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 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