From c01a50533317b9cceb0adf4ffb1a39d84828153e Mon Sep 17 00:00:00 2001
From: Ask Hjorth Larsen <asklarsen@gmail.com>
Date: Fri, 18 Nov 2016 17:20:34 +0100
Subject: [PATCH] fix bug where positions would be defined assuming wrong table
layout
---
parser/parser-molcas/main.py | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/parser/parser-molcas/main.py b/parser/parser-molcas/main.py
index e370d8b..07b012a 100755
--- a/parser/parser-molcas/main.py
+++ b/parser/parser-molcas/main.py
@@ -234,8 +234,10 @@ class MolcasContext(object):
def onClose_section_system(self, backend, gindex, section):
matrix = self.data.pop('coordinates')
- atom_labels = matrix[:, 1]
- coords = matrix[:, 2:5].astype(float)
+ assert matrix.shape[1] == 4
+ atom_labels = matrix[:, 0]
+ coords = matrix[:, 1:4].astype(float)
+ assert coords.shape[1] == 3
coords = convert_unit(coords, 'bohr')
backend.addArrayValues('atom_labels', atom_labels)
--
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