#!/user/bin/env python
# this script caclualtes cdf from rdf
import sys
from common.lnx_util import parseInput , print_help, xvg
import numpy as np
import scipy.integrate
if __name__ == '__main__':
inputP = parseInput(sys.argv[1:] )
paraOpt = '-rdf -o -h -d '.split()
helpdoc = \
'''
Usage ./prog.py -rdf ; rdf file
-o ; output cdf ; if no present, sys.stdout
-d ; dimension
'''
print_help( inputP, paraOpt, helpdoc )
rdfdata = xvg( inputP['-rdf'] )
r= rdfdata[:,0]
g= rdfdata[:,1]
for i in index:
idx_x , idx_y = index2grid(i)
tmp_mol = mol.copy()
# a random rotation around z axis
if random_rotate:
tmp_mol.set_rotate( [0,0,1], 2* np.pi * random.random() )
tmp_mol.set_trans( [idx_x * self.dx, idx_y * self.dy, 0] )
System.add_mol(self, tmp_mol)
if __name__ == '__main__':
inputP = lu.parseInput(sys.argv[1:])
paraOpt = [ '-grid', '-chol', '-dopc', '-o', '-randomRotate' , '-h' ]
helpdoc="Usage! ./prog.py\n"\
" -grid 16 16 ; grid for monolayer\n"\
" -chol chol.base num ; only for monolayer\n"\
" -dopc dopc.base num\n"\
" -randomRotate dopc chol ; set it when you want to a random rotate on each molecule. You may need a much larger box\n"\
" -o out.gro \n"\
" -h ; help message\n"
lu.print_help(inputP, paraOpt, helpdoc)
# build dopc gro