meta 2.0 changes

parser/parser-phonopy/Get_Force_Constants.py

@@ -68,7 +68,7 @@ def parse(name):
     Parse.addArrayValues("atom_labels", super_sym)
     Parse.addArrayValues("atom_positions", super_pos)
     Parse.addArrayValues("simulation_cell", s_cell)
-    Parse.addArrayValues("SC_matrix", supercell_matrix)
+    Parse.addArrayValues("sc_matrix", supercell_matrix)
     Parse.addValue("x_phonopy_original_system_ref", Basesystem)
     Parse.closeSection("section_system", Supercellsystem)
     method = Parse.openSection("section_method")
@@ -77,7 +77,7 @@ def parse(name):
     Parse.closeSection("section_method", method)
     results = Parse.openSection("section_single_configuration_calculation")
     Parse.addValue("single_configuration_calculation_to_system_ref", Supercellsystem)
-    Parse.addValue("single_configuration_to_calculation_method_ref", method)
+    Parse.addValue("single_configuration_calculation_to_method_ref", method)
     Parse.addArrayValues("hessian_matrix", FC2)
     GP = Get_Properties(FC2, cell, positions, symbols, supercell_matrix, sym, displacement)
     GP.prem_emit(Parse, results)

parser/parser-phonopy/Get_Properties.py

@@ -49,7 +49,7 @@ if __name__ == "__main__":
     with open(name) as FORCES:
             data = json.load(FORCES)
     hessian= np.array(data["sections"]["section_single_configuration_calculation-0"]["hessian_matrix"])
-    SC_matrix = np.array(data["sections"]["section_system-1"]["SC_matrix"])
+    sc_matrix = np.array(data["sections"]["section_system-1"]["sc_matrix"])
     cell = np.array(data["sections"]["section_system-0"]["simulation_cell"])
     symbols = np.array(data["sections"]["section_system-0"]["atom_labels"])
     positions = np.array(data["sections"]["section_system-0"]["atom_positions"])
@@ -59,5 +59,5 @@ if __name__ == "__main__":
 
 
     #### omitting
-    get_properties = get_properties(hessian, cell, positions, symbols, SC_matrix, symmetry_thresh, displacement, file_name, metaInfoEnv, parser_info)
+    get_properties = get_properties(hessian, cell, positions, symbols, sc_matrix, symmetry_thresh, displacement, file_name, metaInfoEnv, parser_info)
     get_properties.omit_properties()

parser/parser-phonopy/PhononModulesNomad.py

@@ -183,7 +183,7 @@ class Get_Properties():
                 cell = None, 
                 positions = None, 
                 symbols = None, 
-                SC_matrix = None, 
+                sc_matrix = None, 
                 symmetry_thresh = None, 
                 displacement = None, 
                 name = None, 
@@ -203,7 +203,7 @@ class Get_Properties():
         #### Constructing phonopy_obj
         cell_obj = Atoms(cell = list(cell), symbols= list(symbols), positions= list(positions))
         scaled_positions = cell_obj.get_scaled_positions()
-        phonopy_obj = Phonopy(cell_obj, SC_matrix, distance = displacement, symprec = symmetry_thresh)
+        phonopy_obj = Phonopy(cell_obj, sc_matrix, distance = displacement, symprec = symmetry_thresh)
         phonopy_obj.set_force_constants(hessian)
         ####
 
@@ -390,15 +390,15 @@ class Get_Properties():
         
         #### emitting
         frameSeq = Emit.openSection("section_frame_sequence")
-        Emit.addArrayValues("frame_sequence_local_frames_ref", np.array([sSingleConf]))
+        Emit.addArrayValues("frame_sequence_to_frames_ref", np.array([sSingleConf]))
         sTD = Emit.openSection("section_thermodynamical_properties")
         Emit.addArrayValues("thermodynamical_property_temperature", T)
         Emit.addArrayValues("vibrational_free_energy_at_constant_volume", fe)
-        Emit.addArrayValues("thermodynamical_property_heat_capacity_C_v", cv)
+        Emit.addArrayValues("thermodynamical_property_heat_capacity_c_v", cv)
         sSamplingM = Emit.openSection("section_sampling_method")
         Emit.addValue("sampling_method", "taylor_expansion")
         Emit.addValue("sampling_method_expansion_order", 2)
-        Emit.addValue("frame_sequence_to_sampling_ref", sSamplingM)
+        Emit.addValue("frame_sequence_to_sampling_method_ref", sSamplingM)
         Emit.closeSection("section_thermodynamical_properties", sTD)
         Emit.closeSection("section_sampling_method", sSamplingM)
         Emit.closeSection("section_frame_sequence",frameSeq)

src/main/scala/eu/nomad_lab/parsers/PhonopyParser.scala

@@ -46,7 +46,7 @@ object PhonopyParser extends SimpleExternalParserGenerator(
     "parser-phonopy/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/phonopy.nomadmetainfo.json"
   ) ++ lab.DefaultPythonInterpreter.commonFiles(),
   dirMap = Map(