From ce55910cabb529b7c0751017c5f10e803e2594a3 Mon Sep 17 00:00:00 2001
From: Alvin Noe Ladines <ladinesalvinnoe@gmail.com>
Date: Wed, 3 Feb 2021 22:10:59 +0100
Subject: [PATCH] Fix issue #491
---
phonopyparser/phonopy_parser.py | 38 ++++++++++++++++++++++-----------
1 file changed, 26 insertions(+), 12 deletions(-)
diff --git a/phonopyparser/phonopy_parser.py b/phonopyparser/phonopy_parser.py
index 04d0092..6719030 100644
--- a/phonopyparser/phonopy_parser.py
+++ b/phonopyparser/phonopy_parser.py
@@ -73,10 +73,16 @@ class PhonopyParser(FairdiParser):
displacement = control.phonon["displacement"]
sym = control.phonon["symmetry_thresh"]
- set_of_forces, phonopy_obj, relative_paths = read_forces_aims(
- cell_obj, supercell_matrix, displacement, sym)
- prep_path = self.mainfile.split("phonopy-FHI-aims-displacement-")
+ try:
+ set_of_forces, phonopy_obj, relative_paths = read_forces_aims(
+ cell_obj, supercell_matrix, displacement, sym)
+ except Exception:
+ self.logger.error("Error generating phonopy object.")
+ set_of_forces = []
+ phonopy_obj = None
+ relative_paths = []
+ prep_path = self.mainfile.split("phonopy-FHI-aims-displacement-")
# Try to resolve references as paths relative to the upload root.
try:
for path in relative_paths:
@@ -86,11 +92,12 @@ class PhonopyParser(FairdiParser):
except Exception:
self.logger.warn("Could not resolve path to a referenced calculation within the upload.")
- phonopy_obj.set_forces(set_of_forces)
- phonopy_obj.produce_force_constants()
-
os.chdir(cwd)
+ if set_of_forces:
+ phonopy_obj.set_forces(set_of_forces)
+ phonopy_obj.produce_force_constants()
+
self._phonopy_obj = phonopy_obj
def parse_bandstructure(self):
@@ -182,8 +189,11 @@ class PhonopyParser(FairdiParser):
self._metainfo_env = m_env
+ sec_run = self.archive.m_create(Run)
+ sec_run.program_name = 'Phonopy'
+ sec_run.program_version = phonopy.__version__
+
phonopy_obj = self.phonopy_obj
- self.properties = PhononProperties(self.phonopy_obj, self.logger, **self._kwargs)
pbc = np.array((1, 1, 1), bool)
@@ -206,12 +216,7 @@ class PhonopyParser(FairdiParser):
supercell_matrix = phonopy_obj.supercell_matrix
sym_tol = phonopy_obj.symmetry.tolerance
- force_constants = phonopy_obj.get_force_constants()
- force_constants = pint.Quantity(force_constants, 'eV/(angstrom**2)').to('eV/(m**2)').magnitude
- sec_run = self.archive.m_create(Run)
- sec_run.program_name = 'Phonopy'
- sec_run.program_version = phonopy.__version__
sec_system_unit = sec_run.m_create(System)
sec_system_unit.configuration_periodic_dimensions = pbc
sec_system_unit.atom_labels = unit_sym
@@ -236,11 +241,20 @@ class PhonopyParser(FairdiParser):
sec_method.x_phonopy_symprec = sym_tol
sec_method.x_phonopy_displacement = displacement
+ try:
+ force_constants = phonopy_obj.get_force_constants()
+ force_constants = pint.Quantity(force_constants, 'eV/(angstrom**2)').to('eV/(m**2)').magnitude
+ except Exception:
+ self.logger.error('Error producing force constants.')
+ return
+
sec_scc = sec_run.m_create(SingleConfigurationCalculation)
sec_scc.single_configuration_calculation_to_system_ref = sec_system
sec_scc.single_configuration_to_calculation_method_ref = sec_method
sec_scc.hessian_matrix = force_constants
+ self.properties = PhononProperties(self.phonopy_obj, self.logger, **self._kwargs)
+
self.parse_bandstructure()
self.parse_dos()
self.parse_thermodynamical_properties()
--
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