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parser-namd
Commit b296580f authored by Mohamed, Fawzi Roberto (fawzi)'s avatar Mohamed, Fawzi Roberto (fawzi)
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meta 2.0 changes, to fix

parent d41015e7
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    Showing with 35 additions and 35 deletions
    parser/parser-namd/NAMDDictionary.py
    View file @ b296580f
    ......@@ -403,7 +403,7 @@ 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'},
    ......@@ -617,9 +617,9 @@ 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' : 'POTENTIAL'}],
    valtype='float',
    unitdict=self.unitDict,
    ......@@ -638,7 +638,7 @@ 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),
    ......@@ -661,14 +661,14 @@ 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' : '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']
    ),
    }
    ......@@ -676,13 +676,13 @@ 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,
    ......@@ -691,27 +691,27 @@ 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' : 'TS'}],
    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' : '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' : 'TS'}],
    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' : 'POTENTIAL'}],
    valtype='float',
    unitdict=self.unitDict,
    ......@@ -730,13 +730,13 @@ def get_updateDictionary(self, defname):
    unit='bar',
    lookupdict=self.mddataDict
    ),
    'frame_sequence_pressure_frames' : MetaInfoMap(startpage,
    'xxx_to_rm_frame_sequence_pressure_frames' : MetaInfoMap(startpage,
    depends=[{'store' : 'TS'}],
    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,
    ......@@ -755,13 +755,13 @@ 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' : 'TS'}],
    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,
    ......@@ -943,7 +943,7 @@ 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,
    value=self.minConverged
    ),
    ......@@ -956,7 +956,7 @@ 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'
    # )
    # )
    # ),
    ......@@ -964,7 +964,7 @@ 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'
    )
    )
    ),
    ......@@ -972,7 +972,7 @@ 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'
    )
    )
    ),
    ......@@ -981,7 +981,7 @@ 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'
    )
    )
    ),
    ......@@ -990,7 +990,7 @@ 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'
    )
    )
    ),
    ......@@ -999,7 +999,7 @@ 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'
    )
    )
    ),
    ......@@ -1144,7 +1144,7 @@ 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),
    ......
    parser/parser-namd/NAMDParser.py
    View file @ b296580f
    ......@@ -56,7 +56,7 @@ class NAMDParser(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__(
    ......@@ -214,8 +214,8 @@ class NAMDParser(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
    ......@@ -657,16 +657,16 @@ class NAMDParser(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' : [
    ......@@ -683,7 +683,7 @@ class NAMDParser(SmartParser.ParserBase):
    #if callable(pos_obj):
    if self.trajectory.forces is not None:
    # 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.atompositions.velocities, "kcal/(mol*Angstrom)", self.unitDict))))
    # need to transpose array since its shape is [number_of_atoms,3] in the metadata
    ......
    src/main/scala/eu/nomad_lab/parsers/NAMDParser.scala
    View file @ b296580f
    ......@@ -48,7 +48,7 @@ object NamdParser extends SimpleExternalParserGenerator(
    "parser-namd/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/namd.nomadmetainfo.json"
    ) ++ DefaultPythonInterpreter.commonFiles(),
    dirMap = Map(
    ......
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