def voronoi(ia,aSys):
#=======================================================================
if __name__ == '__main__':
usage= '$ python %prog [options] POSCAR'
parser= optparse.OptionParser(usage=usage)
parser.add_option("-r",dest="rcut",type="float", \
default=5.0, \
help="Cutoff radius in Angstrom. Default is 5.0.")
(options,args)= parser.parse_args()
rcut= options.rcut
infname= args[0]
aSys= AtomSystem()
if not os.path.exists(infname):
print('[Error] File does not exist !!!')
print(infname)
exit()
aSys.read_POSCAR(infname)
#.....make neighbor list
aSys.make_pair_list(rcut)
#.....make Voronoi polygons from Delauney tetrahedra
vrns= []
for ia in range(aSys.num_atoms):
vrn.append(voronoi(ia,aSys))
Expand atomic system from a POSCAR file by copying the system
along a1,a2,a3 direction (n1,n2,n3).
USAGE:
$ python ./expand-POSCAR.py [options] POSCAR n1 n2 n3
INPUT: (these files must be in the working directory)
- POSCAR (for the cell information)
"""
import os
import optparse
from atom_system import AtomSystem
aSys= AtomSystem()
#================================================== main routine
if __name__ == '__main__':
usage= '$ python %prog [options] ./POSCAR n1 n2 n3'
parser= optparse.OptionParser(usage=usage)
parser.add_option("-o",dest="outfname",type="string", \
default="POSCAR.expand", \
help="output file name. Default is POSCAR.expand.")
(options,args)= parser.parse_args()
outfname= options.outfname
#...read POSCAR as 0th step
if not len(args)==4:
sequential files specified by the user.
This script can be only applicable to VASP 5.3, but not to 4.6,
because of the XDATCAR file-format.
USAGE:
$ python ./POSCAR2.py [options] POSCAR
INPUT: (these files must be in the working directory)
- POSCAR (for the cell information)
"""
import os
import optparse
from atom_system import AtomSystem
aSys= AtomSystem()
def change_species(sid1,sid2,sid3):
global aSys
for ia in range(aSys.num_atoms()):
if aSys.atoms[ia].sid == 1:
aSys.atoms[ia].set_sid(sid1)
elif aSys.atoms[ia].sid == 2:
aSys.atoms[ia].set_sid(sid2)
elif aSys.atoms[ia].sid == 3:
aSys.atoms[ia].set_sid(sid3)
#================================================== main routine
if __name__ == '__main__':
usage= 'python %prog [options] ./POSCAR'
if 'NBLOCK' in incar:
nblock=int(incar['NBLOCK'])
else:
nblock= 1
nstep= nstep/nblock
dt= float(incar['POTIM'])*nblock # dt in ft
print "out_format =",out_format
print "nstep =",nstep
print "dt =",dt
#...read POSCAR as 0th step
if not os.path.exists('./POSCAR'):
print ' ERROR: POSCAR does not exist here.'
exit()
aSys= AtomSystem()
aSys.read_POSCAR('./POSCAR')
#...output 0th step
output_AtomSystem(aSys,out_format,0)
#...read XDATCAR after 0th step
if not os.path.exists('./XDATCAR'):
print ' ERROR: XDATCAR does not exist here.'
exit()
f= open('XDATCAR','r')
line1= f.readline()
alc= float(f.readline().split()[0])
a1= [ float(x) for x in f.readline().split()]
a2= [ float(x) for x in f.readline().split()]
a3= [ float(x) for x in f.readline().split()]
