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 creatmini(self):
print('creatmini')
tl.mkdir('minimize')
tl.cd('minimize')
minimize_input(self.m)
tl.write(time.strftime('%Y-%m-%d %H:%M:%S'), 'done')
tl.cd('..')
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 lifenmaq(self, filename="qpoints/qpoints.yaml",
k=[0, 0, 0], correlation_supercell=[10, 10, 1], test=False):
self.test = test
self.pfactor = self.getpfactor(correlation_supercell)
pya = phononyaml(filename)
self.pya = pya
self.testk = k
if not tl.exists('NMA'):
tl.mkdir('NMA')
self.specialk(pya, map(float, k))
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 lifenmaq(self,
filename="qpoints/qpoints.yaml",
k=[0, 0, 0],
correlation_supercell=[10, 10, 1],
test=False):
self.test = test
self.pfactor = self.getpfactor(correlation_supercell)
pya = phononyaml(filename)
self.pya = pya
self.testk = k
if not tl.exists('NMA'):
tl.mkdir('NMA')
self.specialk(pya, map(float, k))
def ineq(m):
now = tl.pwd()
species = m.species
if not (species in ["CN-small"]):
return 0.0
tl.cd('minimize')
tl.mkdir('nonequ')
tl.cd('nonequ')
ie = inequality()
nonequ5 = ie.run()
tl.cd(now)
return nonequ5
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 ineq(m):
now = tl.pwd()
species = m.species
if not (species in ["CN-small"]):
return 0.0
tl.cd('minimize')
tl.mkdir('nonequ')
tl.cd('nonequ')
ie = inequality()
nonequ5 = ie.run()
tl.cd(now)
return nonequ5
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 creatmini(self, m):
print('creatmini')
m.home = pwd()
assert m.home != ''
mkdir('minimize')
cd('minimize')
minimize_input(m)
write(time.strftime('%Y-%m-%d %H:%M:%S'), 'done')
cd('..')
if m.engine == "lammps":
return m.dump2POSCAR(m.home + '/minimize/range')
else:
return io.read(m.home + '/minimize/CONTCAR')
def collect(self):
tl.mkdir('save')
nqpt = len(tl.ls("diam.dyn*")) - 1
for iqpt in np.arange(1, nqpt + 1):
label = str(iqpt)
tl.shell_exec('cp diam.dyn' + str(iqpt) + ' save/diam.dyn_q' +
label)
if (iqpt == 1):
tl.shell_exec('cp _ph0/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('cp -r _ph0/diam.phsave save/')
else:
tl.shell_exec('cp _ph0/diam.q_' + str(iqpt) +
'/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('rm _ph0/diam.q_' + str(iqpt) + '/*wfc*')
def collect(self):
tl.mkdir('save')
nqpt = len(tl.ls("diam.dyn*")) - 1
for iqpt in np.arange(1, nqpt + 1):
label = str(iqpt)
tl.shell_exec('cp diam.dyn' + str(iqpt) + ' save/diam.dyn_q' +
label)
if (iqpt == 1):
tl.shell_exec('cp _ph0/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('cp -r _ph0/diam.phsave save/')
else:
tl.shell_exec('cp _ph0/diam.q_' + str(iqpt) +
'/diam.dvscf1 save/diam.dvscf_q' + label)
tl.shell_exec('rm _ph0/diam.q_' + str(iqpt) + '/*wfc*')
def generate(self):
# m = self.m
self.minimizePOSCAR()
# cp('minimize/POSCAR','.')
mkdir('secondorder')
cd('secondorder')
self.pSecond()
self.fc2()
cd('..')
self.third()
self.vasprun3()
self.force_constant3()
cd('..')
self.pSheng()
self.runsheng()
def sed_band(self, correlation_supercell=[10, 10, 1]):
self.pfactor = self.getpfactor(correlation_supercell)
data = tl.parseyaml('band.yaml')
natom_unitcell = int(data['natom'])
if not tl.exists('SEDBAND'):
tl.mkdir('SEDBAND')
sed = []
db = h5py.File('sed.h5')
def u(phonon):
qp = phonon['q-position']
qps = str(qp)
print(qps)
if qps not in db:
db[qps] = self.calculateSED(map(float, qp), natom_unitcell)
s = db[qps][:]
sed.append(s)
map(u, data['phonon'])
totalStep = self.totalStep
x = np.linspace(0, 1, totalStep / 2 + 1) * 1 / 2.0 / self.timestep
np.save('wtick.npy', x)
np.save('sed.npy', sed)
def sed_band(self, correlation_supercell=[10, 10, 1]):
self.pfactor = self.getpfactor(correlation_supercell)
data = tl.parseyaml('band.yaml')
natom_unitcell = int(data['natom'])
if not tl.exists('SEDBAND'):
tl.mkdir('SEDBAND')
sed = []
db = h5py.File('sed.h5')
def u(phonon):
qp = phonon['q-position']
qps = str(qp)
print(qps)
if qps not in db:
db[qps] = self.calculateSED(map(float, qp), natom_unitcell)
s = db[qps][:]
sed.append(s)
map(u, data['phonon'])
totalStep = self.totalStep
x = np.linspace(0, 1, totalStep / 2 + 1) * 1 / 2.0 / self.timestep
np.save('wtick.npy', x)
np.save('sed.npy', sed)
def third(self):
mkdir('thirdorder')
cd('thirdorder')
cp('../POSCAR', '.')
self.generate_supercells3()
def pSheng(self):
mkdir('SHENG')
cd('SHENG')
cp('../secondorder/FORCE_CONSTANTS', 'FORCE_CONSTANTS_2ND')
cp('../thirdorder/FORCE_CONSTANTS_3RD', '.')
self.getControl()
def creatmini(self, dir):
cur = tl.pwd()
tl.mkdir(dir)
tl.cd(dir)
minimize_input(self.m)
tl.cd(cur)
def creatmini(self, dir):
cur = tl.pwd()
tl.mkdir(dir)
tl.cd(dir)
minimize_input(self.m)
tl.cd(cur)