meta 2.0 changes, to fix

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),

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

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(