meta 2.0 changes, to fix

parent 65077108
Pipeline #42638 failed with stage
in 15 minutes and 52 seconds
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......@@ -60,7 +60,7 @@ class AMBERParser(AmberC.AMBERParserBase):
# 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,
}
AmberC.AMBERParserBase.__init__(
......@@ -433,8 +433,8 @@ class AMBERParser(AmberC.AMBERParserBase):
self.metaStorage.updateBackend(backend,
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
......@@ -603,7 +603,7 @@ class AMBERParser(AmberC.AMBERParserBase):
def onOpen_section_single_configuration_calculation(self, backend, gIndex, section):
# write the references to section_method and section_system
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)
self.singleConfCalcs.append(gIndex)
self.secSingleGIndex = backend.superBackend.openSection("section_single_configuration_calculation")
......@@ -630,16 +630,16 @@ class AMBERParser(AmberC.AMBERParserBase):
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' : [
......@@ -673,10 +673,10 @@ class AMBERParser(AmberC.AMBERParserBase):
# forces_free.append(fi)
# if forces_free:
# # need to transpose array since its shape is [number_of_atoms,3] in the metadata
# backend.addArrayValues('atom_forces_free', np.transpose(np.asarray(forces_free)))
# backend.addArrayValues('atom_forces_xxx_free', np.transpose(np.asarray(forces_free)))
# if self.forces_raw:
# # need to transpose array since its shape is [number_of_atoms,3] in the metadata
# backend.addArrayValues('atom_forces_free_raw', np.transpose(np.asarray(self.forces_raw)))
# backend.addArrayValues('atom_forces_xxx_free_raw', np.transpose(np.asarray(self.forces_raw)))
def setStartingPointCalculation(self, parser):
backend = parser.backend
......
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