Commit 2d437e39 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
Browse files

fixed bug with atomic positions

parent 4b35ff9d
......@@ -5,7 +5,7 @@ from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
from nomadcore.caching_backend import CachingLevel
from nomadcore.unit_conversion import unit_conversion
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_input
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure #, exciting_parser_input
class ExcitingParserContext(object):
......@@ -56,11 +56,11 @@ class ExcitingParserContext(object):
bandFile = os.path.join(dirPath, "bandstructure.xml")
eigvalFile = os.path.join(dirPath, "EIGVAL.OUT")
fermiSurfFile = os.path.join(dirPath, "FERMISURF.bxsf")
inputFile = os.path.join(dirPath, "input.xml")
# inputFile = os.path.join(dirPath, "input.xml")
############# reading input file for atom positions##############
if os.path.exists(inputFile):
with open(inputFile) as f:
exciting_parser_input.parseInput(f, backend)
# if os.path.exists(inputFile):
# with open(inputFile) as f:
# exciting_parser_input.parseInput(f, backend)
if os.path.exists(dosFile):
with open(dosFile) as f:
exciting_parser_dos.parseDos(f, backend)
......@@ -187,7 +187,19 @@ class ExcitingParserContext(object):
# if os.path.exists(inputFile):
# with open(inputFile) as f:
# exciting_parser_input.parseInput(f, backend)
self.secSystemDescriptionIndex = gIndex
atom_pos = []
for i in ['x', 'y', 'z']:
api = section['x_exciting_geometry_atom_positions_' + i]
if api is not None:
atom_pos.append(api)
if atom_pos:
backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos)))
# print("atom_positions==",atom_pos)
atom_labels = section['x_exciting_geometry_atom_labels']
if atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(atom_labels))
mainFileDescription = \
SM(name = "root matcher",
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment