parse atomic positions, total energies, orbital occupancies, atomic charges,...

parse atomic positions, total energies, orbital occupancies, atomic charges, forces and eigenvalues in file detailed.out for molecules/clusters

parser/parser-dftb+/parser_dftb+.py

 import setup_paths
-from nomadcore.simple_parser import SimpleMatcher, mainFunction
+from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
 import os, sys, json
 
 # description of the input
-mainFileDescription = SimpleMatcher(name = 'root',
+mainFileDescription = SM(
+    name = 'root',
     weak = True,
+    forwardMatch = True,
     startReStr = "",
     subMatchers = [
-  SimpleMatcher(name = 'newRun',
-                startReStr = r"\s*# SampleParser #\s*",
-                repeats = True,
+        SM(name = 'newRun',
+           startReStr = r"\s*Fermi distribution function",
+           #repeats = True,
            required = True,
            forwardMatch = True,
            sections   = ['section_run'],
            subMatchers = [
-    SimpleMatcher(name = 'header',
-                  startReStr = r"\s*# SampleParser #\s*")
+               SM(name = 'header',
+                  startReStr = r"\s*Fermi distribution function",
+                  #forwardMatch = True,
+                  #subMatchers=[ ]
+             ),
+               SM(name = 'coordinates',
+                  startReStr = r"\s*Coordinates of moved atoms\s*\(?(au)?\)?:",
+                  #forwardMatch = True,
+                  sections   = ['section_system','section_molecule_type'],
+                  subMatchers = [
+                      SM(r"\s*Coordinates of moved atoms\s*\(?(au)?\)?:"),
+                      SM(r"\s*(?P<atom>\d+)\s*(?P<x_dftbp_atom_positions_X>[+-]?\d+\.\d+)\s*(?P<x_dftbp_atom_positions_Y>[+-]?\d+\.\d+)\s*(?P<x_dftbp_atom_positions_Z>[+-]?\d+\.\d+)\s*", repeats = True),
+                 ],
+             ),
+               SM(name = 'charges',
+                  startReStr = r"\s*Net atomic charges .e.",
+                  #endReStr = r"\s*",
+                  #forwardMatch = True,
+                  sections   = ['section_molecule_type'],
+                  subMatchers = [
+                      SM(r"\s*Atom\s*Net charge"),
+                      SM(r"\s*(?P<atom>\d+)\s*(?P<atom_in_molecule_charge>[+-]?\d+\.\d+)\s*", repeats = True),
+                                 #SM(r"\s*")
+                  ],
+             ),
+               SM(name = 'eigenvalues_H',
+                  startReStr = r"\s*Eigenvalues /H",
+                  #forwardMatch = True,
+                  sections   = ['section_eigenvalues'],
+                  subMatchers = [
+                      SM(r"\s*Eigenvalues /H"),
+                      SM(r"\s*(?P<eigenvalues_values__hartree>[+-]?\d+\.\d+)\s*", repeats = True),
+                  ],
+             ),
+                 SM(name = 'eigenvalues_eV',
+                    startReStr = r"\s*Eigenvalues /eV",
+                    #forwardMatch = True,
+                    sections   = ['section_eigenvalues'],
+                    subMatchers = [
+                        SM(r"\s*Eigenvalues /eV"),
+                        SM(r"\s*(?P<eigenvalues_values>[+-]?\d+\.\d+)\s*", repeats = True),
+                  ],
+             ),
+                  SM(name = 'Occupations',
+                     startReStr = r"\s*Fillings",
+                     #forwardMatch = True,
+                     sections   = ['section_eigenvalues'],
+                     subMatchers = [
+                        SM(r"\s*Fillings"),
+                        SM(r"\s*(?P<eigenvalues_occupation>\d+\.\d+)\s*", repeats = True),
+                  ],
+             ),
+               SM(name = 'energies',
+                  startReStr = r"\s*Fermi energy:.*",
+                  sections   = ['section_single_configuration_calculation'],
+                  subMatchers = [
+                     SM(r"\s*Fermi energy:.*"),
+                     #SM(r"\s*Band energy:.*"),
+                     SM(r"\s*Total energy:\s*(?P<energy_total__hartree>[+-]?\d+\.\d+)\s*H.*"),
+                     SM(r"\s*Total Mermin free energy:\s*(?P<energy_free__hartree>[+-]?\d+\.\d+)\s*H.*"),
+                   ],
+                  #forwardMatch = True,
+                  #required = True,
+             ),
+               SM(name = 'forces',
+                  startReStr = r"\s*Total Forces",
+                  sections   = ['section_single_configuration_calculation'],
+                  subMatchers = [
+                     SM(r"\s*Total Forces*"),
+                     SM(r"\s*(?P<x_dftbp_atom_forces_X>[+-]?\d+\.\d+E?[+-]?\d+)\s*(?P<x_dftbp_atom_forces_Y>[+-]?\d+\.\d+E?[+-]?\d+)\s*(?P<x_dftbp_atom_forces_Z>[+-]?\d+\.\d+E?[+-]?\d+)\s*", repeats = True),
+                     SM(r"\s*Maximal force component:\s*(?P<x_dftbp_force_max>[+-]?\d+\.\d+E?[+-]?\d+)\s*"),
+                     SM(r"\s*Max force for moved atoms::\s*(?P<x_dftbp_force_max>[+-]?\d+\.\d+E?[+-]?\d+)\s*(au)?"),
+                   ],
+
+             ),
            ])
         ])
 
-# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/fhi_aims.nomadmetainfo.json
+# loading metadata from nomad-meta-info/meta_info/nomad_meta_info/dftb-plus.nomadmetainfo.json
 
 parserInfo = {
-  "name": "sample_parser",
+  "name": "parser_dftb+",
   "version": "1.0"
 }
 
-metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/sample_parser.nomadmetainfo.json"))
+metaInfoPath = os.path.normpath(os.path.join(os.path.dirname(os.path.abspath(__file__)),"../../../../nomad-meta-info/meta_info/nomad_meta_info/dftb-plus.nomadmetainfo.json"))
 metaInfoEnv, warnings = loadJsonFile(filePath = metaInfoPath, dependencyLoader = None, extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
 
 if __name__ == "__main__":