From 0076c358e33198e7c8d35134423b28a82ebff878 Mon Sep 17 00:00:00 2001 From: Alvin Noe Ladines <ladinesalvinnoe@gmail.com> Date: Tue, 21 Dec 2021 00:52:53 +0100 Subject: [PATCH] Parser fixes issue #701 --- dependencies/parsers/cp2k | 2 +- dependencies/parsers/crystal | 2 +- dependencies/parsers/exciting | 2 +- dependencies/parsers/fhi-aims | 2 +- dependencies/parsers/gaussian | 2 +- dependencies/parsers/gromacs | 2 +- dependencies/parsers/lammps | 2 +- dependencies/parsers/octopus | 2 +- dependencies/parsers/openkim | 2 +- dependencies/parsers/vasp | 2 +- dependencies/parsers/wien2k | 2 +- nomad/normalizing/results.py | 10 ++++++++-- nomad/normalizing/workflow.py | 6 +++++- 13 files changed, 24 insertions(+), 14 deletions(-) diff --git a/dependencies/parsers/cp2k b/dependencies/parsers/cp2k index 566b1dc900..f3ce55d656 160000 --- a/dependencies/parsers/cp2k +++ b/dependencies/parsers/cp2k @@ -1 +1 @@ -Subproject commit 566b1dc9005f261d7b9338bebd7ba6f03f77064f +Subproject commit f3ce55d656b74d1cdeb86681dd3f104b493a4a18 diff --git a/dependencies/parsers/crystal b/dependencies/parsers/crystal index 2ded98fc63..ba651972b8 160000 --- a/dependencies/parsers/crystal +++ b/dependencies/parsers/crystal @@ -1 +1 @@ -Subproject commit 2ded98fc638765a8ae6b986056d9782b37ab9fac +Subproject commit ba651972b85c14f5c35317400c5f41511fe91611 diff --git a/dependencies/parsers/exciting b/dependencies/parsers/exciting index 650f790435..92b5304f44 160000 --- a/dependencies/parsers/exciting +++ b/dependencies/parsers/exciting @@ -1 +1 @@ -Subproject commit 650f790435cea5a8e4936b4c5119831db9bdb1bd +Subproject commit 92b5304f44de8853e6bc56f22f79fefd6dccbdef diff --git a/dependencies/parsers/fhi-aims b/dependencies/parsers/fhi-aims index a881fb41c5..2e725461e9 160000 --- a/dependencies/parsers/fhi-aims +++ b/dependencies/parsers/fhi-aims @@ -1 +1 @@ -Subproject commit a881fb41c5402f1eb08ffd918c5dc77dbc16fc33 +Subproject commit 2e725461e9463401c75643d603045ffafe3cab4c diff --git a/dependencies/parsers/gaussian b/dependencies/parsers/gaussian index c33fb8ea93..4e1e2cc790 160000 --- a/dependencies/parsers/gaussian +++ b/dependencies/parsers/gaussian @@ -1 +1 @@ -Subproject commit c33fb8ea93184752c580d2f497a2396399f45fe3 +Subproject commit 4e1e2cc790713269232f82b23534be5e1ece6e54 diff --git a/dependencies/parsers/gromacs b/dependencies/parsers/gromacs index 2401385ace..9a4ba02a02 160000 --- a/dependencies/parsers/gromacs +++ b/dependencies/parsers/gromacs @@ -1 +1 @@ -Subproject commit 2401385ace6243b85c2fb7afd84212662c46958a +Subproject commit 9a4ba02a02016f630640a68ad533f847a9343d58 diff --git a/dependencies/parsers/lammps b/dependencies/parsers/lammps index 4e33076b7b..918f29baec 160000 --- a/dependencies/parsers/lammps +++ b/dependencies/parsers/lammps @@ -1 +1 @@ -Subproject commit 4e33076b7b459913ea099ddd5e32aac35600fd98 +Subproject commit 918f29baeceaa0c17b2c5cffd3ef04951c9afdd1 diff --git a/dependencies/parsers/octopus b/dependencies/parsers/octopus index c2318c4b23..c81f95fc41 160000 --- a/dependencies/parsers/octopus +++ b/dependencies/parsers/octopus @@ -1 +1 @@ -Subproject commit c2318c4b2306a3522ebf36f94e3255b240de3e76 +Subproject commit c81f95fc41677153e83534bde23f97d9ada0b477 diff --git a/dependencies/parsers/openkim b/dependencies/parsers/openkim index 59ab830112..b2cf175c43 160000 --- a/dependencies/parsers/openkim +++ b/dependencies/parsers/openkim @@ -1 +1 @@ -Subproject commit 59ab8301128b64e74b4bbfe92035a87c97b5adac +Subproject commit b2cf175c432e2661dea9e5a7788d6439b36b1a9e diff --git a/dependencies/parsers/vasp b/dependencies/parsers/vasp index f51c57a025..40425ea663 160000 --- a/dependencies/parsers/vasp +++ b/dependencies/parsers/vasp @@ -1 +1 @@ -Subproject commit f51c57a0258510645c019b0f935f3e0f01b79282 +Subproject commit 40425ea66319a3390722f63a420e82b2d6277881 diff --git a/dependencies/parsers/wien2k b/dependencies/parsers/wien2k index c8e4fa0a2f..4ac3b4f9fe 160000 --- a/dependencies/parsers/wien2k +++ b/dependencies/parsers/wien2k @@ -1 +1 @@ -Subproject commit c8e4fa0a2fab86d2cefc481fcd00969d81520058 +Subproject commit 4ac3b4f9fe998d36c037ce90fd907ffe5409e027 diff --git a/nomad/normalizing/results.py b/nomad/normalizing/results.py index 44bcd3d437..3755eda9e6 100644 --- a/nomad/normalizing/results.py +++ b/nomad/normalizing/results.py @@ -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 try: # 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() diff --git a/nomad/normalizing/workflow.py b/nomad/normalizing/workflow.py index ca6375c8a6..9b21095cfb 100644 --- a/nomad/normalizing/workflow.py +++ b/nomad/normalizing/workflow.py @@ -420,7 +420,11 @@ class WorkflowNormalizer(Normalizer): def _resolve_workflow_type(self, run): # resolve it from parser workflow_type = None - program_name = run.program.name + try: + program_name = run.program.name + except Exception: + return + if program_name: program_name = program_name.lower() -- GitLab