From 42b2b0ea894aa83cda9588d3d9bf2cdee1f40a92 Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Mon, 12 Aug 2019 10:24:38 +0200
Subject: [PATCH] Fixed insufficient handling of atom positions.
---
bigdftparser/versions/bigdft18/mainparser.py | 14 +++++++++-----
1 file changed, 9 insertions(+), 5 deletions(-)
diff --git a/bigdftparser/versions/bigdft18/mainparser.py b/bigdftparser/versions/bigdft18/mainparser.py
index f0997ae..f833a54 100644
--- a/bigdftparser/versions/bigdft18/mainparser.py
+++ b/bigdftparser/versions/bigdft18/mainparser.py
@@ -1,11 +1,11 @@
# Copyright 2016-2018 Lauri Himanen, Fawzi Mohamed
-#
+#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
-#
+#
# http://www.apache.org/licenses/LICENSE-2.0
-#
+#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
@@ -18,6 +18,7 @@ from yaml import Loader, YAMLError
from yaml import ScalarNode, SequenceNode, MappingNode, MappingEndEvent
from nomadcore.baseclasses import AbstractBaseParser
from bigdftparser.generic.libxc_codes import LIB_XC_MAPPING
+import ase.data
LOGGER = logging.getLogger("nomad")
@@ -143,8 +144,11 @@ class BigDFTMainParser(AbstractBaseParser):
np_labels = []
positions = value["Positions"]
for position in positions:
- np_positions.append(*position.values())
- np_labels.append(*position.keys())
+ for key, value in position.items():
+ # Not all keys are chemical symbols, e.g. spin, etc.
+ if key in ase.data.chemical_symbols:
+ np_positions.append(value)
+ np_labels.append(key)
np_positions = np.array(np_positions)
np_labels = np.array(np_labels)
self.backend.addArrayValues("atom_positions", np_positions, unit="angstrom")
--
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