# print
print
print dir + '========================='
# mirdir = aflowdir+dir+'/'
path = maindir+dir+'/'
print path
os.chdir(path)
# os.system('cp %sKPOINTS .' % maindir)
# os.system('cp %sINCAR .' % maindir)
# os.system('cp %sPOTCAR .' % maindir)
os.system('cp ../../KPOINTS .') #standard files 2 levels up
os.system('cp ../../INCAR .')
os.system('cp ../../POTCAR .')
if vaspexec == 'vasp533mod':
km.writekpts_vasp(maindir,dir+'/','KPOINTS',Nkppra) #correct 2 lines
nameadd = 'mod'
elif vaspexec == 'vasp533':
nameadd = 'clean'
km.writejobfile(maindir,dir+'/','vaspjob',nameadd,vaspexec)
# if len(irrat)>0:
# print dir, irrat
# print irrat
os.system('rm slurm*')
# os.system('cp POSCAR.orig POSCAR') #in case aflow setup went too far.
km.aflow2poscar(path) #generates POSCAR from aflow.in. A
subprocess.call(['rm', 'vasp.out'])
subprocess.call(['rm', 'OUTCAR'])
subprocess.call(['sbatch', 'vaspjob'])
os.chdir(maindir)
#km.checkq('bch') #loops for days
print 'Done'
reallatt = np.zeros((3, 3))
os.chdir(maindir)
dirs = sorted([d for d in os.listdir(os.getcwd()) if os.path.isdir(d)])
for dir in dirs:
if testfile in os.listdir(dir):
# print
print
print dir + '========================='
path = maindir + dir + '/'
os.chdir(path)
# os.system('rm POSCAR*')
os.system('cp ../../KPOINTS .')
os.system('cp ../../INCAR .')
os.system('cp ../../POTCAR .')
totatoms = km.aflow2poscar(path)
# os.system('aconvasp --sprim < POSCAR0 > POSCAR')
# back = subprocess.check_output(["echo", "Hello World!"])
# back = check_out(["echo", "Hello World!"])
# back = os.system('mink_reduction.py < POSCAR0 ')
# back = subprocess.check_output(['mink_reduction.py',' <',' POSCAR0 '], shell=True,)
# back = nstrip(subprocess.check_output(['mink_reduction.py < POSCAR0'], shell=True,).split())
# print 'back'
# print back
N = np.rint(Nkppra / totatoms).astype(int)
pfile = open('POSCAR0', 'r')
rlines = [i.strip() for i in pfile.readlines()]
pos = POSCAR(lines=rlines)
oldROD = pos.rod
oldbvecs = np.array(pos.bvecs)
print "Real lattice orth defect:", pos.orthogonality_defect
print
print dir + '========================='
# mirdir = aflowdir+dir+'/'
path = maindir + dir + '/'
print path
os.chdir(path)
# os.system('cp %sKPOINTS .' % maindir)
# os.system('cp %sINCAR .' % maindir)
# os.system('cp %sPOTCAR .' % maindir)
os.system('cp ../../KPOINTS .') #standard files 2 levels up
os.system('cp ../../INCAR .')
os.system('cp ../../POTCAR .')
if vaspexec == 'vasp533mod':
km.writekpts_vasp(maindir, dir + '/', 'KPOINTS',
Nkppra) #correct 2 lines
nameadd = 'mod'
elif vaspexec == 'vasp533':
nameadd = 'clean'
km.writejobfile(maindir, dir + '/', 'vaspjob', nameadd, vaspexec)
# if len(irrat)>0:
# print dir, irrat
# print irrat
os.system('rm slurm*')
# os.system('cp POSCAR.orig POSCAR') #in case aflow setup went too far.
km.aflow2poscar(path) #generates POSCAR from aflow.in. A
subprocess.call(['rm', 'vasp.out'])
subprocess.call(['rm', 'OUTCAR'])
subprocess.call(['sbatch', 'vaspjob'])
os.chdir(maindir)
#km.checkq('bch') #loops for days
print 'Done'
reallatt = np.zeros((3,3))
os.chdir(maindir)
dirs= sorted([d for d in os.listdir(os.getcwd()) if os.path.isdir(d)])
for dir in dirs:
if testfile in os.listdir(dir):
# print
print
print dir + '========================='
path = maindir+dir+'/'
os.chdir(path)
# os.system('rm POSCAR*')
os.system('cp ../../KPOINTS .')
os.system('cp ../../INCAR .')
os.system('cp ../../POTCAR .')
totatoms = km.aflow2poscar(path)
# os.system('aconvasp --sprim < POSCAR0 > POSCAR')
# back = subprocess.check_output(["echo", "Hello World!"])
# back = check_out(["echo", "Hello World!"])
# back = os.system('mink_reduction.py < POSCAR0 ')
# back = subprocess.check_output(['mink_reduction.py',' <',' POSCAR0 '], shell=True,)
# back = nstrip(subprocess.check_output(['mink_reduction.py < POSCAR0'], shell=True,).split())
# print 'back'
# print back
N = np.rint(Nkppra/totatoms).astype(int)
pfile = open('POSCAR0','r')
rlines = [i.strip() for i in pfile.readlines()]
pos = POSCAR(lines=rlines)
oldROD = pos.rod
oldbvecs = np.array(pos.bvecs)
print "Real lattice orth defect:",pos.orthogonality_defect
