Commit 22bc82b9 authored by Daniel Speckhard's avatar Daniel Speckhard
Browse files

Fixed trajectory file.

parent d7bfc62d
......@@ -66,6 +66,7 @@ def log(msg, highlight=None, enter=endl):
# if osio:
# if highlight==None: hightlight = osio.ww
# osio << highlight << msg << enter
logging.debug(msg)
return
# CONTEXT GUARD
......@@ -109,8 +110,9 @@ def parse_without_class(output_file_name, backend, parser_info):
terminal_gap.ParseOutput(output_file_name, base_dir)
terminal_trj = terminal_gap.trj
logging.debug("Start parsing...")
# osio << "Start parsing ..." << osio.endl
logging.debug('Base directory = %s' % base_dir)
# osio << "Base directory = '%s'" % base_dir << osio.endl
gap = terminal_gap
......
......@@ -23,6 +23,7 @@ import sys
import re
import numpy as np
import xml.dom.minidom
from nomad.utils import create_uuid
try:
import ase
......@@ -197,7 +198,7 @@ class LibAtomsGapParser(LibAtomsParser):
dom = xml.dom.minidom.parse(output_file)
root = XmlGetUnique(dom, 'GAP_params')
# Child keys should be: ['gpSparse', 'command_line', 'GAP_data', 'XYZ_data']
#print(list(child_nodes.keys()))
# print(list(child_nodes.keys()))
child_nodes = XmlGetChildDict(root)
# 'GAP_params'
......@@ -286,16 +287,17 @@ class LibAtomsGapParser(LibAtomsParser):
if key in child_nodes:
node = child_nodes[key][0]
text = XmlGetText(node)
trj_file = 'lib-atoms-gap.from-xml.xyz'
# ofs = open(trj_file, 'w')
# for child in node.childNodes:
# if child.nodeValue == None: continue
# ln = child.nodeValue.strip(' \n')
# if ln == '': continue
# ofs.write(ln+'\n')
# ofs.close()
unique_ID = create_uuid()
trj_file = '/tmp/' + unique_ID + '-lib-atoms-gap.from-xml.xyz'
ofs = open(trj_file, 'w')
for child in node.childNodes:
if child.nodeValue == None: continue
ln = child.nodeValue.strip(' \n')
if ln == '': continue
ofs.write(ln+'\n')
ofs.close()
self.trj = LibAtomsTrajectory(self.log)
# self.trj.ParseOutput(trj_file)
self.trj.ParseOutput(trj_file)
return
class LibAtomsTrajectory(LibAtomsParser):
......
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