def prepareBand(self):
tl.mkcd('band')
# run vasp
tl.cp('../minimize/POSCAR', '.')
self.m.ismear = -1
self.getVaspRun_vasp()
tl.cd('..')
def getvasprun(self, files):
m = self.m
maindir = pwd()
if m.engine == "vasp":
calculator = self.getVaspRun_vasp
elif m.engine == "lammps":
calculator = self.getVaspRun_lammps
self.jm = jobManager()
for file in files:
print(file)
dir = "dirs/dir_" + file
mkdir(dir)
mv(file, dir + '/POSCAR')
cd(dir)
calculator()
cd(maindir)
self.jm.run()
if m.th:
mkdir(m.pbsname)
self.thcode(files, m.pbsname)
cp("dirs", m.pbsname)
passthru("tar zcf %s.tar.gz %s" % (m.pbsname, m.pbsname))
print('start check')
self.jm.check()
if m.engine == "lammps1":
from multiprocessing.dummy import Pool
pool = Pool()
pool.map_async(lammpsvasprun, files)
pool.close()
pool.join()
def getvasprun(self, files):
m = self.m
maindir = pwd()
if m.engine == "vasp":
calculator = self.getVaspRun_vasp
elif m.engine == "lammps":
calculator = self.getVaspRun_lammps
self.jm = jobManager()
for file in files:
print(file)
dir = "dirs/dir_" + file
mkdir(dir)
mv(file, dir + '/POSCAR')
cd(dir)
calculator()
cd(maindir)
self.jm.run()
if m.th:
mkdir(m.pbsname)
self.thcode(files, m.pbsname)
cp("dirs", m.pbsname)
passthru("tar zcf %s.tar.gz %s" % (m.pbsname, m.pbsname))
print('start check')
self.jm.check()
if m.engine == "lammps1":
from multiprocessing.dummy import Pool
pool = Pool()
pool.map_async(lammpsvasprun, files)
pool.close()
pool.join()
def minimizePOSCAR(self):
m = self.m
if m.engine == "lammps":
m.dump2POSCAR(m.home + '/minimize/range', rotate=True)
elif m.engine == "vasp":
cp(m.home + '/minimize/CONTCAR', 'POSCAR')
def minimizePOSCAR(self):
m = self.m
if m.engine == "lammps":
m.dump2POSCAR(m.home + '/minimize/range', rotate=True)
elif m.engine == "vasp":
cp(m.home + '/minimize/CONTCAR', 'POSCAR')
def generate(self):
m = self.m
coordination = self.phontsAtoms()
content0 = "species %d\n" % (len(m.elements)) + m.phontsmasses + """
D3_cutoff %f
kpoints %s 1
delta 0.005
numerical_2der T
numerical_3der T
iter_steps 3
pdos 0. 70. 200 10.
temp 60. 400. 10
AbInitio T F
FP_interface LAMMPS
#phonons_only T
Lattice 1.0
%s
end
""" % (m.shengcut, m.toString(m.kpoints), coordination)
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts) # generate many displacement files
tl.mkdir('lammps')
tl.cd('lammps')
content = "units %s\n" % m.units
content += """atom_style charge
dimension 3
boundary p p p
read_data GENERIC
%s
%s
neighbor 1.1 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 1 *.dump id fx fy fz
dump_modify 1 format "%%d %%30.20f %%30.20f %%30.20f"
dump_modify 1 sort id
run 0
""" % (m.masses, m.potential)
tl.shell_exec("mv ../*.str .")
strs = tl.shell_exec("ls *.str").split("\n")
for str in strs:
dir = str.replace("str", "dir")
tl.mkdir(dir)
tl.write(content.replace("GENERIC", str), dir + "/in")
tl.mv(str, "%s/%s" % (dir, str))
tl.cd(dir)
tl.passthru(config.lammps + " <in >out.dat")
tl.cd('..')
dirs = tl.shell_exec("ls |grep dir").split("\n")
for dir in dirs:
print(dir)
tl.cp(dir + "/0.dump", "../" + dir.replace("dir", "out"))
tl.cp("1.0000.dir/out.dat", "../1.0000.out")
tl.cd('..')
content0 = content0.replace('AbInitio T F', 'AbInitio F T')
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts)
def generate(self):
m = self.m
coordination = self.phontsAtoms()
content0 = "species %d\n" % (len(m.elements)) + m.phontsmasses + """
D3_cutoff %f
kpoints %s 1
delta 0.005
numerical_2der T
numerical_3der T
iter_steps 3
pdos 0. 70. 200 10.
temp 60. 400. 10
AbInitio T F
FP_interface LAMMPS
#phonons_only T
Lattice 1.0
%s
end
""" % (m.shengcut, m.toString(m.kpoints), coordination)
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts) # generate many displacement files
tl.mkdir('lammps')
tl.cd('lammps')
content = "units %s\n" % m.units
content += """atom_style charge
dimension 3
boundary p p p
read_data GENERIC
%s
%s
neighbor 1.1 bin
neigh_modify every 1 delay 1 check yes
dump 1 all custom 1 *.dump id fx fy fz
dump_modify 1 format "%%d %%30.20f %%30.20f %%30.20f"
dump_modify 1 sort id
run 0
""" % (m.masses, m.potential)
tl.shell_exec("mv ../*.str .")
strs = tl.shell_exec("ls *.str").split("\n")
for str in strs:
dir = str.replace("str", "dir")
tl.mkdir(dir)
tl.write(content.replace("GENERIC", str), dir + "/in")
tl.mv(str, "%s/%s" % (dir, str))
tl.cd(dir)
tl.passthru(config.lammps + " <in >out.dat")
tl.cd('..')
dirs = tl.shell_exec("ls |grep dir").split("\n")
for dir in dirs:
print(dir)
tl.cp(dir + "/0.dump", "../" + dir.replace("dir", "out"))
tl.cp("1.0000.dir/out.dat", "../1.0000.out")
tl.cd('..')
content0 = content0.replace('AbInitio T F', 'AbInitio F T')
tl.write(content0, 'phonons_input.dat')
tl.passthru(config.phonts)
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 run(self):
m = self.m
dir0 = 'minimize'
atoms = m.dump2POSCAR('%s/range' % dir0)
tl.cp("POSCAR", "POSCAR_minimize")
cell = atoms.get_cell()
r = np.arange(1.0, 0.5, -0.01) * cell[2][2]
for i, lz in enumerate(r):
dir = 'minimize%d' % i
self.run_next(dir0, dir, lz)
dir0 = dir
def run(self):
m = self.m
dir0 = 'minimize'
atoms = m.dump2POSCAR('%s/range' % dir0)
tl.cp("POSCAR", "POSCAR_minimize")
cell = atoms.get_cell()
r = np.arange(1.0, 0.5, -0.01) * cell[2][2]
for i, lz in enumerate(r):
dir = 'minimize%d' % i
self.run_next(dir0, dir, lz)
dir0 = dir
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 minimize(self):
if (self.m.copyN == -1):
copymini = False
else:
copymini = True
if copymini:
while not tl.exists('../%d/minimize/done' % self.m.copyN):
tl.sleep(30)
print('copymini')
tl.cp('../%d/minimize' % self.m.copyN, '.')
else:
self.creatmini()
def runSPOSCAR(self):
m = self.m
maindir = pwd()
file = "SPOSCAR"
dir = "dir_" + file
mkdir(dir)
cp(file, dir + '/POSCAR')
cd(dir)
if m.engine == "vasp":
self.getVaspRun_vasp()
if m.engine == "lammps":
self.getVaspRun_lammps()
cd(maindir)
def runSPOSCAR(self):
m = self.m
maindir = pwd()
file = "SPOSCAR"
dir = "dir_" + file
mkdir(dir)
cp(file, dir + '/POSCAR')
cd(dir)
if m.engine == "vasp":
self.getVaspRun_vasp()
if m.engine == "lammps":
self.getVaspRun_lammps()
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 generate(self):
m = self.m
self.minimizePOSCAR()
a = time.time()
self.generate_supercells()
tl.debug('generate_supercells:%f s' % (time.time() - a))
tl.shell_exec("rm *-*")
tl.cp("SPOSCAR", "POSCAR001")
a = time.time()
files = ['POSCAR001']
self.getvasprun(files)
tl.debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.force_constant()
tl.debug('force_constant:%f s' % (time.time() - a))
if m.phofc:
return self
self.postp()
def generate(self):
m = self.m
self.minimizePOSCAR()
a = time.time()
self.generate_supercells()
tl.debug('generate_supercells:%f s' % (time.time() - a))
tl.shell_exec("rm *-*")
tl.cp("SPOSCAR", "POSCAR001")
a = time.time()
files = ['POSCAR001']
self.getvasprun(files)
tl.debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.force_constant()
tl.debug('force_constant:%f s' % (time.time() - a))
if m.phofc:
return self
self.postp()
def getVaspRun_vasp(self):
self.writeINCAR()
m = self.m
writePOTCAR(m, m.elements)
if (m.kpointspath):
cp(m.kpointspath, "KPOINTS")
else:
from aces.io.vasp import writeKPOINTS
writeKPOINTS(m.ekpoints)
if 'jm' in self.__dict__:
if not m.th:
path = pwd()
if m.queue == "q3.4":
pb = pbs(
queue=m.queue,
nodes=12,
procs=1,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
pb = pbs(
queue=m.queue,
nodes=1,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
path = pwd()
pb = th(disp=m.pbsname, path=path)
self.jm.reg(pb)
else:
shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
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 getVaspRun_vasp(self):
self.writeINCAR()
m = self.m
writePOTCAR(m, m.elements)
if (m.kpointspath):
cp(m.kpointspath, "KPOINTS")
else:
from aces.io.vasp import writeKPOINTS
writeKPOINTS(m.ekpoints)
if 'jm' in self.__dict__:
if not m.th:
path = pwd()
if m.queue == "q3.4":
pb = pbs(queue=m.queue,
nodes=12,
procs=1,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
pb = pbs(queue=m.queue,
nodes=1,
procs=12,
disp=m.pbsname,
path=path,
content=config.mpirun + " 12 " + config.vasp +
' >log.out')
else:
path = pwd()
pb = th(disp=m.pbsname, path=path)
self.jm.reg(pb)
else:
shell_exec(config.mpirun + " %s " % m.cores + config.vasp +
' >log.out')
def getV(self):
if not exists('groupv'):
mkdir('groupv')
cd('groupv')
cp('../FORCE_CONSTANTS', '.')
cp('../POSCAR', '.')
cp('../disp.yaml', '.')
self.generate_vconf()
passthru(config.phonopy + "--tolerance=1e-4 v.conf")
self.drawV()
cd('..')
def getV(self):
if not exists('groupv'):
mkdir('groupv')
cd('groupv')
cp('../FORCE_CONSTANTS', '.')
cp('../POSCAR', '.')
cp('../disp.yaml', '.')
self.generate_vconf()
passthru(config.phonopy + "--tolerance=1e-4 v.conf")
self.drawV()
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 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 pSecond(self):
cp('../POSCAR', '.')
self.generate_supercells()
files = shell_exec("ls *-*").split('\n')
assert len(files) > 0
self.getvasprun(files)
def generate(self):
tl.cp('minimize/POSCAR', '.')
self.getVaspRun_vasp()
def generate(self):
tl.cp('minimize/POSCAR', '.')
self.getVaspRun_vasp()
def generate(self):
tl.cp('minimize/CONTCAR', 'POSCAR')
self.prepareBand()
self.prepareet()
self.runet()
def pSheng(self):
mkdir('SHENG')
cd('SHENG')
cp('../secondorder/FORCE_CONSTANTS', 'FORCE_CONSTANTS_2ND')
cp('../thirdorder/FORCE_CONSTANTS_3RD', '.')
self.getControl()
def third(self):
mkdir('thirdorder')
cd('thirdorder')
cp('../POSCAR', '.')
self.generate_supercells3()
def minimize_vasp(m):
npar = 1
for i in range(1, int(np.sqrt(m.cores)) + 1):
if m.cores % i == 0:
npar = i
if m.ispin:
ispin = "ISPIN=2"
else:
ispin = ""
if m.soc:
soc = "LSORBIT=T"
else:
soc = ""
if m.isym:
sym = "ISYM = 1"
else:
sym = "ISYM = 0"
s = """SYSTEM = - local optimisation
PREC = high
ENCUT=%f
EDIFF = 1e-8
IBRION = 2
NSW=100
ISIF = 3
ISMEAR = 0 ; SIGMA = 0.1
POTIM=0.01
ISTART = 0
LWAVE = FALSE
LCHARG = FALSE
EDIFFG = -0.01
LREAL=FALSE
NPAR = %d
%s
%s
%s
""" % (m.ecut, npar, sym, ispin, soc)
if m.vdw:
s += """\nIVDW = 1
VDW_RADIUS = 50
VDW_S6 = 0.75
VDW_SR = 1.00
VDW_SCALING = 0.75
VDW_D = 20.0
VDW_C6 = 63.540 31.50
VDW_R0 = 1.898 1.892
"""
tl.write(s, 'INCAR')
m.structure()
from aces.io.vasp import writePOTCAR
writePOTCAR(m, m.elements)
s = """A
0
Monkhorst-Pack
%s
0 0 0
""" % ' '.join(map(str, m.mekpoints))
tl.write(s, 'KPOINTS')
vasp = [config.vasp, config.vasp_2d][m.d2]
if m.useMini:
tl.shell_exec(config.mpirun + " %s " % m.cores + vasp + ' >log.out')
else:
tl.cp('POSCAR', 'CONTCAR')