From dd1d13ba958bcc596911992cdd28b2cb8c2fe1a3 Mon Sep 17 00:00:00 2001
From: Berk Onat <b.onat@warwick.ac.uk>
Date: Sat, 31 Mar 2018 18:53:32 +0100
Subject: [PATCH] Fixing meta info writer for NoneType topology.
---
.../smart_parser/SmartParserCommon.py | 57 +++++++++++++++----
1 file changed, 46 insertions(+), 11 deletions(-)
diff --git a/common/python/nomadcore/smart_parser/SmartParserCommon.py b/common/python/nomadcore/smart_parser/SmartParserCommon.py
index 346dc8e..604d9e5 100644
--- a/common/python/nomadcore/smart_parser/SmartParserCommon.py
+++ b/common/python/nomadcore/smart_parser/SmartParserCommon.py
@@ -233,19 +233,54 @@ class ParserBase(object):
"""
sO = open_section
supB = backend.superBackend
+ topoDict = None
if self.topology:
topoDict = self.topology.topoDict
- types_list = topoDict["types_list"]
- atom_type_list = topoDict["atom_type_list"]
- atomlabelList = topoDict["atom_label_list"]
- name_list = topoDict["name_list"]
- massesList = topoDict["atom_mass_list"]
- elementList = topoDict["element_list"]
- atomelementList = topoDict["atom_element_list"]
- radiusList = topoDict["atom_radius_list"]
- chargeList = topoDict["atom_charge_list"]
- interDict = topoDict["interactions_dict"]
- interTypeDict = topoDict["interactions_type_dict"]
+ if topoDict:
+ if "types_list" in topoDict:
+ types_list = topoDict["types_list"]
+ else:
+ types_list = []
+ if "atom_type_list" in topoDict:
+ atom_type_list = topoDict["atom_type_list"]
+ else:
+ atom_type_list = []
+ if "atom_label_list" in topoDict:
+ atomlabelList = topoDict["atom_label_list"]
+ else:
+ atomlabelList = []
+ if "name_list" in topoDict:
+ name_list = topoDict["name_list"]
+ else:
+ name_list = []
+ if "atom_mass_list" in topoDict:
+ massesList = topoDict["atom_mass_list"]
+ else:
+ massesList = []
+ if "element_list" in topoDict:
+ elementList = topoDict["element_list"]
+ else:
+ elementList = []
+ if "atom_element_list" in topoDict:
+ atomelementList = topoDict["atom_element_list"]
+ else:
+ atomelementList = []
+ if "atom_radius_list" in topoDict:
+ radiusList = topoDict["atom_radius_list"]
+ else:
+ radiusList = []
+ if "atom_charge_list" in topoDict:
+ chargeList = topoDict["atom_charge_list"]
+ else:
+ chargeList = []
+ if "interactions_dict" in topoDict:
+ interDict = topoDict["interactions_dict"]
+ else:
+ interDict = []
+ if "interactions_type_dict" in topoDict:
+ interTypeDict = topoDict["interactions_type_dict"]
+ else:
+ interTypeDict = []
for elm in range(len(types_list)):
with sO(supB, 'section_atom_type'):
# Atom Type NOMAD Name
--
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