Henrik's initial version of quasi harmonic parser

parser/parser-quasi-harmonic-properties/qhp.py

+import numpy as np
+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.units import EvTokJmol, Kb as kBoltzmann
+
+parser_info = {"name": "parser_quasi_harmonic_properties", "version": "1.0"}
+
+path = "../../../../nomad-meta-info/meta_info/nomad_meta_info/quasi-harmonic-properties.nomadmetainfo.json"
+metaInfoPath = os.path.normpath(
+    os.path.join(os.path.dirname(os.path.abspath(__file__)), path))
+metaInfoEnv, warns = loadJsonFile(filePath=metaInfoPath,
+                                  dependencyLoader=None,
+                                  extraArgsHandling=InfoKindEl.ADD_EXTRA_ARGS,
+                                  uri=None)
+
+def parse(name):
+    Parse = JsonParseEventsWriterBackend(metaInfoEnv)
+    Parse.startedParsingSession(name, parser_info)
+    sRun = Parse.openSection("section_run")
+    system = Parse.openSection("section_system")
+    Parse.addValue("spacegroup_3D_number", spacegroup)
+    springermat = Parse.openSection("section_springer_material")
+    Parse.addValue("springer_formula", material)
+    Parse.closeSection("section_springer_material", springermat)
+    Parse.closeSection("section_system", system)
+    results = Parse.openSection("section_single_configuration_calculation")
+    sTD = Parse.openSection("section_thermodynamical_properties")
+    fref = Parse.openSection("section_calculation_to_folder_refs")
+    Parse.addValue("calculation_to_folder_kind", "folder_containing_calculations")
+    Parse.addValue("calculation_to_folder_external_url", name)
+    Parse.closeSection("section_calculation_to_folder_refs", fref)
+    Parse.addArrayValues("thermodynamical_property_temperature", T)
+    Parse.addArrayValues("thermodynamical_property_heat_capacity_C_v", cV)
+    Parse.addArrayValues("x_qhp_quasi_harmonic_free_energy", Free)
+    Parse.addArrayValues("x_qhp_quasi_harmonic_bulk_modulus", B)
+    Parse.addArrayValues("x_qhp_quasi_harmonic_volume", V)
+    Parse.addArrayValues("x_qhp_quasi_harmonic_thermal_expansion", alpha)
+    Parse.closeSection("section_thermodynamical_properties", sTD)
+    Parse.closeSection("section_single_configuration_calculation", results)
+    Parse.closeSection("section_run", sRun)
+    Parse.finishedParsingSession("ParseSuccess", None)
+
+if __name__ == '__main__':
+    import sys
+    parser = argparse.ArgumentParser(description='Parses a txt file containing quasi harmonic data.')
+    parser.add_argument('mainFileUri',
+                        help='The uri of the main file associated with this calculation.')
+    parser.add_argument('mainFilePath', default = None,
+                        help='The path to the main file associated with this calculation.')
+
+    args = parser.parse_args()
+    if args.mainFilePath:
+        mainDir = os.path.dirname(os.path.dirname(os.path.abspath(args.mainFilePath)))
+        os.chdir(mainDir)
+    with open("Quasiharmonic_properties.txt") as qh:
+        for line in qh:
+            if "Quasi-harmonic" in line:
+                spacegroup = line.split()[-1]
+                material = line.split()[-3]
+    name = args.mainFileUri
+    T, V, alpha, B, Free, cV = np.loadtxt("Quasiharmonic_properties.txt")
+    cV = kBoltzmann / JmolToEv * cV
+    cubAtocubm = convert_unit_function('a**3', 'm**3')
+    eVpercubAtoJoulespercubm = convert_unit_function('eV*a**-3', 'joules*m**-3')
+    eVtoJoules = convert_unit_function('eV', 'joules')
+    eVperKtoJoules = convert_unit_function('eV*K**-1', 'joules*K**-1')
+    Free = eVtoJoules(Free)     
+    V = cubAtocubm(V)
+    B = eVpercubAtoJoulespercubm(B)
+    cV = eVperKtoJoules(cV)
+    parse(name)