From 15d0110cbeda05aaea05e4d30ba3aeb0874dafef Mon Sep 17 00:00:00 2001
From: Markus Scheidgen <markus.scheidgen@gmail.com>
Date: Fri, 16 Aug 2019 10:22:46 +0200
Subject: [PATCH] Fixed broken calc to system refs.
---
gaussianparser/parser_gaussian.py | 13 ++++---------
1 file changed, 4 insertions(+), 9 deletions(-)
diff --git a/gaussianparser/parser_gaussian.py b/gaussianparser/parser_gaussian.py
index 655fd36..d8662ee 100644
--- a/gaussianparser/parser_gaussian.py
+++ b/gaussianparser/parser_gaussian.py
@@ -431,7 +431,7 @@ class GaussianParserContext(object):
when the parsing starts and when a section_run closes.
"""
self.secMethodIndex = None
- self.secSystemDescriptionIndex = 0
+ self.secSystemDescriptionIndex = -1
# start with -1 since zeroth iteration is the initialization
self.scfIterNr = -1
self.singleConfCalcs = []
@@ -449,6 +449,9 @@ class GaussianParserContext(object):
# allows to reset values if the same superContext is used to parse different files
self.initialize_values()
+ def onOpen_section_system(self, backend, gIndex, section):
+ self.secSystemDescriptionIndex = gIndex
+
def onClose_section_run(self, backend, gIndex, section):
"""Trigger called when section_run is closed.
@@ -494,18 +497,10 @@ class GaussianParserContext(object):
atom_numbers[i] = numbers[i]
atomic_symbols[i] = ase.data.chemical_symbols[atom_numbers[i]]
- if self.secSystemDescriptionIndex > 0:
- self.secSystemDescriptionIndex = backend.openSection("section_system")
-
backend.addArrayValues("atom_labels", atomic_symbols, self.secSystemDescriptionIndex)
backend.addArrayValues("atom_positions", atom_coords, self.secSystemDescriptionIndex)
backend.addValue("x_gaussian_number_of_atoms",len(atomic_symbols), self.secSystemDescriptionIndex)
- if self.secSystemDescriptionIndex > 0:
- backend.closeSection("section_system", self.secSystemDescriptionIndex)
- else:
- self.secSystemDescriptionIndex = 1
-
def onClose_x_gaussian_section_atom_forces(self, backend, gIndex, section):
xForce = section["x_gaussian_atom_x_force"]
yForce = section["x_gaussian_atom_y_force"]
--
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