def prepareBand(self):
tl.mkcd('band')
# run vasp
tl.cp('../minimize/POSCAR', '.')
self.m.ismear = -1
self.getVaspRun_vasp()
tl.cd('..')
def getPhonons(self):
maindir = tl.pwd()
tl.mkcd('phonons')
self.runscf()
self.runph()
self.collect()
tl.cd(maindir)
def getbol(self):
maindir = tl.pwd()
tl.mkcd('bol')
self.runscf()
self.runnscf()
self.runw()
tl.cd(maindir)
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 phonopy(self, dir, mm):
# if exists(dir+'/FORCE_CONSTANTS'):
# return
mkcd(dir)
self.creatmini(mm)
PRunner(mm).generate()
cd('..')
def getbol(self):
maindir = tl.pwd()
tl.mkcd('bol')
self.runscf()
self.runnscf()
self.runw()
tl.cd(maindir)
def prepareet(self):
fermi = self.get_fermi()
nelect = self.get_nelect()
tl.mkcd('et')
tl.cp('../band/SYMMETRY', '.')
tl.cp('../band/EIGENVAL', '.')
tl.cp('../band/POSCAR', '.')
lpfac = 5
if(self.m.soc):
lpfac = 20
s = """VASP
0 1 0 0.0
%f 0.0005 0.40 %f
CALC
%d
BOLTZ
.15
800. 50.
0.
""" % (fermi, nelect, lpfac)
# Format of DOS
# iskip (not presently used) idebug setgap shiftgap
# Fermilevel (eV, please note), energygrid (Ry),\
# energy span around Fermilevel (Ry), No of electrons
# CALC (calculate expansion coeff), NOCALC read from file
# lpfac, number of latt-points per k-point
# run mode (only BOLTZ is supported)
# (efcut) energy range of chemical potential (Ry)
# Tmax, temperature grid
# energyrange of bands given individual \
# DOS output sig_xxx and dos_xxx (xxx is band number)
tl.write(s, "et.intrans")
tl.cd('..')
def getPhonons(self):
maindir = tl.pwd()
tl.mkcd('phonons')
self.runscf()
self.runph()
self.collect()
tl.cd(maindir)
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 prepareBand(self):
tl.mkcd('band')
# run vasp
tl.cp('../POSCAR', '.')
self.getVaspRun_vasp()
# cp('/home1/xggong/zhouy/tcscripts/sis/
# sis1.1/0/secondorder/dirs/dir_POSCAR-002/EIGENVAL','.')
# cp('/home1/xggong/zhouy/tcscripts/
# sis/sis1.1/0/secondorder/dirs/dir_POSCAR-002/OUTCAR','.')
tl.cd('..')
def prepareBand(self):
tl.mkcd('band')
# run vasp
tl.cp('../POSCAR', '.')
self.getVaspRun_vasp()
# cp('/home1/xggong/zhouy/tcscripts/sis/
# sis1.1/0/secondorder/dirs/dir_POSCAR-002/EIGENVAL','.')
# cp('/home1/xggong/zhouy/tcscripts/
# sis/sis1.1/0/secondorder/dirs/dir_POSCAR-002/OUTCAR','.')
tl.cd('..')
def optimize(self):
mkcd('optimize')
cp('../minimize/POSCAR', '.')
atoms = io.read('POSCAR')
for i in range(100):
dir = "%i" % i
mkcd(dir)
writevasp(atoms)
forces, stress, energy = self.energyForce()
pos = atoms.get_scaled_positions()
pos += forces * 0.01
def optimize(self):
mkcd('optimize')
cp('../minimize/POSCAR', '.')
atoms = io.read('POSCAR')
for i in range(100):
dir = "%i" % i
mkcd(dir)
writevasp(atoms)
forces, stress, energy = self.energyForce()
pos = atoms.get_scaled_positions()
pos += forces * 0.01
def getepw(self):
m = self.m
maindir = tl.pwd()
tl.mkcd('epw')
"""为了保证q+k也在k的格点上，必须要求qs*cell*[nk1,nk2,nk3]为整数，即nk=N*nq
否则可能出现Error in routine createkmap (1):
"""
u = np.array(m.ekpoints) / np.array(m.kpoints)
assert np.allclose(np.floor(u + .5), u, rtol=0.01)
self.runscf()
self.runnscf()
self.runepw()
tl.cd(maindir)
def getepw(self):
m = self.m
maindir = tl.pwd()
tl.mkcd('epw')
"""为了保证q+k也在k的格点上，必须要求qs*cell*[nk1,nk2,nk3]为整数，即nk=N*nq
否则可能出现Error in routine createkmap (1):
"""
u = np.array(m.ekpoints) / np.array(m.kpoints)
assert np.allclose(np.floor(u + .5), u, rtol=0.01)
self.runscf()
self.runnscf()
self.runepw()
tl.cd(maindir)
def sheng(self):
self.writeFC()
m = self.m
from aces.runners.shengbte import runner as shengbte
a = shengbte(m)
tl.mkcd('SHENG')
tl.cp('../FORCE_CONSTANTS_2ND', '.')
tl.cp('../FORCE_CONSTANTS_3RD', '.')
a.getControl()
# Thermal conductivity calculation
print("START SHENGBTE...")
# passthru(config.mpirun+" %s "%m.cores+config.shengbte)
tl.passthru(config.shengbte)
def getlead(self):
cd('center')
left = self.findlead('left')
right = self.findlead('right')
cd('..')
return
from aces.io.vasp import writevasp
mkcd('leftlead')
writevasp(left, 'POSCAR')
self.runlead()
cd('..')
mkcd('rightlead')
writevasp(right, 'POSCAR')
self.runlead()
cd('..')
def tDisorder():
# disorder degree*/
now = tl.pwd()
tl.cd('minimize')
tl.mkcd('disorder')
disorderLine = tl.shell_exec(
"cp %s" % SRCHOME + "/in.disorder .;" + config.lammps +
" <in.disorder 2>err 1>log;tail -1 disorder.txt 2>err;")
k = disorderLine.split()[1:3]
if len(k) == 1:
k.append("")
disorder, rd = k
tl.cd(now)
return (disorder, rd)
def tDisorder():
# disorder degree*/
now = tl.pwd()
tl.cd('minimize')
tl.mkcd('disorder')
disorderLine = tl.shell_exec(
"cp %s" %
SRCHOME +
"/in.disorder .;" +
config.lammps +
" <in.disorder 2>err 1>log;tail -1 disorder.txt 2>err;")
k = disorderLine.split()[1:3]
if len(k) == 1:
k.append("")
disorder, rd = k
tl.cd(now)
return (disorder, rd)
def vfc(self):
c = self.m.correlation_supercell
q = []
u = [int(x / 2) * 2 + 1 for x in c]
for i in range(u[0]):
for j in range(u[1]):
for k in range(u[2]):
b = np.array([
float(i - c[0] / 2) / c[0],
float(j - c[1] / 2) / c[1],
float(k - c[2] / 2) / c[2]
])
q.append(b)
m = self.m
tl.mkcd('vqpoints')
tl.cp('../FORCE_CONSTANTS', '.')
tl.cp('../disp.yaml', '.')
tl.cp('../POSCAR', '.')
Prun(m).getvqpoints(q)
tl.cd('..')
def vfc(self):
c = self.m.correlation_supercell
q = []
u = [int(x / 2) * 2 + 1 for x in c]
for i in range(u[0]):
for j in range(u[1]):
for k in range(u[2]):
b = np.array([
float(i - c[0] / 2) / c[0],
float(j - c[1] / 2) / c[1],
float(k - c[2] / 2) / c[2]
])
q.append(b)
m = self.m
tl.mkcd('vqpoints')
tl.cp('../FORCE_CONSTANTS', '.')
tl.cp('../disp.yaml', '.')
tl.cp('../POSCAR', '.')
Prun(m).getvqpoints(q)
tl.cd('..')
def writeatoms(self, atoms, label='atoms'):
tl.mkcd(label)
self.watoms(atoms)
tl.cd('..')
def writeatoms(self, atoms, label='atoms'):
tl.mkcd(label)
self.watoms(atoms)
tl.cd('..')