print(' Chech the parameters nmeasure and nshift, and input files.')
sys.exit()
#...make output data files
outfname = 'dat.msd-{0}'.format(id)
outfile = open(outfname, 'w')
p0 = np.zeros((nmeasure, 3))
pp = np.zeros(3)
msd = np.zeros((len(infiles), nmeasure, 3))
npbc = np.zeros((3, ), dtype=int)
hmat = np.zeros((3, 3))
for ifile in range(len(infiles)):
file = infiles[ifile]
system = NAPSystem()
system.read_akr(file)
hmat[0] = system.a1 * system.alc
hmat[1] = system.a2 * system.alc
hmat[2] = system.a3 * system.alc
#...human-readable ID to computer-oriented ID
i = id - 1
ai = system.atoms[i]
pi = ai.pos
if ifile == 0:
pp = pi
else:
#...correct periodic motion
dev = pi - pp
if dev[0] > 0.5:
npbc[0] += -1
elif dev[0] < -0.5:
infiles.append(file)
infiles.sort()
#...compute sampling time-window from nmeasure and nshift
ntwindow= len(infiles) -(nmeasure-1)*nshift
print ' ntwindow=',ntwindow
if ntwindow <= 0:
print ' [Error] ntwindow <= 0 !!!'
print ' Chech the parameters nmeasure and nshift, and input files.'
sys.exit()
#...set global values
infile= infiles[0]
system=NAPSystem()
system.read_akr(infile)
natm= len(system.atoms)
psid= np.zeros((natm,),dtype=np.int8)
nas= 0
for ia in range(natm):
if sid == 0:
psid[ia] = 1
nas += 1
elif system.atoms[ia].sid == sid:
psid[ia] = 1
nas += 1
print ' num of all atoms = ',natm
print ' num of atoms to be considered = ',nas
print ' accumurating data',
actmp= np.zeros((nmeasure,ntwindow,3))
sys.exit()
#...make output data files
outfname='dat.msd-{0}'.format(id)
outfile= open(outfname,'w')
p0= np.zeros((nmeasure,3))
pp= np.zeros(3)
msd= np.zeros((len(infiles),nmeasure,3))
npbc= np.zeros((3,),dtype=int)
hmat= np.zeros((3,3))
for ifile in range(len(infiles)):
file= infiles[ifile]
system= NAPSystem()
system.read_akr(file)
hmat[0]= system.a1 *system.alc
hmat[1]= system.a2 *system.alc
hmat[2]= system.a3 *system.alc
#...human-readable ID to computer-oriented ID
i= id-1
ai= system.atoms[i]
pi= ai.pos
if ifile == 0:
pp= pi
else:
#...correct periodic motion
dev= pi -pp
if dev[0] > 0.5:
npbc[0] += -1
elif dev[0] < -0.5:
#!/bin/env python
import sys,os
from napsys import NAPSystem
infname= sys.argv[1]
print 'input file: ',infname
aSys= NAPSystem()
aSys.read_akr(infname)
natm= len(aSys.atoms)
outfname= infname+".voro"
f= open(outfname,'w')
alc= aSys.alc
ax= aSys.a1[0]
ay= aSys.a2[1]
az= aSys.a3[2]
for ia in range(natm):
pos= aSys.atoms[ia].pos
f.write(' {0:4d}'.format(ia+1))
f.write(' {0:10.3f}'.format(alc*ax*pos[0]))
f.write(' {0:10.3f}'.format(alc*ay*pos[1]))
f.write(' {0:10.3f}'.format(alc*az*pos[2]))
f.write('\n')
f.close()
print 'Use voro++ as follows:'
cmd= 'voro++ -p -c " %i %q %v %s %A"' \
+' 0.0 {0:5.1f}'.format(alc*ax) \
+' 0.0 {0:5.1f}'.format(alc*ay) \
+' 0.0 {0:5.1f}'.format(alc*az) \
#!/bin/env python
from __future__ import print_function
import sys, os
from napsys import NAPSystem
infname = sys.argv[1]
print('input file: ', infname)
aSys = NAPSystem()
aSys.read_akr(infname)
natm = len(aSys.atoms)
outfname = infname + ".voro"
f = open(outfname, 'w')
alc = aSys.alc
ax = aSys.a1[0]
ay = aSys.a2[1]
az = aSys.a3[2]
for ia in range(natm):
pos = aSys.atoms[ia].pos
f.write(' {0:4d}'.format(ia + 1))
f.write(' {0:10.3f}'.format(alc * ax * pos[0]))
f.write(' {0:10.3f}'.format(alc * ay * pos[1]))
f.write(' {0:10.3f}'.format(alc * az * pos[2]))
f.write('\n')
f.close()
print('Use voro++ as follows:')
cmd= 'voro++ -p -c " %i %q %v %s %A"' \
+' 0.0 {0:5.1f}'.format(alc*ax) \
