os.system('cp %sPOTCAR .' % mirdir)
os.system('cp %svaspjob .' % mirdir)
os.system('cp %sPOSCAR POSCARaflow' % mirdir)
# 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
pfile = open('POSCARaflow', 'r')
rlines = [i.strip() for i in pfile.readlines()]
pos = POSCAR(lines=rlines)
totatoms = np.sum(pos.types)
N = np.rint(Nkppra / totatoms).astype(int)
oldROD = pos.rod
oldbvecs = np.array(pos.bvecs)
reallatt = np.array((pos.avecs[0], pos.avecs[1], pos.avecs[2]))
print "Real lattice"
print reallatt
print "Recip lattice"
reciplatt = np.array((pos.bvecs[0], pos.bvecs[1], pos.bvecs[2]))
print reciplatt
print "Recip lattice/2pi"
reciplatt = np.array((pos.bvecs[0], pos.bvecs[1], pos.bvecs[2]))
print reciplatt / 2 / np.pi
print "Real lattice orth defect:", pos.orthogonality_defect
print "Recp lattice orth defect:", pos.rod
if __name__ == "__main__":
args= docopt(__doc__)
zmin= float(args['--zmin'])
zmax= float(args['--zmax'])
sfplane= args['--plane']
ndiv= int(args['--ndiv'])
_fname= args['POSCAR']
dr= []
for i in range(len(args['DX'])):
dr.append((float(args['DX'][i]),float(args['DY'][i])))
if not sfplane in ('x','y','z'):
print(' --plane must be x, y, or z !!!')
print(' Now --plane=',sfplane)
exit
if zmin < 0.0 or zmin > 1.0 or zmax < 0.0 or zmax > 1.0 or zmax < zmin:
print(' Should be 0.0 <= zmin < zmax < 1.0 !!!')
print(' zmin, zmax = ',zmin, zmax)
exit
poscar= POSCAR()
poscar.read(fname=_fname)
_shift_and_write(poscar,sfplane,ndiv,zmin,zmax,dr)
############################################################ main
if __name__ == "__main__":
args = docopt(__doc__)
# print args
zmin = float(args['--zmin'])
zmax = float(args['--zmax'])
sfplane = args['--plane']
ndiv = int(args['--ndiv'])
_fname = args['POSCAR']
dr = []
for i in range(len(args['DX'])):
dr.append((float(args['DX'][i]), float(args['DY'][i])))
if not sfplane in ('x', 'y', 'z'):
print ' --plane must be x, y, or z !!!'
print ' Now --plane=', sfplane
exit
if zmin < 0.0 or zmin > 1.0 or zmax < 0.0 or zmax > 1.0 or zmax < zmin:
print ' Should be 0.0 <= zmin < zmax < 1.0 !!!'
print ' zmin, zmax = ', zmin, zmax
exit
poscar = POSCAR()
poscar.read(fname=_fname)
_shift_and_write(poscar, sfplane, ndiv, zmin, zmax, dr)
+" Default value is 0.05.")
parser.add_option("-n","--num-output",dest="nout",
type="int",default=10,
help="number of output files in total."
+" Default value is 10.")
parser.add_option("-o","--offset",dest="offset",
type="int",default=0,
help="offset of sequential number in output file.")
(options,args)= parser.parse_args()
maxdis= options.maxdis
nout= options.nout
offset= options.offset
fname= args[0]
poscar= POSCAR()
poscar.read(fname=fname)
#...original a vectors
ho= poscar.h *poscar.afac
hi= np.linalg.inv(ho)
inc= offset
for i in range(nout):
for ia in range(1,len(poscar.pos)):
r= maxdis*random()
theta= pi*random()
phi= 2.0*pi*random()
dr= get_displacement(r,theta,phi)
os.system('cp %sPOTCAR .' % mirdir)
os.system('cp %svaspjob .' % mirdir)
os.system('cp %sPOSCAR POSCARaflow' % mirdir)
# 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
pfile = open('POSCARaflow','r')
rlines = [i.strip() for i in pfile.readlines()]
pos = POSCAR(lines=rlines)
totatoms = np.sum(pos.types)
N = np.rint(Nkppra/totatoms).astype(int)
oldROD = pos.rod
oldbvecs = np.array(pos.bvecs)
reallatt = np.array((pos.avecs[0],pos.avecs[1],pos.avecs[2]))
print "Real lattice"
print reallatt
print "Recip lattice"
reciplatt = np.array((pos.bvecs[0],pos.bvecs[1],pos.bvecs[2]))
print reciplatt
print "Recip lattice/2pi"
reciplatt = np.array((pos.bvecs[0],pos.bvecs[1],pos.bvecs[2]))
print reciplatt/2/np.pi
print "Real lattice orth defect:",pos.orthogonality_defect
print "Recp lattice orth defect:",pos.rod
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 "Recp lattice orth defect:", pos.rod
pos.kmink_reduce(1e-1)
sys.stdout.flush()
newROD = pos.rod
newbvecs = np.array(pos.bvecs)
reciplatt = np.array((pos.bvecs[0], pos.bvecs[1], pos.bvecs[2]))
# print reciplatt
test = []
if abs(newROD - oldROD) < 1e-3 and np.equal(newbvecs, oldbvecs).all:
# if abs(newROD - oldROD) < 1e-3 :
print "Recip lattice already reduced"
else:
parser= optparse.OptionParser(usage=usage)
parser.add_option("-d","--dev",dest="dev",type="float",default=0.01,
help="maximum value of each strain element.")
parser.add_option("-n","--num-dev",dest="ndev",type="int",default=2,
help="number of devision in each strain element.")
parser.add_option("--offset",dest="offset",type="int",default=0,
help="offset of sequential number in output file.")
(options,args)= parser.parse_args()
dev= options.dev
ndev= options.ndev
offset= options.offset
fname= args[0]
poscar= POSCAR()
poscar.read(fname=fname)
#.....original lattice constant
afac0= copy.deepcopy(poscar.afac)
inc= offset
da= 2*dev/ndev *afac0
al0= afac0 *(1.0 -dev)
print "afac0=",afac0
print "dev =",dev
print "ndev =",ndev
print "da =",da
print "al0 =",al0
for na in range(ndev+1):
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 "Recp lattice orth defect:",pos.rod
pos.kmink_reduce(1e-1)
sys.stdout.flush()
newROD = pos.rod
newbvecs = np.array(pos.bvecs)
reciplatt = np.array((pos.bvecs[0],pos.bvecs[1],pos.bvecs[2]))
# print reciplatt
test = []
if abs(newROD - oldROD) < 1e-3 and np.equal(newbvecs,oldbvecs).all:
# if abs(newROD - oldROD) < 1e-3 :
print "Recip lattice already reduced"
else:
