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Commit a65c9a08 authored by Pardini, Lorenzo (lopa)'s avatar Pardini, Lorenzo (lopa)
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fixed GW parser

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parser/parser-exciting/exciting_parser_bandstructure.py
+ 1
− 1
View file @ a65c9a08
......@@ -41,7 +41,7 @@ class BandHandler(xml.sax.handler.ContentHandler):
elif name == "vertex" and self.inBand:
self.vertexCoord.append(attrs.getValue("coord"))
label = attrs.getValue("label")
if label == "Gamma":
if (label == "Gamma") or (label == "Gamma"):
self.vertexLabels.append('\u0393')
else:
self.vertexLabels.append(label)
......
parser/parser-exciting/exciting_parser_gw.py
+ 38
− 126
View file @ a65c9a08
......@@ -32,7 +32,7 @@ class GWContext(object):
self.parser = parser
self.initialize_values()
def onClose_x_exciting_section_GW_method(self, backend, gIndex, section):
def onClose_x_exciting_section_GW(self, backend, gIndex, section):
dirPath = os.path.dirname(self.parser.fIn.name)
if os.access(os.path.join(dirPath, "EVALQP.DAT"), os.F_OK):
......@@ -41,14 +41,39 @@ class GWContext(object):
eigvalGWFile = os.path.join(dirPath, "EVALQP.TXT")
else:
pass
# eigvalGWFile = os.path.join(dirPath, "EVALQP.DAT")
dosGWFile = os.path.join(dirPath, "TDOS-QP.OUT")
bandCarbGWFile = os.path.join(dirPath, "bandstructure-qp.dat")
bandBorGWFile = os.path.join(dirPath, "BAND-QP.OUT")
# bandGWFile = os.path.join(dirPath, "bandstructure-qp.dat")
vertexGWFile = os.path.join(dirPath, "BANDLINES.OUT")
vertexLabGWFile = os.path.join(dirPath, "bandstructure.xml")
selfCorGWFile = os.path.join(dirPath, "SELFC.DAT")
inputFile = os.path.join(dirPath, "input.xml")
if os.path.exists(inputFile):
selfGWSetGIndex = backend.openSection("x_exciting_section_GW_settings")
singularity = 'mpd'
actype = 'pade'
npol = 0
scrtype = "rpa"
with open(inputFile) as g:
while 1:
s = g.readline()
if not s: break
s = s.strip()
s = s.split('=')
if s[0] == "singularity":
freq_conv = s[1][1:-1]
if s[0] == "actype":
actype = s[1][1:-1]
if s[0] == "npol":
npol = s[1][1:-1]
if s[0] == "scrtype":
scrtype = s[1][1:-1]
backend.addValue("x_exciting_GW_self_energy_singularity_treatment", singularity)
backend.addValue("x_exciting_GW_self_energy_c_analytical_continuation", actype)
backend.addValue("x_exciting_GW_self_energy_c_number_of_poles", npol)
backend.addValue("x_exciting_GW_screened_Coulomb", scrtype)
backend.closeSection("x_exciting_section_GW_settings",selfGWSetGIndex)
if os.path.exists(vertexGWFile):
with open(vertexGWFile) as g:
......@@ -62,9 +87,7 @@ class GWContext(object):
self.vertexDist.append(float(s[0]))
elif float(s[0]) != self.vertexDist[-1]:
self.vertexDist.append(float(s[0]))
# print("vertexDist",self.vertexDist)
self.vertexNum = len(self.vertexDist)-1
# print("vertexNum",self.vertexNum)
if os.path.exists(vertexLabGWFile):
with open(vertexLabGWFile) as g:
......@@ -77,22 +100,10 @@ class GWContext(object):
f = s[4].split("\"")
self.vertexLabels.append(f[1])
if os.path.exists(selfCorGWFile):
selfGWGIndex = backend.openSection("x_exciting_section_GW_self_energy")
with open(selfCorGWFile) as g:
while 1:
s = g.readline()
if not s: break
s = s.strip()
backend.closeSection("x_exciting_section_GW_self_energy",selfGWGIndex)
if os.path.exists(eigvalGWFile):
eigvalGWOutGIndex = backend.openSection("x_exciting_section_GW_output")
eigvalGWGIndex = backend.openSection("x_exciting_section_GW_qp_eigenvalues")
with open(eigvalGWFile) as g:
# print("ggggggggggg=",g)
qpGWKpoint=[]
Sx = [[],[]]
Sc = [[],[]]
......@@ -110,7 +121,6 @@ class GWContext(object):
Sc[i].append([])
qpE[i].append([])
Znk[i].append([])
# x,y,z,weight = float(s.split()[3]),float(s.split()[4]),float(s.split()[5]),float(s.split()[6])
x,y,z = float(s.split()[3]),float(s.split()[4]),float(s.split()[5])
qpGWKpoint[-1].append(x)
qpGWKpoint[-1].append(y)
......@@ -142,10 +152,11 @@ class GWContext(object):
backend.addValue("x_exciting_GW_self_energy_x", Sx)
backend.addValue("x_exciting_GW_self_energy_c", Sc)
backend.closeSection("x_exciting_section_GW_self_energy",selfGWGIndex)
backend.closeSection("x_exciting_section_GW_output",eigvalGWOutGIndex)
####################DOS######################
if os.path.exists(dosGWFile):
dosGWOutGIndex = backend.openSection("x_exciting_section_GW_output")
dosGWGIndex = backend.openSection("x_exciting_section_GW_dos")
fromH = unit_conversion.convert_unit_function("hartree", "J")
with open(dosGWFile) as g:
......@@ -157,7 +168,6 @@ class GWContext(object):
s = s.strip()
s = s.split()
ene, value = fromH(float(s[0])), float(s[1])
# ene, value = float(s[0]), float(s[1])
dosEnergies.append(ene)
if not self.spinTreat:
for i in range(0,2):
......@@ -168,12 +178,12 @@ class GWContext(object):
backend.addValue("x_exciting_GW_dos_values", dosValues)
backend.addValue("x_exciting_GW_number_of_dos_values", len(dosEnergies))
backend.closeSection("x_exciting_section_GW_dos",dosGWGIndex)
backend.closeSection("x_exciting_section_GW_output",dosGWOutGIndex)
##################BANDSTRUCTURE#####################
if os.path.exists(bandCarbGWFile):
bandGWOutGIndex = backend.openSection("x_exciting_section_GW_output")
bandGWGIndex = backend.openSection("x_exciting_section_GW_k_band")
# bandGWSegmGIndex = backend.openSection("x_exciting_section_GW_k_band_segment")
fromH = unit_conversion.convert_unit_function("hartree", "J")
with open(bandCarbGWFile) as g:
......@@ -201,7 +211,6 @@ class GWContext(object):
numK = int(s[3])
elif len(s) > 0:
for i in range(0,2):
# ene = fromH(float(s[6]))
bandEnergies[i][-1].append(fromH(float(s[6])))
if int(s[0]) == 1:
kpoint.append([])
......@@ -213,48 +222,21 @@ class GWContext(object):
for i in range(0,2):
bandEnergies[i].pop()
# print("numBand=",numBand)
# print("numK=",numK)
for i in range(1,numK):
# print("i=",i)
# print("dist[i-1]=",dist[i-1])
# print("dist[i]=",dist[i])
if dist[i] == dist[i-1]:
# pass
Kindex.append(i)
Kindex.append(numK)
# del dist[i]
for i in range(0,len(Kindex)-1):
segmK.append(dist[Kindex[i]:Kindex[i+1]])
for i in range(0,len(segmK)):
# print("i=",i)
# print("segmK[i]=",segmK[i])
segmLength.append(len(segmK[i]))
# bandEnergiesSegm.append([])
for i in range(0,2):
bandEnergiesSegm.append([])
for j in range(0,numBand):
bandEnergiesSegm[i].append([])
for k in range (0,len(Kindex)-1):
# print("l=",k)
# print("len(Kindex)=",len(Kindex))
# print("Kindex[l]=",Kindex[k])
# print("bandEnergies[Kindex[k]:Kindex[k+1]]=",bandEnergies[Kindex[k]:Kindex[k+1]])
bandEnergiesSegm[i][j].append(bandEnergies[i][j][Kindex[k]:Kindex[k+1]])
# print("i=",i)
# print("Kindex[i]=",Kindex[i])
# del dist[Kindex[i]]
# print("bandEnergies=",bandEnergies)
# print("self.vertexDist=",self.vertexDist)
# print("dist=",dist)
# print("len(dist)=",len(dist))
# print("segmK=",segmK)
# print("segmLength=",segmLength)
# print("bandEnergiesSegm=",bandEnergiesSegm)
# print("Kindex=",Kindex)
for i in range(0,len(Kindex)-1):
bandGWBE.append([])
for j in range(0,2):
......@@ -264,28 +246,21 @@ class GWContext(object):
for l in range(0,numBand):
bandGWBE[i][j][-1].append(bandEnergiesSegm[j][l][i][k])
# print("bandGWBE=",bandGWBE)
for i in range(0,len(Kindex)-1):
# print("i=",i)
# print("len(bandGWBE[i])=",len(bandGWBE[i][0]))
bandGWSegmGIndex = backend.openSection("x_exciting_section_GW_k_band_segment")
# print("bandGWBE[i]=",len(bandGWBE[i][0]))
backend.addValue("x_exciting_GW_band_energies", bandGWBE[i])
backend.closeSection("x_exciting_section_GW_k_band_segment",bandGWSegmGIndex)
backend.closeSection("x_exciting_section_GW_k_band",bandGWGIndex)
# backend.closeSection("x_exciting_section_GW_k_band_segment",bandGWSegmGIndex)
backend.closeSection("x_exciting_section_GW_output",bandGWOutGIndex)
if os.path.exists(bandBorGWFile) and not os.path.exists(bandCarbGWFile):
# print("QUI???")
bandGWOutGIndex = backend.openSection("x_exciting_section_GW_output")
bandGWGIndex = backend.openSection("x_exciting_section_GW_k_band")
# bandGWSegmGIndex = backend.openSection("x_exciting_section_GW_k_band_segment")
fromH = unit_conversion.convert_unit_function("hartree", "J")
# fromH = 1.0
with open(bandBorGWFile) as g:
bandEnergies = [[[]],[[]]]
kappa = [[[]],[[]]]
# kpoint = []
dist1 = [[]]
Kindex = [0]
segmK = []
......@@ -303,28 +278,12 @@ class GWContext(object):
bandEnergies[i].append([])
kappa[i].append([])
dist1.append([])
# print("bandEnergies[0]=",bandEnergies[0])
# if not dist1:
# elif s[0] == "#":
# for i in range(0,2):
# bandEnergies[i].append([])
# numBand = int(s[2])
# numK = int(s[3])
elif len(s) > 0:
for i in range(0,2):
# ene = fromH(float(s[6]))
bandEnergies[i][-1].append(fromH(float(s[1])))
kappa[i][-1].append(float(s[0]))
# bandEnergies[i][-1].append(fromH(float(s[1])))
# if int(s[0]) == 1:
# if not dist1:
# print("s[0]=",s[0])
# print("dist1=",dist1)
# kpoint.append([])
dist1[-1].append(float(s[0]))
# kpoint[-1].append([float(s[2]),float(s[3]),float(s[4])])
numK = len(kappa[0][0])
# print("numK=",numK)
for i in kappa[0][0]:
if kappa[0][0].count(i) > 1:
kappa[0][0].remove(i)
......@@ -333,54 +292,21 @@ class GWContext(object):
for i in range(0,2):
bandEnergies[i].pop()
numBand = len(bandEnergies[0])
# numK = len(kappa[0][0])
# print("kappa=",numK)
# print("bandnergies=",numBand)
# vertex = 0
for i in range(1,numK + self.vertexNum-1):
# print("i=",i)
# print("dist1[i-1]=",dist1[0][i-1])
# print("dist1[i]=",dist1[0][i])
if dist1[0][i] == dist1[0][i-1]:
# vertex +=1
# print("vertex=",vertex)
# pass
Kindex.append(i)
# print("vertex=",vertex)
Kindex.append(numK + self.vertexNum-1)
# del dist1[i]
for i in range(0,len(Kindex)-1):
segmK.append(dist1[0][Kindex[i]:Kindex[i+1]])
for i in range(0,len(segmK)):
# print("i=",i)
# print("segmK[i]=",segmK[i])
# print("len(segmK)=",len(segmK))
segmLength.append(len(segmK[i]))
# bandEnergiesSegm.append([])
for i in range(0,2):
bandEnergiesSegm.append([])
for j in range(0,numBand):
bandEnergiesSegm[i].append([])
for k in range (0,len(Kindex)-1):
# for k in range (0,len(Kindex)):
# print("l=",k)
# print("len(Kindex)=",len(Kindex))
# print("Kindex[l]=",Kindex[k])
# print("bandEnergies[Kindex[k]:Kindex[k+1]]=",bandEnergies[Kindex[k]:Kindex[k+1]])
bandEnergiesSegm[i][j].append(bandEnergies[i][j][Kindex[k]:Kindex[k+1]])
# print("i=",i)
# print("Kindex[i]=",Kindex[i])
# del dist1[Kindex[i]]
# print("bandEnergies=",bandEnergies)
# print("self.vertexDist=",self.vertexDist)
# print("dist1=",dist1)
# print("len(dist1)=",len(dist1))
# print("segmK=",segmK)
# print("segmLength=",segmLength)
# print("bandEnergiesSegm=",bandEnergiesSegm)
# print("Kindex=",Kindex)
for i in range(0,len(Kindex)-1):
bandGWBE.append([])
for j in range(0,2):
......@@ -390,38 +316,24 @@ class GWContext(object):
for l in range(0,numBand):
bandGWBE[i][j][-1].append(bandEnergiesSegm[j][l][i][k])
# print("bandGWBE=",bandGWBE)
for i in range(0,len(Kindex)-1):
bandGWSegmGIndex = backend.openSection("x_exciting_section_GW_k_band_segment")
# print("diomerda")
# print("bandGWBE[i]=",len(bandGWBE[i][0]))
backend.addValue("x_exciting_GW_band_energies", bandGWBE[i])
backend.closeSection("x_exciting_section_GW_k_band_segment",bandGWSegmGIndex)
backend.closeSection("x_exciting_section_GW_k_band",bandGWGIndex)
# backend.closeSection("x_exciting_section_GW_k_band_segment",bandGWSegmGIndex)
backend.closeSection("x_exciting_section_GW_output",bandGWOutGIndex)
def buildGWMatchers():
return SM(
name = 'root',
weak = True,
startReStr = "\*\s*GW input parameters\s*\*",
sections = ["x_exciting_section_GW", "x_exciting_section_GW_method"],
sections = ["x_exciting_section_GW","x_exciting_section_GW_settings"],
subMatchers = [
# SM(name = 'GWinput',
# startReStr = r"(?P<x_wien2k_system_nameIn>.*)"),
# startReStr = "\s*GW taskname:\s*"
SM(r"\s*(?P<x_exciting_GW_type>[-a-zA-Z0-9]+)\s*-\s*[-a-zA-Z0-9]+\s*run") #,
# SM(r"\s*(?P<x_exciting_GW_type>[-a-zA-Z0-9]+)\s*-\s*[-a-zA-Z0-9]+\s*run"),
# SM(r"\s*(?P<x_wien2k_in2c_switch>[A-Z]+)\s*.*"),
# SM(r"\s*(?P<x_wien2k_in2c_emin>[-+0-9.]+)\s*(?P<x_wien2k_in2c_ne>[-+0-9.]+)\s*(?P<x_wien2k_in2c_espermin>[-+0-9.]+)\s*(?P<x_wien2k_in2c_esper0>[-+0-9.]+)\s*.*"),
# SM(r"\s*(?P<x_wien2k_smearing_kind>[A-Z]+)\s*\s*(?P<x_wien2k_smearing_width__rydberg>[-+0-9.]+)\s*.*"),
# SM(r"\s*(?P<x_wien2k_in2c_gmax>[-+0-9.]+)\s*GMAX")
# SM(r"\s*GW taskname\:\s*")
SM(r"\s*Number of empty states \(GW\):\s*(?P<x_exciting_GW_polarizability_empty_states>[0-9]+)\s*")
])
def get_cachingLevelForMetaName(metaInfoEnv, CachingLvl):
"""Sets the caching level for the metadata.
......
parser/parser-exciting/parser_exciting.py
+ 14
− 94
View file @ a65c9a08
......@@ -6,20 +6,9 @@ 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
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_gw
import os, sys, json, exciting_parser_dos,exciting_parser_bandstructure, exciting_parser_gw #, exciting_parser_gw_bor
from ase import Atoms
#def elasticCheck(path):
# print("path=", path)
# pat = path.split("/")
# if pat[-1] == "INFO.OUT":
# print("NO", pat)
# else:
# print("YES", pat)
#
#elasticCheck(self.path)
# continue
class ExcitingParserContext(object):
def __init__(self):
......@@ -29,16 +18,6 @@ class ExcitingParserContext(object):
self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
def startedParsing(self, path, parser):
# print("path=", path)
# pat = path.split("/")
# print("pat=", pat)
# if pat[-1] == "INFO.OUT":
# pass
# else:
# pass
# self.initialize_values()
# self.metaInfoEnv = self.parser.parserBuilder.metaInfoEnv
# self.initialize_values()
self.parser=parser
self.initialize_values()
self.atom_pos = []
......@@ -56,20 +35,21 @@ class ExcitingParserContext(object):
def onOpen_section_method(self, backend, gIndex, section):
self.secMethodIndex = gIndex
# gwFile = os.path.join(dirPath,None)
mainFile = self.parser.fIn.fIn.name
dirPath = os.path.dirname(self.parser.fIn.name)
# gwFile = os.path.join(dirPath,"GW_INFO.OUT")
# gwFile = os.path.join(dirPath, "GW_INFO.OUT")
###
if os.access(os.path.join(dirPath, "GW_INFO.OUT"), os.F_OK):
gwFile = os.path.join(dirPath, "GW_INFO.OUT")
elif os.access(os.path.join(dirPath, "GWINFO.OUT"), os.F_OK):
gw_File = os.path.join(dirPath, "GW_INFO.OUT")
gwFile = os.path.join(dirPath, "GWINFO.OUT")
else:
gwFile = os.path.join(dirPath,"GW_INFO.OUT")
###
if os.path.exists(gwFile):
if os.path.exists(gw_File):
subSuperContext = exciting_parser_gw.GWContext()
subParser = AncillaryParser(
fileDescription = exciting_parser_gw.buildGWMatchers(),
parser = self.parser,
cachingLevelForMetaName = exciting_parser_gw.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
superContext = subSuperContext)
with open(gw_File) as fIn:
subParser.parseFile(fIn)
elif os.path.exists(gwFile):
subSuperContext = exciting_parser_gw.GWContext()
subParser = AncillaryParser(
fileDescription = exciting_parser_gw.buildGWMatchers(),
......@@ -87,7 +67,6 @@ class ExcitingParserContext(object):
[latticeX[1],latticeY[1],latticeZ[1]],
[latticeX[2],latticeY[2],latticeZ[2]]]
self.sim_cell = cell
# print("self.sim_cell=",self.sim_cell)
backend.addValue("simulation_cell", cell)
def onClose_x_exciting_section_reciprocal_lattice_vectors(self, backend, gIndex, section):
......@@ -126,14 +105,10 @@ class ExcitingParserContext(object):
dosFile = os.path.join(dirPath, "dos.xml")
bandFile = os.path.join(dirPath, "bandstructure.xml")
fermiSurfFile = os.path.join(dirPath, "FERMISURF.bxsf")
# inputFile = os.path.join(dirPath, "input.xml")
gw_File = os.path.join(dirPath, "GW_INFO.OUT")
gwFile = os.path.join(dirPath, "GWINFO.OUT")
eigvalFile = os.path.join(dirPath, "EIGVAL.OUT")
# if os.path.exists(inputFile):
# with open(inputFile) as f:
# exciting_parser_input.parseInput(f, backend)
if os.path.exists(dosFile):
with open(dosFile) as f:
exciting_parser_dos.parseDos(f, backend, self.spinTreat)
......@@ -141,9 +116,7 @@ class ExcitingParserContext(object):
with open(bandFile) as g:
exciting_parser_bandstructure.parseBand(g, backend, self.spinTreat)
if os.path.exists(gwFile) or os.path.exists(gw_File):
# with open(gwFile) as f:
backend.addValue('electronic_structure_method', "G0W0")
# exciting_parser_gw.parseGW(f, backend, self.spinTreat)
else:
backend.addValue('electronic_structure_method', "DFT")
if os.path.exists(eigvalFile):
......@@ -184,8 +157,6 @@ class ExcitingParserContext(object):
eigvalOccSpin[0].append(eigvalOcc[i][0:nstsv])
eigvalValSpin[1].append(eigvalVal[i][0:nstsv])
eigvalOccSpin[1].append(eigvalOcc[i][0:nstsv])
# backend.addArrayValues("eigenvalues_values", np.asarray(eigvalValSpin))
# backend.addArrayValues("eigenvalues_occupation", np.asarray(eigvalOccSpin))
backend.addValue("eigenvalues_values", eigvalValSpin)
backend.addValue("eigenvalues_occupation", eigvalOccSpin)
else:
......@@ -197,9 +168,6 @@ class ExcitingParserContext(object):
backend.addValue("eigenvalues_values", eigvalValSpin)
backend.addValue("eigenvalues_occupation", eigvalOccSpin)
backend.addValue("eigenvalues_kpoints", eigvalKpoint)
# 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)
##########################Parsing Fermi surface##################
......@@ -272,28 +240,13 @@ class ExcitingParserContext(object):
self.secSystemDescriptionIndex = gIndex
# atoms = Atoms()
if self.atom_pos and self.cell_format[0] == 'cartesian':
backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
# print("self.atom_pos=",np.asarray(self.atom_pos))
elif self.atom_pos and self.cell_format[0] == 'lattice':
# i = 1
atoms = Atoms(self.atom_labels, self.atom_pos, cell=[(1, 0, 0),(0, 1, 0),(0, 0, 1)])
atoms.set_cell(self.sim_cell, scale_atoms=True)
# print("position_lattice",atoms.get_positions()[1])
# while i < len(self.atom_labels):
#
# atoms = Atoms(self.atom_labels, self.atom_pos,self.sim_cell)
# print("attomi=",atoms)
self.atom_pos = atoms.get_positions()
backend.addArrayValues('atom_positions', np.asarray(self.atom_pos))
# print("self.atom_pos_lattice=",np.asarray(self.atom_pos))
# i = 0
# while i < len(self.atom_labels):
# print("self.atom_pos=",np.asarray(self.atom_pos))
# pass
# s##sarrayelf.atom_pos = []
if self.atom_labels is not None:
backend.addArrayValues('atom_labels', np.asarray(self.atom_labels))
self.atom_labels = []
......@@ -303,7 +256,6 @@ class ExcitingParserContext(object):
smearing_internal_map = {
"Gaussian": ['gaussian'],
"Methfessel-Paxton": ['methfessel-paxton'],
# "Methfessel-Paxton 2": ['methfessel-paxton'],
"Fermi-Dirac": ['fermi'],
"Extended": ['tetrahedra']
}
......@@ -315,49 +267,17 @@ class ExcitingParserContext(object):
fromB = unit_conversion.convert_unit_function("bohr", "m")
formt = section['x_exciting_atom_position_format']
self.cell_format = formt
# print("formt=",formt)
pos = [section['x_exciting_geometry_atom_positions_' + i] for i in ['x', 'y', 'z']]
# print("ddd",pos)
pl = [len(comp) for comp in pos]
# print("pelle=",pl)
natom = pl[0]
if pl[1] != natom or pl[2] != natom:
raise Exception("invalid number of atoms in various components %s" % pl)
for i in range(natom):
if formt[0] == 'cartesian':
# print("cartesian?")
self.atom_pos.append([fromB(pos[0][i]), fromB(pos[1][i]), fromB(pos[2][i])])
# print("self.atom_pos=",self.atom_pos)
else:
# atoms = ase.Atoms(self.atom_labels, self.atom_pos,self.sim_cell)
# print("atoms.get_positions()=",atoms.get_positions())
# print("self.sim_cell=",self.sim_cell)
# print("lattice")
self.atom_pos.append([pos[0][i], pos[1][i], pos[2][i]])
# if formt[0] == 'lattice':
#
self.atom_labels = self.atom_labels + (section['x_exciting_geometry_atom_labels'] * natom)
# if formt[0] == 'lattice':
# atoms = ase.Atoms(self.atom_labels, self.atom_pos,self.sim_cell)
# print("atoms.get_positions()=",atoms.get_positions())
# print("self.atom_labels=", self.atom_labels)
# def onClose_section_run(self, backend, gIndex, section):
# self.secGWIndex = gIndex
#
# mainFile = self.parser.fIn.fIn.name
# dirPath = os.path.dirname(self.parser.fIn.name)
# gwFile = os.path.join(dirPath, "GW_INFO.OUT")
# if os.path.exists(gwFile):
# subSuperContext = exciting_parser_gw.GWContext()
# subParser = AncillaryParser(
# fileDescription = exciting_parser_gw.buildGWMatchers(),
# parser = self.parser,
# cachingLevelForMetaName = exciting_parser_gw.get_cachingLevelForMetaName(self.metaInfoEnv, CachingLevel.PreOpenedIgnore),
# superContext = subSuperContext)
# with open(gwFile) as fIn:
# subParser.parseFile(fIn)
def onClose_section_method(self, backend, gIndex, value):
if value["electronic_structure_method"][-1] == "G0W0":
......
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