Reimplemented the fairdi integration.

phonopyparser/Get_Force_Constants.py

@@ -37,6 +37,7 @@ from phonopy.units import *
 from nomadcore.unit_conversion.unit_conversion import convert_unit_function
 from nomadcore.parser_backend import *
 from nomadcore.local_meta_info import loadJsonFile, InfoKindEl
+from phonopy.structure.atoms import PhonopyAtoms as Atoms
 
 phonopy_version = __version__
 parser_info = {"name": "parser_phonopy", "version": "1.0"}
@@ -49,24 +50,31 @@ metaInfoEnv, warnings = loadJsonFile(
     extraArgsHandling = InfoKindEl.ADD_EXTRA_ARGS, uri = None)
 
 
-from phonopy.structure.atoms import PhonopyAtoms as Atoms
+class PhonopyParserWrapper():
+    """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
+    def __init__(self, backend, **kwargs):
+        self.backend_factory = backend
+
+    def parse(self, mainfile):
+        logging.info('phonopy parser started')
+        logging.getLogger('nomadcore').setLevel(logging.WARNING)
+        backend = self.backend_factory(metaInfoEnv)
+        # Call the old parser without a class.
+        mainDir = os.path.dirname(os.path.dirname(os.path.abspath(mainfile)))
+        cwd = os.getcwd()
+        os.chdir(mainDir)
+        try:
+            return parse_without_class(mainfile, backend)
+        finally:
+            os.chdir(cwd)
+
 
-def parse_without_class(name, backend, parser_info):
-    """ Parsing method for phonopy.
-            Args:
-                name: file_name to parse
-                backend: Localbackend object
-                parser_info: information about parser to be saved.
-    """
-
-    # Settings that were previously defined in main().
-    dir_name = os.path.dirname(name)
-    geometry_file = os.path.join(dir_name, "geometry.in")
-    cell_obj = read_aims(geometry_file)
+def parse_without_class(name, backend):
+    cell_obj = read_aims("geometry.in")
     cell = cell_obj.get_cell()
     positions = cell_obj.get_positions()
     symbols = np.array(cell_obj.get_chemical_symbols())
-    control = Control(file = os.path.join(dir_name, "control.in"))
+    control = Control()
     if (len(control.phonon["supercell"]) == 3):
                     supercell_matrix = np.diag(control.phonon["supercell"])
     elif (len(control.phonon["supercell"]) == 9):
@@ -76,8 +84,7 @@ def parse_without_class(name, backend, parser_info):
     ####
 
     #### constructing FORCE_CONSTANTS
-    set_of_forces, phonopy_obj, Relative_Path = Collect_Forces_aims(
-        cell_obj, supercell_matrix, displacement, sym, dir_name)
+    set_of_forces, phonopy_obj, Relative_Path = Collect_Forces_aims(cell_obj, supercell_matrix, displacement, sym)
     Prep_Path = name.split("phonopy-FHI-aims-displacement-")
     Whole_Path = []
     for Path in Relative_Path:
@@ -104,10 +111,9 @@ def parse_without_class(name, backend, parser_info):
     positions = convert_angstrom(positions)
     displacement = convert_angstrom(displacement)
 
-    # Previously was the start of the parser.
+    #### parsing
     pbc = np.array((1, 1, 1), bool)
-    Parse = backend  # Previous dev. called backend Parse.
-    # Parse = JsonParseEventsWriterBackend(metaInfoEnv)
+    Parse = backend
     Parse.startedParsingSession(name, parser_info)
     sRun = Parse.openSection("section_run")
     Parse.addValue("program_name", "Phonopy")
@@ -144,26 +150,10 @@ def parse_without_class(name, backend, parser_info):
     Parse.closeSection("section_single_configuration_calculation", results)
     Parse.closeSection("section_run", sRun)
     Parse.finishedParsingSession("ParseSuccess", None)
-    return Parse  # Return the local backend to which we have been writing.
-
-
-class PhonopyParserWrapper():
-    """ A proper class envolop for running this parser using Noamd-FAIRD infra. """
-    def __init__(self, backend, **kwargs):
-        self.backend_factory = backend
-
-    def parse(self, mainfile):
-        logging.info('phonopy parser started')
-        logging.getLogger('nomadcore').setLevel(logging.WARNING)
-        backend = self.backend_factory(metaInfoEnv)
-        # Call the old parser without a class.
-        parserInfo = parser_info
-        backend = parse_without_class(mainfile, backend, parserInfo)
-        return backend
 
+    return backend
 
 
-#### determening properties of the undisplaced cell
 if __name__ == '__main__':
     import sys
 
@@ -180,47 +170,6 @@ if __name__ == '__main__':
         mainDir = os.path.dirname(os.path.dirname(os.path.abspath(args.mainFilePath)))
         os.chdir(mainDir)
     name = args.mainFileUri
-    cell_obj = read_aims("geometry.in")
-    cell = cell_obj.get_cell()
-    positions = cell_obj.get_positions()
-    symbols = np.array(cell_obj.get_chemical_symbols())
-    control = Control()
-    if (len(control.phonon["supercell"]) == 3):
-                    supercell_matrix = np.diag(control.phonon["supercell"])
-    elif (len(control.phonon["supercell"]) == 9):
-                    supercell_matrix = np.array(control.phonon["supercell"]).reshape(3,3)
-    displacement = control.phonon["displacement"]
-    sym = control.phonon["symmetry_thresh"]
-    ####
-
-    #### constructing FORCE_CONSTANTS
-    set_of_forces, phonopy_obj, Relative_Path = Collect_Forces_aims(cell_obj, supercell_matrix, displacement, sym)
-    Prep_Path = name.split("phonopy-FHI-aims-displacement-")
-    Whole_Path = []
-    for Path in Relative_Path:
-        Whole_Path.append("%s%s" % (Prep_Path[0], Path))
-    phonopy_obj.set_forces(set_of_forces)
-    phonopy_obj.produce_force_constants()
-    FC2 = phonopy_obj.get_force_constants()
-    ####
-
-    #### obtaining information about supercell
-    super_c=phonopy_obj.supercell
-    s_cell = super_c.get_cell()
-    super_pos = super_c.get_positions()
-    super_sym = np.array(super_c.get_chemical_symbols())
-    ####
-
-    #### Converting properties to Si unitis
-    converter_FC2 = convert_unit_function('eV*angstrom**-2', 'joules*meter**-2')
-    convert_angstrom = convert_unit_function('angstrom', 'meter')
-    FC2 = converter_FC2(FC2)
-    cell = convert_angstrom(cell)
-    s_cell = convert_angstrom(s_cell)
-    super_pos = convert_angstrom(super_pos)
-    positions = convert_angstrom(positions)
-    displacement = convert_angstrom(displacement)
-
-    #### parsing
-    parse(name)
+    backend = JsonParseEventsWriterBackend(metaInfoEnv)
 
+    parse_without_class(name, backend)

phonopyparser/PhononModulesNomad.py

@@ -114,7 +114,7 @@ def generate_kPath_ase(cell, symprec):
     return parameters
 ####
 
-def Collect_Forces_aims(cell_obj, supercell_matrix, displacement, sym, dir_name, tol = 1e-6):
+def Collect_Forces_aims(cell_obj, supercell_matrix, displacement, sym, tol = 1e-6):
         symmetry = Symmetry(cell_obj)
         phonopy_obj = Phonopy(cell_obj,
                                 supercell_matrix,
@@ -130,11 +130,8 @@ def Collect_Forces_aims(cell_obj, supercell_matrix, displacement, sym, dir_name,
         Relative_Path = []
         for directory, supercell in zip(directories, supercells):
                 aims_out = os.path.join(directory, directory + ".out")
-                # Added below line for NOMAD-FAIRD
-                aims_out = os.path.join(dir_name, aims_out)
                 if not os.path.isfile(aims_out):
                     logging.warn("!!! file not found: %s" % aims_out)
-                    os.chdir(os.path.join(dir_name, directory))
                     cwd = os.getcwd()
                     con_list = os.listdir(cwd)
                     check_var = False