diff --git a/parser/parser-elk/parser_elk.py b/parser/parser-elk/parser_elk.py index 5c0e8f71e04067fe0010b06fc7a299e74f9a5a9e..fddfbd98602fdfed3f5d2b91ce5a578da766de38 100644 --- a/parser/parser-elk/parser_elk.py +++ b/parser/parser-elk/parser_elk.py @@ -5,29 +5,16 @@ from nomadcore.simple_parser import SimpleMatcher as SM, mainFunction from nomadcore.local_meta_info import loadJsonFile, InfoKindEl from nomadcore.caching_backend import CachingLevel from nomadcore.unit_conversion import unit_conversion -#from nomadcore.simple_parser import mainFunction, AncillaryParser, CachingLevel -#from nomadcore.simple_parser import SimpleMatcher as SM -#from nomadcore.local_meta_info import loadJsonFile, InfoKindEl -#from nomadcore.unit_conversion import unit_conversion import os, sys, json, logging class ElkContext(object): """context for elk parser""" -# def __init__(self): -# self.parser = None - -# def initialize_values(self): -# """allows to reset values if the same superContext is used to parse different files""" -# self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv - def startedParsing(self, path, parser): """called when parsing starts""" self.parser = parser - # allows to reset values if the same superContext is used to parse different files -# self.initialize_values() - self.secMethodIndex = None #LOLLO - self.secSystemIndex = None #LOLLO + self.secMethodIndex = None + self.secSystemIndex = None self.enTot = [] self.atom_pos = [] self.atom_labels = [] @@ -43,11 +30,9 @@ class ElkContext(object): latticeX = section["x_elk_geometry_lattice_vector_x"] latticeY = section["x_elk_geometry_lattice_vector_y"] latticeZ = section["x_elk_geometry_lattice_vector_z"] -# print("latticeZ=",latticeZ) cell = [[latticeX[0],latticeY[0],latticeZ[0]], [latticeX[1],latticeY[1],latticeZ[1]], [latticeX[2],latticeY[2],latticeZ[2]]] -# print ("celll= ", latticeZ) backend.addValue("simulation_cell", cell) def onClose_x_elk_section_reciprocal_lattice_vectors(self, backend, gIndex, section): @@ -107,12 +92,19 @@ class ElkContext(object): eigvalKpoint=[] eigvalVal=[] eigvalOcc=[] + eigvalValSpin = [[],[]] + eigvalOccSpin = [[],[]] fromH = unit_conversion.convert_unit_function("hartree", "J") while 1: s = g.readline() if not s: break s = s.strip() if len(s) < 20: + if "nstsv" in s.split(): + nstsv = int(s.split()[0]) + nstsv2=int(nstsv/2) + elif "nkpt" in s.split(): + nkpt = int(s.split()[0]) continue elif len(s) > 50: eigvalVal.append([]) @@ -126,41 +118,36 @@ class ElkContext(object): n, e, occ = s.split() eigvalVal[-1].append(fromH(float(e))) eigvalOcc[-1].append(float(occ)) + if not self.spinTreat: + backend.addArrayValues("eigenvalues_values", np.asarray([eigvalVal])) + backend.addArrayValues("eigenvalues_occupation", np.asarray([eigvalOcc])) + else: + for i in range(0,nkpt): + eigvalValSpin[0].append(eigvalVal[i][0:nstsv2]) + eigvalOccSpin[0].append(eigvalOcc[i][0:nstsv2]) + eigvalValSpin[1].append(eigvalVal[i][nstsv2:nstsv]) + eigvalOccSpin[1].append(eigvalOcc[i][nstsv2:nstsv]) + backend.addArrayValues("eigenvalues_values", np.asarray(eigvalValSpin)) + backend.addArrayValues("eigenvalues_occupation", np.asarray(eigvalOccSpin)) backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint)) - backend.addArrayValues("eigenvalues_values", np.asarray([eigvalVal])) - backend.addArrayValues("eigenvalues_occupation", np.asarray([eigvalOcc])) backend.closeSection("section_eigenvalues",eigvalGIndex) - +# backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint)) +# backend.addArrayValues("eigenvalues_values", np.asarray([eigvalVal])) +# backend.addArrayValues("eigenvalues_occupation", np.asarray([eigvalOcc])) +# backend.closeSection("section_eigenvalues",eigvalGIndex) backend.addValue("energy_total", self.enTot[-1]) def onClose_x_elk_section_spin(self, backend, gIndex, section): -# pass spin = section["x_elk_spin_treatment"][0] -# print("prima",len(spin)) spin = spin.strip() -# print("dopo",len(spin)) -# print("spin=",spin,"spin", type(spin)) if spin == "spin-polarised": -# print("Vero") self.spinTreat = True else: -# print("Falso") self.spinTreat = False def onClose_section_system(self, backend, gIndex, section): backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True])) self.secSystemDescriptionIndex = gIndex - -# atom_pos = [] -# for i in ['x', 'y', 'z']: -# api = section['x_elk_geometry_atom_positions_' + i] -# if api is not None: -# atom_pos.append(api) -# if atom_pos: -# backend.addArrayValues('atom_positions', np.transpose(np.asarray(atom_pos))) -# atom_labels = section['x_elk_geometry_atom_labels'] -# if atom_labels is not None: -# backend.addArrayValues('atom_labels', np.asarray(atom_labels)) self.secSystemDescriptionIndex = gIndex if self.atom_pos: @@ -169,7 +156,6 @@ class ElkContext(object): if self.atom_labels is not None: backend.addArrayValues('atom_labels', np.asarray(self.atom_labels)) self.atom_labels = [] -# print("self.atom_labels=",self.atom_labels) def onClose_x_elk_section_atoms_group(self, backend, gIndex, section): pos = [section['x_elk_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']] pl = [len(comp) for comp in pos] @@ -286,32 +272,6 @@ mainFileDescription = \ SM(r"\s*valence\s*:\s*(?P[-0-9.]+)"), SM(r"\s*interstitial\s*:\s*(?P[-0-9.]+)"), ]) #, -# SM(name="final_quantities", -# startReStr = r"\sConvergence targets achieved\s*\+", -# endReStr = r"\| Self-consistent loop stopped\s*\|\+", -# subMatchers = [ -# SM(r"\s*Fermi\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*sum of eigenvalues\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*electron kinetic\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*core electron kinetic\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*Coulomb\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*Coulomb potential\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*nuclear-nuclear\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*electron-nuclear\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*Hartree\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*Madelung\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*xc potential\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*exchange\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*correlation\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*electron entropic\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*total energy\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*Density of states at Fermi energy\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*Estimated indirect band gap\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*Estimated direct band gap\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*core\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*valence\s*:\s*(?P[-0-9.]+)"), -# SM(r"\s*interstitial\s*:\s*(?P[-0-9.]+)") -# ]) ] ) ]) @@ -336,6 +296,4 @@ cachingLevelForMetaName = { } if __name__ == "__main__": -# superContext = ElkContext() mainFunction(mainFileDescription, metaInfoEnv, parserInfo, cachingLevelForMetaName = cachingLevelForMetaName, superContext=ElkContext()) -# mainFunction(mainFileDescription, metaInfoEnv, parserInfo, superContext = superContext)