meta 2.0 changes, to fix

parent d41015e7
Pipeline #42787 failed with stage
in 14 minutes and 10 seconds
...@@ -403,7 +403,7 @@ def get_updateDictionary(self, defname): ...@@ -403,7 +403,7 @@ def get_updateDictionary(self, defname):
# 'settings_geometry_optimization' : MetaInfoMap(startpage), # 'settings_geometry_optimization' : MetaInfoMap(startpage),
# 'settings_metadynamics' : MetaInfoMap(startpage), # 'settings_metadynamics' : MetaInfoMap(startpage),
# 'settings_molecular_dynamics' : MetaInfoMap(startpage), # 'settings_molecular_dynamics' : MetaInfoMap(startpage),
# 'settings_Monte_Carlo' : MetaInfoMap(startpage), # 'settings_monte_carlo' : MetaInfoMap(startpage),
# 'geometry_optimization_energy_change' : MetaInfoMap(startpage, # 'geometry_optimization_energy_change' : MetaInfoMap(startpage,
# depends={ # depends={
# '' : {'imin' : '1'}, # '' : {'imin' : '1'},
...@@ -617,9 +617,9 @@ def get_updateDictionary(self, defname): ...@@ -617,9 +617,9 @@ def get_updateDictionary(self, defname):
# depends=[{'assign' : 'Force Field'}], # depends=[{'assign' : 'Force Field'}],
# lookupdict=self.mddataDict # lookupdict=self.mddataDict
# ), # ),
'energy_T0_per_atom' : MetaInfoMap(startpage), 'energy_t0_per_atom' : MetaInfoMap(startpage),
'energy_total_T0_per_atom' : MetaInfoMap(startpage), 'energy_total_t0_per_atom' : MetaInfoMap(startpage),
'energy_total_T0' : MetaInfoMap(startpage, 'energy_total_t0' : MetaInfoMap(startpage,
depends=[{'value' : 'POTENTIAL'}], depends=[{'value' : 'POTENTIAL'}],
valtype='float', valtype='float',
unitdict=self.unitDict, unitdict=self.unitDict,
...@@ -638,7 +638,7 @@ def get_updateDictionary(self, defname): ...@@ -638,7 +638,7 @@ def get_updateDictionary(self, defname):
'hessian_matrix' : MetaInfoMap(startpage), 'hessian_matrix' : MetaInfoMap(startpage),
'single_configuration_calculation_converged' : MetaInfoMap(startpage), 'single_configuration_calculation_converged' : MetaInfoMap(startpage),
'single_configuration_calculation_to_system_ref' : MetaInfoMap(startpage), 'single_configuration_calculation_to_system_ref' : MetaInfoMap(startpage),
'single_configuration_to_calculation_method_ref' : MetaInfoMap(startpage), 'single_configuration_calculation_to_method_ref' : MetaInfoMap(startpage),
'time_calculation' : MetaInfoMap(startpage), 'time_calculation' : MetaInfoMap(startpage),
'time_single_configuration_calculation_cpu1_end' : MetaInfoMap(startpage), 'time_single_configuration_calculation_cpu1_end' : MetaInfoMap(startpage),
'time_single_configuration_calculation_cpu1_start' : MetaInfoMap(startpage), 'time_single_configuration_calculation_cpu1_start' : MetaInfoMap(startpage),
...@@ -661,14 +661,14 @@ def get_updateDictionary(self, defname): ...@@ -661,14 +661,14 @@ def get_updateDictionary(self, defname):
# section_single_energy_van_der_Waals of section_single_configuration_calculation # section_single_energy_van_der_Waals of section_single_configuration_calculation
singlevdw = { singlevdw = {
'energy_van_der_Waals_value' : MetaInfoMap(startpage, 'energy_van_der_waals_value' : MetaInfoMap(startpage,
depends=[{'value' : 'VDW'}], depends=[{'value' : 'VDW'}],
lookupdict=self.mddataDict, lookupdict=self.mddataDict,
valtype='float', valtype='float',
unitdict=self.unitDict, unitdict=self.unitDict,
unit='kilo-joule/mol', unit='kilo-joule/mol',
#autoSections=True, #autoSections=True,
activeSections=['section_energy_van_der_Waals'] activeSections=['section_energy_van_der_waals']
), ),
} }
...@@ -676,13 +676,13 @@ def get_updateDictionary(self, defname): ...@@ -676,13 +676,13 @@ def get_updateDictionary(self, defname):
# Definitions for section_frame_sequence # Definitions for section_frame_sequence
# ------------------------------------------ # ------------------------------------------
frameseq = { frameseq = {
#'frame_sequence_conserved_quantity_frames' : MetaInfoMap(startpage, #'xxx_to_rm_frame_sequence_conserved_quantity_frames' : MetaInfoMap(startpage,
# depends=[{'store' : 'TS'}], # depends=[{'store' : 'TS'}],
# valtype='int', # valtype='int',
# lookupdict=self.mddataDict # lookupdict=self.mddataDict
# ), # ),
#'frame_sequence_conserved_quantity_stats' : MetaInfoMap(startpage), #'frame_sequence_conserved_quantity_stats' : MetaInfoMap(startpage),
#'frame_sequence_conserved_quantity' : MetaInfoMap(startpage, #'xxx_conserved_quantity' : MetaInfoMap(startpage,
# depends=[{'store' : ''}], # depends=[{'store' : ''}],
# valtype='float', # valtype='float',
# unitdict=self.unitDict, # unitdict=self.unitDict,
...@@ -691,27 +691,27 @@ def get_updateDictionary(self, defname): ...@@ -691,27 +691,27 @@ def get_updateDictionary(self, defname):
# ), # ),
'frame_sequence_continuation_kind' : MetaInfoMap(startpage), 'frame_sequence_continuation_kind' : MetaInfoMap(startpage),
'frame_sequence_external_url' : MetaInfoMap(startpage), 'frame_sequence_external_url' : MetaInfoMap(startpage),
'frame_sequence_kinetic_energy_frames' : MetaInfoMap(startpage, 'xxx_to_rm_frame_sequence_kinetic_energy_frames' : MetaInfoMap(startpage,
depends=[{'store' : 'TS'}], depends=[{'store' : 'TS'}],
valtype='int', valtype='int',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
'frame_sequence_kinetic_energy_stats' : MetaInfoMap(startpage), 'frame_sequence_kinetic_energy_stats' : MetaInfoMap(startpage),
'frame_sequence_kinetic_energy' : MetaInfoMap(startpage, 'xxx_kinetic_energy' : MetaInfoMap(startpage,
depends=[{'store' : 'KINETIC'}], depends=[{'store' : 'KINETIC'}],
valtype='float', valtype='float',
unitdict=self.unitDict, unitdict=self.unitDict,
unit='kilo-joule/mol', unit='kilo-joule/mol',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
'frame_sequence_local_frames_ref' : MetaInfoMap(startpage), 'frame_sequence_to_frames_ref' : MetaInfoMap(startpage),
'frame_sequence_potential_energy_frames' : MetaInfoMap(startpage, 'xxx_to_rm_frame_sequence_potential_energy_frames' : MetaInfoMap(startpage,
depends=[{'store' : 'TS'}], depends=[{'store' : 'TS'}],
valtype='int', valtype='int',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
'frame_sequence_potential_energy_stats' : MetaInfoMap(startpage), 'frame_sequence_potential_energy_stats' : MetaInfoMap(startpage),
'frame_sequence_potential_energy' : MetaInfoMap(startpage, 'xxx_potential_energy' : MetaInfoMap(startpage,
depends=[{'store' : 'POTENTIAL'}], depends=[{'store' : 'POTENTIAL'}],
valtype='float', valtype='float',
unitdict=self.unitDict, unitdict=self.unitDict,
...@@ -730,13 +730,13 @@ def get_updateDictionary(self, defname): ...@@ -730,13 +730,13 @@ def get_updateDictionary(self, defname):
unit='bar', unit='bar',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
'frame_sequence_pressure_frames' : MetaInfoMap(startpage, 'xxx_to_rm_frame_sequence_pressure_frames' : MetaInfoMap(startpage,
depends=[{'store' : 'TS'}], depends=[{'store' : 'TS'}],
valtype='int', valtype='int',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
'frame_sequence_pressure_stats' : MetaInfoMap(startpage), 'frame_sequence_pressure_stats' : MetaInfoMap(startpage),
'frame_sequence_pressure' : MetaInfoMap(startpage, 'xxx_instant_pressure' : MetaInfoMap(startpage,
depends=[{'store' : 'PRESSURE'}], depends=[{'store' : 'PRESSURE'}],
valtype='float', valtype='float',
unitdict=self.unitDict, unitdict=self.unitDict,
...@@ -755,13 +755,13 @@ def get_updateDictionary(self, defname): ...@@ -755,13 +755,13 @@ def get_updateDictionary(self, defname):
unit='Kelvin', unit='Kelvin',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
'frame_sequence_temperature_frames' : MetaInfoMap(startpage, 'xxx_to_rm_frame_sequence_temperature_frames' : MetaInfoMap(startpage,
depends=[{'store' : 'TS'}], depends=[{'store' : 'TS'}],
valtype='int', valtype='int',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
'frame_sequence_temperature_stats' : MetaInfoMap(startpage), 'frame_sequence_temperature_stats' : MetaInfoMap(startpage),
'frame_sequence_temperature' : MetaInfoMap(startpage, 'xxx_instant_temperature' : MetaInfoMap(startpage,
depends=[{'store' : 'TEMP'}], depends=[{'store' : 'TEMP'}],
valtype='float', valtype='float',
unitdict=self.unitDict, unitdict=self.unitDict,
...@@ -943,7 +943,7 @@ def get_updateDictionary(self, defname): ...@@ -943,7 +943,7 @@ def get_updateDictionary(self, defname):
unit='kilo-joule/mol', unit='kilo-joule/mol',
lookupdict=self.mddataDict lookupdict=self.mddataDict
), ),
#'frame_sequence_to_sampling_ref' : MetaInfoMap(startpage), #'frame_sequence_to_sampling_method_ref' : MetaInfoMap(startpage),
'geometry_optimization_converged' : MetaInfoMap(startpage, 'geometry_optimization_converged' : MetaInfoMap(startpage,
value=self.minConverged value=self.minConverged
), ),
...@@ -956,7 +956,7 @@ def get_updateDictionary(self, defname): ...@@ -956,7 +956,7 @@ def get_updateDictionary(self, defname):
# value=(lambda x: np.array(x['val']).flatten().shape[0] if( # value=(lambda x: np.array(x['val']).flatten().shape[0] if(
# x is not None and x['val'] is not None) else None)( # x is not None and x['val'] is not None) else None)(
# self.metaStorage.fetchAttrValue( # self.metaStorage.fetchAttrValue(
# 'frame_sequence_conserved_quantity_frames' # 'xxx_to_rm_frame_sequence_conserved_quantity_frames'
# ) # )
# ) # )
# ), # ),
...@@ -964,7 +964,7 @@ def get_updateDictionary(self, defname): ...@@ -964,7 +964,7 @@ def get_updateDictionary(self, defname):
value=(lambda x: np.array(x['val']).flatten().shape[0] if( value=(lambda x: np.array(x['val']).flatten().shape[0] if(
x is not None and x['val'] is not None) else None)( x is not None and x['val'] is not None) else None)(
self.metaStorage.fetchAttrValue( self.metaStorage.fetchAttrValue(
'frame_sequence_potential_energy_frames' 'xxx_to_rm_frame_sequence_potential_energy_frames'
) )
) )
), ),
...@@ -972,7 +972,7 @@ def get_updateDictionary(self, defname): ...@@ -972,7 +972,7 @@ def get_updateDictionary(self, defname):
value=(lambda x: np.array(x['val']).flatten().shape[0] if( value=(lambda x: np.array(x['val']).flatten().shape[0] if(
x is not None and x['val'] is not None) else None)( x is not None and x['val'] is not None) else None)(
self.metaStorage.fetchAttrValue( self.metaStorage.fetchAttrValue(
'frame_sequence_kinetic_energy_frames' 'xxx_to_rm_frame_sequence_kinetic_energy_frames'
) )
) )
), ),
...@@ -981,7 +981,7 @@ def get_updateDictionary(self, defname): ...@@ -981,7 +981,7 @@ def get_updateDictionary(self, defname):
value=(lambda x: np.array(x['val']).flatten().shape[0] if( value=(lambda x: np.array(x['val']).flatten().shape[0] if(
x is not None and x['val'] is not None) else None)( x is not None and x['val'] is not None) else None)(
self.metaStorage.fetchAttrValue( self.metaStorage.fetchAttrValue(
'frame_sequence_potential_energy_frames' 'xxx_to_rm_frame_sequence_potential_energy_frames'
) )
) )
), ),
...@@ -990,7 +990,7 @@ def get_updateDictionary(self, defname): ...@@ -990,7 +990,7 @@ def get_updateDictionary(self, defname):
value=(lambda x: np.array(x['val']).flatten().shape[0] if( value=(lambda x: np.array(x['val']).flatten().shape[0] if(
x is not None and x['val'] is not None) else None)( x is not None and x['val'] is not None) else None)(
self.metaStorage.fetchAttrValue( self.metaStorage.fetchAttrValue(
'frame_sequence_pressure_frames' 'xxx_to_rm_frame_sequence_pressure_frames'
) )
) )
), ),
...@@ -999,7 +999,7 @@ def get_updateDictionary(self, defname): ...@@ -999,7 +999,7 @@ def get_updateDictionary(self, defname):
value=(lambda x: np.array(x['val']).flatten().shape[0] if( value=(lambda x: np.array(x['val']).flatten().shape[0] if(
x is not None and x['val'] is not None) else None)( x is not None and x['val'] is not None) else None)(
self.metaStorage.fetchAttrValue( self.metaStorage.fetchAttrValue(
'frame_sequence_temperature_frames' 'xxx_to_rm_frame_sequence_temperature_frames'
) )
) )
), ),
...@@ -1144,7 +1144,7 @@ def get_updateDictionary(self, defname): ...@@ -1144,7 +1144,7 @@ def get_updateDictionary(self, defname):
'number_of_symmetry_operations' : MetaInfoMap(startpage), 'number_of_symmetry_operations' : MetaInfoMap(startpage),
'reduced_symmetry_matrices' : MetaInfoMap(startpage), 'reduced_symmetry_matrices' : MetaInfoMap(startpage),
'reduced_symmetry_translations' : MetaInfoMap(startpage), 'reduced_symmetry_translations' : MetaInfoMap(startpage),
'SC_matrix' : MetaInfoMap(startpage), 'sc_matrix' : MetaInfoMap(startpage),
'spacegroup_3D_choice' : MetaInfoMap(startpage), 'spacegroup_3D_choice' : MetaInfoMap(startpage),
'spacegroup_3D_hall' : MetaInfoMap(startpage), 'spacegroup_3D_hall' : MetaInfoMap(startpage),
'spacegroup_3D_international' : MetaInfoMap(startpage), 'spacegroup_3D_international' : MetaInfoMap(startpage),
......
...@@ -56,7 +56,7 @@ class NAMDParser(SmartParser.ParserBase): ...@@ -56,7 +56,7 @@ class NAMDParser(SmartParser.ParserBase):
# dictionary of energy values, which are tracked between SCF iterations and written after convergence # dictionary of energy values, which are tracked between SCF iterations and written after convergence
self.totalEnergyList = { self.totalEnergyList = {
'energy_electrostatic': None, 'energy_electrostatic': None,
'energy_total_T0_per_atom': None, 'energy_total_t0_per_atom': None,
'energy_free_per_atom': None, 'energy_free_per_atom': None,
} }
SmartParser.ParserBase.__init__( SmartParser.ParserBase.__init__(
...@@ -214,8 +214,8 @@ class NAMDParser(SmartParser.ParserBase): ...@@ -214,8 +214,8 @@ class NAMDParser(SmartParser.ParserBase):
self.metaStorage.updateBackend(backend.superBackend, self.metaStorage.updateBackend(backend.superBackend,
startsection=['section_frame_sequence'], startsection=['section_frame_sequence'],
autoopenclose=False) autoopenclose=False)
backend.addValue("frame_sequence_to_sampling_ref", self.secSamplingGIndex) backend.addValue("frame_sequence_to_sampling_method_ref", self.secSamplingGIndex)
backend.addArrayValues("frame_sequence_local_frames_ref", np.asarray(self.singleConfCalcs)) backend.addArrayValues("frame_sequence_to_frames_ref", np.asarray(self.singleConfCalcs))
backend.closeSection("section_frame_sequence", frameSequenceGIndex) backend.closeSection("section_frame_sequence", frameSequenceGIndex)
# reset all variables # reset all variables
...@@ -657,16 +657,16 @@ class NAMDParser(SmartParser.ParserBase): ...@@ -657,16 +657,16 @@ class NAMDParser(SmartParser.ParserBase):
section_singlevdw_Dict = get_updateDictionary(self, 'singlevdw') section_singlevdw_Dict = get_updateDictionary(self, 'singlevdw')
updateDictVDW = { updateDictVDW = {
'startSection' : [ 'startSection' : [
['section_energy_van_der_Waals']], ['section_energy_van_der_waals']],
#'muteSections' : [['section_sampling_method']], #'muteSections' : [['section_sampling_method']],
'dictionary' : section_singlevdw_Dict '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.update(updateDictVDW)
self.metaStorage.updateBackend(backend.superBackend, self.metaStorage.updateBackend(backend.superBackend,
startsection=['section_energy_van_der_Waals'], startsection=['section_energy_van_der_waals'],
autoopenclose=False) 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') section_singlecalc_Dict = get_updateDictionary(self, 'singleconfcalc')
updateDict = { updateDict = {
'startSection' : [ 'startSection' : [
...@@ -683,7 +683,7 @@ class NAMDParser(SmartParser.ParserBase): ...@@ -683,7 +683,7 @@ class NAMDParser(SmartParser.ParserBase):
#if callable(pos_obj): #if callable(pos_obj):
if self.trajectory.forces is not None: if self.trajectory.forces is not None:
# Forces in PDB/NAMD binary/DCD files are stored in kcal/mol/A # Forces in PDB/NAMD binary/DCD files are stored in kcal/mol/A
SloppyBackend.addArrayValues('atom_forces', np.transpose(np.asarray( SloppyBackend.addArrayValues('atom_forces_xxx', np.transpose(np.asarray(
self.metaStorage.convertUnits( self.metaStorage.convertUnits(
self.atompositions.velocities, "kcal/(mol*Angstrom)", self.unitDict)))) self.atompositions.velocities, "kcal/(mol*Angstrom)", self.unitDict))))
# need to transpose array since its shape is [number_of_atoms,3] in the metadata # need to transpose array since its shape is [number_of_atoms,3] in the metadata
......
...@@ -48,7 +48,7 @@ object NamdParser extends SimpleExternalParserGenerator( ...@@ -48,7 +48,7 @@ object NamdParser extends SimpleExternalParserGenerator(
"parser-namd/setup_paths.py", "parser-namd/setup_paths.py",
"nomad_meta_info/public.nomadmetainfo.json", "nomad_meta_info/public.nomadmetainfo.json",
"nomad_meta_info/common.nomadmetainfo.json", "nomad_meta_info/common.nomadmetainfo.json",
"nomad_meta_info/meta_types.nomadmetainfo.json", "nomad_meta_info/meta.nomadmetainfo.json",
"nomad_meta_info/namd.nomadmetainfo.json" "nomad_meta_info/namd.nomadmetainfo.json"
) ++ DefaultPythonInterpreter.commonFiles(), ) ++ DefaultPythonInterpreter.commonFiles(),
dirMap = Map( dirMap = Map(
......
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