def setup(self):
self.bandpoints = ibz_points['hexagonal']
self.bandpath = ['Gamma', 'M', 'K', 'Gamma']
if self.pot == 1:
debug("graphene potential chosen:SiC_1994.tersoff")
self.potential = 'pair_style tersoff\npair_coeff * * %s/SiC_1994.tersoff %s' % (
config.lammpspot, ' '.join(['C' for i in self.elements]))
def submit(self):
cmd = "cd %s;qsub %s 2>&1" % (self.path, self.filename)
tl.debug(cmd)
print(cmd)
x = self.ssh_cmd('xggong', 'cluster', cmd)
# assert not x.strip()==''
tl.debug(x)
def submit(self):
cmd = "cd %s;qsub %s 2>&1" % (self.path, self.filename)
tl.debug(cmd)
print(cmd)
x = self.ssh_cmd('xggong', 'cluster', cmd)
# assert not x.strip()==''
tl.debug(x)
def run():
a = time.time()
m = App().m # before cd
tl.debug('one vasprun mv etc.:%f s' % (time.time() - a))
a = time.time()
getVaspRun_lammps(m)
tl.debug('one vasprun lmp:%f s' % (time.time() - a))
def check(self):
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
tl.debug('entering loop waiting for vasp...')
while not jobdone.all():
time.sleep(3)
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
# debug(paths[jobdone])
tl.debug('done')
def check(self):
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
tl.debug('entering loop waiting for vasp...')
while not jobdone.all():
time.sleep(3)
jobdone = np.array(
[tl.exists(job.path + "/done") for job in self.jobs])
# debug(paths[jobdone])
tl.debug('done')
def setup(self):
self.bandpoints = {
'K': [0.5, 0.5, 0],
'Gamma': [0, 0, 0],
'X': [0.5, 0.0, 0],
'Y': [0.0, 0.5, 0]
}
self.bandpath = ['X', 'Gamma', 'Y']
tl.debug("graphene potential chosen:Si.tersoff.mod")
self.potential = 'pair_style tersoff/mod\n' +\
'pair_coeff * * %s/Si.tersoff.mod Si' % (
config.lammpspot)
def run(self):
m = self.m
a = time.time()
self.generate_supercells()
debug('generate_supercells:%f s' % (time.time() - a))
files = shell_exec("ls *-*").split('\n')
assert len(files) > 0 and not files[0] == ""
# self.runSPOSCAR()
a = time.time()
self.getvasprun(files)
debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.fc2()
debug('force_constant:%f s' % (time.time() - a))
if m.phofc:
return self
self.postp()
def run(self):
m = self.m
a = time.time()
self.generate_supercells()
debug('generate_supercells:%f s' % (time.time() - a))
files = shell_exec("ls *-*").split('\n')
assert len(files) > 0 and not files[0] == ""
# self.runSPOSCAR()
a = time.time()
self.getvasprun(files)
debug('getvasprun:%f s' % (time.time() - a))
a = time.time()
self.fc2()
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 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 ssh_cmd(self, user, ip, cmd):
passwd = 'AdminYu@224'
ssh = pexpect.spawn('ssh %s@%s "%s"' % (user, ip, cmd))
try:
i = ssh.expect(
['password:'******'continue connecting (yes/no)?'], timeout=5)
if i == 0:
ssh.sendline(passwd)
elif i == 1:
ssh.sendline('yes')
ssh.expect('password: ')
ssh.sendline(passwd)
except pexpect.EOF:
tl.debug("EOF")
except pexpect.TIMEOUT:
tl.debug("TIMEOUT")
else:
r = ssh.read()
tl.debug(r)
ssh.close()
def ssh_cmd(self, user, ip, cmd):
passwd = 'AdminYu@224'
ssh = pexpect.spawn('ssh %s@%s "%s"' % (user, ip, cmd))
try:
i = ssh.expect(['password:'******'continue connecting (yes/no)?'],
timeout=5)
if i == 0:
ssh.sendline(passwd)
elif i == 1:
ssh.sendline('yes')
ssh.expect('password: ')
ssh.sendline(passwd)
except pexpect.EOF:
tl.debug("EOF")
except pexpect.TIMEOUT:
tl.debug("TIMEOUT")
else:
r = ssh.read()
tl.debug(r)
ssh.close()
def generate(self):
m = self.m
hook = Hook()
if m.method == 'nvt':
nvtDevice(hook, m)
elif m.method == 'muller':
mpDevice(hook, m)
elif m.method == 'inject':
ijDevice(hook, m)
elif m.method == 'greenkubo':
gkDevice(hook, m)
tl.debug("tcfactor=" + str(m.tcfactor))
# settings
print("units %s" % m.units)
print("dimension 3")
pbcx = pbcy = pbcz = 's'
if m.xp == 1:
pbcx = 'p'
if m.yp == 1:
pbcy = 'p'
if m.zp == 1:
pbcz = 'p'
print("boundary %s %s %s" % (pbcx, pbcy, pbcz))
print("atom_style atomic")
print("read_restart minimize/restart.minimize")
print("change_box all boundary %s %s %s" % (pbcx, pbcy, pbcz))
print("lattice fcc 5") # needed to define the regions
print("thermo %d" % m.dumpRate)
print("thermo_modify lost warn")
print("timestep %f" % m.timestep)
# regions and groups
hook.doAction('region')
# computes
print("compute ke all ke/atom")
print("compute pe all pe/atom")
print("compute stress all stress/atom NULL virial")
print("compute jflux all heat/flux ke pe stress")
hook.doAction('compute')
# variables
hook.doAction('variable')
# init atoms to T
print(m.masses)
print(m.potential)
print("reset_timestep 0")
print("velocity all create %f %d mom yes rot yes dist gaussian" %
(m.T, m.seed))
if m.dimension == 1:
print("velocity all set NULL 0.0 0.0 units box")
elif m.dimension == 2:
print("velocity all set NULL NULL 0.0 units box")
hook.doAction('equ')
# /* 定时输出dump文件并按id排序*/
if (m.dumpxyz):
print("dump dump1 all atom %d dump.lammpstrj" % (m.dumpRate))
print("dump_modify dump1 sort id")
print("run %d" % m.equTime)
print("unfix getEqu")
print("reset_timestep 0")
hook.doAction('elimination')
print("fix flux_out all ave/time 1 " +
"%d %d c_jflux[1] c_jflux[2] c_jflux[3] file flux.txt " %
(m.aveRate, m.aveRate))
print("variable T_atom atom c_ke/(1.5*%f)" % m.kb)
print("fix T_atom all ave/atom 1 %d %d v_T_atom " %
(m.aveRate, m.aveRate))
print("dump dump_T all custom %d dump.T type xs ys zs f_T_atom" %
(m.dumpRate))
hook.doAction('temp')
hook.doAction('flux')
hook.doAction('swap')
# /* 定时输出速度文件用于计算速度关联函数*/
if (m.dumpv):
print("dump dump2 all custom %d dump.velocity type vx vy vz" %
(m.dumpRate))
print("dump_modify dump2 sort id")
if m.dimension == 1:
print("fix 1d1 all setforce NULL 0. 0.")
print("run %d" % (m.runTime))