msd = numpy.zeros(args.span-1) #we substract 1 because cpptraj diffusion command does not calculate MSD(0), which is zero by definition
template='''trajin _trajfile_ _t0_ _t0+t_ 1
_rms_
diffusion _dt_ _prefix_ _mask_ average
'''
handle,tmp_prefix = mkstemp(prefix='junk', dir='/tmp')
jump = max(1, int((args.nframe - args.span - 1) / args.nt0)) # consecutive chunks start at positions that differ by 'jump'
for it0 in range(args.nt0):
t0 = 1 + it0*jump # first frame of the chunk
te = t0 + args.span -1 # last frame of the chunk
script = template.replace('_trajfile_', args.trajfile)
script = script.replace('_t0_', '{0}'.format(t0))
script = script.replace('_t0+t_', '{0}'.format(te))
script = script.replace('_mask_', args.mask)
script = script.replace('_dt_', '{0}'.format(args.dt))
script = script.replace('_prefix_', tmp_prefix)
if args.rms2t0 == 'y':
script = script.replace('_rms_', 'rms first')
else:
script = script.replace('_rms_', '#')
#print script
exec_cpptraj(args.topfile, script)
file2mem = numpy.transpose(numpy.loadtxt('{0}_r.xmgr'.format(tmp_prefix))) #read MSD(t) for the chunk and store
msd += file2mem[1]
msd /= args.nt0 # average for all the chunks
buf = '# time MSD\n'
for it in range(1,args.span):
buf += '{0:5f} {1:8f}\n'.format( it*args.dt, msd[it-1] )
open(args.outf, 'w').write(buf)
args=parser.parse_args()
handle, tmpfile = mkstemp(prefix='junk', dir='/tmp')
nsty = nsty_per_polymer * args.npol
solvmask = '(!:1-{0})&(@{1})'.format(nsty, args.tol)
solmask = '(:1-{0})&(@{1})'.format(nsty, args.sty)
lower = args.minimum
upper = lower + args.spacing
buf='# distance number_of_tol/sty\n'
while upper < args.maximum:
script='''trajin {0}
center {1}
watershell {2} {3} lower {4} upper {5} {6}'''.format(args.dcd, solmask, solmask, tmpfile, lower, upper, solvmask)
exec_cpptraj(args.top, script)
#tr()
avgn1=0
avgn2=0
for line in open(tmpfile).readlines()[1:]:
frame, n1, n2 = [float(x) for x in line.split()]
avgn1 += n1
avgn2 += n2
avgn1 /= (frame*nsty)
avgn2 /= (frame*nsty)
buf += '{0:5.2f} {1:6.2f}\n{2:5.2f} {3:6.2f}\n'.format(lower, avgn1, upper, avgn2)
lower = upper + args.spacing
upper = lower + args.spacing
open(args.outf,'w').write(buf)
