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__init__.py
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#****************************************************************************
# Copyright (C) 2013-2015 SUNCAT
# This file is distributed under the terms of the
# GNU General Public License. See the file `COPYING'
# in the root directory of the present distribution,
# or http://www.gnu.org/copyleft/gpl.txt .
#****************************************************************************
import os
from subprocess import Popen, PIPE, call
import warnings
import atexit
import sys
import numpy as np
from ase import Atoms
from ase.units import Rydberg, Bohr, Hartree
from .atomic_configs import hundmag
from .worldstub import world
from . import subdirs
from . import utils
from ase.calculators.calculator import kptdensity2monkhorstpack
try:
from ase.calculators.calculator import FileIOCalculator as Calculator
except BaseException:
from ase.calculators.general import Calculator
try:
from . import espsite
except ImportError:
print(
'*** ase-espresso requires a site-specific espsite.py in PYTHONPATH. '
'*** You may use the espsite.py.example.* in the git checkout as templates.'
)
raise ImportError
site = espsite.config()
gitver = 'GITVERSION'
# ase controlled pw.x's register themselves here, so they can be
# stopped automatically
espresso_calculators = []
# Define types of convergence errors that can be used to handle
# convergence error automatically
class ConvergenceError(Exception):
pass
class KohnShamConvergenceError(ConvergenceError):
pass
class espresso(Calculator):
"""ASE interface for Quantum Espresso"""
implemented_properties = [
'energy', 'free_energy', 'forces', 'stress', 'magmom', 'magmoms'
]
def __init__(
self,
atoms=None,
exedir='', # espresso binary folder, if "./" just take the current environmental variable
pw=350.0,
dw=None,
fw=None,
nbands=-10,
kpts=(1, 1, 1),
kptshift=(0, 0, 0),
fft_grid=None,
mode=None,
calculation='ase3',
opt_algorithm=None,
ion_dynamics='ase3',
nstep=None,
constr_tol=None,
fmax=0.05,
cell_dynamics=None,
press=None, # target pressure
dpress=None, # convergence limit towards target pressure
cell_factor=None,
cell_dofree=None,
dontcalcforces=False,
nosym=False,
noinv=False,
nosym_evc=False,
no_t_rev=False,
xc='PBE',
beefensemble=False,
printensemble=False,
psppath=None,
spinpol=False,
noncollinear=False,
spinorbit=False,
outdir=None,
txt=None,
calcstress=False,
smearing='fd',
sigma=0.1,
fix_magmom=False,
isolated=None,
U=None,
J=None,
U_alpha=None,
U_projection_type='atomic',
nqx1=None,
nqx2=None,
nqx3=None,
exx_fraction=None,
screening_parameter=None,
exxdiv_treatment=None,
ecutvcut=None,
tot_charge=None, # +1 means 1 e missing, -1 means 1 extra e
charge=None, # overrides tot_charge (ase 3.7+ compatibility)
tot_magnetization=-1, # -1 means unspecified, 'hund' means Hund's rule for each atom
occupations='smearing', # 'smearing', 'fixed', 'tetrahedra'
dipole={'status': False},
field={'status': False},
output={
'disk_io':
'default', # how often espresso writes wavefunctions to disk
'avoidio': False, # will overwrite disk_io parameter if True
'removewf': True,
'removesave': False,
'wf_collect': False
},
convergence={
'energy': 1e-6,
'mixing': 0.7,
'maxsteps': 100,
'diag': 'david'
},
startingpot=None,
startingwfc=None,
ion_positions=None,
parflags=None,
onlycreatepwinp=None, # specify filename to only create pw input
single_calculator=True, # if True, only one espresso job will be running
procrange=None, # let this espresso calculator run only on a subset of the requested cpus
numcalcs=None, # used / set by multiespresso class
alwayscreatenewarrayforforces=True,
verbose='low',
# automatically generated list of parameters
# some coincide with ase-style names
iprint=None,
tstress=None,
tprnfor=None,
dt=None,
lkpoint_dir=None,
max_seconds=None,
etot_conv_thr=None,
forc_conv_thr=None,
tefield=None,
dipfield=None,
lelfield=None,
nberrycyc=None,
lorbm=None,
lberry=None,
gdir=None,
nppstr=None,
nbnd=None,
ecutwfc=None,
ecutrho=None,
ecutfock=None,
force_symmorphic=None,
use_all_frac=None,
one_atom_occupations=None,
starting_spin_angle=None,
degauss=None,
nspin=None,
ecfixed=None,
qcutz=None,
q2sigma=None,
x_gamma_extrapolation=None,
lda_plus_u=None,
lda_plus_u_kind=None,
edir=None,
emaxpos=None,
eopreg=None,
eamp=None,
clambda=None,
report=None,
lspinorb=None,
esm_bc=None,
esm_w=None,
esm_efield=None,
esm_nfit=None,
london=None,
london_s6=None,
london_rcut=None,
xdm=None,
xdm_a1=None,
xdm_a2=None,
electron_maxstep=None,
scf_must_converge=None,
conv_thr=None,
adaptive_thr=None,
conv_thr_init=None,
conv_thr_multi=None,
mixing_beta=None,
mixing_ndim=None,
mixing_fixed_ns=None,
ortho_para=None,
diago_thr_init=None,
diago_cg_maxiter=None,
diago_david_ndim=None,
diago_full_acc=None,
efield=None,
tqr=None,
remove_rigid_rot=None,
tempw=None,
tolp=None,
delta_t=None,
nraise=None,
refold_pos=None,
upscale=None,
bfgs_ndim=None,
vdw_corr=None,
ts_vdw_econv_thr=None,
ts_vdw_isolated=None,
lfcpopt=None,
fcp_mu=None,
esm_a=None,
trust_radius_max=None,
trust_radius_min=None,
trust_radius_ini=None,
w_1=None,
w_2=None,
wmass=None,
press_conv_thr=None,
results={},
name='espresso',
restart=None,
ignore_bad_restart_file=False,
label=None,
command=None,
# ENVIRON PART (credit Stefan Ringe)
environ_keys=None, # Environ keys given as dictionary, if given use_environ=True
environ_extra_keys=None
):
"""
Construct an ase-espresso calculator.
Parameters (with defaults in parentheses):
atoms (None)
list of atoms object to be attached to calculator
atoms.set_calculator can be used instead
onlycreatepwinp (None)
if not None but 'filename', create input file 'filename' for pw.x
but do not run pw.x
calc.initialize(atoms) will trigger 'filename' to be written
pw (350.0)
plane-wave cut-off in eV
dw (10*pw)
charge-density cut-off in eV
fw (None)
plane-wave cutoff for evaluation of EXX in eV
nbands (-10)
number of bands, if negative: -n extra bands
kpts ( (1,1,1) )
k-point grid sub-divisions, k-point grid density,
explicit list of k-points, or simply 'gamma' for gamma-point only.
kptshift ( (0,0,0) )
shift of k-point grid
fft_grid ( None )
specify tuple of fft grid points (nr1,nr2,nr3) for q.e.
useful for series of calculations with changing cell size
(e.g. lattice constant optimization) uses q.e. default if not
specified. [RK]
mode (None)
Deprecated, See calculation.
calculation ( 'ase3' )
relaxation mode:
- 'ase3': dynamic communication between Quantum Espresso and python
- 'relax', 'scf', 'nscf': corresponding Quantum Espresso standard modes
opt_algorithm (None)
Deprecated, See ion_dynamics.
ion_dynamics ( 'ase3' )
- 'ase3': ase updates coordinates during relaxation
- 'relax' and other Quantum Espresso standard relaxation modes:
Quantum Espresso own algorithms for structural optimization
are used
Obtaining Quantum Espresso with the ase3 relaxation extensions is
highly recommended, since it allows for using ase's optimizers without
loosing efficiency:
svn co --username anonymous http://qeforge.qe-forge.org/svn/q-e/branches/espresso-dynpy-beef
fmax (0.05)
max force limit for Espresso-internal relaxation (eV/Angstrom)
constr_tol (None)
constraint tolerance for Espresso-internal relaxation
cell_dynamics (None)
algorithm (e.g. 'BFGS') to be used for Espresso-internal
unit-cell optimization
press (None)
target pressure for such an optimization
dpress (None)
convergence limit towards target pressure
cell_factor (None)
should be >>1 if unit-cell volume is expected to shrink a lot during
relaxation (would be more efficient to start with a better guess)
cell_dofree (None)
partially fix lattice vectors
nosym (False)
noinv (False)
nosym_evc (False)
no_t_rev (False)
turn off corresp. symmetries
xc ('PBE')
xc-functional to be used
beefensemble (False)
calculate basis energies for ensemble error estimates based on
the BEEF-vdW functional
printensemble (False)
let Espresso itself calculate 2000 ensemble energies
psppath (None)
Directory containing the pseudo-potentials or paw-setups to be used.
The ase-espresso interface expects all pot. files to be of the type
element.UPF (e.g. H.UPF).
If None, the directory pointed to be ESP_PSP_PATH is used.
spinpol (False)
If True, calculation is spin-polarized
noncollinear (False)
Non-collinear magnetism.
spinorbit (False)
If True, spin-orbit coupling is considered.
Make sure to provide j-dependent pseudo-potentials in psppath
for those elements where spin-orbit coupling is important
outdir (None)
directory where Espresso's output is collected,
default: qe<random>
txt (None)
If not None, direct Espresso's output to a different file than
outdir/log
calcstress (False)
If True, calculate stress
occupations ('smearing')
Controls how Kohn-Sham states are occupied.
Possible values: 'smearing', 'fixed' (molecule or insulator),
or 'tetrahedra'.
smearing ('fd')
method for Fermi surface smearing
- 'fd','Fermi-Dirac': Fermi-Dirac
- 'mv','Marzari-Vanderbilt': Marzari-Vanderbilt cold smearing
- 'gauss','gaussian': Gaussian smearing
- 'mp','Methfessel-Paxton': Methfessel-Paxton
For ase 3.7+ compatibility, smearing can also be a tuple where
the first parameter is the method and the 2nd parameter
is the smearing width which overrides sigma below
sigma (0.1)
smearing width in eV
tot_charge (None)
charge the unit cell,
+1 means 1 e missing, -1 means 1 extra e
charge (None)
overrides tot_charge (ase 3.7+ compatibility)
tot_magnetization (-1)
Fix total magnetization,
-1 means unspecified/free,
'hund' means Hund's rule for each atom
fix_magmom (False)
If True, fix total magnetization to current value.
isolated (None)
invoke an 'assume_isolated' method for screening long-range interactions
across 3D supercells, particularly electrostatics.
Very useful for charged molecules and charged surfaces,
but also improves convergence wrt. vacuum space for neutral molecules.
- 'makov-payne', 'mp': only cubic systems.
- 'dcc': don't use.
- 'martyna-tuckerman', 'mt': method of choice for molecules, works for any supercell geometry.
- 'esm': Effective Screening Medium Method for surfaces and interfaces.
U (None)
specify Hubbard U values (in eV)
U can be list: specify U for each atom
U can be a dictionary ( e.g. U={'Fe':3.5} )
U values are assigned to angular momentum channels
according to Espresso's hard-coded defaults
(i.e. l=2 for transition metals, l=1 for oxygen, etc.)
J (None)
specify exchange J values (in eV)
can be list or dictionary (see U parameter above)
U_alpha
U_alpha (in eV)
can be list or dictionary (see U parameter above)
U_projection_type ('atomic')
type of projectors for calculating density matrices in DFT+U schemes
nqx1, nqx2, nqx3 (all None)
3D mesh for q=k1-k2 sampling of Fock operator. Can be smaller
than number of k-points.
exx_fraction (None)
Default depends on hybrid functional chosen.
screening_parameter (0.106)
Screening parameter for HSE-like functionals.
exxdiv_treatment (gygi-baldereschi)
Method to treat Coulomb potential divergence for small q.
ecutvcut (0)
Cut-off for above.
dipole ( {'status':False} )
If 'status':True, turn on dipole correction; then by default, the
dipole correction is applied along the z-direction, and the dipole is
put in the center of the vacuum region (taking periodic boundary
conditions into account).
This can be overridden with:
- 'edir':1, 2, or 3 for x-, y-, or z-direction
- 'emaxpos':float percentage wrt. unit cell where dip. correction
potential will be max.
- 'eopreg':float percentage wrt. unit cell where potential decreases
- 'eamp':0 (by default) if non-zero overcompensate dipole: i.e. apply
a field
output ( {'disk_io':'default', # how often espresso writes wavefunctions to disk
'avoidio':False, # will overwrite disk_io parameter if True
'removewf':True,
'removesave':False,
'wf_collect':False} )
control how much io is used by espresso;
'removewf':True means wave functions are deleted in scratch area before
job is done and data is copied back to submission directory
'removesave':True means whole .save directory is deleted in scratch area
convergence ( {'energy':1e-6,
'mixing':0.7,
'maxsteps':100,
'diag':'david'} )
Electronic convergence criteria and diag. and mixing algorithms.
Additionally, a preconditioner for the mixing algoritms can be
specified, e.g. 'mixing_mode':'local-TF' or 'mixing_mode':'TF'.
startingpot (None)
By default: 'atomic' (use superposition of atomic orbitals for
initial guess)
'file': construct potential from charge-density.dat
Can be used with load_chg and save_chg methods.
startingwfc (None)
By default: 'atomic'.
Other options: 'atomic+random' or 'random'.
'file': reload wave functions from other calculations.
See load_wf and save_wf methods.
parflags (None)
Parallelization flags for Quantum Espresso.
E.g. parflags='-npool 2' will distribute k-points (and spin if
spin-polarized) over two nodes.
verbose ('low')
Can be 'high' or 'low'
"""
self.exedir = exedir
self.outdir = outdir
self.onlycreatepwinp = onlycreatepwinp
self.pw = pw
self.dw = dw
self.fw = fw
self.nbands = nbands
if type(kpts) == float or type(kpts) == int:
kpts = kptdensity2monkhorstpack(atoms, kpts)
elif isinstance(kpts, str):
assert kpts == 'gamma'
else:
assert len(kpts) == 3
self.kpts = kpts
self.kptshift = kptshift
self.fft_grid = fft_grid # RK
if mode is not None and calculation is None:
warnings.warn(
"mode is deprecated, use calculation instead",
DeprecationWarning)
calculation = mode
self.calculation = calculation
if opt_algorithm is not None and ion_dynamics is None:
warnings.warn(
"opt_algorithm is deprecated, use ion_dynamics instead",
DeprecationWarning)
self.ion_dynamics = ion_dynamics
self.nstep = nstep
self.constr_tol = constr_tol
self.fmax = fmax
self.cell_dynamics = cell_dynamics
self.press = press
self.dpress = dpress
self.cell_factor = cell_factor
self.cell_dofree = cell_dofree
self.dontcalcforces = dontcalcforces
self.nosym = nosym
self.noinv = noinv
self.nosym_evc = nosym_evc
self.no_t_rev = no_t_rev
self.xc = xc
self.beefensemble = beefensemble
self.printensemble = printensemble
if isinstance(smearing, str):
self.smearing = str(smearing)
self.sigma = sigma
else:
self.smearing = smearing[0]
self.sigma = smearing[1]
self.spinpol = spinpol
self.noncollinear = noncollinear
self.spinorbit = spinorbit
self.fix_magmom = fix_magmom
self.isolated = isolated
if charge is None:
self.tot_charge = tot_charge
else:
self.tot_charge = charge
self.tot_magnetization = tot_magnetization
self.occupations = occupations
self.outdir = outdir
self.calcstress = calcstress
self.psppath = psppath
self.dipole = dipole
self.field = field
self.output = output
self.convergence = convergence
self.startingpot = startingpot
self.startingwfc = startingwfc
self.ion_positions = ion_positions
self.verbose = verbose
self.U = U
self.J = J
self.U_alpha = U_alpha
self.U_projection_type = U_projection_type
self.nqx1 = nqx1
self.nqx2 = nqx2
self.nqx3 = nqx3
self.exx_fraction = exx_fraction
self.screening_parameter = screening_parameter
self.exxdiv_treatment = exxdiv_treatment
self.ecutvcut = ecutvcut
self.newforcearray = alwayscreatenewarrayforforces
self.parflags = ''
self.serflags = ''
# ENVIRON IMPLICIT SOLVATION
if environ_keys is not None:
self.parflags = ' -environ '
self.serflags = ' -environ '
self.environ_keys = environ_keys
self.use_environ = True
else:
self.parflags = ''
self.serflags = ''
self.use_environ = False
self.environ_extra_keys=environ_extra_keys
if parflags is not None:
self.parflags += parflags
self.single_calculator = single_calculator
self.txt = txt
self.mypath = os.path.abspath(os.path.dirname(__file__))
self.writeversion = True
self.atoms = None
self.sigma_small = 1e-13
self.started = False
self.got_energy = False
self.only_init = False
# automatically generated list
self.iprint = iprint
self.tstress = tstress
self.tprnfor = tprnfor
self.dt = dt
self.lkpoint_dir = lkpoint_dir
self.max_seconds = max_seconds
self.etot_conv_thr = etot_conv_thr
self.forc_conv_thr = forc_conv_thr
self.tefield = tefield
self.dipfield = dipfield
self.lelfield = lelfield
self.nberrycyc = nberrycyc
self.lorbm = lorbm
self.lberry = lberry
self.gdir = gdir
self.nppstr = nppstr
self.nbnd = nbnd
self.ecutwfc = ecutwfc
self.ecutrho = ecutrho
self.ecutfock = ecutfock
self.force_symmorphic = force_symmorphic
self.use_all_frac = use_all_frac
self.one_atom_occupations = one_atom_occupations
self.starting_spin_angle = starting_spin_angle
self.degauss = degauss
self.nspin = nspin
self.ecfixed = ecfixed
self.qcutz = qcutz
self.q2sigma = q2sigma
self.x_gamma_extrapolation = x_gamma_extrapolation
self.lda_plus_u = lda_plus_u
self.lda_plus_u_kind = lda_plus_u_kind
self.edir = edir
self.emaxpos = emaxpos
self.eopreg = eopreg
self.eamp = eamp
self.clambda = clambda
self.report = report
self.lspinorb = lspinorb
self.esm_bc = esm_bc
self.esm_w = esm_w
self.esm_efield = esm_efield
self.esm_nfit = esm_nfit
self.london = london
self.london_s6 = london_s6
self.london_rcut = london_rcut
self.xdm = xdm
self.xdm_a1 = xdm_a1
self.xdm_a2 = xdm_a2
self.electron_maxstep = electron_maxstep
self.scf_must_converge = scf_must_converge
self.conv_thr = conv_thr
self.adaptive_thr = adaptive_thr
self.conv_thr_init = conv_thr_init
self.conv_thr_multi = conv_thr_multi
self.mixing_beta = mixing_beta
self.mixing_ndim = mixing_ndim
self.mixing_fixed_ns = mixing_fixed_ns
self.ortho_para = ortho_para
self.diago_thr_init = diago_thr_init
self.diago_cg_maxiter = diago_cg_maxiter
self.diago_david_ndim = diago_david_ndim
self.diago_full_acc = diago_full_acc
self.efield = efield
self.tqr = tqr
self.remove_rigid_rot = remove_rigid_rot
self.tempw = tempw
self.tolp = tolp
self.delta_t = delta_t
self.nraise = nraise
self.refold_pos = refold_pos
self.upscale = upscale
self.bfgs_ndim = bfgs_ndim
self.vdw_corr = vdw_corr
self.ts_vdw_econv_thr = ts_vdw_econv_thr
self.ts_vdw_isolated = ts_vdw_isolated
self.lfcpopt = lfcpopt
self.fcp_mu = fcp_mu
self.esm_a = esm_a
self.trust_radius_max = trust_radius_max
self.trust_radius_min = trust_radius_min
self.trust_radius_ini = trust_radius_ini
self.w_1 = w_1
self.w_2 = w_2
self.wmass = wmass
self.press_conv_thr = press_conv_thr
self.results = results
self.name = name
# give original espresso style input names
# preference over ase / dacapo - style names
if ecutwfc is not None:
self.pw = ecutwfc
if ecutrho is not None:
self.dw = ecutwfc
if nbnd is not None:
self.nbands = nbnd
# Variables that cannot be set by inputs
self.nvalence = None
self.nel = None
self.fermi_input = False
self.parameters = {}
# Auto create variables from input
self.input_update()
# Initialize lists of cpu subsets if needed
if procrange is None:
self.proclist = False
else:
self.proclist = True
procs = site.procs + []
procs.sort()
nprocs = len(procs)
self.myncpus = nprocs / numcalcs
i1 = self.myncpus * procrange
self.mycpus = self.localtmp + '/myprocs%04d.txt' % procrange
f = open(self.mycpus, 'w')
for i in range(i1, i1 + self.myncpus):
print(procs[i], file=f)
f.close()
if atoms is not None:
atoms.set_calculator(self)
if hasattr(site, 'mpi_not_setup') and self.onlycreatepwinp is None:
print(
'*** Without cluster-adjusted espsite.py, ase-espresso can only be used\n'
'*** to create input files for pw.x via the option onlycreatepwinp.\n'
'*** Otherwise, ase-espresso requires a site-specific espsite.py\n'
'*** in PYTHONPATH.\n'
'*** You may use the espsite.py.example.* in the git checkout as templates.'
)
raise ImportError
def input_update(self):
"""Run initialization functions, such that this can be called
if variables in espresso are changes using set or directly.
"""
self.create_outdir() # Create the tmp output folder
# sdir is the directory the script is run or submitted from
self.sdir = subdirs.getsubmitorcurrentdir(site)
if self.dw is None:
self.dw = 10. * self.pw
else:
assert self.dw >= self.pw
if self.psppath is None:
try:
self.psppath = os.environ['ESP_PSP_PATH']
except BaseException:
print(
'Unable to find pseudopotential path. Consider '
'setting ESP_PSP_PATH environment variable'
)
raise
if self.dipole is None:
self.dipole = {'status': False}
if self.field is None:
self.field = {'status': False}
if self.convergence is None:
self.conv_thr = 1e-6 / Rydberg
else:
if 'energy' in self.convergence:
self.conv_thr = self.convergence['energy'] / Rydberg
else:
self.conv_thr = 1e-6 / Rydberg
if self.beefensemble:
if self.xc.upper().find('BEEF') < 0:
raise KeyError(
"ensemble-energies only work with xc=BEEF or variants of it!"
)
self.started = False
self.got_energy = False
def create_outdir(self):
if self.onlycreatepwinp is None:
self.localtmp = subdirs.mklocaltmp(self.outdir, site)
if not self.txt:
self.log = self.localtmp + '/log'
elif self.txt[0] != '/':
self.log = self.sdir+'/'+self.txt
else:
self.log = self.txt
self.scratch = subdirs.mkscratch(self.localtmp, site)
if self.output is not None:
if 'removewf' in self.output:
removewf = self.output['removewf']
else:
removewf = True
if 'removesave' in self.output:
removesave = self.output['removesave']
else:
removesave = False
else:
removewf = True
removesave = False
atexit.register(subdirs.cleanup, self.localtmp, self.scratch,
removewf, removesave, self, site)
self.cancalc = True
else:
self.pwinp = self.onlycreatepwinp
self.localtmp = ''
self.cancalc = False
def set(self, **kwargs):
"""Define settings for the Quantum Espresso calculator object
after it has been initialized. This is done in the following way:
>> calc = espresso(...)
>> atoms = set.calculator(calc)
>> calc.set(xc='BEEF')
NB: No input validation is made
"""
for key, value in list(kwargs.items()):
if key == 'outdir':
self.create_outdir()
self.outdir = value
if key == 'startingpot':
self.startingpot = value
if key == 'startingwfc':
self.startingwfc = value
if key == 'ion_positions':
self.ion_positions = value
if key == 'U_alpha':
self.U_alpha = value
if key == 'U':
self.U = value
if key == 'U_projection_type':
self.U_projection_type = value
if key == 'xc':
self.xc = value
if key == 'pw':
self.pw = value
if key == 'dw':
self.dw = value
if key == 'output':
self.output = value
if key == 'convergence':
self.convergence = value
if key == 'kpts':
self.kpts = value
if key == 'kshift':
self.kshift = value
if key == 'fft_grid': # RK
self.fft_grid = value
self.input_update()
self.recalculate = True
self.results = {}
def __del__(self):
try:
self.stop()
except BaseException:
pass
def atoms2species(self):
"""Define several properties of the quantum espresso species
from the ase atoms object. Takes into account that different
spins (or different U etc.) on same kind of chemical elements
are considered different species in quantum espresso.
"""
symbols = self.atoms.get_chemical_symbols()
masses = self.atoms.get_masses()
magmoms = list(self.atoms.get_initial_magnetic_moments())
if len(magmoms) < len(symbols):
magmoms += list(np.zeros(len(symbols) - len(magmoms), np.float))
pos = self.atoms.get_scaled_positions()
if self.U is not None:
if type(self.U) == dict:
Ulist = np.zeros(len(symbols), np.float)
for i, s in enumerate(symbols):
if s in self.U:
Ulist[i] = self.U[s]
else:
Ulist = list(self.U)
if len(Ulist) < len(symbols):
Ulist += list(
np.zeros(len(symbols) - len(Ulist), np.float))
else:
Ulist = np.zeros(len(symbols), np.float)
if self.J is not None:
if type(self.J) == dict:
Jlist = np.zeros(len(symbols), np.float)
for i, s in enumerate(symbols):
if s in self.J:
Jlist[i] = self.J[s]
else:
Jlist = list(self.J)
if len(Jlist) < len(symbols):
Jlist += list(
np.zeros(len(symbols) - len(Jlist), np.float))
else:
Jlist = np.zeros(len(symbols), np.float)
if self.U_alpha is not None:
if type(self.U_alpha) == dict:
U_alphalist = np.zeros(len(symbols), np.float)
for i, s in enumerate(symbols):
if s in self.U_alpha:
U_alphalist[i] = self.U_alpha[s]
else:
U_alphalist = list(self.U_alpha)
if len(U_alphalist) < len(symbols):
U_alphalist += list(
np.zeros(len(symbols) - len(U_alphalist), np.float))
else:
U_alphalist = np.zeros(len(symbols), np.float)
self.species = []
self.specprops = []
dic = {}
symcounter = {}
for s in symbols:
symcounter[s] = 0
for i in range(len(symbols)):
key = symbols[i] + '_m%.14eU%.14eJ%.14eUa%.14e' % (
magmoms[i], Ulist[i], Jlist[i], U_alphalist[i])
if key in dic:
self.specprops.append((dic[key][1], pos[i]))
else:
symcounter[symbols[i]] += 1
spec = symbols[i] + str(symcounter[symbols[i]])
dic[key] = [i, spec]
self.species.append(spec)
self.specprops.append((spec, pos[i]))
self.nspecies = len(self.species)
self.specdict = {}
for i, s in list(dic.values()):
if np.isnan(masses[i]):
mi = 0.0
else:
mi = masses[i]
self.specdict[s] = utils.SpecObject(
s=s.strip('0123456789'), # chemical symbol w/o index
mass=mi,
magmom=magmoms[i],
U=Ulist[i],
J=Jlist[i],
U_alpha=U_alphalist[i])
def get_nvalence(self):
nel = {}
for x in self.species:
el = self.specdict[x].s
# get number of valence electrons from pseudopotential or paw setup
p = Popen(
'egrep -i \'z\ valence|z_valence\' ' + self.psppath +
'/' + el + '.UPF | tr \'"\' \' \'',
shell=True, stdout=PIPE).stdout
out = p.readline().decode('utf-8')
for y in out.split():
if y[0].isdigit() or y[0] == '.':
nel[el] = int(round(float(y)))
break
p.close()
nvalence = np.zeros(len(self.specprops), np.int)
for i, x in enumerate(self.specprops):
nvalence[i] = nel[self.specdict[x[0]].s]
return nvalence, nel
def writeenvinputfile(self, filename='environ.in'):
"""Write Environ input file"""
if self.cancalc:
fname = self.localtmp+'/'+filename
#f = open(self.localtmp+'/pw.inp', 'w')
else:
fname = self.pwinp.split('/')[:-1]+'/'+filename
f = open(fname,'w')
f.write('&ENVIRON\n')
f.write(' !\n')
for key in self.environ_keys:
value=self.environ_keys[key]
if type(value)==bool:
if value:
value='.true.'
else:
value='.false.'
f.write(' {} = {}\n'.format(key,value))
elif type(value)==str:
f.write(' {} = \'{}\'\n'.format(key, value))
elif 'e' in str(value):
value_str=str(value).replace('e','D')
f.write(' {} = {}\n'.format(key, value_str))
else:
f.write(' {} = {}\n'.format(key, self.environ_keys[key]))
f.write(' !\n')
f.write('/\n')
if self.environ_extra_keys is not None:
for key in self.environ_extra_keys:
#f.write('{} {}\n'.format(key,unit))
if key in ['EXTERNAL_CHARGES','DIELECTRIC_REGIONS']:
#CARDs
if 'unit' not in self.environ_extra_keys[key]:
unit='bohr'
else:
unit=self.environ_extra_keys[key]['unit']
f.write('{} {}\n'.format(key,unit))
for vals in self.environ_extra_keys[key]['settings']:
f.write(' {}\n'.format(' '.join([str(vv) for vv in vals])))
else:
#NAMELISTs
f.write('&{}\n'.format(key))
f.write(' !\n')
for key2 in self.environ_extra_keys[key]:
value=self.environ_extra_keys[key][key2]
if type(value)==bool:
if value:
value='.true.'
else:
value='.false.'
f.write(' {} = {}\n'.format(key2,value))
elif type(value)==str:
f.write(' {} = \'{}\'\n'.format(key2,value))
elif 'e' in str(value):
value_str=str(value).replace('e','D')
f.write(' {} = {}\n'.format(key2, value_str))
else:
f.write(' {} = {}\n'.format(key2,value))
f.write(' !\n')
f.write('/\n')
f.close()
def writeinputfile(self,
filename='pw.inp',
mode=None,
overridekpts=None,
overridekptshift=None,
overridenbands=None,
suppressforcecalc=False,
usetetrahedra=False):
if self.atoms is None:
raise ValueError('no atoms defined')
if self.cancalc:
fname = self.localtmp + '/' + filename
else: