diff --git a/parser/parser-gromos/GROMOSDictionary.py b/parser/parser-gromos/GROMOSDictionary.py index d7e51a970905fec63f684a0cd99f6ff449f251bf..f367332649c5e541d7f4413a18dc7c36e4eac61d 100644 --- a/parser/parser-gromos/GROMOSDictionary.py +++ b/parser/parser-gromos/GROMOSDictionary.py @@ -540,7 +540,7 @@ def get_updateDictionary(self, defname): # 'settings_geometry_optimization' : MetaInfoMap(startpage), # 'settings_metadynamics' : MetaInfoMap(startpage), # 'settings_molecular_dynamics' : MetaInfoMap(startpage), -# 'settings_Monte_Carlo' : MetaInfoMap(startpage), +# 'settings_monte_carlo' : MetaInfoMap(startpage), # 'geometry_optimization_energy_change' : MetaInfoMap(startpage, # depends={ # '' : {'imin' : '1'}, @@ -755,9 +755,9 @@ def get_updateDictionary(self, defname): # depends=[{'assign' : 'Force Field'}], # lookupdict=self.mddataDict # ), - 'energy_T0_per_atom' : MetaInfoMap(startpage), - 'energy_total_T0_per_atom' : MetaInfoMap(startpage), - 'energy_total_T0' : MetaInfoMap(startpage, + 'energy_t0_per_atom' : MetaInfoMap(startpage), + 'energy_total_t0_per_atom' : MetaInfoMap(startpage), + 'energy_total_t0' : MetaInfoMap(startpage, depends=[{'value' : 'E_Potential'}], valtype='float', unitdict=self.unitDict, @@ -776,7 +776,7 @@ def get_updateDictionary(self, defname): 'hessian_matrix' : MetaInfoMap(startpage), 'single_configuration_calculation_converged' : 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_single_configuration_calculation_cpu1_end' : MetaInfoMap(startpage), 'time_single_configuration_calculation_cpu1_start' : MetaInfoMap(startpage), @@ -799,14 +799,14 @@ def get_updateDictionary(self, defname): # section_single_energy_van_der_Waals of section_single_configuration_calculation singlevdw = { - 'energy_van_der_Waals_value' : MetaInfoMap(startpage, + 'energy_van_der_waals_value' : MetaInfoMap(startpage, depends=[{'value' : 'E_Vdw'}], lookupdict=self.mddataDict, valtype='float', unitdict=self.unitDict, unit='kilo-joule/mol', #autoSections=True, - activeSections=['section_energy_van_der_Waals'] + activeSections=['section_energy_van_der_waals'] ), } @@ -857,13 +857,13 @@ def get_updateDictionary(self, defname): # Definitions for section_frame_sequence # ------------------------------------------ frameseq = { - #'frame_sequence_conserved_quantity_frames' : MetaInfoMap(startpage, + #'xxx_to_rm_frame_sequence_conserved_quantity_frames' : MetaInfoMap(startpage, # depends=[{'store' : 'TS'}], # valtype='int', # lookupdict=self.mddataDict # ), #'frame_sequence_conserved_quantity_stats' : MetaInfoMap(startpage), - #'frame_sequence_conserved_quantity' : MetaInfoMap(startpage, + #'xxx_conserved_quantity' : MetaInfoMap(startpage, # depends=[{'store' : ''}], # valtype='float', # unitdict=self.unitDict, @@ -872,27 +872,27 @@ def get_updateDictionary(self, defname): # ), 'frame_sequence_continuation_kind' : 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' : 'STEP'}], valtype='int', lookupdict=self.mddataDict ), 'frame_sequence_kinetic_energy_stats' : MetaInfoMap(startpage), - 'frame_sequence_kinetic_energy' : MetaInfoMap(startpage, + 'xxx_kinetic_energy' : MetaInfoMap(startpage, depends=[{'store' : 'E_Kinetic'}], valtype='float', unitdict=self.unitDict, unit='kilo-joule/mol', lookupdict=self.mddataDict ), - 'frame_sequence_local_frames_ref' : MetaInfoMap(startpage), - 'frame_sequence_potential_energy_frames' : MetaInfoMap(startpage, + 'frame_sequence_to_frames_ref' : MetaInfoMap(startpage), + 'xxx_to_rm_frame_sequence_potential_energy_frames' : MetaInfoMap(startpage, depends=[{'store' : 'STEP'}], valtype='int', lookupdict=self.mddataDict ), 'frame_sequence_potential_energy_stats' : MetaInfoMap(startpage), - 'frame_sequence_potential_energy' : MetaInfoMap(startpage, + 'xxx_potential_energy' : MetaInfoMap(startpage, depends=[{'store' : 'E_Potential'}], valtype='float', unitdict=self.unitDict, @@ -911,13 +911,13 @@ def get_updateDictionary(self, defname): # unit='atmosphere', # lookupdict=self.mddataDict # ), - 'frame_sequence_pressure_frames' : MetaInfoMap(startpage, + 'xxx_to_rm_frame_sequence_pressure_frames' : MetaInfoMap(startpage, depends=[{'store' : 'STEP'}], valtype='int', lookupdict=self.mddataDict ), 'frame_sequence_pressure_stats' : MetaInfoMap(startpage), - 'frame_sequence_pressure' : MetaInfoMap(startpage, + 'xxx_instant_pressure' : MetaInfoMap(startpage, depends=[{'store' : 'Pressure'}], valtype='float', unitdict=self.unitDict, @@ -936,13 +936,13 @@ def get_updateDictionary(self, defname): # unit='Kelvin', # lookupdict=self.mddataDict # ), - 'frame_sequence_temperature_frames' : MetaInfoMap(startpage, + 'xxx_to_rm_frame_sequence_temperature_frames' : MetaInfoMap(startpage, depends=[{'store' : 'STEP'}], valtype='int', lookupdict=self.mddataDict ), 'frame_sequence_temperature_stats' : MetaInfoMap(startpage), - 'frame_sequence_temperature' : MetaInfoMap(startpage, + 'xxx_instant_temperature' : MetaInfoMap(startpage, depends=[{'store' : 'T_avg'}], valtype='float', unitdict=self.unitDict, @@ -1139,7 +1139,7 @@ def get_updateDictionary(self, defname): unit='kilo-joule/mol', lookupdict=self.mddataDict ), - #'frame_sequence_to_sampling_ref' : MetaInfoMap(startpage), + #'frame_sequence_to_sampling_method_ref' : MetaInfoMap(startpage), 'geometry_optimization_converged' : MetaInfoMap(startpage, depends=[ {'test' : [["MINI", " is not None"], @@ -1158,7 +1158,7 @@ def get_updateDictionary(self, defname): # value=(lambda x: np.array(x['val']).flatten().shape[0] if( # x is not None and x['val'] is not None) else None)( # self.metaStorage.fetchAttrValue( - # 'frame_sequence_conserved_quantity_frames' + # 'xxx_to_rm_frame_sequence_conserved_quantity_frames' # ) # ) # ), @@ -1166,7 +1166,7 @@ def get_updateDictionary(self, defname): value=(lambda x: np.array(x['val']).flatten().shape[0] if( x is not None and x['val'] is not None) else None)( self.metaStorage.fetchAttrValue( - 'frame_sequence_potential_energy_frames' + 'xxx_to_rm_frame_sequence_potential_energy_frames' ) ) ), @@ -1174,7 +1174,7 @@ def get_updateDictionary(self, defname): value=(lambda x: np.array(x['val']).flatten().shape[0] if( x is not None and x['val'] is not None) else None)( self.metaStorage.fetchAttrValue( - 'frame_sequence_kinetic_energy_frames' + 'xxx_to_rm_frame_sequence_kinetic_energy_frames' ) ) ), @@ -1183,7 +1183,7 @@ def get_updateDictionary(self, defname): value=(lambda x: np.array(x['val']).flatten().shape[0] if( x is not None and x['val'] is not None) else None)( self.metaStorage.fetchAttrValue( - 'frame_sequence_potential_energy_frames' + 'xxx_to_rm_frame_sequence_potential_energy_frames' ) ) ), @@ -1192,7 +1192,7 @@ def get_updateDictionary(self, defname): value=(lambda x: np.array(x['val']).flatten().shape[0] if( x is not None and x['val'] is not None) else None)( self.metaStorage.fetchAttrValue( - 'frame_sequence_pressure_frames' + 'xxx_to_rm_frame_sequence_pressure_frames' ) ) ), @@ -1201,7 +1201,7 @@ def get_updateDictionary(self, defname): value=(lambda x: np.array(x['val']).flatten().shape[0] if( x is not None and x['val'] is not None) else None)( self.metaStorage.fetchAttrValue( - 'frame_sequence_temperature_frames' + 'xxx_to_rm_frame_sequence_temperature_frames' ) ) ), @@ -1326,7 +1326,7 @@ def get_updateDictionary(self, defname): 'number_of_symmetry_operations' : MetaInfoMap(startpage), 'reduced_symmetry_matrices' : MetaInfoMap(startpage), 'reduced_symmetry_translations' : MetaInfoMap(startpage), - 'SC_matrix' : MetaInfoMap(startpage), + 'sc_matrix' : MetaInfoMap(startpage), 'spacegroup_3D_choice' : MetaInfoMap(startpage), 'spacegroup_3D_hall' : MetaInfoMap(startpage), 'spacegroup_3D_international' : MetaInfoMap(startpage), diff --git a/parser/parser-gromos/GROMOSParser.py b/parser/parser-gromos/GROMOSParser.py index ab42ba5dc3c9d8542e15fade3695cbe46c1493d0..2057e21b8f305c66d9727530fbdf695bdf55da44 100644 --- a/parser/parser-gromos/GROMOSParser.py +++ b/parser/parser-gromos/GROMOSParser.py @@ -72,7 +72,7 @@ class GROMOSParser(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__( @@ -275,8 +275,8 @@ class GROMOSParser(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 @@ -884,16 +884,16 @@ class GROMOSParser(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' : [ @@ -910,7 +910,7 @@ class GROMOSParser(SmartParser.ParserBase): #if callable(pos_obj): if self.trajectory.forces is not None: # Forces in PDB/GROMOS 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.atompositions.velocities, "kilo-joule/(mol*nano-meter)", self.unitDict)))) # need to transpose array since its shape is [number_of_atoms,3] in the metadata diff --git a/src/main/scala/eu/nomad_lab/parsers/GromosParser.scala b/src/main/scala/eu/nomad_lab/parsers/GromosParser.scala index 3023bcd31c7024ffd9d01f9d58b09733bb5d2d6d..c9c04f70bf62c21e84dd5776b4812f6830be2768 100644 --- a/src/main/scala/eu/nomad_lab/parsers/GromosParser.scala +++ b/src/main/scala/eu/nomad_lab/parsers/GromosParser.scala @@ -48,7 +48,7 @@ object GromosParser extends SimpleExternalParserGenerator( "parser-gromos/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/gromos.nomadmetainfo.json" ) ++ DefaultPythonInterpreter.commonFiles(), dirMap = Map(