def main(): parser = argparse.ArgumentParser() parser.add_argument("fname", default="ffield", nargs="?", help="force field file name") parser.add_argument("-D", action="store_true", help="Debug the code") parser.add_argument("-trans", action="store_true", help="transform ffield to more readable format") parser.add_argument("-params", action="store_true", help="generate params for training") parser.add_argument("-complete", action="store_true", help="complete the off table") parser.add_argument( "-type", nargs=1, type=int, help="Force field type: 0 for vdw; 1 for lg_inner wall") parser.add_argument("-checkout", nargs='+', help="check out the force field") parser.add_argument("-check", action="store_true", help="check the force field") args = parser.parse_args() #print b.getBondDist(3,2) fname = args.fname assert os.path.exists(fname) if args.D: DEBUG = 1 if args.type: ntype = args.type[0] else: ntype = 0 print "Note: Using default force field type" ff = Ffield(fname, ntype) if args.trans: ff.toEquation() if args.params: ff.toParams() if args.complete: ff.completeOff() toFfield(ff) if args.checkout: atoms = args.checkout ff2 = ff.checkout(atoms) toFfield(ff2) if args.check: ff.checkRedudant()
def main(): parser = argparse.ArgumentParser() parser.add_argument("fname", default="ffield", nargs="?", help="force field file name") parser.add_argument("-D", action="store_true", help="Debug the code") parser.add_argument("-trans", action="store_true", help="transform ffield to more readable format") parser.add_argument("-params", action="store_true", help="generate params for training") parser.add_argument("-complete", action="store_true", help="complete the off table") parser.add_argument("-type", nargs=1, type=int, help="Force field type: 0 for vdw; 1 for lg_inner wall") parser.add_argument("-checkout", nargs='+', help="check out the force field") parser.add_argument("-check", action="store_true", help="check the force field") args = parser.parse_args() #print b.getBondDist(3,2) fname = args.fname assert os.path.exists(fname) if args.D: DEBUG = 1 if args.type: ntype = args.type[0] else: ntype = 0 print "Note: Using default force field type" ff = Ffield(fname, ntype) if args.trans: ff.toEquation() if args.params: ff.toParams() if args.complete: ff.completeOff() toFfield(ff) if args.checkout: atoms = args.checkout ff2 = ff.checkout(atoms) toFfield(ff2) if args.check: ff.checkRedudant()
def test(): fname = "ffield" ntype = 0 ff = Ffield(fname, ntype) ff2 = ff.checkout() toFfield(ff2)
n = int(input("parameter to change: ")) temp = float(t[nt][n]) #r0 in eq (2) scale = float(input("scale factor: ")) flag = input("Continue:yes(1);no(0): ") if int(flag): # Increase if not os.path.exists("in"): os.mkdir("in") os.chdir("in") increase = 1.0 + scale t[nt][n] = "%.4f"%(temp*increase) toFfield(ff, "ffield") os.system("bash ./run.sh") os.chdir("..") # Original if not os.path.exists("or"): os.mkdir("or") os.chdir("or") origin = 1.0 t[nt][n] = "%.4f"%(temp*origin) toFfield(ff, "ffield") os.system("bash ./run.sh") os.chdir("..") # Decrease if not os.path.exists("de"): os.mkdir("de") os.chdir("de")
n = int(raw_input("parameter to change: ")) temp = float(t[nt][n]) #r0 in eq (2) scale = float(raw_input("scale factor: ")) flag = raw_input("Continue:yes(1);no(0): ") if int(flag): # Increase if not os.path.exists("in"): os.mkdir("in") os.chdir("in") increase = 1.0 + scale t[nt][n] = "%.4f"%(temp*increase) toFfield(ff, "ffield") os.system("bash ./run.sh") os.chdir("..") # Original if not os.path.exists("or"): os.mkdir("or") os.chdir("or") origin = 1.0 t[nt][n] = "%.4f"%(temp*origin) toFfield(ff, "ffield") os.system("bash ./run.sh") os.chdir("..") # Decrease if not os.path.exists("de"): os.mkdir("de") os.chdir("de")
def test1(): fname = "ffield" ntype = 0 ff = Ffield(fname, ntype) ff2 = ff.checkout() toFfield(ff2)
import os from ffield import Ffield from output_ff import toFfield ff = Ffield("ffield") toFfield(ff, "ffield.new")