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Add OutcarCollectError and catch it in Vasp.collect #1394

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May 24, 2024
Merged

Add OutcarCollectError and catch it in Vasp.collect #1394

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884f00f
Add OutcarCollectError and catch it in Vasp.collect
pmrv Apr 19, 2024
508ff14
Format black
pyiron-runner Apr 19, 2024
fe1f9d2
Add tests
pmrv May 24, 2024
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10 changes: 7 additions & 3 deletions pyiron_atomistics/vasp/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
dict_group_to_hdf,
)
from pyiron_base import state, GenericParameters, deprecate
from pyiron_atomistics.vasp.parser.outcar import Outcar
from pyiron_atomistics.vasp.parser.outcar import Outcar, OutcarCollectError
from pyiron_atomistics.vasp.parser.oszicar import Oszicar
from pyiron_atomistics.vasp.procar import Procar
from pyiron_atomistics.vasp.structure import read_atoms, write_poscar, vasp_sorter
Expand Down Expand Up @@ -2003,8 +2003,12 @@ def collect(self, directory=os.getcwd(), sorted_indices=None):
if "OSZICAR" in files_present:
self.oszicar.from_file(filename=posixpath.join(directory, "OSZICAR"))
if "OUTCAR" in files_present:
self.outcar.from_file(filename=posixpath.join(directory, "OUTCAR"))
outcar_working = True
try:
self.outcar.from_file(filename=posixpath.join(directory, "OUTCAR"))
outcar_working = True
except OutcarCollectError as e:
state.logger.warning(f"OUTCAR present, but could not be parsed: {e}!")
outcar_working = False
if "vasprun.xml" in files_present:
try:
with warnings.catch_warnings(record=True) as w:
Expand Down
9 changes: 8 additions & 1 deletion pyiron_atomistics/vasp/parser/outcar.py
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Expand Up @@ -24,6 +24,11 @@
)


# derives from ValueError, because that was the exception previously raised
class OutcarCollectError(ValueError):
pass


class Outcar(object):
"""
This module is used to parse VASP OUTCAR files.
Expand Down Expand Up @@ -934,7 +939,9 @@ def get_number_of_atoms(filename="OUTCAR", lines=None):
if len(trigger_indices) != 0:
return int(lines[trigger_indices[0]].split(ions_trigger)[-1])
else:
raise ValueError()
raise OutcarCollectError(
"Failed to read number of atoms, can't find NIONS!"
)

@staticmethod
def get_band_properties(filename="OUTCAR", lines=None):
Expand Down
185 changes: 185 additions & 0 deletions tests/static/vasp_test_files/outcar_without_nions/OUTCAR
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@@ -0,0 +1,185 @@
vasp.5.4.4.18Apr17-6-g9f103f2a35 (build Feb 19 2020 16:12:31) complex

executed on LinuxIFC date 2024.05.24 14:55:29
running on 20 total cores
distrk: each k-point on 20 cores, 1 groups
distr: one band on NCORES_PER_BAND= 20 cores, 1 groups


--------------------------------------------------------------------------------------------------------


INCAR:
POTCAR: PAW_PBE Mg 13Apr2007

-----------------------------------------------------------------------------
| |
| W W AA RRRRR N N II N N GGGG !!! |
| W W A A R R NN N II NN N G G !!! |
| W W A A R R N N N II N N N G !!! |
| W WW W AAAAAA RRRRR N N N II N N N G GGG ! |
| WW WW A A R R N NN II N NN G G |
| W W A A R R N N II N N GGGG !!! |
| |
| For optimal performance we recommend to set |
| NCORE= 4 - approx SQRT( number of cores) |
| NCORE specifies how many cores store one orbital (NPAR=cpu/NCORE). |
| This setting can greatly improve the performance of VASP for DFT. |
| The default, NCORE=1 might be grossly inefficient |
| on modern multi-core architectures or massively parallel machines. |
| Do your own testing !!!! |
| Unfortunately you need to use the default for GW and RPA calculations. |
| (for HF NCORE is supported but not extensively tested yet) |
| |
-----------------------------------------------------------------------------

POTCAR: PAW_PBE Mg 13Apr2007
SHA256 = a90315392b5cf46bd986ff2010bfd53a40dec98e36f8d1f6277412e9d0e81a9f Mg
COPYR = (c) Copyright 13Apr2007 Georg Kresse
COPYR = This file is part of the software VASP. Any use, copying, and all ot
COPYR = If you do not have a valid VASP license, you may not use, copy or di
VRHFIN =Mg: s2p0
LEXCH = PE
EATOM = 23.0369 eV, 1.6932 Ry

TITEL = PAW_PBE Mg 13Apr2007
LULTRA = F use ultrasoft PP ?
IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
RPACOR = 1.500 partial core radius
POMASS = 24.305; ZVAL = 2.000 mass and valenz
RCORE = 2.000 outmost cutoff radius
RWIGS = 2.880; RWIGS = 1.524 wigner-seitz radius (au A)
ENMAX = 200.000; ENMIN = 100.000 eV
RCLOC = 1.506 cutoff for local pot
LCOR = T correct aug charges
LPAW = T paw PP
EAUG = 454.734
DEXC = 0.000
RMAX = 2.045 core radius for proj-oper
RAUG = 1.300 factor for augmentation sphere
RDEP = 2.025 radius for radial grids
RDEPT = 1.942 core radius for aug-charge

Atomic configuration
6 entries
n l j E occ.
1 0 0.50 -1259.6230 2.0000
2 0 0.50 -79.8442 2.0000
2 1 1.50 -46.6121 6.0000
3 0 0.50 -4.7055 2.0000
3 1 0.50 -1.3660 0.0000
3 2 1.50 -1.3606 0.0000
Description
l E TYP RCUT TYP RCUT
0 -4.7054661 23 2.000
0 27.2116520 23 2.000
1 1.3605826 23 2.000
1 27.2116520 23 2.000
2 -1.3605826 23 2.000
local pseudopotential read in
partial core-charges read in
partial kinetic energy density read in
atomic valenz-charges read in
non local Contribution for L= 0 read in
real space projection operators read in
non local Contribution for L= 0 read in
real space projection operators read in
non local Contribution for L= 1 read in
real space projection operators read in
non local Contribution for L= 1 read in
real space projection operators read in
non local Contribution for L= 2 read in
real space projection operators read in
PAW grid and wavefunctions read in

number of l-projection operators is LMAX = 5
number of lm-projection operators is LMMAX = 13

PAW_PBE Mg 13Apr2007 :
energy of atom 1 EATOM= -23.0369
kinetic energy error for atom= 0.0001 (will be added to EATOM!!)


POSCAR: Poscar file generated with pyiron
positions in cartesian coordinates
No initial velocities read in
exchange correlation table for LEXCH = 8
RHO(1)= 0.500 N(1) = 2000
RHO(2)= 100.500 N(2) = 4000



--------------------------------------------------------------------------------------------------------


ion position nearest neighbor table
1 0.500 0.500 0.250-
2 0.500 0.500 0.750-

LATTYP: Found a simple tetragonal cell.
ALAT = 2.8632343400
C/A-ratio = 2.8377866025

Lattice vectors:

A1 = ( 2.8632343400, 0.0000001000, -0.0000006600)
A2 = ( 0.0000001000, 2.8632342300, 0.0000025400)
A3 = ( -0.0000027600, 0.0000097000, 8.1252480500)


Analysis of symmetry for initial positions (statically):
=====================================================================
Subroutine PRICEL returns following result:

LATTYP: Found a simple tetragonal cell.
ALAT = 2.8632343400
C/A-ratio = 1.4188933013

Lattice vectors:

A1 = ( 2.8632343400, 0.0000001000, -0.0000006600)
A2 = ( 0.0000001000, 2.8632342300, 0.0000025400)
A3 = ( -0.0000013800, 0.0000048500, 4.0626240250)

2 primitive cells build up your supercell.


Routine SETGRP: Setting up the symmetry group for a
simple tetragonal supercell.


Subroutine GETGRP returns: Found 16 space group operations
(whereof 16 operations were pure point group operations)
out of a pool of 16 trial point group operations.


The static configuration has the point symmetry D_4h.


Analysis of symmetry for dynamics (positions and initial velocities):
=====================================================================
Subroutine PRICEL returns following result:

LATTYP: Found a simple tetragonal cell.
ALAT = 2.8632343400
C/A-ratio = 1.4188933013

Lattice vectors:

A1 = ( 2.8632343400, 0.0000001000, -0.0000006600)
A2 = ( 0.0000001000, 2.8632342300, 0.0000025400)
A3 = ( -0.0000013800, 0.0000048500, 4.0626240250)

2 primitive cells build up your supercell.


Routine SETGRP: Setting up the symmetry group for a
simple tetragonal supercell.


Subroutine GETGRP returns: Found 16 space group operations
(whereof 16 operations were pure point group operations)
out of a pool of 16 trial point group operations.


The dynamic configuration has the point symmetry D_4h.
3 changes: 3 additions & 0 deletions tests/static/vasp_test_files/outcar_without_nions/README.md
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@@ -0,0 +1,3 @@
Simulates output directory of a VASP job that crashed early in its run.
In particular too early for the OUTCAR to contain the NIONS tag, which the
outcar parser implicitly relies on.
28 changes: 27 additions & 1 deletion tests/vasp/test_outcar.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,8 @@
import os
import posixpath
import numpy as np
from pyiron_atomistics.vasp.parser.outcar import Outcar
from pyiron_atomistics.vasp.base import Output, VaspCollectError
from pyiron_atomistics.vasp.parser.outcar import Outcar, OutcarCollectError


class TestOutcar(unittest.TestCase):
Expand Down Expand Up @@ -1204,5 +1205,30 @@ def test_get_band_properties(self):
self.assertTrue(np.allclose(np.array(cbm_list), np.array([[-0.1332], [0.0219]])))


def test_error_on_parse(self):
"""OutcarCollectError should be raised when vital information cannot be read."""
with self.assertRaises(OutcarCollectError):
Outcar().from_file(os.path.join(self.file_location, "../static/vasp_test_files/outcar_without_nions/OUTCAR"))

def test_no_error_on_incomplete_collect(self):
"""Do not raise an error when collecting output and the OUTCAR is incomplete."""
# the reason being: VaspBase.restart() tries to collect the job before creating a new copy, but if collect fails
# when the OUTCAR is not complete, that would mean this kind of job could not be restarted to apply some fix to
# the input to avoid the crash.
# We want to be able to restart any job, so errors on collect must be silenced or be of the VaspCollectError,
# which is caught during restart
test_folders = ["../static/vasp_test_files/full_job_aborted", "../static/vasp_test_files/outcar_without_nions"]
for folder in test_folders:
with self.subTest(folder=folder):
try:
Output().collect(
os.path.join(self.file_location, folder),
sorted_indices=[] # necessary only because Output object otherwise needs to have a structure defined
)
except VaspCollectError:
pass
except Exception as e:
self.fail(f"collect_output_parser raised {e}, but should be silent!")

if __name__ == "__main__":
unittest.main()
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