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))
(options,args)= parser.parse_args()
out_format= options.format
outfname= options.outfname
sid1= options.sid1
sid2= options.sid2
sid3= options.sid3
#...check output format
if not out_format[0] in ('a','p'):
print ' ERROR: Output format must be akr or pmd.'
exit()
#...read POSCAR as 0th step
if len(args)==0 and not os.path.exists('./POSCAR'):
print ' ERROR: Any POSCAR file have not been specified.'
exit()
elif len(args)==0:
infname= './POSCAR'
else:
infname= args[0]
#aSys= AtomSystem()
aSys.read_POSCAR(infname)
change_species(sid1,sid2,sid3)
if out_format[0] in ('a'):
aSys.write_akr(outfname)
elif out_format[0] in ('p'):
aSys.write_pmd(outfname)
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()]
line6= f.readline() # Species names
