From 526a8b2b51bab122a8cdcd597ed593c2f382fd04 Mon Sep 17 00:00:00 2001
From: Fawzi Mohamed <fawzi.mohamed@fhi-berlin.mpg.de>
Date: Mon, 27 Jun 2016 04:48:31 +0200
Subject: [PATCH] fixing atomic_positions
---
parser/parser-vasp/parser_vasprun.py | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/parser/parser-vasp/parser_vasprun.py b/parser/parser-vasp/parser_vasprun.py
index 6b9a6da..f91869b 100644
--- a/parser/parser-vasp/parser_vasprun.py
+++ b/parser/parser-vasp/parser_vasprun.py
@@ -215,9 +215,9 @@ class VasprunContext(object):
backend = parser.backend
gIndexes = parser.tagSections[pathStr]
self.lastSystemDescription = gIndexes["section_system"]
+ cell = None
for el in element:
if (el.tag == "crystal"):
- cell = None
for cellEl in el:
if cellEl.tag == "varray":
name = cellEl.attrib.get("name", None)
@@ -239,7 +239,7 @@ class VasprunContext(object):
name = el.attrib.get("name", None)
if name == "positions":
pos = getVector(el)
- backend.addArrayValues("atom_positions", np.asarray(pos))
+ backend.addArrayValues("atom_positions", np.dot(np.asarray(pos), np.transpose(cell)))
else:
backend.pwarn("Unexpected varray in structure %s" % el.attrib)
else:
--
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