Planned maintenance on Wednesday, 2021-01-20, 17:00-18:00. Expect some interruptions during that time

applying obvious metadata renames

section_system_description -> section_system
cell_associated -> cell_dependent
parent e50d7ad5
......@@ -18,8 +18,8 @@ class DL_POLYParserContext(object):
def onClose_section_method(self, backend, gIndex, section):
print "<onClose_section_method>"
return
def onClose_section_system_description(self, backend, gIndex, section):
print "<onClose_section_system_description>"
def onClose_section_system(self, backend, gIndex, section):
print "<onClose_section_system>"
return
def onClose_dl_poly_section_md_molecule_type(self, backend, gIndex, section):
print "<onClose_molecule_type>"
......@@ -73,7 +73,7 @@ mainFileDescription = SM(name = 'root',
SM(name = 'mdSystem',
startReStr = r"\s*SYSTEM SPECIFICATION\s*",
required = True,
sections = ['section_system_description'],
sections = ['section_system'],
subMatchers = [
SM(name = 'mdTopology',
startReStr = r"\s*number of molecular types\s*[0-9]*\s*",
......@@ -122,7 +122,7 @@ mainFileDescription = SM(name = 'root',
SM(startReStr = "Number of k-points\s*",
forwardMatch = True,
sections = ["section_system_description"],
sections = ["section_system"],
subMatchers = [
SM(startReStr = "Number of k-points\s*",
......@@ -168,7 +168,7 @@ mainFileDescription = SM(name = 'root',
]), # CLOSING section_single_configuration_calculation
]), # CLOSING section_system_description
]), # CLOSING section_system
]), # CLOSING SM newRun
......
......@@ -202,7 +202,7 @@ def parse(output_file_name):
refs_system_description = []
all_frames = [cfg] + trj.frames # <- Initial config + trajectory
for frame in all_frames:
with open_section(jbe, 'section_system_description') as gid:
with open_section(jbe, 'section_system') as gid:
refs_system_description.append(gid)
# Configuration core
atom_labels = np.array([ atom['atom_name'].As() for atom in frame.atoms ])
......
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