def bdf_read_band(filename):
'''
Read a band structure from bdf output
'''
f = open(filename)
#Read reciporocal vectors
lines = f.readlines()
f.close()
mK = [[float(y) for y in x.split()[1:4]] for x in lines[2:5]]
eig_fermi = float(lines[6].split()[-1])
print(eig_fermi)
list_kpt = []
list_eig = []
for line in lines[7:]:
ar = line.split()
#"A" is marked as non-special k-points
if (ar[1] == "A"):
ar[1] = ""
list_kpt.append(ar[1:2] + [float(x) for x in ar[2:5]] + [1.0])
list_eig.append([float(x) for x in ar[5:]])
kpt = KPointsT()
kpt.stMode = "crystal"
kpt.ReadFromList(list_kpt)
kpt.ConvertUnit("cart", mLatt=f_GetReciprocalLattice(mK))
band = BandsT(kpt, list_eig, eig_fermi, eig_fermi)
band.b_metal = True #Just set to plot fermi
return band
def yaeh_ReadBand(stFileName):
'''
Read k-points and band from yaeh band result.
Fermi energy is not calculated.
@todo spin is always 1
'''
f = open(stFileName)
ar_stLine = f.readlines()
list_kp = []
list_band = []
nbnd = int(ar_stLine[4].split()[0]) #Number of bands in each kpt
nStart = 0 #Start position of band data
for i in range(0, len(ar_stLine)):
if ("Begin band data" in ar_stLine[i]):
nStart = i + 1 #line count that not band data
break
for i in range(0, (len(ar_stLine) - nStart) / (nbnd + 1)):
i2 = (nbnd + 1) * i + nStart
list_kp.append([float(x) for x in ar_stLine[i2][10:].split()])
list_band.append([float(x) for x in ar_stLine[i2 + 1:i2 + nbnd + 1]])
#write
aKPT = KPointsT()
aKPT.ReadFromList(list_kp)
# return aKPT,list_band,0,0,0
band = BandsT(aKPT, list_band)
band.num_spin = 1
return band
def abi_ReadBand_EIG(stFileName):
'''
Read band structure from _EIG file
'''
f = open(stFileName)
stLine = f.readline()
if ("hartree" in stLine): # "(hartree) ="
energy_unit = Ha2eV
else:
energy_unit = 1.0 # energy unit; if it is hartree then convert to eV
if ("Fermi" in stLine): # Find the first equal
ixEqual = stLine.index("=")
dFermi = float(stLine[ixEqual + 1:ixEqual + 10])
stLine = f.readline()
else:
dFermi = None
nKPt = int(stLine[32:36])
listKPt = []
listBand = []
listB1 = []
# for i in xrange(0,nKPt):
while True:
stLine = f.readline()
if not stLine:
break
stLine = stLine[:-1] #Remove \cr for splitting
if ("kpt" in stLine):
listKPt.append([
float(stLine[41:49]),
float(stLine[49:57]),
float(stLine[58:65]),
float(stLine[26:35])
])
if (len(listB1) > 0):
listBand.append(listB1)
listB1 = []
else:
#To avoid two maximum length float recognized as one
# listB1 += [float(x) if not "*" in x else 0.0 * energy_unit for x in stLine.split()]
n = 10
listB1 += [
float(x) if not "*" in x else 0.0
for x in [stLine[i:i + n] for i in xrange(0, len(stLine), n)]
]
#Find band
listBand.append(listB1)
aKPt = KPointsT()
aKPt.ReadFromList(listKPt)
# return aKPt, listBand, dFermi, None, 1
return BandsT(aKPt, listBand, dFermi, None, None, 1)
def abi_ReadBand_GW(stFileName):
'''
Read band structure from _GW file
'''
f = open(stFileName)
nKPt, nSpin = [int(x) for x in f.readline().split()]
listKPt = []
listBand = []
for i in xrange(0, nKPt):
listKPt.append([float(x) for x in f.readline().split()])
n = int(f.readline())
listB = []
for j in xrange(0, n):
listB.append(float(f.readline().split()[1]))
listBand.append(listB)
aKPt = KPointsT()
aKPt.ReadFromList(listKPt)
# return aKPt, listBand, None, None, nSpin
return BandsT(aKPt, listBand, None, None, None, nSpin)
def Main(ArgList):
description = '''Plot band structure or DOS from data including kpoint-energy data, kpoint list, kpoint name list ( for band ) or energy-DOS data, PDOS name ( for DOS). Fermi energy can be used to adjust position in the process.
%prog --fermi 0.5
'''
usage = "%prog "
parser = OptionParser(formatter=EmptyFormatter(),
usage=usage,
description=description)
parser.add_option(
"--band",
dest="BandFileName",
help=
"Specify the energy data filename; This file should be a space or tabular split text file with all states in one k-points in one row"
)
parser.add_option(
"--kpt",
dest="KptFileName",
help=
"Specify the k-point list filename; This file should be a space or tabular split text file with x,y,z coordinate of k-vector in one line. The order must be the same as band file"
)
parser.add_option("--fermi",
dest="FermiFileName",
help="Specify the fermi energy filename.")
parser.add_option(
"-g",
dest="Align",
action="store_true",
default=False,
help=
"If set to true, data will be modified to make E_F=0, otherwise a fermi level will be pointed out at its actual position"
)
parser.add_option(
"--band2",
dest="Band2FileName",
default=None,
help=
"Specify the second energy data filename; the second energy data file will be plotted in dot mode"
)
parser.add_option("--fermi2",
dest="Fermi2FileName",
help="Specify the second fermi energy filename.")
parser.add_option("--ymax",
dest="Ymax",
default=None,
help="Maximum of Y axis")
parser.add_option("--ymin",
dest="Ymin",
default=None,
help="Minimum of Y axis")
(options, args) = parser.parse_args(ArgList)
if (len(args) != 1):
parser.error("incorrect number of arguments.")
#aKPT,list_band = f_ReadBandFile(options.stBandFileName,options.stKptFileName)
list_band = f_Band_ReadFromFile(options.BandFileName)
aKPT = KPointsT(options.KptFileName)
if (options.Band2FileName != None):
list_band2 = f_Band_ReadFromFile(options.Band2FileName)
else:
list_band2 = None
eig_fermi = 0.0
if (options.FermiFileName != None):
eig_fermi = f_ReadFileFloatValue(options.FermiFileName)
if (eig_fermi == None):
print("Warning: fermi file not found, use 0.0 instead")
eig_fermi = 0.0
eig_fermi2 = 0.0
if (options.Fermi2FileName != None):
eig_fermi2 = f_ReadFileFloatValue(options.Fermi2FileName)
if (eig_fermi == None):
print("Warning: second fermi file not found, use 0.0 instead")
eig_fermi2 = 0.0
eig_max = None if options.Ymax == None else float(options.Ymax)
eig_min = None if options.Ymin == None else float(options.Ymin)
f_PlotBand(aKPT,
list_band,
eig_fermi,
bAlignData=options.Align,
list_band2=list_band2,
eig_fermi2=eig_fermi2,
y_min=eig_min,
y_max=eig_max)
def vasp_ReadBand(stFileName="EIGENVAL",filetype=None):
'''
Read k-point and band from vasp EIGENVAL file or OUTCAR file
WARNING: EIGENVAL does not handle non-integer electrons! Use OUTCAR or vasprun.xml if it is that case
Note the structure is always read from vasprun.xml
Another problem is the occuptation numbers are 1 in vasprun.xml and 2 in OUTCAR, if spin unpolarized
:param stFileName: the file to read bandstructure
:param filetype: the file type to read, can be OUTCAR or EIGENVAL. Automatically inferred from stFileName if set to None
'''
if (filetype is None):
if ("EIGENVAL" in stFileName):
filetype = "EIGENVAL"
elif ("vasprun.xml" in stFileName):
filetype = "vasprun.xml"
else:
filetype = "OUTCAR"
f = open(stFileName)
ar_stLine = f.readlines()
f.close()
list_kp = []
list_band = []
list_band2 = []
list_occ = None
bElectronFraction = False
if (filetype == "EIGENVAL"):
#Note we cannot determine LNONCOLLINEAR in EIGENVAL, assume false
b_noncoll = False
num_spin = int(ar_stLine[0].split()[3])
(nElectron,nKPt,nbnd) = [int(x) for x in ar_stLine[5].split()]
for i in range(0,nKPt):
i2 = i * (nbnd+2) + 7
list_kp.append([float(x) for x in ar_stLine[i2].split()])
ar2 =[x.split() for x in ar_stLine[i2+1:i2+nbnd+1]]
list_band.append([float(x[1]) for x in ar2])
if (num_spin == 2):
list_band2.append([float(x[2]) for x in ar2])
if (num_spin == 2):
list_band = [list_band,list_band2]
elif (filetype == "OUTCAR"):
def read_tag(tag, i0):
val = None
for i in xrange(i0, len(ar_stLine)):
line = ar_stLine[i]
if (tag in line):
val = line.split()[2]
break
if (val is None):
raise ValueError("Cannot find tag %s" % tag)
return val, i
list_occ = []
list_occ2 = []
i = 0
num_spin, i = read_tag("ISPIN", i)
num_spin = int(num_spin)
b_noncoll, i = read_tag("LNONCOLLINEAR", i)
b_noncoll = b_noncoll == "T"
nElectron, i = read_tag("NELECT", i)
dElectron = float(nElectron)
nElectron = int(dElectron)
bElectronFraction = abs(dElectron != nElectron) > 1e-7
# if (bElectronFraction):
# print("The number of electrons is not an integer.")
efermi, i = read_tag("E-fermi", i)
efermi = float(efermi)
i += 2
if (num_spin != 1):
i += 2
list_band_now = list_band
list_occ_now = list_occ
while (len(ar_stLine[i+1])>4):
i += 1
if (list_band_now == list_band):
list_kp.append([float(x) for x in ar_stLine[i].split()[-3:]])
i += 2
ar2 = []
ar_occ = []
line = ar_stLine[i]
while (len(line) > 4):
ar_line = line.split()
ar2.append(float(ar_line[1]))
ar_occ.append(float(ar_line[2]))
i += 1
line = ar_stLine[i]
list_band_now.append(ar2)
list_occ_now.append(ar_occ)
if (num_spin != 1 and "spin" in ar_stLine[i+1]):
list_band_now = list_band2
list_occ_now = list_occ2
i += 2
nKPt = len(list_band)
nbnd = len(list_band[0])
# print(nElectron, nKPt, nbnd)
if (num_spin == 2):
list_band = [list_band, list_band2]
list_occ = [list_occ, list_occ2]
elif (filetype == "vasprun.xml"):
#Read from vasprun.xml
for event, elem in ET.iterparse(stFileName,events=('end',)):
if (elem.tag == "parameters"):
node_parameters = elem
elif (elem.tag == "eigenvalues"):
node_eigenvalues = elem
elif (elem.tag == "kpoints"):
node_kpoints = elem
elif (elem.tag == "dos"):
node_dos = elem
break
#Read LNONCOLLINEAR
b_noncoll = node_parameters.find('./separator[@name="electronic"]/separator[@name="electronic spin"]/i[@name="LNONCOLLINEAR"]').text
b_noncoll = b_noncoll.strip() == "T"
#Read NELECT
dElectron = float(node_parameters.find('./separator[@name="electronic"]/i[@name="NELECT"]').text)
nElectron = int(dElectron)
bElectronFraction = abs(dElectron != nElectron) > 1e-7
#Read band
node_band = node_eigenvalues
list_band = []
list_occ = []
list_occ2 = []
#3-level nested , hard to read so split them
for node1 in node_band.findall("./array/set/set"): #Spin
band_spin = []
occ_spin = []
for node2 in node1.findall("./set"): #Kpt
data_kpt = [node3.text.split() for node3 in node2.findall("./r")]
band_spin.append([float(x[0]) for x in data_kpt])
occ_spin.append([float(x[1]) for x in data_kpt])
list_band.append(band_spin)
list_occ.append(occ_spin)
# list_band = reduce(lambda x,y: x+y, list_band)
# list_occ = reduce(lambda x,y: x+y, list_occ)
#Read kpoints coordinates
list_kp = [[float(x) for x in nodek.text.split()] for nodek in node_kpoints.findall('./varray[@name="kpointlist"]/v')]
#Read other properties
num_spin = int(node_parameters.find('./separator[@name="electronic"]/separator[@name="electronic spin"]/i[@name="ISPIN"]').text)
efermi = float(node_dos.find('./i[@name="efermi"]').text)
#Do not use array for each spin if only 1 spin
if (num_spin == 1):
list_band = list_band[0]
list_occ = list_occ[0]
aKPT = KPointsT()
aKPT.ReadFromList(list_kp)
aKPT.stMode = "crystal"
#OUTCAR is not necasseary, it is used to convert k-point unit
try:
latt = vasp_read_latt("initialpos","vasprun.xml")
except ET.ParseError:
matR,matK = vasp_ReadLattVec("OUTCAR")
latt = Lattice()
latt.ReadFromRawCellVector(matR)
aKPT.latt = latt
# aKPT.ConvertUnit("cart",matR)
aKPT.ConvertUnit("cart")
#Each band is assumed to be double occupied in BandsT
#So we use 2 times electron in NONCOLLINEAR where only single occupied
if (b_noncoll):
print("Noncollinear calculation, band.electron = 2*actual electrons")
nElectron *= 2
band = BandsT(aKPT,list_band,None,None,nElectron,num_spin, list_occ=list_occ)
#Calculate VBM
#Only do if the number of electrons is an integer
if (bElectronFraction):
band.fermi = efermi
else:
if (not band.guess_vbm()):
band.fermi = vasp_getout("efer")
# return aKPT,list_band,dVBM,nElectron,1
return band
def yambo_read_band(filename, filename_pw_xml=None):
'''
Read band structure from yambo o-*.qp file
Additional data-file.xml can be used to indicate information
Lattice is a fake and not used
'''
with open(filename, 'r') as f:
lines = f.readlines()
ar = [[float(x) for x in line.split()] for line in lines if line[0] != "#"]
for a1 in ar:
a1[0] = int(a1[0])
a1[1] = int(a1[1])
ix_k = [x[0] for x in ar]
ix_b = [x[1] for x in ar]
ix_k_min = min(ix_k)
ix_k_max = max(ix_k)
ix_b_min = min(ix_b)
ix_b_max = max(ix_b)
#If spin=2, there is 6th column for spin
#If not, only 5 columns
if (len(ar[0]) == 5):
num_spin = 1
elif (len(ar[0]) == 6):
num_spin = 2
else:
raise ValueError("Unknown number of columns %i" % len(ar[0]))
if (filename_pw_xml is not None):
band = qesp_read_band(filename_pw_xml)
if (band.num_spin != num_spin):
raise ValueError("Inconsistent spin for QE file and Yambo file")
#Modify bands
#Set spin
if (num_spin == 1):
for a1 in ar:
a1.append(0)
else:
for a1 in ar:
a1[-1] = int((1 - a1[-1]) / 2)
#Set GW eigenvalues
#Note yambo make a shift to input DFT bands to make KS VBM=0,
#We shuold get it back
#Method 1 : calc shift and apply it to Yambo data
# a = ar[0]
# shift = a[2] - band.prop[a[-1]].eig[a[0]-1][a[1]-1]
# for a in ar:
# band.prop[a[-1]].eig[a[0]-1][a[1]-1] = a[2] + a[3] - shift
#Method 2 : add the correction to DFT instead of reading yambo DFT
for a in ar:
band.prop[a[-1]].eig[a[0] - 1][a[1] - 1] += a[3]
#Calculate properties
if (band.vbm is not None):
#Clear and recalculate
band.vbm = None
band.guess_vbm()
else:
if (num_spin == 1):
list_eig = [[None] * (ix_b_max - ix_b_min + 1)
for x in range(ix_k_max - ix_k_min + 1)]
for x in ar: #Eo + (E-Eo)
list_eig[x[0] - ix_k_min][x[1] - ix_b_min] = x[2] + x[3]
elif (num_spin == 2):
num_spin = 2
list_eig = [[[None] * (ix_b_max - ix_b_min + 1)
for x in range(ix_k_max - ix_k_min + 1)],
[[None] * (ix_b_max - ix_b_min + 1)
for x in range(ix_k_max - ix_k_min + 1)]]
for x in ar: #Eo + (E-Eo)
list_eig[int(
(1 - x[5]) / 2)][x[0] - ix_k_min][x[1] -
ix_b_min] = x[2] + x[3]
#Dummy kpt
latt = Lattice()
latt.ReadFromRawCellVector([[1, 0, 0], [0, 1, 0], [0, 0, 1]])
kpt = KPointsT()
kpt.ReadFromList([[x, 0, 0] for x in range(len(list_eig))])
kpt.unit = "crystal"
kpt.latt = latt
band = BandsT(kpt, list_eig, num_spin=num_spin)
return band
def wann_read_band(filename_band,
filename_kpt=None,
filename_gnu=None,
filename_out=None):
'''
Read band structure information from wannier90 output
Indeed wannier90 output can be directly plotted but sometimes we need to combine two picture!
:param filename_band: the name of eigenvalues ( normally seedname_band.dat )
:param filename_kpt: the name of eigenvalues ( normally seedname_band.kpt;if not provided treated same as filename_band )
:param filename_gnu: the name of gnuplot script ( if not provided treated same as band filename)
:param filename_out: the name of stdout ( if not provided deduced from band filename)
'''
seedname = filename_band[:-9]
if (filename_kpt == None):
filename_kpt = seedname + "_band.kpt"
if (filename_gnu == None):
filename_gnu = seedname + "_band.gnu"
if (filename_out == None):
filename_out = seedname + ".wout"
unit = wann_read_length_unit(filename_out)
#K-points
kpt1 = KPointsT()
f = open(filename_kpt)
n = int(f.readline())
list_k = []
for i in xrange(n):
#Weight is ignored
list_k.append([float(x) for x in f.readline().split()][0:3])
f.close()
kpt1.ReadFromList(list_k)
#Bands
list_band = f_Data_ReadTwoCol(filename_band)
list_kcoord = [float(x[0]) for x in list_band]
list_band = [[float(y) for y in x[1:]] for x in list_band]
#Special k-points from gnuplot
f = open(filename_gnu)
for line in f:
if ("xtics" in line):
line2 = line[line.index("(") + 1:line.index(")")]
ar = line2.split(",")
for spec in ar:
kcoord_last = 0.0
kcoord_now = 0.0
spec_name = spec[spec.index('"') + 1:spec.rindex('"')].strip()
spec_value = float(spec[spec.rindex('"') + 1:])
# print(spec_name,spec_value)
#Search nearest point
for i, value in enumerate(list_kcoord):
# print(value)
if (spec_value <= value): #
if (abs(spec_value - value) <=
abs(kcoord_last - spec_value)):
kpt1.listKPt[i][0] = spec_name
else:
kpt1.listKPt[i - 1][0] = spec_name
break
kcoord_last = value
#Detect the last one if not used
if (i == len(list_kcoord) - 1):
kpt1.listKPt[-1][0] = spec_name
# print("Set kpt%i to %s" % ( i,spec_name))
break
#Convert unit to Bohr
#However list_kcoord is not used later, maybe useful later
if (unit == "Ang"):
print("Convert unit from Angstrom to Bohr")
list_kcoord = [x * Ang2Bohr for x in list_kcoord]
return BandsT(kpt1, list_band, None, None, None, 1)