#!/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