def withPbc(testfile="supper.pdb", args=''):
a = Pdb(testfile)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
b.assignIdNumbers()
b.toFrac()
#b.translate(12.0, "z")
toXyz(b, "out.xyz")
toMusic(b, "out.music")
if len(b.pbc) == 0:
b.geotag = "BIOGRF 200"
else:
b.geotag = "XTLGRF 200"
toReaxLammps(b, "lammps.data")
toGeo(b, "sim.geo")
toMsd(b, "sim.msd")
toPoscar(b, )
toCfg(b, )
toJdft(b, )
toTowheecoords(b)
if args:
if args.element:
toPdb(b, "out.pdb", 1)
else:
toPdb(b, "out.pdb")
unit ntype
3 'H_' 0.4d0
vibration
1
2
improper
0
"""
if len(sys.argv) > 2:
nmol = int(sys.argv[2])
a = Pdb(sys.argv[1])
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
toTowheecoords(b)
rcut = 3.5
xx, xy, xz, yy, yz, zz = lattice2v(b.pbc)
la = [xx, 0.0, 0.0]
lb = [xy, yy, 0.0]
lc = [xz, yz, zz]
print la
print lb
print lc
o = open("towhee_input", "w")
o.write("inputformat\n")
o.write("'Towhee'\n")
o.write("ensemble\n")
o.write("'uvt'\n")