diff --git a/parser/parser-tinker/TINKERDictionary.py b/parser/parser-tinker/TINKERDictionary.py index db0fc89c2802fb1d4d9df077d87148b2fe6a0dd9..2b5d2ac6e41b38b74fded88d1180ecd032915923 100644 --- a/parser/parser-tinker/TINKERDictionary.py +++ b/parser/parser-tinker/TINKERDictionary.py @@ -388,7 +388,7 @@ 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'}, @@ -603,9 +603,9 @@ 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, @@ -624,7 +624,7 @@ 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), @@ -647,14 +647,14 @@ 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='kcal/mol', #autoSections=True, - activeSections=['section_energy_van_der_Waals'] + activeSections=['section_energy_van_der_waals'] ), } @@ -705,13 +705,13 @@ 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, @@ -720,27 +720,27 @@ 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' : 'MD 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='kcal/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' : 'MD 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, @@ -759,13 +759,13 @@ 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' : 'MD Step'}], valtype='int', lookupdict=self.mddataDict ), 'frame_sequence_pressure_stats' : MetaInfoMap(startpage), - 'frame_sequence_pressure' : MetaInfoMap(startpage, + 'xxx_instant_pressure' : MetaInfoMap(startpage, depends=[{'store' : 'Pres'}], valtype='float', unitdict=self.unitDict, @@ -784,13 +784,13 @@ 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' : 'MD Step'}], valtype='int', lookupdict=self.mddataDict ), 'frame_sequence_temperature_stats' : MetaInfoMap(startpage), - 'frame_sequence_temperature' : MetaInfoMap(startpage, + 'xxx_instant_temperature' : MetaInfoMap(startpage, depends=[{'store' : 'Temp'}], valtype='float', unitdict=self.unitDict, @@ -1001,7 +1001,7 @@ 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"], @@ -1020,7 +1020,7 @@ 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' # ) # ) # ), @@ -1028,7 +1028,7 @@ 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' ) ) ), @@ -1036,7 +1036,7 @@ 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' ) ) ), @@ -1045,7 +1045,7 @@ 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' ) ) ), @@ -1054,7 +1054,7 @@ 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' ) ) ), @@ -1063,7 +1063,7 @@ 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' ) ) ), @@ -1188,7 +1188,7 @@ 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-tinker/TINKERParser.py b/parser/parser-tinker/TINKERParser.py index 70354e9f6e068919d29803ba42ea1751cfe032e2..28a3be69b57e2e0cb57c2b4b139e0a09a2b3fbc8 100644 --- a/parser/parser-tinker/TINKERParser.py +++ b/parser/parser-tinker/TINKERParser.py @@ -59,7 +59,7 @@ class TINKERParser(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__( @@ -268,8 +268,8 @@ class TINKERParser(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 @@ -905,16 +905,16 @@ class TINKERParser(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' : [ @@ -931,7 +931,7 @@ class TINKERParser(SmartParser.ParserBase): #if callable(pos_obj): if self.trajectory.forces is not None: # Forces in PDB/TINKER 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/TinkerParser.scala b/src/main/scala/eu/nomad_lab/parsers/TinkerParser.scala index aeeda762df6d131e5c8955b8a37e05f3cc28a15b..22ebffd1b60931f2b63cd45ade6145d7abb760ec 100644 --- a/src/main/scala/eu/nomad_lab/parsers/TinkerParser.scala +++ b/src/main/scala/eu/nomad_lab/parsers/TinkerParser.scala @@ -48,7 +48,7 @@ object TinkerParser extends SimpleExternalParserGenerator( "parser-tinker/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/tinker.nomadmetainfo.json" ) ++ DefaultPythonInterpreter.commonFiles(), dirMap = Map(