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Commit c747ca46 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
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Spin-polarized eigenvalues

parent 94986cef
Pipeline #9241 passed with stage
in 15 minutes and 39 seconds
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parser/parser-elk/parser_elk.py
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......@@ -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))
backend.addArrayValues("eigenvalues_kpoints", np.asarray(eigvalKpoint))
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.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<x_elk_valence_charge_scf_iteration>[-0-9.]+)"),
SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_scf_iteration>[-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<x_elk_fermi_energy__hartree>[-0-9.]+)"),
# SM(r"\s*sum of eigenvalues\s*:\s*(?P<energy_sum_eigenvalues__hartree>[-0-9.]+)"),
# SM(r"\s*electron kinetic\s*:\s*(?P<electronic_kinetic_energy__hartree>[-0-9.]+)"),
# SM(r"\s*core electron kinetic\s*:\s*(?P<x_elk_core_electron_kinetic_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Coulomb\s*:\s*(?P<x_elk_coulomb_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Coulomb potential\s*:\s*(?P<x_elk_coulomb_potential_energy__hartree>[-0-9.]+)"),
# SM(r"\s*nuclear-nuclear\s*:\s*(?P<x_elk_nuclear_nuclear_energy__hartree>[-0-9.]+)"),
# SM(r"\s*electron-nuclear\s*:\s*(?P<x_elk_electron_nuclear_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Hartree\s*:\s*(?P<x_elk_hartree_energy__hartree>[-0-9.]+)"),
# SM(r"\s*Madelung\s*:\s*(?P<x_elk_madelung_energy__hartree>[-0-9.]+)"),
# SM(r"\s*xc potential\s*:\s*(?P<energy_XC_potential__hartree>[-0-9.]+)"),
# SM(r"\s*exchange\s*:\s*(?P<x_elk_exchange_energy__hartree>[-0-9.]+)"),
# SM(r"\s*correlation\s*:\s*(?P<x_elk_correlation_energy__hartree>[-0-9.]+)"),
# SM(r"\s*electron entropic\s*:\s*(?P<x_elk_electron_entropic_energy__hartree>[-0-9.]+)"),
# SM(r"\s*total energy\s*:\s*(?P<energy_total__hartree>[-0-9.]+)"),
# SM(r"\s*Density of states at Fermi energy\s*:\s*(?P<x_elk_dos_fermi__hartree_1>[-0-9.]+)"),
# SM(r"\s*Estimated indirect band gap\s*:\s*(?P<x_elk_indirect_gap__hartree>[-0-9.]+)"),
# SM(r"\s*Estimated direct band gap\s*:\s*(?P<x_elk_direct_gap__hartree>[-0-9.]+)"),
# SM(r"\s*core\s*:\s*(?P<x_elk_core_charge_final>[-0-9.]+)"),
# SM(r"\s*valence\s*:\s*(?P<x_elk_valence_charge_final>[-0-9.]+)"),
# SM(r"\s*interstitial\s*:\s*(?P<x_elk_interstitial_charge_final>[-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)
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