args= docopt(__doc__)
infiles= args['INFILE']
dr= float(args['-d'])
rmax= float(args['-r'])
sigma= int(args['--gsmear'])
ffmt= args['-s']
ofname= args['-o']
nspcs = int(args['--num-species'])
nr= int(rmax/dr) +1
rd,agr= rdf_average(infiles,nspcs,nr,ffmt=ffmt,dr=dr,rmax=rmax,)
if not sigma == 0:
print ' Gaussian smearing...'
rd,agr= gsmear(rd,agr,sigma)
outfile= open(ofname,'w')
outfile.write('# {0:10s} {1:15s}'.format('rd[i],','agr[0,0,i],'))
for isid in range(1,nspcs+1):
for jsid in range(1,nspcs+1):
outfile.write(' {0:10s}'.format('agr[{0:d}-{1:d}]'.format(isid,jsid)))
outfile.write('\n')
for i in range(nr):
outfile.write(' {0:10.4f} {1:15.7f}'.format(rd[i],agr[0,0,i]))
for isid in range(1,nspcs+1):
for jsid in range(1,nspcs+1):
outfile.write(' {0:10.3f}'.format(agr[isid,jsid,i]))
outfile.write('\n')
outfile.close()
print ' Check '+ofname+' with gnuplot, like'
id2= int(args['ID2'])
dang= float(args['-w'])
drad= np.pi *dang/180.0
rcut= float(args['-r'])
sigma= int(args['--gsmear'])
no_average = args['--no-average']
ffmt= args['-f']
ofname= args['-o']
flag_plot= args['--plot']
na= int(180.0/dang) +1
angd,agr= adf_average(infiles,ffmt=ffmt,dang=dang,
rcut=rcut,id0=id0,id1=id1,id2=id2,
no_average=no_average)
if not sigma == 0:
print(' Gaussian smearing...')
agr= gsmear(angd,agr,sigma)
if flag_plot:
plot_figures(angd,agr)
print('')
print(' RDF graphes are plotted.')
print(' Check graph_adf.png')
outfile= open(ofname,'w')
for i in range(na):
outfile.write(' {0:10.4f} {1:15.7f}\n'.format(angd[i],agr[i]))
outfile.close()
print(' Wrote '+ofname)
ofname= args['-o']
nspcs = int(args['--num-species'])
no_average = args['--no-average']
no_normalize = args['--no-normalize']
average = not no_average
normalize = not no_normalize
plot = args['--plot']
nr= int(rmax/dr) +1
rd,agr= rdf_average(infiles,nspcs,nr,ffmt=ffmt,dr=dr,rmax=rmax,
average=average,normalize=normalize)
if not sigma == 0:
print(' Gaussian smearing...')
#...Smearing of total RDF
agrt= gsmear(rd,agr[0,0],sigma)
agr[0,0,:] = agrt[:]
#...Smearing of inter-species RDF
for isid in range(1,nspcs+1):
for jsid in range(1,nspcs+1):
agrt= gsmear(rd,agr[isid,jsid],sigma)
agr[isid,jsid,:] = agrt[:]
outfile= open(ofname,'w')
outfile.write('# 1:{0:10s} 2:{1:13s}'.format('rd[i],','agr[0,0,i],'))
n = 2
for isid in range(1,nspcs+1):
for jsid in range(isid,nspcs+1):
n += 1
outfile.write(' {0:d}:{1:10s}'.format(n,'agr[{0:d}-{1:d}]'.format(isid,jsid)))
outfile.write('\n')
id2 = int(args['ID2'])
dang = float(args['-w'])
drad = np.pi * dang / 180.0
rcut = float(args['-r'])
flag_plot = args['-p']
sigma = int(args['--gsmear'])
ffmt = args['-s']
ofname = args['-o']
na = int(180.0 / dang) + 1
angd, agr = adf_average(infiles,
ffmt=ffmt,
dang=dang,
rcut=rcut,
id0=id0,
id1=id1,
id2=id2)
if not sigma == 0:
print ' Gaussian smearing...'
agr = gsmear(angd, agr, sigma)
if flag_plot:
plt.plot(angd, agr, '-', linewidth=1)
plt.show()
outfile = open(ofname, 'w')
for i in range(na):
outfile.write(' {0:10.4f} {1:15.7f}\n'.format(angd[i], agr[i]))
outfile.close()
