def createdirs(poscarsDir, maindir, vaspinputdir):
'''makes dir in maindir for each structure in poscarsDir'''
potcarDir = "/fslhome/bch/vaspfiles/src/potpaw_PBE"
for file in os.listdir(poscarsDir):
info = file.split('_')
struct = '_'.join(info[1:3])
structDir = '{}/{}'.format(maindir, struct)
atom = info[1]
if not os.path.isdir(structDir):
os.system('mkdir {}'.format(structDir)) #structure is in
os.system('cp {}/{} {}/POSCAR'.format(poscarsDir, file, structDir))
print 'atom', atom
try:
potcar = readfile('{}/{}/POTCAR'.format(potcarDir, atom))
except:
try:
potcar = readfile('{}/{}_pv/POTCAR'.format(potcarDir, atom))
except:
potcar = readfile('{}/{}_sv/POTCAR'.format(potcarDir, atom))
potcar += potcar #multiple atoms in POSCAR have only one POTCAR, so they are really all pure cases
writefile(potcar, '{}/POTCAR'.format(structDir))
os.system('cp {}/INCAR {}'.format(vaspinputdir, structDir))
modIncar(structDir)
os.system('cp -P {}/vasp.x {}'.format(vaspinputdir, structDir))
return
def createStructDirs(dir,poscarsDir,vaspinputdir):
'''makes struct folder in dir for each structure in poscarsDir'''
potcarDir = "/fslhome/bch/vaspfiles/src/potpaw_PBE"
for file in os.listdir(poscarsDir):
info = file.split('_')
struct = '_'.join(info[1:3])
structDir = '{}/{}'.format(dir,struct)
atom = info[1]
if os.path.isdir(structDir):
# os.system('rm -r -f {}'.format(structDir))
output = subprocess.check_output(['rm','-r','-f',structDir])
os.system('mkdir {}'.format(structDir)) #structure is in
meshDet = open('{}/meshDetails.csv'.format(structDir),'w')
meshDet.write('Ntarget,Nmesh,std/mean,energy/N,pack frac\n')
meshDet.close()
os.system('cp {}/{} {}/POSCAR'.format(poscarsDir,file,structDir))
try:
potcar = readfile('{}/{}/POTCAR'.format(potcarDir,atom))
except:
try:
potcar = readfile('{}/{}_pv/POTCAR'.format(potcarDir,atom))
except:
potcar = readfile('{}/{}_sv/POTCAR'.format(potcarDir,atom))
potcar += potcar #multiple atoms in POSCAR have only one POTCAR, so they are really all pure cases
writefile(potcar,'{}/POTCAR'.format(structDir))
os.system ('cp {}/INCAR {}'.format(vaspinputdir,structDir))
modIncar(structDir)
os.system ('cp -P {}/vasp.x {}'.format(vaspinputdir,structDir))
return
def createdirs(poscarsDir,maindir,vaspinputdir):
'''makes dir in maindir for each structure in poscarsDir'''
potcarDir = "/fslhome/bch/vaspfiles/src/potpaw_PBE"
for file in os.listdir(poscarsDir):
info = file.split('_')
struct = '_'.join(info[1:3])
structDir = '{}/{}'.format(maindir,struct)
atom = info[1]
if not os.path.isdir(structDir):
os.system('mkdir {}'.format(structDir)) #structure is in
os.system('cp {}/{} {}/POSCAR'.format(poscarsDir,file,structDir))
print 'atom',atom
try:
potcar = readfile('{}/{}/POTCAR'.format(potcarDir,atom))
except:
try:
potcar = readfile('{}/{}_pv/POTCAR'.format(potcarDir,atom))
except:
potcar = readfile('{}/{}_sv/POTCAR'.format(potcarDir,atom))
potcar += potcar #multiple atoms in POSCAR have only one POTCAR, so they are really all pure cases
writefile(potcar,'{}/POTCAR'.format(structDir))
os.system ('cp {}/INCAR {}'.format(vaspinputdir,structDir))
modIncar(structDir)
os.system ('cp -P {}/vasp.x {}'.format(vaspinputdir,structDir))
return
def modIncar(newdir):
lines = readfile('{}/INCAR'.format(newdir))
plines = readfile('{}/POTCAR'.format(newdir))
for line in plines:
if 'ENMAX' in line:
enmax = 1.4 * float(line.split()[2].replace(';', ''))
break
for i, line in enumerate(deepcopy(lines)):
if 'ENMAX' in line:
lines[i] = 'ENMAX = {}\n'.format(enmax)
break
writefile(lines, '{}/INCAR'.format(newdir))
return
def modIncar(newdir):
lines = readfile('{}/INCAR'.format(newdir))
plines = readfile('{}/POTCAR'.format(newdir))
for line in plines:
if 'ENMAX' in line:
enmax = 1.4*float(line.split()[2].replace(';',''))
break
for i,line in enumerate(npcopy(lines)):
if 'ENMAX' in line:
lines[i] = 'ENMAX = {}\n'.format(enmax)
break
writefile(lines,'{}/INCAR'.format(newdir))
return
def aflowCreatePoscars(structs,aNonPrim,atomic,finalDir):
nsubmit = 50 #number of structures to submit in each execution of aflow
for i in range(len(structs)/nsubmit+1):
if (i+1)*nsubmit < len(structs)-1:
sublist = structs[i*nsubmit:(i+1)*nsubmit]
else:
sublist = structs[i*nsubmit:]
for struc in sublist:
strucstr = 'f%s'% struc
try:
# commstr= 'aconvasp --aflow_proto ' + strucstr+ ':%s' % atomic
commstr = 'aconvasp --proto={} {} | aconvasp --poscar>POSCAR'.format(strucstr,atomic) #for POSCAR creation
print commstr
os.system(commstr)
except:
print 'Error in executing %s' % commstr
structDir = '{}/{}'.format(finalDir,strucstr)
if not os.path.isdir(structDir):
os.mkdir(structDir)
pscr = readfile('POSCAR')
pscr[1] = '{}\n'.format(float(pscr[1])*aNonPrim**3)
writefile(pscr,'POSCAR')
os.system('mv POSCAR {}'.format(structDir))
statusOK,nops = meshc.pack(latticevecs,reciplatt,totatoms,aTypes,postype,transpose(positions),targetNmesh,meshtype,dir,params)
os.chdir(lastDir)
return statusOK,nops
#script:
# os.chdir('/fslhome/bch/cluster_expansion/vcmesh/semiconductors/10OctRnosearchPerp/r0/Si_/bcc_6')
os.chdir('/fslhome/bch/cluster_expansion/vcmesh/semiconductors/sc_SiLP/r0/Si_/bcc_5')
# os.chdir('/fslhome/bch/cluster_expansion/vcmesh/test/r0/Al_1/bcc_5')
# os.chdir('/fslhome/bch/cluster_expansion/vcmesh/semiconductors/28SepRelaxVoidsFine/r2/Si_/bcc_13')
ntarget = 5
type = 'bcc'
paramLabels = ['wallClose','useVoids', 'rcutoff', 'tooClose','tooPlanar' 'rvCutoff','vwPower','wallPower','relax','interPower','wallFactor','wallOffset']
params = ['0.05', '0', '3.0', '-1', '-1', '4.0' , '3.0' , '2.0' , '1', '5.0', '1.3', '0.0'] #0.50 3.00 1.00 0.500. 1. 3. -1. -1. 3. 3. 3. 1. 6. 0.5 0.
'''Best Si from master branch:
params0 = [ 5.0 ]
params1 = [ 2.0 ]#wallPower
params2 = [ 1.3 ] #wallfactor
params3 = [ 0.05] #wallClose
params4 = [ 0.0 ] #wallOffset
params5 = [ 0.5 ] #dw'''
statusOK,nops = getVCmesh(os.getcwd(),ntarget,type,params)
if statusOK:
writefile([],'OK')
elif os.path.exists('OK'):
os.system('rm OK')
from kmeshroutines import nstrip, readposcar,create_poscar,readfile,writefile
import dynamicPacking7
def getVCmesh(dir,targetNmesh,meshtype,params) :
lastDir = os.getcwd()
meshc = dynamicPacking7.dynamicPack() #instance
[descriptor, scale, latticevecs, reciplatt, natoms, postype, positions] = readposcar('POSCAR',dir)
# create_poscar('POSCAR',descriptor, scale, latticevecs, natoms, postype, positions, path) #just to remove the scale problem
os.chdir(dir)
totatoms = sum(natoms)
atype = 1
aTypes = []
for natom in natoms:
for i in range(natom):
aTypes.append(atype)
atype += 1
aTypes = array(aTypes)
statusOK,nops = meshc.pack(latticevecs,reciplatt,totatoms,aTypes,postype,transpose(positions),targetNmesh,meshtype,dir,params)
os.chdir(lastDir)
return statusOK,nops
#script:
ntarget = int(sys.argv[1])
type = sys.argv[2]
params = sys.argv[3:]
statusOK,nops = getVCmesh(os.getcwd(),ntarget,type,params)
if statusOK:
writefile([],'OK')
elif os.path.exists('OK'):
os.system('rm OK')