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Commit 2fc48b51 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
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added electronic_structure_method

parent c9aee2a0
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parser/parser-exciting/parser_exciting.py
View file @ 2fc48b51
......@@ -56,9 +56,9 @@ class ExcitingParserContext(object):
dirPath = os.path.dirname(self.parser.fIn.name)
dosFile = os.path.join(dirPath, "dos.xml")
bandFile = os.path.join(dirPath, "bandstructure.xml")
eigvalFile = os.path.join(dirPath, "EIGVAL.OUT")
fermiSurfFile = os.path.join(dirPath, "FERMISURF.bxsf")
inputFile = os.path.join(dirPath, "input.xml")
gwFile = os.path.join(dirPath, "GW_INFO.OUT")
############# reading input file for atom positions##############
if os.path.exists(inputFile):
with open(inputFile) as f:
......@@ -69,47 +69,10 @@ class ExcitingParserContext(object):
if os.path.exists(bandFile):
with open(bandFile) as g:
exciting_parser_bandstructure.parseBand(g, backend)
if os.path.exists(eigvalFile):
eigvalGIndex = backend.openSection("section_eigenvalues")
with open(eigvalFile) as g:
eigvalKpoint=[]
# eigvalVal=[[],[],[]]
# eigvalOcc=[[],[]]
eigvalVal=[]
eigvalOcc=[]
fromH = unit_conversion.convert_unit_function("hartree", "J")
while 1:
s = g.readline()
if not s: break
s = s.strip()
if len(s) < 20:
continue
elif len(s) > 50:
eigvalVal.append([])
eigvalOcc.append([])
# eigvalVal[1].append([])
# eigvalVal[2].append([])
# eigvalOcc[0].append([])
# eigvalOcc[1].append([])
eigvalKpoint.append([float(x) for x in s.split()[1:4]])
else:
try: int(s[0])
except ValueError:
continue
else:
n, e, occ = s.split()
eigvalVal[-1].append(fromH(float(e)))
eigvalOcc[-1].append(float(occ))
# eigvalVal[1][-1].append(int(n))
# eigvalVal[2][-1].append(fromH(float(e)))
# eigvalOcc[0][-1].append(int(n))
# eigvalOcc[1][-1].append(float(occ))
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)
# print ("values= ", eigvalVal)
# print ("kpoints= ", eigvalKpoint)
if os.path.exists(gwFile):
backend.addValue('electronic_structure_method', "G0W0")
else:
backend.addValue('electronic_structure_method', "DFT")
##########################Parsing Fermi surface##################
......@@ -205,8 +168,65 @@ class ExcitingParserContext(object):
# backend.addArrayValues("x_exciting_atom_forces",np.asarray(f_st))
def onClose_section_system(self, backend, gIndex, section):
# dirPath = os.path.dirname(self.parser.fIn.name)
dirPath = os.path.dirname(self.parser.fIn.name)
backend.addArrayValues('configuration_periodic_dimensions', np.asarray([True, True, True]))
# spin = section["x_exciting_spin_treatment"][0]
# print("spin=",spin, type(spin))
# print ("aqui?",spin[0])
# spinTreat = spin
# print("spinTreat=",spinTreat)
# spinTreat=spin[0].strip()
# print("rispin=",spin)
# if "unpolarised" in spin:
# number_of_spin_channels = 1
# else:
# number_of_spin_channels = 2
# print("number_of_spin_channels=",number_of_spin_channels)
# print("x_exciting_spin_treatment=",section["x_exciting_spin_treatment"])
eigvalFile = os.path.join(dirPath, "EIGVAL.OUT")
if os.path.exists(eigvalFile):
eigvalGIndex = backend.openSection("section_eigenvalues")
with open(eigvalFile) as g:
eigvalKpoint=[]
# eigvalVal=[[],[],[]]
# eigvalOcc=[[],[]]
eigvalVal=[]
eigvalOcc=[]
# print("x_exciting_spin_treatment=",section["x_exciting_spin_treatment"])
fromH = unit_conversion.convert_unit_function("hartree", "J")
while 1:
s = g.readline()
if not s: break
s = s.strip()
if len(s) < 20:
continue
elif len(s) > 50:
eigvalVal.append([])
eigvalOcc.append([])
# eigvalVal[1].append([])
# eigvalVal[2].append([])
# eigvalOcc[0].append([])
# eigvalOcc[1].append([])
eigvalKpoint.append([float(x) for x in s.split()[1:4]])
else:
try: int(s[0])
except ValueError:
continue
else:
n, e, occ = s.split()
eigvalVal[-1].append(fromH(float(e)))
eigvalOcc[-1].append(float(occ))
# eigvalVal[1][-1].append(int(n))
# eigvalVal[2][-1].append(fromH(float(e)))
# eigvalOcc[0][-1].append(int(n))
# eigvalOcc[1][-1].append(float(occ))
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)
# print ("values= ", eigvalVal)
# inputFile = os.path.join(dirPath, "input.xml")
############# reading input file ##############
# if os.path.exists(inputFile):
......@@ -232,6 +252,9 @@ class ExcitingParserContext(object):
self.atom_pos.append([pos[0][i], pos[1][i], pos[2][i]])
self.atom_labels = self.atom_labels + (section['x_exciting_geometry_atom_labels'] * natom)
# def onClose_section_run(self, backend, gIndex, section):
# print("x_exciting_spin_treatment_run=",section["x_exciting_spin_treatment"])
mainFileDescription = \
SM(name = "root matcher",
startReStr = "",
......@@ -273,6 +296,7 @@ mainFileDescription = \
]),
SM(r"\s*Total number of atoms per unit cell\s*:\s*(?P<x_exciting_number_of_atoms>[-0-9.]+)"),
SM(r"\s*Spin treatment\s*:\s*(?P<x_exciting_spin_treatment>[-a-zA-Z\s*]+)"),
# SM(r"\s*Spin treatment\s*:\s*(?P<x_exciting_spin_treatment>[-a-zA-Z+]\s*)"),
SM(r"\s*k-point grid\s*:\s*(?P<x_exciting_number_kpoint_x>[-0-9.]+)\s+(?P<x_exciting_number_kpoint_y>[-0-9.]+)\s+(?P<x_exciting_number_kpoint_z>[-0-9.]+)"),
SM(r"\s*k-point offset\s*:\s*(?P<x_exciting_kpoint_offset_x>[-0-9.]+)\s+(?P<x_exciting_kpoint_offset_y>[-0-9.]+)\s+(?P<x_exciting_kpoint_offset_z>[-0-9.]+)"),
SM(r"\s*Total number of k-points\s*:\s*(?P<x_exciting_number_kpoints>[-0-9.]+)"),
......
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