def __init__(self, filename):
lm = self.lm = lineManager(filename)
self.mesh = sscanf(lm.getLine(0), 'mesh: [ %d, %d, %d ]')
self.nqpoint, = sscanf(lm.getLine(1), 'nqpoint: %d')
self.natom, = sscanf(lm.getLine(2), 'natom: %d')
self.nbranch = 3 * self.natom
self.lenatom = 4
self.leneigvec = self.natom * self.lenatom + 1
self.lenbranch = self.leneigvec + 2
self.lenband = self.lenbranch * self.nbranch + 1
self.lenqpoint = self.lenband + 3
def __init__(self, filename):
lm = self.lm = lineManager(filename)
self.mesh = sscanf(lm.getLine(0), 'mesh: [ %d, %d, %d ]')
self.nqpoint, = sscanf(lm.getLine(1), 'nqpoint: %d')
self.natom, = sscanf(lm.getLine(2), 'natom: %d')
if 'reci' in lm.getLine(3):
self.off = 4
else:
self.off = 0
self.nbranch = 3 * self.natom
self.lenatom = 4
self.leneigvec = self.natom * self.lenatom + 1
self.lenbranch = self.leneigvec + 2
self.lenband = self.lenbranch * self.nbranch + 1
self.lenqpoint = self.lenband + 3
def get_outfermi(self):
file = ls("*.outputtrans")[0]
a = shell_exec("grep FermiE %s|tail -1" % file)
from aces.scanf import sscanf
a = sscanf(a, "FermiE: %f.")[0]
print "E-fermi=" + str(a) + "Ry"
return a
def get_outfermi(self):
file = tl.ls("*.outputtrans")[0]
a = tl.shell_exec("grep FermiE %s|tail -1" % file)
from aces.scanf import sscanf
a = sscanf(a, "FermiE: %f.")[0]
print("E-fermi=" + str(a) + "Ry")
return a
def prepareet(self):
atoms = io.read('POSCAR')
from pyspglib import spglib
s = spglib.get_spacegroup(atoms)
from aces.scanf import sscanf
sgN = sscanf(s, '%s (%d)')[1]
sg = Spacegroup(sgN)
atoms.info = {'spacegroup': sg}
nelect = self.getNelect(outcar='band/OUTCAR')
# The remaining part takes care of writing the files required by
# BoltzTraP.
bandstructure = vasp2boltz.get_vasp_bandstructure(pathname='band/')
tl.mkcd('et')
vasp2boltz.write_bandstructure_boltztrap(bandstructure,
filename='et.energy')
vasp2boltz.write_structure_boltztrap(atoms, filename='et.struct')
vasp2boltz.write_intrans_boltztrap(n_electrons=nelect,
filename='et.intrans')
s = tl.read('et.energy')
s = s.replace('HTE', 'et')
tl.write(s, 'et.energy')
s = tl.read('et.struct')
s = s.replace('HTE', 'et')
tl.write(s, 'et.struct')
tl.cd('..')
def drawdos(self):
from aces.ElectronicDOS.electronicdos import ElectronicDOS
doscar = ElectronicDOS()
# orbital_dos = doscar.sum_ms_dos()
# Create a list of each atom type to sum over.
# type_list = []
# n = 0
# for i in range(len(doscar.unit_cell.atom_types)):
# type_list.append([])
# for j in range(doscar.unit_cell.atom_types[i]):
# type_list[i].append(n)
# n += 1
# Sum dos over sets of atoms.
# partial_dos = doscar.sum_site_dos(type_list,orbital_dos)
dos = doscar.write_dos([doscar.tot_dos])
tl.write(dos, 'dos.txt')
dos = np.loadtxt('dos.txt')
f = tl.shell_exec("grep fermi OUTCAR|tail -1")
from aces.scanf import sscanf
f = sscanf(f, "E-fermi : %f XC(G=0):")
with fig("dos.png"):
pl.xlabel("Energy-Ef (eV)")
pl.ylabel("DOS")
pl.plot(dos[:, 0] - f, dos[:, 1], lw=2)
pl.xlim([-4, 4])
def frequency(self, iqp, ibr, i=False):
lm = self.lm
iline = self.qposition(iqp, i=True) + 3 + ibr * self.lenbranch + 1
if i:
return iline
freq, = sscanf(lm.getLine(iline), ' frequency: %f')
return freq
def qposition(self, iqp, i=False):
lm = self.lm
iline = 4 + self.off + iqp * self.lenqpoint
if i:
return iline
return sscanf(lm.getLine(iline),
'- q-position: [ %f, %f, %f ]')
def frequency(self, iqp, ibr, i=False):
lm = self.lm
iline = self.qposition(iqp, i=True) + 3 + ibr * self.lenbranch + 1
if i:
return iline
freq, = sscanf(lm.getLine(iline), ' frequency: %f')
return freq
def qposition(self, iqp, i=False):
lm = self.lm
iline = 4 + self.off + iqp * self.lenqpoint
if i:
return iline
return sscanf(
lm.getLine(iline), '- q-position: [ %f, %f, %f ]')
def drawdos(self):
from aces.ElectronicDOS.electronicdos import ElectronicDOS
doscar = ElectronicDOS()
#orbital_dos = doscar.sum_ms_dos()
## Create a list of each atom type to sum over.
#type_list = []
#n = 0
#for i in range(len(doscar.unit_cell.atom_types)):
# type_list.append([])
# for j in range(doscar.unit_cell.atom_types[i]):
# type_list[i].append(n)
# n += 1
## Sum dos over sets of atoms.
#partial_dos = doscar.sum_site_dos(type_list,orbital_dos)
dos = doscar.write_dos([doscar.tot_dos])
write(dos, 'dos.txt')
dos = np.loadtxt('dos.txt')
f = shell_exec("grep fermi OUTCAR|tail -1")
from aces.scanf import sscanf
f = sscanf(f, "E-fermi : %f XC(G=0):")
with fig("dos.png"):
pl.xlabel("Energy-Ef (eV)")
pl.ylabel("DOS")
pl.plot(dos[:, 0] - f, dos[:, 1], lw=2)
pl.xlim([-4, 4])
def prepareet(self):
atoms = io.read('POSCAR')
from pyspglib import spglib
s = spglib.get_spacegroup(atoms)
from aces.scanf import sscanf
sgN = sscanf(s, '%s (%d)')[1]
sg = Spacegroup(sgN)
atoms.info = {'spacegroup': sg}
nelect = self.getNelect(outcar='band/OUTCAR')
# The remaining part takes care of writing the files required by
# BoltzTraP.
bandstructure = vasp2boltz.get_vasp_bandstructure(pathname='band/')
tl.mkcd('et')
vasp2boltz.write_bandstructure_boltztrap(
bandstructure, filename='et.energy')
vasp2boltz.write_structure_boltztrap(atoms, filename='et.struct')
vasp2boltz.write_intrans_boltztrap(
n_electrons=nelect, filename='et.intrans')
s = tl.read('et.energy')
s = s.replace('HTE', 'et')
tl.write(s, 'et.energy')
s = tl.read('et.struct')
s = s.replace('HTE', 'et')
tl.write(s, 'et.struct')
tl.cd('..')
def atom(self, iqp, ibr, ia):
lm = self.lm
pos = np.zeros(3, dtype=np.complex)
iline = self.frequency(iqp, ibr, True) + 2 + self.lenatom * ia + 1
lm.moveto(iline)
for i in range(3):
x1, x2 = sscanf(lm.nextLine(), ' - [ %f, %f ]')
pos[i] = x1 + 1j * x2
return pos
def atom(self, iqp, ibr, ia):
lm = self.lm
pos = np.zeros(3, dtype=np.complex)
iline = self.frequency(iqp, ibr, True) + 2 + self.lenatom * ia + 1
lm.moveto(iline)
for i in range(3):
x1, x2 = sscanf(lm.nextLine(), ' - [ %f, %f ]')
pos[i] = x1 + 1j * x2
return pos
def getKlist(self, dir="./"):
file = open(dir + "ph.out")
q = []
from aces.scanf import sscanf
for line in file:
if " N xq(1) xq(2) xq(3)" in line:
while True:
line = file.next().strip()
if (line == ""):
break
k = sscanf(line, "%d %f %f %f")[1:]
q.append(k)
break
assert len(q) > 0
return q
def getKlist(self, dir="./"):
file = open(dir + "ph.out")
q = []
from aces.scanf import sscanf
for line in file:
if " N xq(1) xq(2) xq(3)" in line:
while True:
line = file.next().strip()
if (line == ""):
break
k = sscanf(line, "%d %f %f %f")[1:]
q.append(k)
break
assert len(q) > 0
return q
def energyForce(self):
self.writeINCAR()
m=self.m
m.writePOTCAR()
s="""A
0
Monkhorst-Pack
%s
0 0 0
"""%' '.join(map(str,m.mekpoints))
write(s,'KPOINTS')
shell_exec(config.mpirun+" %s "%m.cores+config.vasp+' >log.out')
try:
from lxml import etree
except ImportError:
print "You need to install python-lxml."
vasprun = etree.iterparse("vasprun.xml", tag='varray')
forces=self.parseVasprun('forces')
stress=self.parseVasprun('stress')
c=shell_exec("grep TOTEN OUTCAR|tail -1")
from aces.scanf import sscanf
energe=sscanf(c,"free energy TOTEN = %f eV")[0]
return forces,stress,energy
def get_fermi(self):
a = tl.shell_exec("grep fermi band/OUTCAR|tail -1")
from aces.scanf import sscanf
a = sscanf(a, "E-fermi : %f XC(G=0): %f alpha+bet :%f")[0]
print("E-fermi=" + str(a) + "eV")
return a
def getfermi(self):
a = tl.shell_exec("grep Fermi nscf.out").strip()
from aces.scanf import sscanf
fermi = sscanf(a, "the Fermi energy is %f ev")[0]
return fermi
def getfermi(self):
a = tl.shell_exec("grep Fermi nscf.out").strip()
from aces.scanf import sscanf
fermi = sscanf(a, "the Fermi energy is %f ev")[0]
return fermi
def get_nelect(self):
a = shell_exec("grep NELECT band/OUTCAR|tail -1")
from aces.scanf import sscanf
a = sscanf(a, "NELECT = %f total number of electrons")[0]
print "NELECT=" + str(a)
return a
def get_nelect(self):
a = tl.shell_exec("grep NELECT band/OUTCAR|tail -1")
from aces.scanf import sscanf
a = sscanf(a, "NELECT = %f total number of electrons")[0]
print("NELECT=" + str(a))
return a
def get_fermi(self):
a = shell_exec("grep fermi band/OUTCAR|tail -1")
from aces.scanf import sscanf
a = sscanf(a, "E-fermi : %f XC(G=0): %f alpha+bet :%f")[0]
print "E-fermi=" + str(a) + "eV"
return a