meta 2.0 changes, to fix

parent 17fb0d6d
Pipeline #42767 failed with stage
in 9 seconds
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......@@ -60,7 +60,7 @@ class GromacsParser(SmartParser.ParserBase):
# dictionary of energy values, which are tracked between SCF iterations and written after convergence
self.totalEnergyList = {
'energy_electrostatic': None,
'energy_total_T0_per_atom': None,
'energy_total_t0_per_atom': None,
'energy_free_per_atom': None,
}
SmartParser.ParserBase.__init__(
......@@ -220,8 +220,8 @@ class GromacsParser(SmartParser.ParserBase):
self.metaStorage.updateBackend(backend.superBackend,
startsection=['section_frame_sequence'],
autoopenclose=False)
backend.addValue("frame_sequence_to_sampling_ref", self.secSamplingGIndex)
backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs))
backend.addValue("frame_sequence_to_sampling_method_ref", self.secSamplingGIndex)
backend.addArrayValues("frame_sequence_to_frames_ref", np.asarray(self.singleConfCalcs))
backend.closeSection("section_frame_sequence", frameSequenceGIndex)
# reset all variables
......@@ -573,16 +573,16 @@ class GromacsParser(SmartParser.ParserBase):
section_singlevdw_Dict = get_updateDictionary(self, 'singlevdw')
updateDictVDW = {
'startSection' : [
['section_energy_van_der_Waals']],
['section_energy_van_der_waals']],
#'muteSections' : [['section_sampling_method']],
'dictionary' : section_singlevdw_Dict
}
self.secVDWGIndex = backend.superBackend.openSection("section_energy_van_der_Waals")
self.secVDWGIndex = backend.superBackend.openSection("section_energy_van_der_waals")
self.metaStorage.update(updateDictVDW)
self.metaStorage.updateBackend(backend.superBackend,
startsection=['section_energy_van_der_Waals'],
startsection=['section_energy_van_der_waals'],
autoopenclose=False)
backend.superBackend.closeSection("section_energy_van_der_Waals", self.secVDWGIndex)
backend.superBackend.closeSection("section_energy_van_der_waals", self.secVDWGIndex)
section_singlecalc_Dict = get_updateDictionary(self, 'singleconfcalc')
updateDict = {
'startSection' : [
......@@ -597,7 +597,7 @@ class GromacsParser(SmartParser.ParserBase):
if self.MDcurrentstep in trajsteps:
self.onOpen_section_system(backend, None, None)
self.onClose_section_system(backend, None, None)
#backend.addValue('single_configuration_to_calculation_method_ref', self.secMethodGIndex)
#backend.addValue('single_configuration_calculation_to_method_ref', self.secMethodGIndex)
backend.addValue('single_configuration_calculation_to_system_ref', self.secSystemGIndex)
else:
if(self.MDcurrentstep in logsteps or
......
......@@ -49,7 +49,7 @@ object GromacsParser extends SimpleExternalParserGenerator(
"parser-gromacs/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json",
"nomad_meta_info/meta.nomadmetainfo.json",
"nomad_meta_info/gromacs.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map(
......
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