frequencies positive!" )
+ opt_outdata = QCOutput ( output_file + ".opt_" + str ( ii )) . data
+ first = False
+ if opt_outdata [ "structure_change" ] == "unconnected_fragments" and not opt_outdata [ "completion" ]:
+ print ( "Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..." )
break
else :
- num_neg_freqs += [ sum ( 1 for freq in outdata . get ( 'frequencies' ) if freq < 0 )]
- if len ( num_neg_freqs ) > 1 :
- if num_neg_freqs [ - 1 ] == num_neg_freqs [ - 2 ] and not reversed_direction :
- reversed_direction = True
- elif num_neg_freqs [ - 1 ] == num_neg_freqs [ - 2 ] and reversed_direction :
- if len ( num_neg_freqs ) < 3 :
- raise AssertionError ( "ERROR: This should only be possible after at least three frequency flattening iterations! Exiting..." )
- else :
- raise Exception ( "ERROR: Reversing the perturbation direction still could not flatten any frequencies. Exiting..." )
- elif num_neg_freqs [ - 1 ] != num_neg_freqs [ - 2 ] and reversed_direction :
- reversed_direction = False
-
- negative_freq_vecs = outdata . get ( "frequency_mode_vectors" )[ 0 ]
- structure_successfully_perturbed = False
-
- for molecule_perturb_scale in np . arange (
- max_molecule_perturb_scale , min_molecule_perturb_scale ,
- - perturb_scale_grid ):
- new_coords = perturb_coordinates (
- old_coords = outdata . get ( "initial_geometry" ),
- negative_freq_vecs = negative_freq_vecs ,
- molecule_perturb_scale = molecule_perturb_scale ,
- reversed_direction = reversed_direction )
- new_molecule = Molecule (
- species = outdata . get ( 'species' ),
- coords = new_coords ,
- charge = outdata . get ( 'charge' ),
- spin_multiplicity = outdata . get ( 'multiplicity' ))
- if check_connectivity :
- old_molgraph = MoleculeGraph . with_local_env_strategy ( outdata . get ( "initial_molecule" ),
- OpenBabelNN (),
- reorder = False ,
- extend_structure = False )
- new_molgraph = MoleculeGraph . with_local_env_strategy ( new_molecule ,
- OpenBabelNN (),
- reorder = False ,
- extend_structure = False )
- if old_molgraph . isomorphic_to ( new_molgraph ):
- structure_successfully_perturbed = True
+ energy_history . append ( opt_outdata . get ( "final_energy" ))
+ freq_QCInput = QCInput (
+ molecule = opt_outdata . get ( "molecule_from_optimized_geometry" ),
+ rem = freq_rem ,
+ opt = orig_input . opt ,
+ pcm = orig_input . pcm ,
+ solvent = orig_input . solvent ,
+ smx = orig_input . smx )
+ freq_QCInput . write_file ( input_file )
+ yield ( QCJob (
+ qchem_command = qchem_command ,
+ multimode = multimode ,
+ input_file = input_file ,
+ output_file = output_file ,
+ qclog_file = qclog_file ,
+ suffix = ".freq_" + str ( ii ),
+ scratch_dir = os . getcwd (),
+ save_scratch = True ,
+ save_name = "chain_scratch" ,
+ backup = first ,
+ ** QCJob_kwargs ))
+ outdata = QCOutput ( output_file + ".freq_" + str ( ii )) . data
+ errors = outdata . get ( "errors" )
+ if len ( errors ) != 0 :
+ raise AssertionError ( 'No errors should be encountered while flattening frequencies!' )
+ if outdata . get ( 'frequencies' )[ 0 ] > 0.0 :
+ print ( "All frequencies positive!" )
+ break
+ elif abs ( outdata . get ( 'frequencies' )[ 0 ]) < 15.0 and outdata . get ( 'frequencies' )[ 1 ] > 0.0 :
+ print ( "One negative frequency smaller than 15.0 - not worth further flattening!" )
+ break
+ else :
+ if len ( energy_history ) > 1 :
+ if abs ( energy_history [ - 1 ] - energy_history [ - 2 ]) < energy_diff_cutoff :
+ print ( "Energy change below cutoff!" )
break
- if not structure_successfully_perturbed :
- raise Exception (
- "ERROR: Unable to perturb coordinates to remove negative frequency without changing the connectivity! Exiting..."
- )
-
- new_opt_QCInput = QCInput (
- molecule = new_molecule ,
- rem = orig_opt_rem ,
+ opt_QCInput = QCInput (
+ molecule = opt_outdata . get ( "molecule_from_optimized_geometry" ),
+ rem = opt_rem ,
+ opt = orig_input . opt ,
+ pcm = orig_input . pcm ,
+ solvent = orig_input . solvent ,
+ smx = orig_input . smx )
+ opt_QCInput . write_file ( input_file )
+ if os . path . exists ( os . path . join ( os . getcwd (), "chain_scratch" )):
+ shutil . rmtree ( os . path . join ( os . getcwd (), "chain_scratch" ))
+
+ else :
+ if not os . path . exists ( input_file ):
+ raise AssertionError ( 'Input file must be present!' )
+ orig_opt_input = QCInput . from_file ( input_file )
+ orig_opt_rem = copy . deepcopy ( orig_opt_input . rem )
+ orig_freq_rem = copy . deepcopy ( orig_opt_input . rem )
+ orig_freq_rem [ "job_type" ] = "freq"
+ first = True
+ history = []
+
+ for ii in range ( max_iterations ):
+ yield ( QCJob (
+ qchem_command = qchem_command ,
+ multimode = multimode ,
+ input_file = input_file ,
+ output_file = output_file ,
+ qclog_file = qclog_file ,
+ suffix = ".opt_" + str ( ii ),
+ backup = first ,
+ ** QCJob_kwargs ))
+ opt_outdata = QCOutput ( output_file + ".opt_" + str ( ii )) . data
+ if first :
+ orig_species = copy . deepcopy ( opt_outdata . get ( 'species' ))
+ orig_charge = copy . deepcopy ( opt_outdata . get ( 'charge' ))
+ orig_multiplicity = copy . deepcopy ( opt_outdata . get ( 'multiplicity' ))
+ orig_energy = copy . deepcopy ( opt_outdata . get ( 'final_energy' ))
+ first = False
+ if opt_outdata [ "structure_change" ] == "unconnected_fragments" and not opt_outdata [ "completion" ]:
+ print ( "Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..." )
+ break
+ else :
+ freq_QCInput = QCInput (
+ molecule = opt_outdata . get ( "molecule_from_optimized_geometry" ),
+ rem = orig_freq_rem ,
opt = orig_opt_input . opt ,
pcm = orig_opt_input . pcm ,
- solvent = orig_opt_input . solvent )
- new_opt_QCInput . write_file ( input_file )
+
solvent = orig_opt_input . solvent ,
+
smx = orig_opt_input . smx )
+
freq_QCInput . write_file ( input_file )
+
yield ( QCJob (
+
qchem_command = qchem_command ,
+
multimode = multimode ,
+
input_file = input_file ,
+
output_file = output_file ,
+
qclog_file = qclog_file ,
+
suffix = ".freq_" + str ( ii ),
+
backup = first ,
+
** QCJob_kwargs ))
+
outdata = QCOutput ( output_file + ".freq_" + str ( ii )) . data
+
errors = outdata . get ( "errors" )
+
if len ( errors ) != 0 :
+
raise AssertionError ( 'No errors should be encountered while flattening frequencies!' )
+
if outdata . get ( 'frequencies' )[ 0 ] > 0.0 :
+
print ( "All frequencies positive!" )
+
if opt_outdata . get ( 'final_energy' ) > orig_energy :
+
print ( "WARNING: Energy increased during frequency flattening!" )
+
break
+
else :
+
hist = {}
+
hist [ "molecule" ] = copy . deepcopy ( outdata . get ( "initial_molecule" ))
+
hist [ "geometry" ] = copy . deepcopy ( outdata . get ( "initial_geometry" ))
+
hist [ "frequencies" ] = copy . deepcopy ( outdata . get ( "frequencies" ))
+
hist [ "frequency_mode_vectors" ] = copy . deepcopy ( outdata . get ( "frequency_mode_vectors" ))
+
hist [ "num_neg_freqs" ] = sum ( 1 for freq in outdata . get ( "frequencies" ) if freq < 0 )
+
hist [ "energy" ] = copy . deepcopy ( opt_outdata . get ( "final_energy" ))
+
hist [ "index" ] = len ( history )
+
hist [ "children" ] = []
+
history . append ( hist )
+
+
ref_mol = history [ - 1 ][ "molecule" ]
+
geom_to_perturb = history [ - 1 ][ "geometry" ]
+
negative_freq_vecs = history [ - 1 ][ "frequency_mode_vectors" ][ 0 ]
+
reversed_direction = False
+
standard = True
+
+
# If we've found one or more negative frequencies in two consecutive iterations, let's dig in
+
# deeper:
+
if len ( history ) > 1 :
+
# Start by finding the latest iteration's parent:
+
if history [ - 1 ][ "index" ] in history [ - 2 ][ "children" ]:
+
parent_hist = history [ - 2 ]
+
history [ - 1 ][ "parent" ] = parent_hist [ "index" ]
+
elif history [ - 1 ][ "index" ] in history [ - 3 ][ "children" ]:
+
parent_hist = history [ - 3 ]
+
history [ - 1 ][ "parent" ] = parent_hist [ "index" ]
+
else :
+
raise AssertionError (
+
"ERROR: your parent should always be one or two iterations behind you! Exiting..." )
+
+
# if the number of negative frequencies has remained constant or increased from parent to
+
# child,
+
if history [ - 1 ][ "num_neg_freqs" ] >= parent_hist [ "num_neg_freqs" ]:
+
# check to see if the parent only has one child, aka only the positive perturbation has
+
# been tried,
+
# in which case just try the negative perturbation from the same parent
+
if len ( parent_hist [ "children" ]) == 1 :
+
ref_mol = parent_hist [ "molecule" ]
+
geom_to_perturb = parent_hist [ "geometry" ]
+
negative_freq_vecs = parent_hist [ "frequency_mode_vectors" ][ 0 ]
+
reversed_direction = True
+
standard = False
+
parent_hist [ "children" ] . append ( len ( history ))
+
# If the parent has two children, aka both directions have been tried, then we have to
+
# get creative:
+
elif len ( parent_hist [ "children" ]) == 2 :
+
# If we're dealing with just one negative frequency,
+
if parent_hist [ "num_neg_freqs" ] == 1 :
+
make_good_child_next_parent = False
+
if history [ parent_hist [ "children" ][ 0 ]][ "energy" ] < history [ - 1 ][ "energy" ]:
+
good_child = copy . deepcopy ( history [ parent_hist [ "children" ][ 0 ]])
+
else :
+
good_child = copy . deepcopy ( history [ - 1 ])
+
if good_child [ "num_neg_freqs" ] > 1 :
+
raise Exception (
+
"ERROR: Child with lower energy has more negative frequencies! "
+
"Exiting..." )
+
elif good_child [ "energy" ] < parent_hist [ "energy" ]:
+
make_good_child_next_parent = True
+
elif vector_list_diff ( good_child [ "frequency_mode_vectors" ][ 0 ],
+
parent_hist [ "frequency_mode_vectors" ][ 0 ]) > 0.2 :
+
make_good_child_next_parent = True
+
else :
+
raise Exception ( "ERROR: Good child not good enough! Exiting..." )
+
if make_good_child_next_parent :
+
good_child [ "index" ] = len ( history )
+
history . append ( good_child )
+
ref_mol = history [ - 1 ][ "molecule" ]
+
geom_to_perturb = history [ - 1 ][ "geometry" ]
+
negative_freq_vecs = history [ - 1 ][ "frequency_mode_vectors" ][ 0 ]
+
else :
+
raise Exception (
+
"ERROR: Can't deal with multiple neg frequencies yet! Exiting..." )
+
else :
+
raise AssertionError ( "ERROR: Parent cannot have more than two childen! Exiting..." )
+
# Implicitly, if the number of negative frequencies decreased from parent to child,
+
# continue normally.
+
if standard :
+
history [ - 1 ][ "children" ] . append ( len ( history ))
+
+
min_molecule_perturb_scale = 0.1
+
scale_grid = 10
+
perturb_scale_grid = (
+
max_molecule_perturb_scale - min_molecule_perturb_scale
+
) / scale_grid
+
+
structure_successfully_perturbed = False
+
for molecule_perturb_scale in np . arange (
+
max_molecule_perturb_scale , min_molecule_perturb_scale ,
+
- perturb_scale_grid ):
+
new_coords = perturb_coordinates (
+
old_coords = geom_to_perturb ,
+
negative_freq_vecs = negative_freq_vecs ,
+
molecule_perturb_scale = molecule_perturb_scale ,
+
reversed_direction = reversed_direction )
+
new_molecule = Molecule (
+
species = orig_species ,
+
coords = new_coords ,
+
charge = orig_charge ,
+
spin_multiplicity = orig_multiplicity )
+
if check_connectivity :
+
structure_successfully_perturbed = check_for_structure_changes (
+
ref_mol , new_molecule ) == "no_change"
+
if structure_successfully_perturbed :
+
break
+
if not structure_successfully_perturbed :
+
raise Exception (
+
"ERROR: Unable to perturb coordinates to remove negative frequency without changing "
+
"the connectivity! Exiting..."
+
)
+
+
new_opt_QCInput = QCInput (
+
molecule = new_molecule ,
+
rem = orig_opt_rem ,
+
opt = orig_opt_input . opt ,
+
pcm = orig_opt_input . pcm ,
+
solvent = orig_opt_input . solvent ,
+
smx = orig_opt_input . smx )
+
new_opt_QCInput . write_file ( input_file ) [docs] def perturb_coordinates ( old_coords , negative_freq_vecs , molecule_perturb_scale ,
reversed_direction ):
max_dis = max (
-
[ math . sqrt ( sum ([ x ** 2 for x in vec ])) for vec in negative_freq_vecs ])
+
[ math . sqrt ( sum ([ x ** 2 for x in vec ])) for vec in negative_freq_vecs ])
scale = molecule_perturb_scale / max_dis
normalized_vecs = [[ x * scale for x in vec ] for vec in negative_freq_vecs ]
direction = 1.0
@@ -331,6 +474,15 @@
Source code for custodian.qchem.jobs
direction = - 1.0
return [[ c + v * direction for c , v in zip ( coord , vec )]
for coord , vec in zip ( old_coords , normalized_vecs )]
+
+
+
[docs] def vector_list_diff ( vecs1 , vecs2 ):
+
diff = 0.0
+
if len ( vecs1 ) != len ( vecs2 ):
+
raise AssertionError ( "ERROR: Vectors must be of equal length! Exiting..." )
+
for ii , vec1 in enumerate ( vecs1 ):
+
diff += np . linalg . norm ( vecs2 [ ii ] - vec1 )
+
return diff custodian.utils — custodian 2019.8.23 documentation
+ custodian.utils — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »Source code for custodian.utils
try :
import socket
host = host or socket . gethostname ()
- except :
+ except Exception :
pass
return host or 'unknown' , cluster or 'unknown' custodian.vasp.handlers — custodian 2019.8.23 documentation
+ custodian.vasp.handlers — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »Source code for custodian.vasp.handlers
self . error_count = Counter ()
# threshold of number of atoms to treat the cell as large.
self . natoms_large_cell = natoms_large_cell
- self . errors_subset_to_catch = errors_subset_to_catch or \
- list ( VaspErrorHandler . error_msgs . keys ())
+ self . errors_subset_to_catch = errors_subset_to_catch or list ( VaspErrorHandler . error_msgs . keys ())
self . logger = logging . getLogger ( self . __class__ . __name__ )
[docs] def check ( self ):
@@ -222,7 +221,7 @@
Source code for custodian.vasp.handlers
try :
assert ( Outcar ( zpath ( os . path . join (
os . getcwd (), "OUTCAR" ))) . is_stopped is False )
- except :
+ except Exception :
self . error_count [ 'brmix' ] += 1
if self . error_count [ 'brmix' ] == 0 :
@@ -241,17 +240,14 @@ Source code for custodian.vasp.handlers
elif self . error_count [ 'brmix' ] == 2 and vi [ "KPOINTS" ] . style \
== Kpoints . supported_modes . Gamma :
actions . append ({ "dict" : "KPOINTS" ,
- "action" : { "_set" : { "generation_style" :
- "Monkhorst" }}})
+ "action" : { "_set" : { "generation_style" : "Monkhorst" }}})
actions . append ({ "dict" : "INCAR" ,
"action" : { "_unset" : { "IMIX" : 1 }}})
self . error_count [ 'brmix' ] += 1
- elif self . error_count [ 'brmix' ] in [ 2 , 3 ] and vi [ "KPOINTS" ] . style \
- == Kpoints . supported_modes . Monkhorst :
+ elif self . error_count [ 'brmix' ] in [ 2 , 3 ] and vi [ "KPOINTS" ] . style == Kpoints . supported_modes . Monkhorst :
actions . append ({ "dict" : "KPOINTS" ,
- "action" : { "_set" : { "generation_style" :
- "Gamma" }}})
+ "action" : { "_set" : { "generation_style" : "Gamma" }}})
actions . append ({ "dict" : "INCAR" ,
"action" : { "_unset" : { "IMIX" : 1 }}})
self . error_count [ 'brmix' ] += 1
@@ -294,7 +290,7 @@ Source code for custodian.vasp.handlers
try :
oszicar = Oszicar ( "OSZICAR" )
nsteps = len ( oszicar . ionic_steps )
- except :
+ except Exception :
nsteps = 0
if nsteps >= 1 :
@@ -406,13 +402,11 @@ Source code for custodian.vasp.handlers
"action" : { "_set" : { "NBANDS" : int ( 1.1 * nbands )}}})
if "pssyevx" in self . errors :
- actions . append ({ "dict" : "INCAR" , "action" :
- { "_set" : { "ALGO" : "Normal" }}})
+ actions . append ({ "dict" : "INCAR" , "action" : { "_set" : { "ALGO" : "Normal" }}})
if "eddrmm" in self . errors :
# RMM algorithm is not stable for this calculation
if vi [ "INCAR" ] . get ( "ALGO" , "Normal" ) in [ "Fast" , "VeryFast" ]:
- actions . append ({ "dict" : "INCAR" , "action" :
- { "_set" : { "ALGO" : "Normal" }}})
+ actions . append ({ "dict" : "INCAR" , "action" : { "_set" : { "ALGO" : "Normal" }}})
else :
potim = float ( vi [ "INCAR" ] . get ( "POTIM" , 0.5 )) / 2.0
actions . append ({ "dict" : "INCAR" ,
@@ -427,8 +421,7 @@ Source code for custodian.vasp.handlers
if vi [ "INCAR" ] . get ( "ICHARG" , 0 ) < 10 :
actions . append ({ "file" : "CHGCAR" ,
"action" : { "_file_delete" : { 'mode' : "actual" }}})
- actions . append ({ "dict" : "INCAR" , "action" :
- { "_set" : { "ALGO" : "All" }}})
+ actions . append ({ "dict" : "INCAR" , "action" : { "_set" : { "ALGO" : "All" }}})
if "grad_not_orth" in self . errors :
if vi [ "INCAR" ] . get ( "ISMEAR" , 1 ) < 0 :
@@ -453,7 +446,7 @@ Source code for custodian.vasp.handlers
if "posmap" in self . errors :
actions . append ({ "dict" : "INCAR" ,
"action" : { "_set" : { "SYMPREC" : 1e-6 }}})
-
+
if "point_group" in self . errors :
actions . append ({ "dict" : "INCAR" ,
"action" : { "_set" : { "ISYM" : 0 }}})
@@ -682,7 +675,8 @@ Source code for custodian.vasp.handlers
"""
Initializes the handler with max drift
Args:
- max_drift (float): This defines the max drift. Leaving this at the default of None gets the max_drift from EDFIFFG
+ max_drift (float): This defines the max drift. Leaving this at the default of None gets the max_drift from
+ EDFIFFG
"""
self . max_drift = max_drift
@@ -702,7 +696,7 @@ Source code for custodian.vasp.handlers
try :
outcar = Outcar ( "OUTCAR" )
- except :
+ except Exception :
# Can't perform check if Outcar not valid
return False
@@ -781,14 +775,14 @@ Source code for custodian.vasp.handlers
# Also disregard if automatic KPOINT generation is used
if ( not vi [ "INCAR" ] . get ( 'ISYM' , True )) or \
vi [
- "KPOINTS" ] . style == Kpoints . supported_modes . Automatic :
+ "KPOINTS" ] . style == Kpoints . supported_modes . Automatic :
return False
try :
v = Vasprun ( self . output_vasprun )
if v . converged :
return False
- except :
+ except Exception :
pass
with open ( self . output_filename , "r" ) as f :
for line in f :
@@ -831,7 +825,7 @@ Source code for custodian.vasp.handlers
v = Vasprun ( self . output_filename )
if not v . converged :
return True
- except :
+ except Exception :
pass
return False Source code for custodian.vasp.handlers
max_force = max ( np . linalg . norm ( forces , axis = 1 ))
if max_force > self . max_force_threshold and v . converged is True :
return True
- except :
+ except Exception :
pass
return False Source code for custodian.vasp.handlers
max_dE = max ([ s [ 'dE' ] for s in oszicar . ionic_steps [ 1 :]]) / n
if max_dE > self . dE_threshold :
return True
- except :
+ except Exception :
return False [docs] def correct ( self ):
@@ -1065,7 +1059,7 @@
Source code for custodian.vasp.handlers
if len ( esteps ) > self . nionic_steps :
return all ([ len ( e ) == nelm
for e in esteps [ - ( self . nionic_steps + 1 ): - 1 ]])
- except :
+ except Exception :
pass
return False
@@ -1107,6 +1101,7 @@
Source code for custodian.vasp.handlers
else :
return { "errors" : [ "Non-converging job" ], "actions" : None } [docs] class WalltimeHandler ( ErrorHandler ):
"""
Check if a run is nearing the walltime. If so, write a STOPCAR with
@@ -1347,7 +1342,7 @@
Source code for custodian.vasp.handlers
oszicar = Oszicar ( self . output_filename )
if oszicar . final_energy > 0 :
return True
- except :
+ except Exception :
pass
return False
diff --git a/docs/_modules/custodian/vasp/interpreter.html b/docs/_modules/custodian/vasp/interpreter.html
index cab14a4a..cd263bbd 100644
--- a/docs/_modules/custodian/vasp/interpreter.html
+++ b/docs/_modules/custodian/vasp/interpreter.html
@@ -4,7 +4,7 @@
-
custodian.vasp.interpreter — custodian 2019.8.23 documentation
+
custodian.vasp.interpreter — custodian 2019.8.24 documentation
@@ -37,7 +37,7 @@
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »custodian.vasp.jobs — custodian 2019.8.23 documentation
+ custodian.vasp.jobs — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »Source code for custodian.vasp.jobs
self . gamma_vasp_cmd = gamma_vasp_cmd
self . copy_magmom = copy_magmom
self . auto_continue = auto_continue
-
+
if SENTRY_DSN :
- # if using Sentry logging, add specific VASP executable to scope
- from sentry_sdk import configure_scope
- with configure_scope () as scope :
- try :
- if isinstance ( vasp_cmd , str ):
- vasp_path = which ( vasp_cmd . split ( ' ' )[ - 1 ])
- elif isinstance ( vasp_cmd , list ):
- vasp_path = which ( vasp_cmd [ - 1 ])
- scope . set_tag ( "vasp_path" , vasp_path )
- scope . set_tag ( "vasp_cmd" , vasp_cmd )
- except :
- logger . error ( "Failed to detect VASP path: {} " . format ( vasp_cmd ), exc_info = True )
- scope . set_tag ( "vasp_cmd" , vasp_cmd )
+ # if using Sentry logging, add specific VASP executable to scope
+ from sentry_sdk import configure_scope
+ with configure_scope () as scope :
+ try :
+ if isinstance ( vasp_cmd , str ):
+ vasp_path = which ( vasp_cmd . split ( ' ' )[ - 1 ])
+ elif isinstance ( vasp_cmd , list ):
+ vasp_path = which ( vasp_cmd [ - 1 ])
+ scope . set_tag ( "vasp_path" , vasp_path )
+ scope . set_tag ( "vasp_cmd" , vasp_cmd )
+ except Exception :
+ logger . error ( "Failed to detect VASP path: {} " . format ( vasp_cmd ), exc_info = True )
+ scope . set_tag ( "vasp_cmd" , vasp_cmd )
[docs] def setup ( self ):
"""
@@ -228,7 +228,7 @@
Source code for custodian.vasp.jobs
incar [ "NPAR" ] = npar
break
incar . write_file ( "INCAR" )
- except :
+ except Exception :
pass
if self . auto_continue :
@@ -297,7 +297,7 @@ Source code for custodian.vasp.jobs
incar = Incar . from_file ( "INCAR" )
incar [ 'MAGMOM' ] = magmom
incar . write_file ( "INCAR" )
- except :
+ except Exception :
logger . error ( 'MAGMOM copy from OUTCAR to INCAR failed' )
# Remove continuation so if a subsequent job is run in
@@ -659,7 +659,7 @@ Source code for custodian.vasp.jobs
if "vasp" in k :
try :
os . system ( "killall %s " % k )
- except :
+ except Exception :
pass Source code for custodian.vasp.jobs
incar [ "NPAR" ] = npar
break
incar . write_file ( "INCAR" )
- except :
+ except Exception :
pass
if self . auto_continue and \
diff --git a/docs/_modules/custodian/vasp/validators.html b/docs/_modules/custodian/vasp/validators.html
index d866767a..ef4a5fd1 100644
--- a/docs/_modules/custodian/vasp/validators.html
+++ b/docs/_modules/custodian/vasp/validators.html
@@ -4,7 +4,7 @@
custodian.vasp.validators — custodian 2019.8.23 documentation
+ custodian.vasp.validators — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Module code »Source code for custodian.vasp.validators
[docs] def check ( self ):
try :
Vasprun ( "vasprun.xml" )
-
except :
+
except Exception :
exception_context = {}
-
+
if os . path . exists ( self . output_file ):
with open ( self . output_file , "r" ) as output_file :
output_file_tail = deque ( output_file , maxlen = 10 )
exception_context [ "output_file_tail" ] = "" . join ( output_file_tail )
-
+
if os . path . exists ( self . stderr_file ):
with open ( self . stderr_file , "r" ) as stderr_file :
stderr_file_tail = deque ( stderr_file , maxlen = 10 )
exception_context [ "stderr_file_tail" ] = "" . join ( stderr_file_tail )
-
+
if os . path . exists ( "vasprun.xml" ):
-
stat = os . stat ( "vasprun.xml" )
exception_context [ "vasprun_st_size" ] = stat . st_size
exception_context [ "vasprun_st_atime" ] = stat . st_atime
exception_context [ "vasprun_st_mtime" ] = stat . st_mtime
exception_context [ "vasprun_st_ctime" ] = stat . st_ctime
-
+
with open ( "vasprun.xml" , "r" ) as vasprun :
vasprun_tail = deque ( vasprun , maxlen = 10 )
exception_context [ "vasprun_tail" ] = "" . join ( vasprun_tail )
-
+
self . logger . error ( "Failed to load vasprun.xml" ,
exc_info = True , extra = exception_context )
-
+
return True
return False Source code for custodian.vasp.validators
+
[docs] class VaspAECCARValidator ( Validator ):
"""
Check if the data in the AECCAR is corrupted
@@ -165,6 +165,7 @@
Source code for custodian.vasp.validators
aeccar = aeccar0 + aeccar2
return check_broken_chgcar ( aeccar )
+
[docs] def check_broken_chgcar ( chgcar ):
chgcar_data = chgcar . data [ 'total' ]
if ( chgcar_data < 0 ) . sum () > 100 :
@@ -172,7 +173,7 @@
Source code for custodian.vasp.validators
return True
diff = chgcar_data [: - 1 , : - 1 , : - 1 ] - chgcar_data [ 1 :, 1 :, 1 :]
- if diff . max () / ( chgcar_data . max () - chgcar_data . min ()) > 0.95 :
+ if diff . max () / ( chgcar_data . max () - chgcar_data . min ()) > 0.95 :
# Some single diagonal finite difference is more than 95% of the entire range
return True
diff --git a/docs/_modules/index.html b/docs/_modules/index.html
index 56a6d705..4dfccac4 100644
--- a/docs/_modules/index.html
+++ b/docs/_modules/index.html
@@ -4,7 +4,7 @@
Overview: module code — custodian 2019.8.23 documentation
+ Overview: module code — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »
diff --git a/docs/_sources/_themes/README.rst.txt b/docs/_sources/_themes/README.rst.txt
deleted file mode 100644
index e8179f96..00000000
--- a/docs/_sources/_themes/README.rst.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-krTheme Sphinx Style
-====================
-
-This repository contains sphinx styles Kenneth Reitz uses in most of
-his projects. It is a drivative of Mitsuhiko's themes for Flask and Flask related
-projects. To use this style in your Sphinx documentation, follow
-this guide:
-
-1. put this folder as _themes into your docs folder. Alternatively
- you can also use git submodules to check out the contents there.
-
-2. add this to your conf.py: ::
-
- sys.path.append(os.path.abspath('_themes'))
- html_theme_path = ['_themes']
- html_theme = 'kr'
-
-The following themes exist:
-
-**kr**
- the standard flask documentation theme for large projects
-
-**kr_small**
- small one-page theme. Intended to be used by very small addon libraries.
-
diff --git a/docs/_sources/changelog.rst.txt b/docs/_sources/changelog.rst.txt
deleted file mode 100644
index c975f125..00000000
--- a/docs/_sources/changelog.rst.txt
+++ /dev/null
@@ -1,218 +0,0 @@
-Change Log
-==========
-
-v2017.12.23
------------
-* cstdn command line tool is now official with docs.
-* Fine-grained control of VaspErrorHandler is now possible using
- `errors_subset_to_catch`.
-* Switched to date-based versioning for custodian like pymatgen.
-
-v1.1.1
-------
-* DriftErrorHandler (Shyam)
-
-v1.1.0
-------
-* Improved error handling for Qchem calculations.
-
-v1.0.4
-------
-* Improved handling of non-zero return codes.
-
-v1.0.2
-------
-* Interrupted run feature. (Shyam Dwaraknath)
-
-v1.0.1
-------
-* Pymatgen 4.0.0 compatible release.
-
-v1.0.0
-------
-* Custodian now comes with a "cstdn" script that enables the arbitrary creation
- of simple job sequences using a yaml file, and the running of calculations
- based on these yaml specifications.
-
-v0.8.8
-------
-1. Fix setup.py.
-
-v0.8.5
-------
-1. Refactoring to support pymatgen 3.1.4.
-
-v0.8.2
-------
-1. Made auto_npar optional for double relaxation VASP run.
-
-v0.8.1
-------
-1. Misc bug fixes (minor).
-
-v0.8.0
-------
-1. Major refactoring of Custodian to introdce Validators,
- which are effectively post-Job checking mechanisms that do not perform
- error correction.
-2. **Backwards incompatibility** BadVasprunXMLHandler is now a validator,
- which must be separately imported to be used.
-3. Miscellaneous cleanup of Py3k fixes.
-v0.7.6
-------
-1. Custodian is now Python 3 compatible and uses the latest versions of
- pymatgen and monty.
-
-v0.7.5
-------
-1. **Major** Custodian now exits with RuntimeError when max_errors or
- unrecoverable_error is encountered.
-2. Added BadVasprunXMLHandler.
-
-v0.7.4
-------
-1. auto_npar option in VaspJob now properly handles Hessian calculations.
-2. WalltimeHandler now supports termination at electronic step (David
- Waroquiers).
-3. Improved handling of BRMIX fixes.
-
-v0.7.3
-------
-1. Improved backwards compatibility for WallTimeHandler.
-2. Improvements to VaspErrorHandler. No longer catches spurious BRMIX error
- messages when NELECT is specified in INCAR, and pricel and rot_mat errors
- are now fixed with symmetry precision and gamma centered KPOINTS instead.
-3. Improved Qchem error handler (Xiaohui Qu).
-
-v0.7.2
-------
-1. Improved WalltimeHandler (PBSWalltimeHandler is a subset and is now
- deprecated).
-2. New monty required version (>= 0.2.2).
-
-v0.7.1
-------
-1. Much improved qchem error handling (Xiaohui Qu).
-2. New Monty required version (>= 0.2.0).
-
-v0.7.0
-------
-1. **Backwards incompatible with v0.6.3. Refactoring to move commonly used
- Python utility functions to `Monty package
`_, which is now a depedency
- for custodian.
-2. Custodian now requires pymatgen >= 2.9.0 for VASP, Qchem and Nwchem jobs
- and handlers.
-3. converge_kpoints script now has increment mode.
-4. ErrorHandlers now have a new API, where the class variables "is_monitor"
- and "is_terminating" are provided to indicate if a particular handler
- runs in the background during a Job and whether a handler should
- terminate the job. Some errors may not be critical or may need to wait
- for some other event to terminate a job. For example,
- a particular error may require a flag to be set to request a job to
- terminate gracefully once it finishes its current task. The handler to
- set the flag should not terminate the job.
-
-0.6.3
------
-1. Added buffer time option in PBSWalltimeHandler.
-2. Improved Qchem jobs and handlers (Xiaohui Qu).
-3. Vastly improved API docs.
-
-0.6.2
------
-1. Bug fix release to support sub dirs in run folder when using scratch.
-2. Improve handling of walltime in PBSWalltimeHander.
-
-0.6.1
------
-1. Bug fix release to address minor issue with checkpointing.
-2. Checkpointing is now turned off by default.
-
-0.6.0
------
-1. Checkpointing implemented for Custodian. Custodian can now checkpoint all
- files in the current working directory after every successful job. If the
- job is resubmitted, it will restore files and start from the last
- checkpoint. Particularly useful for multi-job runs.
-2. Added PBSWalltimeHandler to handle wall times for PBS Vasp Jobs.
-3. Qchem error handlers and jobs.
-
-0.5.0
------
-1. Added scratch_dir option to Custodian class as well as run_vasp and
- run_nwchem scripts. Many supercomputing clusters have a scratch space
- which have significantly faster IO. This option provides a transparent way
- to specify the jobs to be performed in the scratch. Especially useful for
- jobs which have significant file IO.
-
-0.4.5
------
-1. Fix gzip of output.
-
-0.4.3
------
-1. Added handling for ZBRENT error for VASP.
-2. Minor refactoring to consolidate backup and gzip directory methods.
-
-0.4.2
------
-1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
-2. Improved VASP error handling (by Steve Dacek and Will Richards).
-
-0.4.1
------
-1. Added hanlding of PRICEL error in VASP.
-2. Speed and robustness improvements.
-3. BRIONS error now handled by changing ISYM.
-
-0.4.0
------
-1. Many VASP handlers are now consolidated into a single VaspErrorHandler.
-2. Many more fixes for VASP runs, including the "TOO FEW BANDS",
- "TRIPLE PRODUCT", "DENTET" and "BRIONS" errors.
-3. VaspJob now includes the auto_npar and auto_gamma options, which
- automatically optimizes the NPAR setting to be sqrt(number of cores) as
- per the VASP recommendation for DFT runs and tries to search for a
- gamma-only compiled version of VASP for gamma 1x1x1 runs.
-
-0.3.5
------
-1. Bug fix for incorrect shift error handler in VASP.
-2. More robust fix for unconverged VASP runs (switching from ALGO fast to
- normal).
-3. Expanded documentation.
-
-0.3.4
------
-1. Added support for handlers that perform monitor a job as it is progressing
- and terminates it if necessary. Useful for correcting errors that come up
- by do not cause immediate job failures.
-
-0.3.2
------
-1. Important bug fix for VaspJob and converge_kpoints script.
-
-0.3.0
------
-
-1. Major update to custodian API. Custodian now perform more comprehensive
- logging in a file called custodian.json, which logs all jobs and
- corrections performed.
-
-Version 0.2.6
--------------
-1. Bug fix for run_vasp script for static runs.
-
-Version 0.2.5
--------------
-1. run_vasp script that now provides flexible specification of vasp runs.
-2. Vastly improved error handling for VASP runs.
-3. Improved logging system for custodian.
-4. Improved API for custodian return types during run.
-5. First stable release.
-
-Version 0.2.4
--------------
-
-1. Bug fixes for aflow style runs assimilation.
diff --git a/docs/_sources/custodian.ansible.rst.txt b/docs/_sources/custodian.ansible.rst.txt
deleted file mode 100644
index 5840ac5f..00000000
--- a/docs/_sources/custodian.ansible.rst.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-custodian.ansible package
-=========================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.ansible.actions module
---------------------------------
-
-.. automodule:: custodian.ansible.actions
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.ansible.interpreter module
-------------------------------------
-
-.. automodule:: custodian.ansible.interpreter
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.ansible
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/_sources/custodian.cli.rst.txt b/docs/_sources/custodian.cli.rst.txt
deleted file mode 100644
index c83b5d9c..00000000
--- a/docs/_sources/custodian.cli.rst.txt
+++ /dev/null
@@ -1,54 +0,0 @@
-custodian.cli package
-=====================
-
-Submodules
-----------
-
-custodian.cli.converge\_geometry module
----------------------------------------
-
-.. automodule:: custodian.cli.converge_geometry
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.converge\_kpoints module
---------------------------------------
-
-.. automodule:: custodian.cli.converge_kpoints
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.cstdn module
---------------------------
-
-.. automodule:: custodian.cli.cstdn
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.run\_nwchem module
---------------------------------
-
-.. automodule:: custodian.cli.run_nwchem
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.run\_vasp module
-------------------------------
-
-.. automodule:: custodian.cli.run_vasp
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.cli
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/_sources/custodian.feff.rst.txt b/docs/_sources/custodian.feff.rst.txt
deleted file mode 100644
index 753541f9..00000000
--- a/docs/_sources/custodian.feff.rst.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-custodian.feff package
-======================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.feff.handlers module
-------------------------------
-
-.. automodule:: custodian.feff.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.feff.interpreter module
----------------------------------
-
-.. automodule:: custodian.feff.interpreter
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.feff.jobs module
---------------------------
-
-.. automodule:: custodian.feff.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.feff
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/_sources/custodian.nwchem.rst.txt b/docs/_sources/custodian.nwchem.rst.txt
deleted file mode 100644
index be9c01a4..00000000
--- a/docs/_sources/custodian.nwchem.rst.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-custodian.nwchem package
-========================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.nwchem.handlers module
---------------------------------
-
-.. automodule:: custodian.nwchem.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.nwchem.jobs module
-----------------------------
-
-.. automodule:: custodian.nwchem.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.nwchem
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/_sources/custodian.qchem.rst.txt b/docs/_sources/custodian.qchem.rst.txt
deleted file mode 100644
index 6fc3df09..00000000
--- a/docs/_sources/custodian.qchem.rst.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-custodian.qchem package
-=======================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.qchem.handlers module
--------------------------------
-
-.. automodule:: custodian.qchem.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.qchem.jobs module
----------------------------
-
-.. automodule:: custodian.qchem.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.qchem
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/_sources/custodian.rst.txt b/docs/_sources/custodian.rst.txt
deleted file mode 100644
index 97747550..00000000
--- a/docs/_sources/custodian.rst.txt
+++ /dev/null
@@ -1,42 +0,0 @@
-custodian package
-=================
-
-Subpackages
------------
-
-.. toctree::
-
- custodian.ansible
- custodian.cli
- custodian.feff
- custodian.nwchem
- custodian.qchem
- custodian.vasp
-
-Submodules
-----------
-
-custodian.custodian module
---------------------------
-
-.. automodule:: custodian.custodian
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.utils module
-----------------------
-
-.. automodule:: custodian.utils
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/_sources/custodian.vasp.rst.txt b/docs/_sources/custodian.vasp.rst.txt
deleted file mode 100644
index 2d8dbc9b..00000000
--- a/docs/_sources/custodian.vasp.rst.txt
+++ /dev/null
@@ -1,52 +0,0 @@
-custodian.vasp package
-======================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.vasp.handlers module
-------------------------------
-
-.. automodule:: custodian.vasp.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.vasp.interpreter module
----------------------------------
-
-.. automodule:: custodian.vasp.interpreter
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.vasp.jobs module
---------------------------
-
-.. automodule:: custodian.vasp.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.vasp.validators module
---------------------------------
-
-.. automodule:: custodian.vasp.validators
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.vasp
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
deleted file mode 100644
index eaa523f6..00000000
--- a/docs/_sources/index.rst.txt
+++ /dev/null
@@ -1,368 +0,0 @@
-Custodian
-=========
-
-Custodian is a simple, robust and flexible just-in-time (JIT) job management
-framework written in Python. Using custodian, you can create wrappers that
-perform error checking, job management and error recovery. It has a simple
-plugin framework that allows you to develop specific job management workflows
-for different applications.
-
-Error recovery is an important aspect of many *high-throughput* projects that
-generate data on a large scale. When you are running on the order of hundreds
-of thousands of jobs, even an error rate of 1% would mean thousands of errored
-jobs that would be impossible to deal with on a case-by-case basis.
-
-The specific use case for custodian is for long running jobs, with potentially
-random errors. For example, there may be a script that takes several days to
-run on a server, with a 1% chance of some IO error causing the job to fail.
-Using custodian, one can develop a mechanism to gracefully recover from the
-error, and restart the job with modified parameters if necessary.
-
-The current version of Custodian also comes with two sub-packages for error
-handling for Vienna Ab Initio Simulation Package (VASP), NwChem and QChem
-calculations.
-
-Change log
-==========
-
-v2019.2.10
-----------
-* Improved slow convergence handling. (@shyamd)
-
-v2019.2.7
----------
-* Improved error logging.
-* Improved handling of frozen jobs and potim errors.
-* Improved Exceptino handling. (Guido Petretto)
-
-
-:doc:`Older versions `
-
-Getting custodian
-=================
-
-Stable version
---------------
-
-The version at the Python Package Index (PyPI) is always the latest stable
-release that will be hopefully, be relatively bug-free. The easiest way to
-install custodian on any system is to use easy_install or pip, as follows::
-
- easy_install custodian
-
-or::
-
- pip install custodian
-
-Some plugins (e.g., vasp management) require additional setup (please see
-`pymatgen's documentation`_).
-
-Developmental version
----------------------
-
-The bleeding edge developmental version is at the custodian's `Github repo
-`_. The developmental
-version is likely to be more buggy, but may contain new features. The
-Github version include test files as well for complete unit testing. After
-cloning the source, you can type::
-
- python setup.py install
-
-or to install the package in developmental mode::
-
- python setup.py develop
-
-Requirements
-============
-
-Custodian requires Python 2.7+. There are no other required dependencies.
-
-Optional dependencies
----------------------
-
-Optional libraries that are required if you need certain features:
-
-1. Python Materials Genomics (`pymatgen`_) 2.8.10+: To use the plugin for
- VASP, NwChem and Qchem. Please install using::
-
- pip install pymatgen
-
- For more information, please consult `pymatgen's documentation`_.
-2. nose - For complete unittesting.
-
-Usage
-=====
-
-The main class in the workflow is known as Custodian, which manages a series
-of jobs with a list of error handlers. The general workflow for Custodian is
-presented in the figure below.
-
-.. figure:: _static/Custodian.png
- :width: 500px
- :align: center
- :alt: Custodian workflow
- :figclass: align-center
-
- Overview of the Custodian workflow.
-
-The Custodian class takes in two general inputs - a **list of Jobs** and
-a **list of ErrorHandlers**. **Jobs** should be subclasses of the
-:class:`custodian.custodian.Job` abstract base class and **ErrorHandlers**
-should be subclasses of the :class:`custodian.custodian.ErrorHandler` abstract
-base class. To use custodian, you need to implement concrete implementations
-of these abstract base classes.
-
-Simple example
---------------
-
-An very simple example implementation is given in the custodian_examples.py
-script in the scripts directory. We will now go through the example in detail
-here.
-
-The ExampleJob has the following code.
-
-.. code-block:: python
-
- class ExampleJob(Job):
-
- def __init__(self, jobid, params=None):
- if params is None:
- params = {"initial": 0, "total": 0}
- self.jobid = jobid
- self.params = params
-
- def setup(self):
- self.params["initial"] = 0
- self.params["total"] = 0
-
- def run(self):
- sequence = [random.uniform(0, 1) for i in range(100)]
- self.params["total"] = self.params["initial"] + sum(sequence)
-
- def postprocess(self):
- pass
-
- @property
- def name(self):
- return "ExampleJob{}".format(self.jobid)
-
-
-The ExampleJob simply sums a random sequence of 100 numbers between 0 and
-1, adds it to an initial value and puts the value in 'total' variable. The
-ExampleJob subclasses the Job abstract base class, and implements the necessary
-API comprising of just three key methods: **setup(), run(),
-and postprocess()**.
-
-Let us now define an ErrorHandler that will check if the total value is >= 50,
-and if it is not, it will increment the initial value by 1 and rerun the
-ExampleJob again.
-
-.. code-block:: python
-
-
- class ExampleHandler(ErrorHandler):
-
- def __init__(self, params):
- self.params = params
-
- def check(self):
- return self.params["total"] < 50
-
- def correct(self):
- self.params["initial"] += 1
- return {"errors": "total < 50", "actions": "increment by 1"}
-
-As you can see above, the ExampleHandler subclasses the ErrorHandler abstract
-base class, and implements the necessary API comprising of just two key
-methods: **check() and correct()**.
-
-The transfer of information between the Job and ErrorHandler is done using
-the params argument in this example, which is not ideal but is sufficiently
-for demonstrating the Custodian API. In real world usage,
-a more common transfer of information may involve the Job writing the output
-to a file, and the ErrorHandler checking the contents of those files to
-detect error situations.
-
-To run the job, one simply needs to supply a list of ExampleJobs and
-ErrorHandlers to a Custodian.
-
-.. code-block:: python
-
- njobs = 100
- params = {"initial": 0, "total": 0}
- c = Custodian([ExampleHandler(params)],
- [ExampleJob(i, params) for i in xrange(njobs)],
- max_errors=njobs)
- c.run()
-
-If you run custodian_example.py in the scripts directory, you will noticed that
-a **custodian.json** file was generated, which summarizes the jobs that have
-been run and any corrections performed.
-
-Practical example: Electronic structure calculations
-----------------------------------------------------
-
-A practical example where the Custodian framework is particularly useful is
-in the area of electronic structure calculations. Electronic structure
-calculations tend to be long running and often terminates due to errors,
-random or otherwise. Such errors become a major issue in projects that
-performs such calculations in high throughput, such as the `Materials
-Project`_.
-
-The Custodian package comes with a fairly comprehensive plugin to deal
-with jobs (:mod:`custodian.vasp.jobs`) and errors
-(:mod:`custodian.vasp.handlers`) in electronic structure calculations based
-on the Vienna Ab Initio Simulation Package (VASP). To do this,
-Custodian uses the Python Materials Genomics (`pymatgen`_) package to
-perform analysis and io from VASP input and output files.
-
-A simple example of a script using Custodian to run a two-relaxation VASP job
-is as follows:
-
-.. code-block:: python
-
- from custodian.custodian import Custodian
- from custodian.vasp.handlers import VaspErrorHandler, \
- UnconvergedErrorHandler, PoscarErrorHandler, DentetErrorHandler
- from custodian.vasp.jobs import VaspJob
-
- handlers = [VaspErrorHandler(), UnconvergedErrorHandler(),
- PoscarErrorHandler(), DentetErrorHandler()]
- jobs = VaspJob.double_relaxation_run(args.command.split())
- c = Custodian(handlers, jobs, max_errors=10)
- c.run()
-
-The above will gracefully deal with many VASP errors encountered during
-relaxation. For example, it will correct ISMEAR to 0 if there are
-insufficient KPOINTS to use ISMEAR = -5.
-
-Using custodian, you can even setup potentially indefinite jobs,
-e.g. kpoints convergence jobs with a target energy convergence. Please see the
-converge_kpoints script in the scripts for an example.
-
-.. versionadded:: 0.4.3
-
- A new package for dealing with NwChem calculations has been added.
- NwChem is an open-source code for performing computational chemistry
- calculations.
-
-cstdn - A yaml-spec controlled job
-==================================
-
-Custodian now comes with a cstdn script, which allows you to do fine-grained
-control of a job using a yaml spec file. Below is an annotated example of how
-you can specify a double VASP relaxation followed by a static calculation.
-Minor modifications would allow very customizable calculations, though this is
-obviously not meant for highly complex workflows. For those, usage of `FireWorks
-` with parameters specified
- # via the params dict.
-
- jobs:
- - jb: custodian.vasp.jobs.VaspJob
- params:
- final: False
- suffix: .relax1
- - jb: custodian.vasp.jobs.VaspJob
- params:
- final: False
- suffix: .relax2
- settings_override:
- - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
- - jb: custodian.vasp.jobs.VaspJob
- params:
- final: True
- suffix: .static3
- settings_override:
- - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
- - {"dict": "INCAR", "action": {"_set": {"NSW": 0}}}
-
-
- # This key specifies parameters common to all jobs.
- # Keys starting with $ are expanded to the environmental values.
- # The example below means the parameter vasp_cmd is set to the value with
- # $PBS_NODEFILE expanded.
-
- jobs_common_params:
- $vasp_cmd: ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "24", "vasp"]
-
-
- # Specifies a list of error handlers in the same format as jobs. Similarly,
- # parameters passed to the handler __init__ can be configured the same
- # way as for jobs.
- handlers:
- - hdlr: custodian.vasp.handlers.VaspErrorHandler
- - hdlr: custodian.vasp.handlers.AliasingErrorHandler
- - hdlr: custodian.vasp.handlers.MeshSymmetryErrorHandler
-
- # Specifies a list of error handlers in the same format as jobs.
- validators:
- - vldr: custodian.vasp.validators.VasprunXMLValidator
-
- #This sets all custodian running parameters.
- custodian_params:
- max_errors: 10
- scratch_dir: /tmp
- gzipped_output: True
- checkpoint: True
-
-You can then run the job using the following command::
-
- cstdn run
-
-API/Reference Docs
-==================
-
-The API docs are generated using Sphinx auto-doc and outlines the purpose of all
-modules and classes, and the expected argument and returned objects for most
-methods. They are available at the link below.
-
-:doc:`custodian API docs `
-
-How to cite custodian
-=====================
-
-If you use custodian in your research, especially the VASP component, please
-consider citing the following work::
-
- Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier,
- Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
- Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
- Open-Source Python Library for Materials Analysis.* Computational
- Materials Science, 2013, 68, 314–319. `doi:10.1016/j.commatsci.2012.10.028
- `_
-
-License
-=======
-
-Custodian is released under the MIT License. The terms of the license are as
-follows::
-
- The MIT License (MIT)
- Copyright (c) 2011-2012 MIT & LBNL
-
- Permission is hereby granted, free of charge, to any person obtaining a
- copy of this software and associated documentation files (the "Software")
- , to deal in the Software without restriction, including without limitation
- the rights to use, copy, modify, merge, publish, distribute, sublicense,
- and/or sell copies of the Software, and to permit persons to whom the
- Software is furnished to do so, subject to the following conditions:
-
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- DEALINGS IN THE SOFTWARE.
-
-.. _`pymatgen's documentation`: http://pymatgen.org
-.. _`Materials Project`: https://www.materialsproject.org
-.. _`pymatgen`: https://pypi.python.org/pypi/pymatgen
diff --git a/docs/_sources/modules.rst.txt b/docs/_sources/modules.rst.txt
deleted file mode 100644
index c241b4a4..00000000
--- a/docs/_sources/modules.rst.txt
+++ /dev/null
@@ -1,7 +0,0 @@
-custodian
-=========
-
-.. toctree::
- :maxdepth: 6
-
- custodian
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 92680bf2..584dbda4 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '2019.8.23',
+ VERSION: '2019.8.24',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
FILE_SUFFIX: '.html',
diff --git a/docs/_themes/README.html b/docs/_themes/README.html
index 055d525d..5928d650 100644
--- a/docs/_themes/README.html
+++ b/docs/_themes/README.html
@@ -4,7 +4,7 @@
krTheme Sphinx Style — custodian 2019.8.23 documentation
+ krTheme Sphinx Style — custodian 2019.8.24 documentation
Navigation
modules |
- custodian 2019.8.23 documentation »custodian 2019.8.24 documentation »
diff --git a/docs/changelog.html b/docs/changelog.html
index 189415cf..62b7875e 100644
--- a/docs/changelog.html
+++ b/docs/changelog.html
@@ -4,7 +4,7 @@
-
Change Log — custodian 2019.8.23 documentation
+
Change Log — custodian 2019.8.24 documentation
@@ -37,7 +37,7 @@
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Navigation
Change Log
+
+
v2017.12.23
@@ -344,6 +358,8 @@ Version 0.2.4
diff --git a/docs/custodian.cli.html b/docs/custodian.cli.html
index adf3c0d0..d9182556 100644
--- a/docs/custodian.cli.html
+++ b/docs/custodian.cli.html
@@ -4,7 +4,7 @@
-
custodian.cli package — custodian 2019.8.23 documentation
+
custodian.cli package — custodian 2019.8.24 documentation
@@ -37,7 +37,7 @@
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »
diff --git a/docs/custodian.feff.html b/docs/custodian.feff.html
index 95900a3a..4f553247 100644
--- a/docs/custodian.feff.html
+++ b/docs/custodian.feff.html
@@ -4,7 +4,7 @@
custodian.feff package — custodian 2019.8.23 documentation
+ custodian.feff package — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »custodian package — custodian 2019.8.23 documentation
+ custodian package — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »custodian.nwchem package — custodian 2019.8.23 documentation
+ custodian.nwchem package — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »custodian.qchem package — custodian 2019.8.23 documentation
+ custodian.qchem package — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »Submodules
Module contents
diff --git a/docs/custodian.vasp.html b/docs/custodian.vasp.html
index 6dd1ff3e..dbba1db4 100644
--- a/docs/custodian.vasp.html
+++ b/docs/custodian.vasp.html
@@ -4,7 +4,7 @@
-
custodian.vasp package — custodian 2019.8.23 documentation
+
custodian.vasp package — custodian 2019.8.24 documentation
@@ -37,7 +37,7 @@
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »
@@ -180,8 +180,12 @@ Submodules
Corrects for total drift exceeding the force convergence criteria.
Initializes the handler with max drift
-:param max_drift: This defines the max drift. Leaving this at the default of None gets the max_drift from EDFIFFG
-:type max_drift: float
+:param max_drift: This defines the max drift. Leaving this at the default of None gets the max_drift from
+
+
+
+
check( ) [source]
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--- a/docs/genindex.html
+++ b/docs/genindex.html
@@ -5,7 +5,7 @@
Index — custodian 2019.8.23 documentation
+ Index — custodian 2019.8.24 documentation
Navigation
modules |
-
custodian 2019.8.23 documentation »
+
custodian 2019.8.24 documentation »V
VaspNpTMDValidator (class in custodian.vasp.validators)
VasprunXMLValidator (class in custodian.vasp.validators)
+
+
vector_list_diff() (in module custodian.qchem.jobs)
diff --git a/docs/html/.buildinfo b/docs/html/.buildinfo
deleted file mode 100644
index e08b88b0..00000000
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+++ /dev/null
@@ -1,4 +0,0 @@
-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 97de76a622588bfc02d686015cbc7705
-tags: 645f666f9bcd5a90fca523b33c5a78b7
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+++ /dev/null
@@ -1,332 +0,0 @@
-
-
-
-
-
-
-
custodian.ansible.actions — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Source code for custodian.ansible.actions
-# coding: utf-8
-
-from __future__ import unicode_literals , division , print_function
-import os
-import shutil
-
-"""
-This module defines various classes of supported actions. All actions are
-implemented as static methods, but are defined using classes (as opposed to
-modules) so that a set of well-defined actions can be namespaced easily.
-"""
-
-__author__ = "Shyue Ping Ong"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__date__ = "Jun 2, 2012"
-
-
-[docs] def get_nested_dict ( input_dict , key ):
-
current = input_dict
-
toks = key . split ( "->" )
-
n = len ( toks )
-
for i , tok in enumerate ( toks ):
-
if tok not in current and i < n - 1 :
-
current [ tok ] = {}
-
elif i == n - 1 :
-
return current , toks [ - 1 ]
-
current = current [ tok ] [docs] class DictActions ( object ):
-
"""
-
Class to implement the supported mongo-like modifications on a dict.
-
Supported keywords include the following Mongo-based keywords, with the
-
usual meanings (refer to Mongo documentation for information):
-
-
_inc
-
_set
-
_unset
-
_push
-
_push_all
-
_add_to_set (but _each is not supported)
-
_pop
-
_pull
-
_pull_all
-
_rename
-
-
However, note that "_set" does not support modification of nested dicts
-
using the mongo {"a.b":1} notation. This is because mongo does not allow
-
keys with "." to be inserted. Instead, nested dict modification is
-
supported using a special "->" keyword, e.g. {"a->b": 1}
-
"""
-
-
[docs] @staticmethod
-
def set ( input_dict , settings ):
-
for k , v in settings . items ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
d [ key ] = v
-
-
[docs] @staticmethod
-
def unset ( input_dict , settings ):
-
for k in settings . keys ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
del d [ key ]
-
-
[docs] @staticmethod
-
def push ( input_dict , settings ):
-
for k , v in settings . items ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
if key in d :
-
d [ key ] . append ( v )
-
else :
-
d [ key ] = [ v ]
-
-
[docs] @staticmethod
-
def push_all ( input_dict , settings ):
-
for k , v in settings . items ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
if key in d :
-
d [ key ] . extend ( v )
-
else :
-
d [ key ] = v
-
-
[docs] @staticmethod
-
def inc ( input_dict , settings ):
-
for k , v in settings . items ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
if key in d :
-
d [ key ] += v
-
else :
-
d [ key ] = v
-
-
[docs] @staticmethod
-
def rename ( input_dict , settings ):
-
for k , v in settings . items ():
-
if k in input_dict :
-
input_dict [ v ] = input_dict [ k ]
-
del input_dict [ k ]
-
-
[docs] @staticmethod
-
def add_to_set ( input_dict , settings ):
-
for k , v in settings . items ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
if key in d and ( not isinstance ( d [ key ], list )):
-
raise ValueError ( "Keyword {} does not refer to an array."
-
. format ( k ))
-
if key in d and v not in d [ key ]:
-
d [ key ] . append ( v )
-
elif key not in d :
-
d [ key ] = v
-
-
[docs] @staticmethod
-
def pull ( input_dict , settings ):
-
for k , v in settings . items ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
if key in d and ( not isinstance ( d [ key ], list )):
-
raise ValueError ( "Keyword {} does not refer to an array."
-
. format ( k ))
-
if key in d :
-
d [ key ] = [ i for i in d [ key ] if i != v ]
-
-
[docs] @staticmethod
-
def pull_all ( input_dict , settings ):
-
for k , v in settings . items ():
-
if k in input_dict and ( not isinstance ( input_dict [ k ], list )):
-
raise ValueError ( "Keyword {} does not refer to an array."
-
. format ( k ))
-
for i in v :
-
DictActions . pull ( input_dict , { k : i })
-
-
[docs] @staticmethod
-
def pop ( input_dict , settings ):
-
for k , v in settings . items ():
-
( d , key ) = get_nested_dict ( input_dict , k )
-
if key in d and ( not isinstance ( d [ key ], list )):
-
raise ValueError ( "Keyword {} does not refer to an array."
-
. format ( k ))
-
if v == 1 :
-
d [ key ] . pop ()
-
elif v == - 1 :
-
d [ key ] . pop ( 0 ) [docs] class FileActions ( object ):
-
"""
-
Class of supported file actions. For FileActions, the modder class takes in
-
a filename as a string. The filename should preferably be a full path to
-
avoid ambiguity.
-
"""
-
-
[docs] @staticmethod
-
def file_create ( filename , settings ):
-
"""
-
Creates a file.
-
-
Args:
-
filename (str): Filename.
-
settings (dict): Must be {"content": actual_content}
-
"""
-
if len ( settings ) != 1 :
-
raise ValueError ( "Settings must only contain one item with key "
-
"'content'." )
-
for k , v in settings . items ():
-
if k == "content" :
-
with open ( filename , 'w' ) as f :
-
f . write ( v )
-
-
[docs] @staticmethod
-
def file_move ( filename , settings ):
-
"""
-
Moves a file. {'_file_move': {'dest': 'new_file_name'}}
-
-
Args:
-
filename (str): Filename.
-
settings (dict): Must be {"dest": path of new file}
-
"""
-
if len ( settings ) != 1 :
-
raise ValueError ( "Settings must only contain one item with key "
-
"'dest'." )
-
for k , v in settings . items ():
-
if k == "dest" :
-
shutil . move ( filename , v )
-
-
[docs] @staticmethod
-
def file_delete ( filename , settings ):
-
"""
-
Deletes a file. {'_file_delete': {'mode': "actual"}}
-
-
Args:
-
filename (str): Filename.
-
settings (dict): Must be {"mode": actual/simulated}. Simulated
-
mode only prints the action without performing it.
-
"""
-
if len ( settings ) != 1 :
-
raise ValueError ( "Settings must only contain one item with key "
-
"'mode'." )
-
for k , v in settings . items ():
-
if k == "mode" and v == "actual" :
-
try :
-
os . remove ( filename )
-
except OSError :
-
#Skip file not found error.
-
pass
-
elif k == "mode" and v == "simulated" :
-
print ( "Simulated removal of {} " . format ( filename ))
-
-
[docs] @staticmethod
-
def file_copy ( filename , settings ):
-
"""
-
Copies a file. {'_file_copy': {'dest': 'new_file_name'}}
-
-
Args:
-
filename (str): Filename.
-
settings (dict): Must be {"dest": path of new file}
-
"""
-
for k , v in settings . items ():
-
if k . startswith ( "dest" ):
-
shutil . copyfile ( filename , v )
-
-
[docs] @staticmethod
-
def file_modify ( filename , settings ):
-
"""
-
Modifies file access
-
-
Args:
-
filename (str): Filename.
-
settings (dict): Can be "mode" or "owners"
-
"""
-
for k , v in settings . items ():
-
if k == "mode" :
-
os . chmod ( filename , v )
-
if k == "owners" :
-
os . chown ( filename , v )
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/ansible/interpreter.html b/docs/html/_modules/custodian/ansible/interpreter.html
deleted file mode 100644
index 59d22398..00000000
--- a/docs/html/_modules/custodian/ansible/interpreter.html
+++ /dev/null
@@ -1,200 +0,0 @@
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-
custodian.ansible.interpreter — custodian 2019.8.23 documentation
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Source code for custodian.ansible.interpreter
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-"""
-This module implements a Modder class that performs modifications on objects
-using support actions.
-"""
-
-
-__author__ = "Shyue Ping Ong"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__date__ = "Jun 1, 2012"
-
-
-import re
-
-from custodian.ansible.actions import DictActions
-
-
-[docs] class Modder ( object ):
-
"""
-
Class to modify a dict/file/any object using a mongo-like language.
-
Keywords are mostly adopted from mongo's syntax, but instead of $, an
-
underscore precedes action keywords. This is so that the modification can
-
be inserted into a mongo db easily.
-
-
Allowable actions are supplied as a list of classes as an argument. Refer
-
to the action classes on what the actions do. Action classes are in
-
pymatpro.ansible.actions.
-
-
Examples:
-
>>> modder = Modder()
-
>>> d = {"Hello": "World"}
-
>>> mod = {'_set': {'Hello':'Universe', 'Bye': 'World'}}
-
>>> modder.modify(mod, d)
-
>>> d['Bye']
-
'World'
-
>>> d['Hello']
-
'Universe'
-
"""
-
def __init__ ( self , actions = None , strict = True ):
-
"""
-
Initializes a Modder from a list of supported actions.
-
-
Args:
-
actions ([Action]): A sequence of supported actions. See
-
:mod:`custodian.ansible.actions`. Default is None,
-
which means only DictActions are supported.
-
strict (bool): Indicating whether to use strict mode. In non-strict
-
mode, unsupported actions are simply ignored without any
-
errors raised. In strict mode, if an unsupported action is
-
supplied, a ValueError is raised. Defaults to True.
-
"""
-
self . supported_actions = {}
-
actions = actions if actions is not None else [ DictActions ]
-
for action in actions :
-
for i in dir ( action ):
-
if ( not re . match ( '__\w+__' , i )) and \
-
callable ( getattr ( action , i )):
-
self . supported_actions [ "_" + i ] = getattr ( action , i )
-
self . strict = strict
-
-
[docs] def modify ( self , modification , obj ):
-
"""
-
Note that modify makes actual in-place modifications. It does not
-
return a copy.
-
-
Args:
-
modification (dict): Modification must be {action_keyword :
-
settings}. E.g., {'_set': {'Hello':'Universe', 'Bye': 'World'}}
-
obj (dict/str/object): Object to modify depending on actions. For
-
example, for DictActions, obj will be a dict to be modified.
-
For FileActions, obj will be a string with a full pathname to a
-
file.
-
"""
-
for action , settings in modification . items ():
-
if action in self . supported_actions :
-
self . supported_actions [ action ] . __call__ ( obj , settings )
-
elif self . strict :
-
raise ValueError ( " {} is not a supported action!"
-
. format ( action ))
-
-
[docs] def modify_object ( self , modification , obj ):
-
"""
-
Modify an object that supports pymatgen's as_dict() and from_dict API.
-
-
Args:
-
modification (dict): Modification must be {action_keyword :
-
settings}. E.g., {'_set': {'Hello':'Universe', 'Bye': 'World'}}
-
obj (object): Object to modify
-
"""
-
d = obj . as_dict ()
-
self . modify ( modification , d )
-
return obj . from_dict ( d ) if __name__ == "__main__" :
- import doctest
- doctest . testmod ()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/cli/converge_geometry.html b/docs/html/_modules/custodian/cli/converge_geometry.html
deleted file mode 100644
index f59e341c..00000000
--- a/docs/html/_modules/custodian/cli/converge_geometry.html
+++ /dev/null
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custodian.cli.converge_geometry — custodian 2019.8.23 documentation
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Source code for custodian.cli.converge_geometry
-#!/usr/bin/env python
-
-"""
-This is a script to converge the geometry of a system
-"""
-
-from __future__ import division
-
-__author__ = "Stephen Dacek"
-__version__ = "0.1"
-__maintainer__ = "Stephen Dacek"
-__email__ = "sdacek@mit.edu"
-__status__ = "Beta"
-__date__ = "11/3/13"
-
-import logging
-
-from custodian.custodian import Custodian
-from custodian.vasp.handlers import VaspErrorHandler , UnconvergedErrorHandler , \
- MeshSymmetryErrorHandler , NonConvergingErrorHandler , PotimErrorHandler
-from custodian.vasp.jobs import VaspJob
-from pymatgen.io.vasp.outputs import Vasprun
-
-
-FORMAT = ' %(asctime)s %(message)s '
-logging . basicConfig ( format = FORMAT , level = logging . INFO , filename = "run.log" )
-
-
-[docs] def get_runs ( args ):
-
-
vasp_command = args . command . split ()
-
converged = False
-
job_number = 0
-
-
while ( not converged ) and ( job_number < args . max_relax ):
-
-
suffix = ". {}{} " . format ( 'relax' , job_number + 1 )
-
-
if job_number == 0 :
-
backup = True
-
#assume the initial guess is poor,
-
#start with conjugate gradients
-
settings = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "IBRION" : 2 }}}
-
]
-
-
else :
-
backup = False
-
v = Vasprun ( "vasprun.xml" )
-
-
if len ( v . ionic_steps ) == 1 :
-
converged = True
-
-
if job_number < 2 and not converged :
-
-
settings = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISTART" : 1 }}},
-
{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
-
#switch to RMM-DIIS once we are near the
-
#local minimum (assumed after 2 runs of CG)
-
else :
-
settings = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISTART" : 1 , "IBRION" : 1 }}},
-
{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
-
job_number += 1
-
yield VaspJob ( vasp_command , final = converged , backup = backup ,
-
suffix = suffix , settings_override = settings ) [docs] def do_run ( args ):
-
handlers = [ VaspErrorHandler (), MeshSymmetryErrorHandler (),
-
UnconvergedErrorHandler (), NonConvergingErrorHandler (),
-
PotimErrorHandler ()]
-
c = Custodian ( handlers , get_runs ( args ), max_errors = 10 , gzipped_output = args . gzip )
-
c . run ()
-
logging . info ( "Geometry optimization complete" ) if __name__ == "__main__" :
- import argparse
-
- parser = argparse . ArgumentParser ( description = """
- converge_geometry performs a geometry optimization. What this script will do
- is run a particular VASP relaxation repeatedly until the geometry
- is converged within the first ionic step. This is a common practice for
- converging molecular geometries in VASP, especially in situations where
- the geometry needs to be precise: such as frequency calculations.
- """ ,
- epilog = """
- Author: Stephen Dacek
- Version: {} Last updated: {} """ . format ( __version__ , __date__ ))
-
- parser . add_argument (
- "-c" , "--command" , dest = "command" , nargs = "?" ,
- default = "pvasp" , type = str ,
- help = "VASP command. Defaults to pvasp. If you are using mpirun, "
- "set this to something like \" mpirun pvasp \" ." , )
-
- parser . add_argument (
- "-z" , "--gzip" , dest = "gzip" , action = "store_true" ,
- help = "Add this option to gzip the final output. Do not gzip if you "
- "are going to perform an additional static run." )
-
- parser . add_argument (
- "-mr" , "--max_relaxtions" , dest = "max_relax" ,
- default = 10 , type = int ,
- help = "Maximum number of relaxations to allow" )
-
- args = parser . parse_args ()
- do_run ( args )
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/cli/converge_kpoints.html b/docs/html/_modules/custodian/cli/converge_kpoints.html
deleted file mode 100644
index b13a54bf..00000000
--- a/docs/html/_modules/custodian/cli/converge_kpoints.html
+++ /dev/null
@@ -1,222 +0,0 @@
-
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-
custodian.cli.converge_kpoints — custodian 2019.8.23 documentation
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Source code for custodian.cli.converge_kpoints
-#!/usr/bin/env python
-
-"""
-This is a master vasp running script to perform variuos combinations of VASP
-runs.
-"""
-
-from __future__ import division
-
-__author__ = "shyuepingong"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "shyuep@gmail.com"
-__status__ = "Beta"
-__date__ = "2/4/13"
-
-import logging
-
-from custodian.custodian import Custodian
-from custodian.vasp.handlers import VaspErrorHandler , \
- UnconvergedErrorHandler
-from custodian.vasp.jobs import VaspJob
-from pymatgen.io.vasp import VaspInput , Vasprun
-
-
-FORMAT = ' %(asctime)s %(message)s '
-logging . basicConfig ( format = FORMAT , level = logging . INFO , filename = "run.log" )
-
-
-[docs] def get_runs ( vasp_command , target = 1e-3 , max_steps = 10 , mode = "linear" ):
-
energy = 0
-
vinput = VaspInput . from_directory ( "." )
-
kpoints = vinput [ "KPOINTS" ] . kpts [ 0 ]
-
for i in range ( max_steps ):
-
if mode == "linear" :
-
m = [ k * ( i + 1 ) for k in kpoints ]
-
else :
-
m = [ k + 1 for k in kpoints ]
-
if i == 0 :
-
settings = None
-
backup = True
-
else :
-
backup = False
-
v = Vasprun ( "vasprun.xml" )
-
e_per_atom = v . final_energy / len ( v . final_structure )
-
ediff = abs ( e_per_atom - energy )
-
if ediff < target :
-
logging . info ( "Converged to {} eV/atom!" . format ( ediff ))
-
break
-
else :
-
energy = e_per_atom
-
settings = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISTART" : 1 }}},
-
{ 'dict' : 'KPOINTS' ,
-
'action' : { '_set' : { 'kpoints' : [ m ]}}},
-
{ "filename" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
yield VaspJob ( vasp_command , final = False , backup = backup ,
-
suffix = ".kpoints. {} " . format ( "x" . join ( map ( str , m ))),
-
settings_override = settings ) [docs] def do_run ( args ):
-
handlers = [ VaspErrorHandler (), UnconvergedErrorHandler ()]
-
c = Custodian ( handlers , get_runs ( vasp_command = args . command . split (),
-
target = args . target , mode = args . mode ,
-
max_steps = args . max_steps ),
-
max_errors = 10 )
-
c . run () [docs] def main ():
-
import argparse
-
parser = argparse . ArgumentParser ( description = """
-
converge_kpoints perform a KPOINTS convergence. What this script will do
-
is to run a particular VASP run with increasing multiples of the initial
-
KPOINT grid until a target convergence in energy per atom is reached.
-
For example, let's say you have vasp input files that has a k-point grid
-
of 1x1x1. This script will perform sequence jobs with k-point grids of
-
1x1x1, 2x2x2, 3x3x3, 4x4x4, ... until convergence is achieved. The
-
default convergence criteria is 1meV/atom, but this can be set using the
-
--target option.
-
""" ,
-
epilog = """
-
Author: Shyue Ping Ong
-
Version: {}
-
Last updated: {} """ . format ( __version__ , __date__ ))
-
-
parser . add_argument (
-
"-c" , "--command" , dest = "command" , nargs = "?" ,
-
default = "pvasp" , type = str ,
-
help = "VASP command. Defaults to pvasp. If you are using mpirun, "
-
"set this to something like \" mpirun pvasp \" ." )
-
-
parser . add_argument (
-
"-i" , "--increment_mode" , dest = "mode" , nargs = "?" ,
-
default = "linear" , type = str , choices = [ "linear" , "inc" ],
-
help = "Mode for increasing kpoints. In linear mode, multiples of "
-
"the existing kpoints are done. E.g., 2x4x2 -> 4x8x4 -> 6x12x6. "
-
"In inc mode, all KPOINTS are incremented by 1 at each stage, "
-
"i.e., 2x4x2 -> 3x5x3 ->4x6x4. Note that the latter mode does "
-
"not preserve KPOINTS symmetry, though it is probably less "
-
"expensive." )
-
-
parser . add_argument (
-
"-m" , "--max_steps" , dest = "max_steps" , nargs = "?" ,
-
default = 10 , type = int ,
-
help = "The maximum number of KPOINTS increment steps. This puts an "
-
"upper bound on the largest KPOINT converge grid attempted." )
-
-
parser . add_argument (
-
"-t" , "--target" , dest = "target" , nargs = "?" ,
-
default = 0.001 , type = float ,
-
help = "The target converge in energy per atom to achieve "
-
"convergence. E.g., 1e-3 means the KPOINTS will be increased "
-
"until a converged of 1meV is reached."
-
)
-
-
args = parser . parse_args ()
-
do_run ( args ) if __name__ == "__main__" :
- main ()
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/cli/cstdn.html b/docs/html/_modules/custodian/cli/cstdn.html
deleted file mode 100644
index d661e4cb..00000000
--- a/docs/html/_modules/custodian/cli/cstdn.html
+++ /dev/null
@@ -1,215 +0,0 @@
-
-
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-
-
-
-
custodian.cli.cstdn — custodian 2019.8.23 documentation
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Source code for custodian.cli.cstdn
-#!/usr/bin/env python
-# Copyright (c) Materials Virtual Lab.
-# Distributed under the terms of the BSD License.
-
-from __future__ import division , unicode_literals , print_function
-
-import argparse
-
-import sys
-from monty.serialization import loadfn
-
-from custodian.custodian import Custodian
-import logging
-
-
-example_yaml = """
-# This is an example of a Custodian yaml spec file. It shows how you can specify
-# a double relaxation followed by a static calculation. Minor modifications
-# would allow very customizable calculations, though this is obviously not meant
-# for highly complex workflows. For those, you will need to code and usage of
-# FireWorks is highly recommended.
-
-
-# Specifies a list of jobs to run.
-# Each job is specified by a `jb: <full class path>` with parameters specified
-# via the params dict.
-
-jobs:
-- jb: custodian.vasp.jobs.VaspJob
- params:
- final: False
- suffix: .relax1
-- jb: custodian.vasp.jobs.VaspJob
- params:
- final: False
- suffix: .relax2
- settings_override:
- - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
-- jb: custodian.vasp.jobs.VaspJob
- params:
- final: True
- suffix: .static3
- settings_override:
- - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
- - {"dict": "INCAR", "action": {"_set": {"NSW": 0}}}
-
-
-# This key specifies parameters common to all jobs.
-# Keys starting with $ are expanded to the environmental values.
-# The example below means the parameter vasp_cmd is set to the value with
-# $PBS_NODEFILE expanded.
-
-jobs_common_params:
- $vasp_cmd: ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "24", "vasp"]
-
-
-# Specifies a list of error handlers in the same format as jobs.
-handlers:
-- hdlr: custodian.vasp.handlers.VaspErrorHandler
-- hdlr: custodian.vasp.handlers.AliasingErrorHandler
-- hdlr: custodian.vasp.handlers.MeshSymmetryErrorHandler
-
-
-# Specifies a list of error handlers in the same format as jobs.
-validators:
-- vldr: custodian.vasp.validators.VasprunXMLValidator
-
-
-#This sets all custodian running parameters.
-custodian_params:
- max_errors: 10
- scratch_dir: /tmp
- gzipped_output: True
- checkpoint: True
-"""
-
-
-[docs] def run ( args ):
-
FORMAT = ' %(asctime)s %(message)s '
-
logging . basicConfig ( format = FORMAT , level = logging . INFO , filename = "run.log" )
-
logging . info ( "Spec file is %s " % args . spec_file )
-
d = loadfn ( args . spec_file [ 0 ])
-
c = Custodian . from_spec ( d )
-
c . run () [docs] def print_example ( args ):
-
print ( example_yaml ) [docs] def main ():
-
parser = argparse . ArgumentParser ( description = """
-
cstdn is a convenient script to run custodian style jobs using a
-
simple YAML spec.""" , epilog = """Author: Shyue Ping Ong""" )
-
-
subparsers = parser . add_subparsers ()
-
-
prun = subparsers . add_parser ( "run" , help = "Run custodian." )
-
prun . add_argument ( "spec_file" , metavar = "spec_file" , type = str , nargs = 1 ,
-
help = "YAML/JSON spec file." )
-
prun . set_defaults ( func = run )
-
-
prun = subparsers . add_parser (
-
"example" , help = "Print examples. Right now, there is only one example for VASP double relaxation." )
-
prun . set_defaults ( func = print_example )
-
-
args = parser . parse_args ()
-
-
try :
-
a = getattr ( args , "func" )
-
except AttributeError :
-
parser . print_help ()
-
sys . exit ( 0 )
-
args . func ( args ) if __name__ == "__main__" :
- main ()
-
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\ No newline at end of file
diff --git a/docs/html/_modules/custodian/cli/run_nwchem.html b/docs/html/_modules/custodian/cli/run_nwchem.html
deleted file mode 100644
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custodian.cli.run_nwchem — custodian 2019.8.23 documentation
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Source code for custodian.cli.run_nwchem
-#!/usr/bin/env python
-
-"""
-Basic script to run nwchem job.
-"""
-
-from __future__ import division
-
-__author__ = "shyuepingong"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "shyuep@gmail.com"
-__status__ = "Beta"
-__date__ = "6/18/13"
-
-
-import logging
-
-from custodian.custodian import Custodian
-from custodian.nwchem.handlers import NwchemErrorHandler
-from custodian.nwchem.jobs import NwchemJob
-
-
-[docs] def do_run ( args ):
-
logging . basicConfig ( format = ' %(asctime)s %(message)s ' , level = logging . INFO ,
-
filename = "run.log" )
-
job = NwchemJob ( nwchem_cmd = args . command . split (),
-
input_file = args . infile ,
-
output_file = args . outfile )
-
c = Custodian ([ NwchemErrorHandler ( output_filename = args . outfile )], [ job ],
-
max_errors = 5 , scratch_dir = args . scratch ,
-
gzipped_output = args . gzipped , checkpoint = True )
-
c . run () [docs] def main ():
-
import argparse
-
parser = argparse . ArgumentParser ( description = """
-
run_nwchem is a master script to perform various kinds of Nwchem runs.
-
""" ,
-
epilog = """
-
Author: Shyue Ping Ong
-
Version: {}
-
Last updated: {} """ . format ( __version__ , __date__ ))
-
-
parser . add_argument (
-
"-c" , "--command" , dest = "command" , nargs = "?" ,
-
default = "nwchem" , type = str ,
-
help = "Nwchem command. Defaults to nwchem. If you are using mpirun, "
-
"set this to something like \" mpirun nwchem \" ." )
-
-
parser . add_argument (
-
"-s" , "--scratch" , dest = "scratch" , nargs = "?" ,
-
default = None , type = str ,
-
help = "Scratch directory to perform run in. Specify the root scratch "
-
"directory as the code will automatically create a temporary "
-
"subdirectory to run the job." )
-
-
parser . add_argument (
-
"-i" , "--infile" , dest = "infile" , nargs = "?" , default = "mol.nw" ,
-
type = str , help = "Input filename." )
-
-
parser . add_argument (
-
"-o" , "--output" , dest = "outfile" , nargs = "?" , default = "mol.nwout" ,
-
type = str , help = "Output filename."
-
)
-
-
parser . add_argument (
-
"-z" , "--gzip" , dest = "gzip" , action = "store_true" ,
-
help = "Add this option to gzip the final output. Do not gzip if you "
-
"are going to perform an additional static run."
-
)
-
-
args = parser . parse_args ()
-
do_run ( args ) if __name__ == "__main__" :
- main ()
-
-
-
-
-
-
-
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-
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\ No newline at end of file
diff --git a/docs/html/_modules/custodian/cli/run_vasp.html b/docs/html/_modules/custodian/cli/run_vasp.html
deleted file mode 100644
index 04d5fd63..00000000
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custodian.cli.run_vasp — custodian 2019.8.23 documentation
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Source code for custodian.cli.run_vasp
-#!/usr/bin/env python
-
-"""
-This is a master vasp running script to perform various combinations of VASP
-runs.
-"""
-
-from __future__ import division
-
-import logging
-import sys
-import ruamel.yaml as yaml
-
-from custodian.custodian import Custodian
-from custodian.vasp.jobs import VaspJob
-from pymatgen.io.vasp import VaspInput , Incar , Kpoints
-
-__author__ = "Shyue Ping Ong"
-__version__ = "0.5"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__status__ = "Beta"
-__date__ = "12/31/13"
-
-
-[docs] def load_class ( mod , name ):
-
toks = name . split ( "?" )
-
params = {}
-
if len ( toks ) == 2 :
-
for p in toks [ - 1 ] . split ( "," ):
-
ptoks = p . split ( "=" )
-
params [ ptoks [ 0 ]] = yaml . safe_load ( ptoks [ 1 ])
-
elif len ( toks ) > 2 :
-
print ( "Bad handler specification" )
-
sys . exit ( - 1 )
-
mod = __import__ ( mod , globals (), locals (), [ toks [ 0 ]], 0 )
-
return getattr ( mod , toks [ 0 ])( ** params ) [docs] def get_jobs ( args ):
-
# Returns a generator of jobs. Allows of "infinite" jobs.
-
vasp_command = args . command . split ()
-
# save initial INCAR for rampU runs
-
n_ramp_u = args . jobs . count ( 'rampU' )
-
ramps = 0
-
if n_ramp_u :
-
incar = Incar . from_file ( 'INCAR' )
-
ldauu = incar [ 'LDAUU' ]
-
ldauj = incar [ 'LDAUJ' ]
-
-
njobs = len ( args . jobs )
-
post_settings = [] # append to this list to have settings applied on next job
-
for i , job in enumerate ( args . jobs ):
-
final = False if i != njobs - 1 else True
-
if any ( c . isdigit () for c in job ):
-
suffix = "." + job
-
else :
-
suffix = ". {}{} " . format ( job , i + 1 )
-
settings = post_settings
-
post_settings = []
-
backup = True if i == 0 else False
-
copy_magmom = False
-
vinput = VaspInput . from_directory ( "." )
-
if i > 0 :
-
settings . append (
-
{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}})
-
-
job_type = job . lower ()
-
auto_npar = True
-
-
if args . no_auto_npar :
-
auto_npar = False
-
-
if job_type . startswith ( "static_derived" ):
-
from pymatgen.io.vasp.sets import MPStaticSet
-
vis = MPStaticSet . from_prev_calc (
-
"." , user_incar_settings = { "LWAVE" : True , "EDIFF" : 1e-6 },
-
ediff_per_atom = False )
-
settings . extend ([
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : dict ( vis . incar )}},
-
{ 'dict' : 'KPOINTS' ,
-
'action' : { '_set' : vis . kpoints . as_dict ()}}])
-
-
if job_type . startswith ( "static_dielectric_derived" ):
-
from pymatgen.io.vasp.sets import MPStaticSet , MPStaticDielectricDFPTVaspInputSet
-
-
# vis = MPStaticSet.from_prev_calc(
-
# ".", user_incar_settings={"EDIFF": 1e-6, "IBRION": 8,
-
# "LEPSILON": True, 'LREAL':False,
-
# "LPEAD": True, "ISMEAR": 0,
-
# "SIGMA": 0.01},
-
# ediff_per_atom=False)
-
vis = MPStaticDielectricDFPTVaspInputSet ()
-
incar = vis . get_incar ( vinput [ "POSCAR" ] . structure )
-
unset = {}
-
for k in [ "NPAR" , "KPOINT_BSE" , "LAECHG" , "LCHARG" , "LVHAR" ,
-
"NSW" ]:
-
incar . pop ( k , None )
-
if k in vinput [ "INCAR" ]:
-
unset [ k ] = 1
-
kpoints = vis . get_kpoints ( vinput [ "POSCAR" ] . structure )
-
settings . extend ([
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : dict ( incar ),
-
"_unset" : unset }},
-
{ 'dict' : 'KPOINTS' ,
-
'action' : { '_set' : kpoints . as_dict ()}}])
-
auto_npar = False
-
elif job_type . startswith ( "static" ):
-
m = [ i * args . static_kpoint for i in vinput [ "KPOINTS" ] . kpts [ 0 ]]
-
settings . extend ([
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "NSW" : 0 }}},
-
{ 'dict' : 'KPOINTS' ,
-
'action' : { '_set' : { 'kpoints' : [ m ]}}}])
-
-
elif job_type . startswith ( "nonscf_derived" ):
-
from pymatgen.io.vasp.sets import MPNonSCFSet
-
vis = MPNonSCFSet . from_prev_calc ( "." , copy_chgcar = False ,
-
user_incar_settings = { "LWAVE" : True })
-
settings . extend ([
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : dict ( vis . incar )}},
-
{ 'dict' : 'KPOINTS' ,
-
'action' : { '_set' : vis . kpoints . as_dict ()}}])
-
-
elif job_type . startswith ( "optics_derived" ):
-
from pymatgen.io.vasp.sets import MPNonSCFSet
-
vis = MPNonSCFSet . from_prev_calc (
-
"." , optics = True , copy_chgcar = False ,
-
nedos = 2001 , mode = "uniform" , nbands_factor = 5 ,
-
user_incar_settings = { "LWAVE" : True , "ALGO" : "Exact" , "SIGMA" : 0.01 , "EDIFF" : 1e-6 },
-
ediff_per_atom = False )
-
settings . extend ([
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : dict ( vis . incar )}},
-
{ 'dict' : 'KPOINTS' ,
-
'action' : { '_set' : vis . kpoints . as_dict ()}}])
-
-
elif job_type . startswith ( "rampu" ):
-
f = ramps / ( n_ramp_u - 1 )
-
settings . append (
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "LDAUJ" : [ j * f for j in ldauj ],
-
"LDAUU" : [ u * f for u in ldauu ]}}})
-
copy_magmom = True
-
ramps += 1
-
elif job_type . startswith ( "quick_relax" ) or job_type . startswith ( \
-
"quickrelax" ):
-
kpoints = vinput [ "KPOINTS" ]
-
incar = vinput [ "INCAR" ]
-
structure = vinput [ "POSCAR" ] . structure
-
if "ISMEAR" in incar :
-
post_settings . append (
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISMEAR" : incar [ "ISMEAR" ]}}})
-
else :
-
post_settings . append (
-
{ "dict" : "INCAR" ,
-
"action" : { "_unset" : { "ISMEAR" : 1 }}})
-
post_settings . append ({ "dict" : "KPOINTS" ,
-
"action" : { "_set" : kpoints . as_dict ()}})
-
# lattice vectors with length < 9 will get >1 KPOINT
-
low_kpoints = Kpoints . gamma_automatic (
-
[ max ( int ( 18 / l ), 1 ) for l in structure . lattice . abc ])
-
settings . extend ([
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISMEAR" : 0 }}},
-
{ 'dict' : 'KPOINTS' ,
-
'action' : { '_set' : low_kpoints . as_dict ()}}])
-
-
# let vasp determine encut (will be lower than
-
# needed for compatibility with other runs)
-
if "ENCUT" in incar :
-
post_settings . append (
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ENCUT" : incar [ "ENCUT" ]}}})
-
settings . append (
-
{ "dict" : "INCAR" ,
-
"action" : { "_unset" : { "ENCUT" : 1 }}})
-
-
elif job_type . startswith ( "relax" ):
-
pass
-
elif job_type . startswith ( "full_relax" ):
-
for j in VaspJob . full_opt_run (
-
vasp_command ):
-
yield j
-
else :
-
print ( "Unsupported job type: {} " . format ( job ))
-
sys . exit ( - 1 )
-
-
if not job_type . startswith ( "full_relax" ):
-
yield VaspJob ( vasp_command , final = final , suffix = suffix ,
-
backup = backup , settings_override = settings ,
-
copy_magmom = copy_magmom , auto_npar = auto_npar ) [docs] def do_run ( args ):
-
FORMAT = ' %(asctime)s %(message)s '
-
logging . basicConfig ( format = FORMAT , level = logging . INFO , filename = "run.log" )
-
logging . info ( "Handlers used are %s " % args . handlers )
-
handlers = [ load_class ( "custodian.vasp.handlers" , n ) for n in
-
args . handlers ]
-
validators = [ load_class ( "custodian.vasp.validators" , n ) for n in
-
args . validators ]
-
-
c = Custodian ( handlers , get_jobs ( args ), validators ,
-
max_errors = args . max_errors , scratch_dir = args . scratch ,
-
gzipped_output = args . gzip ,
-
checkpoint = True )
-
c . run () [docs] def main ():
-
import argparse
-
parser = argparse . ArgumentParser ( description = """
-
run_vasp is a master script to perform various kinds of VASP runs.
-
""" ,
-
epilog = """
-
Author: Shyue Ping Ong
-
Version: {}
-
Last updated: {} """ . format ( __version__ , __date__ ))
-
-
parser . add_argument (
-
"-c" , "--command" , dest = "command" , nargs = "?" ,
-
default = "pvasp" , type = str ,
-
help = "VASP command. Defaults to pvasp. If you are using mpirun, "
-
"set this to something like \" mpirun pvasp \" ." )
-
-
parser . add_argument (
-
"--no_auto_npar" , action = "store_true" ,
-
help = "Set to true to turn off auto_npar. Useful for certain machines "
-
"and calculations where you want absolute control." )
-
-
-
parser . add_argument (
-
"-z" , "--gzip" , dest = "gzip" , action = "store_true" ,
-
help = "Add this option to gzip the final output. Do not gzip if you "
-
"are going to perform an additional static run."
-
)
-
-
parser . add_argument (
-
"-s" , "--scratch" , dest = "scratch" , nargs = "?" ,
-
default = None , type = str ,
-
help = "Scratch directory to perform run in. Specify the root scratch "
-
"directory as the code will automatically create a temporary "
-
"subdirectory to run the job." )
-
-
parser . add_argument (
-
"-ks" , "--kpoint-static" , dest = "static_kpoint" , nargs = "?" ,
-
default = 1 , type = int ,
-
help = "The multiplier to use for the KPOINTS of a static run (if "
-
"any). For example, setting this to 2 means that if your "
-
"original run was done using a k-point grid of 2x3x3, "
-
"the static run will be done with a k-point grid of 4x6x6. This "
-
"defaults to 1, i.e., static runs are performed with the same "
-
"k-point grid as relaxation runs."
-
)
-
-
parser . add_argument (
-
"-me" , "--max-errors" , dest = "max_errors" , nargs = "?" ,
-
default = 10 , type = int ,
-
help = "Maximum number of errors to allow before quitting" )
-
-
parser . add_argument (
-
"-hd" , "--handlers" , dest = "handlers" , nargs = "+" ,
-
default = [ "VaspErrorHandler" , "MeshSymmetryErrorHandler" ,
-
"UnconvergedErrorHandler" , "NonConvergingErrorHandler" ,
-
"PotimErrorHandler" ], type = str ,
-
help = "The ErrorHandlers to use specified as string class names, "
-
"with optional arguments specified as a url-like string. For "
-
"example, VaspErrorHandler?output_filename=myfile.out specifies a "
-
"VaspErrorHandler with output_name set to myfile.out. Multiple "
-
"arguments are joined by a comma. E.g., MyHandler?myfile=a,"
-
"data=1. The arguments are deserialized using yaml."
-
)
-
-
parser . add_argument (
-
"-vd" , "--validators" , dest = "validators" , nargs = "+" ,
-
default = [ "VasprunXMLValidator" ], type = str ,
-
help = "The Validators to use specified as string class names, "
-
"with optional arguments specified as a url-like string. For "
-
"example, VaspErrorHandler?output_filename=myfile.out specifies a "
-
"VaspErrorHandler with output_name set to myfile.out. Multiple "
-
"arguments are joined by a comma. E.g., MyHandler?myfile=a,"
-
"data=1. The arguments are deserialized using yaml."
-
)
-
-
parser . add_argument (
-
"jobs" , metavar = "jobs" , type = str , nargs = '+' ,
-
default = [ "relax" , "relax" ],
-
help = "Jobs to execute. Only sequences of relax, "
-
"quickrelax, static, rampU, full_relax, static_derived, "
-
"nonscf_derived, optics_derived are "
-
"supported at the moment. For example, \" relax relax static \" "
-
"will run a double relaxation followed by a static "
-
"run. By default, suffixes are given sequential numbering,"
-
"but this can be overrridden by adding a number to the job"
-
"type, e.g. relax5 relax6 relax7" )
-
-
args = parser . parse_args ()
-
do_run ( args )
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/custodian.html b/docs/html/_modules/custodian/custodian.html
deleted file mode 100644
index 0aa53828..00000000
--- a/docs/html/_modules/custodian/custodian.html
+++ /dev/null
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custodian.custodian — custodian 2019.8.23 documentation
-
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Source code for custodian.custodian
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-import logging
-import subprocess
-import sys
-import datetime
-import time
-from glob import glob
-import tarfile
-import os
-from abc import ABCMeta , abstractmethod
-from itertools import islice
-import warnings
-from pprint import pformat
-from ast import literal_eval
-
-import six
-
-from .utils import get_execution_host_info
-
-from monty.tempfile import ScratchDir
-from monty.shutil import gzip_dir
-from monty.json import MSONable , MontyEncoder , MontyDecoder
-from monty.serialization import loadfn , dumpfn
-
-"""
-This module implements the main Custodian class, which manages a list of jobs
-given a set of error handlers, the abstract base classes for the
-ErrorHandlers and Jobs.
-"""
-
-__author__ = "Shyue Ping Ong, William Davidson Richards"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "0.2"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__date__ = "Sep 17 2014"
-
-
-logger = logging . getLogger ( __name__ )
-
-if "SENTRY_DSN" in os . environ :
- # Sentry.io is a service to aggregate logs remotely, this is useful
- # for Custodian to get statistics on which errors are most common.
- # If you do not have a SENTRY_DSN environment variable set, Sentry
- # will not be used.
-
- import sentry_sdk
- sentry_sdk . init ( dsn = os . environ [ "SENTRY_DSN" ])
-
- with sentry_sdk . configure_scope () as scope :
-
- from getpass import getuser
- try :
- scope . user = { "username" : getuser ()}
- except :
- pass
-
-
-
-# Sentry.io is a service to aggregate logs remotely, this is useful
-# for Custodian to get statistics on which errors are most common.
-# If you do not have a SENTRY_DSN environment variable set, or do
-# not have CUSTODIAN_ERROR_REPORTING_OPT_IN set to True, then
-# Sentry will not be enabled.
-
-SENTRY_DSN = None
-if "SENTRY_DSN" in os . environ :
- SENTRY_DSN = os . environ [ "SENTRY_DSN" ]
-elif "CUSTODIAN_REPORTING_OPT_IN" in os . environ :
- # check for environment variable to automatically set SENTRY_DSN
- # will set for True, true, TRUE, etc.
- if literal_eval ( os . environ . get ( "CUSTODIAN_REPORTING_OPT_IN" , "False" ) . title ()):
- SENTRY_DSN = "https://0f7291738eb042a3af671df9fc68ae2a@sentry.io/1470881"
-
-if SENTRY_DSN :
-
- import sentry_sdk
- sentry_sdk . init ( dsn = SENTRY_DSN )
-
- with sentry_sdk . configure_scope () as scope :
-
- from getpass import getuser
- try :
- scope . user = { "username" : getuser ()}
- except :
- pass
-
- import socket
- scope . set_tag ( "hostname" , socket . gethostname ())
-
-
-[docs] class Custodian ( object ):
-
"""
-
The Custodian class is the manager for a list of jobs given a list of
-
error handlers. The way it works is as follows:
-
-
1. Let's say you have defined a list of jobs as [job1, job2, job3, ...] and
-
you have defined a list of possible error handlers as [err1, err2, ...]
-
2. Custodian will run the jobs in the order of job1, job2, ... During each
-
job, custodian will monitor for errors using the handlers that have
-
is_monitor == True. If an error is detected, corrective measures are
-
taken and the particular job is rerun.
-
3. At the end of each individual job, Custodian will run through the list
-
error handlers that have is_monitor == False. If an error is detected,
-
corrective measures are taken and the particular job is rerun.
-
-
.. attribute: max_errors
-
-
Maximum number of errors allowed.
-
-
.. attribute: handlers
-
-
All error handlers (including monitors). All error handlers are used
-
to check for errors at the end of a run.
-
-
.. attribute: monitors
-
-
Error handlers that are Monitors, i.e., handlers that monitors a job
-
as it is being run.
-
-
.. attribute: polling_time_step
-
-
The length of time in seconds between steps in which a job is
-
checked for completion.
-
-
.. attribute: monitor_freq
-
-
The number of polling steps before monitoring occurs. For example,
-
if you have a polling_time_step of 10 seconds and a monitor_freq of
-
30, this means that Custodian uses the monitors to check for errors
-
every 30 x 10 = 300 seconds, i.e., 5 minutes.
-
"""
-
LOG_FILE = "custodian.json"
-
-
def __init__ ( self , handlers , jobs , validators = None ,
-
max_errors_per_job = None ,
-
max_errors = 1 , polling_time_step = 10 , monitor_freq = 30 ,
-
skip_over_errors = False , scratch_dir = None ,
-
gzipped_output = False , checkpoint = False , terminate_func = None ,
-
terminate_on_nonzero_returncode = True ):
-
"""
-
Initializes a Custodian from a list of jobs and error handler.s
-
-
Args:
-
handlers ([ErrorHandler]): Error handlers. In order of priority of
-
fixing.
-
jobs ([Job]): Sequence of Jobs to be run. Note that this can be
-
any sequence or even a generator yielding jobs.
-
validators([Validator]): Validators to ensure job success
-
max_errors_per_job (int): Maximum number of errors per job allowed
-
before exiting. Defaults to None, which means it is set to be
-
equal to max_errors..
-
max_errors (int): Maximum number of total errors allowed before
-
exiting. Defaults to 1.
-
polling_time_step (int): The length of time in seconds between
-
steps in which a job is checked for completion. Defaults to
-
10 secs.
-
monitor_freq (int): The number of polling steps before monitoring
-
occurs. For example, if you have a polling_time_step of 10
-
seconds and a monitor_freq of 30, this means that Custodian
-
uses the monitors to check for errors every 30 x 10 = 300
-
seconds, i.e., 5 minutes.
-
skip_over_errors (bool): If set to True, custodian will skip over
-
error handlers that failed (raised an Exception of some sort).
-
Otherwise, custodian will simply exit on unrecoverable errors.
-
The former will lead to potentially more robust performance,
-
but may make it difficult to improve handlers. The latter
-
will allow one to catch potentially bad error handler
-
implementations. Defaults to False.
-
scratch_dir (str): If this is set, any files in the current
-
directory are copied to a temporary directory in a scratch
-
space first before any jobs are performed, and moved back to
-
the current directory upon completion of all jobs. This is
-
useful in some setups where a scratch partition has much
-
faster IO. To use this, set scratch_dir=root of directory you
-
want to use for runs. There is no need to provide unique
-
directory names; we will use python's tempfile creation
-
mechanisms. A symbolic link is created during the course of
-
the run in the working directory called "scratch_link" as
-
users may want to sometimes check the output during the
-
course of a run. If this is None (the default), the run is
-
performed in the current working directory.
-
gzipped_output (bool): Whether to gzip the final output to save
-
space. Defaults to False.
-
checkpoint (bool): Whether to checkpoint after each successful Job.
-
Checkpoints are stored as custodian.chk.#.tar.gz files. Defaults
-
to False.
-
terminate_func (callable): A function to be called to terminate a
-
running job. If None, the default is to call Popen.terminate.
-
terminate_on_nonzero_returncode (bool): If True, a non-zero return
-
code on any Job will result in a termination. Defaults to True.
-
"""
-
self . max_errors = max_errors
-
self . max_errors_per_job = max_errors_per_job or max_errors
-
self . jobs = jobs
-
self . handlers = handlers
-
self . validators = validators or []
-
self . monitors = [ h for h in handlers if h . is_monitor ]
-
self . polling_time_step = polling_time_step
-
self . monitor_freq = monitor_freq
-
self . skip_over_errors = skip_over_errors
-
self . scratch_dir = scratch_dir
-
self . gzipped_output = gzipped_output
-
self . checkpoint = checkpoint
-
cwd = os . getcwd ()
-
if self . checkpoint :
-
self . restart , self . run_log = Custodian . _load_checkpoint ( cwd )
-
else :
-
self . restart = 0
-
self . run_log = []
-
self . errors_current_job = 0
-
self . total_errors = 0
-
self . terminate_func = terminate_func
-
self . terminate_on_nonzero_returncode = terminate_on_nonzero_returncode
-
self . finished = False
-
-
@staticmethod
-
def _load_checkpoint ( cwd ):
-
restart = 0
-
run_log = []
-
chkpts = glob ( os . path . join ( cwd , "custodian.chk.*.tar.gz" ))
-
if chkpts :
-
chkpt = sorted ( chkpts , key = lambda c : int ( c . split ( "." )[ - 3 ]))[ 0 ]
-
restart = int ( chkpt . split ( "." )[ - 3 ])
-
logger . info ( "Loading from checkpoint file {} ..." . format ( chkpt ))
-
t = tarfile . open ( chkpt )
-
t . extractall ()
-
# Log the corrections to a json file.
-
run_log = loadfn ( Custodian . LOG_FILE , cls = MontyDecoder )
-
-
return restart , run_log
-
-
@staticmethod
-
def _delete_checkpoints ( cwd ):
-
for f in glob ( os . path . join ( cwd , "custodian.chk.*.tar.gz" )):
-
os . remove ( f )
-
-
@staticmethod
-
def _save_checkpoint ( cwd , index ):
-
try :
-
Custodian . _delete_checkpoints ( cwd )
-
n = os . path . join ( cwd , "custodian.chk. {} .tar.gz" . format ( index ))
-
with tarfile . open ( n , mode = "w:gz" , compresslevel = 3 ) as f :
-
f . add ( cwd , arcname = '.' )
-
logger . info ( "Checkpoint written to {} " . format ( n ))
-
except Exception as ex :
-
logger . info ( "Checkpointing failed" )
-
import traceback
-
logger . error ( traceback . format_exc ())
-
-
[docs] @classmethod
-
def from_spec ( cls , spec ):
-
"""
-
Load a Custodian instance where the jobs are specified from a
-
structure and a spec dict. This allows simple
-
custom job sequences to be constructed quickly via a YAML file.
-
-
Args:
-
spec (dict): A dict specifying job. A sample of the dict in
-
YAML format for the usual MP workflow is given as follows
-
-
```
-
jobs:
-
- jb: custodian.vasp.jobs.VaspJob
-
params:
-
final: False
-
suffix: .relax1
-
- jb: custodian.vasp.jobs.VaspJob
-
params:
-
final: True
-
suffix: .relax2
-
settings_override: {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}
-
jobs_common_params:
-
vasp_cmd: /opt/vasp
-
handlers:
-
- hdlr: custodian.vasp.handlers.VaspErrorHandler
-
- hdlr: custodian.vasp.handlers.AliasingErrorHandler
-
- hdlr: custodian.vasp.handlers.MeshSymmetryHandler
-
validators:
-
- vldr: custodian.vasp.validators.VasprunXMLValidator
-
custodian_params:
-
scratch_dir: /tmp
-
```
-
-
The `jobs` key is a list of jobs. Each job is
-
specified via "job": <explicit path>, and all parameters are
-
specified via `params` which is a dict.
-
-
`common_params` specify a common set of parameters that are
-
passed to all jobs, e.g., vasp_cmd.
-
-
Returns:
-
Custodian instance.
-
"""
-
-
dec = MontyDecoder ()
-
-
def load_class ( dotpath ):
-
modname , classname = dotpath . rsplit ( "." , 1 )
-
mod = __import__ ( modname , globals (), locals (), [ classname ], 0 )
-
return getattr ( mod , classname )
-
-
def process_params ( d ):
-
decoded = {}
-
for k , v in d . items ():
-
if k . startswith ( "$" ):
-
if isinstance ( v , list ):
-
v = [ os . path . expandvars ( i ) for i in v ]
-
elif isinstance ( v , dict ):
-
v = { k2 : os . path . expandvars ( v2 ) for k2 , v2 in v . items ()}
-
else :
-
v = os . path . expandvars ( v )
-
decoded [ k . strip ( "$" )] = dec . process_decoded ( v )
-
return decoded
-
-
jobs = []
-
common_params = process_params ( spec . get ( "jobs_common_params" , {}))
-
-
for d in spec [ "jobs" ]:
-
cls_ = load_class ( d [ "jb" ])
-
params = process_params ( d . get ( "params" , {}))
-
params . update ( common_params )
-
jobs . append ( cls_ ( ** params ))
-
-
handlers = []
-
for d in spec . get ( "handlers" , []):
-
cls_ = load_class ( d [ "hdlr" ])
-
params = process_params ( d . get ( "params" , {}))
-
handlers . append ( cls_ ( ** params ))
-
-
validators = []
-
for d in spec . get ( "validators" , []):
-
cls_ = load_class ( d [ "vldr" ])
-
params = process_params ( d . get ( "params" , {}))
-
validators . append ( cls_ ( ** params ))
-
-
custodian_params = process_params ( spec . get ( "custodian_params" , {}))
-
-
return cls ( jobs = jobs , handlers = handlers , validators = validators ,
-
** custodian_params )
-
-
[docs] def run ( self ):
-
"""
-
Runs all jobs.
-
-
Returns:
-
All errors encountered as a list of list.
-
[[error_dicts for job 1], [error_dicts for job 2], ....]
-
-
Raises:
-
ValidationError: if a job fails validation
-
ReturnCodeError: if the process has a return code different from 0
-
NonRecoverableError: if an unrecoverable occurs
-
MaxCorrectionsPerJobError: if max_errors_per_job is reached
-
MaxCorrectionsError: if max_errors is reached
-
MaxCorrectionsPerHandlerError: if max_errors_per_handler is reached
-
"""
-
cwd = os . getcwd ()
-
-
with ScratchDir ( self . scratch_dir , create_symbolic_link = True ,
-
copy_to_current_on_exit = True ,
-
copy_from_current_on_enter = True ) as temp_dir :
-
self . total_errors = 0
-
start = datetime . datetime . now ()
-
logger . info ( "Run started at {} in {} ." . format (
-
start , temp_dir ))
-
v = sys . version . replace ( " \n " , " " )
-
logger . info ( "Custodian running on Python version {} " . format ( v ))
-
logger . info ( "Hostname: {} , Cluster: {} " . format (
-
* get_execution_host_info ()))
-
-
try :
-
# skip jobs until the restart
-
for job_n , job in islice ( enumerate ( self . jobs , 1 ),
-
self . restart , None ):
-
self . _run_job ( job_n , job )
-
# We do a dump of the run log after each job.
-
dumpfn ( self . run_log , Custodian . LOG_FILE , cls = MontyEncoder ,
-
indent = 4 )
-
# Checkpoint after each job so that we can recover from last
-
# point and remove old checkpoints
-
if self . checkpoint :
-
self . restart = job_n
-
Custodian . _save_checkpoint ( cwd , job_n )
-
except CustodianError as ex :
-
logger . error ( ex . message )
-
if ex . raises :
-
raise
-
finally :
-
# Log the corrections to a json file.
-
logger . info ( "Logging to {} ..." . format ( Custodian . LOG_FILE ))
-
dumpfn ( self . run_log , Custodian . LOG_FILE , cls = MontyEncoder ,
-
indent = 4 )
-
end = datetime . datetime . now ()
-
logger . info ( "Run ended at {} ." . format ( end ))
-
run_time = end - start
-
logger . info ( "Run completed. Total time taken = {} ."
-
. format ( run_time ))
-
if self . gzipped_output :
-
gzip_dir ( "." )
-
-
# Cleanup checkpoint files (if any) if run is successful.
-
Custodian . _delete_checkpoints ( cwd )
-
-
return self . run_log
-
-
def _run_job ( self , job_n , job ):
-
"""
-
Runs a single job.
-
-
Args:
-
job_n: job number (1 index)
-
job: Custodian job
-
-
-
Raises:
-
ValidationError: if a job fails validation
-
ReturnCodeError: if the process has a return code different from 0
-
NonRecoverableError: if an unrecoverable occurs
-
MaxCorrectionsPerJobError: if max_errors_per_job is reached
-
MaxCorrectionsError: if max_errors is reached
-
MaxCorrectionsPerHandlerError: if max_errors_per_handler is reached
-
"""
-
self . run_log . append ({ "job" : job . as_dict (), "corrections" : [],
-
"handler" : None , "validator" : None ,
-
"max_errors" : False , "max_errors_per_job" : False ,
-
"max_errors_per_handler" : False ,
-
"nonzero_return_code" : False })
-
self . errors_current_job = 0
-
# reset the counters of the number of times a correction has been
-
# applied for each handler
-
for h in self . handlers :
-
h . n_applied_corrections = 0
-
-
job . setup ()
-
-
attempt = 0
-
while ( self . total_errors < self . max_errors and
-
self . errors_current_job < self . max_errors_per_job ):
-
attempt += 1
-
logger . info (
-
"Starting job no. {} ( {} ) attempt no. {} . Total errors and "
-
"errors in job thus far = {} , {} ." . format (
-
job_n , job . name , attempt , self . total_errors ,
-
self . errors_current_job ))
-
-
p = job . run ()
-
# Check for errors using the error handlers and perform
-
# corrections.
-
has_error = False
-
zero_return_code = True
-
-
# While the job is running, we use the handlers that are
-
# monitors to monitor the job.
-
if isinstance ( p , subprocess . Popen ):
-
if self . monitors :
-
n = 0
-
while True :
-
n += 1
-
time . sleep ( self . polling_time_step )
-
if p . poll () is not None :
-
break
-
terminate = self . terminate_func or p . terminate
-
if n % self . monitor_freq == 0 :
-
has_error = self . _do_check ( self . monitors ,
-
terminate )
-
if terminate is not None and terminate != p . terminate :
-
time . sleep ( self . polling_time_step )
-
else :
-
p . wait ()
-
if self . terminate_func is not None and \
-
self . terminate_func != p . terminate :
-
self . terminate_func ()
-
time . sleep ( self . polling_time_step )
-
-
zero_return_code = p . returncode == 0
-
-
logger . info ( " {} .run has completed. "
-
"Checking remaining handlers" . format ( job . name ))
-
# Check for errors again, since in some cases non-monitor
-
# handlers fix the problems detected by monitors
-
# if an error has been found, not all handlers need to run
-
if has_error :
-
self . _do_check ([ h for h in self . handlers
-
if not h . is_monitor ])
-
else :
-
has_error = self . _do_check ( self . handlers )
-
-
if has_error :
-
# This makes sure the job is killed cleanly for certain systems.
-
job . terminate ()
-
-
# If there are no errors detected, perform
-
# postprocessing and exit.
-
if not has_error :
-
for v in self . validators :
-
if v . check ():
-
self . run_log [ - 1 ][ "validator" ] = v
-
s = "Validation failed: {} " . format ( v . __class__ . __name__ )
-
raise ValidationError ( s , True , v )
-
if not zero_return_code :
-
if self . terminate_on_nonzero_returncode :
-
self . run_log [ - 1 ][ "nonzero_return_code" ] = True
-
s = "Job return code is %d . Terminating..." % \
-
p . returncode
-
logger . info ( s )
-
raise ReturnCodeError ( s , True )
-
else :
-
warnings . warn ( "subprocess returned a non-zero return "
-
"code. Check outputs carefully..." )
-
job . postprocess ()
-
return
-
-
# Check that all errors could be handled
-
for x in self . run_log [ - 1 ][ "corrections" ]:
-
if not x [ "actions" ] and x [ "handler" ] . raises_runtime_error :
-
self . run_log [ - 1 ][ "handler" ] = x [ "handler" ]
-
s = "Unrecoverable error for handler: {} " . format ( x [ "handler" ])
-
raise NonRecoverableError ( s , True , x [ "handler" ])
-
for x in self . run_log [ - 1 ][ "corrections" ]:
-
if not x [ "actions" ]:
-
self . run_log [ - 1 ][ "handler" ] = x [ "handler" ]
-
s = "Unrecoverable error for handler: %s " % x [ "handler" ]
-
raise NonRecoverableError ( s , False , x [ "handler" ])
-
-
if self . errors_current_job >= self . max_errors_per_job :
-
self . run_log [ - 1 ][ "max_errors_per_job" ] = True
-
msg = "Max errors per job reached: {} ." . format ( self . max_errors_per_job )
-
logger . info ( msg )
-
raise MaxCorrectionsPerJobError ( msg , True , self . max_errors_per_job , job )
-
else :
-
self . run_log [ - 1 ][ "max_errors" ] = True
-
msg = "Max errors reached: {} ." . format ( self . max_errors )
-
logger . info ( msg )
-
raise MaxCorrectionsError ( msg , True , self . max_errors )
-
-
[docs] def run_interrupted ( self ):
-
"""
-
Runs custodian in a interuppted mode, which sets up and
-
validates jobs but doesn't run the executable
-
-
Returns:
-
number of remaining jobs
-
-
Raises:
-
ValidationError: if a job fails validation
-
ReturnCodeError: if the process has a return code different from 0
-
NonRecoverableError: if an unrecoverable occurs
-
MaxCorrectionsPerJobError: if max_errors_per_job is reached
-
MaxCorrectionsError: if max_errors is reached
-
MaxCorrectionsPerHandlerError: if max_errors_per_handler is reached
-
"""
-
start = datetime . datetime . now ()
-
try :
-
cwd = os . getcwd ()
-
v = sys . version . replace ( " \n " , " " )
-
logger . info ( "Custodian started in singleshot mode at {} in {} ."
-
. format ( start , cwd ))
-
logger . info ( "Custodian running on Python version {} " . format ( v ))
-
-
# load run log
-
if os . path . exists ( Custodian . LOG_FILE ):
-
self . run_log = loadfn ( Custodian . LOG_FILE , cls = MontyDecoder )
-
-
if len ( self . run_log ) == 0 :
-
# starting up an initial job - setup input and quit
-
job_n = 0
-
job = self . jobs [ job_n ]
-
logger . info ( "Setting up job no. 1 ( {} ) " . format ( job . name ))
-
job . setup ()
-
self . run_log . append ({ "job" : job . as_dict (), "corrections" : [],
-
'job_n' : job_n })
-
return len ( self . jobs )
-
else :
-
# Continuing after running calculation
-
job_n = self . run_log [ - 1 ][ 'job_n' ]
-
job = self . jobs [ job_n ]
-
-
# If we had to fix errors from a previous run, insert clean log
-
# dict
-
if len ( self . run_log [ - 1 ][ 'corrections' ]) > 0 :
-
logger . info ( "Reran {} .run due to fixable errors" . format (
-
job . name ))
-
-
# check error handlers
-
logger . info ( "Checking error handlers for {} .run" . format (
-
job . name ))
-
if self . _do_check ( self . handlers ):
-
logger . info ( "Failed validation based on error handlers" )
-
# raise an error for an unrecoverable error
-
for x in self . run_log [ - 1 ][ "corrections" ]:
-
if not x [ "actions" ] and x [ "handler" ] . raises_runtime_error :
-
self . run_log [ - 1 ][ "handler" ] = x [ "handler" ]
-
s = "Unrecoverable error for handler: {} . " \
-
"Raising RuntimeError" . format ( x [ "handler" ])
-
raise NonRecoverableError ( s , True , x [ "handler" ])
-
logger . info ( "Corrected input based on error handlers" )
-
# Return with more jobs to run if recoverable error caught
-
# and corrected for
-
return len ( self . jobs ) - job_n
-
-
# check validators
-
logger . info ( "Checking validator for {} .run" . format ( job . name ))
-
for v in self . validators :
-
if v . check ():
-
self . run_log [ - 1 ][ "validator" ] = v
-
logger . info ( "Failed validation based on validator" )
-
s = "Validation failed: {} " . format ( v )
-
raise ValidationError ( s , True , v )
-
-
logger . info ( "Postprocessing for {} .run" . format ( job . name ))
-
job . postprocess ()
-
-
# IF DONE WITH ALL JOBS - DELETE ALL CHECKPOINTS AND RETURN
-
# VALIDATED
-
if len ( self . jobs ) == ( job_n + 1 ):
-
self . finished = True
-
return 0
-
-
# Setup next job_n
-
job_n += 1
-
job = self . jobs [ job_n ]
-
self . run_log . append ({ "job" : job . as_dict (), "corrections" : [],
-
'job_n' : job_n })
-
job . setup ()
-
return len ( self . jobs ) - job_n
-
-
except CustodianError as ex :
-
logger . error ( ex . message )
-
if ex . raises :
-
raise
-
-
finally :
-
# Log the corrections to a json file.
-
logger . info ( "Logging to {} ..." . format ( Custodian . LOG_FILE ))
-
dumpfn ( self . run_log , Custodian . LOG_FILE , cls = MontyEncoder ,
-
indent = 4 )
-
end = datetime . datetime . now ()
-
logger . info ( "Run ended at {} ." . format ( end ))
-
run_time = end - start
-
logger . info ( "Run completed. Total time taken = {} ."
-
. format ( run_time ))
-
if self . finished and self . gzipped_output :
-
gzip_dir ( "." )
-
-
def _do_check ( self , handlers , terminate_func = None ):
-
"""
-
checks the specified handlers. Returns True iff errors caught
-
"""
-
corrections = []
-
for h in handlers :
-
try :
-
if h . check ():
-
if h . max_num_corrections is not None \
-
and h . n_applied_corrections >= h . max_num_corrections :
-
msg = "Maximum number of corrections {} reached " \
-
"for handler {} " . format ( h . max_num_corrections , h )
-
if h . raise_on_max :
-
self . run_log [ - 1 ][ "handler" ] = h
-
self . run_log [ - 1 ][ "max_errors_per_handler" ] = True
-
raise MaxCorrectionsPerHandlerError ( msg , True , h . max_num_corrections , h )
-
else :
-
logger . warning ( msg + " Correction not applied." )
-
continue
-
if terminate_func is not None and h . is_terminating :
-
logger . info ( "Terminating job" )
-
terminate_func ()
-
# make sure we don't terminate twice
-
terminate_func = None
-
d = h . correct ()
-
logger . error ( h . __class__ . __name__ , extra = d )
-
d [ "handler" ] = h
-
corrections . append ( d )
-
h . n_applied_corrections += 1
-
except Exception :
-
if not self . skip_over_errors :
-
raise
-
else :
-
import traceback
-
logger . error ( "Bad handler %s " % h )
-
logger . error ( traceback . format_exc ())
-
corrections . append (
-
{ "errors" : [ "Bad handler %s " % h ],
-
"actions" : []})
-
self . total_errors += len ( corrections )
-
self . errors_current_job += len ( corrections )
-
self . run_log [ - 1 ][ "corrections" ] . extend ( corrections )
-
# We do a dump of the run log after each check.
-
dumpfn ( self . run_log , Custodian . LOG_FILE , cls = MontyEncoder ,
-
indent = 4 )
-
return len ( corrections ) > 0 [docs] class Job ( six . with_metaclass ( ABCMeta , MSONable )):
-
"""
-
Abstract base class defining the interface for a Job.
-
"""
-
-
[docs] @abstractmethod
-
def setup ( self ):
-
"""
-
This method is run before the start of a job. Allows for some
-
pre-processing.
-
"""
-
pass
-
-
[docs] @abstractmethod
-
def run ( self ):
-
"""
-
This method perform the actual work for the job. If parallel error
-
checking (monitoring) is desired, this must return a Popen process.
-
"""
-
pass
-
-
[docs] @abstractmethod
-
def postprocess ( self ):
-
"""
-
This method is called at the end of a job, *after* error detection.
-
This allows post-processing, such as cleanup, analysis of results,
-
etc.
-
"""
-
pass
-
-
[docs] def terminate ( self ):
-
return None
-
-
@property
-
def name ( self ):
-
"""
-
A nice string name for the job.
-
"""
-
return self . __class__ . __name__ [docs] class ErrorHandler ( MSONable ):
-
"""
-
Abstract base class defining the interface for an ErrorHandler.
-
"""
-
-
is_monitor = False
-
"""
-
This class property indicates whether the error handler is a monitor,
-
i.e., a handler that monitors a job as it is running. If a
-
monitor-type handler notices an error, the job will be sent a
-
termination signal, the error is then corrected,
-
and then the job is restarted. This is useful for catching errors
-
that occur early in the run but do not cause immediate failure.
-
"""
-
-
is_terminating = True
-
"""
-
Whether this handler terminates a job upon error detection. By
-
default, this is True, which means that the current Job will be
-
terminated upon error detection, corrections applied,
-
and restarted. In some instances, some errors may not need the job to be
-
terminated or may need to wait for some other event to terminate a job.
-
For example, a particular error may require a flag to be set to request
-
a job to terminate gracefully once it finishes its current task. The
-
handler to set the flag should be classified as is_terminating = False to
-
not terminate the job.
-
"""
-
-
raises_runtime_error = True
-
"""
-
Whether this handler causes custodian to raise a runtime error if it cannot
-
handle the error (i.e. if correct returns a dict with "actions":None, or
-
"actions":[])
-
"""
-
-
max_num_corrections = None
-
raise_on_max = False
-
"""
-
Whether corrections from this specific handler should be applied only a
-
fixed maximum number of times on a single job (i.e. the counter is reset
-
at the beginning of each job). If the maximum number is reached the code
-
will either raise a MaxCorrectionsPerHandlerError (raise_on_max==True) or stops
-
considering the correction (raise_on_max==False). If max_num_corrections
-
is None this option is not considered. These options can be overridden
-
as class attributes of the subclass or as customizable options setting
-
an instance attribute from __init__.
-
"""
-
-
[docs] @abstractmethod
-
def check ( self ):
-
"""
-
This method is called during the job (for monitors) or at the end of
-
the job to check for errors.
-
-
Returns:
-
(bool) Indicating if errors are detected.
-
"""
-
pass
-
-
[docs] @abstractmethod
-
def correct ( self ):
-
"""
-
This method is called at the end of a job when an error is detected.
-
It should perform any corrective measures relating to the detected
-
error.
-
-
Returns:
-
(dict) JSON serializable dict that describes the errors and
-
actions taken. E.g.
-
{"errors": list_of_errors, "actions": list_of_actions_taken}.
-
If this is an unfixable error, actions should be set to None.
-
"""
-
pass
-
-
@property
-
def n_applied_corrections ( self ):
-
"""
-
The number of times the handler has given a correction and this
-
has been applied.
-
-
Returns:
-
(int): the number of corrections applied.
-
"""
-
try :
-
return self . _num_applied_corrections
-
except AttributeError :
-
self . _num_applied_corrections = 0
-
return self . _num_applied_corrections
-
-
@n_applied_corrections . setter
-
def n_applied_corrections ( self , value ):
-
"""
-
Setter for the number of corrections applied.
-
-
Args:
-
value(int): the number of corrections applied
-
"""
-
self . _num_applied_corrections = value [docs] class Validator ( six . with_metaclass ( ABCMeta , MSONable )):
-
"""
-
Abstract base class defining the interface for a Validator. A Validator
-
differs from an ErrorHandler in that it does not correct a run and is run
-
only at the end of a Job. If errors are detected by a Validator, a run is
-
immediately terminated.
-
"""
-
-
[docs] @abstractmethod
-
def check ( self ):
-
"""
-
This method is called at the end of a job.
-
-
Returns:
-
(bool) Indicating if errors are detected.
-
"""
-
pass [docs] class CustodianError ( RuntimeError ):
-
"""
-
Exception class for Custodian errors.
-
"""
-
-
def __init__ ( self , message , raises = False ):
-
"""
-
Initializes the error with a message.
-
-
Args:
-
message (str): Message passed to Exception
-
raises (bool): Whether this should be raised outside custodian
-
"""
-
super ( CustodianError , self ) . __init__ ( message )
-
self . raises = raises
-
self . message = message [docs] class ValidationError ( CustodianError ):
-
"""
-
Error raised when a validator does not pass the check
-
"""
-
-
def __init__ ( self , message , raises , validator ):
-
"""
-
Args:
-
message (str): Message passed to Exception
-
raises (bool): Whether this should be raised outside custodian
-
validator (Validator): Validator that caused the exception.
-
"""
-
super ( ValidationError , self ) . __init__ ( message , raises )
-
self . validator = validator [docs] class NonRecoverableError ( CustodianError ):
-
"""
-
Error raised when a handler found an error but could not fix it
-
"""
-
-
def __init__ ( self , message , raises , handler ):
-
"""
-
Args:
-
message (str): Message passed to Exception
-
raises (bool): Whether this should be raised outside custodian
-
handler (Handler): Handler that caused the exception.
-
"""
-
super ( NonRecoverableError , self ) . __init__ ( message , raises )
-
self . handler = handler [docs] class ReturnCodeError ( CustodianError ):
-
"""
-
Error raised when the process gave non zero return code
-
"""
-
pass [docs] class MaxCorrectionsError ( CustodianError ):
-
"""
-
Error raised when the maximum allowed number of errors is reached
-
"""
-
-
def __init__ ( self , message , raises , max_errors ):
-
"""
-
Args:
-
message (str): Message passed to Exception
-
raises (bool): Whether this should be raised outside custodian
-
max_errors (int): the number of errors reached
-
"""
-
super ( MaxCorrectionsError , self ) . __init__ ( message , raises )
-
self . max_errors = max_errors [docs] class MaxCorrectionsPerJobError ( CustodianError ):
-
"""
-
Error raised when the maximum allowed number of errors per job is reached
-
"""
-
-
def __init__ ( self , message , raises , max_errors_per_job , job ):
-
"""
-
Args:
-
message (str): Message passed to Exception
-
raises (bool): Whether this should be raised outside custodian
-
max_errors_per_job (int): the number of errors per job reached
-
job (Job): the job that was stopped
-
"""
-
super ( MaxCorrectionsPerJobError , self ) . __init__ ( message , raises )
-
self . max_errors_per_job = max_errors_per_job
-
self . job = job [docs] class MaxCorrectionsPerHandlerError ( CustodianError ):
-
"""
-
Error raised when the maximum allowed number of errors per handler is reached
-
"""
-
-
def __init__ ( self , message , raises , max_errors_per_handler , handler ):
-
"""
-
Args:
-
message (str): Message passed to Exception
-
raises (bool): Whether this should be raised outside custodian
-
max_errors_per_handler (int): the number of errors per job reached
-
handler (Handler): the handler that caused the exception
-
"""
-
super ( MaxCorrectionsPerHandlerError , self ) . __init__ ( message , raises )
-
self . max_errors_per_handler = max_errors_per_handler
-
self . handler = handler
-
-
-
-
-
-
-
-
-
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-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/feff/handlers.html b/docs/html/_modules/custodian/feff/handlers.html
deleted file mode 100644
index 41572ad8..00000000
--- a/docs/html/_modules/custodian/feff/handlers.html
+++ /dev/null
@@ -1,217 +0,0 @@
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custodian.feff.handlers — custodian 2019.8.23 documentation
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Source code for custodian.feff.handlers
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-from custodian.custodian import ErrorHandler
-import re
-from custodian.utils import backup
-from pymatgen.io.feff.sets import FEFFDictSet
-from custodian.feff.interpreter import FeffModder
-import logging
-
-""" This module implements specific error handler for FEFF runs. """
-
-__author__ = "Chen Zheng"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Chen Zheng"
-__email__ = "chz022@ucsd.edu"
-__date__ = "Oct 18, 2017"
-
-FEFF_BACKUP_FILES = [ "ATOMS" , "HEADER" , "PARAMETERS" , "POTENTIALS" , "feff.inp" , "*.cif" , "pot.bin" ]
-
-logger = logging . getLogger ( __name__ )
-
-
-[docs] class UnconvergedErrorHandler ( ErrorHandler ):
-
"""
-
Correct the unconverged error of FEFF's SCF calculation.
-
"""
-
-
is_monitor = False
-
-
def __init__ ( self , output_filename = 'log1.dat' ):
-
"""
-
Initializes the handler with the output file to check
-
-
Args:
-
output_filename (str): Filename for the log1.dat file. log1.dat file
-
contains the SCF calculation convergence information. Change this only
-
if it is different from the default (unlikely).
-
"""
-
self . output_filename = output_filename
-
-
[docs] def check ( self ):
-
"""
-
If the FEFF run does not converge, the check will return
-
"TRUE"
-
"""
-
return self . _notconverge_check ()
-
-
def _notconverge_check ( self ):
-
-
# Process the output file and get converge information
-
not_converge_pattern = re . compile ( "Convergence not reached.*" )
-
converge_pattern = re . compile ( 'Convergence reached.*' )
-
for _ , line in enumerate ( open ( self . output_filename )):
-
if len ( not_converge_pattern . findall ( line )) > 0 :
-
return True
-
-
elif len ( converge_pattern . findall ( line )) > 0 :
-
return False
-
-
[docs] def correct ( self ):
-
backup ( FEFF_BACKUP_FILES )
-
feff_input = FEFFDictSet . from_directory ( "." )
-
scf_values = feff_input . tags . get ( "SCF" )
-
nscmt = scf_values [ 2 ]
-
ca = scf_values [ 3 ]
-
nmix = scf_values [ 4 ]
-
actions = []
-
-
#Add RESTART card to PARAMETERS
-
if not "RESTART" in feff_input . tags :
-
actions . append ({ "dict" : "PARAMETERS" ,
-
"action" : { "_set" : { "RESTART" : []}}})
-
-
if nscmt < 100 and ca == 0.2 :
-
scf_values [ 2 ] = 100
-
scf_values [ 4 ] = 3 # Set nmix = 3
-
actions . append ({ "dict" : "PARAMETERS" ,
-
"action" : { "_set" : { "SCF" : scf_values }}})
-
FeffModder () . apply_actions ( actions )
-
return { "errors" : [ "Non-converging job" ], "actions" : actions }
-
-
elif nscmt == 100 and nmix == 3 and ca > 0.01 :
-
# Reduce the convergence accelerator factor
-
scf_values [ 3 ] = round ( ca / 2 , 2 )
-
actions . append ({ "dict" : "PARAMETERS" ,
-
"action" : { "_set" : { "SCF" : scf_values }}})
-
FeffModder () . apply_actions ( actions )
-
return { "errors" : [ "Non-converging job" ], "actions" : actions }
-
-
elif nmix == 3 and ca == 0.01 :
-
# Set ca = 0.05 and set nmix
-
scf_values [ 3 ] = 0.05
-
scf_values [ 4 ] = 5
-
actions . append ({ "dict" : "PARAMETERS" ,
-
"action" : { "_set" : { "SCF" : scf_values }}})
-
FeffModder () . apply_actions ( actions )
-
return { "errors" : [ "Non-converging job" ], "actions" : actions }
-
-
elif nmix == 5 and ca == 0.05 :
-
# Set ca = 0.05 and set nmix
-
scf_values [ 3 ] = 0.05
-
scf_values [ 4 ] = 10
-
actions . append ({ "dict" : "PARAMETERS" ,
-
"action" : { "_set" : { "SCF" : scf_values }}})
-
FeffModder () . apply_actions ( actions )
-
return { "errors" : [ "Non-converging job" ], "actions" : actions }
-
-
elif nmix == 10 and ca < 0.2 :
-
# loop through ca with nmix = 10
-
scf_values [ 3 ] = round ( ca * 2 , 2 )
-
actions . append ({ "dict" : "PARAMETERS" ,
-
"action" : { "_set" : { "SCF" : scf_values }}})
-
FeffModder () . apply_actions ( actions )
-
return { "errors" : [ "Non-converging job" ], "actions" : actions }
-
-
# Unfixable error. Just return None for actions.
-
else :
-
return { "errors" : [ "Non-converging job" ], "actions" : None }
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/feff/interpreter.html b/docs/html/_modules/custodian/feff/interpreter.html
deleted file mode 100644
index 2717bfb8..00000000
--- a/docs/html/_modules/custodian/feff/interpreter.html
+++ /dev/null
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custodian.feff.interpreter — custodian 2019.8.23 documentation
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Source code for custodian.feff.interpreter
-# coding: utf-8
-
-from __future__ import unicode_literals
-
-from custodian.ansible.actions import FileActions , DictActions
-from custodian.ansible.interpreter import Modder
-from pymatgen.io.feff.sets import FEFFDictSet
-import six
-import os
-
-
-[docs] class FeffModder ( Modder ):
-
def __init__ ( self , actions = None , strict = True , feffinp = None ):
-
"""
-
Initializes a Modder for FeffInput sets
-
-
Args:
-
actions ([Action]): A sequence of supported actions. See
-
actions ([Action]): A sequence of supported actions. See
-
:mod:`custodian.ansible.actions`. Default is None,
-
which means DictActions and FileActions are supported.
-
strict (bool): Indicating whether to use strict mode. In non-strict
-
mode, unsupported actions are simply ignored without any
-
errors raised. In strict mode, if an unsupported action is
-
supplied, a ValueError is raised. Defaults to True.
-
feffinp (FEFFInput): A FeffInput object from the current directory.
-
Initialized automatically if not passed (but passing it will
-
avoid having to reparse the directory).
-
"""
-
self . feffinp = feffinp or FEFFDictSet . from_directory ( '.' )
-
self . feffinp = self . feffinp . all_input ()
-
actions = actions or [ FileActions , DictActions ]
-
super ( FeffModder , self ) . __init__ ( actions , strict )
-
-
[docs] def apply_actions ( self , actions ):
-
"""
-
Applies a list of actions to the FEFF Input Set and rewrites modified
-
files.
-
-
Args:
-
actions [dict]: A list of actions of the form {'file': filename,
-
'action': moddermodification} or {'dict': feffinput_key,
-
'action': moddermodification}
-
"""
-
modified = []
-
for a in actions :
-
if "dict" in a :
-
k = a [ "dict" ]
-
modified . append ( k )
-
self . feffinp [ k ] = self . modify_object ( a [ "action" ], self . feffinp [ k ])
-
elif "file" in a :
-
self . modify ( a [ "action" ], a [ "file" ])
-
else :
-
raise ValueError ( "Unrecognized format: {} " . format ( a ))
-
if modified :
-
feff = self . feffinp
-
feff_input = " \n\n " . join ( str ( feff [ k ]) for k in
-
[ "HEADER" , "PARAMETERS" , "POTENTIALS" , "ATOMS" ]
-
if k in feff )
-
for k , v in six . iteritems ( feff ):
-
with open ( os . path . join ( '.' , k ), "w" ) as f :
-
f . write ( str ( v ))
-
-
with open ( os . path . join ( '.' , "feff.inp" ), "w" ) as f :
-
f . write ( feff_input )
-
-
-
-
-
-
-
-
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-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/feff/jobs.html b/docs/html/_modules/custodian/feff/jobs.html
deleted file mode 100644
index a2790500..00000000
--- a/docs/html/_modules/custodian/feff/jobs.html
+++ /dev/null
@@ -1,192 +0,0 @@
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custodian.feff.jobs — custodian 2019.8.23 documentation
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Source code for custodian.feff.jobs
-# coding: utf-8
-
-import subprocess
-import os
-import shutil
-import logging
-from monty.shutil import decompress_dir
-
-from custodian.custodian import Job
-from custodian.utils import backup
-
-""" This module implements basic kinds of jobs for FEFF runs."""
-
-logger = logging . getLogger ( __name__ )
-
-__author__ = "Chen Zheng"
-__version__ = "0.1"
-__maintainer__ = "Chen Zheng"
-__email__ = "chz022@ucsd.edu"
-__status__ = "Alpha"
-__date__ = '10/20/17'
-
-FEFF_INPUT_FILES = { "feff.inp" }
-FEFF_BACKUP_FILES = { "ATOMS" , "HEADER" , "PARAMETERS" , "POTENTIALS" }
-
-
-[docs] class FeffJob ( Job ):
-
"""
-
A basic FEFF job, run whatever is in the directory.
-
"""
-
-
def __init__ ( self , feff_cmd , output_file = "feff.out" ,
-
stderr_file = "std_feff_err.txt" , backup = True ,
-
gzipped = False , gzipped_prefix = 'feff_out' ):
-
"""
-
This constructor is used for a standard FEFF initialization
-
-
Args:
-
feff_cmd (str): the name of the full executable for running FEFF
-
output_file (str): Name of file to direct standard out to.
-
Defaults to "feff.out".
-
stderr_file (str): Name of file direct standard error to.
-
Defaults to "std_feff_err.txt".
-
backup (bool): Indicating whether to backup the initial input files.
-
If True, the feff.inp will be copied with a ".orig" appended.
-
Defaults to True.
-
gzipped (bool): Whether to gzip the final output. Defaults to False.
-
gzipped_prefix (str): prefix to the feff output files archive. Defaults
-
to feff_out, which means a series of feff_out.1.tar.gz, feff_out.2.tar.gz, ...
-
will be generated.
-
"""
-
self . feff_cmd = feff_cmd
-
self . output_file = output_file
-
self . stderr_file = stderr_file
-
self . backup = backup
-
self . gzipped = gzipped
-
self . gzipped_prefix = gzipped_prefix
-
-
[docs] def setup ( self ):
-
"""
-
Performs initial setup for FeffJob, do backing up.
-
Returns:
-
-
"""
-
decompress_dir ( '.' )
-
-
if self . backup :
-
for f in FEFF_INPUT_FILES :
-
shutil . copy ( f , " {} .orig" . format ( f ))
-
-
for f in FEFF_BACKUP_FILES :
-
if os . path . isfile ( f ):
-
shutil . copy ( f , " {} .orig" . format ( f ))
-
-
[docs] def run ( self ):
-
-
"""
-
Performs the actual FEFF run
-
Returns:
-
(subprocess.Popen) Used for monitoring.
-
"""
-
with open ( self . output_file , "w" ) as f_std , \
-
open ( self . stderr_file , "w" , buffering = 1 ) as f_err :
-
# Use line buffering for stderr
-
# On TSCC, need to run shell command
-
p = subprocess . Popen ( self . feff_cmd , stdout = f_std , stderr = f_err , shell = True )
-
-
return p
-
-
[docs] def postprocess ( self ):
-
"""
-
Renaming or gzipping all the output as needed
-
"""
-
if self . gzipped :
-
backup ( "*" , prefix = self . gzipped_prefix )
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/nwchem/handlers.html b/docs/html/_modules/custodian/nwchem/handlers.html
deleted file mode 100644
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custodian.nwchem.handlers — custodian 2019.8.23 documentation
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Source code for custodian.nwchem.handlers
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-"""
-This module implements error handlers for Nwchem runs. Currently tested only
-for B3LYP DFT jobs.
-"""
-
-
-__author__ = "Shyue Ping Ong"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__status__ = "Beta"
-__date__ = "5/20/13"
-
-
-from custodian.custodian import ErrorHandler
-from custodian.utils import backup
-from pymatgen.io.nwchem import NwOutput , NwInput
-from custodian.ansible.interpreter import Modder
-
-
-[docs] class NwchemErrorHandler ( ErrorHandler ):
-
"""
-
Error handler for Nwchem Jobs. Currently tested only for B3LYP DFT jobs
-
generated by pymatgen.
-
"""
-
-
def __init__ ( self , output_filename = "mol.nwout" ):
-
"""
-
Initializes with an output file name.
-
-
Args:
-
output_filename (str): This is the file where the stdout for nwchem
-
is being redirected. The error messages that are checked are
-
present in the stdout. Defaults to "mol.nwout", which is the
-
default redirect used by :class:`custodian.nwchem.jobs
-
.NwchemJob`.
-
"""
-
self . output_filename = output_filename
-
-
[docs] def check ( self ):
-
# Checks output file for errors.
-
out = NwOutput ( self . output_filename )
-
self . errors = []
-
self . input_file = out . job_info [ 'input' ]
-
if out . data [ - 1 ][ "has_error" ]:
-
self . errors . extend ( out . data [ - 1 ][ "errors" ])
-
self . errors = list ( set ( self . errors ))
-
self . ntasks = len ( out . data )
-
return len ( self . errors ) > 0
-
-
def _mod_input ( self , search_string_func , mod_string_func ):
-
with open ( self . input_file ) as f :
-
lines = []
-
for l in f :
-
if search_string_func ( l ):
-
lines . append ( mod_string_func ( l ))
-
else :
-
lines . append ( l )
-
-
with open ( self . input_file , "w" ) as fout :
-
fout . write ( "" . join ( lines ))
-
-
[docs] def correct ( self ):
-
backup ( "*.nw*" )
-
actions = []
-
nwi = NwInput . from_file ( self . input_file )
-
for e in self . errors :
-
if e == "autoz error" :
-
action = { "_set" : { "geometry_options" : [ "units" ,
-
"angstroms" ,
-
"noautoz" ]}}
-
actions . append ( action )
-
elif e == "Bad convergence" :
-
t = nwi . tasks [ self . ntasks - 1 ]
-
if "cgmin" in t . theory_directives :
-
nwi . tasks . pop ( self . ntasks - 1 )
-
else :
-
t . theory_directives [ "cgmin" ] = ""
-
for t in nwi . tasks :
-
if t . operation . startswith ( "freq" ):
-
#You cannot calculate hessian with cgmin.
-
t . theory_directives [ "nocgmin" ] = ""
-
action = { "_set" : { "tasks" : [ t . as_dict () for t in nwi . tasks ]}}
-
actions . append ( action )
-
else :
-
# For unimplemented errors, this should just cause the job to
-
# die.
-
return { "errors" : self . errors , "actions" : None }
-
-
m = Modder ()
-
for action in actions :
-
nwi = m . modify_object ( action , nwi )
-
nwi . write_file ( self . input_file )
-
return { "errors" : self . errors , "actions" : actions }
-
-
def __str__ ( self ):
-
return "NwchemErrorHandler"
-
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\ No newline at end of file
diff --git a/docs/html/_modules/custodian/nwchem/jobs.html b/docs/html/_modules/custodian/nwchem/jobs.html
deleted file mode 100644
index 0a597352..00000000
--- a/docs/html/_modules/custodian/nwchem/jobs.html
+++ /dev/null
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custodian.nwchem.jobs — custodian 2019.8.23 documentation
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Source code for custodian.nwchem.jobs
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-import subprocess
-import shutil
-
-from monty.io import zopen
-
-from custodian.custodian import Job
-from monty.shutil import gzip_dir
-
-"""
-This module implements basic kinds of jobs for Nwchem runs.
-"""
-
-__author__ = "Shyue Ping Ong"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__status__ = "Beta"
-__date__ = "5/20/13"
-
-
-[docs] class NwchemJob ( Job ):
-
"""
-
A basic Nwchem job.
-
"""
-
-
def __init__ ( self , nwchem_cmd , input_file = "mol.nw" ,
-
output_file = "mol.nwout" , gzipped = False ,
-
backup = True , settings_override = None ):
-
"""
-
Initializes a basic NwChem job.
-
-
Args:
-
nwchem_cmd ([str]): Command to run Nwchem as a list of args. For
-
example, ["nwchem"].
-
input_file (str): Input file to run. Defaults to "mol.nw".
-
output_file (str): Name of file to direct standard out to.
-
Defaults to "mol.nwout".
-
backup (bool): Whether to backup the initial input files. If True,
-
the input files will be copied with a ".orig" appended.
-
Defaults to True.
-
gzipped (bool): Deprecated. Please use the Custodian class's
-
gzipped_output option instead.
-
settings_override ([dict]):
-
An ansible style list of dict to override changes.
-
#TODO: Not implemented yet.
-
"""
-
self . nwchem_cmd = nwchem_cmd
-
self . input_file = input_file
-
self . output_file = output_file
-
self . backup = backup
-
self . gzipped = gzipped
-
self . settings_override = settings_override
-
-
[docs] def setup ( self ):
-
"""
-
Performs backup if necessary.
-
"""
-
if self . backup :
-
shutil . copy ( self . input_file , " {} .orig" . format ( self . input_file ))
-
-
[docs] def run ( self ):
-
"""
-
Performs actual nwchem run.
-
"""
-
with zopen ( self . output_file , 'w' ) as fout :
-
return subprocess . Popen ( self . nwchem_cmd + [ self . input_file ],
-
stdout = fout )
-
-
[docs] def postprocess ( self ):
-
"""
-
Renaming or gzipping as needed.
-
"""
-
if self . gzipped :
-
gzip_dir ( "." )
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\ No newline at end of file
diff --git a/docs/html/_modules/custodian/qchem/handlers.html b/docs/html/_modules/custodian/qchem/handlers.html
deleted file mode 100644
index 123e4fd9..00000000
--- a/docs/html/_modules/custodian/qchem/handlers.html
+++ /dev/null
@@ -1,331 +0,0 @@
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custodian.qchem.handlers — custodian 2019.8.23 documentation
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Source code for custodian.qchem.handlers
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-# This module implements new error handlers for QChem runs.
-
-import os
-from pymatgen.io.qchem.inputs import QCInput
-from pymatgen.io.qchem.outputs import QCOutput
-from custodian.custodian import ErrorHandler
-from custodian.utils import backup
-
-__author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath"
-__copyright__ = "Copyright 2018, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Samuel Blau"
-__email__ = "samblau1@gmail.com"
-__status__ = "Alpha"
-__date__ = "3/26/18"
-__credits__ = "Xiaohui Qu"
-
-
-[docs] class QChemErrorHandler ( ErrorHandler ):
-
"""
-
Master QChemErrorHandler class that handles a number of common errors
-
that occur during QChem runs.
-
"""
-
-
is_monitor = False
-
-
def __init__ ( self ,
-
input_file = "mol.qin" ,
-
output_file = "mol.qout" ,
-
scf_max_cycles = 200 ,
-
geom_max_cycles = 200 ):
-
"""
-
Initializes the error handler from a set of input and output files.
-
-
Args:
-
input_file (str): Name of the QChem input file.
-
output_file (str): Name of the QChem output file.
-
scf_max_cycles (int): The max iterations to set to fix SCF failure.
-
geom_max_cycles (int): The max iterations to set to fix geometry
-
optimization failure.
-
"""
-
self . input_file = input_file
-
self . output_file = output_file
-
self . scf_max_cycles = scf_max_cycles
-
self . geom_max_cycles = geom_max_cycles
-
self . outdata = None
-
self . errors = []
-
self . opt_error_history = []
-
-
[docs] def check ( self ):
-
# Checks output file for errors.
-
self . outdata = QCOutput ( self . output_file ) . data
-
self . errors = self . outdata . get ( "errors" )
-
# If we aren't out of optimization cycles, but we were in the past, reset the history
-
if "out_of_opt_cycles" not in self . errors and len ( self . opt_error_history ) > 0 :
-
self . opt_error_history = []
-
# If we're out of optimization cycles and we have unconnected fragments, no need to handle any errors
-
if "out_of_opt_cycles" in self . errors and self . outdata [ "structure_change" ] == "unconnected_fragments" :
-
return False
-
return len ( self . errors ) > 0
-
-
[docs] def correct ( self ):
-
backup ({ self . input_file , self . output_file })
-
actions = []
-
self . qcinp = QCInput . from_file ( self . input_file )
-
-
if "SCF_failed_to_converge" in self . errors :
-
# Check number of SCF cycles. If not set or less than scf_max_cycles,
-
# increase to that value and rerun. If already set, check if
-
# scf_algorithm is unset or set to DIIS, in which case set to GDM.
-
# Otherwise, tell user to call SCF error handler and do nothing.
-
if str ( self . qcinp . rem . get ( "max_scf_cycles" )) != str (
-
self . scf_max_cycles ):
-
self . qcinp . rem [ "max_scf_cycles" ] = self . scf_max_cycles
-
actions . append ({ "max_scf_cycles" : self . scf_max_cycles })
-
elif self . qcinp . rem . get ( "scf_algorithm" , "diis" ) . lower () == "diis" :
-
self . qcinp . rem [ "scf_algorithm" ] = "gdm"
-
actions . append ({ "scf_algorithm" : "gdm" })
-
elif self . qcinp . rem . get ( "scf_algorithm" , "gdm" ) . lower () == "gdm" :
-
self . qcinp . rem [ "scf_algorithm" ] = "diis_gdm"
-
actions . append ({ "scf_algorithm" : "diis_gdm" })
-
else :
-
print (
-
"More advanced changes may impact the SCF result. Use the SCF error handler"
-
)
-
-
elif "out_of_opt_cycles" in self . errors :
-
# Check number of opt cycles. If less than geom_max_cycles, increase
-
# to that value, set last geom as new starting geom and rerun.
-
if str ( self . qcinp . rem . get (
-
"geom_opt_max_cycles" )) != str ( self . geom_max_cycles ):
-
self . qcinp . rem [ "geom_opt_max_cycles" ] = self . geom_max_cycles
-
actions . append ({ "geom_max_cycles:" : self . scf_max_cycles })
-
if len ( self . outdata . get ( "energy_trajectory" )) > 1 :
-
self . qcinp . molecule = self . outdata . get (
-
"molecule_from_last_geometry" )
-
actions . append ({ "molecule" : "molecule_from_last_geometry" })
-
# If already at geom_max_cycles, often can just get convergence by restarting
-
# from the geometry of the last cycle. But we'll also save any structural
-
# changes that happened along the way.
-
else :
-
self . opt_error_history += [ self . outdata [ "structure_change" ]]
-
if len ( self . opt_error_history ) > 1 :
-
if self . opt_error_history [ - 1 ] == "no_change" :
-
# If no structural changes occured in two consecutive optimizations,
-
# and we still haven't converged, then just exit.
-
return { "errors" : self . errors , "actions" : None , "opt_error_history" : self . opt_error_history }
-
self . qcinp . molecule = self . outdata . get ( "molecule_from_last_geometry" )
-
actions . append ({ "molecule" : "molecule_from_last_geometry" })
-
-
elif "unable_to_determine_lamda" in self . errors :
-
# Set last geom as new starting geom and rerun. If no opt cycles,
-
# use diff SCF strat? Diff initial guess? Change basis?
-
if len ( self . outdata . get ( "energy_trajectory" )) > 1 :
-
self . qcinp . molecule = self . outdata . get (
-
"molecule_from_last_geometry" )
-
actions . append ({ "molecule" : "molecule_from_last_geometry" })
-
elif self . qcinp . rem . get ( "scf_algorithm" , "diis" ) . lower () == "diis" :
-
self . qcinp . rem [ "scf_algorithm" ] = "rca_diis"
-
actions . append ({ "scf_algorithm" : "rca_diis" })
-
if self . qcinp . rem . get ( "gen_scfman" ):
-
self . qcinp . rem [ "gen_scfman" ] = False
-
actions . append ({ "gen_scfman" : False })
-
else :
-
print (
-
"Use a different initial guess? Perhaps a different basis?"
-
)
-
-
elif "linear_dependent_basis" in self . errors :
-
# DIIS -> RCA_DIIS. If already RCA_DIIS, change basis?
-
if self . qcinp . rem . get ( "scf_algorithm" , "diis" ) . lower () == "diis" :
-
self . qcinp . rem [ "scf_algorithm" ] = "rca_diis"
-
actions . append ({ "scf_algorithm" : "rca_diis" })
-
if self . qcinp . rem . get ( "gen_scfman" ):
-
self . qcinp . rem [ "gen_scfman" ] = False
-
actions . append ({ "gen_scfman" : False })
-
else :
-
print ( "Perhaps use a better basis?" )
-
-
elif "failed_to_transform_coords" in self . errors :
-
# Check for symmetry flag in rem. If not False, set to False and rerun.
-
# If already False, increase threshold?
-
if not self . qcinp . rem . get ( "sym_ignore" ) or self . qcinp . rem . get (
-
"symmetry" ):
-
self . qcinp . rem [ "sym_ignore" ] = True
-
self . qcinp . rem [ "symmetry" ] = False
-
actions . append ({ "sym_ignore" : True })
-
actions . append ({ "symmetry" : False })
-
else :
-
print ( "Perhaps increase the threshold?" )
-
-
elif "input_file_error" in self . errors :
-
print (
-
"Something is wrong with the input file. Examine error message by hand."
-
)
-
return { "errors" : self . errors , "actions" : None }
-
-
elif "failed_to_read_input" in self . errors :
-
# Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
-
actions . append ({ "rerun job as-is" })
-
-
elif "IO_error" in self . errors :
-
# Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
-
actions . append ({ "rerun job as-is" })
-
-
elif "read_molecule_error" in self . errors :
-
# Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
-
actions . append ({ "rerun job as-is" })
-
-
elif "never_called_qchem" in self . errors :
-
# Almost certainly just a temporary problem that will not be encountered again. Rerun job as-is.
-
actions . append ({ "rerun job as-is" })
-
-
elif "unknown_error" in self . errors :
-
print ( "Examine error message by hand." )
-
return { "errors" : self . errors , "actions" : None }
-
-
else :
-
# You should never get here. If correct is being called then errors should have at least one entry,
-
# in which case it should have been caught by the if/elifs above.
-
print (
-
"If you get this message, something has gone terribly wrong!" )
-
return { "errors" : self . errors , "actions" : None }
-
-
os . rename ( self . input_file , self . input_file + ".last" )
-
self . qcinp . write_file ( self . input_file )
-
return { "errors" : self . errors , "actions" : actions } [docs] class QChemSCFErrorHandler ( ErrorHandler ):
-
"""
-
QChem ErrorHandler class that addresses SCF non-convergence.
-
"""
-
-
is_monitor = False
-
-
def __init__ ( self ,
-
input_file = "mol.qin" ,
-
output_file = "mol.qout" ,
-
rca_gdm_thresh = 1.0E-3 ,
-
scf_max_cycles = 200 ):
-
"""
-
Initializes the error handler from a set of input and output files.
-
-
Args:
-
input_file (str): Name of the QChem input file.
-
output_file (str): Name of the QChem output file.
-
rca_gdm_thresh (float): The threshold for the prior scf algorithm.
-
If last deltaE is larger than the threshold try RCA_DIIS
-
first, else, try DIIS_GDM first.
-
scf_max_cycles (int): The max iterations to set to fix SCF failure.
-
"""
-
self . input_file = input_file
-
self . output_file = output_file
-
self . scf_max_cycles = scf_max_cycles
-
self . geom_max_cycles = geom_max_cycles
-
self . qcinp = QCInput . from_file ( self . input_file )
-
self . outdata = None
-
self . errors = None
-
self . qchem_job = qchem_job
-
-
[docs] def check ( self ):
-
# Checks output file for errors.
-
self . outdata = QCOutput ( self . output_file ) . data
-
self . errors = self . outdata . get ( "errors" )
-
return len ( self . errors ) > 0
-
-
[docs] def correct ( self ):
-
print ( "This hasn't been implemented yet!" )
-
return { "errors" : self . errors , "actions" : None }
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/qchem/jobs.html b/docs/html/_modules/custodian/qchem/jobs.html
deleted file mode 100644
index 81f8756a..00000000
--- a/docs/html/_modules/custodian/qchem/jobs.html
+++ /dev/null
@@ -1,380 +0,0 @@
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custodian.qchem.jobs — custodian 2019.8.23 documentation
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Source code for custodian.qchem.jobs
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-import math
-
-# New QChem job module
-
-
-import os
-import shutil
-import copy
-import subprocess
-import numpy as np
-from pymatgen.core import Molecule
-from pymatgen.io.qchem.inputs import QCInput
-from pymatgen.io.qchem.outputs import QCOutput
-from pymatgen.analysis.graphs import MoleculeGraph
-from pymatgen.analysis.local_env import OpenBabelNN
-from custodian.custodian import Job
-
-
-__author__ = "Samuel Blau, Brandon Wood, Shyam Dwaraknath"
-__copyright__ = "Copyright 2018, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Samuel Blau"
-__email__ = "samblau1@gmail.com"
-__status__ = "Alpha"
-__date__ = "3/20/18"
-__credits__ = "Xiaohui Qu"
-
-
-[docs] class QCJob ( Job ):
-
"""
-
A basic QChem Job.
-
"""
-
-
def __init__ ( self ,
-
qchem_command ,
-
max_cores ,
-
multimode = "openmp" ,
-
input_file = "mol.qin" ,
-
output_file = "mol.qout" ,
-
qclog_file = "mol.qclog" ,
-
suffix = "" ,
-
scratch_dir = "/dev/shm/qcscratch/" ,
-
save_scratch = False ,
-
save_name = "default_save_name" ,
-
backup = True ):
-
"""
-
Args:
-
qchem_command (str): Command to run QChem.
-
max_cores (int): Maximum number of cores to parallelize over.
-
multimode (str): Parallelization scheme, either openmp or mpi.
-
input_file (str): Name of the QChem input file.
-
output_file (str): Name of the QChem output file.
-
qclog_file (str): Name of the file to redirect the standard output
-
to. None means not to record the standard output.
-
suffix (str): String to append to the file in postprocess.
-
scratch_dir (str): QCSCRATCH directory. Defaults to "/dev/shm/qcscratch/".
-
save_scratch (bool): Whether to save scratch directory contents.
-
Defaults to False.
-
save_name (str): Name of the saved scratch directory. Defaults to
-
to "default_save_name".
-
backup (bool): Whether to backup the initial input file. If True, the
-
input will be copied with a ".orig" appended. Defaults to True.
-
"""
-
self . qchem_command = qchem_command . split ( " " )
-
self . multimode = multimode
-
self . input_file = input_file
-
self . output_file = output_file
-
self . max_cores = max_cores
-
self . qclog_file = qclog_file
-
self . suffix = suffix
-
self . scratch_dir = scratch_dir
-
self . save_scratch = save_scratch
-
self . save_name = save_name
-
self . backup = backup
-
-
@property
-
def current_command ( self ):
-
multimode_index = 0
-
if self . save_scratch :
-
command = [
-
"-save" , "" ,
-
str ( self . max_cores ), self . input_file , self . output_file ,
-
self . save_name
-
]
-
multimode_index = 1
-
else :
-
command = [
-
"" , str ( self . max_cores ), self . input_file , self . output_file
-
]
-
if self . multimode == 'openmp' :
-
command [ multimode_index ] = "-nt"
-
elif self . multimode == 'mpi' :
-
command [ multimode_index ] = "-np"
-
else :
-
print ( "ERROR: Multimode should only be set to openmp or mpi" )
-
command = self . qchem_command + command
-
return command
-
-
[docs] def setup ( self ):
-
if self . backup :
-
shutil . copy ( self . input_file , " {} .orig" . format ( self . input_file ))
-
os . putenv ( "QCSCRATCH" , self . scratch_dir )
-
if self . multimode == 'openmp' :
-
os . putenv ( 'QCTHREADS' , str ( self . max_cores ))
-
os . putenv ( 'OMP_NUM_THREADS' , str ( self . max_cores ))
-
-
[docs] def postprocess ( self ):
-
if self . save_scratch :
-
shutil . copytree (
-
os . path . join ( self . scratch_dir , self . save_name ),
-
os . path . join ( os . path . dirname ( self . input_file ), self . save_name ))
-
if self . suffix != "" :
-
shutil . move ( self . input_file , self . input_file + self . suffix )
-
shutil . move ( self . output_file , self . output_file + self . suffix )
-
shutil . move ( self . qclog_file , self . qclog_file + self . suffix )
-
-
[docs] def run ( self ):
-
"""
-
Perform the actual QChem run.
-
-
Returns:
-
(subprocess.Popen) Used for monitoring.
-
"""
-
qclog = open ( self . qclog_file , 'w' )
-
p = subprocess . Popen ( self . current_command , stdout = qclog )
-
return p
-
-
[docs] @classmethod
-
def opt_with_frequency_flattener ( cls ,
-
qchem_command ,
-
multimode = "openmp" ,
-
input_file = "mol.qin" ,
-
output_file = "mol.qout" ,
-
qclog_file = "mol.qclog" ,
-
max_iterations = 10 ,
-
max_molecule_perturb_scale = 0.3 ,
-
check_connectivity = True ,
-
** QCJob_kwargs ):
-
"""
-
Optimize a structure and calculate vibrational frequencies to check if the
-
structure is in a true minima. If a frequency is negative, iteratively
-
perturbe the geometry, optimize, and recalculate frequencies until all are
-
positive, aka a true minima has been found.
-
-
Args:
-
qchem_command (str): Command to run QChem.
-
multimode (str): Parallelization scheme, either openmp or mpi.
-
input_file (str): Name of the QChem input file.
-
output_file (str): Name of the QChem output file.
-
max_iterations (int): Number of perturbation -> optimization -> frequency
-
iterations to perform. Defaults to 10.
-
max_molecule_perturb_scale (float): The maximum scaled perturbation that
-
can be applied to the molecule. Defaults to 0.3.
-
check_connectivity (bool): Whether to check differences in connectivity
-
introduced by structural perturbation. Defaults to True.
-
**QCJob_kwargs: Passthrough kwargs to QCJob. See
-
:class:`custodian.qchem.jobs.QCJob`.
-
"""
-
-
min_molecule_perturb_scale = 0.1
-
scale_grid = 10
-
perturb_scale_grid = (
-
max_molecule_perturb_scale - min_molecule_perturb_scale
-
) / scale_grid
-
-
if not os . path . exists ( input_file ):
-
raise AssertionError ( 'Input file must be present!' )
-
orig_opt_input = QCInput . from_file ( input_file )
-
orig_opt_rem = copy . deepcopy ( orig_opt_input . rem )
-
orig_freq_rem = copy . deepcopy ( orig_opt_input . rem )
-
orig_freq_rem [ "job_type" ] = "freq"
-
first = True
-
reversed_direction = False
-
num_neg_freqs = []
-
-
for ii in range ( max_iterations ):
-
yield ( QCJob (
-
qchem_command = qchem_command ,
-
multimode = multimode ,
-
input_file = input_file ,
-
output_file = output_file ,
-
qclog_file = qclog_file ,
-
suffix = ".opt_" + str ( ii ),
-
backup = first ,
-
** QCJob_kwargs ))
-
first = False
-
opt_outdata = QCOutput ( output_file + ".opt_" + str ( ii )) . data
-
if opt_outdata [ "structure_change" ] == "unconnected_fragments" and not opt_outdata [ "completion" ]:
-
print ( "Unstable molecule broke into unconnected fragments which failed to optimize! Exiting..." )
-
break
-
else :
-
freq_QCInput = QCInput (
-
molecule = opt_outdata . get ( "molecule_from_optimized_geometry" ),
-
rem = orig_freq_rem ,
-
opt = orig_opt_input . opt ,
-
pcm = orig_opt_input . pcm ,
-
solvent = orig_opt_input . solvent )
-
freq_QCInput . write_file ( input_file )
-
yield ( QCJob (
-
qchem_command = qchem_command ,
-
multimode = multimode ,
-
input_file = input_file ,
-
output_file = output_file ,
-
qclog_file = qclog_file ,
-
suffix = ".freq_" + str ( ii ),
-
backup = first ,
-
** QCJob_kwargs ))
-
outdata = QCOutput ( output_file + ".freq_" + str ( ii )) . data
-
errors = outdata . get ( "errors" )
-
if len ( errors ) != 0 :
-
raise AssertionError ( 'No errors should be encountered while flattening frequencies!' )
-
if outdata . get ( 'frequencies' )[ 0 ] > 0.0 :
-
print ( "All frequencies positive!" )
-
break
-
else :
-
num_neg_freqs += [ sum ( 1 for freq in outdata . get ( 'frequencies' ) if freq < 0 )]
-
if len ( num_neg_freqs ) > 1 :
-
if num_neg_freqs [ - 1 ] == num_neg_freqs [ - 2 ] and not reversed_direction :
-
reversed_direction = True
-
elif num_neg_freqs [ - 1 ] == num_neg_freqs [ - 2 ] and reversed_direction :
-
if len ( num_neg_freqs ) < 3 :
-
raise AssertionError ( "ERROR: This should only be possible after at least three frequency flattening iterations! Exiting..." )
-
else :
-
raise Exception ( "ERROR: Reversing the perturbation direction still could not flatten any frequencies. Exiting..." )
-
elif num_neg_freqs [ - 1 ] != num_neg_freqs [ - 2 ] and reversed_direction :
-
reversed_direction = False
-
-
negative_freq_vecs = outdata . get ( "frequency_mode_vectors" )[ 0 ]
-
structure_successfully_perturbed = False
-
-
for molecule_perturb_scale in np . arange (
-
max_molecule_perturb_scale , min_molecule_perturb_scale ,
-
- perturb_scale_grid ):
-
new_coords = perturb_coordinates (
-
old_coords = outdata . get ( "initial_geometry" ),
-
negative_freq_vecs = negative_freq_vecs ,
-
molecule_perturb_scale = molecule_perturb_scale ,
-
reversed_direction = reversed_direction )
-
new_molecule = Molecule (
-
species = outdata . get ( 'species' ),
-
coords = new_coords ,
-
charge = outdata . get ( 'charge' ),
-
spin_multiplicity = outdata . get ( 'multiplicity' ))
-
if check_connectivity :
-
old_molgraph = MoleculeGraph . with_local_env_strategy ( outdata . get ( "initial_molecule" ),
-
OpenBabelNN (),
-
reorder = False ,
-
extend_structure = False )
-
new_molgraph = MoleculeGraph . with_local_env_strategy ( new_molecule ,
-
OpenBabelNN (),
-
reorder = False ,
-
extend_structure = False )
-
if old_molgraph . isomorphic_to ( new_molgraph ):
-
structure_successfully_perturbed = True
-
break
-
if not structure_successfully_perturbed :
-
raise Exception (
-
"ERROR: Unable to perturb coordinates to remove negative frequency without changing the connectivity! Exiting..."
-
)
-
-
new_opt_QCInput = QCInput (
-
molecule = new_molecule ,
-
rem = orig_opt_rem ,
-
opt = orig_opt_input . opt ,
-
pcm = orig_opt_input . pcm ,
-
solvent = orig_opt_input . solvent )
-
new_opt_QCInput . write_file ( input_file ) [docs] def perturb_coordinates ( old_coords , negative_freq_vecs , molecule_perturb_scale ,
-
reversed_direction ):
-
max_dis = max (
-
[ math . sqrt ( sum ([ x ** 2 for x in vec ])) for vec in negative_freq_vecs ])
-
scale = molecule_perturb_scale / max_dis
-
normalized_vecs = [[ x * scale for x in vec ] for vec in negative_freq_vecs ]
-
direction = 1.0
-
if reversed_direction :
-
direction = - 1.0
-
return [[ c + v * direction for c , v in zip ( coord , vec )]
-
for coord , vec in zip ( old_coords , normalized_vecs )]
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/utils.html b/docs/html/_modules/custodian/utils.html
deleted file mode 100644
index 2eaa52a8..00000000
--- a/docs/html/_modules/custodian/utils.html
+++ /dev/null
@@ -1,157 +0,0 @@
-
-
-
-
-
-
-
custodian.utils — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Source code for custodian.utils
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-"""
-Utility function and classes.
-"""
-
-
-__author__ = "Shyue Ping Ong"
-__copyright__ = "Copyright 2012, The Materials Project"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "shyuep@gmail.com"
-__date__ = "1/12/14"
-
-from glob import glob
-import logging
-import os
-import tarfile
-
-
-[docs] def backup ( filenames , prefix = "error" ):
-
"""
-
Backup files to a tar.gz file. Used, for example, in backing up the
-
files of an errored run before performing corrections.
-
-
Args:
-
filenames ([str]): List of files to backup. Supports wildcards, e.g.,
-
*.*.
-
prefix (str): prefix to the files. Defaults to error, which means a
-
series of error.1.tar.gz, error.2.tar.gz, ... will be generated.
-
"""
-
num = max ([ 0 ] + [ int ( f . split ( "." )[ 1 ])
-
for f in glob ( " {} .*.tar.gz" . format ( prefix ))])
-
filename = " {} . {} .tar.gz" . format ( prefix , num + 1 )
-
logging . info ( "Backing up run to {} ." . format ( filename ))
-
with tarfile . open ( filename , "w:gz" ) as tar :
-
for fname in filenames :
-
for f in glob ( fname ):
-
tar . add ( f ) [docs] def get_execution_host_info ():
-
"""
-
Tries to return a tuple describing the execution host.
-
Doesn't work for all queueing systems
-
-
Returns:
-
(HOSTNAME, CLUSTER_NAME)
-
"""
-
host = os . environ . get ( 'HOSTNAME' , None )
-
cluster = os . environ . get ( 'SGE_O_HOST' , None )
-
if host is None :
-
try :
-
import socket
-
host = host or socket . gethostname ()
-
except :
-
pass
-
return host or 'unknown' , cluster or 'unknown'
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/vasp/handlers.html b/docs/html/_modules/custodian/vasp/handlers.html
deleted file mode 100644
index a928e363..00000000
--- a/docs/html/_modules/custodian/vasp/handlers.html
+++ /dev/null
@@ -1,1419 +0,0 @@
-
-
-
-
-
-
-
custodian.vasp.handlers — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Source code for custodian.vasp.handlers
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-from monty.os.path import zpath
-import os
-import time
-import datetime
-import operator
-import shutil
-import logging
-from functools import reduce
-from collections import Counter
-import re
-
-import numpy as np
-
-from monty.dev import deprecated
-from monty.serialization import loadfn
-
-from custodian.custodian import ErrorHandler
-from custodian.utils import backup
-from pymatgen.io.vasp import Poscar , VaspInput , Incar , Kpoints , Vasprun , \
- Oszicar , Outcar
-from pymatgen.transformations.standard_transformations import \
- SupercellTransformation
-
-from custodian.ansible.interpreter import Modder
-from custodian.ansible.actions import FileActions
-from custodian.vasp.interpreter import VaspModder
-
-"""
-This module implements specific error handlers for VASP runs. These handlers
-tries to detect common errors in vasp runs and attempt to fix them on the fly
-by modifying the input files.
-"""
-
-__author__ = "Shyue Ping Ong, William Davidson Richards, Anubhav Jain, " \
- "Wei Chen, Stephen Dacek"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "ongsp@ucsd.edu"
-__status__ = "Beta"
-__date__ = "2/4/13"
-
-VASP_BACKUP_FILES = { "INCAR" , "KPOINTS" , "POSCAR" , "OUTCAR" , "CONTCAR" ,
- "OSZICAR" , "vasprun.xml" , "vasp.out" , "std_err.txt" }
-
-
-[docs] class VaspErrorHandler ( ErrorHandler ):
-
"""
-
Master VaspErrorHandler class that handles a number of common errors
-
that occur during VASP runs.
-
"""
-
-
is_monitor = True
-
-
error_msgs = {
-
"tet" : [ "Tetrahedron method fails for NKPT<4" ,
-
"Fatal error detecting k-mesh" ,
-
"Fatal error: unable to match k-point" ,
-
"Routine TETIRR needs special values" ,
-
"Tetrahedron method fails (number of k-points < 4)" ],
-
"inv_rot_mat" : [ "inverse of rotation matrix was not found (increase "
-
"SYMPREC)" ],
-
"brmix" : [ "BRMIX: very serious problems" ],
-
"subspacematrix" : [ "WARNING: Sub-Space-Matrix is not hermitian in "
-
"DAV" ],
-
"tetirr" : [ "Routine TETIRR needs special values" ],
-
"incorrect_shift" : [ "Could not get correct shifts" ],
-
"real_optlay" : [ "REAL_OPTLAY: internal error" ,
-
"REAL_OPT: internal ERROR" ],
-
"rspher" : [ "ERROR RSPHER" ],
-
"dentet" : [ "DENTET" ],
-
"too_few_bands" : [ "TOO FEW BANDS" ],
-
"triple_product" : [ "ERROR: the triple product of the basis vectors" ],
-
"rot_matrix" : [ "Found some non-integer element in rotation matrix" ],
-
"brions" : [ "BRIONS problems: POTIM should be increased" ],
-
"pricel" : [ "internal error in subroutine PRICEL" ],
-
"zpotrf" : [ "LAPACK: Routine ZPOTRF failed" ],
-
"amin" : [ "One of the lattice vectors is very long (>50 A), but AMIN" ],
-
"zbrent" : [ "ZBRENT: fatal internal in" ,
-
"ZBRENT: fatal error in bracketing" ],
-
"pssyevx" : [ "ERROR in subspace rotation PSSYEVX" ],
-
"eddrmm" : [ "WARNING in EDDRMM: call to ZHEGV failed" ],
-
"edddav" : [ "Error EDDDAV: Call to ZHEGV failed" ],
-
"grad_not_orth" : [
-
"EDWAV: internal error, the gradient is not orthogonal" ],
-
"nicht_konv" : [ "ERROR: SBESSELITER : nicht konvergent" ],
-
"zheev" : [ "ERROR EDDIAG: Call to routine ZHEEV failed!" ],
-
"elf_kpar" : [ "ELF: KPAR>1 not implemented" ],
-
"elf_ncl" : [ "WARNING: ELF not implemented for non collinear case" ],
-
"rhosyg" : [ "RHOSYG internal error" ],
-
"posmap" : [ "POSMAP internal error: symmetry equivalent atom not found" ],
-
"point_group" : [ "Error: point group operation missing" ]
-
}
-
-
def __init__ ( self , output_filename = "vasp.out" , natoms_large_cell = 100 ,
-
errors_subset_to_catch = None ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_filename (str): This is the file where the stdout for vasp
-
is being redirected. The error messages that are checked are
-
present in the stdout. Defaults to "vasp.out", which is the
-
default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
-
natoms_large_cell (int): Number of atoms threshold to treat cell
-
as large. Affects the correction of certain errors. Defaults to
-
100.
-
errors_subset_to_detect (list): A subset of errors to catch. The
-
default is None, which means all supported errors are detected.
-
Use this to only catch only a subset of supported errors.
-
E.g., ["eddrrm", "zheev"] will only catch the eddrmm and zheev
-
errors, and not others. If you wish to only excluded one or
-
two of the errors, you can create this list by the following
-
lines:
-
-
```
-
subset = list(VaspErrorHandler.error_msgs.keys())
-
subset.pop("eddrrm")
-
-
handler = VaspErrorHandler(errors_subset_to_catch=subset)
-
```
-
"""
-
self . output_filename = output_filename
-
self . errors = set ()
-
self . error_count = Counter ()
-
# threshold of number of atoms to treat the cell as large.
-
self . natoms_large_cell = natoms_large_cell
-
self . errors_subset_to_catch = errors_subset_to_catch or \
-
list ( VaspErrorHandler . error_msgs . keys ())
-
self . logger = logging . getLogger ( self . __class__ . __name__ )
-
-
[docs] def check ( self ):
-
incar = Incar . from_file ( "INCAR" )
-
self . errors = set ()
-
with open ( self . output_filename , "r" ) as f :
-
for line in f :
-
l = line . strip ()
-
for err , msgs in VaspErrorHandler . error_msgs . items ():
-
if err in self . errors_subset_to_catch :
-
for msg in msgs :
-
if l . find ( msg ) != - 1 :
-
# this checks if we want to run a charged
-
# computation (e.g., defects) if yes we don't
-
# want to kill it because there is a change in
-
# e-density (brmix error)
-
if err == "brmix" and 'NELECT' in incar :
-
continue
-
self . errors . add ( err )
-
self . logger . error ( msg , extra = { "incar" : incar . as_dict ()})
-
return len ( self . errors ) > 0
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES | { self . output_filename })
-
actions = []
-
vi = VaspInput . from_directory ( "." )
-
-
if self . errors . intersection ([ "tet" , "dentet" ]):
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISMEAR" : 0 , "SIGMA" : 0.05 }}})
-
-
if "inv_rot_mat" in self . errors :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "SYMPREC" : 1e-8 }}})
-
-
if "brmix" in self . errors :
-
# If there is not a valid OUTCAR already, increment
-
# error count to 1 to skip first fix
-
if self . error_count [ 'brmix' ] == 0 :
-
try :
-
assert ( Outcar ( zpath ( os . path . join (
-
os . getcwd (), "OUTCAR" ))) . is_stopped is False )
-
except :
-
self . error_count [ 'brmix' ] += 1
-
-
if self . error_count [ 'brmix' ] == 0 :
-
# Valid OUTCAR - simply rerun the job and increment
-
# error count for next time
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISTART" : 1 }}})
-
self . error_count [ 'brmix' ] += 1
-
-
elif self . error_count [ 'brmix' ] == 1 :
-
# Use Kerker mixing w/default values for other parameters
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "IMIX" : 1 }}})
-
self . error_count [ 'brmix' ] += 1
-
-
elif self . error_count [ 'brmix' ] == 2 and vi [ "KPOINTS" ] . style \
-
== Kpoints . supported_modes . Gamma :
-
actions . append ({ "dict" : "KPOINTS" ,
-
"action" : { "_set" : { "generation_style" :
-
"Monkhorst" }}})
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_unset" : { "IMIX" : 1 }}})
-
self . error_count [ 'brmix' ] += 1
-
-
elif self . error_count [ 'brmix' ] in [ 2 , 3 ] and vi [ "KPOINTS" ] . style \
-
== Kpoints . supported_modes . Monkhorst :
-
actions . append ({ "dict" : "KPOINTS" ,
-
"action" : { "_set" : { "generation_style" :
-
"Gamma" }}})
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_unset" : { "IMIX" : 1 }}})
-
self . error_count [ 'brmix' ] += 1
-
-
if vi [ "KPOINTS" ] . num_kpts < 1 :
-
all_kpts_even = all ([
-
bool ( n % 2 == 0 ) for n in vi [ "KPOINTS" ] . kpts [ 0 ]
-
])
-
if all_kpts_even :
-
new_kpts = (
-
tuple ( n + 1 for n in vi [ "KPOINTS" ] . kpts [ 0 ]),)
-
actions . append ({ "dict" : "KPOINTS" , "action" : { "_set" : {
-
"kpoints" : new_kpts
-
}}})
-
-
else :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISYM" : 0 }}})
-
-
if vi [ "KPOINTS" ] . style == Kpoints . supported_modes . Monkhorst :
-
actions . append ({ "dict" : "KPOINTS" ,
-
"action" : {
-
"_set" : { "generation_style" : "Gamma" }}})
-
-
# Based on VASP forum's recommendation, you should delete the
-
# CHGCAR and WAVECAR when dealing with this error.
-
if vi [ "INCAR" ] . get ( "ICHARG" , 0 ) < 10 :
-
actions . append ({ "file" : "CHGCAR" ,
-
"action" : {
-
"_file_delete" : { 'mode' : "actual" }}})
-
actions . append ({ "file" : "WAVECAR" ,
-
"action" : {
-
"_file_delete" : { 'mode' : "actual" }}})
-
-
if "zpotrf" in self . errors :
-
# Usually caused by short bond distances. If on the first step,
-
# volume needs to be increased. Otherwise, it was due to a step
-
# being too big and POTIM should be decreased. If a static run
-
# try turning off symmetry.
-
try :
-
oszicar = Oszicar ( "OSZICAR" )
-
nsteps = len ( oszicar . ionic_steps )
-
except :
-
nsteps = 0
-
-
if nsteps >= 1 :
-
potim = float ( vi [ "INCAR" ] . get ( "POTIM" , 0.5 )) / 2.0
-
actions . append (
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISYM" : 0 , "POTIM" : potim }}})
-
elif vi [ "INCAR" ] . get ( "NSW" , 0 ) == 0 \
-
or vi [ "INCAR" ] . get ( "ISIF" , 0 ) in range ( 3 ):
-
actions . append (
-
{ "dict" : "INCAR" , "action" : { "_set" : { "ISYM" : 0 }}})
-
else :
-
s = vi [ "POSCAR" ] . structure
-
s . apply_strain ( 0.2 )
-
actions . append ({ "dict" : "POSCAR" ,
-
"action" : { "_set" : { "structure" : s . as_dict ()}}})
-
-
# Based on VASP forum's recommendation, you should delete the
-
# CHGCAR and WAVECAR when dealing with this error.
-
if vi [ "INCAR" ] . get ( "ICHARG" , 0 ) < 10 :
-
actions . append ({ "file" : "CHGCAR" ,
-
"action" : { "_file_delete" : { 'mode' : "actual" }}})
-
actions . append ({ "file" : "WAVECAR" ,
-
"action" : { "_file_delete" : { 'mode' : "actual" }}})
-
-
if self . errors . intersection ([ "subspacematrix" ]):
-
if self . error_count [ "subspacematrix" ] == 0 :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "LREAL" : False }}})
-
else :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "PREC" : "Accurate" }}})
-
self . error_count [ "subspacematrix" ] += 1
-
-
if self . errors . intersection ([ "rspher" , "real_optlay" , "nicht_konv" ]):
-
s = vi [ "POSCAR" ] . structure
-
if len ( s ) < self . natoms_large_cell :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "LREAL" : False }}})
-
else :
-
# for large supercell, try an in-between option LREAL = True
-
# prior to LREAL = False
-
if self . error_count [ 'real_optlay' ] == 0 :
-
# use real space projectors generated by pot
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "LREAL" : True }}})
-
elif self . error_count [ 'real_optlay' ] == 1 :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "LREAL" : False }}})
-
self . error_count [ 'real_optlay' ] += 1
-
-
if self . errors . intersection ([ "tetirr" , "incorrect_shift" ]):
-
-
if vi [ "KPOINTS" ] . style == Kpoints . supported_modes . Monkhorst :
-
actions . append ({ "dict" : "KPOINTS" ,
-
"action" : {
-
"_set" : { "generation_style" : "Gamma" }}})
-
-
if "rot_matrix" in self . errors :
-
if vi [ "KPOINTS" ] . style == Kpoints . supported_modes . Monkhorst :
-
actions . append ({ "dict" : "KPOINTS" ,
-
"action" : {
-
"_set" : { "generation_style" : "Gamma" }}})
-
else :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISYM" : 0 }}})
-
-
if "amin" in self . errors :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "AMIN" : "0.01" }}})
-
-
if "triple_product" in self . errors :
-
s = vi [ "POSCAR" ] . structure
-
trans = SupercellTransformation ((( 1 , 0 , 0 ), ( 0 , 0 , 1 ), ( 0 , 1 , 0 )))
-
new_s = trans . apply_transformation ( s )
-
actions . append ({ "dict" : "POSCAR" ,
-
"action" : { "_set" : { "structure" : new_s . as_dict ()}},
-
"transformation" : trans . as_dict ()})
-
-
if "pricel" in self . errors :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "SYMPREC" : 1e-8 , "ISYM" : 0 }}})
-
-
if "brions" in self . errors :
-
potim = float ( vi [ "INCAR" ] . get ( "POTIM" , 0.5 )) + 0.1
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "POTIM" : potim }}})
-
-
if "zbrent" in self . errors :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "IBRION" : 1 }}})
-
actions . append ({ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}})
-
-
if "too_few_bands" in self . errors :
-
if "NBANDS" in vi [ "INCAR" ]:
-
nbands = int ( vi [ "INCAR" ][ "NBANDS" ])
-
else :
-
with open ( "OUTCAR" ) as f :
-
for line in f :
-
if "NBANDS" in line :
-
try :
-
d = line . split ( "=" )
-
nbands = int ( d [ - 1 ] . strip ())
-
break
-
except ( IndexError , ValueError ):
-
pass
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "NBANDS" : int ( 1.1 * nbands )}}})
-
-
if "pssyevx" in self . errors :
-
actions . append ({ "dict" : "INCAR" , "action" :
-
{ "_set" : { "ALGO" : "Normal" }}})
-
if "eddrmm" in self . errors :
-
# RMM algorithm is not stable for this calculation
-
if vi [ "INCAR" ] . get ( "ALGO" , "Normal" ) in [ "Fast" , "VeryFast" ]:
-
actions . append ({ "dict" : "INCAR" , "action" :
-
{ "_set" : { "ALGO" : "Normal" }}})
-
else :
-
potim = float ( vi [ "INCAR" ] . get ( "POTIM" , 0.5 )) / 2.0
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "POTIM" : potim }}})
-
if vi [ "INCAR" ] . get ( "ICHARG" , 0 ) < 10 :
-
actions . append ({ "file" : "CHGCAR" ,
-
"action" : { "_file_delete" : { 'mode' : "actual" }}})
-
actions . append ({ "file" : "WAVECAR" ,
-
"action" : { "_file_delete" : { 'mode' : "actual" }}})
-
-
if "edddav" in self . errors :
-
if vi [ "INCAR" ] . get ( "ICHARG" , 0 ) < 10 :
-
actions . append ({ "file" : "CHGCAR" ,
-
"action" : { "_file_delete" : { 'mode' : "actual" }}})
-
actions . append ({ "dict" : "INCAR" , "action" :
-
{ "_set" : { "ALGO" : "All" }}})
-
-
if "grad_not_orth" in self . errors :
-
if vi [ "INCAR" ] . get ( "ISMEAR" , 1 ) < 0 :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISMEAR" : 0 , "SIGMA" : 0.05 }}})
-
-
if "zheev" in self . errors :
-
if vi [ "INCAR" ] . get ( "ALGO" , "Fast" ) . lower () != "exact" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "Exact" }}})
-
if "elf_kpar" in self . errors :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "KPAR" : 1 }}})
-
-
if "rhosyg" in self . errors :
-
if vi [ "INCAR" ] . get ( "SYMPREC" , 1e-4 ) == 1e-4 :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISYM" : 0 }}})
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "SYMPREC" : 1e-4 }}})
-
-
if "posmap" in self . errors :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "SYMPREC" : 1e-6 }}})
-
-
if "point_group" in self . errors :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISYM" : 0 }}})
-
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : list ( self . errors ), "actions" : actions } [docs] class LrfCommutatorHandler ( ErrorHandler ):
-
"""
-
Corrects LRF_COMMUTATOR errors by setting LPEAD=True if not already set.
-
Note that switching LPEAD=T can slightly change results versus the
-
default due to numerical evaluation of derivatives.
-
"""
-
-
is_monitor = True
-
-
error_msgs = {
-
"lrf_comm" : [ "LRF_COMMUTATOR internal error" ],
-
}
-
-
def __init__ ( self , output_filename = "std_err.txt" ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_filename (str): This is the file where the stderr for vasp
-
is being redirected. The error messages that are checked are
-
present in the stderr. Defaults to "std_err.txt", which is the
-
default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
-
"""
-
self . output_filename = output_filename
-
self . errors = set ()
-
self . error_count = Counter ()
-
-
[docs] def check ( self ):
-
self . errors = set ()
-
with open ( self . output_filename , "r" ) as f :
-
for line in f :
-
l = line . strip ()
-
for err , msgs in LrfCommutatorHandler . error_msgs . items ():
-
for msg in msgs :
-
if l . find ( msg ) != - 1 :
-
self . errors . add ( err )
-
return len ( self . errors ) > 0
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES | { self . output_filename })
-
actions = []
-
vi = VaspInput . from_directory ( "." )
-
-
if "lrf_comm" in self . errors :
-
if Outcar ( zpath ( os . path . join (
-
os . getcwd (), "OUTCAR" ))) . is_stopped is False :
-
if not vi [ "INCAR" ] . get ( "LPEAD" ):
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "LPEAD" : True }}})
-
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : list ( self . errors ), "actions" : actions } [docs] class StdErrHandler ( ErrorHandler ):
-
"""
-
Master StdErr class that handles a number of common errors
-
that occur during VASP runs with error messages only in
-
the standard error.
-
"""
-
-
is_monitor = True
-
-
error_msgs = {
-
"kpoints_trans" : [ "internal error in GENERATE_KPOINTS_TRANS: "
-
"number of G-vector changed in star" ],
-
"out_of_memory" : [ "Allocation would exceed memory limit" ]
-
}
-
-
def __init__ ( self , output_filename = "std_err.txt" ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_filename (str): This is the file where the stderr for vasp
-
is being redirected. The error messages that are checked are
-
present in the stderr. Defaults to "std_err.txt", which is the
-
default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
-
"""
-
self . output_filename = output_filename
-
self . errors = set ()
-
self . error_count = Counter ()
-
-
[docs] def check ( self ):
-
self . errors = set ()
-
with open ( self . output_filename , "r" ) as f :
-
for line in f :
-
l = line . strip ()
-
for err , msgs in StdErrHandler . error_msgs . items ():
-
for msg in msgs :
-
if l . find ( msg ) != - 1 :
-
self . errors . add ( err )
-
return len ( self . errors ) > 0
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES | { self . output_filename })
-
actions = []
-
vi = VaspInput . from_directory ( "." )
-
-
if "kpoints_trans" in self . errors :
-
if self . error_count [ "kpoints_trans" ] == 0 :
-
m = reduce ( operator . mul , vi [ "KPOINTS" ] . kpts [ 0 ])
-
m = max ( int ( round ( m ** ( 1 / 3 ))), 1 )
-
if vi [ "KPOINTS" ] . style . name . lower () . startswith ( "m" ):
-
m += m % 2
-
actions . append ({ "dict" : "KPOINTS" ,
-
"action" : { "_set" : { "kpoints" : [[ m ] * 3 ]}}})
-
self . error_count [ 'kpoints_trans' ] += 1
-
-
if "out_of_memory" in self . errors :
-
if vi [ "INCAR" ] . get ( "KPAR" , 1 ) > 1 :
-
reduced_kpar = max ( vi [ "INCAR" ] . get ( "KPAR" , 1 ) // 2 , 1 )
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "KPAR" : reduced_kpar }}})
-
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : list ( self . errors ), "actions" : actions } [docs] class AliasingErrorHandler ( ErrorHandler ):
-
"""
-
Master VaspErrorHandler class that handles a number of common errors
-
that occur during VASP runs.
-
"""
-
-
is_monitor = True
-
-
error_msgs = {
-
"aliasing" : [
-
"WARNING: small aliasing (wrap around) errors must be expected" ],
-
"aliasing_incar" : [ "Your FFT grids (NGX,NGY,NGZ) are not sufficient "
-
"for an accurate" ]
-
}
-
-
def __init__ ( self , output_filename = "vasp.out" ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_filename (str): This is the file where the stdout for vasp
-
is being redirected. The error messages that are checked are
-
present in the stdout. Defaults to "vasp.out", which is the
-
default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
-
"""
-
self . output_filename = output_filename
-
self . errors = set ()
-
-
[docs] def check ( self ):
-
incar = Incar . from_file ( "INCAR" )
-
self . errors = set ()
-
with open ( self . output_filename , "r" ) as f :
-
for line in f :
-
l = line . strip ()
-
for err , msgs in AliasingErrorHandler . error_msgs . items ():
-
for msg in msgs :
-
if l . find ( msg ) != - 1 :
-
# this checks if we want to run a charged
-
# computation (e.g., defects) if yes we don't
-
# want to kill it because there is a change in e-
-
# density (brmix error)
-
if err == "brmix" and 'NELECT' in incar :
-
continue
-
self . errors . add ( err )
-
return len ( self . errors ) > 0
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES | { self . output_filename })
-
actions = []
-
vi = VaspInput . from_directory ( "." )
-
-
if "aliasing" in self . errors :
-
with open ( "OUTCAR" ) as f :
-
grid_adjusted = False
-
changes_dict = {}
-
r = re . compile ( ".+aliasing errors.*(NG.)\s*to\s*(\d+)" )
-
for line in f :
-
m = r . match ( line )
-
if m :
-
changes_dict [ m . group ( 1 )] = int ( m . group ( 2 ))
-
grid_adjusted = True
-
# Ensure that all NGX, NGY, NGZ have been checked
-
if grid_adjusted and 'NGZ' in line :
-
actions . append (
-
{ "dict" : "INCAR" , "action" : { "_set" : changes_dict }})
-
if vi [ "INCAR" ] . get ( "ICHARG" , 0 ) < 10 :
-
actions . extend ([{ "file" : "CHGCAR" ,
-
"action" : { "_file_delete" : {
-
'mode' : "actual" }}},
-
{ "file" : "WAVECAR" ,
-
"action" : { "_file_delete" : {
-
'mode' : "actual" }}}])
-
break
-
-
if "aliasing_incar" in self . errors :
-
# vasp seems to give different warnings depending on whether the
-
# aliasing error was caused by user supplied inputs
-
d = { k : 1 for k in [ 'NGX' , 'NGY' , 'NGZ' ] if k in vi [ 'INCAR' ] . keys ()}
-
actions . append ({ "dict" : "INCAR" , "action" : { "_unset" : d }})
-
-
if vi [ "INCAR" ] . get ( "ICHARG" , 0 ) < 10 :
-
actions . extend ([{ "file" : "CHGCAR" ,
-
"action" : {
-
"_file_delete" : { 'mode' : "actual" }}},
-
{ "file" : "WAVECAR" ,
-
"action" : {
-
"_file_delete" : { 'mode' : "actual" }}}])
-
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : list ( self . errors ), "actions" : actions } [docs] class DriftErrorHandler ( ErrorHandler ):
-
"""
-
Corrects for total drift exceeding the force convergence criteria.
-
"""
-
-
def __init__ ( self , max_drift = None , to_average = 3 , enaug_multiply = 2 ):
-
"""
-
Initializes the handler with max drift
-
Args:
-
max_drift (float): This defines the max drift. Leaving this at the default of None gets the max_drift from EDFIFFG
-
"""
-
-
self . max_drift = max_drift
-
self . to_average = int ( to_average )
-
self . enaug_multiply = enaug_multiply
-
-
[docs] def check ( self ):
-
-
incar = Incar . from_file ( "INCAR" )
-
if incar . get ( "EDIFFG" , 0.1 ) >= 0 or incar . get ( "NSW" , 0 ) == 0 :
-
# Only activate when force relaxing and ionic steps
-
# NSW check prevents accidental effects when running DFPT
-
return False
-
-
if not self . max_drift :
-
self . max_drift = incar [ "EDIFFG" ] * - 1
-
-
try :
-
outcar = Outcar ( "OUTCAR" )
-
except :
-
# Can't perform check if Outcar not valid
-
return False
-
-
if len ( outcar . data . get ( 'drift' , [])) < self . to_average :
-
# Ensure enough steps to get average drift
-
return False
-
else :
-
curr_drift = outcar . data . get ( "drift" , [])[:: - 1 ][: self . to_average ]
-
curr_drift = np . average ([ np . linalg . norm ( d ) for d in curr_drift ])
-
return curr_drift > self . max_drift
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES )
-
actions = []
-
vi = VaspInput . from_directory ( "." )
-
-
incar = vi [ "INCAR" ]
-
outcar = Outcar ( "OUTCAR" )
-
-
# Move CONTCAR to POSCAR
-
actions . append ({ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}})
-
-
# First try adding ADDGRID
-
if not incar . get ( "ADDGRID" , False ):
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ADDGRID" : True }}})
-
# Otherwise set PREC to High so ENAUG can be used to control Augmentation Grid Size
-
elif incar . get ( "PREC" , "Accurate" ) . lower () != "high" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "PREC" : "High" }}})
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ENAUG" : incar . get ( "ENCUT" , 520 ) * 2 }}})
-
# PREC is already high and ENAUG set so just increase it
-
else :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ENAUG" : int ( incar . get ( "ENAUG" , 1040 ) * self . enaug_multiply )}}})
-
-
curr_drift = outcar . data . get ( "drift" , [])[:: - 1 ][: self . to_average ]
-
curr_drift = np . average ([ np . linalg . norm ( d ) for d in curr_drift ])
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : "Excessive drift {} > {} " . format ( curr_drift , self . max_drift ), "actions" : actions } [docs] class MeshSymmetryErrorHandler ( ErrorHandler ):
-
"""
-
Corrects the mesh symmetry error in VASP. This error is sometimes
-
non-fatal. So this error handler only checks at the end of the run,
-
and if the run has converged, no error is recorded.
-
"""
-
is_monitor = False
-
-
def __init__ ( self , output_filename = "vasp.out" ,
-
output_vasprun = "vasprun.xml" ):
-
"""
-
Initializes the handler with the output files to check.
-
-
Args:
-
output_filename (str): This is the file where the stdout for vasp
-
is being redirected. The error messages that are checked are
-
present in the stdout. Defaults to "vasp.out", which is the
-
default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
-
output_vasprun (str): Filename for the vasprun.xml file. Change
-
this only if it is different from the default (unlikely).
-
"""
-
self . output_filename = output_filename
-
self . output_vasprun = output_vasprun
-
-
[docs] def check ( self ):
-
msg = "Reciprocal lattice and k-lattice belong to different class of" \
-
" lattices."
-
-
vi = VaspInput . from_directory ( '.' )
-
# According to VASP admins, you can disregard this error
-
# if symmetry is off
-
# Also disregard if automatic KPOINT generation is used
-
if ( not vi [ "INCAR" ] . get ( 'ISYM' , True )) or \
-
vi [
-
"KPOINTS" ] . style == Kpoints . supported_modes . Automatic :
-
return False
-
-
try :
-
v = Vasprun ( self . output_vasprun )
-
if v . converged :
-
return False
-
except :
-
pass
-
with open ( self . output_filename , "r" ) as f :
-
for line in f :
-
l = line . strip ()
-
if l . find ( msg ) != - 1 :
-
return True
-
return False
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES | { self . output_filename })
-
vi = VaspInput . from_directory ( "." )
-
m = reduce ( operator . mul , vi [ "KPOINTS" ] . kpts [ 0 ])
-
m = max ( int ( round ( m ** ( 1 / 3 ))), 1 )
-
if vi [ "KPOINTS" ] . style . name . lower () . startswith ( "m" ):
-
m += m % 2
-
actions = [{ "dict" : "KPOINTS" ,
-
"action" : { "_set" : { "kpoints" : [[ m ] * 3 ]}}}]
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : [ "mesh_symmetry" ], "actions" : actions } [docs] class UnconvergedErrorHandler ( ErrorHandler ):
-
"""
-
Check if a run is converged.
-
"""
-
is_monitor = False
-
-
def __init__ ( self , output_filename = "vasprun.xml" ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_vasprun (str): Filename for the vasprun.xml file. Change
-
this only if it is different from the default (unlikely).
-
"""
-
self . output_filename = output_filename
-
-
[docs] def check ( self ):
-
try :
-
v = Vasprun ( self . output_filename )
-
if not v . converged :
-
return True
-
except :
-
pass
-
return False
-
-
[docs] def correct ( self ):
-
v = Vasprun ( self . output_filename )
-
actions = []
-
if not v . converged_electronic :
-
# Ladder from VeryFast to Fast to Fast to All
-
# These progressively switches to more stable but more
-
# expensive algorithms
-
algo = v . incar . get ( "ALGO" , "Normal" )
-
if algo == "VeryFast" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "Fast" }}})
-
elif algo == "Fast" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "Normal" }}})
-
elif algo == "Normal" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "All" }}})
-
else :
-
# Try mixing as last resort
-
new_settings = { "ISTART" : 1 ,
-
"ALGO" : "Normal" ,
-
"NELMDL" : - 6 ,
-
"BMIX" : 0.001 ,
-
"AMIX_MAG" : 0.8 ,
-
"BMIX_MAG" : 0.001 }
-
-
if not all ([ v . incar . get ( k , "" ) == val for k , val in new_settings . items ()]):
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : new_settings }})
-
-
elif not v . converged_ionic :
-
# Just continue optimizing and let other handles fix ionic
-
# optimizer parameters
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "IBRION" : 1 }}})
-
actions . append ({ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}})
-
-
if actions :
-
vi = VaspInput . from_directory ( "." )
-
backup ( VASP_BACKUP_FILES )
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : [ "Unconverged" ], "actions" : actions }
-
else :
-
# Unfixable error. Just return None for actions.
-
return { "errors" : [ "Unconverged" ], "actions" : None } [docs] class MaxForceErrorHandler ( ErrorHandler ):
-
"""
-
Checks that the desired force convergence has been achieved. Otherwise
-
restarts the run with smaller EDIFF. (This is necessary since energy
-
and force convergence criteria cannot be set simultaneously)
-
"""
-
is_monitor = False
-
-
def __init__ ( self , output_filename = "vasprun.xml" ,
-
max_force_threshold = 0.25 ):
-
"""
-
Args:
-
input_filename (str): name of the vasp INCAR file
-
output_filename (str): name to look for the vasprun
-
max_force_threshold (float): Threshold for max force for
-
restarting the run. (typically should be set to the value
-
that the creator looks for)
-
"""
-
self . output_filename = output_filename
-
self . max_force_threshold = max_force_threshold
-
-
[docs] def check ( self ):
-
try :
-
v = Vasprun ( self . output_filename )
-
forces = np . array ( v . ionic_steps [ - 1 ][ 'forces' ])
-
sdyn = v . final_structure . site_properties . get ( 'selective_dynamics' )
-
if sdyn :
-
forces [ np . logical_not ( sdyn )] = 0
-
max_force = max ( np . linalg . norm ( forces , axis = 1 ))
-
if max_force > self . max_force_threshold and v . converged is True :
-
return True
-
except :
-
pass
-
return False
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES | { self . output_filename })
-
vi = VaspInput . from_directory ( "." )
-
ediff = float ( vi [ "INCAR" ] . get ( "EDIFF" , 1e-4 ))
-
ediffg = float ( vi [ "INCAR" ] . get ( "EDIFFG" , ediff * 10 ))
-
actions = [{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}},
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "EDIFFG" : ediffg * 0.5 }}}]
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
-
return { "errors" : [ "MaxForce" ], "actions" : actions } [docs] class PotimErrorHandler ( ErrorHandler ):
-
"""
-
Check if a run has excessively large positive energy changes.
-
This is typically caused by too large a POTIM. Runs typically
-
end up crashing with some other error (e.g. BRMIX) as the geometry
-
gets progressively worse.
-
"""
-
is_monitor = True
-
-
def __init__ ( self , input_filename = "POSCAR" , output_filename = "OSZICAR" ,
-
dE_threshold = 1 ):
-
"""
-
Initializes the handler with the input and output files to check.
-
-
Args:
-
input_filename (str): This is the POSCAR file that the run
-
started from. Defaults to "POSCAR". Change
-
this only if it is different from the default (unlikely).
-
output_filename (str): This is the OSZICAR file. Change
-
this only if it is different from the default (unlikely).
-
dE_threshold (float): The threshold energy change. Defaults to 1eV.
-
"""
-
self . input_filename = input_filename
-
self . output_filename = output_filename
-
self . dE_threshold = dE_threshold
-
-
[docs] def check ( self ):
-
try :
-
oszicar = Oszicar ( self . output_filename )
-
n = len ( Poscar . from_file ( self . input_filename ) . structure )
-
max_dE = max ([ s [ 'dE' ] for s in oszicar . ionic_steps [ 1 :]]) / n
-
if max_dE > self . dE_threshold :
-
return True
-
except :
-
return False
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES )
-
vi = VaspInput . from_directory ( "." )
-
potim = float ( vi [ "INCAR" ] . get ( "POTIM" , 0.5 ))
-
ibrion = int ( vi [ "INCAR" ] . get ( "IBRION" , 0 ))
-
if potim < 0.2 and ibrion != 3 :
-
actions = [{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "IBRION" : 3 ,
-
"SMASS" : 0.75 }}}]
-
elif potim < 0.1 :
-
actions = [{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "SYMPREC" : 1e-8 }}}]
-
else :
-
actions = [{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "POTIM" : potim * 0.5 }}}]
-
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : [ "POTIM" ], "actions" : actions } [docs] class FrozenJobErrorHandler ( ErrorHandler ):
-
"""
-
Detects an error when the output file has not been updated
-
in timeout seconds. Changes ALGO to Normal from Fast
-
"""
-
-
is_monitor = True
-
-
def __init__ ( self , output_filename = "vasp.out" , timeout = 21600 ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_filename (str): This is the file where the stdout for vasp
-
is being redirected. The error messages that are checked are
-
present in the stdout. Defaults to "vasp.out", which is the
-
default redirect used by :class:`custodian.vasp.jobs.VaspJob`.
-
timeout (int): The time in seconds between checks where if there
-
is no activity on the output file, the run is considered
-
frozen. Defaults to 3600 seconds, i.e., 1 hour.
-
"""
-
self . output_filename = output_filename
-
self . timeout = timeout
-
-
[docs] def check ( self ):
-
st = os . stat ( self . output_filename )
-
if time . time () - st . st_mtime > self . timeout :
-
return True
-
-
[docs] def correct ( self ):
-
backup ( VASP_BACKUP_FILES | { self . output_filename })
-
-
vi = VaspInput . from_directory ( '.' )
-
actions = []
-
if vi [ "INCAR" ] . get ( "ALGO" , "Normal" ) == "Fast" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "Normal" }}})
-
else :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "SYMPREC" : 1e-8 }}})
-
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
-
return { "errors" : [ "Frozen job" ], "actions" : actions } [docs] class NonConvergingErrorHandler ( ErrorHandler ):
-
"""
-
Check if a run is hitting the maximum number of electronic steps at the
-
last nionic_steps ionic steps (default=10). If so, change ALGO from Fast to
-
Normal or kill the job.
-
"""
-
is_monitor = True
-
-
def __init__ ( self , output_filename = "OSZICAR" , nionic_steps = 10 ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_filename (str): This is the OSZICAR file. Change
-
this only if it is different from the default (unlikely).
-
nionic_steps (int): The threshold number of ionic steps that
-
needs to hit the maximum number of electronic steps for the
-
run to be considered non-converging.
-
"""
-
self . output_filename = output_filename
-
self . nionic_steps = nionic_steps
-
-
[docs] def check ( self ):
-
vi = VaspInput . from_directory ( "." )
-
nelm = vi [ "INCAR" ] . get ( "NELM" , 60 )
-
try :
-
oszicar = Oszicar ( self . output_filename )
-
esteps = oszicar . electronic_steps
-
if len ( esteps ) > self . nionic_steps :
-
return all ([ len ( e ) == nelm
-
for e in esteps [ - ( self . nionic_steps + 1 ): - 1 ]])
-
except :
-
pass
-
return False
-
-
[docs] def correct ( self ):
-
vi = VaspInput . from_directory ( "." )
-
algo = vi [ "INCAR" ] . get ( "ALGO" , "Normal" )
-
amix = vi [ "INCAR" ] . get ( "AMIX" , 0.4 )
-
bmix = vi [ "INCAR" ] . get ( "BMIX" , 1.0 )
-
amin = vi [ "INCAR" ] . get ( "AMIN" , 0.1 )
-
actions = []
-
# Ladder from VeryFast to Fast to Fast to All
-
# These progressively switches to more stable but more
-
# expensive algorithms
-
if algo == "VeryFast" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "Fast" }}})
-
elif algo == "Fast" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "Normal" }}})
-
elif algo == "Normal" :
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "All" }}})
-
elif amix > 0.1 and bmix > 0.01 :
-
# Try linear mixing
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "AMIX" : 0.1 , "BMIX" : 0.01 ,
-
"ICHARG" : 2 }}})
-
elif bmix < 3.0 and amin > 0.01 :
-
# Try increasing bmix
-
actions . append ({ "dict" : "INCAR" ,
-
"action" : { "_set" : { "AMIN" : 0.01 , "BMIX" : 3.0 ,
-
"ICHARG" : 2 }}})
-
-
if actions :
-
backup ( VASP_BACKUP_FILES )
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : [ "Non-converging job" ], "actions" : actions }
-
# Unfixable error. Just return None for actions.
-
else :
-
return { "errors" : [ "Non-converging job" ], "actions" : None } [docs] class WalltimeHandler ( ErrorHandler ):
-
"""
-
Check if a run is nearing the walltime. If so, write a STOPCAR with
-
LSTOP or LABORT = .True.. You can specify the walltime either in the init (
-
which is unfortunately necessary for SGE and SLURM systems. If you happen
-
to be running on a PBS system and the PBS_WALLTIME variable is in the run
-
environment, the wall time will be automatically determined if not set.
-
"""
-
is_monitor = True
-
-
# The WalltimeHandler should not terminate as we want VASP to terminate
-
# itself naturally with the STOPCAR.
-
is_terminating = False
-
-
# This handler will be unrecoverable, but custodian shouldn't raise an
-
# error
-
raises_runtime_error = False
-
-
def __init__ ( self , wall_time = None , buffer_time = 300 ,
-
electronic_step_stop = False ):
-
"""
-
Initializes the handler with a buffer time.
-
-
Args:
-
wall_time (int): Total walltime in seconds. If this is None and
-
the job is running on a PBS system, the handler will attempt to
-
determine the walltime from the PBS_WALLTIME environment
-
variable. If the wall time cannot be determined or is not
-
set, this handler will have no effect.
-
buffer_time (int): The min amount of buffer time in secs at the
-
end that the STOPCAR will be written. The STOPCAR is written
-
when the time remaining is < the higher of 3 x the average
-
time for each ionic step and the buffer time. Defaults to
-
300 secs, which is the default polling time of Custodian.
-
This is typically sufficient for the current ionic step to
-
complete. But if other operations are being performed after
-
the run has stopped, the buffer time may need to be increased
-
accordingly.
-
electronic_step_stop (bool): Whether to check for electronic steps
-
instead of ionic steps (e.g. for static runs on large systems or
-
static HSE runs, ...). Be careful that results such as density
-
or wavefunctions might not be converged at the electronic level.
-
Should be used with LWAVE = .True. to be useful. If this is
-
True, the STOPCAR is written with LABORT = .TRUE. instead of
-
LSTOP = .TRUE.
-
"""
-
if wall_time is not None :
-
self . wall_time = wall_time
-
elif "PBS_WALLTIME" in os . environ :
-
self . wall_time = int ( os . environ [ "PBS_WALLTIME" ])
-
elif "SBATCH_TIMELIMIT" in os . environ :
-
self . wall_time = int ( os . environ [ "SBATCH_TIMELIMIT" ])
-
else :
-
self . wall_time = None
-
self . buffer_time = buffer_time
-
# Sets CUSTODIAN_WALLTIME_START as the start time to use for
-
# future jobs in the same batch environment. Can also be
-
# set manually be the user in the batch environment.
-
if "CUSTODIAN_WALLTIME_START" in os . environ :
-
self . start_time = datetime . datetime . strptime (
-
os . environ [ "CUSTODIAN_WALLTIME_START" ], " %a %b %d %H:%M:%S %Z %Y" )
-
else :
-
self . start_time = datetime . datetime . now ()
-
os . environ [ "CUSTODIAN_WALLTIME_START" ] = datetime . datetime . strftime (
-
self . start_time , " %a %b %d %H:%M:%S UTC %Y" )
-
-
self . electronic_step_stop = electronic_step_stop
-
self . electronic_steps_timings = [ 0 ]
-
self . prev_check_time = self . start_time
-
-
[docs] def check ( self ):
-
if self . wall_time :
-
run_time = datetime . datetime . now () - self . start_time
-
total_secs = run_time . total_seconds ()
-
outcar = Outcar ( "OUTCAR" )
-
if not self . electronic_step_stop :
-
# Determine max time per ionic step.
-
outcar . read_pattern ({ "timings" : "LOOP\+.+real time(.+)" },
-
postprocess = float )
-
time_per_step = np . max ( outcar . data . get ( 'timings' )) if outcar . data . get ( "timings" , []) else 0
-
else :
-
# Determine max time per electronic step.
-
outcar . read_pattern ({ "timings" : "LOOP:.+real time(.+)" },
-
postprocess = float )
-
time_per_step = np . max ( outcar . data . get ( 'timings' )) if outcar . data . get ( "timings" , []) else 0
-
-
# If the remaining time is less than average time for 3
-
# steps or buffer_time.
-
time_left = self . wall_time - total_secs
-
if time_left < max ( time_per_step * 3 , self . buffer_time ):
-
return True
-
-
return False
-
-
[docs] def correct ( self ):
-
-
content = "LSTOP = .TRUE." if not self . electronic_step_stop else \
-
"LABORT = .TRUE."
-
# Write STOPCAR
-
actions = [{ "file" : "STOPCAR" ,
-
"action" : { "_file_create" : { 'content' : content }}}]
-
-
m = Modder ( actions = [ FileActions ])
-
for a in actions :
-
m . modify ( a [ "action" ], a [ "file" ])
-
return { "errors" : [ "Walltime reached" ], "actions" : None } @deprecated ( replacement = WalltimeHandler )
-class PBSWalltimeHandler ( WalltimeHandler ):
-
- def __init__ ( self , buffer_time = 300 ):
- super ( PBSWalltimeHandler , self ) . __init__ ( None , buffer_time = buffer_time )
-
-
-[docs] class CheckpointHandler ( ErrorHandler ):
-
"""
-
This is not an error handler per se, but rather a checkpointer. What this
-
does is that every X seconds, a STOPCAR and CHKPT will be written. This
-
forces VASP to stop at the end of the next ionic step. The files are then
-
copied into a subdir, and then the job is restarted. To use this proper,
-
max_errors in Custodian must be set to a very high value, and you
-
probably wouldn't want to use any standard VASP error handlers. The
-
checkpoint will be stored in subdirs chk_#. This should be used in
-
combiantion with the StoppedRunHandler.
-
"""
-
is_monitor = True
-
-
# The CheckpointHandler should not terminate as we want VASP to terminate
-
# itself naturally with the STOPCAR.
-
is_terminating = False
-
-
def __init__ ( self , interval = 3600 ):
-
"""
-
Initializes the handler with an interval.
-
-
Args:
-
interval (int): Interval at which to checkpoint in seconds.
-
Defaults to 3600 (1 hr).
-
"""
-
self . interval = interval
-
self . start_time = datetime . datetime . now ()
-
self . chk_counter = 0
-
-
[docs] def check ( self ):
-
run_time = datetime . datetime . now () - self . start_time
-
total_secs = run_time . seconds + run_time . days * 3600 * 24
-
if total_secs > self . interval :
-
return True
-
return False
-
-
[docs] def correct ( self ):
-
content = "LSTOP = .TRUE."
-
chkpt_content = "Index: %d \n Time: \" %s \" " % ( self . chk_counter ,
-
datetime . datetime . now ())
-
self . chk_counter += 1
-
-
# Write STOPCAR
-
actions = [{ "file" : "STOPCAR" ,
-
"action" : { "_file_create" : { 'content' : content }}},
-
{ "file" : "chkpt.yaml" ,
-
"action" : { "_file_create" : { 'content' : chkpt_content }}}]
-
-
m = Modder ( actions = [ FileActions ])
-
for a in actions :
-
m . modify ( a [ "action" ], a [ "file" ])
-
-
# Reset the clock.
-
self . start_time = datetime . datetime . now ()
-
-
return { "errors" : [ "Checkpoint reached" ], "actions" : actions }
-
-
def __str__ ( self ):
-
return "CheckpointHandler with interval %d " % self . interval [docs] class StoppedRunHandler ( ErrorHandler ):
-
"""
-
This is not an error handler per se, but rather a checkpointer. What this
-
does is that every X seconds, a STOPCAR will be written. This forces VASP to
-
stop at the end of the next ionic step. The files are then copied into a
-
subdir, and then the job is restarted. To use this proper, max_errors in
-
Custodian must be set to a very high value, and you probably wouldn't
-
want to use any standard VASP error handlers. The checkpoint will be
-
stored in subdirs chk_#. This should be used in combination with the
-
StoppedRunHandler.
-
"""
-
is_monitor = False
-
-
# The CheckpointHandler should not terminate as we want VASP to terminate
-
# itself naturally with the STOPCAR.
-
is_terminating = False
-
-
def __init__ ( self ):
-
pass
-
-
[docs] def check ( self ):
-
return os . path . exists ( "chkpt.yaml" )
-
-
[docs] def correct ( self ):
-
d = loadfn ( "chkpt.yaml" )
-
i = d [ "Index" ]
-
name = shutil . make_archive (
-
os . path . join ( os . getcwd (), "vasp.chk. %d " % i ), "gztar" )
-
-
actions = [{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
-
m = Modder ( actions = [ FileActions ])
-
for a in actions :
-
m . modify ( a [ "action" ], a [ "file" ])
-
-
actions . append ({ "Checkpoint" : name })
-
-
return { "errors" : [ "Stopped run." ],
-
"actions" : actions } [docs] class PositiveEnergyErrorHandler ( ErrorHandler ):
-
"""
-
Check if a run has positive absolute energy.
-
If so, change ALGO from Fast to Normal or kill the job.
-
"""
-
is_monitor = True
-
-
def __init__ ( self , output_filename = "OSZICAR" ):
-
"""
-
Initializes the handler with the output file to check.
-
-
Args:
-
output_filename (str): This is the OSZICAR file. Change
-
this only if it is different from the default (unlikely).
-
"""
-
self . output_filename = output_filename
-
-
[docs] def check ( self ):
-
try :
-
oszicar = Oszicar ( self . output_filename )
-
if oszicar . final_energy > 0 :
-
return True
-
except :
-
pass
-
return False
-
-
[docs] def correct ( self ):
-
# change ALGO = Fast to Normal if ALGO is !Normal
-
vi = VaspInput . from_directory ( "." )
-
algo = vi [ "INCAR" ] . get ( "ALGO" , "Normal" )
-
if algo . lower () not in [ 'normal' , 'n' ]:
-
backup ( VASP_BACKUP_FILES )
-
actions = [{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ALGO" : "Normal" }}}]
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : [ "Positive energy" ], "actions" : actions }
-
elif algo == "Normal" :
-
potim = float ( vi [ "INCAR" ] . get ( "POTIM" , 0.5 )) / 2.0
-
actions = [{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "POTIM" : potim }}}]
-
VaspModder ( vi = vi ) . apply_actions ( actions )
-
return { "errors" : [ "Positive energy" ], "actions" : actions }
-
# Unfixable error. Just return None for actions.
-
else :
-
return { "errors" : [ "Positive energy" ], "actions" : None }
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/vasp/interpreter.html b/docs/html/_modules/custodian/vasp/interpreter.html
deleted file mode 100644
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+++ /dev/null
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custodian.vasp.interpreter — custodian 2019.8.23 documentation
-
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Source code for custodian.vasp.interpreter
-# coding: utf-8
-
-from __future__ import unicode_literals
-
-from custodian.ansible.actions import FileActions , DictActions
-from custodian.ansible.interpreter import Modder
-from pymatgen.io.vasp import VaspInput
-
-
-[docs] class VaspModder ( Modder ):
-
def __init__ ( self , actions = None , strict = True , vi = None ):
-
"""
-
Initializes a Modder for VaspInput sets
-
-
Args:
-
actions ([Action]): A sequence of supported actions. See
-
:mod:`custodian.ansible.actions`. Default is None,
-
which means DictActions and FileActions are supported.
-
strict (bool): Indicating whether to use strict mode. In non-strict
-
mode, unsupported actions are simply ignored without any
-
errors raised. In strict mode, if an unsupported action is
-
supplied, a ValueError is raised. Defaults to True.
-
vi (VaspInput): A VaspInput object from the current directory.
-
Initialized automatically if not passed (but passing it will
-
avoid having to reparse the directory).
-
"""
-
self . vi = vi or VaspInput . from_directory ( '.' )
-
actions = actions or [ FileActions , DictActions ]
-
super ( VaspModder , self ) . __init__ ( actions , strict )
-
-
[docs] def apply_actions ( self , actions ):
-
"""
-
Applies a list of actions to the Vasp Input Set and rewrites modified
-
files.
-
Args:
-
actions [dict]: A list of actions of the form {'file': filename,
-
'action': moddermodification} or {'dict': vaspinput_key,
-
'action': moddermodification}
-
"""
-
modified = []
-
for a in actions :
-
if "dict" in a :
-
k = a [ "dict" ]
-
modified . append ( k )
-
self . vi [ k ] = self . modify_object ( a [ "action" ], self . vi [ k ])
-
elif "file" in a :
-
self . modify ( a [ "action" ], a [ "file" ])
-
else :
-
raise ValueError ( "Unrecognized format: {} " . format ( a ))
-
for f in modified :
-
self . vi [ f ] . write_file ( f )
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
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custodian.vasp.jobs — custodian 2019.8.23 documentation
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Source code for custodian.vasp.jobs
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-import subprocess
-import os
-import shutil
-import math
-import logging
-
-import numpy as np
-
-from pymatgen import Structure
-from pymatgen.io.vasp import VaspInput , Incar , Poscar , Outcar , Kpoints , Vasprun
-from monty.os.path import which
-from monty.shutil import decompress_dir
-from monty.serialization import dumpfn , loadfn
-
-from custodian.custodian import Job , SENTRY_DSN
-from custodian.utils import backup
-from custodian.vasp.interpreter import VaspModder
-from custodian.vasp.handlers import VASP_BACKUP_FILES
-
-"""
-This module implements basic kinds of jobs for VASP runs.
-"""
-
-
-logger = logging . getLogger ( __name__ )
-
-
-__author__ = "Shyue Ping Ong"
-__version__ = "0.1"
-__maintainer__ = "Shyue Ping Ong"
-__email__ = "shyuep@gmail.com"
-__status__ = "Beta"
-__date__ = "2/4/13"
-
-
-VASP_INPUT_FILES = { "INCAR" , "POSCAR" , "POTCAR" , "KPOINTS" }
-
-VASP_OUTPUT_FILES = [ 'DOSCAR' , 'INCAR' , 'KPOINTS' , 'POSCAR' , 'PROCAR' ,
- 'vasprun.xml' , 'CHGCAR' , 'CHG' , 'EIGENVAL' , 'OSZICAR' ,
- 'WAVECAR' , 'CONTCAR' , 'IBZKPT' , 'OUTCAR' ]
-
-VASP_NEB_INPUT_FILES = { 'INCAR' , 'POTCAR' , 'KPOINTS' }
-
-VASP_NEB_OUTPUT_FILES = [ 'INCAR' , 'KPOINTS' , 'POTCAR' , 'vasprun.xml' ]
-
-VASP_NEB_OUTPUT_SUB_FILES = [ 'CHG' , 'CHGCAR' , 'CONTCAR' , 'DOSCAR' ,
- 'EIGENVAL' , 'IBZKPT' , 'PCDAT' , 'POSCAR' ,
- 'REPORT' , 'PROCAR' , 'OSZICAR' , 'OUTCAR' ,
- 'WAVECAR' , 'XDATCAR' ]
-
-
-[docs] class VaspJob ( Job ):
-
"""
-
A basic vasp job. Just runs whatever is in the directory. But conceivably
-
can be a complex processing of inputs etc. with initialization.
-
"""
-
-
def __init__ ( self , vasp_cmd , output_file = "vasp.out" ,
-
stderr_file = "std_err.txt" , suffix = "" , final = True ,
-
backup = True , auto_npar = False , auto_gamma = True ,
-
settings_override = None , gamma_vasp_cmd = None ,
-
copy_magmom = False , auto_continue = False ):
-
"""
-
This constructor is necessarily complex due to the need for
-
flexibility. For standard kinds of runs, it's often better to use one
-
of the static constructors. The defaults are usually fine too.
-
-
Args:
-
vasp_cmd (str): Command to run vasp as a list of args. For example,
-
if you are using mpirun, it can be something like
-
["mpirun", "pvasp.5.2.11"]
-
output_file (str): Name of file to direct standard out to.
-
Defaults to "vasp.out".
-
stderr_file (str): Name of file to direct standard error to.
-
Defaults to "std_err.txt".
-
suffix (str): A suffix to be appended to the final output. E.g.,
-
to rename all VASP output from say vasp.out to
-
vasp.out.relax1, provide ".relax1" as the suffix.
-
final (bool): Indicating whether this is the final vasp job in a
-
series. Defaults to True.
-
backup (bool): Whether to backup the initial input files. If True,
-
the INCAR, KPOINTS, POSCAR and POTCAR will be copied with a
-
".orig" appended. Defaults to True.
-
auto_npar (bool): Whether to automatically tune NPAR to be sqrt(
-
number of cores) as recommended by VASP for DFT calculations.
-
Generally, this results in significant speedups. Defaults to
-
True. Set to False for HF, GW and RPA calculations.
-
auto_gamma (bool): Whether to automatically check if run is a
-
Gamma 1x1x1 run, and whether a Gamma optimized version of
-
VASP exists with ".gamma" appended to the name of the VASP
-
executable (typical setup in many systems). If so, run the
-
gamma optimized version of VASP instead of regular VASP. You
-
can also specify the gamma vasp command using the
-
gamma_vasp_cmd argument if the command is named differently.
-
settings_override ([dict]): An ansible style list of dict to
-
override changes. For example, to set ISTART=1 for subsequent
-
runs and to copy the CONTCAR to the POSCAR, you will provide::
-
-
[{"dict": "INCAR", "action": {"_set": {"ISTART": 1}}},
-
{"file": "CONTCAR",
-
"action": {"_file_copy": {"dest": "POSCAR"}}}]
-
gamma_vasp_cmd (str): Command for gamma vasp version when
-
auto_gamma is True. Should follow the list style of
-
subprocess. Defaults to None, which means ".gamma" is added
-
to the last argument of the standard vasp_cmd.
-
copy_magmom (bool): Whether to copy the final magmom from the
-
OUTCAR to the next INCAR. Useful for multi-relaxation runs
-
where the CHGCAR and WAVECAR are sometimes deleted (due to
-
changes in fft grid, etc.). Only applies to non-final runs.
-
auto_continue (bool): Whether to automatically continue a run
-
if a STOPCAR is present. This is very useful if using the
-
wall-time handler which will write a read-only STOPCAR to
-
prevent VASP from deleting it once it finishes
-
"""
-
self . vasp_cmd = vasp_cmd
-
self . output_file = output_file
-
self . stderr_file = stderr_file
-
self . final = final
-
self . backup = backup
-
self . suffix = suffix
-
self . settings_override = settings_override
-
self . auto_npar = auto_npar
-
self . auto_gamma = auto_gamma
-
self . gamma_vasp_cmd = gamma_vasp_cmd
-
self . copy_magmom = copy_magmom
-
self . auto_continue = auto_continue
-
-
if SENTRY_DSN :
-
# if using Sentry logging, add specific VASP executable to scope
-
from sentry_sdk import configure_scope
-
with configure_scope () as scope :
-
try :
-
if isinstance ( vasp_cmd , str ):
-
vasp_path = which ( vasp_cmd . split ( ' ' )[ - 1 ])
-
elif isinstance ( vasp_cmd , list ):
-
vasp_path = which ( vasp_cmd [ - 1 ])
-
scope . set_tag ( "vasp_path" , vasp_path )
-
scope . set_tag ( "vasp_cmd" , vasp_cmd )
-
except :
-
logger . error ( "Failed to detect VASP path: {} " . format ( vasp_cmd ), exc_info = True )
-
scope . set_tag ( "vasp_cmd" , vasp_cmd )
-
-
[docs] def setup ( self ):
-
"""
-
Performs initial setup for VaspJob, including overriding any settings
-
and backing up.
-
"""
-
decompress_dir ( '.' )
-
-
if self . backup :
-
for f in VASP_INPUT_FILES :
-
shutil . copy ( f , " {} .orig" . format ( f ))
-
-
if self . auto_npar :
-
try :
-
incar = Incar . from_file ( "INCAR" )
-
# Only optimized NPAR for non-HF and non-RPA calculations.
-
if not ( incar . get ( "LHFCALC" ) or incar . get ( "LRPA" ) or
-
incar . get ( "LEPSILON" )):
-
if incar . get ( "IBRION" ) in [ 5 , 6 , 7 , 8 ]:
-
# NPAR should not be set for Hessian matrix
-
# calculations, whether in DFPT or otherwise.
-
del incar [ "NPAR" ]
-
else :
-
import multiprocessing
-
# try sge environment variable first
-
# (since multiprocessing counts cores on the current
-
# machine only)
-
ncores = os . environ . get ( 'NSLOTS' ) or \
-
multiprocessing . cpu_count ()
-
ncores = int ( ncores )
-
for npar in range ( int ( math . sqrt ( ncores )),
-
ncores ):
-
if ncores % npar == 0 :
-
incar [ "NPAR" ] = npar
-
break
-
incar . write_file ( "INCAR" )
-
except :
-
pass
-
-
if self . auto_continue :
-
if os . path . exists ( "continue.json" ):
-
actions = loadfn ( "continue.json" ) . get ( "actions" )
-
logger . info ( "Continuing previous VaspJob. Actions: {} " . format ( actions ))
-
backup ( VASP_BACKUP_FILES , prefix = "prev_run" )
-
VaspModder () . apply_actions ( actions )
-
-
else :
-
# Default functionality is to copy CONTCAR to POSCAR and set
-
# ISTART to 1 in the INCAR, but other actions can be specified
-
if self . auto_continue is True :
-
actions = [{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}},
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISTART" : 1 }}}]
-
else :
-
actions = self . auto_continue
-
dumpfn ({ "actions" : actions }, "continue.json" )
-
-
if self . settings_override is not None :
-
VaspModder () . apply_actions ( self . settings_override )
-
-
[docs] def run ( self ):
-
"""
-
Perform the actual VASP run.
-
-
Returns:
-
(subprocess.Popen) Used for monitoring.
-
"""
-
cmd = list ( self . vasp_cmd )
-
if self . auto_gamma :
-
vi = VaspInput . from_directory ( "." )
-
kpts = vi [ "KPOINTS" ]
-
if kpts . style == Kpoints . supported_modes . Gamma \
-
and tuple ( kpts . kpts [ 0 ]) == ( 1 , 1 , 1 ):
-
if self . gamma_vasp_cmd is not None and which (
-
self . gamma_vasp_cmd [ - 1 ]):
-
cmd = self . gamma_vasp_cmd
-
elif which ( cmd [ - 1 ] + ".gamma" ):
-
cmd [ - 1 ] += ".gamma"
-
logger . info ( "Running {} " . format ( " " . join ( cmd )))
-
with open ( self . output_file , 'w' ) as f_std , \
-
open ( self . stderr_file , "w" , buffering = 1 ) as f_err :
-
# use line buffering for stderr
-
p = subprocess . Popen ( cmd , stdout = f_std , stderr = f_err )
-
return p
-
-
[docs] def postprocess ( self ):
-
"""
-
Postprocessing includes renaming and gzipping where necessary.
-
Also copies the magmom to the incar if necessary
-
"""
-
for f in VASP_OUTPUT_FILES + [ self . output_file ]:
-
if os . path . exists ( f ):
-
if self . final and self . suffix != "" :
-
shutil . move ( f , " {}{} " . format ( f , self . suffix ))
-
elif self . suffix != "" :
-
shutil . copy ( f , " {}{} " . format ( f , self . suffix ))
-
-
if self . copy_magmom and not self . final :
-
try :
-
outcar = Outcar ( "OUTCAR" )
-
magmom = [ m [ 'tot' ] for m in outcar . magnetization ]
-
incar = Incar . from_file ( "INCAR" )
-
incar [ 'MAGMOM' ] = magmom
-
incar . write_file ( "INCAR" )
-
except :
-
logger . error ( 'MAGMOM copy from OUTCAR to INCAR failed' )
-
-
# Remove continuation so if a subsequent job is run in
-
# the same directory, will not restart this job.
-
if os . path . exists ( "continue.json" ):
-
os . remove ( "continue.json" )
-
-
[docs] @classmethod
-
def double_relaxation_run ( cls , vasp_cmd , auto_npar = True , ediffg =- 0.05 ,
-
half_kpts_first_relax = False , auto_continue = False ):
-
"""
-
Returns a list of two jobs corresponding to an AFLOW style double
-
relaxation run.
-
-
Args:
-
vasp_cmd (str): Command to run vasp as a list of args. For example,
-
if you are using mpirun, it can be something like
-
["mpirun", "pvasp.5.2.11"]
-
auto_npar (bool): Whether to automatically tune NPAR to be sqrt(
-
number of cores) as recommended by VASP for DFT calculations.
-
Generally, this results in significant speedups. Defaults to
-
True. Set to False for HF, GW and RPA calculations.
-
ediffg (float): Force convergence criteria for subsequent runs (
-
ignored for the initial run.)
-
half_kpts_first_relax (bool): Whether to halve the kpoint grid
-
for the first relaxation. Speeds up difficult convergence
-
considerably. Defaults to False.
-
-
Returns:
-
List of two jobs corresponding to an AFLOW style run.
-
"""
-
incar_update = { "ISTART" : 1 }
-
if ediffg :
-
incar_update [ "EDIFFG" ] = ediffg
-
settings_overide_1 = None
-
settings_overide_2 = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : incar_update }},
-
{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
if half_kpts_first_relax and os . path . exists ( "KPOINTS" ) and \
-
os . path . exists ( "POSCAR" ):
-
kpts = Kpoints . from_file ( "KPOINTS" )
-
orig_kpts_dict = kpts . as_dict ()
-
# lattice vectors with length < 8 will get >1 KPOINT
-
kpts . kpts = np . round ( np . maximum ( np . array ( kpts . kpts ) / 2 ,
-
1 )) . astype ( int ) . tolist ()
-
low_kpts_dict = kpts . as_dict ()
-
settings_overide_1 = [
-
{ "dict" : "KPOINTS" ,
-
"action" : { "_set" : low_kpts_dict }}
-
]
-
settings_overide_2 . append (
-
{ "dict" : "KPOINTS" ,
-
"action" : { "_set" : orig_kpts_dict }}
-
)
-
-
return [ VaspJob ( vasp_cmd , final = False , suffix = ".relax1" ,
-
auto_npar = auto_npar , auto_continue = auto_continue ,
-
settings_override = settings_overide_1 ),
-
VaspJob ( vasp_cmd , final = True , backup = False , suffix = ".relax2" ,
-
auto_npar = auto_npar , auto_continue = auto_continue ,
-
settings_override = settings_overide_2 )]
-
-
-
-
[docs] @classmethod
-
def full_opt_run ( cls , vasp_cmd , vol_change_tol = 0.02 ,
-
max_steps = 10 , ediffg =- 0.05 , half_kpts_first_relax = False ,
-
** vasp_job_kwargs ):
-
"""
-
Returns a generator of jobs for a full optimization run. Basically,
-
this runs an infinite series of geometry optimization jobs until the
-
% vol change in a particular optimization is less than vol_change_tol.
-
-
Args:
-
vasp_cmd (str): Command to run vasp as a list of args. For example,
-
if you are using mpirun, it can be something like
-
["mpirun", "pvasp.5.2.11"]
-
vol_change_tol (float): The tolerance at which to stop a run.
-
Defaults to 0.05, i.e., 5%.
-
max_steps (int): The maximum number of runs. Defaults to 10 (
-
highly unlikely that this limit is ever reached).
-
ediffg (float): Force convergence criteria for subsequent runs (
-
ignored for the initial run.)
-
half_kpts_first_relax (bool): Whether to halve the kpoint grid
-
for the first relaxation. Speeds up difficult convergence
-
considerably. Defaults to False.
-
\*\*vasp_job_kwargs: Passthrough kwargs to VaspJob. See
-
:class:`custodian.vasp.jobs.VaspJob`.
-
-
Returns:
-
Generator of jobs.
-
"""
-
for i in range ( max_steps ):
-
if i == 0 :
-
settings = None
-
backup = True
-
if half_kpts_first_relax and os . path . exists ( "KPOINTS" ) and \
-
os . path . exists ( "POSCAR" ):
-
kpts = Kpoints . from_file ( "KPOINTS" )
-
orig_kpts_dict = kpts . as_dict ()
-
kpts . kpts = np . maximum ( np . array ( kpts . kpts ) / 2 , 1 ) . tolist ()
-
low_kpts_dict = kpts . as_dict ()
-
settings = [
-
{ "dict" : "KPOINTS" ,
-
"action" : { "_set" : low_kpts_dict }}
-
]
-
else :
-
backup = False
-
initial = Poscar . from_file ( "POSCAR" ) . structure
-
final = Poscar . from_file ( "CONTCAR" ) . structure
-
vol_change = ( final . volume - initial . volume ) / initial . volume
-
-
logger . info ( "Vol change = %.1f %% !" % ( vol_change * 100 ))
-
if abs ( vol_change ) < vol_change_tol :
-
logger . info ( "Stopping optimization!" )
-
break
-
else :
-
incar_update = { "ISTART" : 1 }
-
if ediffg :
-
incar_update [ "EDIFFG" ] = ediffg
-
settings = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : incar_update }},
-
{ "file" : "CONTCAR" ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
if i == 1 and half_kpts_first_relax :
-
settings . append ({ "dict" : "KPOINTS" ,
-
"action" : { "_set" : orig_kpts_dict }})
-
logger . info ( "Generating job = %d !" % ( i + 1 ))
-
yield VaspJob ( vasp_cmd , final = False , backup = backup ,
-
suffix = ".relax %d " % ( i + 1 ), settings_override = settings ,
-
** vasp_job_kwargs )
-
-
[docs] @classmethod
-
def constrained_opt_run ( cls , vasp_cmd , lattice_direction , initial_strain ,
-
atom_relax = True , max_steps = 20 , algo = "bfgs" ,
-
** vasp_job_kwargs ):
-
"""
-
Returns a generator of jobs for a constrained optimization run. Typical
-
use case is when you want to approximate a biaxial strain situation,
-
e.g., you apply a defined strain to a and b directions of the lattice,
-
but allows the c-direction to relax.
-
-
Some guidelines on the use of this method:
-
i. It is recommended you do not use the Auto kpoint generation. The
-
grid generated via Auto may fluctuate with changes in lattice
-
param, resulting in numerical noise.
-
ii. Make sure your EDIFF/EDIFFG is properly set in your INCAR. The
-
optimization relies on these values to determine convergence.
-
-
Args:
-
vasp_cmd (str): Command to run vasp as a list of args. For example,
-
if you are using mpirun, it can be something like
-
["mpirun", "pvasp.5.2.11"]
-
lattice_direction (str): Which direction to relax. Valid values are
-
"a", "b" or "c".
-
initial_strain (float): An initial strain to be applied to the
-
lattice_direction. This can usually be estimated as the
-
negative of the strain applied in the other two directions.
-
E.g., if you apply a tensile strain of 0.05 to the a and b
-
directions, you can use -0.05 as a reasonable first guess for
-
initial strain.
-
atom_relax (bool): Whether to relax atomic positions.
-
max_steps (int): The maximum number of runs. Defaults to 20 (
-
highly unlikely that this limit is ever reached).
-
algo (str): Algorithm to use to find minimum. Default is "bfgs",
-
which is fast, but can be sensitive to numerical noise
-
in energy calculations. The alternative is "bisection",
-
which is more robust but can be a bit slow. The code does fall
-
back on the bisection when bfgs gives a non-sensical result,
-
e.g., negative lattice params.
-
\*\*vasp_job_kwargs: Passthrough kwargs to VaspJob. See
-
:class:`custodian.vasp.jobs.VaspJob`.
-
-
Returns:
-
Generator of jobs. At the end of the run, an "EOS.txt" is written
-
which provides a quick look at the E vs lattice parameter.
-
"""
-
nsw = 99 if atom_relax else 0
-
-
incar = Incar . from_file ( "INCAR" )
-
-
# Set the energy convergence criteria as the EDIFFG (if present) or
-
# 10 x EDIFF (which itself defaults to 1e-4 if not present).
-
if incar . get ( "EDIFFG" ) and incar . get ( "EDIFFG" ) > 0 :
-
etol = incar [ "EDIFFG" ]
-
else :
-
etol = incar . get ( "EDIFF" , 1e-4 ) * 10
-
-
if lattice_direction == "a" :
-
lattice_index = 0
-
elif lattice_direction == "b" :
-
lattice_index = 1
-
else :
-
lattice_index = 2
-
-
energies = {}
-
-
for i in range ( max_steps ):
-
if i == 0 :
-
settings = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : { "ISIF" : 2 , "NSW" : nsw }}}]
-
structure = Poscar . from_file ( "POSCAR" ) . structure
-
x = structure . lattice . abc [ lattice_index ]
-
backup = True
-
else :
-
backup = False
-
v = Vasprun ( "vasprun.xml" )
-
structure = v . final_structure
-
energy = v . final_energy
-
lattice = structure . lattice
-
-
x = lattice . abc [ lattice_index ]
-
-
energies [ x ] = energy
-
-
if i == 1 :
-
x *= ( 1 + initial_strain )
-
else :
-
# Sort the lattice parameter by energies.
-
min_x = min ( energies . keys (), key = lambda e : energies [ e ])
-
sorted_x = sorted ( energies . keys ())
-
ind = sorted_x . index ( min_x )
-
if ind == 0 :
-
other = ind + 1
-
elif ind == len ( sorted_x ) - 1 :
-
other = ind - 1
-
else :
-
other = ind + 1 \
-
if energies [ sorted_x [ ind + 1 ]] \
-
< energies [ sorted_x [ ind - 1 ]] \
-
else ind - 1
-
if abs ( energies [ min_x ]
-
- energies [ sorted_x [ other ]]) < etol :
-
logger . info ( "Stopping optimization! Final %s = %f "
-
% ( lattice_direction , min_x ))
-
break
-
-
if ind == 0 and len ( sorted_x ) > 2 :
-
# Lowest energy lies outside of range of lowest value.
-
# we decrease the lattice parameter in the next
-
# iteration to find a minimum. This applies only when
-
# there are at least 3 values.
-
x = sorted_x [ 0 ] - abs ( sorted_x [ 1 ] - sorted_x [ 0 ])
-
logger . info ( "Lowest energy lies below bounds. "
-
"Setting %s = %f ." % ( lattice_direction , x ))
-
elif ind == len ( sorted_x ) - 1 and len ( sorted_x ) > 2 :
-
# Lowest energy lies outside of range of highest value.
-
# we increase the lattice parameter in the next
-
# iteration to find a minimum. This applies only when
-
# there are at least 3 values.
-
x = sorted_x [ - 1 ] + abs ( sorted_x [ - 1 ] - sorted_x [ - 2 ])
-
logger . info ( "Lowest energy lies above bounds. "
-
"Setting %s = %f ." % ( lattice_direction , x ))
-
else :
-
if algo . lower () == "bfgs" and len ( sorted_x ) >= 4 :
-
try :
-
# If there are more than 4 data points, we will
-
# do a quadratic fit to accelerate convergence.
-
x1 = list ( energies . keys ())
-
y1 = [ energies [ j ] for j in x1 ]
-
z1 = np . polyfit ( x1 , y1 , 2 )
-
pp = np . poly1d ( z1 )
-
from scipy.optimize import minimize
-
result = minimize (
-
pp , min_x ,
-
bounds = [( sorted_x [ 0 ], sorted_x [ - 1 ])])
-
if ( not result . success ) or result . x [ 0 ] < 0 :
-
raise ValueError (
-
"Negative lattice constant!" )
-
x = result . x [ 0 ]
-
logger . info ( "BFGS minimized %s = %f ."
-
% ( lattice_direction , x ))
-
except ValueError as ex :
-
# Fall back on bisection algo if the bfgs fails.
-
logger . info ( str ( ex ))
-
x = ( min_x + sorted_x [ other ]) / 2
-
logger . info ( "Falling back on bisection %s = %f ."
-
% ( lattice_direction , x ))
-
else :
-
x = ( min_x + sorted_x [ other ]) / 2
-
logger . info ( "Bisection %s = %f ."
-
% ( lattice_direction , x ))
-
-
lattice = lattice . matrix
-
lattice [ lattice_index ] = lattice [ lattice_index ] / \
-
np . linalg . norm ( lattice [ lattice_index ]) * x
-
-
s = Structure ( lattice , structure . species , structure . frac_coords )
-
fname = "POSCAR. %f " % x
-
s . to ( filename = fname )
-
-
incar_update = { "ISTART" : 1 , "NSW" : nsw , "ISIF" : 2 }
-
-
settings = [
-
{ "dict" : "INCAR" ,
-
"action" : { "_set" : incar_update }},
-
{ "file" : fname ,
-
"action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
-
logger . info ( "Generating job = %d with parameter %f !" % ( i + 1 , x ))
-
yield VaspJob ( vasp_cmd , final = False , backup = backup ,
-
suffix = ".static. %f " % x ,
-
settings_override = settings , ** vasp_job_kwargs )
-
-
with open ( "EOS.txt" , "wt" ) as f :
-
f . write ( "# %s energy \n " % lattice_direction )
-
for k in sorted ( energies . keys ()):
-
f . write ( " %f %f \n " % ( k , energies [ k ]))
-
-
[docs] def terminate ( self ):
-
for k in self . vasp_cmd :
-
if "vasp" in k :
-
try :
-
os . system ( "killall %s " % k )
-
except :
-
pass [docs] class VaspNEBJob ( Job ):
-
"""
-
A NEB vasp job, especially for CI-NEB running at PBS clusters.
-
The class is added for the purpose of handling a different folder
-
arrangement in NEB calculation.
-
"""
-
-
def __init__ ( self , vasp_cmd ,
-
output_file = "neb_vasp.out" , stderr_file = "neb_std_err.txt" ,
-
suffix = "" , final = True , backup = True , auto_npar = True ,
-
half_kpts = False , auto_gamma = True , auto_continue = False ,
-
gamma_vasp_cmd = None , settings_override = None ):
-
"""
-
This constructor is a simplified version of VaspJob, which satisfies
-
the need for flexibility. For standard kinds of runs, it's often
-
better to use one of the static constructors. The defaults are
-
usually fine too.
-
-
Args:
-
vasp_cmd (str): Command to run vasp as a list of args. For example,
-
if you are using mpirun, it can be something like
-
["mpirun", "pvasp.5.2.11"]
-
output_file (str): Name of file to direct standard out to.
-
Defaults to "vasp.out".
-
stderr_file (str): Name of file to direct standard error to.
-
Defaults to "std_err.txt".
-
suffix (str): A suffix to be appended to the final output. E.g.,
-
to rename all VASP output from say vasp.out to
-
vasp.out.relax1, provide ".relax1" as the suffix.
-
final (bool): Indicating whether this is the final vasp job in a
-
series. Defaults to True.
-
backup (bool): Whether to backup the initial input files. If True,
-
the INCAR, KPOINTS, POSCAR and POTCAR will be copied with a
-
".orig" appended. Defaults to True.
-
auto_npar (bool): Whether to automatically tune NPAR to be sqrt(
-
number of cores) as recommended by VASP for DFT calculations.
-
Generally, this results in significant speedups. Defaults to
-
True. Set to False for HF, GW and RPA calculations.
-
half_kpts (bool): Whether to halve the kpoint grid for NEB.
-
Speeds up convergence considerably. Defaults to False.
-
auto_gamma (bool): Whether to automatically check if run is a
-
Gamma 1x1x1 run, and whether a Gamma optimized version of
-
VASP exists with ".gamma" appended to the name of the VASP
-
executable (typical setup in many systems). If so, run the
-
gamma optimized version of VASP instead of regular VASP. You
-
can also specify the gamma vasp command using the
-
gamma_vasp_cmd argument if the command is named differently.
-
auto_continue (bool): Whether to automatically continue a run
-
if a STOPCAR is present. This is very useful if using the
-
wall-time handler which will write a read-only STOPCAR to
-
prevent VASP from deleting it once it finishes.
-
gamma_vasp_cmd (str): Command for gamma vasp version when
-
auto_gamma is True. Should follow the list style of
-
subprocess. Defaults to None, which means ".gamma" is added
-
to the last argument of the standard vasp_cmd.
-
settings_override ([dict]): An ansible style list of dict to
-
override changes. For example, to set ISTART=1 for subsequent
-
runs and to copy the CONTCAR to the POSCAR, you will provide::
-
-
[{"dict": "INCAR", "action": {"_set": {"ISTART": 1}}},
-
{"file": "CONTCAR",
-
"action": {"_file_copy": {"dest": "POSCAR"}}}]
-
"""
-
-
self . vasp_cmd = vasp_cmd
-
self . output_file = output_file
-
self . stderr_file = stderr_file
-
self . final = final
-
self . backup = backup
-
self . suffix = suffix
-
self . auto_npar = auto_npar
-
self . half_kpts = half_kpts
-
self . auto_gamma = auto_gamma
-
self . gamma_vasp_cmd = gamma_vasp_cmd
-
self . auto_continue = auto_continue
-
self . settings_override = settings_override
-
self . neb_dirs = [] # 00, 01, etc.
-
self . neb_sub = [] # 01, 02, etc.
-
-
for path in os . listdir ( "." ):
-
if os . path . isdir ( path ) and path . isdigit ():
-
self . neb_dirs . append ( path )
-
self . neb_dirs = sorted ( self . neb_dirs )
-
self . neb_sub = self . neb_dirs [ 1 : - 1 ]
-
-
[docs] def setup ( self ):
-
"""
-
Performs initial setup for VaspNEBJob, including overriding any settings
-
and backing up.
-
"""
-
neb_dirs = self . neb_dirs
-
-
if self . backup :
-
# Back up KPOINTS, INCAR, POTCAR
-
for f in VASP_NEB_INPUT_FILES :
-
shutil . copy ( f , " {} .orig" . format ( f ))
-
# Back up POSCARs
-
for path in neb_dirs :
-
poscar = os . path . join ( path , "POSCAR" )
-
shutil . copy ( poscar , " {} .orig" . format ( poscar ))
-
-
if self . half_kpts and os . path . exists ( "KPOINTS" ):
-
kpts = Kpoints . from_file ( "KPOINTS" )
-
kpts . kpts = np . maximum ( np . array ( kpts . kpts ) / 2 , 1 )
-
kpts . kpts = kpts . kpts . astype ( int ) . tolist ()
-
if tuple ( kpts . kpts [ 0 ]) == ( 1 , 1 , 1 ):
-
kpt_dic = kpts . as_dict ()
-
kpt_dic [ "generation_style" ] = 'Gamma'
-
kpts = Kpoints . from_dict ( kpt_dic )
-
kpts . write_file ( "KPOINTS" )
-
-
if self . auto_npar :
-
try :
-
incar = Incar . from_file ( "INCAR" )
-
import multiprocessing
-
# Try sge environment variable first
-
# (since multiprocessing counts cores on the current
-
# machine only)
-
ncores = os . environ . get ( 'NSLOTS' ) or multiprocessing . cpu_count ()
-
ncores = int ( ncores )
-
for npar in range ( int ( math . sqrt ( ncores )),
-
ncores ):
-
if ncores % npar == 0 :
-
incar [ "NPAR" ] = npar
-
break
-
incar . write_file ( "INCAR" )
-
except :
-
pass
-
-
if self . auto_continue and \
-
os . path . exists ( "STOPCAR" ) and \
-
not os . access ( "STOPCAR" , os . W_OK ):
-
# Remove STOPCAR
-
os . chmod ( "STOPCAR" , 0o644 )
-
os . remove ( "STOPCAR" )
-
-
# Copy CONTCAR to POSCAR
-
for path in self . neb_sub :
-
contcar = os . path . join ( path , "CONTCAR" )
-
poscar = os . path . join ( path , "POSCAR" )
-
shutil . copy ( contcar , poscar )
-
-
if self . settings_override is not None :
-
VaspModder () . apply_actions ( self . settings_override )
-
-
[docs] def run ( self ):
-
"""
-
Perform the actual VASP run.
-
-
Returns:
-
(subprocess.Popen) Used for monitoring.
-
"""
-
cmd = list ( self . vasp_cmd )
-
if self . auto_gamma :
-
kpts = Kpoints . from_file ( "KPOINTS" )
-
if kpts . style == Kpoints . supported_modes . Gamma \
-
and tuple ( kpts . kpts [ 0 ]) == ( 1 , 1 , 1 ):
-
if self . gamma_vasp_cmd is not None and which (
-
self . gamma_vasp_cmd [ - 1 ]):
-
cmd = self . gamma_vasp_cmd
-
elif which ( cmd [ - 1 ] + ".gamma" ):
-
cmd [ - 1 ] += ".gamma"
-
logger . info ( "Running {} " . format ( " " . join ( cmd )))
-
with open ( self . output_file , 'w' ) as f_std , \
-
open ( self . stderr_file , "w" , buffering = 1 ) as f_err :
-
-
# Use line buffering for stderr
-
p = subprocess . Popen ( cmd , stdout = f_std , stderr = f_err )
-
return p
-
-
[docs] def postprocess ( self ):
-
"""
-
Postprocessing includes renaming and gzipping where necessary.
-
"""
-
# Add suffix to all sub_dir/{items}
-
for path in self . neb_dirs :
-
for f in VASP_NEB_OUTPUT_SUB_FILES :
-
f = os . path . join ( path , f )
-
if os . path . exists ( f ):
-
if self . final and self . suffix != "" :
-
shutil . move ( f , " {}{} " . format ( f , self . suffix ))
-
elif self . suffix != "" :
-
shutil . copy ( f , " {}{} " . format ( f , self . suffix ))
-
-
# Add suffix to all output files
-
for f in VASP_NEB_OUTPUT_FILES + [ self . output_file ]:
-
if os . path . exists ( f ):
-
if self . final and self . suffix != "" :
-
shutil . move ( f , " {}{} " . format ( f , self . suffix ))
-
elif self . suffix != "" :
-
shutil . copy ( f , " {}{} " . format ( f , self . suffix ))
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/custodian/vasp/validators.html b/docs/html/_modules/custodian/vasp/validators.html
deleted file mode 100644
index d866767a..00000000
--- a/docs/html/_modules/custodian/vasp/validators.html
+++ /dev/null
@@ -1,226 +0,0 @@
-
-
-
-
-
-
-
custodian.vasp.validators — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
Source code for custodian.vasp.validators
-# coding: utf-8
-
-from __future__ import unicode_literals , division
-
-from custodian.custodian import Validator
-from pymatgen.io.vasp import Vasprun , Incar , Outcar , Chgcar
-from collections import deque
-
-import os
-import logging
-
-
-[docs] class VasprunXMLValidator ( Validator ):
-
"""
-
Checks that a valid vasprun.xml was generated
-
"""
-
-
def __init__ ( self , output_file = "vasp.out" , stderr_file = "std_err.txt" ):
-
"""
-
Args:
-
output_file (str): Name of file VASP standard output is directed to.
-
Defaults to "vasp.out".
-
stderr_file (str): Name of file VASP standard error is direct to.
-
Defaults to "std_err.txt".
-
"""
-
self . output_file = output_file
-
self . stderr_file = stderr_file
-
self . logger = logging . getLogger ( self . __class__ . __name__ )
-
-
[docs] def check ( self ):
-
try :
-
Vasprun ( "vasprun.xml" )
-
except :
-
exception_context = {}
-
-
if os . path . exists ( self . output_file ):
-
with open ( self . output_file , "r" ) as output_file :
-
output_file_tail = deque ( output_file , maxlen = 10 )
-
exception_context [ "output_file_tail" ] = "" . join ( output_file_tail )
-
-
if os . path . exists ( self . stderr_file ):
-
with open ( self . stderr_file , "r" ) as stderr_file :
-
stderr_file_tail = deque ( stderr_file , maxlen = 10 )
-
exception_context [ "stderr_file_tail" ] = "" . join ( stderr_file_tail )
-
-
if os . path . exists ( "vasprun.xml" ):
-
-
stat = os . stat ( "vasprun.xml" )
-
exception_context [ "vasprun_st_size" ] = stat . st_size
-
exception_context [ "vasprun_st_atime" ] = stat . st_atime
-
exception_context [ "vasprun_st_mtime" ] = stat . st_mtime
-
exception_context [ "vasprun_st_ctime" ] = stat . st_ctime
-
-
with open ( "vasprun.xml" , "r" ) as vasprun :
-
vasprun_tail = deque ( vasprun , maxlen = 10 )
-
exception_context [ "vasprun_tail" ] = "" . join ( vasprun_tail )
-
-
self . logger . error ( "Failed to load vasprun.xml" ,
-
exc_info = True , extra = exception_context )
-
-
return True
-
return False [docs] class VaspFilesValidator ( Validator ):
-
"""
-
Check for existence of some of the files that VASP
-
normally create upon running.
-
"""
-
-
def __init__ ( self ):
-
pass
-
-
[docs] def check ( self ):
-
for vfile in [ "CONTCAR" , "OSZICAR" , "OUTCAR" ]:
-
if not os . path . exists ( vfile ):
-
return True
-
return False [docs] class VaspNpTMDValidator ( Validator ):
-
"""
-
Check NpT-AIMD settings is loaded by VASP compiled with -Dtbdyn.
-
Currently, VASP only have Langevin thermostat (MDALGO = 3) for NpT ensemble.
-
"""
-
-
def __init__ ( self ):
-
pass
-
-
[docs] def check ( self ):
-
incar = Incar . from_file ( "INCAR" )
-
is_npt = incar . get ( "MDALGO" ) == 3
-
if not is_npt :
-
return False
-
-
outcar = Outcar ( "OUTCAR" )
-
patterns = { "MDALGO" : "MDALGO\s+=\s+([\d]+)" }
-
outcar . read_pattern ( patterns = patterns )
-
if outcar . data [ "MDALGO" ] == [[ '3' ]]:
-
return False
-
else :
-
return True [docs] class VaspAECCARValidator ( Validator ):
-
"""
-
Check if the data in the AECCAR is corrupted
-
"""
-
-
def __init__ ( self ):
-
pass
-
-
[docs] def check ( self ):
-
aeccar0 = Chgcar . from_file ( "AECCAR0" )
-
aeccar2 = Chgcar . from_file ( "AECCAR2" )
-
aeccar = aeccar0 + aeccar2
-
return check_broken_chgcar ( aeccar ) [docs] def check_broken_chgcar ( chgcar ):
-
chgcar_data = chgcar . data [ 'total' ]
-
if ( chgcar_data < 0 ) . sum () > 100 :
-
# a decent bunch of the values are negative
-
return True
-
-
diff = chgcar_data [: - 1 , : - 1 , : - 1 ] - chgcar_data [ 1 :, 1 :, 1 :]
-
if diff . max () / ( chgcar_data . max () - chgcar_data . min ()) > 0.95 :
-
# Some single diagonal finite difference is more than 95% of the entire range
-
return True
-
-
return False
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_modules/index.html b/docs/html/_modules/index.html
deleted file mode 100644
index 56a6d705..00000000
--- a/docs/html/_modules/index.html
+++ /dev/null
@@ -1,114 +0,0 @@
-
-
-
-
-
-
-
Overview: module code — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
-
All modules for which code is available
-
-
-
-
-
-
-
-
-
-
-
-
-
-
\ No newline at end of file
diff --git a/docs/html/_sources/_themes/README.rst.txt b/docs/html/_sources/_themes/README.rst.txt
deleted file mode 100644
index e8179f96..00000000
--- a/docs/html/_sources/_themes/README.rst.txt
+++ /dev/null
@@ -1,25 +0,0 @@
-krTheme Sphinx Style
-====================
-
-This repository contains sphinx styles Kenneth Reitz uses in most of
-his projects. It is a drivative of Mitsuhiko's themes for Flask and Flask related
-projects. To use this style in your Sphinx documentation, follow
-this guide:
-
-1. put this folder as _themes into your docs folder. Alternatively
- you can also use git submodules to check out the contents there.
-
-2. add this to your conf.py: ::
-
- sys.path.append(os.path.abspath('_themes'))
- html_theme_path = ['_themes']
- html_theme = 'kr'
-
-The following themes exist:
-
-**kr**
- the standard flask documentation theme for large projects
-
-**kr_small**
- small one-page theme. Intended to be used by very small addon libraries.
-
diff --git a/docs/html/_sources/changelog.rst.txt b/docs/html/_sources/changelog.rst.txt
deleted file mode 100644
index c975f125..00000000
--- a/docs/html/_sources/changelog.rst.txt
+++ /dev/null
@@ -1,218 +0,0 @@
-Change Log
-==========
-
-v2017.12.23
------------
-* cstdn command line tool is now official with docs.
-* Fine-grained control of VaspErrorHandler is now possible using
- `errors_subset_to_catch`.
-* Switched to date-based versioning for custodian like pymatgen.
-
-v1.1.1
-------
-* DriftErrorHandler (Shyam)
-
-v1.1.0
-------
-* Improved error handling for Qchem calculations.
-
-v1.0.4
-------
-* Improved handling of non-zero return codes.
-
-v1.0.2
-------
-* Interrupted run feature. (Shyam Dwaraknath)
-
-v1.0.1
-------
-* Pymatgen 4.0.0 compatible release.
-
-v1.0.0
-------
-* Custodian now comes with a "cstdn" script that enables the arbitrary creation
- of simple job sequences using a yaml file, and the running of calculations
- based on these yaml specifications.
-
-v0.8.8
-------
-1. Fix setup.py.
-
-v0.8.5
-------
-1. Refactoring to support pymatgen 3.1.4.
-
-v0.8.2
-------
-1. Made auto_npar optional for double relaxation VASP run.
-
-v0.8.1
-------
-1. Misc bug fixes (minor).
-
-v0.8.0
-------
-1. Major refactoring of Custodian to introdce Validators,
- which are effectively post-Job checking mechanisms that do not perform
- error correction.
-2. **Backwards incompatibility** BadVasprunXMLHandler is now a validator,
- which must be separately imported to be used.
-3. Miscellaneous cleanup of Py3k fixes.
-v0.7.6
-------
-1. Custodian is now Python 3 compatible and uses the latest versions of
- pymatgen and monty.
-
-v0.7.5
-------
-1. **Major** Custodian now exits with RuntimeError when max_errors or
- unrecoverable_error is encountered.
-2. Added BadVasprunXMLHandler.
-
-v0.7.4
-------
-1. auto_npar option in VaspJob now properly handles Hessian calculations.
-2. WalltimeHandler now supports termination at electronic step (David
- Waroquiers).
-3. Improved handling of BRMIX fixes.
-
-v0.7.3
-------
-1. Improved backwards compatibility for WallTimeHandler.
-2. Improvements to VaspErrorHandler. No longer catches spurious BRMIX error
- messages when NELECT is specified in INCAR, and pricel and rot_mat errors
- are now fixed with symmetry precision and gamma centered KPOINTS instead.
-3. Improved Qchem error handler (Xiaohui Qu).
-
-v0.7.2
-------
-1. Improved WalltimeHandler (PBSWalltimeHandler is a subset and is now
- deprecated).
-2. New monty required version (>= 0.2.2).
-
-v0.7.1
-------
-1. Much improved qchem error handling (Xiaohui Qu).
-2. New Monty required version (>= 0.2.0).
-
-v0.7.0
-------
-1. **Backwards incompatible with v0.6.3. Refactoring to move commonly used
- Python utility functions to `Monty package
`_, which is now a depedency
- for custodian.
-2. Custodian now requires pymatgen >= 2.9.0 for VASP, Qchem and Nwchem jobs
- and handlers.
-3. converge_kpoints script now has increment mode.
-4. ErrorHandlers now have a new API, where the class variables "is_monitor"
- and "is_terminating" are provided to indicate if a particular handler
- runs in the background during a Job and whether a handler should
- terminate the job. Some errors may not be critical or may need to wait
- for some other event to terminate a job. For example,
- a particular error may require a flag to be set to request a job to
- terminate gracefully once it finishes its current task. The handler to
- set the flag should not terminate the job.
-
-0.6.3
------
-1. Added buffer time option in PBSWalltimeHandler.
-2. Improved Qchem jobs and handlers (Xiaohui Qu).
-3. Vastly improved API docs.
-
-0.6.2
------
-1. Bug fix release to support sub dirs in run folder when using scratch.
-2. Improve handling of walltime in PBSWalltimeHander.
-
-0.6.1
------
-1. Bug fix release to address minor issue with checkpointing.
-2. Checkpointing is now turned off by default.
-
-0.6.0
------
-1. Checkpointing implemented for Custodian. Custodian can now checkpoint all
- files in the current working directory after every successful job. If the
- job is resubmitted, it will restore files and start from the last
- checkpoint. Particularly useful for multi-job runs.
-2. Added PBSWalltimeHandler to handle wall times for PBS Vasp Jobs.
-3. Qchem error handlers and jobs.
-
-0.5.0
------
-1. Added scratch_dir option to Custodian class as well as run_vasp and
- run_nwchem scripts. Many supercomputing clusters have a scratch space
- which have significantly faster IO. This option provides a transparent way
- to specify the jobs to be performed in the scratch. Especially useful for
- jobs which have significant file IO.
-
-0.4.5
------
-1. Fix gzip of output.
-
-0.4.3
------
-1. Added handling for ZBRENT error for VASP.
-2. Minor refactoring to consolidate backup and gzip directory methods.
-
-0.4.2
------
-1. Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
-2. Improved VASP error handling (by Steve Dacek and Will Richards).
-
-0.4.1
------
-1. Added hanlding of PRICEL error in VASP.
-2. Speed and robustness improvements.
-3. BRIONS error now handled by changing ISYM.
-
-0.4.0
------
-1. Many VASP handlers are now consolidated into a single VaspErrorHandler.
-2. Many more fixes for VASP runs, including the "TOO FEW BANDS",
- "TRIPLE PRODUCT", "DENTET" and "BRIONS" errors.
-3. VaspJob now includes the auto_npar and auto_gamma options, which
- automatically optimizes the NPAR setting to be sqrt(number of cores) as
- per the VASP recommendation for DFT runs and tries to search for a
- gamma-only compiled version of VASP for gamma 1x1x1 runs.
-
-0.3.5
------
-1. Bug fix for incorrect shift error handler in VASP.
-2. More robust fix for unconverged VASP runs (switching from ALGO fast to
- normal).
-3. Expanded documentation.
-
-0.3.4
------
-1. Added support for handlers that perform monitor a job as it is progressing
- and terminates it if necessary. Useful for correcting errors that come up
- by do not cause immediate job failures.
-
-0.3.2
------
-1. Important bug fix for VaspJob and converge_kpoints script.
-
-0.3.0
------
-
-1. Major update to custodian API. Custodian now perform more comprehensive
- logging in a file called custodian.json, which logs all jobs and
- corrections performed.
-
-Version 0.2.6
--------------
-1. Bug fix for run_vasp script for static runs.
-
-Version 0.2.5
--------------
-1. run_vasp script that now provides flexible specification of vasp runs.
-2. Vastly improved error handling for VASP runs.
-3. Improved logging system for custodian.
-4. Improved API for custodian return types during run.
-5. First stable release.
-
-Version 0.2.4
--------------
-
-1. Bug fixes for aflow style runs assimilation.
diff --git a/docs/html/_sources/custodian.ansible.rst.txt b/docs/html/_sources/custodian.ansible.rst.txt
deleted file mode 100644
index 5840ac5f..00000000
--- a/docs/html/_sources/custodian.ansible.rst.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-custodian.ansible package
-=========================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.ansible.actions module
---------------------------------
-
-.. automodule:: custodian.ansible.actions
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.ansible.interpreter module
-------------------------------------
-
-.. automodule:: custodian.ansible.interpreter
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.ansible
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/html/_sources/custodian.cli.rst.txt b/docs/html/_sources/custodian.cli.rst.txt
deleted file mode 100644
index c83b5d9c..00000000
--- a/docs/html/_sources/custodian.cli.rst.txt
+++ /dev/null
@@ -1,54 +0,0 @@
-custodian.cli package
-=====================
-
-Submodules
-----------
-
-custodian.cli.converge\_geometry module
----------------------------------------
-
-.. automodule:: custodian.cli.converge_geometry
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.converge\_kpoints module
---------------------------------------
-
-.. automodule:: custodian.cli.converge_kpoints
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.cstdn module
---------------------------
-
-.. automodule:: custodian.cli.cstdn
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.run\_nwchem module
---------------------------------
-
-.. automodule:: custodian.cli.run_nwchem
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.cli.run\_vasp module
-------------------------------
-
-.. automodule:: custodian.cli.run_vasp
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.cli
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/html/_sources/custodian.feff.rst.txt b/docs/html/_sources/custodian.feff.rst.txt
deleted file mode 100644
index 753541f9..00000000
--- a/docs/html/_sources/custodian.feff.rst.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-custodian.feff package
-======================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.feff.handlers module
-------------------------------
-
-.. automodule:: custodian.feff.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.feff.interpreter module
----------------------------------
-
-.. automodule:: custodian.feff.interpreter
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.feff.jobs module
---------------------------
-
-.. automodule:: custodian.feff.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.feff
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/html/_sources/custodian.nwchem.rst.txt b/docs/html/_sources/custodian.nwchem.rst.txt
deleted file mode 100644
index be9c01a4..00000000
--- a/docs/html/_sources/custodian.nwchem.rst.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-custodian.nwchem package
-========================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.nwchem.handlers module
---------------------------------
-
-.. automodule:: custodian.nwchem.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.nwchem.jobs module
-----------------------------
-
-.. automodule:: custodian.nwchem.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.nwchem
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/html/_sources/custodian.qchem.rst.txt b/docs/html/_sources/custodian.qchem.rst.txt
deleted file mode 100644
index 6fc3df09..00000000
--- a/docs/html/_sources/custodian.qchem.rst.txt
+++ /dev/null
@@ -1,36 +0,0 @@
-custodian.qchem package
-=======================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.qchem.handlers module
--------------------------------
-
-.. automodule:: custodian.qchem.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.qchem.jobs module
----------------------------
-
-.. automodule:: custodian.qchem.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.qchem
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/html/_sources/custodian.rst.txt b/docs/html/_sources/custodian.rst.txt
deleted file mode 100644
index 97747550..00000000
--- a/docs/html/_sources/custodian.rst.txt
+++ /dev/null
@@ -1,42 +0,0 @@
-custodian package
-=================
-
-Subpackages
------------
-
-.. toctree::
-
- custodian.ansible
- custodian.cli
- custodian.feff
- custodian.nwchem
- custodian.qchem
- custodian.vasp
-
-Submodules
-----------
-
-custodian.custodian module
---------------------------
-
-.. automodule:: custodian.custodian
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.utils module
-----------------------
-
-.. automodule:: custodian.utils
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/html/_sources/custodian.vasp.rst.txt b/docs/html/_sources/custodian.vasp.rst.txt
deleted file mode 100644
index 2d8dbc9b..00000000
--- a/docs/html/_sources/custodian.vasp.rst.txt
+++ /dev/null
@@ -1,52 +0,0 @@
-custodian.vasp package
-======================
-
-Subpackages
------------
-
-.. toctree::
-
-
-Submodules
-----------
-
-custodian.vasp.handlers module
-------------------------------
-
-.. automodule:: custodian.vasp.handlers
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.vasp.interpreter module
----------------------------------
-
-.. automodule:: custodian.vasp.interpreter
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.vasp.jobs module
---------------------------
-
-.. automodule:: custodian.vasp.jobs
- :members:
- :undoc-members:
- :show-inheritance:
-
-custodian.vasp.validators module
---------------------------------
-
-.. automodule:: custodian.vasp.validators
- :members:
- :undoc-members:
- :show-inheritance:
-
-
-Module contents
----------------
-
-.. automodule:: custodian.vasp
- :members:
- :undoc-members:
- :show-inheritance:
diff --git a/docs/html/_sources/index.rst.txt b/docs/html/_sources/index.rst.txt
deleted file mode 100644
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--- a/docs/html/_sources/index.rst.txt
+++ /dev/null
@@ -1,368 +0,0 @@
-Custodian
-=========
-
-Custodian is a simple, robust and flexible just-in-time (JIT) job management
-framework written in Python. Using custodian, you can create wrappers that
-perform error checking, job management and error recovery. It has a simple
-plugin framework that allows you to develop specific job management workflows
-for different applications.
-
-Error recovery is an important aspect of many *high-throughput* projects that
-generate data on a large scale. When you are running on the order of hundreds
-of thousands of jobs, even an error rate of 1% would mean thousands of errored
-jobs that would be impossible to deal with on a case-by-case basis.
-
-The specific use case for custodian is for long running jobs, with potentially
-random errors. For example, there may be a script that takes several days to
-run on a server, with a 1% chance of some IO error causing the job to fail.
-Using custodian, one can develop a mechanism to gracefully recover from the
-error, and restart the job with modified parameters if necessary.
-
-The current version of Custodian also comes with two sub-packages for error
-handling for Vienna Ab Initio Simulation Package (VASP), NwChem and QChem
-calculations.
-
-Change log
-==========
-
-v2019.2.10
-----------
-* Improved slow convergence handling. (@shyamd)
-
-v2019.2.7
----------
-* Improved error logging.
-* Improved handling of frozen jobs and potim errors.
-* Improved Exceptino handling. (Guido Petretto)
-
-
-:doc:`Older versions `
-
-Getting custodian
-=================
-
-Stable version
---------------
-
-The version at the Python Package Index (PyPI) is always the latest stable
-release that will be hopefully, be relatively bug-free. The easiest way to
-install custodian on any system is to use easy_install or pip, as follows::
-
- easy_install custodian
-
-or::
-
- pip install custodian
-
-Some plugins (e.g., vasp management) require additional setup (please see
-`pymatgen's documentation`_).
-
-Developmental version
----------------------
-
-The bleeding edge developmental version is at the custodian's `Github repo
-`_. The developmental
-version is likely to be more buggy, but may contain new features. The
-Github version include test files as well for complete unit testing. After
-cloning the source, you can type::
-
- python setup.py install
-
-or to install the package in developmental mode::
-
- python setup.py develop
-
-Requirements
-============
-
-Custodian requires Python 2.7+. There are no other required dependencies.
-
-Optional dependencies
----------------------
-
-Optional libraries that are required if you need certain features:
-
-1. Python Materials Genomics (`pymatgen`_) 2.8.10+: To use the plugin for
- VASP, NwChem and Qchem. Please install using::
-
- pip install pymatgen
-
- For more information, please consult `pymatgen's documentation`_.
-2. nose - For complete unittesting.
-
-Usage
-=====
-
-The main class in the workflow is known as Custodian, which manages a series
-of jobs with a list of error handlers. The general workflow for Custodian is
-presented in the figure below.
-
-.. figure:: _static/Custodian.png
- :width: 500px
- :align: center
- :alt: Custodian workflow
- :figclass: align-center
-
- Overview of the Custodian workflow.
-
-The Custodian class takes in two general inputs - a **list of Jobs** and
-a **list of ErrorHandlers**. **Jobs** should be subclasses of the
-:class:`custodian.custodian.Job` abstract base class and **ErrorHandlers**
-should be subclasses of the :class:`custodian.custodian.ErrorHandler` abstract
-base class. To use custodian, you need to implement concrete implementations
-of these abstract base classes.
-
-Simple example
---------------
-
-An very simple example implementation is given in the custodian_examples.py
-script in the scripts directory. We will now go through the example in detail
-here.
-
-The ExampleJob has the following code.
-
-.. code-block:: python
-
- class ExampleJob(Job):
-
- def __init__(self, jobid, params=None):
- if params is None:
- params = {"initial": 0, "total": 0}
- self.jobid = jobid
- self.params = params
-
- def setup(self):
- self.params["initial"] = 0
- self.params["total"] = 0
-
- def run(self):
- sequence = [random.uniform(0, 1) for i in range(100)]
- self.params["total"] = self.params["initial"] + sum(sequence)
-
- def postprocess(self):
- pass
-
- @property
- def name(self):
- return "ExampleJob{}".format(self.jobid)
-
-
-The ExampleJob simply sums a random sequence of 100 numbers between 0 and
-1, adds it to an initial value and puts the value in 'total' variable. The
-ExampleJob subclasses the Job abstract base class, and implements the necessary
-API comprising of just three key methods: **setup(), run(),
-and postprocess()**.
-
-Let us now define an ErrorHandler that will check if the total value is >= 50,
-and if it is not, it will increment the initial value by 1 and rerun the
-ExampleJob again.
-
-.. code-block:: python
-
-
- class ExampleHandler(ErrorHandler):
-
- def __init__(self, params):
- self.params = params
-
- def check(self):
- return self.params["total"] < 50
-
- def correct(self):
- self.params["initial"] += 1
- return {"errors": "total < 50", "actions": "increment by 1"}
-
-As you can see above, the ExampleHandler subclasses the ErrorHandler abstract
-base class, and implements the necessary API comprising of just two key
-methods: **check() and correct()**.
-
-The transfer of information between the Job and ErrorHandler is done using
-the params argument in this example, which is not ideal but is sufficiently
-for demonstrating the Custodian API. In real world usage,
-a more common transfer of information may involve the Job writing the output
-to a file, and the ErrorHandler checking the contents of those files to
-detect error situations.
-
-To run the job, one simply needs to supply a list of ExampleJobs and
-ErrorHandlers to a Custodian.
-
-.. code-block:: python
-
- njobs = 100
- params = {"initial": 0, "total": 0}
- c = Custodian([ExampleHandler(params)],
- [ExampleJob(i, params) for i in xrange(njobs)],
- max_errors=njobs)
- c.run()
-
-If you run custodian_example.py in the scripts directory, you will noticed that
-a **custodian.json** file was generated, which summarizes the jobs that have
-been run and any corrections performed.
-
-Practical example: Electronic structure calculations
-----------------------------------------------------
-
-A practical example where the Custodian framework is particularly useful is
-in the area of electronic structure calculations. Electronic structure
-calculations tend to be long running and often terminates due to errors,
-random or otherwise. Such errors become a major issue in projects that
-performs such calculations in high throughput, such as the `Materials
-Project`_.
-
-The Custodian package comes with a fairly comprehensive plugin to deal
-with jobs (:mod:`custodian.vasp.jobs`) and errors
-(:mod:`custodian.vasp.handlers`) in electronic structure calculations based
-on the Vienna Ab Initio Simulation Package (VASP). To do this,
-Custodian uses the Python Materials Genomics (`pymatgen`_) package to
-perform analysis and io from VASP input and output files.
-
-A simple example of a script using Custodian to run a two-relaxation VASP job
-is as follows:
-
-.. code-block:: python
-
- from custodian.custodian import Custodian
- from custodian.vasp.handlers import VaspErrorHandler, \
- UnconvergedErrorHandler, PoscarErrorHandler, DentetErrorHandler
- from custodian.vasp.jobs import VaspJob
-
- handlers = [VaspErrorHandler(), UnconvergedErrorHandler(),
- PoscarErrorHandler(), DentetErrorHandler()]
- jobs = VaspJob.double_relaxation_run(args.command.split())
- c = Custodian(handlers, jobs, max_errors=10)
- c.run()
-
-The above will gracefully deal with many VASP errors encountered during
-relaxation. For example, it will correct ISMEAR to 0 if there are
-insufficient KPOINTS to use ISMEAR = -5.
-
-Using custodian, you can even setup potentially indefinite jobs,
-e.g. kpoints convergence jobs with a target energy convergence. Please see the
-converge_kpoints script in the scripts for an example.
-
-.. versionadded:: 0.4.3
-
- A new package for dealing with NwChem calculations has been added.
- NwChem is an open-source code for performing computational chemistry
- calculations.
-
-cstdn - A yaml-spec controlled job
-==================================
-
-Custodian now comes with a cstdn script, which allows you to do fine-grained
-control of a job using a yaml spec file. Below is an annotated example of how
-you can specify a double VASP relaxation followed by a static calculation.
-Minor modifications would allow very customizable calculations, though this is
-obviously not meant for highly complex workflows. For those, usage of `FireWorks
-` with parameters specified
- # via the params dict.
-
- jobs:
- - jb: custodian.vasp.jobs.VaspJob
- params:
- final: False
- suffix: .relax1
- - jb: custodian.vasp.jobs.VaspJob
- params:
- final: False
- suffix: .relax2
- settings_override:
- - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
- - jb: custodian.vasp.jobs.VaspJob
- params:
- final: True
- suffix: .static3
- settings_override:
- - {"file": "CONTCAR", "action": {"_file_copy": {"dest": "POSCAR"}}}
- - {"dict": "INCAR", "action": {"_set": {"NSW": 0}}}
-
-
- # This key specifies parameters common to all jobs.
- # Keys starting with $ are expanded to the environmental values.
- # The example below means the parameter vasp_cmd is set to the value with
- # $PBS_NODEFILE expanded.
-
- jobs_common_params:
- $vasp_cmd: ["mpirun", "-machinefile", "$PBS_NODEFILE", "-np", "24", "vasp"]
-
-
- # Specifies a list of error handlers in the same format as jobs. Similarly,
- # parameters passed to the handler __init__ can be configured the same
- # way as for jobs.
- handlers:
- - hdlr: custodian.vasp.handlers.VaspErrorHandler
- - hdlr: custodian.vasp.handlers.AliasingErrorHandler
- - hdlr: custodian.vasp.handlers.MeshSymmetryErrorHandler
-
- # Specifies a list of error handlers in the same format as jobs.
- validators:
- - vldr: custodian.vasp.validators.VasprunXMLValidator
-
- #This sets all custodian running parameters.
- custodian_params:
- max_errors: 10
- scratch_dir: /tmp
- gzipped_output: True
- checkpoint: True
-
-You can then run the job using the following command::
-
- cstdn run
-
-API/Reference Docs
-==================
-
-The API docs are generated using Sphinx auto-doc and outlines the purpose of all
-modules and classes, and the expected argument and returned objects for most
-methods. They are available at the link below.
-
-:doc:`custodian API docs `
-
-How to cite custodian
-=====================
-
-If you use custodian in your research, especially the VASP component, please
-consider citing the following work::
-
- Shyue Ping Ong, William Davidson Richards, Anubhav Jain, Geoffroy Hautier,
- Michael Kocher, Shreyas Cholia, Dan Gunter, Vincent Chevrier, Kristin A.
- Persson, Gerbrand Ceder. *Python Materials Genomics (pymatgen) : A Robust,
- Open-Source Python Library for Materials Analysis.* Computational
- Materials Science, 2013, 68, 314–319. `doi:10.1016/j.commatsci.2012.10.028
- `_
-
-License
-=======
-
-Custodian is released under the MIT License. The terms of the license are as
-follows::
-
- The MIT License (MIT)
- Copyright (c) 2011-2012 MIT & LBNL
-
- Permission is hereby granted, free of charge, to any person obtaining a
- copy of this software and associated documentation files (the "Software")
- , to deal in the Software without restriction, including without limitation
- the rights to use, copy, modify, merge, publish, distribute, sublicense,
- and/or sell copies of the Software, and to permit persons to whom the
- Software is furnished to do so, subject to the following conditions:
-
- The above copyright notice and this permission notice shall be included in
- all copies or substantial portions of the Software.
-
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
- DEALINGS IN THE SOFTWARE.
-
-.. _`pymatgen's documentation`: http://pymatgen.org
-.. _`Materials Project`: https://www.materialsproject.org
-.. _`pymatgen`: https://pypi.python.org/pypi/pymatgen
diff --git a/docs/html/_sources/modules.rst.txt b/docs/html/_sources/modules.rst.txt
deleted file mode 100644
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+++ /dev/null
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-custodian
-=========
-
-.. toctree::
- :maxdepth: 6
-
- custodian
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index c41d718e..00000000
--- a/docs/html/_static/basic.css
+++ /dev/null
@@ -1,763 +0,0 @@
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\ No newline at end of file
diff --git a/docs/html/_static/doctools.js b/docs/html/_static/doctools.js
deleted file mode 100644
index b33f87fc..00000000
--- a/docs/html/_static/doctools.js
+++ /dev/null
@@ -1,314 +0,0 @@
-/*
- * doctools.js
- * ~~~~~~~~~~~
- *
- * Sphinx JavaScript utilities for all documentation.
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- * :copyright: Copyright 2007-2019 by the Sphinx team, see AUTHORS.
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- jQuery(addItems[i].parent).before(addItems[i].target);
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-
-/*
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- * This will be supported until firefox bug is fixed.
- */
-if (!jQuery.browser) {
- jQuery.uaMatch = function(ua) {
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-
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- },
-
- /**
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-
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-
- /**
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- addContextElements : function() {
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- $('dt[id]').each(function() {
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-
- /**
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-
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- .appendTo($('#searchbox'));
- }
- },
-
- /**
- * init the domain index toggle buttons
- */
- initIndexTable : function() {
- var togglers = $('img.toggler').click(function() {
- var src = $(this).attr('src');
- var idnum = $(this).attr('id').substr(7);
- $('tr.cg-' + idnum).toggle();
- if (src.substr(-9) === 'minus.png')
- $(this).attr('src', src.substr(0, src.length-9) + 'plus.png');
- else
- $(this).attr('src', src.substr(0, src.length-8) + 'minus.png');
- }).css('display', '');
- if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) {
- togglers.click();
- }
- },
-
- /**
- * helper function to hide the search marks again
- */
- hideSearchWords : function() {
- $('#searchbox .highlight-link').fadeOut(300);
- $('span.highlighted').removeClass('highlighted');
- },
-
- /**
- * make the url absolute
- */
- makeURL : function(relativeURL) {
- return DOCUMENTATION_OPTIONS.URL_ROOT + '/' + relativeURL;
- },
-
- /**
- * get the current relative url
- */
- getCurrentURL : function() {
- var path = document.location.pathname;
- var parts = path.split(/\//);
- $.each(DOCUMENTATION_OPTIONS.URL_ROOT.split(/\//), function() {
- if (this === '..')
- parts.pop();
- });
- var url = parts.join('/');
- return path.substring(url.lastIndexOf('/') + 1, path.length - 1);
- },
-
- initOnKeyListeners: function() {
- $(document).keyup(function(event) {
- var activeElementType = document.activeElement.tagName;
- // don't navigate when in search box or textarea
- if (activeElementType !== 'TEXTAREA' && activeElementType !== 'INPUT' && activeElementType !== 'SELECT') {
- switch (event.keyCode) {
- case 37: // left
- var prevHref = $('link[rel="prev"]').prop('href');
- if (prevHref) {
- window.location.href = prevHref;
- return false;
- }
- case 39: // right
- var nextHref = $('link[rel="next"]').prop('href');
- if (nextHref) {
- window.location.href = nextHref;
- return false;
- }
- }
- }
- });
- }
-};
-
-// quick alias for translations
-_ = Documentation.gettext;
-
-$(document).ready(function() {
- Documentation.init();
-});
diff --git a/docs/html/_static/documentation_options.js b/docs/html/_static/documentation_options.js
deleted file mode 100644
index 92680bf2..00000000
--- a/docs/html/_static/documentation_options.js
+++ /dev/null
@@ -1,10 +0,0 @@
-var DOCUMENTATION_OPTIONS = {
- URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '2019.8.23',
- LANGUAGE: 'None',
- COLLAPSE_INDEX: false,
- FILE_SUFFIX: '.html',
- HAS_SOURCE: true,
- SOURCELINK_SUFFIX: '.txt',
- NAVIGATION_WITH_KEYS: false
-};
\ No newline at end of file
diff --git a/docs/html/_static/favicon.ico b/docs/html/_static/favicon.ico
deleted file mode 100644
index d086b444..00000000
Binary files a/docs/html/_static/favicon.ico and /dev/null differ
diff --git a/docs/html/_static/file.png b/docs/html/_static/file.png
deleted file mode 100644
index a858a410..00000000
Binary files a/docs/html/_static/file.png and /dev/null differ
diff --git a/docs/html/_static/flasky.css b/docs/html/_static/flasky.css
deleted file mode 100644
index f764eb5e..00000000
--- a/docs/html/_static/flasky.css
+++ /dev/null
@@ -1,445 +0,0 @@
-/*
- * flasky.css_t
- * ~~~~~~~~~~~~
- *
- * :copyright: Copyright 2010 by Armin Ronacher. Modifications by Kenneth Reitz.
- * :license: Flask Design License, see LICENSE for details.
- */
-
-
-
-
-@import url("basic.css");
-
-/* -- page layout ----------------------------------------------------------- */
-
-body {
- font-family: 'goudy old style', 'minion pro', 'bell mt', Georgia, 'Hiragino Mincho Pro';
- font-size: 17px;
- background-color: white;
- color: #000;
- margin: 0;
- padding: 0;
-}
-
-div.document {
- width: 940px;
- margin: 30px auto 0 auto;
-}
-
-div.documentwrapper {
- float: left;
- width: 100%;
-}
-
-div.bodywrapper {
- margin: 0 0 0 220px;
-}
-
-div.sphinxsidebar {
- width: 220px;
-}
-
-hr {
- border: 1px solid #B1B4B6;
-}
-
-div.body {
- background-color: #ffffff;
- color: #3E4349;
- padding: 0 30px 0 30px;
-}
-
-img.floatingflask {
- padding: 0 0 10px 10px;
- float: right;
-}
-
-div.footer {
- width: 940px;
- margin: 20px auto 30px auto;
- font-size: 14px;
- color: #888;
- text-align: right;
-}
-
-div.footer a {
- color: #888;
-}
-
-div.related {
- display: none;
-}
-
-div.sphinxsidebar a {
- color: #444;
- text-decoration: none;
- border-bottom: 1px dotted #999;
-}
-
-div.sphinxsidebar a:hover {
- border-bottom: 1px solid #999;
-}
-
-div.sphinxsidebar {
- font-size: 14px;
- line-height: 1.5;
-}
-
-div.sphinxsidebarwrapper {
- padding: 18px 10px;
-}
-
-div.sphinxsidebarwrapper p.logo {
- padding: 0;
- margin: -10px 0 0 -20px;
- text-align: center;
-}
-
-div.sphinxsidebar h3,
-div.sphinxsidebar h4 {
- font-family: 'Garamond', 'Georgia', serif;
- color: #444;
- font-size: 24px;
- font-weight: normal;
- margin: 0 0 5px 0;
- padding: 0;
-}
-
-div.sphinxsidebar h4 {
- font-size: 20px;
-}
-
-div.sphinxsidebar h3 a {
- color: #444;
-}
-
-div.sphinxsidebar p.logo a,
-div.sphinxsidebar h3 a,
-div.sphinxsidebar p.logo a:hover,
-div.sphinxsidebar h3 a:hover {
- border: none;
-}
-
-div.sphinxsidebar p {
- color: #555;
- margin: 10px 0;
-}
-
-div.sphinxsidebar ul {
- margin: 10px 0;
- padding: 0;
- color: #000;
-}
-
-div.sphinxsidebar input {
- border: 1px solid #ccc;
- font-family: 'Georgia', serif;
- font-size: 1em;
-}
-
-/* -- body styles ----------------------------------------------------------- */
-
-a {
- color: #004B6B;
- text-decoration: underline;
-}
-
-a:hover {
- color: #6D4100;
- text-decoration: underline;
-}
-
-div.body h1,
-div.body h2,
-div.body h3,
-div.body h4,
-div.body h5,
-div.body h6 {
- font-family: 'Garamond', 'Georgia', serif;
- font-weight: normal;
- margin: 30px 0px 10px 0px;
- padding: 0;
-}
-
-div.body h1 { margin-top: 0; padding-top: 0; font-size: 240%; }
-div.body h2 { font-size: 180%; }
-div.body h3 { font-size: 150%; }
-div.body h4 { font-size: 130%; }
-div.body h5 { font-size: 100%; }
-div.body h6 { font-size: 100%; }
-
-a.headerlink {
- color: #ddd;
- padding: 0 4px;
- text-decoration: none;
-}
-
-a.headerlink:hover {
- color: #444;
- background: #eaeaea;
-}
-
-div.body p, div.body dd, div.body li {
- line-height: 1.4em;
-}
-
-div.admonition {
- background: #fafafa;
- margin: 20px -30px;
- padding: 10px 30px;
- border-top: 1px solid #ccc;
- border-bottom: 1px solid #ccc;
-}
-
-div.admonition tt.xref, div.admonition a tt {
- border-bottom: 1px solid #fafafa;
-}
-
-dd div.admonition {
- margin-left: -60px;
- padding-left: 60px;
-}
-
-div.admonition p.admonition-title {
- font-family: 'Garamond', 'Georgia', serif;
- font-weight: normal;
- font-size: 24px;
- margin: 0 0 10px 0;
- padding: 0;
- line-height: 1;
-}
-
-div.admonition p.last {
- margin-bottom: 0;
-}
-
-div.highlight {
- background-color: white;
-}
-
-dt:target, .highlight {
- background: #FAF3E8;
-}
-
-div.note {
- background-color: #eee;
- border: 1px solid #ccc;
-}
-
-div.seealso {
- background-color: #ffc;
- border: 1px solid #ff6;
-}
-
-div.topic {
- background-color: #eee;
-}
-
-p.admonition-title {
- display: inline;
-}
-
-p.admonition-title:after {
- content: ":";
-}
-
-pre, tt {
- font-family: 'Consolas', 'Menlo', 'Deja Vu Sans Mono', 'Bitstream Vera Sans Mono', monospace;
- font-size: 0.9em;
-}
-
-img.screenshot {
-}
-
-tt.descname, tt.descclassname {
- font-size: 0.95em;
-}
-
-tt.descname {
- padding-right: 0.08em;
-}
-
-img.screenshot {
- -moz-box-shadow: 2px 2px 4px #eee;
- -webkit-box-shadow: 2px 2px 4px #eee;
- box-shadow: 2px 2px 4px #eee;
-}
-
-table.docutils {
- border: 1px solid #888;
- -moz-box-shadow: 2px 2px 4px #eee;
- -webkit-box-shadow: 2px 2px 4px #eee;
- box-shadow: 2px 2px 4px #eee;
-}
-
-table.docutils td, table.docutils th {
- border: 1px solid #888;
- padding: 0.25em 0.7em;
-}
-
-table.field-list, table.footnote {
- border: none;
- -moz-box-shadow: none;
- -webkit-box-shadow: none;
- box-shadow: none;
-}
-
-table.footnote {
- margin: 15px 0;
- width: 100%;
- border: 1px solid #eee;
- background: #fdfdfd;
- font-size: 0.9em;
-}
-
-table.footnote + table.footnote {
- margin-top: -15px;
- border-top: none;
-}
-
-table.field-list th {
- padding: 0 0.8em 0 0;
-}
-
-table.field-list td {
- padding: 0;
-}
-
-table.footnote td.label {
- width: 0px;
- padding: 0.3em 0 0.3em 0.5em;
-}
-
-table.footnote td {
- padding: 0.3em 0.5em;
-}
-
-dl {
- margin: 0;
- padding: 0;
-}
-
-dl dd {
- margin-left: 30px;
-}
-
-blockquote {
- margin: 0 0 0 30px;
- padding: 0;
-}
-
-ul, ol {
- margin: 10px 0 10px 30px;
- padding: 0;
-}
-
-pre {
- background: #eee;
- padding: 7px 30px;
- margin: 15px -30px;
- line-height: 1.3em;
-}
-
-dl pre, blockquote pre, li pre {
- margin-left: -60px;
- padding-left: 60px;
-}
-
-dl dl pre {
- margin-left: -90px;
- padding-left: 90px;
-}
-
-tt {
- background-color: #ecf0f3;
- color: #222;
- /* padding: 1px 2px; */
-}
-
-tt.xref, a tt {
- background-color: #FBFBFB;
- border-bottom: 1px solid white;
-}
-
-a.reference {
- text-decoration: none;
- border-bottom: 1px dotted #004B6B;
-}
-
-a.reference:hover {
- border-bottom: 1px solid #6D4100;
-}
-
-a.footnote-reference {
- text-decoration: none;
- font-size: 0.7em;
- vertical-align: top;
- border-bottom: 1px dotted #004B6B;
-}
-
-a.footnote-reference:hover {
- border-bottom: 1px solid #6D4100;
-}
-
-a:hover tt {
- background: #EEE;
-}
-
-
-@media screen and (max-width: 600px) {
-
- div.sphinxsidebar {
- display: none;
- }
-
- div.document {
- width: 100%;
-
- }
-
- div.documentwrapper {
- margin-left: 0;
- margin-top: 0;
- margin-right: 0;
- margin-bottom: 0;
- }
-
- div.bodywrapper {
- margin-top: 0;
- margin-right: 0;
- margin-bottom: 0;
- margin-left: 0;
- }
-
- ul {
- margin-left: 0;
- }
-
- .document {
- width: auto;
- }
-
- .footer {
- width: auto;
- }
-
- .bodywrapper {
- margin: 0;
- }
-
- .footer {
- width: auto;
- }
-
- .github {
- display: none;
- }
-
-}
-
-/* misc. */
-
-.revsys-inline {
- display: none!important;
-}
\ No newline at end of file
diff --git a/docs/html/_static/jquery-3.2.1.js b/docs/html/_static/jquery-3.2.1.js
deleted file mode 100644
index d2d8ca47..00000000
--- a/docs/html/_static/jquery-3.2.1.js
+++ /dev/null
@@ -1,10253 +0,0 @@
-/*!
- * jQuery JavaScript Library v3.2.1
- * https://jquery.com/
- *
- * Includes Sizzle.js
- * https://sizzlejs.com/
- *
- * Copyright JS Foundation and other contributors
- * Released under the MIT license
- * https://jquery.org/license
- *
- * Date: 2017-03-20T18:59Z
- */
-( function( global, factory ) {
-
- "use strict";
-
- if ( typeof module === "object" && typeof module.exports === "object" ) {
-
- // For CommonJS and CommonJS-like environments where a proper `window`
- // is present, execute the factory and get jQuery.
- // For environments that do not have a `window` with a `document`
- // (such as Node.js), expose a factory as module.exports.
- // This accentuates the need for the creation of a real `window`.
- // e.g. var jQuery = require("jquery")(window);
- // See ticket #14549 for more info.
- module.exports = global.document ?
- factory( global, true ) :
- function( w ) {
- if ( !w.document ) {
- throw new Error( "jQuery requires a window with a document" );
- }
- return factory( w );
- };
- } else {
- factory( global );
- }
-
-// Pass this if window is not defined yet
-} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
-
-// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
-// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
-// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
-// enough that all such attempts are guarded in a try block.
-"use strict";
-
-var arr = [];
-
-var document = window.document;
-
-var getProto = Object.getPrototypeOf;
-
-var slice = arr.slice;
-
-var concat = arr.concat;
-
-var push = arr.push;
-
-var indexOf = arr.indexOf;
-
-var class2type = {};
-
-var toString = class2type.toString;
-
-var hasOwn = class2type.hasOwnProperty;
-
-var fnToString = hasOwn.toString;
-
-var ObjectFunctionString = fnToString.call( Object );
-
-var support = {};
-
-
-
- function DOMEval( code, doc ) {
- doc = doc || document;
-
- var script = doc.createElement( "script" );
-
- script.text = code;
- doc.head.appendChild( script ).parentNode.removeChild( script );
- }
-/* global Symbol */
-// Defining this global in .eslintrc.json would create a danger of using the global
-// unguarded in another place, it seems safer to define global only for this module
-
-
-
-var
- version = "3.2.1",
-
- // Define a local copy of jQuery
- jQuery = function( selector, context ) {
-
- // The jQuery object is actually just the init constructor 'enhanced'
- // Need init if jQuery is called (just allow error to be thrown if not included)
- return new jQuery.fn.init( selector, context );
- },
-
- // Support: Android <=4.0 only
- // Make sure we trim BOM and NBSP
- rtrim = /^[\s\uFEFF\xA0]+|[\s\uFEFF\xA0]+$/g,
-
- // Matches dashed string for camelizing
- rmsPrefix = /^-ms-/,
- rdashAlpha = /-([a-z])/g,
-
- // Used by jQuery.camelCase as callback to replace()
- fcamelCase = function( all, letter ) {
- return letter.toUpperCase();
- };
-
-jQuery.fn = jQuery.prototype = {
-
- // The current version of jQuery being used
- jquery: version,
-
- constructor: jQuery,
-
- // The default length of a jQuery object is 0
- length: 0,
-
- toArray: function() {
- return slice.call( this );
- },
-
- // Get the Nth element in the matched element set OR
- // Get the whole matched element set as a clean array
- get: function( num ) {
-
- // Return all the elements in a clean array
- if ( num == null ) {
- return slice.call( this );
- }
-
- // Return just the one element from the set
- return num < 0 ? this[ num + this.length ] : this[ num ];
- },
-
- // Take an array of elements and push it onto the stack
- // (returning the new matched element set)
- pushStack: function( elems ) {
-
- // Build a new jQuery matched element set
- var ret = jQuery.merge( this.constructor(), elems );
-
- // Add the old object onto the stack (as a reference)
- ret.prevObject = this;
-
- // Return the newly-formed element set
- return ret;
- },
-
- // Execute a callback for every element in the matched set.
- each: function( callback ) {
- return jQuery.each( this, callback );
- },
-
- map: function( callback ) {
- return this.pushStack( jQuery.map( this, function( elem, i ) {
- return callback.call( elem, i, elem );
- } ) );
- },
-
- slice: function() {
- return this.pushStack( slice.apply( this, arguments ) );
- },
-
- first: function() {
- return this.eq( 0 );
- },
-
- last: function() {
- return this.eq( -1 );
- },
-
- eq: function( i ) {
- var len = this.length,
- j = +i + ( i < 0 ? len : 0 );
- return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] );
- },
-
- end: function() {
- return this.prevObject || this.constructor();
- },
-
- // For internal use only.
- // Behaves like an Array's method, not like a jQuery method.
- push: push,
- sort: arr.sort,
- splice: arr.splice
-};
-
-jQuery.extend = jQuery.fn.extend = function() {
- var options, name, src, copy, copyIsArray, clone,
- target = arguments[ 0 ] || {},
- i = 1,
- length = arguments.length,
- deep = false;
-
- // Handle a deep copy situation
- if ( typeof target === "boolean" ) {
- deep = target;
-
- // Skip the boolean and the target
- target = arguments[ i ] || {};
- i++;
- }
-
- // Handle case when target is a string or something (possible in deep copy)
- if ( typeof target !== "object" && !jQuery.isFunction( target ) ) {
- target = {};
- }
-
- // Extend jQuery itself if only one argument is passed
- if ( i === length ) {
- target = this;
- i--;
- }
-
- for ( ; i < length; i++ ) {
-
- // Only deal with non-null/undefined values
- if ( ( options = arguments[ i ] ) != null ) {
-
- // Extend the base object
- for ( name in options ) {
- src = target[ name ];
- copy = options[ name ];
-
- // Prevent never-ending loop
- if ( target === copy ) {
- continue;
- }
-
- // Recurse if we're merging plain objects or arrays
- if ( deep && copy && ( jQuery.isPlainObject( copy ) ||
- ( copyIsArray = Array.isArray( copy ) ) ) ) {
-
- if ( copyIsArray ) {
- copyIsArray = false;
- clone = src && Array.isArray( src ) ? src : [];
-
- } else {
- clone = src && jQuery.isPlainObject( src ) ? src : {};
- }
-
- // Never move original objects, clone them
- target[ name ] = jQuery.extend( deep, clone, copy );
-
- // Don't bring in undefined values
- } else if ( copy !== undefined ) {
- target[ name ] = copy;
- }
- }
- }
- }
-
- // Return the modified object
- return target;
-};
-
-jQuery.extend( {
-
- // Unique for each copy of jQuery on the page
- expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
-
- // Assume jQuery is ready without the ready module
- isReady: true,
-
- error: function( msg ) {
- throw new Error( msg );
- },
-
- noop: function() {},
-
- isFunction: function( obj ) {
- return jQuery.type( obj ) === "function";
- },
-
- isWindow: function( obj ) {
- return obj != null && obj === obj.window;
- },
-
- isNumeric: function( obj ) {
-
- // As of jQuery 3.0, isNumeric is limited to
- // strings and numbers (primitives or objects)
- // that can be coerced to finite numbers (gh-2662)
- var type = jQuery.type( obj );
- return ( type === "number" || type === "string" ) &&
-
- // parseFloat NaNs numeric-cast false positives ("")
- // ...but misinterprets leading-number strings, particularly hex literals ("0x...")
- // subtraction forces infinities to NaN
- !isNaN( obj - parseFloat( obj ) );
- },
-
- isPlainObject: function( obj ) {
- var proto, Ctor;
-
- // Detect obvious negatives
- // Use toString instead of jQuery.type to catch host objects
- if ( !obj || toString.call( obj ) !== "[object Object]" ) {
- return false;
- }
-
- proto = getProto( obj );
-
- // Objects with no prototype (e.g., `Object.create( null )`) are plain
- if ( !proto ) {
- return true;
- }
-
- // Objects with prototype are plain iff they were constructed by a global Object function
- Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor;
- return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString;
- },
-
- isEmptyObject: function( obj ) {
-
- /* eslint-disable no-unused-vars */
- // See https://github.com/eslint/eslint/issues/6125
- var name;
-
- for ( name in obj ) {
- return false;
- }
- return true;
- },
-
- type: function( obj ) {
- if ( obj == null ) {
- return obj + "";
- }
-
- // Support: Android <=2.3 only (functionish RegExp)
- return typeof obj === "object" || typeof obj === "function" ?
- class2type[ toString.call( obj ) ] || "object" :
- typeof obj;
- },
-
- // Evaluates a script in a global context
- globalEval: function( code ) {
- DOMEval( code );
- },
-
- // Convert dashed to camelCase; used by the css and data modules
- // Support: IE <=9 - 11, Edge 12 - 13
- // Microsoft forgot to hump their vendor prefix (#9572)
- camelCase: function( string ) {
- return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
- },
-
- each: function( obj, callback ) {
- var length, i = 0;
-
- if ( isArrayLike( obj ) ) {
- length = obj.length;
- for ( ; i < length; i++ ) {
- if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
- break;
- }
- }
- } else {
- for ( i in obj ) {
- if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
- break;
- }
- }
- }
-
- return obj;
- },
-
- // Support: Android <=4.0 only
- trim: function( text ) {
- return text == null ?
- "" :
- ( text + "" ).replace( rtrim, "" );
- },
-
- // results is for internal usage only
- makeArray: function( arr, results ) {
- var ret = results || [];
-
- if ( arr != null ) {
- if ( isArrayLike( Object( arr ) ) ) {
- jQuery.merge( ret,
- typeof arr === "string" ?
- [ arr ] : arr
- );
- } else {
- push.call( ret, arr );
- }
- }
-
- return ret;
- },
-
- inArray: function( elem, arr, i ) {
- return arr == null ? -1 : indexOf.call( arr, elem, i );
- },
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- merge: function( first, second ) {
- var len = +second.length,
- j = 0,
- i = first.length;
-
- for ( ; j < len; j++ ) {
- first[ i++ ] = second[ j ];
- }
-
- first.length = i;
-
- return first;
- },
-
- grep: function( elems, callback, invert ) {
- var callbackInverse,
- matches = [],
- i = 0,
- length = elems.length,
- callbackExpect = !invert;
-
- // Go through the array, only saving the items
- // that pass the validator function
- for ( ; i < length; i++ ) {
- callbackInverse = !callback( elems[ i ], i );
- if ( callbackInverse !== callbackExpect ) {
- matches.push( elems[ i ] );
- }
- }
-
- return matches;
- },
-
- // arg is for internal usage only
- map: function( elems, callback, arg ) {
- var length, value,
- i = 0,
- ret = [];
-
- // Go through the array, translating each of the items to their new values
- if ( isArrayLike( elems ) ) {
- length = elems.length;
- for ( ; i < length; i++ ) {
- value = callback( elems[ i ], i, arg );
-
- if ( value != null ) {
- ret.push( value );
- }
- }
-
- // Go through every key on the object,
- } else {
- for ( i in elems ) {
- value = callback( elems[ i ], i, arg );
-
- if ( value != null ) {
- ret.push( value );
- }
- }
- }
-
- // Flatten any nested arrays
- return concat.apply( [], ret );
- },
-
- // A global GUID counter for objects
- guid: 1,
-
- // Bind a function to a context, optionally partially applying any
- // arguments.
- proxy: function( fn, context ) {
- var tmp, args, proxy;
-
- if ( typeof context === "string" ) {
- tmp = fn[ context ];
- context = fn;
- fn = tmp;
- }
-
- // Quick check to determine if target is callable, in the spec
- // this throws a TypeError, but we will just return undefined.
- if ( !jQuery.isFunction( fn ) ) {
- return undefined;
- }
-
- // Simulated bind
- args = slice.call( arguments, 2 );
- proxy = function() {
- return fn.apply( context || this, args.concat( slice.call( arguments ) ) );
- };
-
- // Set the guid of unique handler to the same of original handler, so it can be removed
- proxy.guid = fn.guid = fn.guid || jQuery.guid++;
-
- return proxy;
- },
-
- now: Date.now,
-
- // jQuery.support is not used in Core but other projects attach their
- // properties to it so it needs to exist.
- support: support
-} );
-
-if ( typeof Symbol === "function" ) {
- jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ];
-}
-
-// Populate the class2type map
-jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ),
-function( i, name ) {
- class2type[ "[object " + name + "]" ] = name.toLowerCase();
-} );
-
-function isArrayLike( obj ) {
-
- // Support: real iOS 8.2 only (not reproducible in simulator)
- // `in` check used to prevent JIT error (gh-2145)
- // hasOwn isn't used here due to false negatives
- // regarding Nodelist length in IE
- var length = !!obj && "length" in obj && obj.length,
- type = jQuery.type( obj );
-
- if ( type === "function" || jQuery.isWindow( obj ) ) {
- return false;
- }
-
- return type === "array" || length === 0 ||
- typeof length === "number" && length > 0 && ( length - 1 ) in obj;
-}
-var Sizzle =
-/*!
- * Sizzle CSS Selector Engine v2.3.3
- * https://sizzlejs.com/
- *
- * Copyright jQuery Foundation and other contributors
- * Released under the MIT license
- * http://jquery.org/license
- *
- * Date: 2016-08-08
- */
-(function( window ) {
-
-var i,
- support,
- Expr,
- getText,
- isXML,
- tokenize,
- compile,
- select,
- outermostContext,
- sortInput,
- hasDuplicate,
-
- // Local document vars
- setDocument,
- document,
- docElem,
- documentIsHTML,
- rbuggyQSA,
- rbuggyMatches,
- matches,
- contains,
-
- // Instance-specific data
- expando = "sizzle" + 1 * new Date(),
- preferredDoc = window.document,
- dirruns = 0,
- done = 0,
- classCache = createCache(),
- tokenCache = createCache(),
- compilerCache = createCache(),
- sortOrder = function( a, b ) {
- if ( a === b ) {
- hasDuplicate = true;
- }
- return 0;
- },
-
- // Instance methods
- hasOwn = ({}).hasOwnProperty,
- arr = [],
- pop = arr.pop,
- push_native = arr.push,
- push = arr.push,
- slice = arr.slice,
- // Use a stripped-down indexOf as it's faster than native
- // https://jsperf.com/thor-indexof-vs-for/5
- indexOf = function( list, elem ) {
- var i = 0,
- len = list.length;
- for ( ; i < len; i++ ) {
- if ( list[i] === elem ) {
- return i;
- }
- }
- return -1;
- },
-
- booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|ismap|loop|multiple|open|readonly|required|scoped",
-
- // Regular expressions
-
- // http://www.w3.org/TR/css3-selectors/#whitespace
- whitespace = "[\\x20\\t\\r\\n\\f]",
-
- // http://www.w3.org/TR/CSS21/syndata.html#value-def-identifier
- identifier = "(?:\\\\.|[\\w-]|[^\0-\\xa0])+",
-
- // Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
- attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace +
- // Operator (capture 2)
- "*([*^$|!~]?=)" + whitespace +
- // "Attribute values must be CSS identifiers [capture 5] or strings [capture 3 or capture 4]"
- "*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" + whitespace +
- "*\\]",
-
- pseudos = ":(" + identifier + ")(?:\\((" +
- // To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
- // 1. quoted (capture 3; capture 4 or capture 5)
- "('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
- // 2. simple (capture 6)
- "((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
- // 3. anything else (capture 2)
- ".*" +
- ")\\)|)",
-
- // Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
- rwhitespace = new RegExp( whitespace + "+", "g" ),
- rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" + whitespace + "+$", "g" ),
-
- rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
- rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace + "*" ),
-
- rattributeQuotes = new RegExp( "=" + whitespace + "*([^\\]'\"]*?)" + whitespace + "*\\]", "g" ),
-
- rpseudo = new RegExp( pseudos ),
- ridentifier = new RegExp( "^" + identifier + "$" ),
-
- matchExpr = {
- "ID": new RegExp( "^#(" + identifier + ")" ),
- "CLASS": new RegExp( "^\\.(" + identifier + ")" ),
- "TAG": new RegExp( "^(" + identifier + "|[*])" ),
- "ATTR": new RegExp( "^" + attributes ),
- "PSEUDO": new RegExp( "^" + pseudos ),
- "CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" + whitespace +
- "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" + whitespace +
- "*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
- "bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
- // For use in libraries implementing .is()
- // We use this for POS matching in `select`
- "needsContext": new RegExp( "^" + whitespace + "*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" +
- whitespace + "*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
- },
-
- rinputs = /^(?:input|select|textarea|button)$/i,
- rheader = /^h\d$/i,
-
- rnative = /^[^{]+\{\s*\[native \w/,
-
- // Easily-parseable/retrievable ID or TAG or CLASS selectors
- rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
-
- rsibling = /[+~]/,
-
- // CSS escapes
- // http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
- runescape = new RegExp( "\\\\([\\da-f]{1,6}" + whitespace + "?|(" + whitespace + ")|.)", "ig" ),
- funescape = function( _, escaped, escapedWhitespace ) {
- var high = "0x" + escaped - 0x10000;
- // NaN means non-codepoint
- // Support: Firefox<24
- // Workaround erroneous numeric interpretation of +"0x"
- return high !== high || escapedWhitespace ?
- escaped :
- high < 0 ?
- // BMP codepoint
- String.fromCharCode( high + 0x10000 ) :
- // Supplemental Plane codepoint (surrogate pair)
- String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
- },
-
- // CSS string/identifier serialization
- // https://drafts.csswg.org/cssom/#common-serializing-idioms
- rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,
- fcssescape = function( ch, asCodePoint ) {
- if ( asCodePoint ) {
-
- // U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER
- if ( ch === "\0" ) {
- return "\uFFFD";
- }
-
- // Control characters and (dependent upon position) numbers get escaped as code points
- return ch.slice( 0, -1 ) + "\\" + ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " ";
- }
-
- // Other potentially-special ASCII characters get backslash-escaped
- return "\\" + ch;
- },
-
- // Used for iframes
- // See setDocument()
- // Removing the function wrapper causes a "Permission Denied"
- // error in IE
- unloadHandler = function() {
- setDocument();
- },
-
- disabledAncestor = addCombinator(
- function( elem ) {
- return elem.disabled === true && ("form" in elem || "label" in elem);
- },
- { dir: "parentNode", next: "legend" }
- );
-
-// Optimize for push.apply( _, NodeList )
-try {
- push.apply(
- (arr = slice.call( preferredDoc.childNodes )),
- preferredDoc.childNodes
- );
- // Support: Android<4.0
- // Detect silently failing push.apply
- arr[ preferredDoc.childNodes.length ].nodeType;
-} catch ( e ) {
- push = { apply: arr.length ?
-
- // Leverage slice if possible
- function( target, els ) {
- push_native.apply( target, slice.call(els) );
- } :
-
- // Support: IE<9
- // Otherwise append directly
- function( target, els ) {
- var j = target.length,
- i = 0;
- // Can't trust NodeList.length
- while ( (target[j++] = els[i++]) ) {}
- target.length = j - 1;
- }
- };
-}
-
-function Sizzle( selector, context, results, seed ) {
- var m, i, elem, nid, match, groups, newSelector,
- newContext = context && context.ownerDocument,
-
- // nodeType defaults to 9, since context defaults to document
- nodeType = context ? context.nodeType : 9;
-
- results = results || [];
-
- // Return early from calls with invalid selector or context
- if ( typeof selector !== "string" || !selector ||
- nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
-
- return results;
- }
-
- // Try to shortcut find operations (as opposed to filters) in HTML documents
- if ( !seed ) {
-
- if ( ( context ? context.ownerDocument || context : preferredDoc ) !== document ) {
- setDocument( context );
- }
- context = context || document;
-
- if ( documentIsHTML ) {
-
- // If the selector is sufficiently simple, try using a "get*By*" DOM method
- // (excepting DocumentFragment context, where the methods don't exist)
- if ( nodeType !== 11 && (match = rquickExpr.exec( selector )) ) {
-
- // ID selector
- if ( (m = match[1]) ) {
-
- // Document context
- if ( nodeType === 9 ) {
- if ( (elem = context.getElementById( m )) ) {
-
- // Support: IE, Opera, Webkit
- // TODO: identify versions
- // getElementById can match elements by name instead of ID
- if ( elem.id === m ) {
- results.push( elem );
- return results;
- }
- } else {
- return results;
- }
-
- // Element context
- } else {
-
- // Support: IE, Opera, Webkit
- // TODO: identify versions
- // getElementById can match elements by name instead of ID
- if ( newContext && (elem = newContext.getElementById( m )) &&
- contains( context, elem ) &&
- elem.id === m ) {
-
- results.push( elem );
- return results;
- }
- }
-
- // Type selector
- } else if ( match[2] ) {
- push.apply( results, context.getElementsByTagName( selector ) );
- return results;
-
- // Class selector
- } else if ( (m = match[3]) && support.getElementsByClassName &&
- context.getElementsByClassName ) {
-
- push.apply( results, context.getElementsByClassName( m ) );
- return results;
- }
- }
-
- // Take advantage of querySelectorAll
- if ( support.qsa &&
- !compilerCache[ selector + " " ] &&
- (!rbuggyQSA || !rbuggyQSA.test( selector )) ) {
-
- if ( nodeType !== 1 ) {
- newContext = context;
- newSelector = selector;
-
- // qSA looks outside Element context, which is not what we want
- // Thanks to Andrew Dupont for this workaround technique
- // Support: IE <=8
- // Exclude object elements
- } else if ( context.nodeName.toLowerCase() !== "object" ) {
-
- // Capture the context ID, setting it first if necessary
- if ( (nid = context.getAttribute( "id" )) ) {
- nid = nid.replace( rcssescape, fcssescape );
- } else {
- context.setAttribute( "id", (nid = expando) );
- }
-
- // Prefix every selector in the list
- groups = tokenize( selector );
- i = groups.length;
- while ( i-- ) {
- groups[i] = "#" + nid + " " + toSelector( groups[i] );
- }
- newSelector = groups.join( "," );
-
- // Expand context for sibling selectors
- newContext = rsibling.test( selector ) && testContext( context.parentNode ) ||
- context;
- }
-
- if ( newSelector ) {
- try {
- push.apply( results,
- newContext.querySelectorAll( newSelector )
- );
- return results;
- } catch ( qsaError ) {
- } finally {
- if ( nid === expando ) {
- context.removeAttribute( "id" );
- }
- }
- }
- }
- }
- }
-
- // All others
- return select( selector.replace( rtrim, "$1" ), context, results, seed );
-}
-
-/**
- * Create key-value caches of limited size
- * @returns {function(string, object)} Returns the Object data after storing it on itself with
- * property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
- * deleting the oldest entry
- */
-function createCache() {
- var keys = [];
-
- function cache( key, value ) {
- // Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
- if ( keys.push( key + " " ) > Expr.cacheLength ) {
- // Only keep the most recent entries
- delete cache[ keys.shift() ];
- }
- return (cache[ key + " " ] = value);
- }
- return cache;
-}
-
-/**
- * Mark a function for special use by Sizzle
- * @param {Function} fn The function to mark
- */
-function markFunction( fn ) {
- fn[ expando ] = true;
- return fn;
-}
-
-/**
- * Support testing using an element
- * @param {Function} fn Passed the created element and returns a boolean result
- */
-function assert( fn ) {
- var el = document.createElement("fieldset");
-
- try {
- return !!fn( el );
- } catch (e) {
- return false;
- } finally {
- // Remove from its parent by default
- if ( el.parentNode ) {
- el.parentNode.removeChild( el );
- }
- // release memory in IE
- el = null;
- }
-}
-
-/**
- * Adds the same handler for all of the specified attrs
- * @param {String} attrs Pipe-separated list of attributes
- * @param {Function} handler The method that will be applied
- */
-function addHandle( attrs, handler ) {
- var arr = attrs.split("|"),
- i = arr.length;
-
- while ( i-- ) {
- Expr.attrHandle[ arr[i] ] = handler;
- }
-}
-
-/**
- * Checks document order of two siblings
- * @param {Element} a
- * @param {Element} b
- * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
- */
-function siblingCheck( a, b ) {
- var cur = b && a,
- diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
- a.sourceIndex - b.sourceIndex;
-
- // Use IE sourceIndex if available on both nodes
- if ( diff ) {
- return diff;
- }
-
- // Check if b follows a
- if ( cur ) {
- while ( (cur = cur.nextSibling) ) {
- if ( cur === b ) {
- return -1;
- }
- }
- }
-
- return a ? 1 : -1;
-}
-
-/**
- * Returns a function to use in pseudos for input types
- * @param {String} type
- */
-function createInputPseudo( type ) {
- return function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return name === "input" && elem.type === type;
- };
-}
-
-/**
- * Returns a function to use in pseudos for buttons
- * @param {String} type
- */
-function createButtonPseudo( type ) {
- return function( elem ) {
- var name = elem.nodeName.toLowerCase();
- return (name === "input" || name === "button") && elem.type === type;
- };
-}
-
-/**
- * Returns a function to use in pseudos for :enabled/:disabled
- * @param {Boolean} disabled true for :disabled; false for :enabled
- */
-function createDisabledPseudo( disabled ) {
-
- // Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable
- return function( elem ) {
-
- // Only certain elements can match :enabled or :disabled
- // https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled
- // https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled
- if ( "form" in elem ) {
-
- // Check for inherited disabledness on relevant non-disabled elements:
- // * listed form-associated elements in a disabled fieldset
- // https://html.spec.whatwg.org/multipage/forms.html#category-listed
- // https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled
- // * option elements in a disabled optgroup
- // https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled
- // All such elements have a "form" property.
- if ( elem.parentNode && elem.disabled === false ) {
-
- // Option elements defer to a parent optgroup if present
- if ( "label" in elem ) {
- if ( "label" in elem.parentNode ) {
- return elem.parentNode.disabled === disabled;
- } else {
- return elem.disabled === disabled;
- }
- }
-
- // Support: IE 6 - 11
- // Use the isDisabled shortcut property to check for disabled fieldset ancestors
- return elem.isDisabled === disabled ||
-
- // Where there is no isDisabled, check manually
- /* jshint -W018 */
- elem.isDisabled !== !disabled &&
- disabledAncestor( elem ) === disabled;
- }
-
- return elem.disabled === disabled;
-
- // Try to winnow out elements that can't be disabled before trusting the disabled property.
- // Some victims get caught in our net (label, legend, menu, track), but it shouldn't
- // even exist on them, let alone have a boolean value.
- } else if ( "label" in elem ) {
- return elem.disabled === disabled;
- }
-
- // Remaining elements are neither :enabled nor :disabled
- return false;
- };
-}
-
-/**
- * Returns a function to use in pseudos for positionals
- * @param {Function} fn
- */
-function createPositionalPseudo( fn ) {
- return markFunction(function( argument ) {
- argument = +argument;
- return markFunction(function( seed, matches ) {
- var j,
- matchIndexes = fn( [], seed.length, argument ),
- i = matchIndexes.length;
-
- // Match elements found at the specified indexes
- while ( i-- ) {
- if ( seed[ (j = matchIndexes[i]) ] ) {
- seed[j] = !(matches[j] = seed[j]);
- }
- }
- });
- });
-}
-
-/**
- * Checks a node for validity as a Sizzle context
- * @param {Element|Object=} context
- * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
- */
-function testContext( context ) {
- return context && typeof context.getElementsByTagName !== "undefined" && context;
-}
-
-// Expose support vars for convenience
-support = Sizzle.support = {};
-
-/**
- * Detects XML nodes
- * @param {Element|Object} elem An element or a document
- * @returns {Boolean} True iff elem is a non-HTML XML node
- */
-isXML = Sizzle.isXML = function( elem ) {
- // documentElement is verified for cases where it doesn't yet exist
- // (such as loading iframes in IE - #4833)
- var documentElement = elem && (elem.ownerDocument || elem).documentElement;
- return documentElement ? documentElement.nodeName !== "HTML" : false;
-};
-
-/**
- * Sets document-related variables once based on the current document
- * @param {Element|Object} [doc] An element or document object to use to set the document
- * @returns {Object} Returns the current document
- */
-setDocument = Sizzle.setDocument = function( node ) {
- var hasCompare, subWindow,
- doc = node ? node.ownerDocument || node : preferredDoc;
-
- // Return early if doc is invalid or already selected
- if ( doc === document || doc.nodeType !== 9 || !doc.documentElement ) {
- return document;
- }
-
- // Update global variables
- document = doc;
- docElem = document.documentElement;
- documentIsHTML = !isXML( document );
-
- // Support: IE 9-11, Edge
- // Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936)
- if ( preferredDoc !== document &&
- (subWindow = document.defaultView) && subWindow.top !== subWindow ) {
-
- // Support: IE 11, Edge
- if ( subWindow.addEventListener ) {
- subWindow.addEventListener( "unload", unloadHandler, false );
-
- // Support: IE 9 - 10 only
- } else if ( subWindow.attachEvent ) {
- subWindow.attachEvent( "onunload", unloadHandler );
- }
- }
-
- /* Attributes
- ---------------------------------------------------------------------- */
-
- // Support: IE<8
- // Verify that getAttribute really returns attributes and not properties
- // (excepting IE8 booleans)
- support.attributes = assert(function( el ) {
- el.className = "i";
- return !el.getAttribute("className");
- });
-
- /* getElement(s)By*
- ---------------------------------------------------------------------- */
-
- // Check if getElementsByTagName("*") returns only elements
- support.getElementsByTagName = assert(function( el ) {
- el.appendChild( document.createComment("") );
- return !el.getElementsByTagName("*").length;
- });
-
- // Support: IE<9
- support.getElementsByClassName = rnative.test( document.getElementsByClassName );
-
- // Support: IE<10
- // Check if getElementById returns elements by name
- // The broken getElementById methods don't pick up programmatically-set names,
- // so use a roundabout getElementsByName test
- support.getById = assert(function( el ) {
- docElem.appendChild( el ).id = expando;
- return !document.getElementsByName || !document.getElementsByName( expando ).length;
- });
-
- // ID filter and find
- if ( support.getById ) {
- Expr.filter["ID"] = function( id ) {
- var attrId = id.replace( runescape, funescape );
- return function( elem ) {
- return elem.getAttribute("id") === attrId;
- };
- };
- Expr.find["ID"] = function( id, context ) {
- if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
- var elem = context.getElementById( id );
- return elem ? [ elem ] : [];
- }
- };
- } else {
- Expr.filter["ID"] = function( id ) {
- var attrId = id.replace( runescape, funescape );
- return function( elem ) {
- var node = typeof elem.getAttributeNode !== "undefined" &&
- elem.getAttributeNode("id");
- return node && node.value === attrId;
- };
- };
-
- // Support: IE 6 - 7 only
- // getElementById is not reliable as a find shortcut
- Expr.find["ID"] = function( id, context ) {
- if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
- var node, i, elems,
- elem = context.getElementById( id );
-
- if ( elem ) {
-
- // Verify the id attribute
- node = elem.getAttributeNode("id");
- if ( node && node.value === id ) {
- return [ elem ];
- }
-
- // Fall back on getElementsByName
- elems = context.getElementsByName( id );
- i = 0;
- while ( (elem = elems[i++]) ) {
- node = elem.getAttributeNode("id");
- if ( node && node.value === id ) {
- return [ elem ];
- }
- }
- }
-
- return [];
- }
- };
- }
-
- // Tag
- Expr.find["TAG"] = support.getElementsByTagName ?
- function( tag, context ) {
- if ( typeof context.getElementsByTagName !== "undefined" ) {
- return context.getElementsByTagName( tag );
-
- // DocumentFragment nodes don't have gEBTN
- } else if ( support.qsa ) {
- return context.querySelectorAll( tag );
- }
- } :
-
- function( tag, context ) {
- var elem,
- tmp = [],
- i = 0,
- // By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
- results = context.getElementsByTagName( tag );
-
- // Filter out possible comments
- if ( tag === "*" ) {
- while ( (elem = results[i++]) ) {
- if ( elem.nodeType === 1 ) {
- tmp.push( elem );
- }
- }
-
- return tmp;
- }
- return results;
- };
-
- // Class
- Expr.find["CLASS"] = support.getElementsByClassName && function( className, context ) {
- if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) {
- return context.getElementsByClassName( className );
- }
- };
-
- /* QSA/matchesSelector
- ---------------------------------------------------------------------- */
-
- // QSA and matchesSelector support
-
- // matchesSelector(:active) reports false when true (IE9/Opera 11.5)
- rbuggyMatches = [];
-
- // qSa(:focus) reports false when true (Chrome 21)
- // We allow this because of a bug in IE8/9 that throws an error
- // whenever `document.activeElement` is accessed on an iframe
- // So, we allow :focus to pass through QSA all the time to avoid the IE error
- // See https://bugs.jquery.com/ticket/13378
- rbuggyQSA = [];
-
- if ( (support.qsa = rnative.test( document.querySelectorAll )) ) {
- // Build QSA regex
- // Regex strategy adopted from Diego Perini
- assert(function( el ) {
- // Select is set to empty string on purpose
- // This is to test IE's treatment of not explicitly
- // setting a boolean content attribute,
- // since its presence should be enough
- // https://bugs.jquery.com/ticket/12359
- docElem.appendChild( el ).innerHTML = "" +
- " ";
-
- // Support: IE8, Opera 11-12.16
- // Nothing should be selected when empty strings follow ^= or $= or *=
- // The test attribute must be unknown in Opera but "safe" for WinRT
- // https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
- if ( el.querySelectorAll("[msallowcapture^='']").length ) {
- rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
- }
-
- // Support: IE8
- // Boolean attributes and "value" are not treated correctly
- if ( !el.querySelectorAll("[selected]").length ) {
- rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
- }
-
- // Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+
- if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
- rbuggyQSA.push("~=");
- }
-
- // Webkit/Opera - :checked should return selected option elements
- // http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
- // IE8 throws error here and will not see later tests
- if ( !el.querySelectorAll(":checked").length ) {
- rbuggyQSA.push(":checked");
- }
-
- // Support: Safari 8+, iOS 8+
- // https://bugs.webkit.org/show_bug.cgi?id=136851
- // In-page `selector#id sibling-combinator selector` fails
- if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) {
- rbuggyQSA.push(".#.+[+~]");
- }
- });
-
- assert(function( el ) {
- el.innerHTML = ") matching elements by id
- for ( ; i !== len && (elem = elems[i]) != null; i++ ) {
- if ( byElement && elem ) {
- j = 0;
- if ( !context && elem.ownerDocument !== document ) {
- setDocument( elem );
- xml = !documentIsHTML;
- }
- while ( (matcher = elementMatchers[j++]) ) {
- if ( matcher( elem, context || document, xml) ) {
- results.push( elem );
- break;
- }
- }
- if ( outermost ) {
- dirruns = dirrunsUnique;
- }
- }
-
- // Track unmatched elements for set filters
- if ( bySet ) {
- // They will have gone through all possible matchers
- if ( (elem = !matcher && elem) ) {
- matchedCount--;
- }
-
- // Lengthen the array for every element, matched or not
- if ( seed ) {
- unmatched.push( elem );
- }
- }
- }
-
- // `i` is now the count of elements visited above, and adding it to `matchedCount`
- // makes the latter nonnegative.
- matchedCount += i;
-
- // Apply set filters to unmatched elements
- // NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount`
- // equals `i`), unless we didn't visit _any_ elements in the above loop because we have
- // no element matchers and no seed.
- // Incrementing an initially-string "0" `i` allows `i` to remain a string only in that
- // case, which will result in a "00" `matchedCount` that differs from `i` but is also
- // numerically zero.
- if ( bySet && i !== matchedCount ) {
- j = 0;
- while ( (matcher = setMatchers[j++]) ) {
- matcher( unmatched, setMatched, context, xml );
- }
-
- if ( seed ) {
- // Reintegrate element matches to eliminate the need for sorting
- if ( matchedCount > 0 ) {
- while ( i-- ) {
- if ( !(unmatched[i] || setMatched[i]) ) {
- setMatched[i] = pop.call( results );
- }
- }
- }
-
- // Discard index placeholder values to get only actual matches
- setMatched = condense( setMatched );
- }
-
- // Add matches to results
- push.apply( results, setMatched );
-
- // Seedless set matches succeeding multiple successful matchers stipulate sorting
- if ( outermost && !seed && setMatched.length > 0 &&
- ( matchedCount + setMatchers.length ) > 1 ) {
-
- Sizzle.uniqueSort( results );
- }
- }
-
- // Override manipulation of globals by nested matchers
- if ( outermost ) {
- dirruns = dirrunsUnique;
- outermostContext = contextBackup;
- }
-
- return unmatched;
- };
-
- return bySet ?
- markFunction( superMatcher ) :
- superMatcher;
-}
-
-compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
- var i,
- setMatchers = [],
- elementMatchers = [],
- cached = compilerCache[ selector + " " ];
-
- if ( !cached ) {
- // Generate a function of recursive functions that can be used to check each element
- if ( !match ) {
- match = tokenize( selector );
- }
- i = match.length;
- while ( i-- ) {
- cached = matcherFromTokens( match[i] );
- if ( cached[ expando ] ) {
- setMatchers.push( cached );
- } else {
- elementMatchers.push( cached );
- }
- }
-
- // Cache the compiled function
- cached = compilerCache( selector, matcherFromGroupMatchers( elementMatchers, setMatchers ) );
-
- // Save selector and tokenization
- cached.selector = selector;
- }
- return cached;
-};
-
-/**
- * A low-level selection function that works with Sizzle's compiled
- * selector functions
- * @param {String|Function} selector A selector or a pre-compiled
- * selector function built with Sizzle.compile
- * @param {Element} context
- * @param {Array} [results]
- * @param {Array} [seed] A set of elements to match against
- */
-select = Sizzle.select = function( selector, context, results, seed ) {
- var i, tokens, token, type, find,
- compiled = typeof selector === "function" && selector,
- match = !seed && tokenize( (selector = compiled.selector || selector) );
-
- results = results || [];
-
- // Try to minimize operations if there is only one selector in the list and no seed
- // (the latter of which guarantees us context)
- if ( match.length === 1 ) {
-
- // Reduce context if the leading compound selector is an ID
- tokens = match[0] = match[0].slice( 0 );
- if ( tokens.length > 2 && (token = tokens[0]).type === "ID" &&
- context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[1].type ] ) {
-
- context = ( Expr.find["ID"]( token.matches[0].replace(runescape, funescape), context ) || [] )[0];
- if ( !context ) {
- return results;
-
- // Precompiled matchers will still verify ancestry, so step up a level
- } else if ( compiled ) {
- context = context.parentNode;
- }
-
- selector = selector.slice( tokens.shift().value.length );
- }
-
- // Fetch a seed set for right-to-left matching
- i = matchExpr["needsContext"].test( selector ) ? 0 : tokens.length;
- while ( i-- ) {
- token = tokens[i];
-
- // Abort if we hit a combinator
- if ( Expr.relative[ (type = token.type) ] ) {
- break;
- }
- if ( (find = Expr.find[ type ]) ) {
- // Search, expanding context for leading sibling combinators
- if ( (seed = find(
- token.matches[0].replace( runescape, funescape ),
- rsibling.test( tokens[0].type ) && testContext( context.parentNode ) || context
- )) ) {
-
- // If seed is empty or no tokens remain, we can return early
- tokens.splice( i, 1 );
- selector = seed.length && toSelector( tokens );
- if ( !selector ) {
- push.apply( results, seed );
- return results;
- }
-
- break;
- }
- }
- }
- }
-
- // Compile and execute a filtering function if one is not provided
- // Provide `match` to avoid retokenization if we modified the selector above
- ( compiled || compile( selector, match ) )(
- seed,
- context,
- !documentIsHTML,
- results,
- !context || rsibling.test( selector ) && testContext( context.parentNode ) || context
- );
- return results;
-};
-
-// One-time assignments
-
-// Sort stability
-support.sortStable = expando.split("").sort( sortOrder ).join("") === expando;
-
-// Support: Chrome 14-35+
-// Always assume duplicates if they aren't passed to the comparison function
-support.detectDuplicates = !!hasDuplicate;
-
-// Initialize against the default document
-setDocument();
-
-// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
-// Detached nodes confoundingly follow *each other*
-support.sortDetached = assert(function( el ) {
- // Should return 1, but returns 4 (following)
- return el.compareDocumentPosition( document.createElement("fieldset") ) & 1;
-});
-
-// Support: IE<8
-// Prevent attribute/property "interpolation"
-// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !assert(function( el ) {
- el.innerHTML = " to avoid XSS via location.hash (#9521)
- // Strict HTML recognition (#11290: must start with <)
- // Shortcut simple #id case for speed
- rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/,
-
- init = jQuery.fn.init = function( selector, context, root ) {
- var match, elem;
-
- // HANDLE: $(""), $(null), $(undefined), $(false)
- if ( !selector ) {
- return this;
- }
-
- // Method init() accepts an alternate rootjQuery
- // so migrate can support jQuery.sub (gh-2101)
- root = root || rootjQuery;
-
- // Handle HTML strings
- if ( typeof selector === "string" ) {
- if ( selector[ 0 ] === "<" &&
- selector[ selector.length - 1 ] === ">" &&
- selector.length >= 3 ) {
-
- // Assume that strings that start and end with <> are HTML and skip the regex check
- match = [ null, selector, null ];
-
- } else {
- match = rquickExpr.exec( selector );
- }
-
- // Match html or make sure no context is specified for #id
- if ( match && ( match[ 1 ] || !context ) ) {
-
- // HANDLE: $(html) -> $(array)
- if ( match[ 1 ] ) {
- context = context instanceof jQuery ? context[ 0 ] : context;
-
- // Option to run scripts is true for back-compat
- // Intentionally let the error be thrown if parseHTML is not present
- jQuery.merge( this, jQuery.parseHTML(
- match[ 1 ],
- context && context.nodeType ? context.ownerDocument || context : document,
- true
- ) );
-
- // HANDLE: $(html, props)
- if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) {
- for ( match in context ) {
-
- // Properties of context are called as methods if possible
- if ( jQuery.isFunction( this[ match ] ) ) {
- this[ match ]( context[ match ] );
-
- // ...and otherwise set as attributes
- } else {
- this.attr( match, context[ match ] );
- }
- }
- }
-
- return this;
-
- // HANDLE: $(#id)
- } else {
- elem = document.getElementById( match[ 2 ] );
-
- if ( elem ) {
-
- // Inject the element directly into the jQuery object
- this[ 0 ] = elem;
- this.length = 1;
- }
- return this;
- }
-
- // HANDLE: $(expr, $(...))
- } else if ( !context || context.jquery ) {
- return ( context || root ).find( selector );
-
- // HANDLE: $(expr, context)
- // (which is just equivalent to: $(context).find(expr)
- } else {
- return this.constructor( context ).find( selector );
- }
-
- // HANDLE: $(DOMElement)
- } else if ( selector.nodeType ) {
- this[ 0 ] = selector;
- this.length = 1;
- return this;
-
- // HANDLE: $(function)
- // Shortcut for document ready
- } else if ( jQuery.isFunction( selector ) ) {
- return root.ready !== undefined ?
- root.ready( selector ) :
-
- // Execute immediately if ready is not present
- selector( jQuery );
- }
-
- return jQuery.makeArray( selector, this );
- };
-
-// Give the init function the jQuery prototype for later instantiation
-init.prototype = jQuery.fn;
-
-// Initialize central reference
-rootjQuery = jQuery( document );
-
-
-var rparentsprev = /^(?:parents|prev(?:Until|All))/,
-
- // Methods guaranteed to produce a unique set when starting from a unique set
- guaranteedUnique = {
- children: true,
- contents: true,
- next: true,
- prev: true
- };
-
-jQuery.fn.extend( {
- has: function( target ) {
- var targets = jQuery( target, this ),
- l = targets.length;
-
- return this.filter( function() {
- var i = 0;
- for ( ; i < l; i++ ) {
- if ( jQuery.contains( this, targets[ i ] ) ) {
- return true;
- }
- }
- } );
- },
-
- closest: function( selectors, context ) {
- var cur,
- i = 0,
- l = this.length,
- matched = [],
- targets = typeof selectors !== "string" && jQuery( selectors );
-
- // Positional selectors never match, since there's no _selection_ context
- if ( !rneedsContext.test( selectors ) ) {
- for ( ; i < l; i++ ) {
- for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) {
-
- // Always skip document fragments
- if ( cur.nodeType < 11 && ( targets ?
- targets.index( cur ) > -1 :
-
- // Don't pass non-elements to Sizzle
- cur.nodeType === 1 &&
- jQuery.find.matchesSelector( cur, selectors ) ) ) {
-
- matched.push( cur );
- break;
- }
- }
- }
- }
-
- return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched );
- },
-
- // Determine the position of an element within the set
- index: function( elem ) {
-
- // No argument, return index in parent
- if ( !elem ) {
- return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1;
- }
-
- // Index in selector
- if ( typeof elem === "string" ) {
- return indexOf.call( jQuery( elem ), this[ 0 ] );
- }
-
- // Locate the position of the desired element
- return indexOf.call( this,
-
- // If it receives a jQuery object, the first element is used
- elem.jquery ? elem[ 0 ] : elem
- );
- },
-
- add: function( selector, context ) {
- return this.pushStack(
- jQuery.uniqueSort(
- jQuery.merge( this.get(), jQuery( selector, context ) )
- )
- );
- },
-
- addBack: function( selector ) {
- return this.add( selector == null ?
- this.prevObject : this.prevObject.filter( selector )
- );
- }
-} );
-
-function sibling( cur, dir ) {
- while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {}
- return cur;
-}
-
-jQuery.each( {
- parent: function( elem ) {
- var parent = elem.parentNode;
- return parent && parent.nodeType !== 11 ? parent : null;
- },
- parents: function( elem ) {
- return dir( elem, "parentNode" );
- },
- parentsUntil: function( elem, i, until ) {
- return dir( elem, "parentNode", until );
- },
- next: function( elem ) {
- return sibling( elem, "nextSibling" );
- },
- prev: function( elem ) {
- return sibling( elem, "previousSibling" );
- },
- nextAll: function( elem ) {
- return dir( elem, "nextSibling" );
- },
- prevAll: function( elem ) {
- return dir( elem, "previousSibling" );
- },
- nextUntil: function( elem, i, until ) {
- return dir( elem, "nextSibling", until );
- },
- prevUntil: function( elem, i, until ) {
- return dir( elem, "previousSibling", until );
- },
- siblings: function( elem ) {
- return siblings( ( elem.parentNode || {} ).firstChild, elem );
- },
- children: function( elem ) {
- return siblings( elem.firstChild );
- },
- contents: function( elem ) {
- if ( nodeName( elem, "iframe" ) ) {
- return elem.contentDocument;
- }
-
- // Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only
- // Treat the template element as a regular one in browsers that
- // don't support it.
- if ( nodeName( elem, "template" ) ) {
- elem = elem.content || elem;
- }
-
- return jQuery.merge( [], elem.childNodes );
- }
-}, function( name, fn ) {
- jQuery.fn[ name ] = function( until, selector ) {
- var matched = jQuery.map( this, fn, until );
-
- if ( name.slice( -5 ) !== "Until" ) {
- selector = until;
- }
-
- if ( selector && typeof selector === "string" ) {
- matched = jQuery.filter( selector, matched );
- }
-
- if ( this.length > 1 ) {
-
- // Remove duplicates
- if ( !guaranteedUnique[ name ] ) {
- jQuery.uniqueSort( matched );
- }
-
- // Reverse order for parents* and prev-derivatives
- if ( rparentsprev.test( name ) ) {
- matched.reverse();
- }
- }
-
- return this.pushStack( matched );
- };
-} );
-var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g );
-
-
-
-// Convert String-formatted options into Object-formatted ones
-function createOptions( options ) {
- var object = {};
- jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) {
- object[ flag ] = true;
- } );
- return object;
-}
-
-/*
- * Create a callback list using the following parameters:
- *
- * options: an optional list of space-separated options that will change how
- * the callback list behaves or a more traditional option object
- *
- * By default a callback list will act like an event callback list and can be
- * "fired" multiple times.
- *
- * Possible options:
- *
- * once: will ensure the callback list can only be fired once (like a Deferred)
- *
- * memory: will keep track of previous values and will call any callback added
- * after the list has been fired right away with the latest "memorized"
- * values (like a Deferred)
- *
- * unique: will ensure a callback can only be added once (no duplicate in the list)
- *
- * stopOnFalse: interrupt callings when a callback returns false
- *
- */
-jQuery.Callbacks = function( options ) {
-
- // Convert options from String-formatted to Object-formatted if needed
- // (we check in cache first)
- options = typeof options === "string" ?
- createOptions( options ) :
- jQuery.extend( {}, options );
-
- var // Flag to know if list is currently firing
- firing,
-
- // Last fire value for non-forgettable lists
- memory,
-
- // Flag to know if list was already fired
- fired,
-
- // Flag to prevent firing
- locked,
-
- // Actual callback list
- list = [],
-
- // Queue of execution data for repeatable lists
- queue = [],
-
- // Index of currently firing callback (modified by add/remove as needed)
- firingIndex = -1,
-
- // Fire callbacks
- fire = function() {
-
- // Enforce single-firing
- locked = locked || options.once;
-
- // Execute callbacks for all pending executions,
- // respecting firingIndex overrides and runtime changes
- fired = firing = true;
- for ( ; queue.length; firingIndex = -1 ) {
- memory = queue.shift();
- while ( ++firingIndex < list.length ) {
-
- // Run callback and check for early termination
- if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false &&
- options.stopOnFalse ) {
-
- // Jump to end and forget the data so .add doesn't re-fire
- firingIndex = list.length;
- memory = false;
- }
- }
- }
-
- // Forget the data if we're done with it
- if ( !options.memory ) {
- memory = false;
- }
-
- firing = false;
-
- // Clean up if we're done firing for good
- if ( locked ) {
-
- // Keep an empty list if we have data for future add calls
- if ( memory ) {
- list = [];
-
- // Otherwise, this object is spent
- } else {
- list = "";
- }
- }
- },
-
- // Actual Callbacks object
- self = {
-
- // Add a callback or a collection of callbacks to the list
- add: function() {
- if ( list ) {
-
- // If we have memory from a past run, we should fire after adding
- if ( memory && !firing ) {
- firingIndex = list.length - 1;
- queue.push( memory );
- }
-
- ( function add( args ) {
- jQuery.each( args, function( _, arg ) {
- if ( jQuery.isFunction( arg ) ) {
- if ( !options.unique || !self.has( arg ) ) {
- list.push( arg );
- }
- } else if ( arg && arg.length && jQuery.type( arg ) !== "string" ) {
-
- // Inspect recursively
- add( arg );
- }
- } );
- } )( arguments );
-
- if ( memory && !firing ) {
- fire();
- }
- }
- return this;
- },
-
- // Remove a callback from the list
- remove: function() {
- jQuery.each( arguments, function( _, arg ) {
- var index;
- while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
- list.splice( index, 1 );
-
- // Handle firing indexes
- if ( index <= firingIndex ) {
- firingIndex--;
- }
- }
- } );
- return this;
- },
-
- // Check if a given callback is in the list.
- // If no argument is given, return whether or not list has callbacks attached.
- has: function( fn ) {
- return fn ?
- jQuery.inArray( fn, list ) > -1 :
- list.length > 0;
- },
-
- // Remove all callbacks from the list
- empty: function() {
- if ( list ) {
- list = [];
- }
- return this;
- },
-
- // Disable .fire and .add
- // Abort any current/pending executions
- // Clear all callbacks and values
- disable: function() {
- locked = queue = [];
- list = memory = "";
- return this;
- },
- disabled: function() {
- return !list;
- },
-
- // Disable .fire
- // Also disable .add unless we have memory (since it would have no effect)
- // Abort any pending executions
- lock: function() {
- locked = queue = [];
- if ( !memory && !firing ) {
- list = memory = "";
- }
- return this;
- },
- locked: function() {
- return !!locked;
- },
-
- // Call all callbacks with the given context and arguments
- fireWith: function( context, args ) {
- if ( !locked ) {
- args = args || [];
- args = [ context, args.slice ? args.slice() : args ];
- queue.push( args );
- if ( !firing ) {
- fire();
- }
- }
- return this;
- },
-
- // Call all the callbacks with the given arguments
- fire: function() {
- self.fireWith( this, arguments );
- return this;
- },
-
- // To know if the callbacks have already been called at least once
- fired: function() {
- return !!fired;
- }
- };
-
- return self;
-};
-
-
-function Identity( v ) {
- return v;
-}
-function Thrower( ex ) {
- throw ex;
-}
-
-function adoptValue( value, resolve, reject, noValue ) {
- var method;
-
- try {
-
- // Check for promise aspect first to privilege synchronous behavior
- if ( value && jQuery.isFunction( ( method = value.promise ) ) ) {
- method.call( value ).done( resolve ).fail( reject );
-
- // Other thenables
- } else if ( value && jQuery.isFunction( ( method = value.then ) ) ) {
- method.call( value, resolve, reject );
-
- // Other non-thenables
- } else {
-
- // Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer:
- // * false: [ value ].slice( 0 ) => resolve( value )
- // * true: [ value ].slice( 1 ) => resolve()
- resolve.apply( undefined, [ value ].slice( noValue ) );
- }
-
- // For Promises/A+, convert exceptions into rejections
- // Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in
- // Deferred#then to conditionally suppress rejection.
- } catch ( value ) {
-
- // Support: Android 4.0 only
- // Strict mode functions invoked without .call/.apply get global-object context
- reject.apply( undefined, [ value ] );
- }
-}
-
-jQuery.extend( {
-
- Deferred: function( func ) {
- var tuples = [
-
- // action, add listener, callbacks,
- // ... .then handlers, argument index, [final state]
- [ "notify", "progress", jQuery.Callbacks( "memory" ),
- jQuery.Callbacks( "memory" ), 2 ],
- [ "resolve", "done", jQuery.Callbacks( "once memory" ),
- jQuery.Callbacks( "once memory" ), 0, "resolved" ],
- [ "reject", "fail", jQuery.Callbacks( "once memory" ),
- jQuery.Callbacks( "once memory" ), 1, "rejected" ]
- ],
- state = "pending",
- promise = {
- state: function() {
- return state;
- },
- always: function() {
- deferred.done( arguments ).fail( arguments );
- return this;
- },
- "catch": function( fn ) {
- return promise.then( null, fn );
- },
-
- // Keep pipe for back-compat
- pipe: function( /* fnDone, fnFail, fnProgress */ ) {
- var fns = arguments;
-
- return jQuery.Deferred( function( newDefer ) {
- jQuery.each( tuples, function( i, tuple ) {
-
- // Map tuples (progress, done, fail) to arguments (done, fail, progress)
- var fn = jQuery.isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ];
-
- // deferred.progress(function() { bind to newDefer or newDefer.notify })
- // deferred.done(function() { bind to newDefer or newDefer.resolve })
- // deferred.fail(function() { bind to newDefer or newDefer.reject })
- deferred[ tuple[ 1 ] ]( function() {
- var returned = fn && fn.apply( this, arguments );
- if ( returned && jQuery.isFunction( returned.promise ) ) {
- returned.promise()
- .progress( newDefer.notify )
- .done( newDefer.resolve )
- .fail( newDefer.reject );
- } else {
- newDefer[ tuple[ 0 ] + "With" ](
- this,
- fn ? [ returned ] : arguments
- );
- }
- } );
- } );
- fns = null;
- } ).promise();
- },
- then: function( onFulfilled, onRejected, onProgress ) {
- var maxDepth = 0;
- function resolve( depth, deferred, handler, special ) {
- return function() {
- var that = this,
- args = arguments,
- mightThrow = function() {
- var returned, then;
-
- // Support: Promises/A+ section 2.3.3.3.3
- // https://promisesaplus.com/#point-59
- // Ignore double-resolution attempts
- if ( depth < maxDepth ) {
- return;
- }
-
- returned = handler.apply( that, args );
-
- // Support: Promises/A+ section 2.3.1
- // https://promisesaplus.com/#point-48
- if ( returned === deferred.promise() ) {
- throw new TypeError( "Thenable self-resolution" );
- }
-
- // Support: Promises/A+ sections 2.3.3.1, 3.5
- // https://promisesaplus.com/#point-54
- // https://promisesaplus.com/#point-75
- // Retrieve `then` only once
- then = returned &&
-
- // Support: Promises/A+ section 2.3.4
- // https://promisesaplus.com/#point-64
- // Only check objects and functions for thenability
- ( typeof returned === "object" ||
- typeof returned === "function" ) &&
- returned.then;
-
- // Handle a returned thenable
- if ( jQuery.isFunction( then ) ) {
-
- // Special processors (notify) just wait for resolution
- if ( special ) {
- then.call(
- returned,
- resolve( maxDepth, deferred, Identity, special ),
- resolve( maxDepth, deferred, Thrower, special )
- );
-
- // Normal processors (resolve) also hook into progress
- } else {
-
- // ...and disregard older resolution values
- maxDepth++;
-
- then.call(
- returned,
- resolve( maxDepth, deferred, Identity, special ),
- resolve( maxDepth, deferred, Thrower, special ),
- resolve( maxDepth, deferred, Identity,
- deferred.notifyWith )
- );
- }
-
- // Handle all other returned values
- } else {
-
- // Only substitute handlers pass on context
- // and multiple values (non-spec behavior)
- if ( handler !== Identity ) {
- that = undefined;
- args = [ returned ];
- }
-
- // Process the value(s)
- // Default process is resolve
- ( special || deferred.resolveWith )( that, args );
- }
- },
-
- // Only normal processors (resolve) catch and reject exceptions
- process = special ?
- mightThrow :
- function() {
- try {
- mightThrow();
- } catch ( e ) {
-
- if ( jQuery.Deferred.exceptionHook ) {
- jQuery.Deferred.exceptionHook( e,
- process.stackTrace );
- }
-
- // Support: Promises/A+ section 2.3.3.3.4.1
- // https://promisesaplus.com/#point-61
- // Ignore post-resolution exceptions
- if ( depth + 1 >= maxDepth ) {
-
- // Only substitute handlers pass on context
- // and multiple values (non-spec behavior)
- if ( handler !== Thrower ) {
- that = undefined;
- args = [ e ];
- }
-
- deferred.rejectWith( that, args );
- }
- }
- };
-
- // Support: Promises/A+ section 2.3.3.3.1
- // https://promisesaplus.com/#point-57
- // Re-resolve promises immediately to dodge false rejection from
- // subsequent errors
- if ( depth ) {
- process();
- } else {
-
- // Call an optional hook to record the stack, in case of exception
- // since it's otherwise lost when execution goes async
- if ( jQuery.Deferred.getStackHook ) {
- process.stackTrace = jQuery.Deferred.getStackHook();
- }
- window.setTimeout( process );
- }
- };
- }
-
- return jQuery.Deferred( function( newDefer ) {
-
- // progress_handlers.add( ... )
- tuples[ 0 ][ 3 ].add(
- resolve(
- 0,
- newDefer,
- jQuery.isFunction( onProgress ) ?
- onProgress :
- Identity,
- newDefer.notifyWith
- )
- );
-
- // fulfilled_handlers.add( ... )
- tuples[ 1 ][ 3 ].add(
- resolve(
- 0,
- newDefer,
- jQuery.isFunction( onFulfilled ) ?
- onFulfilled :
- Identity
- )
- );
-
- // rejected_handlers.add( ... )
- tuples[ 2 ][ 3 ].add(
- resolve(
- 0,
- newDefer,
- jQuery.isFunction( onRejected ) ?
- onRejected :
- Thrower
- )
- );
- } ).promise();
- },
-
- // Get a promise for this deferred
- // If obj is provided, the promise aspect is added to the object
- promise: function( obj ) {
- return obj != null ? jQuery.extend( obj, promise ) : promise;
- }
- },
- deferred = {};
-
- // Add list-specific methods
- jQuery.each( tuples, function( i, tuple ) {
- var list = tuple[ 2 ],
- stateString = tuple[ 5 ];
-
- // promise.progress = list.add
- // promise.done = list.add
- // promise.fail = list.add
- promise[ tuple[ 1 ] ] = list.add;
-
- // Handle state
- if ( stateString ) {
- list.add(
- function() {
-
- // state = "resolved" (i.e., fulfilled)
- // state = "rejected"
- state = stateString;
- },
-
- // rejected_callbacks.disable
- // fulfilled_callbacks.disable
- tuples[ 3 - i ][ 2 ].disable,
-
- // progress_callbacks.lock
- tuples[ 0 ][ 2 ].lock
- );
- }
-
- // progress_handlers.fire
- // fulfilled_handlers.fire
- // rejected_handlers.fire
- list.add( tuple[ 3 ].fire );
-
- // deferred.notify = function() { deferred.notifyWith(...) }
- // deferred.resolve = function() { deferred.resolveWith(...) }
- // deferred.reject = function() { deferred.rejectWith(...) }
- deferred[ tuple[ 0 ] ] = function() {
- deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments );
- return this;
- };
-
- // deferred.notifyWith = list.fireWith
- // deferred.resolveWith = list.fireWith
- // deferred.rejectWith = list.fireWith
- deferred[ tuple[ 0 ] + "With" ] = list.fireWith;
- } );
-
- // Make the deferred a promise
- promise.promise( deferred );
-
- // Call given func if any
- if ( func ) {
- func.call( deferred, deferred );
- }
-
- // All done!
- return deferred;
- },
-
- // Deferred helper
- when: function( singleValue ) {
- var
-
- // count of uncompleted subordinates
- remaining = arguments.length,
-
- // count of unprocessed arguments
- i = remaining,
-
- // subordinate fulfillment data
- resolveContexts = Array( i ),
- resolveValues = slice.call( arguments ),
-
- // the master Deferred
- master = jQuery.Deferred(),
-
- // subordinate callback factory
- updateFunc = function( i ) {
- return function( value ) {
- resolveContexts[ i ] = this;
- resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
- if ( !( --remaining ) ) {
- master.resolveWith( resolveContexts, resolveValues );
- }
- };
- };
-
- // Single- and empty arguments are adopted like Promise.resolve
- if ( remaining <= 1 ) {
- adoptValue( singleValue, master.done( updateFunc( i ) ).resolve, master.reject,
- !remaining );
-
- // Use .then() to unwrap secondary thenables (cf. gh-3000)
- if ( master.state() === "pending" ||
- jQuery.isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) {
-
- return master.then();
- }
- }
-
- // Multiple arguments are aggregated like Promise.all array elements
- while ( i-- ) {
- adoptValue( resolveValues[ i ], updateFunc( i ), master.reject );
- }
-
- return master.promise();
- }
-} );
-
-
-// These usually indicate a programmer mistake during development,
-// warn about them ASAP rather than swallowing them by default.
-var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/;
-
-jQuery.Deferred.exceptionHook = function( error, stack ) {
-
- // Support: IE 8 - 9 only
- // Console exists when dev tools are open, which can happen at any time
- if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) {
- window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack );
- }
-};
-
-
-
-
-jQuery.readyException = function( error ) {
- window.setTimeout( function() {
- throw error;
- } );
-};
-
-
-
-
-// The deferred used on DOM ready
-var readyList = jQuery.Deferred();
-
-jQuery.fn.ready = function( fn ) {
-
- readyList
- .then( fn )
-
- // Wrap jQuery.readyException in a function so that the lookup
- // happens at the time of error handling instead of callback
- // registration.
- .catch( function( error ) {
- jQuery.readyException( error );
- } );
-
- return this;
-};
-
-jQuery.extend( {
-
- // Is the DOM ready to be used? Set to true once it occurs.
- isReady: false,
-
- // A counter to track how many items to wait for before
- // the ready event fires. See #6781
- readyWait: 1,
-
- // Handle when the DOM is ready
- ready: function( wait ) {
-
- // Abort if there are pending holds or we're already ready
- if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
- return;
- }
-
- // Remember that the DOM is ready
- jQuery.isReady = true;
-
- // If a normal DOM Ready event fired, decrement, and wait if need be
- if ( wait !== true && --jQuery.readyWait > 0 ) {
- return;
- }
-
- // If there are functions bound, to execute
- readyList.resolveWith( document, [ jQuery ] );
- }
-} );
-
-jQuery.ready.then = readyList.then;
-
-// The ready event handler and self cleanup method
-function completed() {
- document.removeEventListener( "DOMContentLoaded", completed );
- window.removeEventListener( "load", completed );
- jQuery.ready();
-}
-
-// Catch cases where $(document).ready() is called
-// after the browser event has already occurred.
-// Support: IE <=9 - 10 only
-// Older IE sometimes signals "interactive" too soon
-if ( document.readyState === "complete" ||
- ( document.readyState !== "loading" && !document.documentElement.doScroll ) ) {
-
- // Handle it asynchronously to allow scripts the opportunity to delay ready
- window.setTimeout( jQuery.ready );
-
-} else {
-
- // Use the handy event callback
- document.addEventListener( "DOMContentLoaded", completed );
-
- // A fallback to window.onload, that will always work
- window.addEventListener( "load", completed );
-}
-
-
-
-
-// Multifunctional method to get and set values of a collection
-// The value/s can optionally be executed if it's a function
-var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
- var i = 0,
- len = elems.length,
- bulk = key == null;
-
- // Sets many values
- if ( jQuery.type( key ) === "object" ) {
- chainable = true;
- for ( i in key ) {
- access( elems, fn, i, key[ i ], true, emptyGet, raw );
- }
-
- // Sets one value
- } else if ( value !== undefined ) {
- chainable = true;
-
- if ( !jQuery.isFunction( value ) ) {
- raw = true;
- }
-
- if ( bulk ) {
-
- // Bulk operations run against the entire set
- if ( raw ) {
- fn.call( elems, value );
- fn = null;
-
- // ...except when executing function values
- } else {
- bulk = fn;
- fn = function( elem, key, value ) {
- return bulk.call( jQuery( elem ), value );
- };
- }
- }
-
- if ( fn ) {
- for ( ; i < len; i++ ) {
- fn(
- elems[ i ], key, raw ?
- value :
- value.call( elems[ i ], i, fn( elems[ i ], key ) )
- );
- }
- }
- }
-
- if ( chainable ) {
- return elems;
- }
-
- // Gets
- if ( bulk ) {
- return fn.call( elems );
- }
-
- return len ? fn( elems[ 0 ], key ) : emptyGet;
-};
-var acceptData = function( owner ) {
-
- // Accepts only:
- // - Node
- // - Node.ELEMENT_NODE
- // - Node.DOCUMENT_NODE
- // - Object
- // - Any
- return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType );
-};
-
-
-
-
-function Data() {
- this.expando = jQuery.expando + Data.uid++;
-}
-
-Data.uid = 1;
-
-Data.prototype = {
-
- cache: function( owner ) {
-
- // Check if the owner object already has a cache
- var value = owner[ this.expando ];
-
- // If not, create one
- if ( !value ) {
- value = {};
-
- // We can accept data for non-element nodes in modern browsers,
- // but we should not, see #8335.
- // Always return an empty object.
- if ( acceptData( owner ) ) {
-
- // If it is a node unlikely to be stringify-ed or looped over
- // use plain assignment
- if ( owner.nodeType ) {
- owner[ this.expando ] = value;
-
- // Otherwise secure it in a non-enumerable property
- // configurable must be true to allow the property to be
- // deleted when data is removed
- } else {
- Object.defineProperty( owner, this.expando, {
- value: value,
- configurable: true
- } );
- }
- }
- }
-
- return value;
- },
- set: function( owner, data, value ) {
- var prop,
- cache = this.cache( owner );
-
- // Handle: [ owner, key, value ] args
- // Always use camelCase key (gh-2257)
- if ( typeof data === "string" ) {
- cache[ jQuery.camelCase( data ) ] = value;
-
- // Handle: [ owner, { properties } ] args
- } else {
-
- // Copy the properties one-by-one to the cache object
- for ( prop in data ) {
- cache[ jQuery.camelCase( prop ) ] = data[ prop ];
- }
- }
- return cache;
- },
- get: function( owner, key ) {
- return key === undefined ?
- this.cache( owner ) :
-
- // Always use camelCase key (gh-2257)
- owner[ this.expando ] && owner[ this.expando ][ jQuery.camelCase( key ) ];
- },
- access: function( owner, key, value ) {
-
- // In cases where either:
- //
- // 1. No key was specified
- // 2. A string key was specified, but no value provided
- //
- // Take the "read" path and allow the get method to determine
- // which value to return, respectively either:
- //
- // 1. The entire cache object
- // 2. The data stored at the key
- //
- if ( key === undefined ||
- ( ( key && typeof key === "string" ) && value === undefined ) ) {
-
- return this.get( owner, key );
- }
-
- // When the key is not a string, or both a key and value
- // are specified, set or extend (existing objects) with either:
- //
- // 1. An object of properties
- // 2. A key and value
- //
- this.set( owner, key, value );
-
- // Since the "set" path can have two possible entry points
- // return the expected data based on which path was taken[*]
- return value !== undefined ? value : key;
- },
- remove: function( owner, key ) {
- var i,
- cache = owner[ this.expando ];
-
- if ( cache === undefined ) {
- return;
- }
-
- if ( key !== undefined ) {
-
- // Support array or space separated string of keys
- if ( Array.isArray( key ) ) {
-
- // If key is an array of keys...
- // We always set camelCase keys, so remove that.
- key = key.map( jQuery.camelCase );
- } else {
- key = jQuery.camelCase( key );
-
- // If a key with the spaces exists, use it.
- // Otherwise, create an array by matching non-whitespace
- key = key in cache ?
- [ key ] :
- ( key.match( rnothtmlwhite ) || [] );
- }
-
- i = key.length;
-
- while ( i-- ) {
- delete cache[ key[ i ] ];
- }
- }
-
- // Remove the expando if there's no more data
- if ( key === undefined || jQuery.isEmptyObject( cache ) ) {
-
- // Support: Chrome <=35 - 45
- // Webkit & Blink performance suffers when deleting properties
- // from DOM nodes, so set to undefined instead
- // https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted)
- if ( owner.nodeType ) {
- owner[ this.expando ] = undefined;
- } else {
- delete owner[ this.expando ];
- }
- }
- },
- hasData: function( owner ) {
- var cache = owner[ this.expando ];
- return cache !== undefined && !jQuery.isEmptyObject( cache );
- }
-};
-var dataPriv = new Data();
-
-var dataUser = new Data();
-
-
-
-// Implementation Summary
-//
-// 1. Enforce API surface and semantic compatibility with 1.9.x branch
-// 2. Improve the module's maintainability by reducing the storage
-// paths to a single mechanism.
-// 3. Use the same single mechanism to support "private" and "user" data.
-// 4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData)
-// 5. Avoid exposing implementation details on user objects (eg. expando properties)
-// 6. Provide a clear path for implementation upgrade to WeakMap in 2014
-
-var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
- rmultiDash = /[A-Z]/g;
-
-function getData( data ) {
- if ( data === "true" ) {
- return true;
- }
-
- if ( data === "false" ) {
- return false;
- }
-
- if ( data === "null" ) {
- return null;
- }
-
- // Only convert to a number if it doesn't change the string
- if ( data === +data + "" ) {
- return +data;
- }
-
- if ( rbrace.test( data ) ) {
- return JSON.parse( data );
- }
-
- return data;
-}
-
-function dataAttr( elem, key, data ) {
- var name;
-
- // If nothing was found internally, try to fetch any
- // data from the HTML5 data-* attribute
- if ( data === undefined && elem.nodeType === 1 ) {
- name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase();
- data = elem.getAttribute( name );
-
- if ( typeof data === "string" ) {
- try {
- data = getData( data );
- } catch ( e ) {}
-
- // Make sure we set the data so it isn't changed later
- dataUser.set( elem, key, data );
- } else {
- data = undefined;
- }
- }
- return data;
-}
-
-jQuery.extend( {
- hasData: function( elem ) {
- return dataUser.hasData( elem ) || dataPriv.hasData( elem );
- },
-
- data: function( elem, name, data ) {
- return dataUser.access( elem, name, data );
- },
-
- removeData: function( elem, name ) {
- dataUser.remove( elem, name );
- },
-
- // TODO: Now that all calls to _data and _removeData have been replaced
- // with direct calls to dataPriv methods, these can be deprecated.
- _data: function( elem, name, data ) {
- return dataPriv.access( elem, name, data );
- },
-
- _removeData: function( elem, name ) {
- dataPriv.remove( elem, name );
- }
-} );
-
-jQuery.fn.extend( {
- data: function( key, value ) {
- var i, name, data,
- elem = this[ 0 ],
- attrs = elem && elem.attributes;
-
- // Gets all values
- if ( key === undefined ) {
- if ( this.length ) {
- data = dataUser.get( elem );
-
- if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) {
- i = attrs.length;
- while ( i-- ) {
-
- // Support: IE 11 only
- // The attrs elements can be null (#14894)
- if ( attrs[ i ] ) {
- name = attrs[ i ].name;
- if ( name.indexOf( "data-" ) === 0 ) {
- name = jQuery.camelCase( name.slice( 5 ) );
- dataAttr( elem, name, data[ name ] );
- }
- }
- }
- dataPriv.set( elem, "hasDataAttrs", true );
- }
- }
-
- return data;
- }
-
- // Sets multiple values
- if ( typeof key === "object" ) {
- return this.each( function() {
- dataUser.set( this, key );
- } );
- }
-
- return access( this, function( value ) {
- var data;
-
- // The calling jQuery object (element matches) is not empty
- // (and therefore has an element appears at this[ 0 ]) and the
- // `value` parameter was not undefined. An empty jQuery object
- // will result in `undefined` for elem = this[ 0 ] which will
- // throw an exception if an attempt to read a data cache is made.
- if ( elem && value === undefined ) {
-
- // Attempt to get data from the cache
- // The key will always be camelCased in Data
- data = dataUser.get( elem, key );
- if ( data !== undefined ) {
- return data;
- }
-
- // Attempt to "discover" the data in
- // HTML5 custom data-* attrs
- data = dataAttr( elem, key );
- if ( data !== undefined ) {
- return data;
- }
-
- // We tried really hard, but the data doesn't exist.
- return;
- }
-
- // Set the data...
- this.each( function() {
-
- // We always store the camelCased key
- dataUser.set( this, key, value );
- } );
- }, null, value, arguments.length > 1, null, true );
- },
-
- removeData: function( key ) {
- return this.each( function() {
- dataUser.remove( this, key );
- } );
- }
-} );
-
-
-jQuery.extend( {
- queue: function( elem, type, data ) {
- var queue;
-
- if ( elem ) {
- type = ( type || "fx" ) + "queue";
- queue = dataPriv.get( elem, type );
-
- // Speed up dequeue by getting out quickly if this is just a lookup
- if ( data ) {
- if ( !queue || Array.isArray( data ) ) {
- queue = dataPriv.access( elem, type, jQuery.makeArray( data ) );
- } else {
- queue.push( data );
- }
- }
- return queue || [];
- }
- },
-
- dequeue: function( elem, type ) {
- type = type || "fx";
-
- var queue = jQuery.queue( elem, type ),
- startLength = queue.length,
- fn = queue.shift(),
- hooks = jQuery._queueHooks( elem, type ),
- next = function() {
- jQuery.dequeue( elem, type );
- };
-
- // If the fx queue is dequeued, always remove the progress sentinel
- if ( fn === "inprogress" ) {
- fn = queue.shift();
- startLength--;
- }
-
- if ( fn ) {
-
- // Add a progress sentinel to prevent the fx queue from being
- // automatically dequeued
- if ( type === "fx" ) {
- queue.unshift( "inprogress" );
- }
-
- // Clear up the last queue stop function
- delete hooks.stop;
- fn.call( elem, next, hooks );
- }
-
- if ( !startLength && hooks ) {
- hooks.empty.fire();
- }
- },
-
- // Not public - generate a queueHooks object, or return the current one
- _queueHooks: function( elem, type ) {
- var key = type + "queueHooks";
- return dataPriv.get( elem, key ) || dataPriv.access( elem, key, {
- empty: jQuery.Callbacks( "once memory" ).add( function() {
- dataPriv.remove( elem, [ type + "queue", key ] );
- } )
- } );
- }
-} );
-
-jQuery.fn.extend( {
- queue: function( type, data ) {
- var setter = 2;
-
- if ( typeof type !== "string" ) {
- data = type;
- type = "fx";
- setter--;
- }
-
- if ( arguments.length < setter ) {
- return jQuery.queue( this[ 0 ], type );
- }
-
- return data === undefined ?
- this :
- this.each( function() {
- var queue = jQuery.queue( this, type, data );
-
- // Ensure a hooks for this queue
- jQuery._queueHooks( this, type );
-
- if ( type === "fx" && queue[ 0 ] !== "inprogress" ) {
- jQuery.dequeue( this, type );
- }
- } );
- },
- dequeue: function( type ) {
- return this.each( function() {
- jQuery.dequeue( this, type );
- } );
- },
- clearQueue: function( type ) {
- return this.queue( type || "fx", [] );
- },
-
- // Get a promise resolved when queues of a certain type
- // are emptied (fx is the type by default)
- promise: function( type, obj ) {
- var tmp,
- count = 1,
- defer = jQuery.Deferred(),
- elements = this,
- i = this.length,
- resolve = function() {
- if ( !( --count ) ) {
- defer.resolveWith( elements, [ elements ] );
- }
- };
-
- if ( typeof type !== "string" ) {
- obj = type;
- type = undefined;
- }
- type = type || "fx";
-
- while ( i-- ) {
- tmp = dataPriv.get( elements[ i ], type + "queueHooks" );
- if ( tmp && tmp.empty ) {
- count++;
- tmp.empty.add( resolve );
- }
- }
- resolve();
- return defer.promise( obj );
- }
-} );
-var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source;
-
-var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" );
-
-
-var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
-
-var isHiddenWithinTree = function( elem, el ) {
-
- // isHiddenWithinTree might be called from jQuery#filter function;
- // in that case, element will be second argument
- elem = el || elem;
-
- // Inline style trumps all
- return elem.style.display === "none" ||
- elem.style.display === "" &&
-
- // Otherwise, check computed style
- // Support: Firefox <=43 - 45
- // Disconnected elements can have computed display: none, so first confirm that elem is
- // in the document.
- jQuery.contains( elem.ownerDocument, elem ) &&
-
- jQuery.css( elem, "display" ) === "none";
- };
-
-var swap = function( elem, options, callback, args ) {
- var ret, name,
- old = {};
-
- // Remember the old values, and insert the new ones
- for ( name in options ) {
- old[ name ] = elem.style[ name ];
- elem.style[ name ] = options[ name ];
- }
-
- ret = callback.apply( elem, args || [] );
-
- // Revert the old values
- for ( name in options ) {
- elem.style[ name ] = old[ name ];
- }
-
- return ret;
-};
-
-
-
-
-function adjustCSS( elem, prop, valueParts, tween ) {
- var adjusted,
- scale = 1,
- maxIterations = 20,
- currentValue = tween ?
- function() {
- return tween.cur();
- } :
- function() {
- return jQuery.css( elem, prop, "" );
- },
- initial = currentValue(),
- unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
-
- // Starting value computation is required for potential unit mismatches
- initialInUnit = ( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) &&
- rcssNum.exec( jQuery.css( elem, prop ) );
-
- if ( initialInUnit && initialInUnit[ 3 ] !== unit ) {
-
- // Trust units reported by jQuery.css
- unit = unit || initialInUnit[ 3 ];
-
- // Make sure we update the tween properties later on
- valueParts = valueParts || [];
-
- // Iteratively approximate from a nonzero starting point
- initialInUnit = +initial || 1;
-
- do {
-
- // If previous iteration zeroed out, double until we get *something*.
- // Use string for doubling so we don't accidentally see scale as unchanged below
- scale = scale || ".5";
-
- // Adjust and apply
- initialInUnit = initialInUnit / scale;
- jQuery.style( elem, prop, initialInUnit + unit );
-
- // Update scale, tolerating zero or NaN from tween.cur()
- // Break the loop if scale is unchanged or perfect, or if we've just had enough.
- } while (
- scale !== ( scale = currentValue() / initial ) && scale !== 1 && --maxIterations
- );
- }
-
- if ( valueParts ) {
- initialInUnit = +initialInUnit || +initial || 0;
-
- // Apply relative offset (+=/-=) if specified
- adjusted = valueParts[ 1 ] ?
- initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] :
- +valueParts[ 2 ];
- if ( tween ) {
- tween.unit = unit;
- tween.start = initialInUnit;
- tween.end = adjusted;
- }
- }
- return adjusted;
-}
-
-
-var defaultDisplayMap = {};
-
-function getDefaultDisplay( elem ) {
- var temp,
- doc = elem.ownerDocument,
- nodeName = elem.nodeName,
- display = defaultDisplayMap[ nodeName ];
-
- if ( display ) {
- return display;
- }
-
- temp = doc.body.appendChild( doc.createElement( nodeName ) );
- display = jQuery.css( temp, "display" );
-
- temp.parentNode.removeChild( temp );
-
- if ( display === "none" ) {
- display = "block";
- }
- defaultDisplayMap[ nodeName ] = display;
-
- return display;
-}
-
-function showHide( elements, show ) {
- var display, elem,
- values = [],
- index = 0,
- length = elements.length;
-
- // Determine new display value for elements that need to change
- for ( ; index < length; index++ ) {
- elem = elements[ index ];
- if ( !elem.style ) {
- continue;
- }
-
- display = elem.style.display;
- if ( show ) {
-
- // Since we force visibility upon cascade-hidden elements, an immediate (and slow)
- // check is required in this first loop unless we have a nonempty display value (either
- // inline or about-to-be-restored)
- if ( display === "none" ) {
- values[ index ] = dataPriv.get( elem, "display" ) || null;
- if ( !values[ index ] ) {
- elem.style.display = "";
- }
- }
- if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) {
- values[ index ] = getDefaultDisplay( elem );
- }
- } else {
- if ( display !== "none" ) {
- values[ index ] = "none";
-
- // Remember what we're overwriting
- dataPriv.set( elem, "display", display );
- }
- }
- }
-
- // Set the display of the elements in a second loop to avoid constant reflow
- for ( index = 0; index < length; index++ ) {
- if ( values[ index ] != null ) {
- elements[ index ].style.display = values[ index ];
- }
- }
-
- return elements;
-}
-
-jQuery.fn.extend( {
- show: function() {
- return showHide( this, true );
- },
- hide: function() {
- return showHide( this );
- },
- toggle: function( state ) {
- if ( typeof state === "boolean" ) {
- return state ? this.show() : this.hide();
- }
-
- return this.each( function() {
- if ( isHiddenWithinTree( this ) ) {
- jQuery( this ).show();
- } else {
- jQuery( this ).hide();
- }
- } );
- }
-} );
-var rcheckableType = ( /^(?:checkbox|radio)$/i );
-
-var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]+)/i );
-
-var rscriptType = ( /^$|\/(?:java|ecma)script/i );
-
-
-
-// We have to close these tags to support XHTML (#13200)
-var wrapMap = {
-
- // Support: IE <=9 only
- option: [ 1, "", " " ],
-
- // XHTML parsers do not magically insert elements in the
- // same way that tag soup parsers do. So we cannot shorten
- // this by omitting or other required elements.
- thead: [ 1, "" ],
- col: [ 2, "" ],
- tr: [ 2, "" ],
- td: [ 3, "" ],
-
- _default: [ 0, "", "" ]
-};
-
-// Support: IE <=9 only
-wrapMap.optgroup = wrapMap.option;
-
-wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
-wrapMap.th = wrapMap.td;
-
-
-function getAll( context, tag ) {
-
- // Support: IE <=9 - 11 only
- // Use typeof to avoid zero-argument method invocation on host objects (#15151)
- var ret;
-
- if ( typeof context.getElementsByTagName !== "undefined" ) {
- ret = context.getElementsByTagName( tag || "*" );
-
- } else if ( typeof context.querySelectorAll !== "undefined" ) {
- ret = context.querySelectorAll( tag || "*" );
-
- } else {
- ret = [];
- }
-
- if ( tag === undefined || tag && nodeName( context, tag ) ) {
- return jQuery.merge( [ context ], ret );
- }
-
- return ret;
-}
-
-
-// Mark scripts as having already been evaluated
-function setGlobalEval( elems, refElements ) {
- var i = 0,
- l = elems.length;
-
- for ( ; i < l; i++ ) {
- dataPriv.set(
- elems[ i ],
- "globalEval",
- !refElements || dataPriv.get( refElements[ i ], "globalEval" )
- );
- }
-}
-
-
-var rhtml = /<|&#?\w+;/;
-
-function buildFragment( elems, context, scripts, selection, ignored ) {
- var elem, tmp, tag, wrap, contains, j,
- fragment = context.createDocumentFragment(),
- nodes = [],
- i = 0,
- l = elems.length;
-
- for ( ; i < l; i++ ) {
- elem = elems[ i ];
-
- if ( elem || elem === 0 ) {
-
- // Add nodes directly
- if ( jQuery.type( elem ) === "object" ) {
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
-
- // Convert non-html into a text node
- } else if ( !rhtml.test( elem ) ) {
- nodes.push( context.createTextNode( elem ) );
-
- // Convert html into DOM nodes
- } else {
- tmp = tmp || fragment.appendChild( context.createElement( "div" ) );
-
- // Deserialize a standard representation
- tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase();
- wrap = wrapMap[ tag ] || wrapMap._default;
- tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ];
-
- // Descend through wrappers to the right content
- j = wrap[ 0 ];
- while ( j-- ) {
- tmp = tmp.lastChild;
- }
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- jQuery.merge( nodes, tmp.childNodes );
-
- // Remember the top-level container
- tmp = fragment.firstChild;
-
- // Ensure the created nodes are orphaned (#12392)
- tmp.textContent = "";
- }
- }
- }
-
- // Remove wrapper from fragment
- fragment.textContent = "";
-
- i = 0;
- while ( ( elem = nodes[ i++ ] ) ) {
-
- // Skip elements already in the context collection (trac-4087)
- if ( selection && jQuery.inArray( elem, selection ) > -1 ) {
- if ( ignored ) {
- ignored.push( elem );
- }
- continue;
- }
-
- contains = jQuery.contains( elem.ownerDocument, elem );
-
- // Append to fragment
- tmp = getAll( fragment.appendChild( elem ), "script" );
-
- // Preserve script evaluation history
- if ( contains ) {
- setGlobalEval( tmp );
- }
-
- // Capture executables
- if ( scripts ) {
- j = 0;
- while ( ( elem = tmp[ j++ ] ) ) {
- if ( rscriptType.test( elem.type || "" ) ) {
- scripts.push( elem );
- }
- }
- }
- }
-
- return fragment;
-}
-
-
-( function() {
- var fragment = document.createDocumentFragment(),
- div = fragment.appendChild( document.createElement( "div" ) ),
- input = document.createElement( "input" );
-
- // Support: Android 4.0 - 4.3 only
- // Check state lost if the name is set (#11217)
- // Support: Windows Web Apps (WWA)
- // `name` and `type` must use .setAttribute for WWA (#14901)
- input.setAttribute( "type", "radio" );
- input.setAttribute( "checked", "checked" );
- input.setAttribute( "name", "t" );
-
- div.appendChild( input );
-
- // Support: Android <=4.1 only
- // Older WebKit doesn't clone checked state correctly in fragments
- support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
-
- // Support: IE <=11 only
- // Make sure textarea (and checkbox) defaultValue is properly cloned
- div.innerHTML = "";
- support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
-} )();
-var documentElement = document.documentElement;
-
-
-
-var
- rkeyEvent = /^key/,
- rmouseEvent = /^(?:mouse|pointer|contextmenu|drag|drop)|click/,
- rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
-
-function returnTrue() {
- return true;
-}
-
-function returnFalse() {
- return false;
-}
-
-// Support: IE <=9 only
-// See #13393 for more info
-function safeActiveElement() {
- try {
- return document.activeElement;
- } catch ( err ) { }
-}
-
-function on( elem, types, selector, data, fn, one ) {
- var origFn, type;
-
- // Types can be a map of types/handlers
- if ( typeof types === "object" ) {
-
- // ( types-Object, selector, data )
- if ( typeof selector !== "string" ) {
-
- // ( types-Object, data )
- data = data || selector;
- selector = undefined;
- }
- for ( type in types ) {
- on( elem, type, selector, data, types[ type ], one );
- }
- return elem;
- }
-
- if ( data == null && fn == null ) {
-
- // ( types, fn )
- fn = selector;
- data = selector = undefined;
- } else if ( fn == null ) {
- if ( typeof selector === "string" ) {
-
- // ( types, selector, fn )
- fn = data;
- data = undefined;
- } else {
-
- // ( types, data, fn )
- fn = data;
- data = selector;
- selector = undefined;
- }
- }
- if ( fn === false ) {
- fn = returnFalse;
- } else if ( !fn ) {
- return elem;
- }
-
- if ( one === 1 ) {
- origFn = fn;
- fn = function( event ) {
-
- // Can use an empty set, since event contains the info
- jQuery().off( event );
- return origFn.apply( this, arguments );
- };
-
- // Use same guid so caller can remove using origFn
- fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
- }
- return elem.each( function() {
- jQuery.event.add( this, types, fn, data, selector );
- } );
-}
-
-/*
- * Helper functions for managing events -- not part of the public interface.
- * Props to Dean Edwards' addEvent library for many of the ideas.
- */
-jQuery.event = {
-
- global: {},
-
- add: function( elem, types, handler, data, selector ) {
-
- var handleObjIn, eventHandle, tmp,
- events, t, handleObj,
- special, handlers, type, namespaces, origType,
- elemData = dataPriv.get( elem );
-
- // Don't attach events to noData or text/comment nodes (but allow plain objects)
- if ( !elemData ) {
- return;
- }
-
- // Caller can pass in an object of custom data in lieu of the handler
- if ( handler.handler ) {
- handleObjIn = handler;
- handler = handleObjIn.handler;
- selector = handleObjIn.selector;
- }
-
- // Ensure that invalid selectors throw exceptions at attach time
- // Evaluate against documentElement in case elem is a non-element node (e.g., document)
- if ( selector ) {
- jQuery.find.matchesSelector( documentElement, selector );
- }
-
- // Make sure that the handler has a unique ID, used to find/remove it later
- if ( !handler.guid ) {
- handler.guid = jQuery.guid++;
- }
-
- // Init the element's event structure and main handler, if this is the first
- if ( !( events = elemData.events ) ) {
- events = elemData.events = {};
- }
- if ( !( eventHandle = elemData.handle ) ) {
- eventHandle = elemData.handle = function( e ) {
-
- // Discard the second event of a jQuery.event.trigger() and
- // when an event is called after a page has unloaded
- return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ?
- jQuery.event.dispatch.apply( elem, arguments ) : undefined;
- };
- }
-
- // Handle multiple events separated by a space
- types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
- t = types.length;
- while ( t-- ) {
- tmp = rtypenamespace.exec( types[ t ] ) || [];
- type = origType = tmp[ 1 ];
- namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
-
- // There *must* be a type, no attaching namespace-only handlers
- if ( !type ) {
- continue;
- }
-
- // If event changes its type, use the special event handlers for the changed type
- special = jQuery.event.special[ type ] || {};
-
- // If selector defined, determine special event api type, otherwise given type
- type = ( selector ? special.delegateType : special.bindType ) || type;
-
- // Update special based on newly reset type
- special = jQuery.event.special[ type ] || {};
-
- // handleObj is passed to all event handlers
- handleObj = jQuery.extend( {
- type: type,
- origType: origType,
- data: data,
- handler: handler,
- guid: handler.guid,
- selector: selector,
- needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
- namespace: namespaces.join( "." )
- }, handleObjIn );
-
- // Init the event handler queue if we're the first
- if ( !( handlers = events[ type ] ) ) {
- handlers = events[ type ] = [];
- handlers.delegateCount = 0;
-
- // Only use addEventListener if the special events handler returns false
- if ( !special.setup ||
- special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
-
- if ( elem.addEventListener ) {
- elem.addEventListener( type, eventHandle );
- }
- }
- }
-
- if ( special.add ) {
- special.add.call( elem, handleObj );
-
- if ( !handleObj.handler.guid ) {
- handleObj.handler.guid = handler.guid;
- }
- }
-
- // Add to the element's handler list, delegates in front
- if ( selector ) {
- handlers.splice( handlers.delegateCount++, 0, handleObj );
- } else {
- handlers.push( handleObj );
- }
-
- // Keep track of which events have ever been used, for event optimization
- jQuery.event.global[ type ] = true;
- }
-
- },
-
- // Detach an event or set of events from an element
- remove: function( elem, types, handler, selector, mappedTypes ) {
-
- var j, origCount, tmp,
- events, t, handleObj,
- special, handlers, type, namespaces, origType,
- elemData = dataPriv.hasData( elem ) && dataPriv.get( elem );
-
- if ( !elemData || !( events = elemData.events ) ) {
- return;
- }
-
- // Once for each type.namespace in types; type may be omitted
- types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
- t = types.length;
- while ( t-- ) {
- tmp = rtypenamespace.exec( types[ t ] ) || [];
- type = origType = tmp[ 1 ];
- namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
-
- // Unbind all events (on this namespace, if provided) for the element
- if ( !type ) {
- for ( type in events ) {
- jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
- }
- continue;
- }
-
- special = jQuery.event.special[ type ] || {};
- type = ( selector ? special.delegateType : special.bindType ) || type;
- handlers = events[ type ] || [];
- tmp = tmp[ 2 ] &&
- new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" );
-
- // Remove matching events
- origCount = j = handlers.length;
- while ( j-- ) {
- handleObj = handlers[ j ];
-
- if ( ( mappedTypes || origType === handleObj.origType ) &&
- ( !handler || handler.guid === handleObj.guid ) &&
- ( !tmp || tmp.test( handleObj.namespace ) ) &&
- ( !selector || selector === handleObj.selector ||
- selector === "**" && handleObj.selector ) ) {
- handlers.splice( j, 1 );
-
- if ( handleObj.selector ) {
- handlers.delegateCount--;
- }
- if ( special.remove ) {
- special.remove.call( elem, handleObj );
- }
- }
- }
-
- // Remove generic event handler if we removed something and no more handlers exist
- // (avoids potential for endless recursion during removal of special event handlers)
- if ( origCount && !handlers.length ) {
- if ( !special.teardown ||
- special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
-
- jQuery.removeEvent( elem, type, elemData.handle );
- }
-
- delete events[ type ];
- }
- }
-
- // Remove data and the expando if it's no longer used
- if ( jQuery.isEmptyObject( events ) ) {
- dataPriv.remove( elem, "handle events" );
- }
- },
-
- dispatch: function( nativeEvent ) {
-
- // Make a writable jQuery.Event from the native event object
- var event = jQuery.event.fix( nativeEvent );
-
- var i, j, ret, matched, handleObj, handlerQueue,
- args = new Array( arguments.length ),
- handlers = ( dataPriv.get( this, "events" ) || {} )[ event.type ] || [],
- special = jQuery.event.special[ event.type ] || {};
-
- // Use the fix-ed jQuery.Event rather than the (read-only) native event
- args[ 0 ] = event;
-
- for ( i = 1; i < arguments.length; i++ ) {
- args[ i ] = arguments[ i ];
- }
-
- event.delegateTarget = this;
-
- // Call the preDispatch hook for the mapped type, and let it bail if desired
- if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
- return;
- }
-
- // Determine handlers
- handlerQueue = jQuery.event.handlers.call( this, event, handlers );
-
- // Run delegates first; they may want to stop propagation beneath us
- i = 0;
- while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) {
- event.currentTarget = matched.elem;
-
- j = 0;
- while ( ( handleObj = matched.handlers[ j++ ] ) &&
- !event.isImmediatePropagationStopped() ) {
-
- // Triggered event must either 1) have no namespace, or 2) have namespace(s)
- // a subset or equal to those in the bound event (both can have no namespace).
- if ( !event.rnamespace || event.rnamespace.test( handleObj.namespace ) ) {
-
- event.handleObj = handleObj;
- event.data = handleObj.data;
-
- ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle ||
- handleObj.handler ).apply( matched.elem, args );
-
- if ( ret !== undefined ) {
- if ( ( event.result = ret ) === false ) {
- event.preventDefault();
- event.stopPropagation();
- }
- }
- }
- }
- }
-
- // Call the postDispatch hook for the mapped type
- if ( special.postDispatch ) {
- special.postDispatch.call( this, event );
- }
-
- return event.result;
- },
-
- handlers: function( event, handlers ) {
- var i, handleObj, sel, matchedHandlers, matchedSelectors,
- handlerQueue = [],
- delegateCount = handlers.delegateCount,
- cur = event.target;
-
- // Find delegate handlers
- if ( delegateCount &&
-
- // Support: IE <=9
- // Black-hole SVG instance trees (trac-13180)
- cur.nodeType &&
-
- // Support: Firefox <=42
- // Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861)
- // https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click
- // Support: IE 11 only
- // ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343)
- !( event.type === "click" && event.button >= 1 ) ) {
-
- for ( ; cur !== this; cur = cur.parentNode || this ) {
-
- // Don't check non-elements (#13208)
- // Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
- if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) {
- matchedHandlers = [];
- matchedSelectors = {};
- for ( i = 0; i < delegateCount; i++ ) {
- handleObj = handlers[ i ];
-
- // Don't conflict with Object.prototype properties (#13203)
- sel = handleObj.selector + " ";
-
- if ( matchedSelectors[ sel ] === undefined ) {
- matchedSelectors[ sel ] = handleObj.needsContext ?
- jQuery( sel, this ).index( cur ) > -1 :
- jQuery.find( sel, this, null, [ cur ] ).length;
- }
- if ( matchedSelectors[ sel ] ) {
- matchedHandlers.push( handleObj );
- }
- }
- if ( matchedHandlers.length ) {
- handlerQueue.push( { elem: cur, handlers: matchedHandlers } );
- }
- }
- }
- }
-
- // Add the remaining (directly-bound) handlers
- cur = this;
- if ( delegateCount < handlers.length ) {
- handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } );
- }
-
- return handlerQueue;
- },
-
- addProp: function( name, hook ) {
- Object.defineProperty( jQuery.Event.prototype, name, {
- enumerable: true,
- configurable: true,
-
- get: jQuery.isFunction( hook ) ?
- function() {
- if ( this.originalEvent ) {
- return hook( this.originalEvent );
- }
- } :
- function() {
- if ( this.originalEvent ) {
- return this.originalEvent[ name ];
- }
- },
-
- set: function( value ) {
- Object.defineProperty( this, name, {
- enumerable: true,
- configurable: true,
- writable: true,
- value: value
- } );
- }
- } );
- },
-
- fix: function( originalEvent ) {
- return originalEvent[ jQuery.expando ] ?
- originalEvent :
- new jQuery.Event( originalEvent );
- },
-
- special: {
- load: {
-
- // Prevent triggered image.load events from bubbling to window.load
- noBubble: true
- },
- focus: {
-
- // Fire native event if possible so blur/focus sequence is correct
- trigger: function() {
- if ( this !== safeActiveElement() && this.focus ) {
- this.focus();
- return false;
- }
- },
- delegateType: "focusin"
- },
- blur: {
- trigger: function() {
- if ( this === safeActiveElement() && this.blur ) {
- this.blur();
- return false;
- }
- },
- delegateType: "focusout"
- },
- click: {
-
- // For checkbox, fire native event so checked state will be right
- trigger: function() {
- if ( this.type === "checkbox" && this.click && nodeName( this, "input" ) ) {
- this.click();
- return false;
- }
- },
-
- // For cross-browser consistency, don't fire native .click() on links
- _default: function( event ) {
- return nodeName( event.target, "a" );
- }
- },
-
- beforeunload: {
- postDispatch: function( event ) {
-
- // Support: Firefox 20+
- // Firefox doesn't alert if the returnValue field is not set.
- if ( event.result !== undefined && event.originalEvent ) {
- event.originalEvent.returnValue = event.result;
- }
- }
- }
- }
-};
-
-jQuery.removeEvent = function( elem, type, handle ) {
-
- // This "if" is needed for plain objects
- if ( elem.removeEventListener ) {
- elem.removeEventListener( type, handle );
- }
-};
-
-jQuery.Event = function( src, props ) {
-
- // Allow instantiation without the 'new' keyword
- if ( !( this instanceof jQuery.Event ) ) {
- return new jQuery.Event( src, props );
- }
-
- // Event object
- if ( src && src.type ) {
- this.originalEvent = src;
- this.type = src.type;
-
- // Events bubbling up the document may have been marked as prevented
- // by a handler lower down the tree; reflect the correct value.
- this.isDefaultPrevented = src.defaultPrevented ||
- src.defaultPrevented === undefined &&
-
- // Support: Android <=2.3 only
- src.returnValue === false ?
- returnTrue :
- returnFalse;
-
- // Create target properties
- // Support: Safari <=6 - 7 only
- // Target should not be a text node (#504, #13143)
- this.target = ( src.target && src.target.nodeType === 3 ) ?
- src.target.parentNode :
- src.target;
-
- this.currentTarget = src.currentTarget;
- this.relatedTarget = src.relatedTarget;
-
- // Event type
- } else {
- this.type = src;
- }
-
- // Put explicitly provided properties onto the event object
- if ( props ) {
- jQuery.extend( this, props );
- }
-
- // Create a timestamp if incoming event doesn't have one
- this.timeStamp = src && src.timeStamp || jQuery.now();
-
- // Mark it as fixed
- this[ jQuery.expando ] = true;
-};
-
-// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
-// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
-jQuery.Event.prototype = {
- constructor: jQuery.Event,
- isDefaultPrevented: returnFalse,
- isPropagationStopped: returnFalse,
- isImmediatePropagationStopped: returnFalse,
- isSimulated: false,
-
- preventDefault: function() {
- var e = this.originalEvent;
-
- this.isDefaultPrevented = returnTrue;
-
- if ( e && !this.isSimulated ) {
- e.preventDefault();
- }
- },
- stopPropagation: function() {
- var e = this.originalEvent;
-
- this.isPropagationStopped = returnTrue;
-
- if ( e && !this.isSimulated ) {
- e.stopPropagation();
- }
- },
- stopImmediatePropagation: function() {
- var e = this.originalEvent;
-
- this.isImmediatePropagationStopped = returnTrue;
-
- if ( e && !this.isSimulated ) {
- e.stopImmediatePropagation();
- }
-
- this.stopPropagation();
- }
-};
-
-// Includes all common event props including KeyEvent and MouseEvent specific props
-jQuery.each( {
- altKey: true,
- bubbles: true,
- cancelable: true,
- changedTouches: true,
- ctrlKey: true,
- detail: true,
- eventPhase: true,
- metaKey: true,
- pageX: true,
- pageY: true,
- shiftKey: true,
- view: true,
- "char": true,
- charCode: true,
- key: true,
- keyCode: true,
- button: true,
- buttons: true,
- clientX: true,
- clientY: true,
- offsetX: true,
- offsetY: true,
- pointerId: true,
- pointerType: true,
- screenX: true,
- screenY: true,
- targetTouches: true,
- toElement: true,
- touches: true,
-
- which: function( event ) {
- var button = event.button;
-
- // Add which for key events
- if ( event.which == null && rkeyEvent.test( event.type ) ) {
- return event.charCode != null ? event.charCode : event.keyCode;
- }
-
- // Add which for click: 1 === left; 2 === middle; 3 === right
- if ( !event.which && button !== undefined && rmouseEvent.test( event.type ) ) {
- if ( button & 1 ) {
- return 1;
- }
-
- if ( button & 2 ) {
- return 3;
- }
-
- if ( button & 4 ) {
- return 2;
- }
-
- return 0;
- }
-
- return event.which;
- }
-}, jQuery.event.addProp );
-
-// Create mouseenter/leave events using mouseover/out and event-time checks
-// so that event delegation works in jQuery.
-// Do the same for pointerenter/pointerleave and pointerover/pointerout
-//
-// Support: Safari 7 only
-// Safari sends mouseenter too often; see:
-// https://bugs.chromium.org/p/chromium/issues/detail?id=470258
-// for the description of the bug (it existed in older Chrome versions as well).
-jQuery.each( {
- mouseenter: "mouseover",
- mouseleave: "mouseout",
- pointerenter: "pointerover",
- pointerleave: "pointerout"
-}, function( orig, fix ) {
- jQuery.event.special[ orig ] = {
- delegateType: fix,
- bindType: fix,
-
- handle: function( event ) {
- var ret,
- target = this,
- related = event.relatedTarget,
- handleObj = event.handleObj;
-
- // For mouseenter/leave call the handler if related is outside the target.
- // NB: No relatedTarget if the mouse left/entered the browser window
- if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) {
- event.type = handleObj.origType;
- ret = handleObj.handler.apply( this, arguments );
- event.type = fix;
- }
- return ret;
- }
- };
-} );
-
-jQuery.fn.extend( {
-
- on: function( types, selector, data, fn ) {
- return on( this, types, selector, data, fn );
- },
- one: function( types, selector, data, fn ) {
- return on( this, types, selector, data, fn, 1 );
- },
- off: function( types, selector, fn ) {
- var handleObj, type;
- if ( types && types.preventDefault && types.handleObj ) {
-
- // ( event ) dispatched jQuery.Event
- handleObj = types.handleObj;
- jQuery( types.delegateTarget ).off(
- handleObj.namespace ?
- handleObj.origType + "." + handleObj.namespace :
- handleObj.origType,
- handleObj.selector,
- handleObj.handler
- );
- return this;
- }
- if ( typeof types === "object" ) {
-
- // ( types-object [, selector] )
- for ( type in types ) {
- this.off( type, selector, types[ type ] );
- }
- return this;
- }
- if ( selector === false || typeof selector === "function" ) {
-
- // ( types [, fn] )
- fn = selector;
- selector = undefined;
- }
- if ( fn === false ) {
- fn = returnFalse;
- }
- return this.each( function() {
- jQuery.event.remove( this, types, fn, selector );
- } );
- }
-} );
-
-
-var
-
- /* eslint-disable max-len */
-
- // See https://github.com/eslint/eslint/issues/3229
- rxhtmlTag = /<(?!area|br|col|embed|hr|img|input|link|meta|param)(([a-z][^\/\0>\x20\t\r\n\f]*)[^>]*)\/>/gi,
-
- /* eslint-enable */
-
- // Support: IE <=10 - 11, Edge 12 - 13
- // In IE/Edge using regex groups here causes severe slowdowns.
- // See https://connect.microsoft.com/IE/feedback/details/1736512/
- rnoInnerhtml = /\s*$/g;
-
-// Prefer a tbody over its parent table for containing new rows
-function manipulationTarget( elem, content ) {
- if ( nodeName( elem, "table" ) &&
- nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) {
-
- return jQuery( ">tbody", elem )[ 0 ] || elem;
- }
-
- return elem;
-}
-
-// Replace/restore the type attribute of script elements for safe DOM manipulation
-function disableScript( elem ) {
- elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type;
- return elem;
-}
-function restoreScript( elem ) {
- var match = rscriptTypeMasked.exec( elem.type );
-
- if ( match ) {
- elem.type = match[ 1 ];
- } else {
- elem.removeAttribute( "type" );
- }
-
- return elem;
-}
-
-function cloneCopyEvent( src, dest ) {
- var i, l, type, pdataOld, pdataCur, udataOld, udataCur, events;
-
- if ( dest.nodeType !== 1 ) {
- return;
- }
-
- // 1. Copy private data: events, handlers, etc.
- if ( dataPriv.hasData( src ) ) {
- pdataOld = dataPriv.access( src );
- pdataCur = dataPriv.set( dest, pdataOld );
- events = pdataOld.events;
-
- if ( events ) {
- delete pdataCur.handle;
- pdataCur.events = {};
-
- for ( type in events ) {
- for ( i = 0, l = events[ type ].length; i < l; i++ ) {
- jQuery.event.add( dest, type, events[ type ][ i ] );
- }
- }
- }
- }
-
- // 2. Copy user data
- if ( dataUser.hasData( src ) ) {
- udataOld = dataUser.access( src );
- udataCur = jQuery.extend( {}, udataOld );
-
- dataUser.set( dest, udataCur );
- }
-}
-
-// Fix IE bugs, see support tests
-function fixInput( src, dest ) {
- var nodeName = dest.nodeName.toLowerCase();
-
- // Fails to persist the checked state of a cloned checkbox or radio button.
- if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
- dest.checked = src.checked;
-
- // Fails to return the selected option to the default selected state when cloning options
- } else if ( nodeName === "input" || nodeName === "textarea" ) {
- dest.defaultValue = src.defaultValue;
- }
-}
-
-function domManip( collection, args, callback, ignored ) {
-
- // Flatten any nested arrays
- args = concat.apply( [], args );
-
- var fragment, first, scripts, hasScripts, node, doc,
- i = 0,
- l = collection.length,
- iNoClone = l - 1,
- value = args[ 0 ],
- isFunction = jQuery.isFunction( value );
-
- // We can't cloneNode fragments that contain checked, in WebKit
- if ( isFunction ||
- ( l > 1 && typeof value === "string" &&
- !support.checkClone && rchecked.test( value ) ) ) {
- return collection.each( function( index ) {
- var self = collection.eq( index );
- if ( isFunction ) {
- args[ 0 ] = value.call( this, index, self.html() );
- }
- domManip( self, args, callback, ignored );
- } );
- }
-
- if ( l ) {
- fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored );
- first = fragment.firstChild;
-
- if ( fragment.childNodes.length === 1 ) {
- fragment = first;
- }
-
- // Require either new content or an interest in ignored elements to invoke the callback
- if ( first || ignored ) {
- scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
- hasScripts = scripts.length;
-
- // Use the original fragment for the last item
- // instead of the first because it can end up
- // being emptied incorrectly in certain situations (#8070).
- for ( ; i < l; i++ ) {
- node = fragment;
-
- if ( i !== iNoClone ) {
- node = jQuery.clone( node, true, true );
-
- // Keep references to cloned scripts for later restoration
- if ( hasScripts ) {
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // push.apply(_, arraylike) throws on ancient WebKit
- jQuery.merge( scripts, getAll( node, "script" ) );
- }
- }
-
- callback.call( collection[ i ], node, i );
- }
-
- if ( hasScripts ) {
- doc = scripts[ scripts.length - 1 ].ownerDocument;
-
- // Reenable scripts
- jQuery.map( scripts, restoreScript );
-
- // Evaluate executable scripts on first document insertion
- for ( i = 0; i < hasScripts; i++ ) {
- node = scripts[ i ];
- if ( rscriptType.test( node.type || "" ) &&
- !dataPriv.access( node, "globalEval" ) &&
- jQuery.contains( doc, node ) ) {
-
- if ( node.src ) {
-
- // Optional AJAX dependency, but won't run scripts if not present
- if ( jQuery._evalUrl ) {
- jQuery._evalUrl( node.src );
- }
- } else {
- DOMEval( node.textContent.replace( rcleanScript, "" ), doc );
- }
- }
- }
- }
- }
- }
-
- return collection;
-}
-
-function remove( elem, selector, keepData ) {
- var node,
- nodes = selector ? jQuery.filter( selector, elem ) : elem,
- i = 0;
-
- for ( ; ( node = nodes[ i ] ) != null; i++ ) {
- if ( !keepData && node.nodeType === 1 ) {
- jQuery.cleanData( getAll( node ) );
- }
-
- if ( node.parentNode ) {
- if ( keepData && jQuery.contains( node.ownerDocument, node ) ) {
- setGlobalEval( getAll( node, "script" ) );
- }
- node.parentNode.removeChild( node );
- }
- }
-
- return elem;
-}
-
-jQuery.extend( {
- htmlPrefilter: function( html ) {
- return html.replace( rxhtmlTag, "<$1>" );
- },
-
- clone: function( elem, dataAndEvents, deepDataAndEvents ) {
- var i, l, srcElements, destElements,
- clone = elem.cloneNode( true ),
- inPage = jQuery.contains( elem.ownerDocument, elem );
-
- // Fix IE cloning issues
- if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) &&
- !jQuery.isXMLDoc( elem ) ) {
-
- // We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2
- destElements = getAll( clone );
- srcElements = getAll( elem );
-
- for ( i = 0, l = srcElements.length; i < l; i++ ) {
- fixInput( srcElements[ i ], destElements[ i ] );
- }
- }
-
- // Copy the events from the original to the clone
- if ( dataAndEvents ) {
- if ( deepDataAndEvents ) {
- srcElements = srcElements || getAll( elem );
- destElements = destElements || getAll( clone );
-
- for ( i = 0, l = srcElements.length; i < l; i++ ) {
- cloneCopyEvent( srcElements[ i ], destElements[ i ] );
- }
- } else {
- cloneCopyEvent( elem, clone );
- }
- }
-
- // Preserve script evaluation history
- destElements = getAll( clone, "script" );
- if ( destElements.length > 0 ) {
- setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
- }
-
- // Return the cloned set
- return clone;
- },
-
- cleanData: function( elems ) {
- var data, elem, type,
- special = jQuery.event.special,
- i = 0;
-
- for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) {
- if ( acceptData( elem ) ) {
- if ( ( data = elem[ dataPriv.expando ] ) ) {
- if ( data.events ) {
- for ( type in data.events ) {
- if ( special[ type ] ) {
- jQuery.event.remove( elem, type );
-
- // This is a shortcut to avoid jQuery.event.remove's overhead
- } else {
- jQuery.removeEvent( elem, type, data.handle );
- }
- }
- }
-
- // Support: Chrome <=35 - 45+
- // Assign undefined instead of using delete, see Data#remove
- elem[ dataPriv.expando ] = undefined;
- }
- if ( elem[ dataUser.expando ] ) {
-
- // Support: Chrome <=35 - 45+
- // Assign undefined instead of using delete, see Data#remove
- elem[ dataUser.expando ] = undefined;
- }
- }
- }
- }
-} );
-
-jQuery.fn.extend( {
- detach: function( selector ) {
- return remove( this, selector, true );
- },
-
- remove: function( selector ) {
- return remove( this, selector );
- },
-
- text: function( value ) {
- return access( this, function( value ) {
- return value === undefined ?
- jQuery.text( this ) :
- this.empty().each( function() {
- if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
- this.textContent = value;
- }
- } );
- }, null, value, arguments.length );
- },
-
- append: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
- var target = manipulationTarget( this, elem );
- target.appendChild( elem );
- }
- } );
- },
-
- prepend: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
- var target = manipulationTarget( this, elem );
- target.insertBefore( elem, target.firstChild );
- }
- } );
- },
-
- before: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.parentNode ) {
- this.parentNode.insertBefore( elem, this );
- }
- } );
- },
-
- after: function() {
- return domManip( this, arguments, function( elem ) {
- if ( this.parentNode ) {
- this.parentNode.insertBefore( elem, this.nextSibling );
- }
- } );
- },
-
- empty: function() {
- var elem,
- i = 0;
-
- for ( ; ( elem = this[ i ] ) != null; i++ ) {
- if ( elem.nodeType === 1 ) {
-
- // Prevent memory leaks
- jQuery.cleanData( getAll( elem, false ) );
-
- // Remove any remaining nodes
- elem.textContent = "";
- }
- }
-
- return this;
- },
-
- clone: function( dataAndEvents, deepDataAndEvents ) {
- dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
- deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
-
- return this.map( function() {
- return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
- } );
- },
-
- html: function( value ) {
- return access( this, function( value ) {
- var elem = this[ 0 ] || {},
- i = 0,
- l = this.length;
-
- if ( value === undefined && elem.nodeType === 1 ) {
- return elem.innerHTML;
- }
-
- // See if we can take a shortcut and just use innerHTML
- if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
- !wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) {
-
- value = jQuery.htmlPrefilter( value );
-
- try {
- for ( ; i < l; i++ ) {
- elem = this[ i ] || {};
-
- // Remove element nodes and prevent memory leaks
- if ( elem.nodeType === 1 ) {
- jQuery.cleanData( getAll( elem, false ) );
- elem.innerHTML = value;
- }
- }
-
- elem = 0;
-
- // If using innerHTML throws an exception, use the fallback method
- } catch ( e ) {}
- }
-
- if ( elem ) {
- this.empty().append( value );
- }
- }, null, value, arguments.length );
- },
-
- replaceWith: function() {
- var ignored = [];
-
- // Make the changes, replacing each non-ignored context element with the new content
- return domManip( this, arguments, function( elem ) {
- var parent = this.parentNode;
-
- if ( jQuery.inArray( this, ignored ) < 0 ) {
- jQuery.cleanData( getAll( this ) );
- if ( parent ) {
- parent.replaceChild( elem, this );
- }
- }
-
- // Force callback invocation
- }, ignored );
- }
-} );
-
-jQuery.each( {
- appendTo: "append",
- prependTo: "prepend",
- insertBefore: "before",
- insertAfter: "after",
- replaceAll: "replaceWith"
-}, function( name, original ) {
- jQuery.fn[ name ] = function( selector ) {
- var elems,
- ret = [],
- insert = jQuery( selector ),
- last = insert.length - 1,
- i = 0;
-
- for ( ; i <= last; i++ ) {
- elems = i === last ? this : this.clone( true );
- jQuery( insert[ i ] )[ original ]( elems );
-
- // Support: Android <=4.0 only, PhantomJS 1 only
- // .get() because push.apply(_, arraylike) throws on ancient WebKit
- push.apply( ret, elems.get() );
- }
-
- return this.pushStack( ret );
- };
-} );
-var rmargin = ( /^margin/ );
-
-var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
-
-var getStyles = function( elem ) {
-
- // Support: IE <=11 only, Firefox <=30 (#15098, #14150)
- // IE throws on elements created in popups
- // FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
- var view = elem.ownerDocument.defaultView;
-
- if ( !view || !view.opener ) {
- view = window;
- }
-
- return view.getComputedStyle( elem );
- };
-
-
-
-( function() {
-
- // Executing both pixelPosition & boxSizingReliable tests require only one layout
- // so they're executed at the same time to save the second computation.
- function computeStyleTests() {
-
- // This is a singleton, we need to execute it only once
- if ( !div ) {
- return;
- }
-
- div.style.cssText =
- "box-sizing:border-box;" +
- "position:relative;display:block;" +
- "margin:auto;border:1px;padding:1px;" +
- "top:1%;width:50%";
- div.innerHTML = "";
- documentElement.appendChild( container );
-
- var divStyle = window.getComputedStyle( div );
- pixelPositionVal = divStyle.top !== "1%";
-
- // Support: Android 4.0 - 4.3 only, Firefox <=3 - 44
- reliableMarginLeftVal = divStyle.marginLeft === "2px";
- boxSizingReliableVal = divStyle.width === "4px";
-
- // Support: Android 4.0 - 4.3 only
- // Some styles come back with percentage values, even though they shouldn't
- div.style.marginRight = "50%";
- pixelMarginRightVal = divStyle.marginRight === "4px";
-
- documentElement.removeChild( container );
-
- // Nullify the div so it wouldn't be stored in the memory and
- // it will also be a sign that checks already performed
- div = null;
- }
-
- var pixelPositionVal, boxSizingReliableVal, pixelMarginRightVal, reliableMarginLeftVal,
- container = document.createElement( "div" ),
- div = document.createElement( "div" );
-
- // Finish early in limited (non-browser) environments
- if ( !div.style ) {
- return;
- }
-
- // Support: IE <=9 - 11 only
- // Style of cloned element affects source element cloned (#8908)
- div.style.backgroundClip = "content-box";
- div.cloneNode( true ).style.backgroundClip = "";
- support.clearCloneStyle = div.style.backgroundClip === "content-box";
-
- container.style.cssText = "border:0;width:8px;height:0;top:0;left:-9999px;" +
- "padding:0;margin-top:1px;position:absolute";
- container.appendChild( div );
-
- jQuery.extend( support, {
- pixelPosition: function() {
- computeStyleTests();
- return pixelPositionVal;
- },
- boxSizingReliable: function() {
- computeStyleTests();
- return boxSizingReliableVal;
- },
- pixelMarginRight: function() {
- computeStyleTests();
- return pixelMarginRightVal;
- },
- reliableMarginLeft: function() {
- computeStyleTests();
- return reliableMarginLeftVal;
- }
- } );
-} )();
-
-
-function curCSS( elem, name, computed ) {
- var width, minWidth, maxWidth, ret,
-
- // Support: Firefox 51+
- // Retrieving style before computed somehow
- // fixes an issue with getting wrong values
- // on detached elements
- style = elem.style;
-
- computed = computed || getStyles( elem );
-
- // getPropertyValue is needed for:
- // .css('filter') (IE 9 only, #12537)
- // .css('--customProperty) (#3144)
- if ( computed ) {
- ret = computed.getPropertyValue( name ) || computed[ name ];
-
- if ( ret === "" && !jQuery.contains( elem.ownerDocument, elem ) ) {
- ret = jQuery.style( elem, name );
- }
-
- // A tribute to the "awesome hack by Dean Edwards"
- // Android Browser returns percentage for some values,
- // but width seems to be reliably pixels.
- // This is against the CSSOM draft spec:
- // https://drafts.csswg.org/cssom/#resolved-values
- if ( !support.pixelMarginRight() && rnumnonpx.test( ret ) && rmargin.test( name ) ) {
-
- // Remember the original values
- width = style.width;
- minWidth = style.minWidth;
- maxWidth = style.maxWidth;
-
- // Put in the new values to get a computed value out
- style.minWidth = style.maxWidth = style.width = ret;
- ret = computed.width;
-
- // Revert the changed values
- style.width = width;
- style.minWidth = minWidth;
- style.maxWidth = maxWidth;
- }
- }
-
- return ret !== undefined ?
-
- // Support: IE <=9 - 11 only
- // IE returns zIndex value as an integer.
- ret + "" :
- ret;
-}
-
-
-function addGetHookIf( conditionFn, hookFn ) {
-
- // Define the hook, we'll check on the first run if it's really needed.
- return {
- get: function() {
- if ( conditionFn() ) {
-
- // Hook not needed (or it's not possible to use it due
- // to missing dependency), remove it.
- delete this.get;
- return;
- }
-
- // Hook needed; redefine it so that the support test is not executed again.
- return ( this.get = hookFn ).apply( this, arguments );
- }
- };
-}
-
-
-var
-
- // Swappable if display is none or starts with table
- // except "table", "table-cell", or "table-caption"
- // See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
- rdisplayswap = /^(none|table(?!-c[ea]).+)/,
- rcustomProp = /^--/,
- cssShow = { position: "absolute", visibility: "hidden", display: "block" },
- cssNormalTransform = {
- letterSpacing: "0",
- fontWeight: "400"
- },
-
- cssPrefixes = [ "Webkit", "Moz", "ms" ],
- emptyStyle = document.createElement( "div" ).style;
-
-// Return a css property mapped to a potentially vendor prefixed property
-function vendorPropName( name ) {
-
- // Shortcut for names that are not vendor prefixed
- if ( name in emptyStyle ) {
- return name;
- }
-
- // Check for vendor prefixed names
- var capName = name[ 0 ].toUpperCase() + name.slice( 1 ),
- i = cssPrefixes.length;
-
- while ( i-- ) {
- name = cssPrefixes[ i ] + capName;
- if ( name in emptyStyle ) {
- return name;
- }
- }
-}
-
-// Return a property mapped along what jQuery.cssProps suggests or to
-// a vendor prefixed property.
-function finalPropName( name ) {
- var ret = jQuery.cssProps[ name ];
- if ( !ret ) {
- ret = jQuery.cssProps[ name ] = vendorPropName( name ) || name;
- }
- return ret;
-}
-
-function setPositiveNumber( elem, value, subtract ) {
-
- // Any relative (+/-) values have already been
- // normalized at this point
- var matches = rcssNum.exec( value );
- return matches ?
-
- // Guard against undefined "subtract", e.g., when used as in cssHooks
- Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) :
- value;
-}
-
-function augmentWidthOrHeight( elem, name, extra, isBorderBox, styles ) {
- var i,
- val = 0;
-
- // If we already have the right measurement, avoid augmentation
- if ( extra === ( isBorderBox ? "border" : "content" ) ) {
- i = 4;
-
- // Otherwise initialize for horizontal or vertical properties
- } else {
- i = name === "width" ? 1 : 0;
- }
-
- for ( ; i < 4; i += 2 ) {
-
- // Both box models exclude margin, so add it if we want it
- if ( extra === "margin" ) {
- val += jQuery.css( elem, extra + cssExpand[ i ], true, styles );
- }
-
- if ( isBorderBox ) {
-
- // border-box includes padding, so remove it if we want content
- if ( extra === "content" ) {
- val -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
- }
-
- // At this point, extra isn't border nor margin, so remove border
- if ( extra !== "margin" ) {
- val -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
- }
- } else {
-
- // At this point, extra isn't content, so add padding
- val += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
-
- // At this point, extra isn't content nor padding, so add border
- if ( extra !== "padding" ) {
- val += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
- }
- }
- }
-
- return val;
-}
-
-function getWidthOrHeight( elem, name, extra ) {
-
- // Start with computed style
- var valueIsBorderBox,
- styles = getStyles( elem ),
- val = curCSS( elem, name, styles ),
- isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
-
- // Computed unit is not pixels. Stop here and return.
- if ( rnumnonpx.test( val ) ) {
- return val;
- }
-
- // Check for style in case a browser which returns unreliable values
- // for getComputedStyle silently falls back to the reliable elem.style
- valueIsBorderBox = isBorderBox &&
- ( support.boxSizingReliable() || val === elem.style[ name ] );
-
- // Fall back to offsetWidth/Height when value is "auto"
- // This happens for inline elements with no explicit setting (gh-3571)
- if ( val === "auto" ) {
- val = elem[ "offset" + name[ 0 ].toUpperCase() + name.slice( 1 ) ];
- }
-
- // Normalize "", auto, and prepare for extra
- val = parseFloat( val ) || 0;
-
- // Use the active box-sizing model to add/subtract irrelevant styles
- return ( val +
- augmentWidthOrHeight(
- elem,
- name,
- extra || ( isBorderBox ? "border" : "content" ),
- valueIsBorderBox,
- styles
- )
- ) + "px";
-}
-
-jQuery.extend( {
-
- // Add in style property hooks for overriding the default
- // behavior of getting and setting a style property
- cssHooks: {
- opacity: {
- get: function( elem, computed ) {
- if ( computed ) {
-
- // We should always get a number back from opacity
- var ret = curCSS( elem, "opacity" );
- return ret === "" ? "1" : ret;
- }
- }
- }
- },
-
- // Don't automatically add "px" to these possibly-unitless properties
- cssNumber: {
- "animationIterationCount": true,
- "columnCount": true,
- "fillOpacity": true,
- "flexGrow": true,
- "flexShrink": true,
- "fontWeight": true,
- "lineHeight": true,
- "opacity": true,
- "order": true,
- "orphans": true,
- "widows": true,
- "zIndex": true,
- "zoom": true
- },
-
- // Add in properties whose names you wish to fix before
- // setting or getting the value
- cssProps: {
- "float": "cssFloat"
- },
-
- // Get and set the style property on a DOM Node
- style: function( elem, name, value, extra ) {
-
- // Don't set styles on text and comment nodes
- if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
- return;
- }
-
- // Make sure that we're working with the right name
- var ret, type, hooks,
- origName = jQuery.camelCase( name ),
- isCustomProp = rcustomProp.test( name ),
- style = elem.style;
-
- // Make sure that we're working with the right name. We don't
- // want to query the value if it is a CSS custom property
- // since they are user-defined.
- if ( !isCustomProp ) {
- name = finalPropName( origName );
- }
-
- // Gets hook for the prefixed version, then unprefixed version
- hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
- // Check if we're setting a value
- if ( value !== undefined ) {
- type = typeof value;
-
- // Convert "+=" or "-=" to relative numbers (#7345)
- if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) {
- value = adjustCSS( elem, name, ret );
-
- // Fixes bug #9237
- type = "number";
- }
-
- // Make sure that null and NaN values aren't set (#7116)
- if ( value == null || value !== value ) {
- return;
- }
-
- // If a number was passed in, add the unit (except for certain CSS properties)
- if ( type === "number" ) {
- value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" );
- }
-
- // background-* props affect original clone's values
- if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) {
- style[ name ] = "inherit";
- }
-
- // If a hook was provided, use that value, otherwise just set the specified value
- if ( !hooks || !( "set" in hooks ) ||
- ( value = hooks.set( elem, value, extra ) ) !== undefined ) {
-
- if ( isCustomProp ) {
- style.setProperty( name, value );
- } else {
- style[ name ] = value;
- }
- }
-
- } else {
-
- // If a hook was provided get the non-computed value from there
- if ( hooks && "get" in hooks &&
- ( ret = hooks.get( elem, false, extra ) ) !== undefined ) {
-
- return ret;
- }
-
- // Otherwise just get the value from the style object
- return style[ name ];
- }
- },
-
- css: function( elem, name, extra, styles ) {
- var val, num, hooks,
- origName = jQuery.camelCase( name ),
- isCustomProp = rcustomProp.test( name );
-
- // Make sure that we're working with the right name. We don't
- // want to modify the value if it is a CSS custom property
- // since they are user-defined.
- if ( !isCustomProp ) {
- name = finalPropName( origName );
- }
-
- // Try prefixed name followed by the unprefixed name
- hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
- // If a hook was provided get the computed value from there
- if ( hooks && "get" in hooks ) {
- val = hooks.get( elem, true, extra );
- }
-
- // Otherwise, if a way to get the computed value exists, use that
- if ( val === undefined ) {
- val = curCSS( elem, name, styles );
- }
-
- // Convert "normal" to computed value
- if ( val === "normal" && name in cssNormalTransform ) {
- val = cssNormalTransform[ name ];
- }
-
- // Make numeric if forced or a qualifier was provided and val looks numeric
- if ( extra === "" || extra ) {
- num = parseFloat( val );
- return extra === true || isFinite( num ) ? num || 0 : val;
- }
-
- return val;
- }
-} );
-
-jQuery.each( [ "height", "width" ], function( i, name ) {
- jQuery.cssHooks[ name ] = {
- get: function( elem, computed, extra ) {
- if ( computed ) {
-
- // Certain elements can have dimension info if we invisibly show them
- // but it must have a current display style that would benefit
- return rdisplayswap.test( jQuery.css( elem, "display" ) ) &&
-
- // Support: Safari 8+
- // Table columns in Safari have non-zero offsetWidth & zero
- // getBoundingClientRect().width unless display is changed.
- // Support: IE <=11 only
- // Running getBoundingClientRect on a disconnected node
- // in IE throws an error.
- ( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ?
- swap( elem, cssShow, function() {
- return getWidthOrHeight( elem, name, extra );
- } ) :
- getWidthOrHeight( elem, name, extra );
- }
- },
-
- set: function( elem, value, extra ) {
- var matches,
- styles = extra && getStyles( elem ),
- subtract = extra && augmentWidthOrHeight(
- elem,
- name,
- extra,
- jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
- styles
- );
-
- // Convert to pixels if value adjustment is needed
- if ( subtract && ( matches = rcssNum.exec( value ) ) &&
- ( matches[ 3 ] || "px" ) !== "px" ) {
-
- elem.style[ name ] = value;
- value = jQuery.css( elem, name );
- }
-
- return setPositiveNumber( elem, value, subtract );
- }
- };
-} );
-
-jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft,
- function( elem, computed ) {
- if ( computed ) {
- return ( parseFloat( curCSS( elem, "marginLeft" ) ) ||
- elem.getBoundingClientRect().left -
- swap( elem, { marginLeft: 0 }, function() {
- return elem.getBoundingClientRect().left;
- } )
- ) + "px";
- }
- }
-);
-
-// These hooks are used by animate to expand properties
-jQuery.each( {
- margin: "",
- padding: "",
- border: "Width"
-}, function( prefix, suffix ) {
- jQuery.cssHooks[ prefix + suffix ] = {
- expand: function( value ) {
- var i = 0,
- expanded = {},
-
- // Assumes a single number if not a string
- parts = typeof value === "string" ? value.split( " " ) : [ value ];
-
- for ( ; i < 4; i++ ) {
- expanded[ prefix + cssExpand[ i ] + suffix ] =
- parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
- }
-
- return expanded;
- }
- };
-
- if ( !rmargin.test( prefix ) ) {
- jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
- }
-} );
-
-jQuery.fn.extend( {
- css: function( name, value ) {
- return access( this, function( elem, name, value ) {
- var styles, len,
- map = {},
- i = 0;
-
- if ( Array.isArray( name ) ) {
- styles = getStyles( elem );
- len = name.length;
-
- for ( ; i < len; i++ ) {
- map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
- }
-
- return map;
- }
-
- return value !== undefined ?
- jQuery.style( elem, name, value ) :
- jQuery.css( elem, name );
- }, name, value, arguments.length > 1 );
- }
-} );
-
-
-function Tween( elem, options, prop, end, easing ) {
- return new Tween.prototype.init( elem, options, prop, end, easing );
-}
-jQuery.Tween = Tween;
-
-Tween.prototype = {
- constructor: Tween,
- init: function( elem, options, prop, end, easing, unit ) {
- this.elem = elem;
- this.prop = prop;
- this.easing = easing || jQuery.easing._default;
- this.options = options;
- this.start = this.now = this.cur();
- this.end = end;
- this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
- },
- cur: function() {
- var hooks = Tween.propHooks[ this.prop ];
-
- return hooks && hooks.get ?
- hooks.get( this ) :
- Tween.propHooks._default.get( this );
- },
- run: function( percent ) {
- var eased,
- hooks = Tween.propHooks[ this.prop ];
-
- if ( this.options.duration ) {
- this.pos = eased = jQuery.easing[ this.easing ](
- percent, this.options.duration * percent, 0, 1, this.options.duration
- );
- } else {
- this.pos = eased = percent;
- }
- this.now = ( this.end - this.start ) * eased + this.start;
-
- if ( this.options.step ) {
- this.options.step.call( this.elem, this.now, this );
- }
-
- if ( hooks && hooks.set ) {
- hooks.set( this );
- } else {
- Tween.propHooks._default.set( this );
- }
- return this;
- }
-};
-
-Tween.prototype.init.prototype = Tween.prototype;
-
-Tween.propHooks = {
- _default: {
- get: function( tween ) {
- var result;
-
- // Use a property on the element directly when it is not a DOM element,
- // or when there is no matching style property that exists.
- if ( tween.elem.nodeType !== 1 ||
- tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) {
- return tween.elem[ tween.prop ];
- }
-
- // Passing an empty string as a 3rd parameter to .css will automatically
- // attempt a parseFloat and fallback to a string if the parse fails.
- // Simple values such as "10px" are parsed to Float;
- // complex values such as "rotate(1rad)" are returned as-is.
- result = jQuery.css( tween.elem, tween.prop, "" );
-
- // Empty strings, null, undefined and "auto" are converted to 0.
- return !result || result === "auto" ? 0 : result;
- },
- set: function( tween ) {
-
- // Use step hook for back compat.
- // Use cssHook if its there.
- // Use .style if available and use plain properties where available.
- if ( jQuery.fx.step[ tween.prop ] ) {
- jQuery.fx.step[ tween.prop ]( tween );
- } else if ( tween.elem.nodeType === 1 &&
- ( tween.elem.style[ jQuery.cssProps[ tween.prop ] ] != null ||
- jQuery.cssHooks[ tween.prop ] ) ) {
- jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
- } else {
- tween.elem[ tween.prop ] = tween.now;
- }
- }
- }
-};
-
-// Support: IE <=9 only
-// Panic based approach to setting things on disconnected nodes
-Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
- set: function( tween ) {
- if ( tween.elem.nodeType && tween.elem.parentNode ) {
- tween.elem[ tween.prop ] = tween.now;
- }
- }
-};
-
-jQuery.easing = {
- linear: function( p ) {
- return p;
- },
- swing: function( p ) {
- return 0.5 - Math.cos( p * Math.PI ) / 2;
- },
- _default: "swing"
-};
-
-jQuery.fx = Tween.prototype.init;
-
-// Back compat <1.8 extension point
-jQuery.fx.step = {};
-
-
-
-
-var
- fxNow, inProgress,
- rfxtypes = /^(?:toggle|show|hide)$/,
- rrun = /queueHooks$/;
-
-function schedule() {
- if ( inProgress ) {
- if ( document.hidden === false && window.requestAnimationFrame ) {
- window.requestAnimationFrame( schedule );
- } else {
- window.setTimeout( schedule, jQuery.fx.interval );
- }
-
- jQuery.fx.tick();
- }
-}
-
-// Animations created synchronously will run synchronously
-function createFxNow() {
- window.setTimeout( function() {
- fxNow = undefined;
- } );
- return ( fxNow = jQuery.now() );
-}
-
-// Generate parameters to create a standard animation
-function genFx( type, includeWidth ) {
- var which,
- i = 0,
- attrs = { height: type };
-
- // If we include width, step value is 1 to do all cssExpand values,
- // otherwise step value is 2 to skip over Left and Right
- includeWidth = includeWidth ? 1 : 0;
- for ( ; i < 4; i += 2 - includeWidth ) {
- which = cssExpand[ i ];
- attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
- }
-
- if ( includeWidth ) {
- attrs.opacity = attrs.width = type;
- }
-
- return attrs;
-}
-
-function createTween( value, prop, animation ) {
- var tween,
- collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ),
- index = 0,
- length = collection.length;
- for ( ; index < length; index++ ) {
- if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) {
-
- // We're done with this property
- return tween;
- }
- }
-}
-
-function defaultPrefilter( elem, props, opts ) {
- var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display,
- isBox = "width" in props || "height" in props,
- anim = this,
- orig = {},
- style = elem.style,
- hidden = elem.nodeType && isHiddenWithinTree( elem ),
- dataShow = dataPriv.get( elem, "fxshow" );
-
- // Queue-skipping animations hijack the fx hooks
- if ( !opts.queue ) {
- hooks = jQuery._queueHooks( elem, "fx" );
- if ( hooks.unqueued == null ) {
- hooks.unqueued = 0;
- oldfire = hooks.empty.fire;
- hooks.empty.fire = function() {
- if ( !hooks.unqueued ) {
- oldfire();
- }
- };
- }
- hooks.unqueued++;
-
- anim.always( function() {
-
- // Ensure the complete handler is called before this completes
- anim.always( function() {
- hooks.unqueued--;
- if ( !jQuery.queue( elem, "fx" ).length ) {
- hooks.empty.fire();
- }
- } );
- } );
- }
-
- // Detect show/hide animations
- for ( prop in props ) {
- value = props[ prop ];
- if ( rfxtypes.test( value ) ) {
- delete props[ prop ];
- toggle = toggle || value === "toggle";
- if ( value === ( hidden ? "hide" : "show" ) ) {
-
- // Pretend to be hidden if this is a "show" and
- // there is still data from a stopped show/hide
- if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
- hidden = true;
-
- // Ignore all other no-op show/hide data
- } else {
- continue;
- }
- }
- orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
- }
- }
-
- // Bail out if this is a no-op like .hide().hide()
- propTween = !jQuery.isEmptyObject( props );
- if ( !propTween && jQuery.isEmptyObject( orig ) ) {
- return;
- }
-
- // Restrict "overflow" and "display" styles during box animations
- if ( isBox && elem.nodeType === 1 ) {
-
- // Support: IE <=9 - 11, Edge 12 - 13
- // Record all 3 overflow attributes because IE does not infer the shorthand
- // from identically-valued overflowX and overflowY
- opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
-
- // Identify a display type, preferring old show/hide data over the CSS cascade
- restoreDisplay = dataShow && dataShow.display;
- if ( restoreDisplay == null ) {
- restoreDisplay = dataPriv.get( elem, "display" );
- }
- display = jQuery.css( elem, "display" );
- if ( display === "none" ) {
- if ( restoreDisplay ) {
- display = restoreDisplay;
- } else {
-
- // Get nonempty value(s) by temporarily forcing visibility
- showHide( [ elem ], true );
- restoreDisplay = elem.style.display || restoreDisplay;
- display = jQuery.css( elem, "display" );
- showHide( [ elem ] );
- }
- }
-
- // Animate inline elements as inline-block
- if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) {
- if ( jQuery.css( elem, "float" ) === "none" ) {
-
- // Restore the original display value at the end of pure show/hide animations
- if ( !propTween ) {
- anim.done( function() {
- style.display = restoreDisplay;
- } );
- if ( restoreDisplay == null ) {
- display = style.display;
- restoreDisplay = display === "none" ? "" : display;
- }
- }
- style.display = "inline-block";
- }
- }
- }
-
- if ( opts.overflow ) {
- style.overflow = "hidden";
- anim.always( function() {
- style.overflow = opts.overflow[ 0 ];
- style.overflowX = opts.overflow[ 1 ];
- style.overflowY = opts.overflow[ 2 ];
- } );
- }
-
- // Implement show/hide animations
- propTween = false;
- for ( prop in orig ) {
-
- // General show/hide setup for this element animation
- if ( !propTween ) {
- if ( dataShow ) {
- if ( "hidden" in dataShow ) {
- hidden = dataShow.hidden;
- }
- } else {
- dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } );
- }
-
- // Store hidden/visible for toggle so `.stop().toggle()` "reverses"
- if ( toggle ) {
- dataShow.hidden = !hidden;
- }
-
- // Show elements before animating them
- if ( hidden ) {
- showHide( [ elem ], true );
- }
-
- /* eslint-disable no-loop-func */
-
- anim.done( function() {
-
- /* eslint-enable no-loop-func */
-
- // The final step of a "hide" animation is actually hiding the element
- if ( !hidden ) {
- showHide( [ elem ] );
- }
- dataPriv.remove( elem, "fxshow" );
- for ( prop in orig ) {
- jQuery.style( elem, prop, orig[ prop ] );
- }
- } );
- }
-
- // Per-property setup
- propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
- if ( !( prop in dataShow ) ) {
- dataShow[ prop ] = propTween.start;
- if ( hidden ) {
- propTween.end = propTween.start;
- propTween.start = 0;
- }
- }
- }
-}
-
-function propFilter( props, specialEasing ) {
- var index, name, easing, value, hooks;
-
- // camelCase, specialEasing and expand cssHook pass
- for ( index in props ) {
- name = jQuery.camelCase( index );
- easing = specialEasing[ name ];
- value = props[ index ];
- if ( Array.isArray( value ) ) {
- easing = value[ 1 ];
- value = props[ index ] = value[ 0 ];
- }
-
- if ( index !== name ) {
- props[ name ] = value;
- delete props[ index ];
- }
-
- hooks = jQuery.cssHooks[ name ];
- if ( hooks && "expand" in hooks ) {
- value = hooks.expand( value );
- delete props[ name ];
-
- // Not quite $.extend, this won't overwrite existing keys.
- // Reusing 'index' because we have the correct "name"
- for ( index in value ) {
- if ( !( index in props ) ) {
- props[ index ] = value[ index ];
- specialEasing[ index ] = easing;
- }
- }
- } else {
- specialEasing[ name ] = easing;
- }
- }
-}
-
-function Animation( elem, properties, options ) {
- var result,
- stopped,
- index = 0,
- length = Animation.prefilters.length,
- deferred = jQuery.Deferred().always( function() {
-
- // Don't match elem in the :animated selector
- delete tick.elem;
- } ),
- tick = function() {
- if ( stopped ) {
- return false;
- }
- var currentTime = fxNow || createFxNow(),
- remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
-
- // Support: Android 2.3 only
- // Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497)
- temp = remaining / animation.duration || 0,
- percent = 1 - temp,
- index = 0,
- length = animation.tweens.length;
-
- for ( ; index < length; index++ ) {
- animation.tweens[ index ].run( percent );
- }
-
- deferred.notifyWith( elem, [ animation, percent, remaining ] );
-
- // If there's more to do, yield
- if ( percent < 1 && length ) {
- return remaining;
- }
-
- // If this was an empty animation, synthesize a final progress notification
- if ( !length ) {
- deferred.notifyWith( elem, [ animation, 1, 0 ] );
- }
-
- // Resolve the animation and report its conclusion
- deferred.resolveWith( elem, [ animation ] );
- return false;
- },
- animation = deferred.promise( {
- elem: elem,
- props: jQuery.extend( {}, properties ),
- opts: jQuery.extend( true, {
- specialEasing: {},
- easing: jQuery.easing._default
- }, options ),
- originalProperties: properties,
- originalOptions: options,
- startTime: fxNow || createFxNow(),
- duration: options.duration,
- tweens: [],
- createTween: function( prop, end ) {
- var tween = jQuery.Tween( elem, animation.opts, prop, end,
- animation.opts.specialEasing[ prop ] || animation.opts.easing );
- animation.tweens.push( tween );
- return tween;
- },
- stop: function( gotoEnd ) {
- var index = 0,
-
- // If we are going to the end, we want to run all the tweens
- // otherwise we skip this part
- length = gotoEnd ? animation.tweens.length : 0;
- if ( stopped ) {
- return this;
- }
- stopped = true;
- for ( ; index < length; index++ ) {
- animation.tweens[ index ].run( 1 );
- }
-
- // Resolve when we played the last frame; otherwise, reject
- if ( gotoEnd ) {
- deferred.notifyWith( elem, [ animation, 1, 0 ] );
- deferred.resolveWith( elem, [ animation, gotoEnd ] );
- } else {
- deferred.rejectWith( elem, [ animation, gotoEnd ] );
- }
- return this;
- }
- } ),
- props = animation.props;
-
- propFilter( props, animation.opts.specialEasing );
-
- for ( ; index < length; index++ ) {
- result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts );
- if ( result ) {
- if ( jQuery.isFunction( result.stop ) ) {
- jQuery._queueHooks( animation.elem, animation.opts.queue ).stop =
- jQuery.proxy( result.stop, result );
- }
- return result;
- }
- }
-
- jQuery.map( props, createTween, animation );
-
- if ( jQuery.isFunction( animation.opts.start ) ) {
- animation.opts.start.call( elem, animation );
- }
-
- // Attach callbacks from options
- animation
- .progress( animation.opts.progress )
- .done( animation.opts.done, animation.opts.complete )
- .fail( animation.opts.fail )
- .always( animation.opts.always );
-
- jQuery.fx.timer(
- jQuery.extend( tick, {
- elem: elem,
- anim: animation,
- queue: animation.opts.queue
- } )
- );
-
- return animation;
-}
-
-jQuery.Animation = jQuery.extend( Animation, {
-
- tweeners: {
- "*": [ function( prop, value ) {
- var tween = this.createTween( prop, value );
- adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween );
- return tween;
- } ]
- },
-
- tweener: function( props, callback ) {
- if ( jQuery.isFunction( props ) ) {
- callback = props;
- props = [ "*" ];
- } else {
- props = props.match( rnothtmlwhite );
- }
-
- var prop,
- index = 0,
- length = props.length;
-
- for ( ; index < length; index++ ) {
- prop = props[ index ];
- Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || [];
- Animation.tweeners[ prop ].unshift( callback );
- }
- },
-
- prefilters: [ defaultPrefilter ],
-
- prefilter: function( callback, prepend ) {
- if ( prepend ) {
- Animation.prefilters.unshift( callback );
- } else {
- Animation.prefilters.push( callback );
- }
- }
-} );
-
-jQuery.speed = function( speed, easing, fn ) {
- var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
- complete: fn || !fn && easing ||
- jQuery.isFunction( speed ) && speed,
- duration: speed,
- easing: fn && easing || easing && !jQuery.isFunction( easing ) && easing
- };
-
- // Go to the end state if fx are off
- if ( jQuery.fx.off ) {
- opt.duration = 0;
-
- } else {
- if ( typeof opt.duration !== "number" ) {
- if ( opt.duration in jQuery.fx.speeds ) {
- opt.duration = jQuery.fx.speeds[ opt.duration ];
-
- } else {
- opt.duration = jQuery.fx.speeds._default;
- }
- }
- }
-
- // Normalize opt.queue - true/undefined/null -> "fx"
- if ( opt.queue == null || opt.queue === true ) {
- opt.queue = "fx";
- }
-
- // Queueing
- opt.old = opt.complete;
-
- opt.complete = function() {
- if ( jQuery.isFunction( opt.old ) ) {
- opt.old.call( this );
- }
-
- if ( opt.queue ) {
- jQuery.dequeue( this, opt.queue );
- }
- };
-
- return opt;
-};
-
-jQuery.fn.extend( {
- fadeTo: function( speed, to, easing, callback ) {
-
- // Show any hidden elements after setting opacity to 0
- return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show()
-
- // Animate to the value specified
- .end().animate( { opacity: to }, speed, easing, callback );
- },
- animate: function( prop, speed, easing, callback ) {
- var empty = jQuery.isEmptyObject( prop ),
- optall = jQuery.speed( speed, easing, callback ),
- doAnimation = function() {
-
- // Operate on a copy of prop so per-property easing won't be lost
- var anim = Animation( this, jQuery.extend( {}, prop ), optall );
-
- // Empty animations, or finishing resolves immediately
- if ( empty || dataPriv.get( this, "finish" ) ) {
- anim.stop( true );
- }
- };
- doAnimation.finish = doAnimation;
-
- return empty || optall.queue === false ?
- this.each( doAnimation ) :
- this.queue( optall.queue, doAnimation );
- },
- stop: function( type, clearQueue, gotoEnd ) {
- var stopQueue = function( hooks ) {
- var stop = hooks.stop;
- delete hooks.stop;
- stop( gotoEnd );
- };
-
- if ( typeof type !== "string" ) {
- gotoEnd = clearQueue;
- clearQueue = type;
- type = undefined;
- }
- if ( clearQueue && type !== false ) {
- this.queue( type || "fx", [] );
- }
-
- return this.each( function() {
- var dequeue = true,
- index = type != null && type + "queueHooks",
- timers = jQuery.timers,
- data = dataPriv.get( this );
-
- if ( index ) {
- if ( data[ index ] && data[ index ].stop ) {
- stopQueue( data[ index ] );
- }
- } else {
- for ( index in data ) {
- if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
- stopQueue( data[ index ] );
- }
- }
- }
-
- for ( index = timers.length; index--; ) {
- if ( timers[ index ].elem === this &&
- ( type == null || timers[ index ].queue === type ) ) {
-
- timers[ index ].anim.stop( gotoEnd );
- dequeue = false;
- timers.splice( index, 1 );
- }
- }
-
- // Start the next in the queue if the last step wasn't forced.
- // Timers currently will call their complete callbacks, which
- // will dequeue but only if they were gotoEnd.
- if ( dequeue || !gotoEnd ) {
- jQuery.dequeue( this, type );
- }
- } );
- },
- finish: function( type ) {
- if ( type !== false ) {
- type = type || "fx";
- }
- return this.each( function() {
- var index,
- data = dataPriv.get( this ),
- queue = data[ type + "queue" ],
- hooks = data[ type + "queueHooks" ],
- timers = jQuery.timers,
- length = queue ? queue.length : 0;
-
- // Enable finishing flag on private data
- data.finish = true;
-
- // Empty the queue first
- jQuery.queue( this, type, [] );
-
- if ( hooks && hooks.stop ) {
- hooks.stop.call( this, true );
- }
-
- // Look for any active animations, and finish them
- for ( index = timers.length; index--; ) {
- if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
- timers[ index ].anim.stop( true );
- timers.splice( index, 1 );
- }
- }
-
- // Look for any animations in the old queue and finish them
- for ( index = 0; index < length; index++ ) {
- if ( queue[ index ] && queue[ index ].finish ) {
- queue[ index ].finish.call( this );
- }
- }
-
- // Turn off finishing flag
- delete data.finish;
- } );
- }
-} );
-
-jQuery.each( [ "toggle", "show", "hide" ], function( i, name ) {
- var cssFn = jQuery.fn[ name ];
- jQuery.fn[ name ] = function( speed, easing, callback ) {
- return speed == null || typeof speed === "boolean" ?
- cssFn.apply( this, arguments ) :
- this.animate( genFx( name, true ), speed, easing, callback );
- };
-} );
-
-// Generate shortcuts for custom animations
-jQuery.each( {
- slideDown: genFx( "show" ),
- slideUp: genFx( "hide" ),
- slideToggle: genFx( "toggle" ),
- fadeIn: { opacity: "show" },
- fadeOut: { opacity: "hide" },
- fadeToggle: { opacity: "toggle" }
-}, function( name, props ) {
- jQuery.fn[ name ] = function( speed, easing, callback ) {
- return this.animate( props, speed, easing, callback );
- };
-} );
-
-jQuery.timers = [];
-jQuery.fx.tick = function() {
- var timer,
- i = 0,
- timers = jQuery.timers;
-
- fxNow = jQuery.now();
-
- for ( ; i < timers.length; i++ ) {
- timer = timers[ i ];
-
- // Run the timer and safely remove it when done (allowing for external removal)
- if ( !timer() && timers[ i ] === timer ) {
- timers.splice( i--, 1 );
- }
- }
-
- if ( !timers.length ) {
- jQuery.fx.stop();
- }
- fxNow = undefined;
-};
-
-jQuery.fx.timer = function( timer ) {
- jQuery.timers.push( timer );
- jQuery.fx.start();
-};
-
-jQuery.fx.interval = 13;
-jQuery.fx.start = function() {
- if ( inProgress ) {
- return;
- }
-
- inProgress = true;
- schedule();
-};
-
-jQuery.fx.stop = function() {
- inProgress = null;
-};
-
-jQuery.fx.speeds = {
- slow: 600,
- fast: 200,
-
- // Default speed
- _default: 400
-};
-
-
-// Based off of the plugin by Clint Helfers, with permission.
-// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/
-jQuery.fn.delay = function( time, type ) {
- time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
- type = type || "fx";
-
- return this.queue( type, function( next, hooks ) {
- var timeout = window.setTimeout( next, time );
- hooks.stop = function() {
- window.clearTimeout( timeout );
- };
- } );
-};
-
-
-( function() {
- var input = document.createElement( "input" ),
- select = document.createElement( "select" ),
- opt = select.appendChild( document.createElement( "option" ) );
-
- input.type = "checkbox";
-
- // Support: Android <=4.3 only
- // Default value for a checkbox should be "on"
- support.checkOn = input.value !== "";
-
- // Support: IE <=11 only
- // Must access selectedIndex to make default options select
- support.optSelected = opt.selected;
-
- // Support: IE <=11 only
- // An input loses its value after becoming a radio
- input = document.createElement( "input" );
- input.value = "t";
- input.type = "radio";
- support.radioValue = input.value === "t";
-} )();
-
-
-var boolHook,
- attrHandle = jQuery.expr.attrHandle;
-
-jQuery.fn.extend( {
- attr: function( name, value ) {
- return access( this, jQuery.attr, name, value, arguments.length > 1 );
- },
-
- removeAttr: function( name ) {
- return this.each( function() {
- jQuery.removeAttr( this, name );
- } );
- }
-} );
-
-jQuery.extend( {
- attr: function( elem, name, value ) {
- var ret, hooks,
- nType = elem.nodeType;
-
- // Don't get/set attributes on text, comment and attribute nodes
- if ( nType === 3 || nType === 8 || nType === 2 ) {
- return;
- }
-
- // Fallback to prop when attributes are not supported
- if ( typeof elem.getAttribute === "undefined" ) {
- return jQuery.prop( elem, name, value );
- }
-
- // Attribute hooks are determined by the lowercase version
- // Grab necessary hook if one is defined
- if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
- hooks = jQuery.attrHooks[ name.toLowerCase() ] ||
- ( jQuery.expr.match.bool.test( name ) ? boolHook : undefined );
- }
-
- if ( value !== undefined ) {
- if ( value === null ) {
- jQuery.removeAttr( elem, name );
- return;
- }
-
- if ( hooks && "set" in hooks &&
- ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
- return ret;
- }
-
- elem.setAttribute( name, value + "" );
- return value;
- }
-
- if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
- return ret;
- }
-
- ret = jQuery.find.attr( elem, name );
-
- // Non-existent attributes return null, we normalize to undefined
- return ret == null ? undefined : ret;
- },
-
- attrHooks: {
- type: {
- set: function( elem, value ) {
- if ( !support.radioValue && value === "radio" &&
- nodeName( elem, "input" ) ) {
- var val = elem.value;
- elem.setAttribute( "type", value );
- if ( val ) {
- elem.value = val;
- }
- return value;
- }
- }
- }
- },
-
- removeAttr: function( elem, value ) {
- var name,
- i = 0,
-
- // Attribute names can contain non-HTML whitespace characters
- // https://html.spec.whatwg.org/multipage/syntax.html#attributes-2
- attrNames = value && value.match( rnothtmlwhite );
-
- if ( attrNames && elem.nodeType === 1 ) {
- while ( ( name = attrNames[ i++ ] ) ) {
- elem.removeAttribute( name );
- }
- }
- }
-} );
-
-// Hooks for boolean attributes
-boolHook = {
- set: function( elem, value, name ) {
- if ( value === false ) {
-
- // Remove boolean attributes when set to false
- jQuery.removeAttr( elem, name );
- } else {
- elem.setAttribute( name, name );
- }
- return name;
- }
-};
-
-jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( i, name ) {
- var getter = attrHandle[ name ] || jQuery.find.attr;
-
- attrHandle[ name ] = function( elem, name, isXML ) {
- var ret, handle,
- lowercaseName = name.toLowerCase();
-
- if ( !isXML ) {
-
- // Avoid an infinite loop by temporarily removing this function from the getter
- handle = attrHandle[ lowercaseName ];
- attrHandle[ lowercaseName ] = ret;
- ret = getter( elem, name, isXML ) != null ?
- lowercaseName :
- null;
- attrHandle[ lowercaseName ] = handle;
- }
- return ret;
- };
-} );
-
-
-
-
-var rfocusable = /^(?:input|select|textarea|button)$/i,
- rclickable = /^(?:a|area)$/i;
-
-jQuery.fn.extend( {
- prop: function( name, value ) {
- return access( this, jQuery.prop, name, value, arguments.length > 1 );
- },
-
- removeProp: function( name ) {
- return this.each( function() {
- delete this[ jQuery.propFix[ name ] || name ];
- } );
- }
-} );
-
-jQuery.extend( {
- prop: function( elem, name, value ) {
- var ret, hooks,
- nType = elem.nodeType;
-
- // Don't get/set properties on text, comment and attribute nodes
- if ( nType === 3 || nType === 8 || nType === 2 ) {
- return;
- }
-
- if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
-
- // Fix name and attach hooks
- name = jQuery.propFix[ name ] || name;
- hooks = jQuery.propHooks[ name ];
- }
-
- if ( value !== undefined ) {
- if ( hooks && "set" in hooks &&
- ( ret = hooks.set( elem, value, name ) ) !== undefined ) {
- return ret;
- }
-
- return ( elem[ name ] = value );
- }
-
- if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
- return ret;
- }
-
- return elem[ name ];
- },
-
- propHooks: {
- tabIndex: {
- get: function( elem ) {
-
- // Support: IE <=9 - 11 only
- // elem.tabIndex doesn't always return the
- // correct value when it hasn't been explicitly set
- // https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
- // Use proper attribute retrieval(#12072)
- var tabindex = jQuery.find.attr( elem, "tabindex" );
-
- if ( tabindex ) {
- return parseInt( tabindex, 10 );
- }
-
- if (
- rfocusable.test( elem.nodeName ) ||
- rclickable.test( elem.nodeName ) &&
- elem.href
- ) {
- return 0;
- }
-
- return -1;
- }
- }
- },
-
- propFix: {
- "for": "htmlFor",
- "class": "className"
- }
-} );
-
-// Support: IE <=11 only
-// Accessing the selectedIndex property
-// forces the browser to respect setting selected
-// on the option
-// The getter ensures a default option is selected
-// when in an optgroup
-// eslint rule "no-unused-expressions" is disabled for this code
-// since it considers such accessions noop
-if ( !support.optSelected ) {
- jQuery.propHooks.selected = {
- get: function( elem ) {
-
- /* eslint no-unused-expressions: "off" */
-
- var parent = elem.parentNode;
- if ( parent && parent.parentNode ) {
- parent.parentNode.selectedIndex;
- }
- return null;
- },
- set: function( elem ) {
-
- /* eslint no-unused-expressions: "off" */
-
- var parent = elem.parentNode;
- if ( parent ) {
- parent.selectedIndex;
-
- if ( parent.parentNode ) {
- parent.parentNode.selectedIndex;
- }
- }
- }
- };
-}
-
-jQuery.each( [
- "tabIndex",
- "readOnly",
- "maxLength",
- "cellSpacing",
- "cellPadding",
- "rowSpan",
- "colSpan",
- "useMap",
- "frameBorder",
- "contentEditable"
-], function() {
- jQuery.propFix[ this.toLowerCase() ] = this;
-} );
-
-
-
-
- // Strip and collapse whitespace according to HTML spec
- // https://html.spec.whatwg.org/multipage/infrastructure.html#strip-and-collapse-whitespace
- function stripAndCollapse( value ) {
- var tokens = value.match( rnothtmlwhite ) || [];
- return tokens.join( " " );
- }
-
-
-function getClass( elem ) {
- return elem.getAttribute && elem.getAttribute( "class" ) || "";
-}
-
-jQuery.fn.extend( {
- addClass: function( value ) {
- var classes, elem, cur, curValue, clazz, j, finalValue,
- i = 0;
-
- if ( jQuery.isFunction( value ) ) {
- return this.each( function( j ) {
- jQuery( this ).addClass( value.call( this, j, getClass( this ) ) );
- } );
- }
-
- if ( typeof value === "string" && value ) {
- classes = value.match( rnothtmlwhite ) || [];
-
- while ( ( elem = this[ i++ ] ) ) {
- curValue = getClass( elem );
- cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
-
- if ( cur ) {
- j = 0;
- while ( ( clazz = classes[ j++ ] ) ) {
- if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
- cur += clazz + " ";
- }
- }
-
- // Only assign if different to avoid unneeded rendering.
- finalValue = stripAndCollapse( cur );
- if ( curValue !== finalValue ) {
- elem.setAttribute( "class", finalValue );
- }
- }
- }
- }
-
- return this;
- },
-
- removeClass: function( value ) {
- var classes, elem, cur, curValue, clazz, j, finalValue,
- i = 0;
-
- if ( jQuery.isFunction( value ) ) {
- return this.each( function( j ) {
- jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) );
- } );
- }
-
- if ( !arguments.length ) {
- return this.attr( "class", "" );
- }
-
- if ( typeof value === "string" && value ) {
- classes = value.match( rnothtmlwhite ) || [];
-
- while ( ( elem = this[ i++ ] ) ) {
- curValue = getClass( elem );
-
- // This expression is here for better compressibility (see addClass)
- cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
-
- if ( cur ) {
- j = 0;
- while ( ( clazz = classes[ j++ ] ) ) {
-
- // Remove *all* instances
- while ( cur.indexOf( " " + clazz + " " ) > -1 ) {
- cur = cur.replace( " " + clazz + " ", " " );
- }
- }
-
- // Only assign if different to avoid unneeded rendering.
- finalValue = stripAndCollapse( cur );
- if ( curValue !== finalValue ) {
- elem.setAttribute( "class", finalValue );
- }
- }
- }
- }
-
- return this;
- },
-
- toggleClass: function( value, stateVal ) {
- var type = typeof value;
-
- if ( typeof stateVal === "boolean" && type === "string" ) {
- return stateVal ? this.addClass( value ) : this.removeClass( value );
- }
-
- if ( jQuery.isFunction( value ) ) {
- return this.each( function( i ) {
- jQuery( this ).toggleClass(
- value.call( this, i, getClass( this ), stateVal ),
- stateVal
- );
- } );
- }
-
- return this.each( function() {
- var className, i, self, classNames;
-
- if ( type === "string" ) {
-
- // Toggle individual class names
- i = 0;
- self = jQuery( this );
- classNames = value.match( rnothtmlwhite ) || [];
-
- while ( ( className = classNames[ i++ ] ) ) {
-
- // Check each className given, space separated list
- if ( self.hasClass( className ) ) {
- self.removeClass( className );
- } else {
- self.addClass( className );
- }
- }
-
- // Toggle whole class name
- } else if ( value === undefined || type === "boolean" ) {
- className = getClass( this );
- if ( className ) {
-
- // Store className if set
- dataPriv.set( this, "__className__", className );
- }
-
- // If the element has a class name or if we're passed `false`,
- // then remove the whole classname (if there was one, the above saved it).
- // Otherwise bring back whatever was previously saved (if anything),
- // falling back to the empty string if nothing was stored.
- if ( this.setAttribute ) {
- this.setAttribute( "class",
- className || value === false ?
- "" :
- dataPriv.get( this, "__className__" ) || ""
- );
- }
- }
- } );
- },
-
- hasClass: function( selector ) {
- var className, elem,
- i = 0;
-
- className = " " + selector + " ";
- while ( ( elem = this[ i++ ] ) ) {
- if ( elem.nodeType === 1 &&
- ( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) {
- return true;
- }
- }
-
- return false;
- }
-} );
-
-
-
-
-var rreturn = /\r/g;
-
-jQuery.fn.extend( {
- val: function( value ) {
- var hooks, ret, isFunction,
- elem = this[ 0 ];
-
- if ( !arguments.length ) {
- if ( elem ) {
- hooks = jQuery.valHooks[ elem.type ] ||
- jQuery.valHooks[ elem.nodeName.toLowerCase() ];
-
- if ( hooks &&
- "get" in hooks &&
- ( ret = hooks.get( elem, "value" ) ) !== undefined
- ) {
- return ret;
- }
-
- ret = elem.value;
-
- // Handle most common string cases
- if ( typeof ret === "string" ) {
- return ret.replace( rreturn, "" );
- }
-
- // Handle cases where value is null/undef or number
- return ret == null ? "" : ret;
- }
-
- return;
- }
-
- isFunction = jQuery.isFunction( value );
-
- return this.each( function( i ) {
- var val;
-
- if ( this.nodeType !== 1 ) {
- return;
- }
-
- if ( isFunction ) {
- val = value.call( this, i, jQuery( this ).val() );
- } else {
- val = value;
- }
-
- // Treat null/undefined as ""; convert numbers to string
- if ( val == null ) {
- val = "";
-
- } else if ( typeof val === "number" ) {
- val += "";
-
- } else if ( Array.isArray( val ) ) {
- val = jQuery.map( val, function( value ) {
- return value == null ? "" : value + "";
- } );
- }
-
- hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
-
- // If set returns undefined, fall back to normal setting
- if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) {
- this.value = val;
- }
- } );
- }
-} );
-
-jQuery.extend( {
- valHooks: {
- option: {
- get: function( elem ) {
-
- var val = jQuery.find.attr( elem, "value" );
- return val != null ?
- val :
-
- // Support: IE <=10 - 11 only
- // option.text throws exceptions (#14686, #14858)
- // Strip and collapse whitespace
- // https://html.spec.whatwg.org/#strip-and-collapse-whitespace
- stripAndCollapse( jQuery.text( elem ) );
- }
- },
- select: {
- get: function( elem ) {
- var value, option, i,
- options = elem.options,
- index = elem.selectedIndex,
- one = elem.type === "select-one",
- values = one ? null : [],
- max = one ? index + 1 : options.length;
-
- if ( index < 0 ) {
- i = max;
-
- } else {
- i = one ? index : 0;
- }
-
- // Loop through all the selected options
- for ( ; i < max; i++ ) {
- option = options[ i ];
-
- // Support: IE <=9 only
- // IE8-9 doesn't update selected after form reset (#2551)
- if ( ( option.selected || i === index ) &&
-
- // Don't return options that are disabled or in a disabled optgroup
- !option.disabled &&
- ( !option.parentNode.disabled ||
- !nodeName( option.parentNode, "optgroup" ) ) ) {
-
- // Get the specific value for the option
- value = jQuery( option ).val();
-
- // We don't need an array for one selects
- if ( one ) {
- return value;
- }
-
- // Multi-Selects return an array
- values.push( value );
- }
- }
-
- return values;
- },
-
- set: function( elem, value ) {
- var optionSet, option,
- options = elem.options,
- values = jQuery.makeArray( value ),
- i = options.length;
-
- while ( i-- ) {
- option = options[ i ];
-
- /* eslint-disable no-cond-assign */
-
- if ( option.selected =
- jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1
- ) {
- optionSet = true;
- }
-
- /* eslint-enable no-cond-assign */
- }
-
- // Force browsers to behave consistently when non-matching value is set
- if ( !optionSet ) {
- elem.selectedIndex = -1;
- }
- return values;
- }
- }
- }
-} );
-
-// Radios and checkboxes getter/setter
-jQuery.each( [ "radio", "checkbox" ], function() {
- jQuery.valHooks[ this ] = {
- set: function( elem, value ) {
- if ( Array.isArray( value ) ) {
- return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 );
- }
- }
- };
- if ( !support.checkOn ) {
- jQuery.valHooks[ this ].get = function( elem ) {
- return elem.getAttribute( "value" ) === null ? "on" : elem.value;
- };
- }
-} );
-
-
-
-
-// Return jQuery for attributes-only inclusion
-
-
-var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/;
-
-jQuery.extend( jQuery.event, {
-
- trigger: function( event, data, elem, onlyHandlers ) {
-
- var i, cur, tmp, bubbleType, ontype, handle, special,
- eventPath = [ elem || document ],
- type = hasOwn.call( event, "type" ) ? event.type : event,
- namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : [];
-
- cur = tmp = elem = elem || document;
-
- // Don't do events on text and comment nodes
- if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
- return;
- }
-
- // focus/blur morphs to focusin/out; ensure we're not firing them right now
- if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
- return;
- }
-
- if ( type.indexOf( "." ) > -1 ) {
-
- // Namespaced trigger; create a regexp to match event type in handle()
- namespaces = type.split( "." );
- type = namespaces.shift();
- namespaces.sort();
- }
- ontype = type.indexOf( ":" ) < 0 && "on" + type;
-
- // Caller can pass in a jQuery.Event object, Object, or just an event type string
- event = event[ jQuery.expando ] ?
- event :
- new jQuery.Event( type, typeof event === "object" && event );
-
- // Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
- event.isTrigger = onlyHandlers ? 2 : 3;
- event.namespace = namespaces.join( "." );
- event.rnamespace = event.namespace ?
- new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) :
- null;
-
- // Clean up the event in case it is being reused
- event.result = undefined;
- if ( !event.target ) {
- event.target = elem;
- }
-
- // Clone any incoming data and prepend the event, creating the handler arg list
- data = data == null ?
- [ event ] :
- jQuery.makeArray( data, [ event ] );
-
- // Allow special events to draw outside the lines
- special = jQuery.event.special[ type ] || {};
- if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
- return;
- }
-
- // Determine event propagation path in advance, per W3C events spec (#9951)
- // Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
- if ( !onlyHandlers && !special.noBubble && !jQuery.isWindow( elem ) ) {
-
- bubbleType = special.delegateType || type;
- if ( !rfocusMorph.test( bubbleType + type ) ) {
- cur = cur.parentNode;
- }
- for ( ; cur; cur = cur.parentNode ) {
- eventPath.push( cur );
- tmp = cur;
- }
-
- // Only add window if we got to document (e.g., not plain obj or detached DOM)
- if ( tmp === ( elem.ownerDocument || document ) ) {
- eventPath.push( tmp.defaultView || tmp.parentWindow || window );
- }
- }
-
- // Fire handlers on the event path
- i = 0;
- while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) {
-
- event.type = i > 1 ?
- bubbleType :
- special.bindType || type;
-
- // jQuery handler
- handle = ( dataPriv.get( cur, "events" ) || {} )[ event.type ] &&
- dataPriv.get( cur, "handle" );
- if ( handle ) {
- handle.apply( cur, data );
- }
-
- // Native handler
- handle = ontype && cur[ ontype ];
- if ( handle && handle.apply && acceptData( cur ) ) {
- event.result = handle.apply( cur, data );
- if ( event.result === false ) {
- event.preventDefault();
- }
- }
- }
- event.type = type;
-
- // If nobody prevented the default action, do it now
- if ( !onlyHandlers && !event.isDefaultPrevented() ) {
-
- if ( ( !special._default ||
- special._default.apply( eventPath.pop(), data ) === false ) &&
- acceptData( elem ) ) {
-
- // Call a native DOM method on the target with the same name as the event.
- // Don't do default actions on window, that's where global variables be (#6170)
- if ( ontype && jQuery.isFunction( elem[ type ] ) && !jQuery.isWindow( elem ) ) {
-
- // Don't re-trigger an onFOO event when we call its FOO() method
- tmp = elem[ ontype ];
-
- if ( tmp ) {
- elem[ ontype ] = null;
- }
-
- // Prevent re-triggering of the same event, since we already bubbled it above
- jQuery.event.triggered = type;
- elem[ type ]();
- jQuery.event.triggered = undefined;
-
- if ( tmp ) {
- elem[ ontype ] = tmp;
- }
- }
- }
- }
-
- return event.result;
- },
-
- // Piggyback on a donor event to simulate a different one
- // Used only for `focus(in | out)` events
- simulate: function( type, elem, event ) {
- var e = jQuery.extend(
- new jQuery.Event(),
- event,
- {
- type: type,
- isSimulated: true
- }
- );
-
- jQuery.event.trigger( e, null, elem );
- }
-
-} );
-
-jQuery.fn.extend( {
-
- trigger: function( type, data ) {
- return this.each( function() {
- jQuery.event.trigger( type, data, this );
- } );
- },
- triggerHandler: function( type, data ) {
- var elem = this[ 0 ];
- if ( elem ) {
- return jQuery.event.trigger( type, data, elem, true );
- }
- }
-} );
-
-
-jQuery.each( ( "blur focus focusin focusout resize scroll click dblclick " +
- "mousedown mouseup mousemove mouseover mouseout mouseenter mouseleave " +
- "change select submit keydown keypress keyup contextmenu" ).split( " " ),
- function( i, name ) {
-
- // Handle event binding
- jQuery.fn[ name ] = function( data, fn ) {
- return arguments.length > 0 ?
- this.on( name, null, data, fn ) :
- this.trigger( name );
- };
-} );
-
-jQuery.fn.extend( {
- hover: function( fnOver, fnOut ) {
- return this.mouseenter( fnOver ).mouseleave( fnOut || fnOver );
- }
-} );
-
-
-
-
-support.focusin = "onfocusin" in window;
-
-
-// Support: Firefox <=44
-// Firefox doesn't have focus(in | out) events
-// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787
-//
-// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1
-// focus(in | out) events fire after focus & blur events,
-// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order
-// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857
-if ( !support.focusin ) {
- jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) {
-
- // Attach a single capturing handler on the document while someone wants focusin/focusout
- var handler = function( event ) {
- jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) );
- };
-
- jQuery.event.special[ fix ] = {
- setup: function() {
- var doc = this.ownerDocument || this,
- attaches = dataPriv.access( doc, fix );
-
- if ( !attaches ) {
- doc.addEventListener( orig, handler, true );
- }
- dataPriv.access( doc, fix, ( attaches || 0 ) + 1 );
- },
- teardown: function() {
- var doc = this.ownerDocument || this,
- attaches = dataPriv.access( doc, fix ) - 1;
-
- if ( !attaches ) {
- doc.removeEventListener( orig, handler, true );
- dataPriv.remove( doc, fix );
-
- } else {
- dataPriv.access( doc, fix, attaches );
- }
- }
- };
- } );
-}
-var location = window.location;
-
-var nonce = jQuery.now();
-
-var rquery = ( /\?/ );
-
-
-
-// Cross-browser xml parsing
-jQuery.parseXML = function( data ) {
- var xml;
- if ( !data || typeof data !== "string" ) {
- return null;
- }
-
- // Support: IE 9 - 11 only
- // IE throws on parseFromString with invalid input.
- try {
- xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" );
- } catch ( e ) {
- xml = undefined;
- }
-
- if ( !xml || xml.getElementsByTagName( "parsererror" ).length ) {
- jQuery.error( "Invalid XML: " + data );
- }
- return xml;
-};
-
-
-var
- rbracket = /\[\]$/,
- rCRLF = /\r?\n/g,
- rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
- rsubmittable = /^(?:input|select|textarea|keygen)/i;
-
-function buildParams( prefix, obj, traditional, add ) {
- var name;
-
- if ( Array.isArray( obj ) ) {
-
- // Serialize array item.
- jQuery.each( obj, function( i, v ) {
- if ( traditional || rbracket.test( prefix ) ) {
-
- // Treat each array item as a scalar.
- add( prefix, v );
-
- } else {
-
- // Item is non-scalar (array or object), encode its numeric index.
- buildParams(
- prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]",
- v,
- traditional,
- add
- );
- }
- } );
-
- } else if ( !traditional && jQuery.type( obj ) === "object" ) {
-
- // Serialize object item.
- for ( name in obj ) {
- buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
- }
-
- } else {
-
- // Serialize scalar item.
- add( prefix, obj );
- }
-}
-
-// Serialize an array of form elements or a set of
-// key/values into a query string
-jQuery.param = function( a, traditional ) {
- var prefix,
- s = [],
- add = function( key, valueOrFunction ) {
-
- // If value is a function, invoke it and use its return value
- var value = jQuery.isFunction( valueOrFunction ) ?
- valueOrFunction() :
- valueOrFunction;
-
- s[ s.length ] = encodeURIComponent( key ) + "=" +
- encodeURIComponent( value == null ? "" : value );
- };
-
- // If an array was passed in, assume that it is an array of form elements.
- if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
-
- // Serialize the form elements
- jQuery.each( a, function() {
- add( this.name, this.value );
- } );
-
- } else {
-
- // If traditional, encode the "old" way (the way 1.3.2 or older
- // did it), otherwise encode params recursively.
- for ( prefix in a ) {
- buildParams( prefix, a[ prefix ], traditional, add );
- }
- }
-
- // Return the resulting serialization
- return s.join( "&" );
-};
-
-jQuery.fn.extend( {
- serialize: function() {
- return jQuery.param( this.serializeArray() );
- },
- serializeArray: function() {
- return this.map( function() {
-
- // Can add propHook for "elements" to filter or add form elements
- var elements = jQuery.prop( this, "elements" );
- return elements ? jQuery.makeArray( elements ) : this;
- } )
- .filter( function() {
- var type = this.type;
-
- // Use .is( ":disabled" ) so that fieldset[disabled] works
- return this.name && !jQuery( this ).is( ":disabled" ) &&
- rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
- ( this.checked || !rcheckableType.test( type ) );
- } )
- .map( function( i, elem ) {
- var val = jQuery( this ).val();
-
- if ( val == null ) {
- return null;
- }
-
- if ( Array.isArray( val ) ) {
- return jQuery.map( val, function( val ) {
- return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- } );
- }
-
- return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
- } ).get();
- }
-} );
-
-
-var
- r20 = /%20/g,
- rhash = /#.*$/,
- rantiCache = /([?&])_=[^&]*/,
- rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg,
-
- // #7653, #8125, #8152: local protocol detection
- rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
- rnoContent = /^(?:GET|HEAD)$/,
- rprotocol = /^\/\//,
-
- /* Prefilters
- * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
- * 2) These are called:
- * - BEFORE asking for a transport
- * - AFTER param serialization (s.data is a string if s.processData is true)
- * 3) key is the dataType
- * 4) the catchall symbol "*" can be used
- * 5) execution will start with transport dataType and THEN continue down to "*" if needed
- */
- prefilters = {},
-
- /* Transports bindings
- * 1) key is the dataType
- * 2) the catchall symbol "*" can be used
- * 3) selection will start with transport dataType and THEN go to "*" if needed
- */
- transports = {},
-
- // Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
- allTypes = "*/".concat( "*" ),
-
- // Anchor tag for parsing the document origin
- originAnchor = document.createElement( "a" );
- originAnchor.href = location.href;
-
-// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
-function addToPrefiltersOrTransports( structure ) {
-
- // dataTypeExpression is optional and defaults to "*"
- return function( dataTypeExpression, func ) {
-
- if ( typeof dataTypeExpression !== "string" ) {
- func = dataTypeExpression;
- dataTypeExpression = "*";
- }
-
- var dataType,
- i = 0,
- dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || [];
-
- if ( jQuery.isFunction( func ) ) {
-
- // For each dataType in the dataTypeExpression
- while ( ( dataType = dataTypes[ i++ ] ) ) {
-
- // Prepend if requested
- if ( dataType[ 0 ] === "+" ) {
- dataType = dataType.slice( 1 ) || "*";
- ( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func );
-
- // Otherwise append
- } else {
- ( structure[ dataType ] = structure[ dataType ] || [] ).push( func );
- }
- }
- }
- };
-}
-
-// Base inspection function for prefilters and transports
-function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
-
- var inspected = {},
- seekingTransport = ( structure === transports );
-
- function inspect( dataType ) {
- var selected;
- inspected[ dataType ] = true;
- jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
- var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
- if ( typeof dataTypeOrTransport === "string" &&
- !seekingTransport && !inspected[ dataTypeOrTransport ] ) {
-
- options.dataTypes.unshift( dataTypeOrTransport );
- inspect( dataTypeOrTransport );
- return false;
- } else if ( seekingTransport ) {
- return !( selected = dataTypeOrTransport );
- }
- } );
- return selected;
- }
-
- return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
-}
-
-// A special extend for ajax options
-// that takes "flat" options (not to be deep extended)
-// Fixes #9887
-function ajaxExtend( target, src ) {
- var key, deep,
- flatOptions = jQuery.ajaxSettings.flatOptions || {};
-
- for ( key in src ) {
- if ( src[ key ] !== undefined ) {
- ( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
- }
- }
- if ( deep ) {
- jQuery.extend( true, target, deep );
- }
-
- return target;
-}
-
-/* Handles responses to an ajax request:
- * - finds the right dataType (mediates between content-type and expected dataType)
- * - returns the corresponding response
- */
-function ajaxHandleResponses( s, jqXHR, responses ) {
-
- var ct, type, finalDataType, firstDataType,
- contents = s.contents,
- dataTypes = s.dataTypes;
-
- // Remove auto dataType and get content-type in the process
- while ( dataTypes[ 0 ] === "*" ) {
- dataTypes.shift();
- if ( ct === undefined ) {
- ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" );
- }
- }
-
- // Check if we're dealing with a known content-type
- if ( ct ) {
- for ( type in contents ) {
- if ( contents[ type ] && contents[ type ].test( ct ) ) {
- dataTypes.unshift( type );
- break;
- }
- }
- }
-
- // Check to see if we have a response for the expected dataType
- if ( dataTypes[ 0 ] in responses ) {
- finalDataType = dataTypes[ 0 ];
- } else {
-
- // Try convertible dataTypes
- for ( type in responses ) {
- if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) {
- finalDataType = type;
- break;
- }
- if ( !firstDataType ) {
- firstDataType = type;
- }
- }
-
- // Or just use first one
- finalDataType = finalDataType || firstDataType;
- }
-
- // If we found a dataType
- // We add the dataType to the list if needed
- // and return the corresponding response
- if ( finalDataType ) {
- if ( finalDataType !== dataTypes[ 0 ] ) {
- dataTypes.unshift( finalDataType );
- }
- return responses[ finalDataType ];
- }
-}
-
-/* Chain conversions given the request and the original response
- * Also sets the responseXXX fields on the jqXHR instance
- */
-function ajaxConvert( s, response, jqXHR, isSuccess ) {
- var conv2, current, conv, tmp, prev,
- converters = {},
-
- // Work with a copy of dataTypes in case we need to modify it for conversion
- dataTypes = s.dataTypes.slice();
-
- // Create converters map with lowercased keys
- if ( dataTypes[ 1 ] ) {
- for ( conv in s.converters ) {
- converters[ conv.toLowerCase() ] = s.converters[ conv ];
- }
- }
-
- current = dataTypes.shift();
-
- // Convert to each sequential dataType
- while ( current ) {
-
- if ( s.responseFields[ current ] ) {
- jqXHR[ s.responseFields[ current ] ] = response;
- }
-
- // Apply the dataFilter if provided
- if ( !prev && isSuccess && s.dataFilter ) {
- response = s.dataFilter( response, s.dataType );
- }
-
- prev = current;
- current = dataTypes.shift();
-
- if ( current ) {
-
- // There's only work to do if current dataType is non-auto
- if ( current === "*" ) {
-
- current = prev;
-
- // Convert response if prev dataType is non-auto and differs from current
- } else if ( prev !== "*" && prev !== current ) {
-
- // Seek a direct converter
- conv = converters[ prev + " " + current ] || converters[ "* " + current ];
-
- // If none found, seek a pair
- if ( !conv ) {
- for ( conv2 in converters ) {
-
- // If conv2 outputs current
- tmp = conv2.split( " " );
- if ( tmp[ 1 ] === current ) {
-
- // If prev can be converted to accepted input
- conv = converters[ prev + " " + tmp[ 0 ] ] ||
- converters[ "* " + tmp[ 0 ] ];
- if ( conv ) {
-
- // Condense equivalence converters
- if ( conv === true ) {
- conv = converters[ conv2 ];
-
- // Otherwise, insert the intermediate dataType
- } else if ( converters[ conv2 ] !== true ) {
- current = tmp[ 0 ];
- dataTypes.unshift( tmp[ 1 ] );
- }
- break;
- }
- }
- }
- }
-
- // Apply converter (if not an equivalence)
- if ( conv !== true ) {
-
- // Unless errors are allowed to bubble, catch and return them
- if ( conv && s.throws ) {
- response = conv( response );
- } else {
- try {
- response = conv( response );
- } catch ( e ) {
- return {
- state: "parsererror",
- error: conv ? e : "No conversion from " + prev + " to " + current
- };
- }
- }
- }
- }
- }
- }
-
- return { state: "success", data: response };
-}
-
-jQuery.extend( {
-
- // Counter for holding the number of active queries
- active: 0,
-
- // Last-Modified header cache for next request
- lastModified: {},
- etag: {},
-
- ajaxSettings: {
- url: location.href,
- type: "GET",
- isLocal: rlocalProtocol.test( location.protocol ),
- global: true,
- processData: true,
- async: true,
- contentType: "application/x-www-form-urlencoded; charset=UTF-8",
-
- /*
- timeout: 0,
- data: null,
- dataType: null,
- username: null,
- password: null,
- cache: null,
- throws: false,
- traditional: false,
- headers: {},
- */
-
- accepts: {
- "*": allTypes,
- text: "text/plain",
- html: "text/html",
- xml: "application/xml, text/xml",
- json: "application/json, text/javascript"
- },
-
- contents: {
- xml: /\bxml\b/,
- html: /\bhtml/,
- json: /\bjson\b/
- },
-
- responseFields: {
- xml: "responseXML",
- text: "responseText",
- json: "responseJSON"
- },
-
- // Data converters
- // Keys separate source (or catchall "*") and destination types with a single space
- converters: {
-
- // Convert anything to text
- "* text": String,
-
- // Text to html (true = no transformation)
- "text html": true,
-
- // Evaluate text as a json expression
- "text json": JSON.parse,
-
- // Parse text as xml
- "text xml": jQuery.parseXML
- },
-
- // For options that shouldn't be deep extended:
- // you can add your own custom options here if
- // and when you create one that shouldn't be
- // deep extended (see ajaxExtend)
- flatOptions: {
- url: true,
- context: true
- }
- },
-
- // Creates a full fledged settings object into target
- // with both ajaxSettings and settings fields.
- // If target is omitted, writes into ajaxSettings.
- ajaxSetup: function( target, settings ) {
- return settings ?
-
- // Building a settings object
- ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
-
- // Extending ajaxSettings
- ajaxExtend( jQuery.ajaxSettings, target );
- },
-
- ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
- ajaxTransport: addToPrefiltersOrTransports( transports ),
-
- // Main method
- ajax: function( url, options ) {
-
- // If url is an object, simulate pre-1.5 signature
- if ( typeof url === "object" ) {
- options = url;
- url = undefined;
- }
-
- // Force options to be an object
- options = options || {};
-
- var transport,
-
- // URL without anti-cache param
- cacheURL,
-
- // Response headers
- responseHeadersString,
- responseHeaders,
-
- // timeout handle
- timeoutTimer,
-
- // Url cleanup var
- urlAnchor,
-
- // Request state (becomes false upon send and true upon completion)
- completed,
-
- // To know if global events are to be dispatched
- fireGlobals,
-
- // Loop variable
- i,
-
- // uncached part of the url
- uncached,
-
- // Create the final options object
- s = jQuery.ajaxSetup( {}, options ),
-
- // Callbacks context
- callbackContext = s.context || s,
-
- // Context for global events is callbackContext if it is a DOM node or jQuery collection
- globalEventContext = s.context &&
- ( callbackContext.nodeType || callbackContext.jquery ) ?
- jQuery( callbackContext ) :
- jQuery.event,
-
- // Deferreds
- deferred = jQuery.Deferred(),
- completeDeferred = jQuery.Callbacks( "once memory" ),
-
- // Status-dependent callbacks
- statusCode = s.statusCode || {},
-
- // Headers (they are sent all at once)
- requestHeaders = {},
- requestHeadersNames = {},
-
- // Default abort message
- strAbort = "canceled",
-
- // Fake xhr
- jqXHR = {
- readyState: 0,
-
- // Builds headers hashtable if needed
- getResponseHeader: function( key ) {
- var match;
- if ( completed ) {
- if ( !responseHeaders ) {
- responseHeaders = {};
- while ( ( match = rheaders.exec( responseHeadersString ) ) ) {
- responseHeaders[ match[ 1 ].toLowerCase() ] = match[ 2 ];
- }
- }
- match = responseHeaders[ key.toLowerCase() ];
- }
- return match == null ? null : match;
- },
-
- // Raw string
- getAllResponseHeaders: function() {
- return completed ? responseHeadersString : null;
- },
-
- // Caches the header
- setRequestHeader: function( name, value ) {
- if ( completed == null ) {
- name = requestHeadersNames[ name.toLowerCase() ] =
- requestHeadersNames[ name.toLowerCase() ] || name;
- requestHeaders[ name ] = value;
- }
- return this;
- },
-
- // Overrides response content-type header
- overrideMimeType: function( type ) {
- if ( completed == null ) {
- s.mimeType = type;
- }
- return this;
- },
-
- // Status-dependent callbacks
- statusCode: function( map ) {
- var code;
- if ( map ) {
- if ( completed ) {
-
- // Execute the appropriate callbacks
- jqXHR.always( map[ jqXHR.status ] );
- } else {
-
- // Lazy-add the new callbacks in a way that preserves old ones
- for ( code in map ) {
- statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
- }
- }
- }
- return this;
- },
-
- // Cancel the request
- abort: function( statusText ) {
- var finalText = statusText || strAbort;
- if ( transport ) {
- transport.abort( finalText );
- }
- done( 0, finalText );
- return this;
- }
- };
-
- // Attach deferreds
- deferred.promise( jqXHR );
-
- // Add protocol if not provided (prefilters might expect it)
- // Handle falsy url in the settings object (#10093: consistency with old signature)
- // We also use the url parameter if available
- s.url = ( ( url || s.url || location.href ) + "" )
- .replace( rprotocol, location.protocol + "//" );
-
- // Alias method option to type as per ticket #12004
- s.type = options.method || options.type || s.method || s.type;
-
- // Extract dataTypes list
- s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ];
-
- // A cross-domain request is in order when the origin doesn't match the current origin.
- if ( s.crossDomain == null ) {
- urlAnchor = document.createElement( "a" );
-
- // Support: IE <=8 - 11, Edge 12 - 13
- // IE throws exception on accessing the href property if url is malformed,
- // e.g. http://example.com:80x/
- try {
- urlAnchor.href = s.url;
-
- // Support: IE <=8 - 11 only
- // Anchor's host property isn't correctly set when s.url is relative
- urlAnchor.href = urlAnchor.href;
- s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !==
- urlAnchor.protocol + "//" + urlAnchor.host;
- } catch ( e ) {
-
- // If there is an error parsing the URL, assume it is crossDomain,
- // it can be rejected by the transport if it is invalid
- s.crossDomain = true;
- }
- }
-
- // Convert data if not already a string
- if ( s.data && s.processData && typeof s.data !== "string" ) {
- s.data = jQuery.param( s.data, s.traditional );
- }
-
- // Apply prefilters
- inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
-
- // If request was aborted inside a prefilter, stop there
- if ( completed ) {
- return jqXHR;
- }
-
- // We can fire global events as of now if asked to
- // Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
- fireGlobals = jQuery.event && s.global;
-
- // Watch for a new set of requests
- if ( fireGlobals && jQuery.active++ === 0 ) {
- jQuery.event.trigger( "ajaxStart" );
- }
-
- // Uppercase the type
- s.type = s.type.toUpperCase();
-
- // Determine if request has content
- s.hasContent = !rnoContent.test( s.type );
-
- // Save the URL in case we're toying with the If-Modified-Since
- // and/or If-None-Match header later on
- // Remove hash to simplify url manipulation
- cacheURL = s.url.replace( rhash, "" );
-
- // More options handling for requests with no content
- if ( !s.hasContent ) {
-
- // Remember the hash so we can put it back
- uncached = s.url.slice( cacheURL.length );
-
- // If data is available, append data to url
- if ( s.data ) {
- cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data;
-
- // #9682: remove data so that it's not used in an eventual retry
- delete s.data;
- }
-
- // Add or update anti-cache param if needed
- if ( s.cache === false ) {
- cacheURL = cacheURL.replace( rantiCache, "$1" );
- uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce++ ) + uncached;
- }
-
- // Put hash and anti-cache on the URL that will be requested (gh-1732)
- s.url = cacheURL + uncached;
-
- // Change '%20' to '+' if this is encoded form body content (gh-2658)
- } else if ( s.data && s.processData &&
- ( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) {
- s.data = s.data.replace( r20, "+" );
- }
-
- // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
- if ( s.ifModified ) {
- if ( jQuery.lastModified[ cacheURL ] ) {
- jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
- }
- if ( jQuery.etag[ cacheURL ] ) {
- jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
- }
- }
-
- // Set the correct header, if data is being sent
- if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
- jqXHR.setRequestHeader( "Content-Type", s.contentType );
- }
-
- // Set the Accepts header for the server, depending on the dataType
- jqXHR.setRequestHeader(
- "Accept",
- s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ?
- s.accepts[ s.dataTypes[ 0 ] ] +
- ( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
- s.accepts[ "*" ]
- );
-
- // Check for headers option
- for ( i in s.headers ) {
- jqXHR.setRequestHeader( i, s.headers[ i ] );
- }
-
- // Allow custom headers/mimetypes and early abort
- if ( s.beforeSend &&
- ( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) {
-
- // Abort if not done already and return
- return jqXHR.abort();
- }
-
- // Aborting is no longer a cancellation
- strAbort = "abort";
-
- // Install callbacks on deferreds
- completeDeferred.add( s.complete );
- jqXHR.done( s.success );
- jqXHR.fail( s.error );
-
- // Get transport
- transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
-
- // If no transport, we auto-abort
- if ( !transport ) {
- done( -1, "No Transport" );
- } else {
- jqXHR.readyState = 1;
-
- // Send global event
- if ( fireGlobals ) {
- globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
- }
-
- // If request was aborted inside ajaxSend, stop there
- if ( completed ) {
- return jqXHR;
- }
-
- // Timeout
- if ( s.async && s.timeout > 0 ) {
- timeoutTimer = window.setTimeout( function() {
- jqXHR.abort( "timeout" );
- }, s.timeout );
- }
-
- try {
- completed = false;
- transport.send( requestHeaders, done );
- } catch ( e ) {
-
- // Rethrow post-completion exceptions
- if ( completed ) {
- throw e;
- }
-
- // Propagate others as results
- done( -1, e );
- }
- }
-
- // Callback for when everything is done
- function done( status, nativeStatusText, responses, headers ) {
- var isSuccess, success, error, response, modified,
- statusText = nativeStatusText;
-
- // Ignore repeat invocations
- if ( completed ) {
- return;
- }
-
- completed = true;
-
- // Clear timeout if it exists
- if ( timeoutTimer ) {
- window.clearTimeout( timeoutTimer );
- }
-
- // Dereference transport for early garbage collection
- // (no matter how long the jqXHR object will be used)
- transport = undefined;
-
- // Cache response headers
- responseHeadersString = headers || "";
-
- // Set readyState
- jqXHR.readyState = status > 0 ? 4 : 0;
-
- // Determine if successful
- isSuccess = status >= 200 && status < 300 || status === 304;
-
- // Get response data
- if ( responses ) {
- response = ajaxHandleResponses( s, jqXHR, responses );
- }
-
- // Convert no matter what (that way responseXXX fields are always set)
- response = ajaxConvert( s, response, jqXHR, isSuccess );
-
- // If successful, handle type chaining
- if ( isSuccess ) {
-
- // Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
- if ( s.ifModified ) {
- modified = jqXHR.getResponseHeader( "Last-Modified" );
- if ( modified ) {
- jQuery.lastModified[ cacheURL ] = modified;
- }
- modified = jqXHR.getResponseHeader( "etag" );
- if ( modified ) {
- jQuery.etag[ cacheURL ] = modified;
- }
- }
-
- // if no content
- if ( status === 204 || s.type === "HEAD" ) {
- statusText = "nocontent";
-
- // if not modified
- } else if ( status === 304 ) {
- statusText = "notmodified";
-
- // If we have data, let's convert it
- } else {
- statusText = response.state;
- success = response.data;
- error = response.error;
- isSuccess = !error;
- }
- } else {
-
- // Extract error from statusText and normalize for non-aborts
- error = statusText;
- if ( status || !statusText ) {
- statusText = "error";
- if ( status < 0 ) {
- status = 0;
- }
- }
- }
-
- // Set data for the fake xhr object
- jqXHR.status = status;
- jqXHR.statusText = ( nativeStatusText || statusText ) + "";
-
- // Success/Error
- if ( isSuccess ) {
- deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
- } else {
- deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
- }
-
- // Status-dependent callbacks
- jqXHR.statusCode( statusCode );
- statusCode = undefined;
-
- if ( fireGlobals ) {
- globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
- [ jqXHR, s, isSuccess ? success : error ] );
- }
-
- // Complete
- completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
-
- if ( fireGlobals ) {
- globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
-
- // Handle the global AJAX counter
- if ( !( --jQuery.active ) ) {
- jQuery.event.trigger( "ajaxStop" );
- }
- }
- }
-
- return jqXHR;
- },
-
- getJSON: function( url, data, callback ) {
- return jQuery.get( url, data, callback, "json" );
- },
-
- getScript: function( url, callback ) {
- return jQuery.get( url, undefined, callback, "script" );
- }
-} );
-
-jQuery.each( [ "get", "post" ], function( i, method ) {
- jQuery[ method ] = function( url, data, callback, type ) {
-
- // Shift arguments if data argument was omitted
- if ( jQuery.isFunction( data ) ) {
- type = type || callback;
- callback = data;
- data = undefined;
- }
-
- // The url can be an options object (which then must have .url)
- return jQuery.ajax( jQuery.extend( {
- url: url,
- type: method,
- dataType: type,
- data: data,
- success: callback
- }, jQuery.isPlainObject( url ) && url ) );
- };
-} );
-
-
-jQuery._evalUrl = function( url ) {
- return jQuery.ajax( {
- url: url,
-
- // Make this explicit, since user can override this through ajaxSetup (#11264)
- type: "GET",
- dataType: "script",
- cache: true,
- async: false,
- global: false,
- "throws": true
- } );
-};
-
-
-jQuery.fn.extend( {
- wrapAll: function( html ) {
- var wrap;
-
- if ( this[ 0 ] ) {
- if ( jQuery.isFunction( html ) ) {
- html = html.call( this[ 0 ] );
- }
-
- // The elements to wrap the target around
- wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true );
-
- if ( this[ 0 ].parentNode ) {
- wrap.insertBefore( this[ 0 ] );
- }
-
- wrap.map( function() {
- var elem = this;
-
- while ( elem.firstElementChild ) {
- elem = elem.firstElementChild;
- }
-
- return elem;
- } ).append( this );
- }
-
- return this;
- },
-
- wrapInner: function( html ) {
- if ( jQuery.isFunction( html ) ) {
- return this.each( function( i ) {
- jQuery( this ).wrapInner( html.call( this, i ) );
- } );
- }
-
- return this.each( function() {
- var self = jQuery( this ),
- contents = self.contents();
-
- if ( contents.length ) {
- contents.wrapAll( html );
-
- } else {
- self.append( html );
- }
- } );
- },
-
- wrap: function( html ) {
- var isFunction = jQuery.isFunction( html );
-
- return this.each( function( i ) {
- jQuery( this ).wrapAll( isFunction ? html.call( this, i ) : html );
- } );
- },
-
- unwrap: function( selector ) {
- this.parent( selector ).not( "body" ).each( function() {
- jQuery( this ).replaceWith( this.childNodes );
- } );
- return this;
- }
-} );
-
-
-jQuery.expr.pseudos.hidden = function( elem ) {
- return !jQuery.expr.pseudos.visible( elem );
-};
-jQuery.expr.pseudos.visible = function( elem ) {
- return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length );
-};
-
-
-
-
-jQuery.ajaxSettings.xhr = function() {
- try {
- return new window.XMLHttpRequest();
- } catch ( e ) {}
-};
-
-var xhrSuccessStatus = {
-
- // File protocol always yields status code 0, assume 200
- 0: 200,
-
- // Support: IE <=9 only
- // #1450: sometimes IE returns 1223 when it should be 204
- 1223: 204
- },
- xhrSupported = jQuery.ajaxSettings.xhr();
-
-support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
-support.ajax = xhrSupported = !!xhrSupported;
-
-jQuery.ajaxTransport( function( options ) {
- var callback, errorCallback;
-
- // Cross domain only allowed if supported through XMLHttpRequest
- if ( support.cors || xhrSupported && !options.crossDomain ) {
- return {
- send: function( headers, complete ) {
- var i,
- xhr = options.xhr();
-
- xhr.open(
- options.type,
- options.url,
- options.async,
- options.username,
- options.password
- );
-
- // Apply custom fields if provided
- if ( options.xhrFields ) {
- for ( i in options.xhrFields ) {
- xhr[ i ] = options.xhrFields[ i ];
- }
- }
-
- // Override mime type if needed
- if ( options.mimeType && xhr.overrideMimeType ) {
- xhr.overrideMimeType( options.mimeType );
- }
-
- // X-Requested-With header
- // For cross-domain requests, seeing as conditions for a preflight are
- // akin to a jigsaw puzzle, we simply never set it to be sure.
- // (it can always be set on a per-request basis or even using ajaxSetup)
- // For same-domain requests, won't change header if already provided.
- if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) {
- headers[ "X-Requested-With" ] = "XMLHttpRequest";
- }
-
- // Set headers
- for ( i in headers ) {
- xhr.setRequestHeader( i, headers[ i ] );
- }
-
- // Callback
- callback = function( type ) {
- return function() {
- if ( callback ) {
- callback = errorCallback = xhr.onload =
- xhr.onerror = xhr.onabort = xhr.onreadystatechange = null;
-
- if ( type === "abort" ) {
- xhr.abort();
- } else if ( type === "error" ) {
-
- // Support: IE <=9 only
- // On a manual native abort, IE9 throws
- // errors on any property access that is not readyState
- if ( typeof xhr.status !== "number" ) {
- complete( 0, "error" );
- } else {
- complete(
-
- // File: protocol always yields status 0; see #8605, #14207
- xhr.status,
- xhr.statusText
- );
- }
- } else {
- complete(
- xhrSuccessStatus[ xhr.status ] || xhr.status,
- xhr.statusText,
-
- // Support: IE <=9 only
- // IE9 has no XHR2 but throws on binary (trac-11426)
- // For XHR2 non-text, let the caller handle it (gh-2498)
- ( xhr.responseType || "text" ) !== "text" ||
- typeof xhr.responseText !== "string" ?
- { binary: xhr.response } :
- { text: xhr.responseText },
- xhr.getAllResponseHeaders()
- );
- }
- }
- };
- };
-
- // Listen to events
- xhr.onload = callback();
- errorCallback = xhr.onerror = callback( "error" );
-
- // Support: IE 9 only
- // Use onreadystatechange to replace onabort
- // to handle uncaught aborts
- if ( xhr.onabort !== undefined ) {
- xhr.onabort = errorCallback;
- } else {
- xhr.onreadystatechange = function() {
-
- // Check readyState before timeout as it changes
- if ( xhr.readyState === 4 ) {
-
- // Allow onerror to be called first,
- // but that will not handle a native abort
- // Also, save errorCallback to a variable
- // as xhr.onerror cannot be accessed
- window.setTimeout( function() {
- if ( callback ) {
- errorCallback();
- }
- } );
- }
- };
- }
-
- // Create the abort callback
- callback = callback( "abort" );
-
- try {
-
- // Do send the request (this may raise an exception)
- xhr.send( options.hasContent && options.data || null );
- } catch ( e ) {
-
- // #14683: Only rethrow if this hasn't been notified as an error yet
- if ( callback ) {
- throw e;
- }
- }
- },
-
- abort: function() {
- if ( callback ) {
- callback();
- }
- }
- };
- }
-} );
-
-
-
-
-// Prevent auto-execution of scripts when no explicit dataType was provided (See gh-2432)
-jQuery.ajaxPrefilter( function( s ) {
- if ( s.crossDomain ) {
- s.contents.script = false;
- }
-} );
-
-// Install script dataType
-jQuery.ajaxSetup( {
- accepts: {
- script: "text/javascript, application/javascript, " +
- "application/ecmascript, application/x-ecmascript"
- },
- contents: {
- script: /\b(?:java|ecma)script\b/
- },
- converters: {
- "text script": function( text ) {
- jQuery.globalEval( text );
- return text;
- }
- }
-} );
-
-// Handle cache's special case and crossDomain
-jQuery.ajaxPrefilter( "script", function( s ) {
- if ( s.cache === undefined ) {
- s.cache = false;
- }
- if ( s.crossDomain ) {
- s.type = "GET";
- }
-} );
-
-// Bind script tag hack transport
-jQuery.ajaxTransport( "script", function( s ) {
-
- // This transport only deals with cross domain requests
- if ( s.crossDomain ) {
- var script, callback;
- return {
- send: function( _, complete ) {
- script = jQuery( "
-
-
-
-
-
-
-
-
-
-
-
krTheme Sphinx Style
-
This repository contains sphinx styles Kenneth Reitz uses in most of
-his projects. It is a drivative of Mitsuhiko’s themes for Flask and Flask related
-projects. To use this style in your Sphinx documentation, follow
-this guide:
-
-put this folder as _themes into your docs folder. Alternatively
-you can also use git submodules to check out the contents there.
add this to your conf.py:
-sys . path . append ( os . path . abspath ( '_themes' ))
-html_theme_path = [ '_themes' ]
-html_theme = 'kr'
-
-
-
The following themes exist:
-
-kr the standard flask documentation theme for large projects
-kr_small small one-page theme. Intended to be used by very small addon libraries.
-
-
-
-
-
-
-
-
-
-
Change Log — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
Change Log
-
-
v2017.12.23
-
-cstdn command line tool is now official with docs.
Fine-grained control of VaspErrorHandler is now possible using
-errors_subset_to_catch .
Switched to date-based versioning for custodian like pymatgen.
-
-
-
-
-
-
-
-
-
v0.8.8
-
-Fix setup.py.
-
-
-
v0.8.5
-
-Refactoring to support pymatgen 3.1.4.
-
-
-
v0.8.2
-
-Made auto_npar optional for double relaxation VASP run.
-
-
-
v0.8.1
-
-Misc bug fixes (minor).
-
-
-
v0.8.0
-
-Major refactoring of Custodian to introdce Validators,
-which are effectively post-Job checking mechanisms that do not perform
-error correction.
Backwards incompatibility BadVasprunXMLHandler is now a validator,
-which must be separately imported to be used.
-
3. Miscellaneous cleanup of Py3k fixes.
-v0.7.6
-——
-1. Custodian is now Python 3 compatible and uses the latest versions of
-
-
-
-
-
v0.7.5
-
-Major Custodian now exits with RuntimeError when max_errors or
-unrecoverable_error is encountered.
Added BadVasprunXMLHandler.
-
-
-
v0.7.4
-
-auto_npar option in VaspJob now properly handles Hessian calculations.
WalltimeHandler now supports termination at electronic step (David
-Waroquiers).
Improved handling of BRMIX fixes.
-
-
-
v0.7.3
-
-Improved backwards compatibility for WallTimeHandler.
Improvements to VaspErrorHandler. No longer catches spurious BRMIX error
-messages when NELECT is specified in INCAR, and pricel and rot_mat errors
-are now fixed with symmetry precision and gamma centered KPOINTS instead.
Improved Qchem error handler (Xiaohui Qu).
-
-
-
v0.7.2
-
-Improved WalltimeHandler (PBSWalltimeHandler is a subset and is now
-deprecated).
New monty required version (>= 0.2.2).
-
-
-
v0.7.1
-
-Much improved qchem error handling (Xiaohui Qu).
New Monty required version (>= 0.2.0).
-
-
-
v0.7.0
-
-** Monty package , which is now a depedency
-for custodian.
Custodian now requires pymatgen >= 2.9.0 for VASP, Qchem and Nwchem jobs
-and handlers.
converge_kpoints script now has increment mode.
ErrorHandlers now have a new API, where the class variables “is_monitor”
-and “is_terminating” are provided to indicate if a particular handler
-runs in the background during a Job and whether a handler should
-terminate the job. Some errors may not be critical or may need to wait
-for some other event to terminate a job. For example,
-a particular error may require a flag to be set to request a job to
-terminate gracefully once it finishes its current task. The handler to
-set the flag should not terminate the job.
-
-
-
0.6.3
-
-Added buffer time option in PBSWalltimeHandler.
Improved Qchem jobs and handlers (Xiaohui Qu).
Vastly improved API docs.
-
-
-
0.6.2
-
-Bug fix release to support sub dirs in run folder when using scratch.
Improve handling of walltime in PBSWalltimeHander.
-
-
-
0.6.1
-
-Bug fix release to address minor issue with checkpointing.
Checkpointing is now turned off by default.
-
-
-
0.6.0
-
-Checkpointing implemented for Custodian. Custodian can now checkpoint all
-files in the current working directory after every successful job. If the
-job is resubmitted, it will restore files and start from the last
-checkpoint. Particularly useful for multi-job runs.
Added PBSWalltimeHandler to handle wall times for PBS Vasp Jobs.
Qchem error handlers and jobs.
-
-
-
0.5.0
-
-Added scratch_dir option to Custodian class as well as run_vasp and
-run_nwchem scripts. Many supercomputing clusters have a scratch space
-which have significantly faster IO. This option provides a transparent way
-to specify the jobs to be performed in the scratch. Especially useful for
-jobs which have significant file IO.
-
-
-
0.4.5
-
-Fix gzip of output.
-
-
-
0.4.3
-
-Added handling for ZBRENT error for VASP.
Minor refactoring to consolidate backup and gzip directory methods.
-
-
-
0.4.2
-
-Rudimentary support for Nwchem error handling (by Shyue Ping Ong).
Improved VASP error handling (by Steve Dacek and Will Richards).
-
-
-
0.4.1
-
-Added hanlding of PRICEL error in VASP.
Speed and robustness improvements.
BRIONS error now handled by changing ISYM.
-
-
-
0.4.0
-
-Many VASP handlers are now consolidated into a single VaspErrorHandler.
Many more fixes for VASP runs, including the “TOO FEW BANDS”,
-“TRIPLE PRODUCT”, “DENTET” and “BRIONS” errors.
VaspJob now includes the auto_npar and auto_gamma options, which
-automatically optimizes the NPAR setting to be sqrt(number of cores) as
-per the VASP recommendation for DFT runs and tries to search for a
-gamma-only compiled version of VASP for gamma 1x1x1 runs.
-
-
-
0.3.5
-
-Bug fix for incorrect shift error handler in VASP.
More robust fix for unconverged VASP runs (switching from ALGO fast to
-normal).
Expanded documentation.
-
-
-
0.3.4
-
-Added support for handlers that perform monitor a job as it is progressing
-and terminates it if necessary. Useful for correcting errors that come up
-by do not cause immediate job failures.
-
-
-
0.3.2
-
-Important bug fix for VaspJob and converge_kpoints script.
-
-
-
0.3.0
-
-Major update to custodian API. Custodian now perform more comprehensive
-logging in a file called custodian.json, which logs all jobs and
-corrections performed.
-
-
-
Version 0.2.6
-
-Bug fix for run_vasp script for static runs.
-
-
-
Version 0.2.5
-
-run_vasp script that now provides flexible specification of vasp runs.
Vastly improved error handling for VASP runs.
Improved logging system for custodian.
Improved API for custodian return types during run.
First stable release.
-
-
-
Version 0.2.4
-
-Bug fixes for aflow style runs assimilation.
-
-
-
-
-
-
-
-
-
-
custodian.ansible package — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
custodian.ansible package
-
-
-
Submodules
-
-
-
custodian.ansible.actions module
-
-
-class DictActions[source]
-Bases: object
-Class to implement the supported mongo-like modifications on a dict.
-Supported keywords include the following Mongo-based keywords, with the
-usual meanings (refer to Mongo documentation for information):
-
-_inc
-_set
-_unset
-_push
-_push_all
-_add_to_set (but _each is not supported)
-_pop
-_pull
-_pull_all
-_rename
-
-However, note that “_set” does not support modification of nested dicts
-using the mongo {“a.b”:1} notation. This is because mongo does not allow
-keys with “.” to be inserted. Instead, nested dict modification is
-supported using a special “->” keyword, e.g. {“a->b”: 1}
-
-
-static add_to_set( input_dict , settings ) [source]
-
-
-
-
-static inc( input_dict , settings ) [source]
-
-
-
-
-static pop( input_dict , settings ) [source]
-
-
-
-
-static pull( input_dict , settings ) [source]
-
-
-
-
-static pull_all( input_dict , settings ) [source]
-
-
-
-
-static push( input_dict , settings ) [source]
-
-
-
-
-static push_all( input_dict , settings ) [source]
-
-
-
-
-static rename( input_dict , settings ) [source]
-
-
-
-
-static set( input_dict , settings ) [source]
-
-
-
-
-static unset( input_dict , settings ) [source]
-
-
-
-
-
-
-class FileActions[source]
-Bases: object
-Class of supported file actions. For FileActions, the modder class takes in
-a filename as a string. The filename should preferably be a full path to
-avoid ambiguity.
-
-
-static file_copy( filename , settings ) [source]
-Copies a file. {‘_file_copy’: {‘dest’: ‘new_file_name’}}
-
-Parameters
-
-
-
-
-
-
-
-static file_create( filename , settings ) [source]
-Creates a file.
-
-Parameters
-
-
-
-
-
-
-
-static file_delete( filename , settings ) [source]
-Deletes a file. {‘_file_delete’: {‘mode’: “actual”}}
-
-Parameters
-
-
-
-
-
-
-
-static file_modify( filename , settings ) [source]
-Modifies file access
-
-Parameters
-
-
-
-
-
-
-
-static file_move( filename , settings ) [source]
-Moves a file. {‘_file_move’: {‘dest’: ‘new_file_name’}}
-
-Parameters
-
-
-
-
-
-
-
-
-
-get_nested_dict( input_dict , key ) [source]
-
-
-
-
-
custodian.ansible.interpreter module
-
-
-class Modder( actions=None , strict=True ) [source]
-Bases: object
-Class to modify a dict/file/any object using a mongo-like language.
-Keywords are mostly adopted from mongo’s syntax, but instead of $, an
-underscore precedes action keywords. This is so that the modification can
-be inserted into a mongo db easily.
-Allowable actions are supplied as a list of classes as an argument. Refer
-to the action classes on what the actions do. Action classes are in
-pymatpro.ansible.actions.
-Examples:
->>> modder = Modder()
->>> d = {“Hello”: “World”}
->>> mod = {‘_set’: {‘Hello’:’Universe’, ‘Bye’: ‘World’}}
->>> modder.modify(mod, d)
->>> d[‘Bye’]
-‘World’
->>> d[‘Hello’]
-‘Universe’
-Initializes a Modder from a list of supported actions.
-
-Parameters
-
-actions ([ Action ] ) – A sequence of supported actions. See
-custodian.ansible.actions
strict (bool ) – Indicating whether to use strict mode. In non-strict
-mode, unsupported actions are simply ignored without any
-errors raised. In strict mode, if an unsupported action is
-supplied, a ValueError is raised. Defaults to True.
-
-
-
-modify( modification , obj ) [source]
-Note that modify makes actual in-place modifications. It does not
-return a copy.
-
-Parameters
-
-modification (dict ) – Modification must be {action_keyword :
-settings}. E.g., {‘_set’: {‘Hello’:’Universe’, ‘Bye’: ‘World’}}
obj (dict/str/object ) – Object to modify depending on actions. For
-example, for DictActions, obj will be a dict to be modified.
-For FileActions, obj will be a string with a full pathname to a
-file.
-
-
-
-
-
-modify_object( modification , obj ) [source]
-Modify an object that supports pymatgen’s as_dict() and from_dict API.
-
-Parameters
-
-modification (dict ) – Modification must be {action_keyword :
-settings}. E.g., {‘_set’: {‘Hello’:’Universe’, ‘Bye’: ‘World’}}
obj (object ) – Object to modify
-
-
-
-
-
-
-
-
Module contents
-
-
-
-
-
-
-
-
-
-
custodian.cli package — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
custodian.cli package
-
-
Submodules
-
-
-
custodian.cli.converge_geometry module
-
This is a script to converge the geometry of a system
-
-
-do_run( args ) [source]
-
-
-
-
-get_runs( args ) [source]
-
-
-
-
-
custodian.cli.converge_kpoints module
-
This is a master vasp running script to perform variuos combinations of VASP
-runs.
-
-
-do_run( args ) [source]
-
-
-
-
-get_runs( vasp_command , target=0.001 , max_steps=10 , mode='linear' ) [source]
-
-
-
-
-main( ) [source]
-
-
-
-
-
-
custodian.cli.run_nwchem module
-
Basic script to run nwchem job.
-
-
-do_run( args ) [source]
-
-
-
-
-main( ) [source]
-
-
-
-
-
custodian.cli.run_vasp module
-
This is a master vasp running script to perform various combinations of VASP
-runs.
-
-
-do_run( args ) [source]
-
-
-
-
-get_jobs( args ) [source]
-
-
-
-
-load_class( mod , name ) [source]
-
-
-
-
-main( ) [source]
-
-
-
-
-
Module contents
-
-
-
-
-
-
-
-
-
-
custodian.feff package — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
custodian.feff package
-
-
-
Submodules
-
-
-
custodian.feff.handlers module
-
-
-class UnconvergedErrorHandler( output_filename='log1.dat' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Correct the unconverged error of FEFF’s SCF calculation.
-Initializes the handler with the output file to check
-
-Parameters
-output_filename (str ) – Filename for the log1.dat file. log1.dat file
-contains the SCF calculation convergence information. Change this only
-if it is different from the default (unlikely).
-
-
-
-check( ) [source]
-If the FEFF run does not converge, the check will return
-“TRUE”
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-
-
-
-
-
-
-
custodian.feff.interpreter module
-
-
-class FeffModder( actions=None , strict=True , feffinp=None ) [source]
-Bases: custodian.ansible.interpreter.Modder
-Initializes a Modder for FeffInput sets
-
-Parameters
-
-actions ([ Action ] ) – A sequence of supported actions. See
actions – A sequence of supported actions. See
-custodian.ansible.actions
strict (bool ) – Indicating whether to use strict mode. In non-strict
-mode, unsupported actions are simply ignored without any
-errors raised. In strict mode, if an unsupported action is
-supplied, a ValueError is raised. Defaults to True.
feffinp (FEFFInput ) – A FeffInput object from the current directory.
-Initialized automatically if not passed (but passing it will
-avoid having to reparse the directory).
-
-
-
-apply_actions( actions ) [source]
-Applies a list of actions to the FEFF Input Set and rewrites modified
-files.
-
-Parameters
-[ dict ] (actions ) – A list of actions of the form {‘file’: filename,
-‘action’: moddermodification} or {‘dict’: feffinput_key,
-‘action’: moddermodification}
-
-
-
-
-
-
-
-
custodian.feff.jobs module
-
-
-class FeffJob( feff_cmd , output_file='feff.out' , stderr_file='std_feff_err.txt' , backup=True , gzipped=False , gzipped_prefix='feff_out' ) [source]
-Bases: custodian.custodian.Job
-A basic FEFF job, run whatever is in the directory.
-This constructor is used for a standard FEFF initialization
-
-Parameters
-
-feff_cmd (str ) – the name of the full executable for running FEFF
output_file (str ) – Name of file to direct standard out to.
-Defaults to “feff.out”.
stderr_file (str ) – Name of file direct standard error to.
-Defaults to “std_feff_err.txt”.
backup (bool ) – Indicating whether to backup the initial input files.
-If True, the feff.inp will be copied with a “.orig” appended.
-Defaults to True.
gzipped (bool ) – Whether to gzip the final output. Defaults to False.
gzipped_prefix (str ) – prefix to the feff output files archive. Defaults
-to feff_out, which means a series of feff_out.1.tar.gz, feff_out.2.tar.gz, …
-will be generated.
-
-
-
-postprocess( ) [source]
-Renaming or gzipping all the output as needed
-
-
-
-
-run( ) [source]
-Performs the actual FEFF run
-:returns: (subprocess.Popen) Used for monitoring.
-
-
-
-
-setup( ) [source]
-Performs initial setup for FeffJob, do backing up.
-Returns:
-
-
-
-
-
-
-
Module contents
-
-
-
-
-
-
-
-
-
-
custodian package — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
custodian package
-
-
-
Submodules
-
-
-
custodian.custodian module
-
-
-class Custodian( handlers , jobs , validators=None , max_errors_per_job=None , max_errors=1 , polling_time_step=10 , monitor_freq=30 , skip_over_errors=False , scratch_dir=None , gzipped_output=False , checkpoint=False , terminate_func=None , terminate_on_nonzero_returncode=True ) [source]
-Bases: object
-The Custodian class is the manager for a list of jobs given a list of
-error handlers. The way it works is as follows:
-
-Let’s say you have defined a list of jobs as [job1, job2, job3, …] and
-you have defined a list of possible error handlers as [err1, err2, …]
Custodian will run the jobs in the order of job1, job2, … During each
-job, custodian will monitor for errors using the handlers that have
-is_monitor == True. If an error is detected, corrective measures are
-taken and the particular job is rerun.
At the end of each individual job, Custodian will run through the list
-error handlers that have is_monitor == False. If an error is detected,
-corrective measures are taken and the particular job is rerun.
-Initializes a Custodian from a list of jobs and error handler.s
-
-Parameters
-
-handlers ([ ErrorHandler ] ) – Error handlers. In order of priority of
-fixing.
jobs ([ Job ] ) – Sequence of Jobs to be run. Note that this can be
-any sequence or even a generator yielding jobs.
validators ([ Validator ] ) – Validators to ensure job success
max_errors_per_job (int ) – Maximum number of errors per job allowed
-before exiting. Defaults to None, which means it is set to be
-equal to max_errors..
max_errors (int ) – Maximum number of total errors allowed before
-exiting. Defaults to 1.
polling_time_step (int ) – The length of time in seconds between
-steps in which a job is checked for completion. Defaults to
-10 secs.
monitor_freq (int ) – The number of polling steps before monitoring
-occurs. For example, if you have a polling_time_step of 10
-seconds and a monitor_freq of 30, this means that Custodian
-uses the monitors to check for errors every 30 x 10 = 300
-seconds, i.e., 5 minutes.
skip_over_errors (bool ) – If set to True, custodian will skip over
-error handlers that failed (raised an Exception of some sort).
-Otherwise, custodian will simply exit on unrecoverable errors.
-The former will lead to potentially more robust performance,
-but may make it difficult to improve handlers. The latter
-will allow one to catch potentially bad error handler
-implementations. Defaults to False.
scratch_dir (str ) – If this is set, any files in the current
-directory are copied to a temporary directory in a scratch
-space first before any jobs are performed, and moved back to
-the current directory upon completion of all jobs. This is
-useful in some setups where a scratch partition has much
-faster IO. To use this, set scratch_dir=root of directory you
-want to use for runs. There is no need to provide unique
-directory names; we will use python’s tempfile creation
-mechanisms. A symbolic link is created during the course of
-the run in the working directory called “scratch_link” as
-users may want to sometimes check the output during the
-course of a run. If this is None (the default), the run is
-performed in the current working directory.
gzipped_output (bool ) – Whether to gzip the final output to save
-space. Defaults to False.
checkpoint (bool ) – Whether to checkpoint after each successful Job.
-Checkpoints are stored as custodian.chk.#.tar.gz files. Defaults
-to False.
terminate_func (callable ) – A function to be called to terminate a
-running job. If None, the default is to call Popen.terminate.
terminate_on_nonzero_returncode (bool ) – If True, a non-zero return
-code on any Job will result in a termination. Defaults to True.
-
-
-
-LOG_FILE = 'custodian.json'
-
-
-
-
-classmethod from_spec( spec ) [source]
-Load a Custodian instance where the jobs are specified from a
-structure and a spec dict. This allows simple
-custom job sequences to be constructed quickly via a YAML file.
-
-Parameters
-spec (dict ) –
A dict specifying job. A sample of the dict in
-YAML format for the usual MP workflow is given as follows
-``
-
-
-params: final: False
-suffix: .relax1
-
-
-
-
-jobs_common_params: vasp_cmd: /opt/vasp
-
-handlers:
-- hdlr: custodian.vasp.handlers.VaspErrorHandler
-- hdlr: custodian.vasp.handlers.AliasingErrorHandler
-- hdlr: custodian.vasp.handlers.MeshSymmetryHandler
-validators:
-- vldr: custodian.vasp.validators.VasprunXMLValidator
-custodian_params:
-
-
-`` `
-The jobs key is a list of jobs. Each job is
-specified via “job”: <explicit path>, and all parameters are
-specified via params which is a dict.
-common_params specify a common set of parameters that are
-passed to all jobs, e.g., vasp_cmd.
-
-Returns
-Custodian instance.
-
-
-
-
-
-run( ) [source]
-Runs all jobs.
-
-Returns
-All errors encountered as a list of list.
-[[error_dicts for job 1], [error_dicts for job 2], ….]
-Raises
-
-
-
-
-
-
-
-run_interrupted( ) [source]
-Runs custodian in a interuppted mode, which sets up and
-validates jobs but doesn’t run the executable
-
-Returns
-number of remaining jobs
-Raises
-
-
-
-
-
-
-
-
-
-exception CustodianError( message , raises=False ) [source]
-Bases: RuntimeError
-Exception class for Custodian errors.
-Initializes the error with a message.
-
-Parameters
-
-
-
-
-
-
-
-class ErrorHandler[source]
-Bases: monty.json.MSONable
-Abstract base class defining the interface for an ErrorHandler.
-
-
-abstract check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-abstract correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-This class property indicates whether the error handler is a monitor,
-i.e., a handler that monitors a job as it is running. If a
-monitor-type handler notices an error, the job will be sent a
-termination signal, the error is then corrected,
-and then the job is restarted. This is useful for catching errors
-that occur early in the run but do not cause immediate failure.
-
-
-
-
-is_terminating = True
-Whether this handler terminates a job upon error detection. By
-default, this is True, which means that the current Job will be
-terminated upon error detection, corrections applied,
-and restarted. In some instances, some errors may not need the job to be
-terminated or may need to wait for some other event to terminate a job.
-For example, a particular error may require a flag to be set to request
-a job to terminate gracefully once it finishes its current task. The
-handler to set the flag should be classified as is_terminating = False to
-not terminate the job.
-
-
-
-
-max_num_corrections = None
-
-
-
-
-property n_applied_corrections
-The number of times the handler has given a correction and this
-has been applied.
-
-Returns
-the number of corrections applied.
-Return type
-(int)
-
-
-
-
-
-raise_on_max = False
-Whether corrections from this specific handler should be applied only a
-fixed maximum number of times on a single job (i.e. the counter is reset
-at the beginning of each job). If the maximum number is reached the code
-will either raise a MaxCorrectionsPerHandlerError (raise_on_max==True) or stops
-considering the correction (raise_on_max==False). If max_num_corrections
-is None this option is not considered. These options can be overridden
-as class attributes of the subclass or as customizable options setting
-an instance attribute from __init__.
-
-
-
-
-raises_runtime_error = True
-Whether this handler causes custodian to raise a runtime error if it cannot
-handle the error (i.e. if correct returns a dict with “actions”:None, or
-“actions”:[])
-
-
-
-
-
-
-class Job[source]
-Bases: monty.json.MSONable
-Abstract base class defining the interface for a Job.
-
-
-property name
-A nice string name for the job.
-
-
-
-
-abstract postprocess( ) [source]
-This method is called at the end of a job, after error detection.
-This allows post-processing, such as cleanup, analysis of results,
-etc.
-
-
-
-
-abstract run( ) [source]
-This method perform the actual work for the job. If parallel error
-checking (monitoring) is desired, this must return a Popen process.
-
-
-
-
-abstract setup( ) [source]
-This method is run before the start of a job. Allows for some
-pre-processing.
-
-
-
-
-terminate( ) [source]
-
-
-
-
-
-
-exception MaxCorrectionsError( message , raises , max_errors ) [source]
-Bases: custodian.custodian.CustodianError
-Error raised when the maximum allowed number of errors is reached
-
-Parameters
-
-message (str ) – Message passed to Exception
raises (bool ) – Whether this should be raised outside custodian
max_errors (int ) – the number of errors reached
-
-
-
-
-
-exception MaxCorrectionsPerHandlerError( message , raises , max_errors_per_handler , handler ) [source]
-Bases: custodian.custodian.CustodianError
-Error raised when the maximum allowed number of errors per handler is reached
-
-Parameters
-
-message (str ) – Message passed to Exception
raises (bool ) – Whether this should be raised outside custodian
max_errors_per_handler (int ) – the number of errors per job reached
handler (Handler ) – the handler that caused the exception
-
-
-
-
-
-exception MaxCorrectionsPerJobError( message , raises , max_errors_per_job , job ) [source]
-Bases: custodian.custodian.CustodianError
-Error raised when the maximum allowed number of errors per job is reached
-
-Parameters
-
-message (str ) – Message passed to Exception
raises (bool ) – Whether this should be raised outside custodian
max_errors_per_job (int ) – the number of errors per job reached
job (Job
-
-
-
-
-
-exception NonRecoverableError( message , raises , handler ) [source]
-Bases: custodian.custodian.CustodianError
-Error raised when a handler found an error but could not fix it
-
-Parameters
-
-message (str ) – Message passed to Exception
raises (bool ) – Whether this should be raised outside custodian
handler (Handler ) – Handler that caused the exception.
-
-
-
-
-
-exception ReturnCodeError( message , raises=False ) [source]
-Bases: custodian.custodian.CustodianError
-Error raised when the process gave non zero return code
-Initializes the error with a message.
-
-Parameters
-
-
-
-
-
-
-
-exception ValidationError( message , raises , validator ) [source]
-Bases: custodian.custodian.CustodianError
-Error raised when a validator does not pass the check
-
-Parameters
-
-message (str ) – Message passed to Exception
raises (bool ) – Whether this should be raised outside custodian
validator (Validator
-
-
-
-
-
-class Validator[source]
-Bases: monty.json.MSONable
-Abstract base class defining the interface for a Validator. A Validator
-differs from an ErrorHandler in that it does not correct a run and is run
-only at the end of a Job. If errors are detected by a Validator, a run is
-immediately terminated.
-
-
-abstract check( ) [source]
-This method is called at the end of a job.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-
-
-
custodian.utils module
-
-
-backup( filenames , prefix='error' ) [source]
-Backup files to a tar.gz file. Used, for example, in backing up the
-files of an errored run before performing corrections.
-
-Parameters
-
-filenames ([ str ] ) – List of files to backup. Supports wildcards, e.g.,
-. .
prefix (str ) – prefix to the files. Defaults to error, which means a
-series of error.1.tar.gz, error.2.tar.gz, … will be generated.
-
-
-
-
-
-get_execution_host_info( ) [source]
-Tries to return a tuple describing the execution host.
-Doesn’t work for all queueing systems
-
-Returns
-(HOSTNAME, CLUSTER_NAME)
-
-
-
-
-
-
Module contents
-
-
-
-
-
-
-
-
-
-
custodian.nwchem package — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
custodian.nwchem package
-
-
-
Submodules
-
-
-
custodian.nwchem.handlers module
-
-
-class NwchemErrorHandler( output_filename='mol.nwout' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Error handler for Nwchem Jobs. Currently tested only for B3LYP DFT jobs
-generated by pymatgen.
-Initializes with an output file name.
-
-Parameters
-output_filename (str ) – This is the file where the stdout for nwchem
-is being redirected. The error messages that are checked are
-present in the stdout. Defaults to “mol.nwout”, which is the
-default redirect used by custodian.nwchem.jobs
-.NwchemJob
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-
-
-
custodian.nwchem.jobs module
-
-
-class NwchemJob( nwchem_cmd , input_file='mol.nw' , output_file='mol.nwout' , gzipped=False , backup=True , settings_override=None ) [source]
-Bases: custodian.custodian.Job
-A basic Nwchem job.
-Initializes a basic NwChem job.
-
-Parameters
-
-nwchem_cmd ([ str ] ) – Command to run Nwchem as a list of args. For
-example, [“nwchem”].
input_file (str ) – Input file to run. Defaults to “mol.nw”.
output_file (str ) – Name of file to direct standard out to.
-Defaults to “mol.nwout”.
backup (bool ) – Whether to backup the initial input files. If True,
-the input files will be copied with a “.orig” appended.
-Defaults to True.
gzipped (bool ) – Deprecated. Please use the Custodian class’s
-gzipped_output option instead.
settings_override ([ dict ] ) – An ansible style list of dict to override changes.
-#TODO: Not implemented yet.
-
-
-
-postprocess( ) [source]
-Renaming or gzipping as needed.
-
-
-
-
-run( ) [source]
-Performs actual nwchem run.
-
-
-
-
-setup( ) [source]
-Performs backup if necessary.
-
-
-
-
-
-
-
Module contents
-
-
-
-
-
-
-
-
-
-
custodian.qchem package — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
custodian.qchem package
-
-
-
Submodules
-
-
-
custodian.qchem.handlers module
-
-
-class QChemErrorHandler( input_file='mol.qin' , output_file='mol.qout' , scf_max_cycles=200 , geom_max_cycles=200 ) [source]
-Bases: custodian.custodian.ErrorHandler
-Master QChemErrorHandler class that handles a number of common errors
-that occur during QChem runs.
-Initializes the error handler from a set of input and output files.
-
-Parameters
-
-input_file (str ) – Name of the QChem input file.
output_file (str ) – Name of the QChem output file.
scf_max_cycles (int ) – The max iterations to set to fix SCF failure.
geom_max_cycles (int ) – The max iterations to set to fix geometry
-optimization failure.
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-
-
-
-
-
-
-class QChemSCFErrorHandler( input_file='mol.qin' , output_file='mol.qout' , rca_gdm_thresh=0.001 , scf_max_cycles=200 ) [source]
-Bases: custodian.custodian.ErrorHandler
-QChem ErrorHandler class that addresses SCF non-convergence.
-Initializes the error handler from a set of input and output files.
-
-Parameters
-
-input_file (str ) – Name of the QChem input file.
output_file (str ) – Name of the QChem output file.
rca_gdm_thresh (float ) – The threshold for the prior scf algorithm.
-If last deltaE is larger than the threshold try RCA_DIIS
-first, else, try DIIS_GDM first.
scf_max_cycles (int ) – The max iterations to set to fix SCF failure.
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-
-
-
-
-
-
-
custodian.qchem.jobs module
-
-
-class QCJob( qchem_command , max_cores , multimode='openmp' , input_file='mol.qin' , output_file='mol.qout' , qclog_file='mol.qclog' , suffix='' , scratch_dir='/dev/shm/qcscratch/' , save_scratch=False , save_name='default_save_name' , backup=True ) [source]
-Bases: custodian.custodian.Job
-A basic QChem Job.
-
-Parameters
-
-qchem_command (str ) – Command to run QChem.
max_cores (int ) – Maximum number of cores to parallelize over.
multimode (str ) – Parallelization scheme, either openmp or mpi.
input_file (str ) – Name of the QChem input file.
output_file (str ) – Name of the QChem output file.
qclog_file (str ) – Name of the file to redirect the standard output
-to. None means not to record the standard output.
suffix (str ) – String to append to the file in postprocess.
scratch_dir (str ) – QCSCRATCH directory. Defaults to “/dev/shm/qcscratch/”.
save_scratch (bool ) – Whether to save scratch directory contents.
-Defaults to False.
save_name (str ) – Name of the saved scratch directory. Defaults to
-to “default_save_name”.
backup (bool ) – Whether to backup the initial input file. If True, the
-input will be copied with a “.orig” appended. Defaults to True.
-
-
-
-property current_command
-
-
-
-
-classmethod opt_with_frequency_flattener( qchem_command , multimode='openmp' , input_file='mol.qin' , output_file='mol.qout' , qclog_file='mol.qclog' , max_iterations=10 , max_molecule_perturb_scale=0.3 , check_connectivity=True , **QCJob_kwargs ) [source]
-Optimize a structure and calculate vibrational frequencies to check if the
-structure is in a true minima. If a frequency is negative, iteratively
-perturbe the geometry, optimize, and recalculate frequencies until all are
-positive, aka a true minima has been found.
-
-Parameters
-
-qchem_command (str ) – Command to run QChem.
multimode (str ) – Parallelization scheme, either openmp or mpi.
input_file (str ) – Name of the QChem input file.
output_file (str ) – Name of the QChem output file.
max_iterations (int ) – Number of perturbation -> optimization -> frequency
-iterations to perform. Defaults to 10.
max_molecule_perturb_scale (float ) – The maximum scaled perturbation that
-can be applied to the molecule. Defaults to 0.3.
check_connectivity (bool ) – Whether to check differences in connectivity
-introduced by structural perturbation. Defaults to True.
**QCJob_kwargs – Passthrough kwargs to QCJob. See
-custodian.qchem.jobs.QCJob
-
-
-
-
-
-postprocess( ) [source]
-This method is called at the end of a job, after error detection.
-This allows post-processing, such as cleanup, analysis of results,
-etc.
-
-
-
-
-run( ) [source]
-Perform the actual QChem run.
-
-Returns
-(subprocess.Popen) Used for monitoring.
-
-
-
-
-
-setup( ) [source]
-This method is run before the start of a job. Allows for some
-pre-processing.
-
-
-
-
-
-
-perturb_coordinates( old_coords , negative_freq_vecs , molecule_perturb_scale , reversed_direction ) [source]
-
-
-
-
-
Module contents
-
-
-
-
-
-
-
-
-
-
custodian.vasp package — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
custodian.vasp package
-
-
-
Submodules
-
-
-
custodian.vasp.handlers module
-
-
-class AliasingErrorHandler( output_filename='vasp.out' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Master VaspErrorHandler class that handles a number of common errors
-that occur during VASP runs.
-Initializes the handler with the output file to check.
-
-Parameters
-output_filename (str ) – This is the file where the stdout for vasp
-is being redirected. The error messages that are checked are
-present in the stdout. Defaults to “vasp.out”, which is the
-default redirect used by custodian.vasp.jobs.VaspJob
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-error_msgs = {'aliasing': ['WARNING: small aliasing (wrap around) errors must be expected'], 'aliasing_incar': ['Your FFT grids (NGX,NGY,NGZ) are not sufficient for an accurate']}
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class CheckpointHandler( interval=3600 ) [source]
-Bases: custodian.custodian.ErrorHandler
-This is not an error handler per se, but rather a checkpointer. What this
-does is that every X seconds, a STOPCAR and CHKPT will be written. This
-forces VASP to stop at the end of the next ionic step. The files are then
-copied into a subdir, and then the job is restarted. To use this proper,
-max_errors in Custodian must be set to a very high value, and you
-probably wouldn’t want to use any standard VASP error handlers. The
-checkpoint will be stored in subdirs chk_#. This should be used in
-combiantion with the StoppedRunHandler.
-Initializes the handler with an interval.
-
-Parameters
-
-
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = True
-
-
-
-
-is_terminating = False
-
-
-
-
-
-
-class DriftErrorHandler( max_drift=None , to_average=3 , enaug_multiply=2 ) [source]
-Bases: custodian.custodian.ErrorHandler
-Corrects for total drift exceeding the force convergence criteria.
-Initializes the handler with max drift
-:param max_drift: This defines the max drift. Leaving this at the default of None gets the max_drift from EDFIFFG
-:type max_drift: float
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-
-
-class FrozenJobErrorHandler( output_filename='vasp.out' , timeout=21600 ) [source]
-Bases: custodian.custodian.ErrorHandler
-Detects an error when the output file has not been updated
-in timeout seconds. Changes ALGO to Normal from Fast
-Initializes the handler with the output file to check.
-
-Parameters
-
-output_filename (str ) – This is the file where the stdout for vasp
-is being redirected. The error messages that are checked are
-present in the stdout. Defaults to “vasp.out”, which is the
-default redirect used by custodian.vasp.jobs.VaspJob
timeout (int ) – The time in seconds between checks where if there
-is no activity on the output file, the run is considered
-frozen. Defaults to 3600 seconds, i.e., 1 hour.
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class LrfCommutatorHandler( output_filename='std_err.txt' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Corrects LRF_COMMUTATOR errors by setting LPEAD=True if not already set.
-Note that switching LPEAD=T can slightly change results versus the
-default due to numerical evaluation of derivatives.
-Initializes the handler with the output file to check.
-
-Parameters
-output_filename (str ) – This is the file where the stderr for vasp
-is being redirected. The error messages that are checked are
-present in the stderr. Defaults to “std_err.txt”, which is the
-default redirect used by custodian.vasp.jobs.VaspJob
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-error_msgs = {'lrf_comm': ['LRF_COMMUTATOR internal error']}
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class MaxForceErrorHandler( output_filename='vasprun.xml' , max_force_threshold=0.25 ) [source]
-Bases: custodian.custodian.ErrorHandler
-Checks that the desired force convergence has been achieved. Otherwise
-restarts the run with smaller EDIFF. (This is necessary since energy
-and force convergence criteria cannot be set simultaneously)
-
-Parameters
-
-input_filename (str ) – name of the vasp INCAR file
output_filename (str ) – name to look for the vasprun
max_force_threshold (float ) – Threshold for max force for
-restarting the run. (typically should be set to the value
-that the creator looks for)
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-
-
-
-
-
-
-class MeshSymmetryErrorHandler( output_filename='vasp.out' , output_vasprun='vasprun.xml' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Corrects the mesh symmetry error in VASP. This error is sometimes
-non-fatal. So this error handler only checks at the end of the run,
-and if the run has converged, no error is recorded.
-Initializes the handler with the output files to check.
-
-Parameters
-
-output_filename (str ) – This is the file where the stdout for vasp
-is being redirected. The error messages that are checked are
-present in the stdout. Defaults to “vasp.out”, which is the
-default redirect used by custodian.vasp.jobs.VaspJob
output_vasprun (str ) – Filename for the vasprun.xml file. Change
-this only if it is different from the default (unlikely).
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-
-
-
-
-
-
-class NonConvergingErrorHandler( output_filename='OSZICAR' , nionic_steps=10 ) [source]
-Bases: custodian.custodian.ErrorHandler
-Check if a run is hitting the maximum number of electronic steps at the
-last nionic_steps ionic steps (default=10). If so, change ALGO from Fast to
-Normal or kill the job.
-Initializes the handler with the output file to check.
-
-Parameters
-
-output_filename (str ) – This is the OSZICAR file. Change
-this only if it is different from the default (unlikely).
nionic_steps (int ) – The threshold number of ionic steps that
-needs to hit the maximum number of electronic steps for the
-run to be considered non-converging.
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class PositiveEnergyErrorHandler( output_filename='OSZICAR' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Check if a run has positive absolute energy.
-If so, change ALGO from Fast to Normal or kill the job.
-Initializes the handler with the output file to check.
-
-Parameters
-output_filename (str ) – This is the OSZICAR file. Change
-this only if it is different from the default (unlikely).
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class PotimErrorHandler( input_filename='POSCAR' , output_filename='OSZICAR' , dE_threshold=1 ) [source]
-Bases: custodian.custodian.ErrorHandler
-Check if a run has excessively large positive energy changes.
-This is typically caused by too large a POTIM. Runs typically
-end up crashing with some other error (e.g. BRMIX) as the geometry
-gets progressively worse.
-Initializes the handler with the input and output files to check.
-
-Parameters
-
-input_filename (str ) – This is the POSCAR file that the run
-started from. Defaults to “POSCAR”. Change
-this only if it is different from the default (unlikely).
output_filename (str ) – This is the OSZICAR file. Change
-this only if it is different from the default (unlikely).
dE_threshold (float ) – The threshold energy change. Defaults to 1eV.
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class StdErrHandler( output_filename='std_err.txt' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Master StdErr class that handles a number of common errors
-that occur during VASP runs with error messages only in
-the standard error.
-Initializes the handler with the output file to check.
-
-Parameters
-output_filename (str ) – This is the file where the stderr for vasp
-is being redirected. The error messages that are checked are
-present in the stderr. Defaults to “std_err.txt”, which is the
-default redirect used by custodian.vasp.jobs.VaspJob
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-error_msgs = {'kpoints_trans': ['internal error in GENERATE_KPOINTS_TRANS: number of G-vector changed in star'], 'out_of_memory': ['Allocation would exceed memory limit']}
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class StoppedRunHandler[source]
-Bases: custodian.custodian.ErrorHandler
-This is not an error handler per se, but rather a checkpointer. What this
-does is that every X seconds, a STOPCAR will be written. This forces VASP to
-stop at the end of the next ionic step. The files are then copied into a
-subdir, and then the job is restarted. To use this proper, max_errors in
-Custodian must be set to a very high value, and you probably wouldn’t
-want to use any standard VASP error handlers. The checkpoint will be
-stored in subdirs chk_#. This should be used in combination with the
-StoppedRunHandler.
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-
-
-
-
-is_terminating = False
-
-
-
-
-
-
-class UnconvergedErrorHandler( output_filename='vasprun.xml' ) [source]
-Bases: custodian.custodian.ErrorHandler
-Check if a run is converged.
-Initializes the handler with the output file to check.
-
-Parameters
-output_vasprun (str ) – Filename for the vasprun.xml file. Change
-this only if it is different from the default (unlikely).
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = False
-
-
-
-
-
-
-class VaspErrorHandler( output_filename='vasp.out' , natoms_large_cell=100 , errors_subset_to_catch=None ) [source]
-Bases: custodian.custodian.ErrorHandler
-Master VaspErrorHandler class that handles a number of common errors
-that occur during VASP runs.
-Initializes the handler with the output file to check.
-
-Parameters
-
-output_filename (str ) – This is the file where the stdout for vasp
-is being redirected. The error messages that are checked are
-present in the stdout. Defaults to “vasp.out”, which is the
-default redirect used by custodian.vasp.jobs.VaspJob
natoms_large_cell (int ) – Number of atoms threshold to treat cell
-as large. Affects the correction of certain errors. Defaults to
-100.
errors_subset_to_detect (list ) –
A subset of errors to catch. The
-default is None, which means all supported errors are detected.
-Use this to only catch only a subset of supported errors.
-E.g., [“eddrrm”, “zheev”] will only catch the eddrmm and zheev
-errors, and not others. If you wish to only excluded one or
-two of the errors, you can create this list by the following
-lines:
-``
-handler = VaspErrorHandler(errors_subset_to_catch=subset)
-`` `
-
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-error_msgs = {'amin': ['One of the lattice vectors is very long (>50 A), but AMIN'], 'brions': ['BRIONS problems: POTIM should be increased'], 'brmix': ['BRMIX: very serious problems'], 'dentet': ['DENTET'], 'edddav': ['Error EDDDAV: Call to ZHEGV failed'], 'eddrmm': ['WARNING in EDDRMM: call to ZHEGV failed'], 'elf_kpar': ['ELF: KPAR>1 not implemented'], 'elf_ncl': ['WARNING: ELF not implemented for non collinear case'], 'grad_not_orth': ['EDWAV: internal error, the gradient is not orthogonal'], 'incorrect_shift': ['Could not get correct shifts'], 'inv_rot_mat': ['inverse of rotation matrix was not found (increase SYMPREC)'], 'nicht_konv': ['ERROR: SBESSELITER : nicht konvergent'], 'point_group': ['Error: point group operation missing'], 'posmap': ['POSMAP internal error: symmetry equivalent atom not found'], 'pricel': ['internal error in subroutine PRICEL'], 'pssyevx': ['ERROR in subspace rotation PSSYEVX'], 'real_optlay': ['REAL_OPTLAY: internal error', 'REAL_OPT: internal ERROR'], 'rhosyg': ['RHOSYG internal error'], 'rot_matrix': ['Found some non-integer element in rotation matrix'], 'rspher': ['ERROR RSPHER'], 'subspacematrix': ['WARNING: Sub-Space-Matrix is not hermitian in DAV'], 'tet': ['Tetrahedron method fails for NKPT<4', 'Fatal error detecting k-mesh', 'Fatal error: unable to match k-point', 'Routine TETIRR needs special values', 'Tetrahedron method fails (number of k-points < 4)'], 'tetirr': ['Routine TETIRR needs special values'], 'too_few_bands': ['TOO FEW BANDS'], 'triple_product': ['ERROR: the triple product of the basis vectors'], 'zbrent': ['ZBRENT: fatal internal in', 'ZBRENT: fatal error in bracketing'], 'zheev': ['ERROR EDDIAG: Call to routine ZHEEV failed!'], 'zpotrf': ['LAPACK: Routine ZPOTRF failed']}
-
-
-
-
-is_monitor = True
-
-
-
-
-
-
-class WalltimeHandler( wall_time=None , buffer_time=300 , electronic_step_stop=False ) [source]
-Bases: custodian.custodian.ErrorHandler
-Check if a run is nearing the walltime. If so, write a STOPCAR with
-LSTOP or LABORT = .True.. You can specify the walltime either in the init (
-which is unfortunately necessary for SGE and SLURM systems. If you happen
-to be running on a PBS system and the PBS_WALLTIME variable is in the run
-environment, the wall time will be automatically determined if not set.
-Initializes the handler with a buffer time.
-
-Parameters
-
-wall_time (int ) – Total walltime in seconds. If this is None and
-the job is running on a PBS system, the handler will attempt to
-determine the walltime from the PBS_WALLTIME environment
-variable. If the wall time cannot be determined or is not
-set, this handler will have no effect.
buffer_time (int ) – The min amount of buffer time in secs at the
-end that the STOPCAR will be written. The STOPCAR is written
-when the time remaining is < the higher of 3 x the average
-time for each ionic step and the buffer time. Defaults to
-300 secs, which is the default polling time of Custodian.
-This is typically sufficient for the current ionic step to
-complete. But if other operations are being performed after
-the run has stopped, the buffer time may need to be increased
-accordingly.
electronic_step_stop (bool ) – Whether to check for electronic steps
-instead of ionic steps (e.g. for static runs on large systems or
-static HSE runs, …). Be careful that results such as density
-or wavefunctions might not be converged at the electronic level.
-Should be used with LWAVE = .True. to be useful. If this is
-True, the STOPCAR is written with LABORT = .TRUE. instead of
-LSTOP = .TRUE.
-
-
-
-check( ) [source]
-This method is called during the job (for monitors) or at the end of
-the job to check for errors.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-correct( ) [source]
-This method is called at the end of a job when an error is detected.
-It should perform any corrective measures relating to the detected
-error.
-
-Returns
-(dict) JSON serializable dict that describes the errors and
-actions taken. E.g.
-{“errors”: list_of_errors, “actions”: list_of_actions_taken}.
-If this is an unfixable error, actions should be set to None.
-
-
-
-
-
-is_monitor = True
-
-
-
-
-is_terminating = False
-
-
-
-
-raises_runtime_error = False
-
-
-
-
-
-
-
custodian.vasp.interpreter module
-
-
-class VaspModder( actions=None , strict=True , vi=None ) [source]
-Bases: custodian.ansible.interpreter.Modder
-Initializes a Modder for VaspInput sets
-
-Parameters
-
-actions ([ Action ] ) – A sequence of supported actions. See
-custodian.ansible.actions
strict (bool ) – Indicating whether to use strict mode. In non-strict
-mode, unsupported actions are simply ignored without any
-errors raised. In strict mode, if an unsupported action is
-supplied, a ValueError is raised. Defaults to True.
vi (VaspInput ) – A VaspInput object from the current directory.
-Initialized automatically if not passed (but passing it will
-avoid having to reparse the directory).
-
-
-
-apply_actions( actions ) [source]
-Applies a list of actions to the Vasp Input Set and rewrites modified
-files.
-:param actions [dict]: A list of actions of the form {‘file’: filename,
-
-‘action’: moddermodification} or {‘dict’: vaspinput_key,
-‘action’: moddermodification}
-
-
-
-
-
-
-
-
custodian.vasp.jobs module
-
-
-class GenerateVaspInputJob( input_set , contcar_only=True , **kwargs ) [source]
-Bases: custodian.custodian.Job
-Generates a VASP input based on an existing directory. This is typically
-used to modify the VASP input files before the next VaspJob.
-
-Parameters
-
-input_set (str ) – Full path to the input set. E.g.,
-“pymatgen.io.vasp.sets.MPNonSCFSet”.
contcar_only (bool ) – If True (default), only CONTCAR structures
-are used as input to the input set.
-
-
-
-postprocess( ) [source]
-This method is called at the end of a job, after error detection.
-This allows post-processing, such as cleanup, analysis of results,
-etc.
-
-
-
-
-run( ) [source]
-This method perform the actual work for the job. If parallel error
-checking (monitoring) is desired, this must return a Popen process.
-
-
-
-
-setup( ) [source]
-This method is run before the start of a job. Allows for some
-pre-processing.
-
-
-
-
-
-
-class VaspJob( vasp_cmd , output_file='vasp.out' , stderr_file='std_err.txt' , suffix='' , final=True , backup=True , auto_npar=False , auto_gamma=True , settings_override=None , gamma_vasp_cmd=None , copy_magmom=False , auto_continue=False ) [source]
-Bases: custodian.custodian.Job
-A basic vasp job. Just runs whatever is in the directory. But conceivably
-can be a complex processing of inputs etc. with initialization.
-This constructor is necessarily complex due to the need for
-flexibility. For standard kinds of runs, it’s often better to use one
-of the static constructors. The defaults are usually fine too.
-
-Parameters
-
-vasp_cmd (str ) – Command to run vasp as a list of args. For example,
-if you are using mpirun, it can be something like
-[“mpirun”, “pvasp.5.2.11”]
output_file (str ) – Name of file to direct standard out to.
-Defaults to “vasp.out”.
stderr_file (str ) – Name of file to direct standard error to.
-Defaults to “std_err.txt”.
suffix (str ) – A suffix to be appended to the final output. E.g.,
-to rename all VASP output from say vasp.out to
-vasp.out.relax1, provide “.relax1” as the suffix.
final (bool ) – Indicating whether this is the final vasp job in a
-series. Defaults to True.
backup (bool ) – Whether to backup the initial input files. If True,
-the INCAR, KPOINTS, POSCAR and POTCAR will be copied with a
-“.orig” appended. Defaults to True.
auto_npar (bool ) – Whether to automatically tune NPAR to be sqrt(
-number of cores) as recommended by VASP for DFT calculations.
-Generally, this results in significant speedups. Defaults to
-True. Set to False for HF, GW and RPA calculations.
auto_gamma (bool ) – Whether to automatically check if run is a
-Gamma 1x1x1 run, and whether a Gamma optimized version of
-VASP exists with “.gamma” appended to the name of the VASP
-executable (typical setup in many systems). If so, run the
-gamma optimized version of VASP instead of regular VASP. You
-can also specify the gamma vasp command using the
-gamma_vasp_cmd argument if the command is named differently.
settings_override ([ dict ] ) –
An ansible style list of dict to
-override changes. For example, to set ISTART=1 for subsequent
-runs and to copy the CONTCAR to the POSCAR, you will provide:
-[{ "dict" : "INCAR" , "action" : { "_set" : { "ISTART" : 1 }}},
- { "file" : "CONTCAR" ,
- "action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
-
gamma_vasp_cmd (str ) – Command for gamma vasp version when
-auto_gamma is True. Should follow the list style of
-subprocess. Defaults to None, which means “.gamma” is added
-to the last argument of the standard vasp_cmd.
copy_magmom (bool ) – Whether to copy the final magmom from the
-OUTCAR to the next INCAR. Useful for multi-relaxation runs
-where the CHGCAR and WAVECAR are sometimes deleted (due to
-changes in fft grid, etc.). Only applies to non-final runs.
auto_continue (bool ) – Whether to automatically continue a run
-if a STOPCAR is present. This is very useful if using the
-wall-time handler which will write a read-only STOPCAR to
-prevent VASP from deleting it once it finishes
-
-
-
-classmethod constrained_opt_run( vasp_cmd , lattice_direction , initial_strain , atom_relax=True , max_steps=20 , algo='bfgs' , **vasp_job_kwargs ) [source]
-Returns a generator of jobs for a constrained optimization run. Typical
-use case is when you want to approximate a biaxial strain situation,
-e.g., you apply a defined strain to a and b directions of the lattice,
-but allows the c-direction to relax.
-Some guidelines on the use of this method:
-i. It is recommended you do not use the Auto kpoint generation. The
-
-grid generated via Auto may fluctuate with changes in lattice
-param, resulting in numerical noise.
-
-
-Make sure your EDIFF/EDIFFG is properly set in your INCAR. The
-optimization relies on these values to determine convergence.
-
-Parameters
-
-vasp_cmd (str ) – Command to run vasp as a list of args. For example,
-if you are using mpirun, it can be something like
-[“mpirun”, “pvasp.5.2.11”]
lattice_direction (str ) – Which direction to relax. Valid values are
-“a”, “b” or “c”.
initial_strain (float ) – An initial strain to be applied to the
-lattice_direction. This can usually be estimated as the
-negative of the strain applied in the other two directions.
-E.g., if you apply a tensile strain of 0.05 to the a and b
-directions, you can use -0.05 as a reasonable first guess for
-initial strain.
atom_relax (bool ) – Whether to relax atomic positions.
max_steps (int ) – The maximum number of runs. Defaults to 20 (
-highly unlikely that this limit is ever reached).
algo (str ) – Algorithm to use to find minimum. Default is “bfgs”,
-which is fast, but can be sensitive to numerical noise
-in energy calculations. The alternative is “bisection”,
-which is more robust but can be a bit slow. The code does fall
-back on the bisection when bfgs gives a non-sensical result,
-e.g., negative lattice params.
**vasp_job_kwargs – Passthrough kwargs to VaspJob. See
-custodian.vasp.jobs.VaspJob
-Returns
-Generator of jobs. At the end of the run, an “EOS.txt” is written
-which provides a quick look at the E vs lattice parameter.
-
-
-
-
-
-classmethod double_relaxation_run( vasp_cmd , auto_npar=True , ediffg=-0.05 , half_kpts_first_relax=False , auto_continue=False ) [source]
-Returns a list of two jobs corresponding to an AFLOW style double
-relaxation run.
-
-Parameters
-
-vasp_cmd (str ) – Command to run vasp as a list of args. For example,
-if you are using mpirun, it can be something like
-[“mpirun”, “pvasp.5.2.11”]
auto_npar (bool ) – Whether to automatically tune NPAR to be sqrt(
-number of cores) as recommended by VASP for DFT calculations.
-Generally, this results in significant speedups. Defaults to
-True. Set to False for HF, GW and RPA calculations.
ediffg (float ) – Force convergence criteria for subsequent runs (
-ignored for the initial run.)
half_kpts_first_relax (bool ) – Whether to halve the kpoint grid
-for the first relaxation. Speeds up difficult convergence
-considerably. Defaults to False.
-Returns
-List of two jobs corresponding to an AFLOW style run.
-
-
-
-
-
-classmethod full_opt_run( vasp_cmd , vol_change_tol=0.02 , max_steps=10 , ediffg=-0.05 , half_kpts_first_relax=False , **vasp_job_kwargs ) [source]
-Returns a generator of jobs for a full optimization run. Basically,
-this runs an infinite series of geometry optimization jobs until the
-% vol change in a particular optimization is less than vol_change_tol.
-
-Parameters
-
-vasp_cmd (str ) – Command to run vasp as a list of args. For example,
-if you are using mpirun, it can be something like
-[“mpirun”, “pvasp.5.2.11”]
vol_change_tol (float ) – The tolerance at which to stop a run.
-Defaults to 0.05, i.e., 5%.
max_steps (int ) – The maximum number of runs. Defaults to 10 (
-highly unlikely that this limit is ever reached).
ediffg (float ) – Force convergence criteria for subsequent runs (
-ignored for the initial run.)
half_kpts_first_relax (bool ) – Whether to halve the kpoint grid
-for the first relaxation. Speeds up difficult convergence
-considerably. Defaults to False.
**vasp_job_kwargs – Passthrough kwargs to VaspJob. See
-custodian.vasp.jobs.VaspJob
-Returns
-Generator of jobs.
-
-
-
-
-
-classmethod metagga_opt_run( vasp_cmd , auto_npar=True , ediffg=-0.05 , half_kpts_first_relax=False , auto_continue=False ) [source]
-Returns a list of thres jobs to perform an optimization for any
-metaGGA functional. There is an initial calculation of the
-GGA wavefunction which is fed into the initial metaGGA optimization
-to precondition the electronic structure optimizer. The metaGGA
-optimization is performed using the double relaxation scheme
-
-
-
-
-postprocess( ) [source]
-Postprocessing includes renaming and gzipping where necessary.
-Also copies the magmom to the incar if necessary
-
-
-
-
-run( ) [source]
-Perform the actual VASP run.
-
-Returns
-(subprocess.Popen) Used for monitoring.
-
-
-
-
-
-setup( ) [source]
-Performs initial setup for VaspJob, including overriding any settings
-and backing up.
-
-
-
-
-terminate( ) [source]
-
-
-
-
-
-
-class VaspNEBJob( vasp_cmd , output_file='neb_vasp.out' , stderr_file='neb_std_err.txt' , suffix='' , final=True , backup=True , auto_npar=True , half_kpts=False , auto_gamma=True , auto_continue=False , gamma_vasp_cmd=None , settings_override=None ) [source]
-Bases: custodian.custodian.Job
-A NEB vasp job, especially for CI-NEB running at PBS clusters.
-The class is added for the purpose of handling a different folder
-arrangement in NEB calculation.
-This constructor is a simplified version of VaspJob, which satisfies
-the need for flexibility. For standard kinds of runs, it’s often
-better to use one of the static constructors. The defaults are
-usually fine too.
-
-Parameters
-
-vasp_cmd (str ) – Command to run vasp as a list of args. For example,
-if you are using mpirun, it can be something like
-[“mpirun”, “pvasp.5.2.11”]
output_file (str ) – Name of file to direct standard out to.
-Defaults to “vasp.out”.
stderr_file (str ) – Name of file to direct standard error to.
-Defaults to “std_err.txt”.
suffix (str ) – A suffix to be appended to the final output. E.g.,
-to rename all VASP output from say vasp.out to
-vasp.out.relax1, provide “.relax1” as the suffix.
final (bool ) – Indicating whether this is the final vasp job in a
-series. Defaults to True.
backup (bool ) – Whether to backup the initial input files. If True,
-the INCAR, KPOINTS, POSCAR and POTCAR will be copied with a
-“.orig” appended. Defaults to True.
auto_npar (bool ) – Whether to automatically tune NPAR to be sqrt(
-number of cores) as recommended by VASP for DFT calculations.
-Generally, this results in significant speedups. Defaults to
-True. Set to False for HF, GW and RPA calculations.
half_kpts (bool ) – Whether to halve the kpoint grid for NEB.
-Speeds up convergence considerably. Defaults to False.
auto_gamma (bool ) – Whether to automatically check if run is a
-Gamma 1x1x1 run, and whether a Gamma optimized version of
-VASP exists with “.gamma” appended to the name of the VASP
-executable (typical setup in many systems). If so, run the
-gamma optimized version of VASP instead of regular VASP. You
-can also specify the gamma vasp command using the
-gamma_vasp_cmd argument if the command is named differently.
auto_continue (bool ) – Whether to automatically continue a run
-if a STOPCAR is present. This is very useful if using the
-wall-time handler which will write a read-only STOPCAR to
-prevent VASP from deleting it once it finishes.
gamma_vasp_cmd (str ) – Command for gamma vasp version when
-auto_gamma is True. Should follow the list style of
-subprocess. Defaults to None, which means “.gamma” is added
-to the last argument of the standard vasp_cmd.
settings_override ([ dict ] ) –
An ansible style list of dict to
-override changes. For example, to set ISTART=1 for subsequent
-runs and to copy the CONTCAR to the POSCAR, you will provide:
-[{ "dict" : "INCAR" , "action" : { "_set" : { "ISTART" : 1 }}},
- { "file" : "CONTCAR" ,
- "action" : { "_file_copy" : { "dest" : "POSCAR" }}}]
-
-
-
-
-
-postprocess( ) [source]
-Postprocessing includes renaming and gzipping where necessary.
-
-
-
-
-run( ) [source]
-Perform the actual VASP run.
-
-Returns
-(subprocess.Popen) Used for monitoring.
-
-
-
-
-
-setup( ) [source]
-Performs initial setup for VaspNEBJob, including overriding any settings
-and backing up.
-
-
-
-
-
-
-
custodian.vasp.validators module
-
-
-class VaspAECCARValidator[source]
-Bases: custodian.custodian.Validator
-Check if the data in the AECCAR is corrupted
-
-
-check( ) [source]
-This method is called at the end of a job.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-
-
-class VaspFilesValidator[source]
-Bases: custodian.custodian.Validator
-
-Check for existence of some of the files that VASP normally create upon running.
-
-
-
-check( ) [source]
-This method is called at the end of a job.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-
-
-class VaspNpTMDValidator[source]
-Bases: custodian.custodian.Validator
-Check NpT-AIMD settings is loaded by VASP compiled with -Dtbdyn.
-Currently, VASP only have Langevin thermostat (MDALGO = 3) for NpT ensemble.
-
-
-check( ) [source]
-This method is called at the end of a job.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-
-
-class VasprunXMLValidator( output_file='vasp.out' , stderr_file='std_err.txt' ) [source]
-Bases: custodian.custodian.Validator
-Checks that a valid vasprun.xml was generated
-
-Parameters
-
-
-
-
-
-check( ) [source]
-This method is called at the end of a job.
-
-Returns
-(bool) Indicating if errors are detected.
-
-
-
-
-
-
-
-check_broken_chgcar( chgcar ) [source]
-
-
-
-
-
Module contents
-
-
-
-
-
-
-
-
-
-
Index — custodian 2019.8.23 documentation
-
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Index
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Custodian — custodian 2019.8.23 documentation
-
-
-
-
-
-
-
Custodian
-
Custodian is a simple, robust and flexible just-in-time (JIT) job management
-framework written in Python. Using custodian, you can create wrappers that
-perform error checking, job management and error recovery. It has a simple
-plugin framework that allows you to develop specific job management workflows
-for different applications.
-
Error recovery is an important aspect of many high-throughput projects that
-generate data on a large scale. When you are running on the order of hundreds
-of thousands of jobs, even an error rate of 1% would mean thousands of errored
-jobs that would be impossible to deal with on a case-by-case basis.
-
The specific use case for custodian is for long running jobs, with potentially
-random errors. For example, there may be a script that takes several days to
-run on a server, with a 1% chance of some IO error causing the job to fail.
-Using custodian, one can develop a mechanism to gracefully recover from the
-error, and restart the job with modified parameters if necessary.
-
The current version of Custodian also comes with two sub-packages for error
-handling for Vienna Ab Initio Simulation Package (VASP), NwChem and QChem
-calculations.
-
-
-
-
Getting custodian
-
-
Stable version
-
The version at the Python Package Index (PyPI) is always the latest stable
-release that will be hopefully, be relatively bug-free. The easiest way to
-install custodian on any system is to use easy_install or pip, as follows:
-
-
or:
-
-
Some plugins (e.g., vasp management) require additional setup (please see
-pymatgen’s documentation ).
-
-
-
Developmental version
-
The bleeding edge developmental version is at the custodian’s Github repo . The developmental
-version is likely to be more buggy, but may contain new features. The
-Github version include test files as well for complete unit testing. After
-cloning the source, you can type:
-
python setup . py install
-
-
-
or to install the package in developmental mode:
-
python setup . py develop
-
-
-
-
-
-
Requirements
-
Custodian requires Python 2.7+. There are no other required dependencies.
-
-
Optional dependencies
-
Optional libraries that are required if you need certain features:
-
-Python Materials Genomics (pymatgen ) 2.8.10+: To use the plugin for
-VASP, NwChem and Qchem. Please install using:
-
-For more information, please consult pymatgen’s documentation .
-nose - For complete unittesting.
-
-
-
-
Usage
-
The main class in the workflow is known as Custodian, which manages a series
-of jobs with a list of error handlers. The general workflow for Custodian is
-presented in the figure below.
-
-
The Custodian class takes in two general inputs - a list of Jobs and
-a list of ErrorHandlers . Jobs should be subclasses of the
-custodian.custodian.Job ErrorHandlers
-should be subclasses of the custodian.custodian.ErrorHandler
-
-
Simple example
-
An very simple example implementation is given in the custodian_examples.py
-script in the scripts directory. We will now go through the example in detail
-here.
-
The ExampleJob has the following code.
-
class ExampleJob ( Job ):
-
- def __init__ ( self , jobid , params = None ):
- if params is None :
- params = { "initial" : 0 , "total" : 0 }
- self . jobid = jobid
- self . params = params
-
- def setup ( self ):
- self . params [ "initial" ] = 0
- self . params [ "total" ] = 0
-
- def run ( self ):
- sequence = [ random . uniform ( 0 , 1 ) for i in range ( 100 )]
- self . params [ "total" ] = self . params [ "initial" ] + sum ( sequence )
-
- def postprocess ( self ):
- pass
-
- @property
- def name ( self ):
- return "ExampleJob{}" . format ( self . jobid )
-
-
-
The ExampleJob simply sums a random sequence of 100 numbers between 0 and
-1, adds it to an initial value and puts the value in ‘total’ variable. The
-ExampleJob subclasses the Job abstract base class, and implements the necessary
-API comprising of just three key methods: setup(), run(),
-and postprocess() .
-
Let us now define an ErrorHandler that will check if the total value is >= 50,
-and if it is not, it will increment the initial value by 1 and rerun the
-ExampleJob again.
-
class ExampleHandler ( ErrorHandler ):
-
- def __init__ ( self , params ):
- self . params = params
-
- def check ( self ):
- return self . params [ "total" ] < 50
-
- def correct ( self ):
- self . params [ "initial" ] += 1
- return { "errors" : "total < 50" , "actions" : "increment by 1" }
-
-
-
As you can see above, the ExampleHandler subclasses the ErrorHandler abstract
-base class, and implements the necessary API comprising of just two key
-methods: check() and correct() .
-
The transfer of information between the Job and ErrorHandler is done using
-the params argument in this example, which is not ideal but is sufficiently
-for demonstrating the Custodian API. In real world usage,
-a more common transfer of information may involve the Job writing the output
-to a file, and the ErrorHandler checking the contents of those files to
-detect error situations.
-
To run the job, one simply needs to supply a list of ExampleJobs and
-ErrorHandlers to a Custodian.
-
njobs = 100
-params = { "initial" : 0 , "total" : 0 }
-c = Custodian ([ ExampleHandler ( params )],
- [ ExampleJob ( i , params ) for i in xrange ( njobs )],
- max_errors = njobs )
-c . run ()
-
-
-
If you run custodian_example.py in the scripts directory, you will noticed that
-a custodian.json file was generated, which summarizes the jobs that have
-been run and any corrections performed.
-
-
-
Practical example: Electronic structure calculations
-
A practical example where the Custodian framework is particularly useful is
-in the area of electronic structure calculations. Electronic structure
-calculations tend to be long running and often terminates due to errors,
-random or otherwise. Such errors become a major issue in projects that
-performs such calculations in high throughput, such as the Materials
-Project .
-
The Custodian package comes with a fairly comprehensive plugin to deal
-with jobs (custodian.vasp.jobs custodian.vasp.handlers pymatgen ) package to
-perform analysis and io from VASP input and output files.
-
A simple example of a script using Custodian to run a two-relaxation VASP job
-is as follows:
-
from custodian.custodian import Custodian
-from custodian.vasp.handlers import VaspErrorHandler , \
- UnconvergedErrorHandler , PoscarErrorHandler , DentetErrorHandler
-from custodian.vasp.jobs import VaspJob
-
-handlers = [ VaspErrorHandler (), UnconvergedErrorHandler (),
- PoscarErrorHandler (), DentetErrorHandler ()]
-jobs = VaspJob . double_relaxation_run ( args . command . split ())
-c = Custodian ( handlers , jobs , max_errors = 10 )
-c . run ()
-
-
-
The above will gracefully deal with many VASP errors encountered during
-relaxation. For example, it will correct ISMEAR to 0 if there are
-insufficient KPOINTS to use ISMEAR = -5.
-
Using custodian, you can even setup potentially indefinite jobs,
-e.g. kpoints convergence jobs with a target energy convergence. Please see the
-converge_kpoints script in the scripts for an example.
-
-
New in version 0.4.3: A new package for dealing with NwChem calculations has been added.
-NwChem is an open-source code for performing computational chemistry
-calculations.
-
-
-
-
-
cstdn - A yaml-spec controlled job
-
Custodian now comes with a cstdn script, which allows you to do fine-grained
-control of a job using a yaml spec file. Below is an annotated example of how
-you can specify a double VASP relaxation followed by a static calculation.
-Minor modifications would allow very customizable calculations, though this is
-obviously not meant for highly complex workflows. For those, usage of FireWorks is highly recommended.
-
Sample yaml spec:
-
-
-
You can then run the job using the following command:
-
cstdn run < path to yaml file >
-
-
-
-
-
API/Reference Docs
-
The API docs are generated using Sphinx auto-doc and outlines the purpose of all
-modules and classes, and the expected argument and returned objects for most
-methods. They are available at the link below.
-
custodian API docs
-
-
-
How to cite custodian
-
If you use custodian in your research, especially the VASP component, please
-consider citing the following work:
-
-
-
-
-
License
-
Custodian is released under the MIT License. The terms of the license are as
-follows:
-
The MIT License ( MIT )
-Copyright ( c ) 2011 - 2012 MIT & LBNL
-
-Permission is hereby granted , free of charge , to any person obtaining a
-copy of this software and associated documentation files ( the "Software" )
-, to deal in the Software without restriction , including without limitation
-the rights to use , copy , modify , merge , publish , distribute , sublicense ,
-and / or sell copies of the Software , and to permit persons to whom the
-Software is furnished to do so , subject to the following conditions :
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software .
-
-THE SOFTWARE IS PROVIDED "AS IS" , WITHOUT WARRANTY OF ANY KIND , EXPRESS OR
-IMPLIED , INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY ,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT . IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM , DAMAGES OR OTHER
-LIABILITY , WHETHER IN AN ACTION OF CONTRACT , TORT OR OTHERWISE , ARISING
-FROM , OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
-DEALINGS IN THE SOFTWARE .
-
-
-
-
-
-
-
-
-
-
-
custodian — custodian 2019.8.23 documentation
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