From c7811d4c7fcba9226a58ad32a626efe041655b0b Mon Sep 17 00:00:00 2001
From: jrudz <rudzinski@mpip-mainz.mpg.de>
Date: Mon, 20 Mar 2023 14:39:31 +0100
Subject: [PATCH] fixed errors when unable to create universe
---
nomad/atomutils.py | 15 ++++++++-------
1 file changed, 8 insertions(+), 7 deletions(-)
diff --git a/nomad/atomutils.py b/nomad/atomutils.py
index 40f84b5760..d4eb43055e 100644
--- a/nomad/atomutils.py
+++ b/nomad/atomutils.py
@@ -1038,15 +1038,16 @@ def archive_to_universe(archive, system_index: int = 0, method_index: int = -1,
sec_atoms = sec_system_top.atoms
sec_atoms_group = sec_system_top.atoms_group
sec_method = sec_run.method[method_index] if sec_run.get('method') is not None else None
- sec_model = sec_method.force_field.model[model_index] if sec_method is not None else None
+ sec_force_field = sec_method.force_field if sec_method is not None else None
+ sec_model = sec_force_field.model[model_index] if sec_force_field is not None else None
except IndexError:
- logging.error('Supplied indices do not exist in archive.')
- return []
+ logging.warning('Supplied indices or necessary sections do not exist in archive. Cannot build the MDA universe.')
+ return None
n_atoms = sec_atoms.get('n_atoms')
if n_atoms is None:
- logging.error('No atoms found in the archive. Cannot build the MDA universe.')
- return []
+ logging.warning('No atoms found in the archive. Cannot build the MDA universe.')
+ return None
n_frames = len(sec_system) if sec_system is not None else None
atom_names = sec_atoms.get('labels')
@@ -1188,8 +1189,8 @@ def archive_to_universe(archive, system_index: int = 0, method_index: int = -1,
# add the bonds
if hasattr(metainfo_universe, 'bonds'):
- logging.error('archive_to_universe() failed, universe already has bonds.')
- return []
+ logging.warning('archive_to_universe() failed, universe already has bonds.')
+ return None
metainfo_universe.add_TopologyAttr('bonds', bonds)
return metainfo_universe
--
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