def gen_cry2qwalk(dftfn):
loc = '/'.join([os.getcwd()] + dftfn.split('/')[:-1])
root = dftfn.split('/')[-1].replace('.d12', '')
propfn = root + '.d3'
dftdat = read_cryinp(open(dftfn, 'r'))
shrink = dftdat['kdens']
proplines = []
proplines.append('NEWK')
proplines.append('{0} {1}'.format(shrink, 2 * shrink))
proplines.append('0 1')
proplines.append('67 999')
proplines.append('END')
with open('/'.join((loc, propfn)), 'w') as propf:
propf.write('\n'.join(proplines))
exe = '~/bin/properties < {0}'.format(propfn)
out = propfn + '.out'
fc = []
fc.append('cat {root}.d12.out {root}.d3.out > tmp'.format(root=root))
fc.append(
'addline=`grep -n "HAMILTONIAN EIGENVECTORS" tmp | head -1 | cut -d":" -f1`'
)
fc.append('sed "$addline i NEWK EIGENVECTORS" tmp > crystal2qmc.inp')
fc.append('rm -f tmp')
fc.append(
'~/bin/crystal2qmc -o {root} crystal2qmc.inp &>> crystal2qmc.out'.
format(root=root))
return gen_qsub(exe,
stdout=out,
loc=loc,
name=loc + ' gen_cry2qwalk',
time='02:00:00',
queue='secondary',
final_commands=fc)
def gen_cry2qwalk(dftfn):
loc = '/'.join([os.getcwd()]+dftfn.split('/')[:-1])
root = dftfn.split('/')[-1].replace('.d12','')
propfn = root+'.d3'
dftdat = read_cryinp(open(dftfn,'r'))
shrink = dftdat['kdens']
proplines = []
proplines.append('NEWK')
proplines.append('{0} {1}'.format(shrink,2*shrink))
proplines.append('0 1')
proplines.append('67 999')
proplines.append('END')
with open('/'.join((loc,propfn)),'w') as propf:
propf.write('\n'.join(proplines))
exe = '~/bin/properties < {0}'.format(propfn)
out = propfn+'.out'
fc = []
fc.append('cat {root}.d12.out {root}.d3.out > tmp'.format(root=root))
fc.append('addline=`grep -n "HAMILTONIAN EIGENVECTORS" tmp | head -1 | cut -d":" -f1`')
fc.append('sed "$addline i NEWK EIGENVECTORS" tmp > crystal2qmc.inp')
fc.append('rm -f tmp')
fc.append('~/bin/crystal2qmc -o {root} crystal2qmc.inp &>> crystal2qmc.out'.format(root=root))
return gen_qsub(exe,stdout=out,loc=loc,
name=loc+' gen_cry2qwalk',
time='02:00:00',
queue='secondary',
final_commands=fc)
def submit_job(base, lines, cwd):
if not os.path.exists(base): os.mkdir(base)
os.chdir(base)
with open("%s.inp" % base, 'w') as outf:
outf.write("\n".join([" ".join(l) for l in lines]))
pc = ["module load openmpi/1.4-gcc+ifort"]
qin = gen_qsub("~/bin/pw.x < %s.inp" % (base),
stdout="%s.out" % (base),
queue="physics",
name="%s/%s.out" % (cwd, base),
time="72:00:00",
nn=1,
prep_commands=pc)
print sp.check_output("qsub %s" % qin, shell=True)
os.chdir(cwd)
def submit_job(base, lines, cwd):
if not os.path.exists(base):
os.mkdir(base)
os.chdir(base)
with open("%s.inp" % base, "w") as outf:
outf.write("\n".join([" ".join(l) for l in lines]))
pc = ["module load openmpi/1.4-gcc+ifort"]
qin = gen_qsub(
"~/bin/pw.x < %s.inp" % (base),
stdout="%s.out" % (base),
queue="physics",
name="%s/%s.out" % (cwd, base),
time="72:00:00",
nn=1,
prep_commands=pc,
)
print sp.check_output("qsub %s" % qin, shell=True)
os.chdir(cwd)
def gen_optimize(dftfn,time='02:00:00'):
loc = '/'.join([os.getcwd()]+dftfn.split('/')[:-1])
root = dftfn.split('/')[-1].replace('.d12','')
opt1fn = root+'_0.opt1'
with open('/'.join((loc,opt1fn)),'w') as opt1f:
opt1lines = []
opt1lines.append('method{ optimize }')
opt1lines.append('include %s_0.sys'%root)
opt1lines.append('trialfunc{ slater-jastrow ')
opt1lines.append('wf1{ include %s_0.slater }'%root)
opt1lines.append('wf2{ include %s.jast2 }'%root)
opt1lines.append('}')
opt1f.write('\n'.join(opt1lines))
optfn = root+'_0.opt'
with open('/'.join((loc,optfn)),'w') as optf:
optlines = []
optlines.append('method{ optimize }')
optlines.append('include %s_0.sys'%root)
optlines.append('trialfunc{ include %s_0.opt.wfout }'%root)
optf.write('\n'.join(optlines))
exe = '~/bin/qwalk $inpfile'
out = optfn+'.out'
pc = ['module load openmpi/1.4-gcc+ifort']
pc += ['if [ -f {root}_0.opt.wfout ]'.format(root=root)]
pc += ['then inpfile={0}'.format(optfn)]
pc += ['else inpfile={0}'.format(opt1fn)]
pc += ['fi']
fc = []
fc += ['if [ ! -f {root}_0.opt.wfout ]'.format(root=root)]
fc += ['then cp {root}_0.opt1.wfout {root}_0.opt.wfout'.format(root=root)]
fc += ['fi']
fc += ['~/bin/separate_jastrow {root}_0.opt.wfout > {root}_0.opt.jast2'.format(root=root)]
return my.gen_qsub(exe,stdout=out,loc=loc,
name=loc+' gen_optimize',
time=time,
nn=2,np=12,
queue='secondary',
prep_commands=pc,
final_commands=fc)
def gen_optimize(dftfn,time='02:00:00'):
loc = '/'.join([os.getcwd()]+dftfn.split('/')[:-1])
root = dftfn.split('/')[-1].replace('.d12','')
opt1fn = root+'_0.opt1'
with open('/'.join((loc,opt1fn)),'w') as opt1f:
opt1lines = []
opt1lines.append('method{ optimize }')
opt1lines.append('include %s_0.sys'%root)
opt1lines.append('trialfunc{ slater-jastrow ')
opt1lines.append('wf1{ include %s_0.slater }'%root)
opt1lines.append('wf2{ include %s.jast2 }'%root)
opt1lines.append('}')
opt1f.write('\n'.join(opt1lines))
optfn = root+'_0.opt'
with open('/'.join((loc,optfn)),'w') as optf:
optlines = []
optlines.append('method{ optimize }')
optlines.append('include %s_0.sys'%root)
optlines.append('trialfunc{ include %s_0.opt.wfout }'%root)
optf.write('\n'.join(optlines))
exe = '~/bin/qwalk $inpfile'
out = optfn+'.out'
pc = ['module load openmpi/1.4-gcc+ifort']
pc += ['if [ -f {root}_0.opt.wfout ]'.format(root=root)]
pc += ['then inpfile={0}'.format(optfn)]
pc += ['else inpfile={0}'.format(opt1fn)]
pc += ['fi']
fc = []
fc += ['if [ ! -f {root}_0.opt.wfout ]'.format(root=root)]
fc += ['then cp {root}_0.opt1.wfout {root}_0.opt.wfout'.format(root=root)]
fc += ['fi']
fc += ['~/bin/separate_jastrow {root}_0.opt.wfout > {root}_0.opt.jast2'.format(root=root)]
return my.gen_qsub(exe,stdout=out,loc=loc,
name=loc+' gen_optimize',
time=time,
nn=2,np=12,
queue='secondary',
prep_commands=pc,
final_commands=fc)
sh.copyfile(use_fort,name+'/fort.20')
os.chdir(name)
tmplines[4] = " ".join(map(str,geo[:2]))
se_part = tmplines[7].split(" ")
se_part[-1] = str(geo[-1])
tmplines[7] = " ".join(se_part)
with open(name+".d12",'w') as outf:
outf.write("\n".join(tmplines))
pc[-1] = "cp %s.d12 INPUT"%name
qsub = my.gen_qsub(exe,
stdout = name+".d12.out",
loc = os.getcwd(),
name = "%s %s"%(os.getcwd(),name),
time = time,
nn = nn,
queue = queue,
prep_commands = pc,
final_commands = fc
)
print name, sub.check_output("qsub %s"%qsub,shell=True)
os.chdir(cwd)
################################################################################
# Edit options.
shrinklist = []#[2,4,6,8,10,12]
tmplines = deepcopy(baselines)
for shrink in shrinklist:
name = "shrink_%d"%shrink
if not os.path.isdir(name):
inplines = inpstr.split("\n")
if needs_guessp:
i = 0
while inplines[-i] != "END":
i += 1
inplines[-i] = "GUESSP"
try:
inplines[-i + 1] = "END"
except IndexError:
inplines.append("END")
newinpfn = "new." + inpfn
with open(newinpfn, 'w') as outf:
outf.write("\n".join(inplines))
sh.copyfile(use_fort, "fort.20")
pc[-1] = "cp %s INPUT" % newinpfn
qsub = my.gen_qsub(exe,
stdout=newinpfn + ".out",
loc=os.getcwd(),
name="%s %s" % (os.getcwd(), newinpfn),
time=time,
nn=nn,
queue=queue,
prep_commands=pc,
final_commands=fc)
print newinpfn, sub.check_output("qsub %s" % qsub, shell=True)
os.chdir(cwd)
import qefiles_io as qeio
import os
import mython as my
import sys
import subprocess as sub
qpts = [(0.0, 0.0, 0.0), (0.25, 0.0, 0.0), (0.5, 0.0, 0.0), (0.75, 0.0, 0.0)]
scfinp = open(sys.argv[1], 'r')
inps = qeio.gen_phonon(qpts, scfinp, bundle=True)
cwd = os.getcwd()
for fname in inps:
if '/' in fname:
dname = '/'.join(fname.split('/')[:-1])
fname = fname.split('/')[-1]
os.chdir(dname)
qsub = my.gen_qsub('~/bin/ph.x < %s' % fname,
stdout=fname.replace('inp', 'out'),
loc=os.getcwd(),
nn=1,
np=8)
print sub.check_output("qsub %s" % qsub, shell=True)
os.chdir(cwd)
with open('base.d12','w') as outf:
outf.write(lines2str(baselines))
for hy in hyb_list:
for dx in dx_list:
dr = 'hy_%d_dx_%.2f'%(hy,dx)
baselines[spot[0]][spot[1]] = val+dx
baselines[hyb_spot][0] = hy
if not os.path.exists(dr):
os.makedirs(dr)
with open('{dr}/{dr}.d12'.format(dr=dr),'w') as outf:
outf.write(lines2str(baselines))
loc = '/'.join((os.getcwd(),dr))
pc = ['module load openmpi/1.4-gcc+ifort',
'cp {dr}.d12 INPUT'.format(dr=dr)]
fc = ['rm *.pe[0-9] *.pe[0-9][0-9]']
qin = gen_qsub('~/bin/Pcrystal',
loc=loc,
name='_'.join((sys.argv[1][:3],dr)),
stdout=dr+'.d12.out',
time='4:00:00',
nn=2,np=12,
queue='secondary',
prep_commands = pc,
final_commands = fc)
#print check_output('cp -v {0}/fort.79 {0}/fort.20'.format(dr),shell=True)
print check_output('cp -v fort.9 {0}/fort.20'.format(dr),shell=True)
print check_output('qsub {0}'.format(qin),shell=True)
qsub = []
qsub.append('qsub')
qsub.append('-q prod')
qsub.append('-A SuperMatSim')
qsub.append('-t {time}'.format(time=time))
qsub.append('-n {nproc}'.format(nproc=nproc))
qsub.append('--mode c32')
qsub.append('-o {gamma}.dmc.out'.format(gamma=gamma))
qsub.append('~/bin/qwalk')
qsub += dmcfns
qin = ' '.join(qsub)
print check_output(qin, shell=True)
#print qin
elif system == 'taub':
pc = ['module load openmpi/1.4-gcc+ifort']
for dmcfn in dmcfns:
qin = gen_qsub('~/bin/qwalk {0}'.format(dmcfn),
stdout=dmcfn + '.out',
name='/'.join((os.getcwd(), dmcfn)),
time='4:00:00',
nn=4,
np=12,
queue='secondary',
prep_commands=pc)
print check_output('qsub ' + qin, shell=True)
#print qin
else:
print "You need to add appropriate submission routine."
os.chdir(wd)
import qefiles_io as qeio
import os
import mython as my
import sys
import subprocess as sub
qpts = [(0.0,0.0,0.0),(0.25,0.0,0.0),(0.5,0.0,0.0),(0.75,0.0,0.0)]
scfinp = open(sys.argv[1],'r')
inps = qeio.gen_phonon(qpts,scfinp,bundle=True)
cwd = os.getcwd()
for fname in inps:
if '/' in fname:
dname = '/'.join(fname.split('/')[:-1])
fname = fname.split('/')[-1]
os.chdir(dname)
qsub = my.gen_qsub(
'~/bin/ph.x < %s'%fname,
stdout=fname.replace('inp','out'),
loc=os.getcwd(),
nn=1,np=8)
print sub.check_output("qsub %s"%qsub,shell=True)
os.chdir(cwd)
nproc=512*4
qsub = []
qsub.append('qsub')
qsub.append('-q prod')
qsub.append('-A SuperMatSim')
qsub.append('-t {time}'.format(time=time))
qsub.append('-n {nproc}'.format(nproc=nproc))
qsub.append('--mode c32')
qsub.append('-o {gamma}.dmc.out'.format(gamma=gamma))
qsub.append('~/bin/qwalk')
qsub += dmcfns
qin = ' '.join(qsub)
print check_output(qin,shell=True)
#print qin
elif system == 'taub':
pc = ['module load openmpi/1.4-gcc+ifort']
for dmcfn in dmcfns:
qin = gen_qsub('~/bin/qwalk {0}'.format(dmcfn),
stdout=dmcfn+'.out',
name='/'.join((os.getcwd(),dmcfn)),
time='4:00:00',
nn=4,np=12,
queue='secondary',
prep_commands=pc)
print check_output('qsub '+qin,shell=True)
#print qin
else:
print "You need to add appropriate submission routine."
os.chdir(wd)
pprfns = [
gen_ppr(root,
gosling="/home/busemey2/bin/gosling",
jast=gamma + '.opt.jast2') for root in roots
]
pc = []
pc += ['module load openmpi/1.4-gcc+ifort']
pc += ['module load gcc/4.7.1']
pc += ['module load intel/11.1']
for root in roots:
if not os.path.isfile(root + ".dmc.tracele"):
print "Swapping endian of %s." % (root + ".dmc.trace")
sub.call("/home/busemey2/bin/swap_endian {0} {1}".format(
root + ".dmc.trace", root + ".dmc.tracele"),
shell=True)
for pprfn in pprfns:
qin = gen_qsub('~/bin/qwalk {0}'.format(pprfn),
stdout=pprfn + '.out',
name='/'.join((os.getcwd(), pprfn)),
time='04:00:00',
nn=2,
queue='secondary',
prep_commands=pc)
print sub.check_output('qsub ' + qin, shell=True)
os.chdir(wd)
loc = '/'.join(dftloc.split('/')[:-1])
os.chdir(wd + '/' + loc)
pprfns = [gen_ppr(root,gosling="/home/busemey2/bin/gosling",
jast=gamma+'.opt.jast2') for root in roots]
pc = []
pc += ['module load openmpi/1.4-gcc+ifort']
pc += ['module load gcc/4.7.1']
pc += ['module load intel/11.1']
for root in roots:
if not os.path.isfile(root+".dmc.tracele"):
print "Swapping endian of %s."%(root+".dmc.trace")
sub.call("/home/busemey2/bin/swap_endian {0} {1}".format(
root+".dmc.trace",root+".dmc.tracele"),
shell=True)
for pprfn in pprfns:
qin = gen_qsub('~/bin/qwalk {0}'.format(pprfn),
stdout=pprfn+'.out',
name='/'.join((os.getcwd(),pprfn)),
time='04:00:00',
nn=2,
queue='secondary',
prep_commands=pc)
print sub.check_output('qsub '+qin,shell=True)
os.chdir(wd)
if needs_guessp:
i=0
while inplines[-i] != "END":
i += 1
inplines[-i] = "GUESSP"
try:
inplines[-i+1] = "END"
except IndexError:
inplines.append("END")
newinpfn = "new."+inpfn
with open(newinpfn,'w') as outf:
outf.write("\n".join(inplines))
sh.copyfile(use_fort,"fort.20")
pc[-1] = "cp %s INPUT"%newinpfn
qsub = my.gen_qsub(exe,
stdout = newinpfn+".out",
loc = os.getcwd(),
name = "%s %s"%(os.getcwd(),newinpfn),
time = time,
nn = nn,
queue = queue,
prep_commands = pc,
final_commands = fc
)
print newinpfn, sub.check_output("qsub %s"%qsub,shell=True)
os.chdir(cwd)
for hy in hyb_list:
for dx in dx_list:
dr = 'hy_%d_dx_%.2f' % (hy, dx)
baselines[spot[0]][spot[1]] = val + dx
baselines[hyb_spot][0] = hy
if not os.path.exists(dr):
os.makedirs(dr)
with open('{dr}/{dr}.d12'.format(dr=dr), 'w') as outf:
outf.write(lines2str(baselines))
loc = '/'.join((os.getcwd(), dr))
pc = [
'module load openmpi/1.4-gcc+ifort',
'cp {dr}.d12 INPUT'.format(dr=dr)
]
fc = ['rm *.pe[0-9] *.pe[0-9][0-9]']
qin = gen_qsub('~/bin/Pcrystal',
loc=loc,
name='_'.join((sys.argv[1][:3], dr)),
stdout=dr + '.d12.out',
time='4:00:00',
nn=2,
np=12,
queue='secondary',
prep_commands=pc,
final_commands=fc)
#print check_output('cp -v {0}/fort.79 {0}/fort.20'.format(dr),shell=True)
print check_output('cp -v fort.9 {0}/fort.20'.format(dr), shell=True)
print check_output('qsub {0}'.format(qin), shell=True)