Commit 0076c358 authored by Alvin Noe Ladines's avatar Alvin Noe Ladines
Browse files

Parser fixes issue #701

parent af5d77cb
Pipeline #118309 passed with stages
in 27 minutes and 25 seconds
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......@@ -568,6 +568,10 @@ class ResultsNormalizer(Normalizer):
return conv_atoms, prim_atoms, wyckoff_sets, spg_number
def structures_2d(self, original_atoms):
conv_atoms = None
prim_atoms = None
wyckoff_sets = None
spg_number = None
# Get dimension of system by also taking into account the covalent radii
dimensions = matid.geometry.get_dimensions(original_atoms, [True, True, True])
......@@ -580,7 +584,8 @@ class ResultsNormalizer(Normalizer):
# unsufficient (the structure is "wavy" making also the gap highly
# nonlinear).
if sum(periodicity) != 2:
raise ValueError("could not detect the periodic dimensions in a 2D system")
self.logger.error("could not detect the periodic dimensions in a 2D system")
return conv_atoms, prim_atoms, wyckoff_sets, spg_number
# Center the system in the non-periodic direction, also taking
# periodicity into account. The get_center_of_mass()-function in MatID
......@@ -655,7 +660,8 @@ class ResultsNormalizer(Normalizer):
# If one axis is not periodic, return. This only happens if the vacuum
# gap is not aligned with a cell vector.
if sum(periodicity) != 1:
raise ValueError("could not detect the periodic dimensions in a 1D system")
self.logger.error("could not detect the periodic dimensions in a 1D system")
return conv_atoms, prim_atoms
# Translate to center of mass
conv_atoms = prim_atoms.copy()
......@@ -420,7 +420,11 @@ class WorkflowNormalizer(Normalizer):
def _resolve_workflow_type(self, run):
# resolve it from parser
workflow_type = None
program_name =
except Exception:
if program_name:
program_name = program_name.lower()
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