def main(filePrefix):
# filePrefix='140415c'
quenchFileInit = 'quench_asi_nofilename.lmp'
# quenchFile='quench_asi_'+filePrefix+'.lmpc'
nemdFileInit = 'nemd_asi_nofilename.lmp'
# nemdFile='nemd_asi_'+filePrefix+'.lmpc'
dataFile = filePrefix + '_Si.dat'
restartFile = filePrefix + '.quenched.restart'
LAMMPSParams = '-var filename ' + filePrefix
length = 200 # Length of the system in Angstroms
width = 70 # Width of the system in Angstroms
# width=30 # Width of the system in Angstroms
mass = 28.0 # Mass to be used in writing the LAMMPS data file
rho = 2.291 # Density in g/cm^3
# rho=2.33 # Larkin Si.sw
Natoms = np.int(
np.round(rho * 1e-3 / 1e-6 * length * width**2 * 1e-30 /
(mass * 1.6605e-27)))
print "The system contains %d atoms." % (Natoms)
timeQuench = '0-12:00:00'
timeNemd = '0-12:00:00'
# partition='test'
# partition='parallel'
partition = 'small'
nodes = 4
if os.path.isfile(restartFile):
answer = raw_input(
'The restartfile ' + restartFile +
' exists, do you want to perform the quenching anyway ([y/n], default=y)?.\n'
)
# print answer
if answer == 'n':
runQuench = False
print 'Skipping the quenching.'
else:
runQuench = True
print 'Performing the quenching.'
else:
runQuench = True
# sys.exit()
# Determine the system from the hostname
p = Popen(["hostname"], shell=True, stdout=PIPE, stderr=PIPE)
out, err = p.communicate()
host = out.split('-')[0]
print "Running in " + host + "."
system = host.upper()
if system == 'SISU':
LammpsExec = '/wrk/kisaaski/lammps_sisu/lmp_sisu'
ncpus = nodes * 24
elif system == 'TAITO':
LammpsExec = '/wrk/kisaaski/lammps_sisu/lmp_taito_040215'
ncpus = nodes * 16
else:
raise StandardError, "Could not determine the system."
print "%d atoms per core." % (round(Natoms / ncpus))
# sys.exit()
if runQuench:
# Create the box of silicon atoms, write to datafile
ab = atombox(length, width, Natoms)
ab.fillBox(seed=1234)
ab.writeToFile(dataFile, mass)
del ab
batchQuenchScript = 'batch_quench_' + filePrefix + '.sh'
# Prepare the batch script
prepareBatch(batchQuenchScript,
LammpsExec,
quenchFileInit,
execParams=LAMMPSParams,
outputFile=filePrefix + '_quench.out',
ntasks=ncpus,
nodes=nodes,
time=timeQuench,
partition=partition,
system=system,
out=filePrefix + '_quench.slurm',
jobname=filePrefix + '_quench.job')
# sys.exit()
# Submit the batch script
try:
command1 = "sbatch " + batchQuenchScript
print "Shell command: " + command1
p = Popen([command1],
shell=True,
stdin=PIPE,
stdout=PIPE,
stderr=PIPE)
out, err = p.communicate()
p.wait()
if err != '': # Failed the submission
raise SubmissionError("Failed the submission of quench job.",
err)
if out != '':
print "Output from the first submission: " + out.strip('\n')
quenchJobId = str(out.split(' ')[-1]).strip(' ').strip('\n')
print "Job id=" + str(quenchJobId)
except SubmissionError as S:
# if err!='':
print "Error: ", S.message
print "Output: " + S.error
sys.exit()
else: # Quench not run, set quenchJobId to empty string so that no dependency is created for the NEMD job.
quenchJobId = ''
# sys.exit()
# Prepare the second batch script
batchNemdScript = 'batch_nemd_' + filePrefix + '.sh'
# Prepare the NEMD batch script
prepareBatch(batchNemdScript,
LammpsExec,
nemdFileInit,
execParams=LAMMPSParams,
outputFile=filePrefix + '_nemd.out',
ntasks=ncpus,
time=timeNemd,
nodes=nodes,
partition=partition,
system=system,
dependency='afterany:' + quenchJobId,
out=filePrefix + '_nemd.slurm',
jobname=filePrefix + '_nemd.job')
# Submit the batch script
try:
command2 = "sbatch " + batchNemdScript
print "Shell command: " + command2
# p=Popen([command2],shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE)
p = Popen([command2], shell=True, stdout=PIPE, stderr=PIPE)
out, err = p.communicate()
p.wait()
if err != '': # Failed the submission
raise SubmissionError("Failed the submission of NEMD job.", err)
if out != '':
print "Output from the second submission: " + out.strip('\n')
NemdJobId = str(out.split(' ')[-1]).strip(' ').strip('\n')
# print "Job id="+str(NemdJobId)
except SubmissionError as S:
# if err!='':
print "Error: ", S.message
print "Error output from the submission: " + S.error
sys.exit()
def main(filePrefix):
# filePrefix='090415a'
dataFile=filePrefix+'_Si.dat'
restartFile=filePrefix+'.quenched.restart'
length=200
width=20
mass=28.0
rho=2.291 # Density in g/cm^3
Natoms=np.int(np.round(rho*1e-3/1e-6*length*width**2*1e-30/(mass*1.66e-27)))
# Create the box of silicon atoms, write to datafile
ab=atombox(length,width,Natoms)
ab.fillBox(seed=1234)
ab.writeToFile(dataFile,mass)
del ab
# Minimize the atom positions
lmp=lammps()
lmp.command("variable filename string '"+filePrefix+"'")
lmp.command("variable datafile string '"+dataFile+"'")
lmp.command("variable restartfile string '"+restartFile+"'")
def iterateFile(lmp,filename):
'''
Do the same as lmp.file(filename) but allow the script to be continued after quit.
'''
with open(filename,"r") as f:
for line in f:
print line
if "quit" in line and line[0]!="#":
return
else:
lmp.command(line)
return
# lmp.file("quench_Si.lmp") # If quit is found, python quits
iterateFile(lmp,"quench_Si.lmp")
lmp.close()
# Create a new LAMMPS object
lmp=lammps()
lmp.command("variable filename string '"+filePrefix+"'")
lmp.command("variable restartfile string '"+restartFile+"'")
iterateFile(lmp,"amorphous_interface.lmp")
# lmp.file("amorphous_interface.lmp")
fileCompactVels=filePrefix+'.vels.dat.compact'
fileVels=filePrefix+'.vels.dat'
widthWin=0.5e12
KijFilePrefix=filePrefix
scaleFactor=1.602e-19/(1e-20)*1e4
dt_md=2.5e-15
pP=SHCPostProc.SHCPostProc(fileCompactVels,KijFilePrefix,
dt_md=dt_md,scaleFactor=scaleFactor,
LAMMPSDumpFile=fileVels,
widthWin=widthWin,
NChunks=20,chunkSize=50000,
backupPrefix=filePrefix,
LAMMPSRestartFile=restartFile,
reCalcVels=True,
reCalcFC=True)
pP.postProcess()
# Pickling the post-processing object into file
import cPickle as pickle
with open(filePrefix+'_PP.pckl','w') as f:
pickle.dump(pP,f)
# Saving into numpy files
np.save(filePrefix+'_oms.npy',pP.oms_fft)
np.save(filePrefix+'_SHC.npy',pP.SHC_smooth)
# Saving the frequencies and heat currents to file
np.savetxt(fileprefix+'_SHC.txt',np.column_stack((oms,pP.SHC_smooth)))
def main(filePrefix):
# filePrefix='140415c'
quenchFileInit='quench_asi_nofilename_press.lmp'
# quenchFile='quench_asi_'+filePrefix+'.lmpc'
nemdFileInit='nemd_asi_nofilename.lmp'
# nemdFile='nemd_asi_'+filePrefix+'.lmpc'
dataFile=filePrefix+'_Si.dat'
restartFile=filePrefix+'.quenched.restart'
LAMMPSParams='-var filename '+filePrefix
length=200 # Length of the system in Angstroms
width=70 # Width of the system in Angstroms
# width=30 # Width of the system in Angstroms
mass=28.0 # Mass to be used in writing the LAMMPS data file
rho=2.291 # Density in g/cm^3
# rho=2.33 # Larkin Si.sw
Natoms=np.int(np.round(rho*1e-3/1e-6*length*width**2*1e-30/(mass*1.6605e-27)))
print "The system contains %d atoms." % (Natoms)
timeQuench='0-12:00:00'
timeNemd='0-12:00:00'
# partition='test'
# partition='parallel'
partition='small'
nodes=4
if os.path.isfile(restartFile):
answer=raw_input('The restartfile '+restartFile+' exists, do you want to perform the quenching anyway ([y/n], default=y)?.\n')
# print answer
if answer=='n':
runQuench=False
print 'Skipping the quenching.'
else:
runQuench=True
print 'Performing the quenching.'
else:
runQuench=True
# sys.exit()
# Determine the system from the hostname
p=Popen(["hostname"],shell=True, stdout=PIPE, stderr=PIPE)
out,err=p.communicate()
host=out.split('-')[0]
print "Running in "+host+"."
system=host.upper()
if system=='SISU':
LammpsExec='/wrk/kisaaski/lammps_sisu/lmp_sisu'
ncpus=nodes*24
elif system=='TAITO':
LammpsExec='/wrk/kisaaski/lammps_sisu/lmp_taito_040215'
ncpus=nodes*16
else:
raise StandardError, "Could not determine the system."
print "%d atoms per core." % (round(Natoms/ncpus))
# sys.exit()
if runQuench:
# Create the box of silicon atoms, write to datafile
ab=atombox(length,width,Natoms)
ab.fillBox(seed=1234)
ab.writeToFile(dataFile,mass)
del ab
batchQuenchScript='batch_quench_'+filePrefix+'.sh'
# Prepare the batch script
prepareBatch(batchQuenchScript,LammpsExec,quenchFileInit,execParams=LAMMPSParams,outputFile=filePrefix+'_quench.out',ntasks=ncpus,nodes=nodes,time=timeQuench,partition=partition,system=system,out=filePrefix+'_quench.slurm',jobname=filePrefix+'_quench.job')
# sys.exit()
# Submit the batch script
try:
command1="sbatch "+batchQuenchScript
print "Shell command: " + command1
p=Popen([command1],shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE)
out,err=p.communicate()
p.wait()
if err!='': # Failed the submission
raise SubmissionError("Failed the submission of quench job.",err)
if out!='':
print "Output from the first submission: "+ out.strip('\n')
quenchJobId=str(out.split(' ')[-1]).strip(' ').strip('\n')
print "Job id="+str(quenchJobId)
except SubmissionError as S:
# if err!='':
print "Error: ", S.message
print "Output: " + S.error
sys.exit()
else: # Quench not run, set quenchJobId to empty string so that no dependency is created for the NEMD job.
quenchJobId=''
# sys.exit()
# Prepare the second batch script
batchNemdScript='batch_nemd_'+filePrefix+'.sh'
# Prepare the NEMD batch script
prepareBatch(batchNemdScript,LammpsExec,nemdFileInit,execParams=LAMMPSParams,outputFile=filePrefix+'_nemd.out',ntasks=ncpus,time=timeNemd,nodes=nodes,partition=partition,system=system,dependency='afterany:'+quenchJobId,out=filePrefix+'_nemd.slurm',jobname=filePrefix+'_nemd.job')
# Submit the batch script
try:
command2="sbatch "+batchNemdScript
print "Shell command: " + command2
# p=Popen([command2],shell=True, stdin=PIPE, stdout=PIPE, stderr=PIPE)
p=Popen([command2],shell=True, stdout=PIPE, stderr=PIPE)
out,err=p.communicate()
p.wait()
if err!='': # Failed the submission
raise SubmissionError("Failed the submission of NEMD job.",err)
if out!='':
print "Output from the second submission: "+ out.strip('\n')
NemdJobId=str(out.split(' ')[-1]).strip(' ').strip('\n')
# print "Job id="+str(NemdJobId)
except SubmissionError as S:
# if err!='':
print "Error: ", S.message
print "Error output from the submission: " + S.error
sys.exit()
def main(filePrefix):
# filePrefix='090415a'
dataFile = filePrefix + '_Si.dat'
restartFile = filePrefix + '.quenched.restart'
length = 200
width = 20
mass = 28.0
rho = 2.291 # Density in g/cm^3
Natoms = np.int(
np.round(rho * 1e-3 / 1e-6 * length * width**2 * 1e-30 /
(mass * 1.66e-27)))
# Create the box of silicon atoms, write to datafile
ab = atombox(length, width, Natoms)
ab.fillBox(seed=1234)
ab.writeToFile(dataFile, mass)
del ab
# Minimize the atom positions
lmp = lammps()
lmp.command("variable filename string '" + filePrefix + "'")
lmp.command("variable datafile string '" + dataFile + "'")
lmp.command("variable restartfile string '" + restartFile + "'")
def iterateFile(lmp, filename):
'''
Do the same as lmp.file(filename) but allow the script to be continued after quit.
'''
with open(filename, "r") as f:
for line in f:
print line
if "quit" in line and line[0] != "#":
return
else:
lmp.command(line)
return
# lmp.file("quench_Si.lmp") # If quit is found, python quits
iterateFile(lmp, "quench_Si.lmp")
lmp.close()
# Create a new LAMMPS object
lmp = lammps()
lmp.command("variable filename string '" + filePrefix + "'")
lmp.command("variable restartfile string '" + restartFile + "'")
iterateFile(lmp, "amorphous_interface.lmp")
# lmp.file("amorphous_interface.lmp")
fileCompactVels = filePrefix + '.vels.dat.compact'
fileVels = filePrefix + '.vels.dat'
widthWin = 0.5e12
KijFilePrefix = filePrefix
scaleFactor = 1.602e-19 / (1e-20) * 1e4
dt_md = 2.5e-15
pP = SHCPostProc.SHCPostProc(fileCompactVels,
KijFilePrefix,
dt_md=dt_md,
scaleFactor=scaleFactor,
LAMMPSDumpFile=fileVels,
widthWin=widthWin,
NChunks=20,
chunkSize=50000,
backupPrefix=filePrefix,
LAMMPSRestartFile=restartFile,
reCalcVels=True,
reCalcFC=True)
pP.postProcess()
# Pickling the post-processing object into file
import cPickle as pickle
with open(filePrefix + '_PP.pckl', 'w') as f:
pickle.dump(pP, f)
# Saving into numpy files
np.save(filePrefix + '_oms.npy', pP.oms_fft)
np.save(filePrefix + '_SHC.npy', pP.SHC_smooth)
# Saving the frequencies and heat currents to file
np.savetxt(fileprefix + '_SHC.txt', np.column_stack((oms, pP.SHC_smooth)))
