def reduce(self, nd, *pn):
from aces.qpointsyaml import phononyaml
pya = phononyaml("qpoints/qpoints.yaml")
nq = pya.nqpoint
nbr = pya.nbranch
import h5py
nma = h5py.File('lifenma.h5')
q = np.array(nma['/q/0/0'])
n = len(q)
v = np.zeros([nq * nbr, n])
def onedir(dir, num):
for idir in num:
print(idir)
nma = h5py.File(dir + '/%d/lifenma.h5' % idir)
for i in range(nq):
for j in range(nbr):
node = '/q/%d/%d' % (i, j)
v[i * nbr + j, :] += np.array(nma[node])
return len(num)
N = 0
for i in range(nd):
dir, num = pn[i * 2:i * 2 + 2]
N += onedir(dir, num)
# N+=onedir('../q3.1',30)
# N+=onedir('../q3.2',90)
v /= N
if tl.exists('phis.h5'):
tl.passthru('rm phis.h5')
phis = h5py.File('phis.h5')
for i in range(nq):
for j in range(nbr):
node = '/%d/%d' % (i, j)
phis[node] = v[i * nbr + j, :]
def reduce(self, nd, *pn):
from aces.qpointsyaml import phononyaml
pya = phononyaml("qpoints/qpoints.yaml")
nq = pya.nqpoint
nbr = pya.nbranch
import h5py
nma = h5py.File('lifenma.h5')
q = np.array(nma['/q/0/0'])
n = len(q)
v = np.zeros([nq * nbr, n])
def onedir(dir, num):
for idir in num:
print(idir)
nma = h5py.File(dir + '/%d/lifenma.h5' % idir)
for i in range(nq):
for j in range(nbr):
node = '/q/%d/%d' % (i, j)
v[i * nbr + j, :] += np.array(nma[node])
return len(num)
N = 0
for i in range(nd):
dir, num = pn[i * 2:i * 2 + 2]
N += onedir(dir, num)
# N+=onedir('../q3.1',30)
# N+=onedir('../q3.2',90)
v /= N
if tl.exists('phis.h5'):
tl.passthru('rm phis.h5')
phis = h5py.File('phis.h5')
for i in range(nq):
for j in range(nbr):
node = '/%d/%d' % (i, j)
phis[node] = v[i * nbr + j, :]
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 runepw1(self):
m = self.m
subcores = m.cores
epw = config.mpirun + str(subcores) + \
config.epw + " -npool " + str(subcores)
cmd3 = epw + " <epw1.in > epw1.out"
tl.passthru(cmd3)
def runepw1(self):
m = self.m
subcores = m.cores
epw = config.mpirun + str(subcores) + \
config.epw + " -npool " + str(subcores)
cmd3 = epw + " <epw1.in > epw1.out"
tl.passthru(cmd3)
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 run(name):
path=home(name)
if not exists(path):
workdir=shell_exec('pwd')
cd(dirname(path))
passthru("make")
cd(workdir)
passthru(path)
def runbol(self):
self.getwin()
p = config.espresso + "bin/postw90.x"
if not tl.exists(p):
print("p not exists")
return
postw90 = self.getx("postw90", pool=False)
tl.passthru(postw90 + " diam")
def runet(self):
tl.cd('et')
m = self.m
if(m.soc):
tl.passthru(config.x_trans_vasp + " BoltzTrap_vasp -so")
else:
tl.passthru(config.x_trans_vasp + " BoltzTrap_vasp")
tl.cd('..')
def runbol(self):
self.getwin()
p = config.espresso + "bin/postw90.x"
if not tl.exists(p):
print("p not exists")
return
postw90 = self.getx("postw90", pool=False)
tl.passthru(postw90 + " diam")
def rerunepw(self):
m = self.m
subcores = m.cores
if not tl.exists('epw.in'):
self.getepwin()
epw = config.mpirun + str(subcores) + \
config.epw + " -npool " + str(subcores)
cmd3 = epw + " <epw.in > epw.out"
tl.passthru(cmd3)
def caltc(self):
m = self.m
tl.passthru(config.phono3py + ' --dim="' + m.dim +
'" -c POSCAR --mesh="' + ' '.join(map(str, m.kpoints)) +
'" --fc3 --fc2 --thm --br')
filename = "kappa-m%s.hdf5" % ''.join(map(str, m.kpoints))
tl.passthru(config.pypath + 'kaccum --mesh="' +
' '.join(map(str, m.kpoints)) + '" POSCAR ' + filename +
' |tee kaccum.dat')
def rerunepw(self):
m = self.m
subcores = m.cores
if not tl.exists('epw.in'):
self.getepwin()
epw = config.mpirun + str(subcores) + \
config.epw + " -npool " + str(subcores)
cmd3 = epw + " <epw.in > epw.out"
tl.passthru(cmd3)
def modulation(self):
m = self.m
conf = """
DIM = %s
MODULATION = 1 1 1, 0 0 0 0 1 0
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'modulation.conf')
passthru(config.phonopy + "--tolerance=1e-4 modulation.conf")
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 modulation(self):
m = self.m
conf = """
DIM = %s
MODULATION = 1 1 1, 0 0 0 0 1 0
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'modulation.conf')
passthru(config.phonopy + "--tolerance=1e-4 modulation.conf")
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 force_constant(self, files):
cmd = config.phono3py + "--cf3 "
for file in files:
dir = "dirs/dir_" + file
cmd += dir + '/vasprun.xml '
tl.write(cmd, 'post.sh')
# generate FORCE_SETS
tl.passthru("sh post.sh")
m = self.m
print("Create fc2.hdf and fc3.hdf")
tl.passthru(config.phono3py + "-c POSCAR --dim='%s'" % (m.dim))
def animate(self):
m = self.m
conf = """
DIM = %s
ANIME = 0 5 20
ANIME_TYPE = xyz
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'animate.conf')
passthru(config.phonopy + "--tolerance=1e-4 animate.conf")
def animate(self):
m = self.m
conf = """
DIM = %s
ANIME = 0 5 20
ANIME_TYPE = xyz
ATOM_NAME = %s
FORCE_CONSTANTS = READ
""" % (m.dim, ' '.join(m.elements))
write(conf, 'animate.conf')
passthru(config.phonopy + "--tolerance=1e-4 animate.conf")
def force_constant(self, files):
cmd = config.phonopy + "-f "
if exists("dir_SPOSCAR/vasprun.xml"):
cmd = config.phonopy + "--fz dir_SPOSCAR/vasprun.xml "
for file in files:
dir = "dirs/dir_" + file
cmd += dir + '/vasprun.xml '
# generate FORCE_SETS
passthru(cmd)
m = self.m
# Create FORCE_CONSTANTS
passthru(config.phonopy + "--tolerance=1e-4 --writefc --dim='%s'" %
(m.dim))
def force_constant(self, files):
cmd = config.phonopy + "-f "
if exists("dir_SPOSCAR/vasprun.xml"):
cmd = config.phonopy + "--fz dir_SPOSCAR/vasprun.xml "
for file in files:
dir = "dirs/dir_" + file
cmd += dir + '/vasprun.xml '
# generate FORCE_SETS
passthru(cmd)
m = self.m
# Create FORCE_CONSTANTS
passthru(config.phonopy + "--tolerance=1e-4 --writefc --dim='%s'" %
(m.dim))
def phanados(self):
from aces.tools import read
m = self.m
s = """20
1
1
%s
2
y
1000
y
phana.dos.txt
0
""" % tl.toString(m.kpoints)
s = s.replace(r'^\s+', '')
tl.write(s, 'phana.dos.in')
tl.passthru(config.phana + 'phonon.bin.%d <phana.dos.in' % m.Ctime)
s = read('pdos.gnuplot')
s = s.replace('pdos.eps', 'phana.dos.eps')
tl.write(s, 'phana.dos.gnuplot')
tl.passthru('rm pdos.gnuplot')
tl.passthru('gnuplot phana.dos.gnuplot')
tl.passthru('convert -rotate 90 phana.dos.eps phana.dos.png')
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 phana(self):
from aces.tools import read
m = self.m
bp = m.bandpath
bpp = m.bandpoints
v = ""
for i in range(len(bp) - 1):
v += "%s\n%s\n101\n" % (tl.toString(bpp[bp[i]]),
tl.toString(bpp[bp[i + 1]]))
s = """20
1
2
phana.band.txt
%sq
0
""" % v
s = s.replace(r'^\s+', '')
tl.write(s, 'phana.in')
tl.passthru(config.phana + 'phonon.bin.%d <phana.in' % m.Ctime)
s = read('pdisp.gnuplot')
s = s.replace('pdisp.eps', 'phana.band.eps')
tl.write(s, 'phana.band.gnuplot')
tl.passthru('rm pdisp.gnuplot')
tl.passthru('gnuplot phana.band.gnuplot')
tl.passthru('convert -rotate 90 phana.band.eps phana.band.png')
def __exit__(self, type, value, trace):
if self.legend:
setLegend(pl, ncol=self.ncol)
pl.savefig(self.filename, bbox_inches='tight', transparent=True)
pl.close()
if self.filename.find(".eps") > 0:
try:
import aces.tools as tl
cmd = "convert %s %s" % (self.filename,
self.filename.replace(
".eps",
".png"))
tl.passthru(cmd)
except Exception as e:
print(e)
def getvqpoints(self, q):
self.generate_vqconf(q)
passthru(config.phonopy + "--tolerance=1e-4 q.conf")
data = parseyaml('qpoints.yaml')
file = open("v.txt", 'w')
for phonon in data['phonon']:
qp = phonon['q-position']
for band in phonon['band']:
frequency = band['frequency']
v = np.array(band['group_velocity'])
v = np.linalg.norm(v)
print >> file, "%s\t%f\t%f" % ('\t'.join(map(
str, qp)), frequency, v)
file.close()
v = np.loadtxt('v.txt')
plot((v[:, 3], 'Frequency (THz)'),
(v[:, 4], 'Group Velocity (Angstrom/ps)'),
'v_freq.png',
grid=True,
scatter=True)
def getvqpoints(self, q):
self.generate_vqconf(q)
passthru(config.phonopy + "--tolerance=1e-4 q.conf")
data = parseyaml('qpoints.yaml')
file = open("v.txt", 'w')
for phonon in data['phonon']:
qp = phonon['q-position']
for band in phonon['band']:
frequency = band['frequency']
v = np.array(band['group_velocity'])
v = np.linalg.norm(v)
print >> file, "%s\t%f\t%f" % ('\t'.join(map(str, qp)),
frequency, v)
file.close()
v = np.loadtxt('v.txt')
plot(
(v[:, 3], 'Frequency (THz)'), (v[:, 4],
'Group Velocity (Angstrom/ps)'),
'v_freq.png',
grid=True,
scatter=True)
def run_anphonin(self):
tl.passthru(config.mpirun + str(self.m.cores) + config.anphon +
" band.in > band.out")
tl.passthru(config.mpirun + str(self.m.cores) + config.anphon +
" dos.in > dos.out")
tl.passthru(config.mpirun + str(self.m.cores) + config.anphon +
" tc.in > tc.out")
def run_anphonin(self):
tl.passthru(config.mpirun + str(self.m.cores) + config.anphon +
" band.in > band.out")
tl.passthru(config.mpirun + str(self.m.cores) + config.anphon +
" dos.in > dos.out")
tl.passthru(config.mpirun + str(self.m.cores) + config.anphon +
" tc.in > tc.out")
def writePOTCAR(options, elements):
dir = 'pot' # LDA
# paw：PAW-LDA
# paw_gga：PAW-GGA-PW91
# paw_pbe：PAW-GGA-PBE
# pot：USPP-LDA
# pot_GGA：USPP-GGA
if not options.paw:
if options.gga:
dir = 'pot_GGA'
else:
dir = 'pot'
else:
if not options.gga:
dir = 'paw'
else:
if options.pbe:
dir = 'paw_pbe'
else:
dir = 'paw_gga'
tl.passthru('cat "" >POTCAR')
for ele in elements:
file = config.vasppot + "/%s/%s/POTCAR" % (dir, ele)
z = False
if not tl.exists(file):
file += '.Z'
z = True
assert tl.exists(file)
if z:
tl.passthru('zcat %s >> POTCAR' % file)
else:
tl.passthru('cat %s >> POTCAR' % file)
def writePOTCAR(options, elements):
dir = 'pot' # LDA
# paw：PAW-LDA
# paw_gga：PAW-GGA-PW91
# paw_pbe：PAW-GGA-PBE
# pot：USPP-LDA
# pot_GGA：USPP-GGA
if not options.paw:
if options.gga:
dir = 'pot_GGA'
else:
dir = 'pot'
else:
if not options.gga:
dir = 'paw'
else:
if options.pbe:
dir = 'paw_pbe'
else:
dir = 'paw_gga'
tl.passthru('cat "" >POTCAR')
for ele in elements:
file = config.vasppot + "/%s/%s/POTCAR" % (dir, ele)
z = False
if not tl.exists(file):
file += '.Z'
z = True
assert tl.exists(file)
if z:
tl.passthru('zcat %s >> POTCAR' % file)
else:
tl.passthru('cat %s >> POTCAR' % file)
def runw(self):
self.getwin()
wannier = self.getx("wannier90", pa=False)
tl.passthru(wannier + " -pp diam")
pw2w = self.getx("pw2wannier90", pool=False)
tl.passthru(pw2w + "<diam.pw2wan >pw2wan.out")
tl.passthru(wannier + " diam")
self.runbol()
def runw(self):
self.getwin()
wannier = self.getx("wannier90", pa=False)
tl.passthru(wannier + " -pp diam")
pw2w = self.getx("pw2wannier90", pool=False)
tl.passthru(pw2w + "<diam.pw2wan >pw2wan.out")
tl.passthru(wannier + " diam")
self.runbol()
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)
if __name__=='__main__': from aces.tools import passthru from aces import config passthru(config.python+"setup.py build --build-lib=. --build-platlib=.")
def runph(self):
if not tl.exists('ph.in'):
self.getphin()
ph = self.getx("ph")
tl.passthru(ph + " < ph.in > ph.out ")
def runnscf(self):
if not tl.exists('nscf.in'):
self.getnscfin()
pw = self.getx("pw")
tl.passthru(pw + " <nscf.in > nscf.out")
def getfcs(self):
tl.passthru(config.alm + "< fit.in > fit.out")
assert tl.exists("alm.fcs")
assert tl.exists("alm.xml")
def displacements(self):
tl.passthru(config.alm + "< alm.in > alm.out")
files = tl.shell_exec("ls *pattern*").split()
tl.passthru(config.almdisp + self.m.toString(files))
def pix(self, cmd):
if tl.exists('dy.h5'):
v = "-lv dy.h5"
else:
v = "dynaphopy.lammpstrj"
tl.passthru("dynaphopy in.dy %s -ts %f %s" % (v, self.m.timestep, cmd))
def generate_supercells(self):
m = self.m
# generate supercells
tl.passthru(config.phono3py + "-d --dim='%s' -c POSCAR" % (m.dim))
def getfcs(self):
tl.passthru(config.alm + "< fit.in > fit.out")
assert tl.exists("alm.fcs")
assert tl.exists("alm.xml")
def runph(self):
if not tl.exists('ph.in'):
self.getphin()
ph = self.getx("ph")
tl.passthru(ph + " < ph.in > ph.out ")
def runnscf(self):
if not tl.exists('nscf.in'):
self.getnscfin()
pw = self.getx("pw")
tl.passthru(pw + " <nscf.in > nscf.out")
def calculateLife(self, eigen, iqp, ibr):
q = self.modeSed(eigen, iqp, ibr)
if tl.exists('velocity.h5md'):
tl.passthru('rm velocity.h5md')
k, freq, vec = eigen
return self.modefit(iqp, ibr, k, freq, q)
def force_constant(self):
cmd = config.phonopy + "--fc dirs/dir_POSCAR001/vasprun.xml"
tl.passthru(cmd)
def generate_supercells3(self):
# generate supercells
cmd = config.thirdorder + "sow" + self.getcut()
print(cmd)
passthru(cmd)
def displacements(self):
tl.passthru(config.alm + "< alm.in > alm.out")
files = tl.shell_exec("ls *pattern*").split()
tl.passthru(config.almdisp + self.m.toString(files))
def runsheng(self):
# Thermal conductivity calculation
m = self.m
print("START SHENGBTE...")
passthru(config.mpirun + " %s " % (m.nodes * m.procs) +
config.shengbte)
def generate(self):
m = self.m
self.get_structure()
f = open("strain.lmp", "w")
print >> f, "units %s" % m.units
print >> f, "dimension 3"
pbcx = "f"
if m.vStrain:
pbcx = "s"
pbcy = pbcz = 's'
if m.xp == 1:
pbcx = 'p'
if m.yp == 1:
pbcy = 'p'
if m.zp == 1:
pbcz = 'p'
print >> f, "boundary %s %s %s" % (pbcx, pbcy, pbcz)
print >> f, "atom_style atomic"
print >> f, "read_data strain_structure"
print >> f, "change_box all boundary %s %s %s" % (pbcx, pbcy, pbcz)
print >> f, "lattice fcc 5" # needed to define the regions
print >> f, "thermo %d" % m.dumpRate
print >> f, "thermo_modify lost warn"
print >> f, m.masses
print >> f, m.potential
print >> f, "timestep %f" % m.timestep
print >> f, "reset_timestep 0"
box = m.box
deta = m.deta
wfix = m.wfix
xlo, xhi, ylo, yhi, zlo, zhi, lx, ly, lz = box
fixl1 = xlo - deta
fixl2 = fixl1 + deta * wfix
fixr2 = xhi + deta
fixr1 = fixr2 - deta * wfix
if m.vStrain:
runTime, content = self.vDeform()
else:
runTime, content = self.deform()
print >> f, "region stayl block %s %s INF INF INF INF units box" % (
fixl1, fixl2)
print >> f, "region stayr block %s %s INF INF INF INF units box" % (
fixr1, fixr2)
print >> f, "region stay union 2 stayl stayr"
print >> f, "region main block %s %s INF INF INF INF units box" % (
fixl2, fixr1)
print >> f, "group stayl region stayl"
print >> f, "group stayr region stayr"
print >> f, "group stay region stay"
print >> f, "group main region main"
print >> f, "velocity stay set 0 0 0"
print >> f, "velocity main create %f %d mom yes rot yes dist gaussian" % (
m.T, m.seed)
#print >>f,"velocity stay set NULL 0 0"
#print >>f,"fix force stay setforce NULL 0 0"
print >> f, "fix getEqu main nvt temp %f %f %f" % (m.T, m.T, m.dtime)
print >> f, "dump dump1 all atom %d dump.lammpstrj" % (max(
runTime / 1000, 1))
print >> f, "dump_modify dump1 sort id"
print >> f, "run %d" % m.equTime
print >> f, "unfix getEqu"
print >> f, "reset_timestep 0"
print >> f, "fix nve main nve"
print >> f, "compute disp all displace/atom"
print >> f, "compute s1 all stress/atom NULL"
print >> f, "compute rr stayr com"
print >> f, "compute rl stayl com"
print >> f, "fix 2 main temp/berendsen %f %f 1" % (m.T, m.T)
print >> f, "fix s all ave/atom 1 %d %d c_disp[1] c_s1[1] c_s1[2] c_s1[3] c_s1[4] c_s1[5] c_s1[6]" % (
m.strainStep, m.strainStep)
print >> f, "dump 1 all custom %d dump.tensile id type xs ys zs f_s[1] f_s[1] f_s[2] f_s[3] f_s[4] f_s[5] f_s[6] f_s[7]" % m.strainStep
print >> f, "dump_modify 1 sort id"
print >> f, "variable lx equal c_rr[1]-c_rl[1]"
print >> f, "variable pxx equal pxx"
print >> f, "fix p all ave/time 1 %d %d v_lx v_pxx file strain_stress.txt" % (
m.strainStep, m.strainStep)
#print >>f,"dump lala main custom %s velocity.txt id type vx vy vz"%m.Cinterval
print >> f, content
f.close()
tl.passthru(config.mpirun + " %s " % self.m.cores + config.lammps +
" <strain.lmp >out.dat")
self.post()
