Exemple #1
0
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")
Exemple #2
0
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")