Exemple #1
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def replicate(xyz_info, args):
    fname = args.f[0]
    nlines = xyz_info.natoms + 2
    nframe = xyzBlock(fname, nlines)

    na, nb, nc = args.nbox
    if nframe >= 0:
        for i in range(nframe+1):
            if not xyz_info.restart:
                a = Xyz("output%05d.xyz"%i)
                b = a.parser()
                b.pbc = xyz_info.pbc
                b.step = i
                toPdb(b, "output%05d.pdb"%i)
            # replicate the box using external code (genconf in Gromacs)
            subprocess.Popen(["genconf", "-f", "output%05d.pdb"%i, 
                              "-o", "s_%05d.pdb"%i, "-nbox",
                                "%d"%na, "%d"%nb, "%d"%nc],
                             stdout=subprocess.PIPE, stderr=subprocess.PIPE)
    subprocess.Popen(["cat s_*.pdb > movie_%d_%d_%d.pdb"%(na, nb, nc)],
                     shell=True)
    # clear up
    o = open("clear.sh", "w")
    o.write("rm output*.xyz\n")
    o.write("rm output*.pdb\n")
    o.write("rm s_*.pdb\n")
    o.close()
    st = os.stat('clear.sh')
    os.chmod('clear.sh', st.st_mode | stat.S_IEXEC)
Exemple #2
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def sort_with_connect(fname):
    """Sort the atoms: gather the same atoms, and atoms in same
    molecules according to connectivity (.mdf). This is very good 
    for generating gromacs input files, and organize the atoms into 
    a well defined order.
    """
    mdffile = "%s.mdf" % fname
    carfile = "%s.car" % fname
    mdf = Mdf(mdffile)
    car = Car(carfile)
    a = car.parser()
    Li = []
    Ge = []
    P = []
    atom_names = mdf.atom_names
    for i in range(len(mdf.atoms)):
        if mdf.atoms[i].element == "Li":
            Li.append(i)
        elif mdf.atoms[i].element == "Ge":
            Ge.append(i)
            for j in mdf.atoms[i].connect:
                Ge.append(atom_names.index(j))
        elif mdf.atoms[i].element == "P":
            P.append(i)
            for j in mdf.atoms[i].connect:
                P.append(__get_index(atom_names, j))
    seq_new = Li + Ge + P
    a.sortNdx(seq_new)
    toPdb(a)
Exemple #3
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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 #4
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def main(args):
    xyz_info = XyzInfo()

    if args.f:
        fname = args.f[0]
    else:
        fname = "movie.xyz"
        sys.stderr.write("Using default xyz file: movie.xyz\n")

    if args.c:
	a = Xyz(fname)
        b = a.parser()
        b.pbc = [100, 100, 100, 90, 90, 90]
        toPdb(b)

    if args.s:
        config = ConfigParser.ConfigParser() 
        config.read(args.s[0])
        read_info(xyz_info, config)

    if args.nbox:
        if not args.s:
            sys.stderr.write("No configure file found!\n")
            sys.stderr.write("Prepare a sample configure file (test.ini)\n")
            write_config()
            sys.exit()
        else:
            replicate(xyz_info, args)
Exemple #5
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def main(args):
    xyz_info = XyzInfo()

    if args.f:
        fname = args.f[0]
    else:
        fname = "movie.xyz"
        sys.stderr.write("Using default xyz file: movie.xyz\n")

    if args.c:
        a = Xyz(fname)
        b = a.parser()
        if args.pbc:
            b.pbc = args.pbc
        else:
            b.pbc = [20, 20, 23, 90, 90, 90]
        toPdb(b)

    if args.s:
        config = ConfigParser.ConfigParser()
        config.read(args.s[0])
        read_info(xyz_info, config)

    if args.nbox:
        if not args.s:
            sys.stderr.write("No configure file found!\n")
            sys.stderr.write("Prepare a sample configure file (test.ini)\n")
            write_config()
            sys.exit()
        else:
            replicate(xyz_info, args)
Exemple #6
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def add_h(b, centers, cn):
    dx = DELTA_X
    zl = b.pbc[2]
    b1 = copy.deepcopy(b)
    n_cut = 10
    for i in range(len(cn)):
        n = int(cn[i])
        print "processing %d"%(n*1.0/8183*100)
        if n < n_cut:
            a = Atom()
            a.name = "H"
            a.element = "H"
            x0 = b.atoms[i].x[0]
            y0 = b.atoms[i].x[1]
            z0 = b.atoms[i].x[2]
            z0 = z0 - int(z0/zl)*zl
            n_sl = int(z0/dx)
            x1 = centers[n_sl][0]
            y1 = centers[n_sl][1]
            z1 = centers[n_sl][2]
            r2 = (x0-x1)*(x0-x1)
            r2 += (y0-y1)*(y0-y1)
            r2 += (z0-z1)*(z0-z1)
            r1 = math.sqrt(r2)
            r = r1 + 1.5
            s = r/r1
            x = s*(x0-x1) + x1
            y = s*(y0-y1) + y1
            z = s*(z0-z1) + z1
            a.x[0] = x 
            a.x[1] = y
            a.x[2] = z
            b1.atoms.append(a)
    toPdb(b1, "add_h.pdb")
Exemple #7
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def replicate(xyz_info, args):
    fname = args.f[0]
    nlines = xyz_info.natoms + 2
    nframe = xyzBlock(fname, nlines)

    na, nb, nc = args.nbox
    if nframe >= 0:
        for i in range(nframe + 1):
            if not xyz_info.restart:
                a = Xyz("output%05d.xyz" % i)
                b = a.parser()
                b.pbc = xyz_info.pbc
                b.step = i
                toPdb(b, "output%05d.pdb" % i)
            # replicate the box using external code (genconf in Gromacs)
            subprocess.Popen([
                "gmx", "genconf", "-f",
                "output%05d.pdb" % i, "-o",
                "s_%05d.pdb" % i, "-nbox",
                "%d" % na,
                "%d" % nb,
                "%d" % nc
            ],
                             stdout=subprocess.PIPE,
                             stderr=subprocess.PIPE)
    subprocess.Popen(["cat s_*.pdb > movie_%d_%d_%d.pdb" % (na, nb, nc)],
                     shell=True)
    # clear up
    o = open("clear.sh", "w")
    o.write("rm output*.xyz\n")
    o.write("rm output*.pdb\n")
    o.write("rm s_*.pdb\n")
    o.close()
    st = os.stat('clear.sh')
    os.chmod('clear.sh', st.st_mode | stat.S_IEXEC)
Exemple #8
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def convertors(b):
    #toGeo(b, b.name+'.geo')
    toGeo(b, 'geo')
    toXyz(b, b.name+'.xyz')
    toGjf(b, b.name+'.gjf')
    toPdb(b, b.name+'.pdb')
    toReaxLammps(b)
Exemple #9
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def sort_with_connect(fname):
    """Sort the atoms: gather the same atoms, and atoms in same
    molecules according to connectivity (.mdf). This is very good 
    for generating gromacs input files, and organize the atoms into 
    a well defined order.
    """
    mdffile = "%s.mdf" % fname
    carfile = "%s.car" % fname
    mdf = Mdf(mdffile)
    car = Car(carfile)
    a = car.parser()
    Li = []
    Ge = []
    P = []
    atom_names = mdf.atom_names
    for i in range(len(mdf.atoms)):
        if mdf.atoms[i].element == "Li":
            Li.append(i)
        elif mdf.atoms[i].element == "Ge":
            Ge.append(i)
            for j in mdf.atoms[i].connect:
                Ge.append(atom_names.index(j))
        elif mdf.atoms[i].element == "P":
            P.append(i)
            for j in mdf.atoms[i].connect:
                P.append(__get_index(atom_names, j))
    seq_new = Li + Ge + P
    a.sortNdx(seq_new)
    toPdb(a)
Exemple #10
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def convert(fname):
    a = Jaguar(fname)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    toXyz(b, "out.xyz")
    toPdb(b, "output.pdb", 1)
    toReaxLammps(b, "lammps.data")
Exemple #11
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def convert(fname):
    a = Jaguar(fname)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    toXyz(b, "out.xyz")
    toPdb(b, "output.pdb", 1)
    toReaxLammps(b, "lammps.data")
Exemple #12
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def surface_atoms_read(b):
    sur = np.loadtxt("sur_sas.dat")
    b1 = copy.deepcopy(b)
    atoms = []
    for i in range(len(sur)):
        if int(sur[i]) == 1:
            atoms.append(b.atoms[i])
    b1.atoms = atoms
    toPdb(b1, "surface_atoms.pdb")
    toXyz(b1, "surface_atoms.xyz")
Exemple #13
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def main(log):
    d1_file = "lammps.data.3"
    d2_file = "./slice_03/conf2/lammps.data"
    d1 = read_data(d1_file)
    d2 = read_data(d2_file)
    logfile = "./slice_03/conf2/build.log"
    z0, ndx = read_build_log(logfile)
    toPdb(d1, "t0.pdb")
    update_coords(d1, d2, z0, ndx)
    toPdb(d1, "t1.pdb")
    toReaxLammps(d1, "lammps.data.4")
Exemple #14
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def main(log):
    d1_file = "lammps.data.3"
    d2_file = "./slice_03/conf2/lammps.data"
    d1 = read_data(d1_file)
    d2 = read_data(d2_file)
    logfile = "./slice_03/conf2/build.log"
    z0, ndx = read_build_log(logfile)
    toPdb(d1, "t0.pdb")
    update_coords(d1, d2, z0, ndx)
    toPdb(d1, "t1.pdb")
    toReaxLammps(d1, "lammps.data.4")
Exemple #15
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def filter_center(center, dx, nl, b):
    o = open("ndx_original.dat", "w")
    atoms = []
    for i in range(len(b.atoms)):
        x = b.atoms[i].x[0]
        z = b.atoms[i].x[2]
        an = b.atoms[i].an
        zn = int(z/dx)
        if x >= center[zn][0]:
            atoms.append(b.atoms[i])
            o.write("%d\n"%an)
    o.close()
    b.atoms = atoms
    toPdb(b)
Exemple #16
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def filter_center(center, dx, nl, b):
    o = open("ndx_original.dat", "w")
    atoms = []
    for i in range(len(b.atoms)):
        x = b.atoms[i].x[0]
        z = b.atoms[i].x[2]
        an = b.atoms[i].an
        zn = int(z / dx)
        if x >= center[zn][0]:
            atoms.append(b.atoms[i])
            o.write("%d\n" % an)
    o.close()
    b.atoms = atoms
    toPdb(b)
Exemple #17
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def fortranOut(testfile="output.pdb", args=''):
    a = Pdb(testfile)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    b.pbc = [50.00, 50.00, 50.00, 90.0, 90.0, 90.0]
    b.geotag = "XTLGRF 200"
    toReaxLammps(b, "lammps.data")
    if args:
        if args.element:
            toPdb(b, "out.pdb", 1)
    else:
        toPdb(b, "out.pdb")
    toMsd(b, "sim.msd")
    toGeo(b, "sim.geo")
Exemple #18
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def fortranOut(testfile = "output.pdb", args=''):
    a = Pdb(testfile)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    b.pbc = [50.00, 50.00, 50.00, 90.0, 90.0, 90.0]
    b.geotag = "XTLGRF 200"
    toReaxLammps(b, "lammps.data")
    if args:
        if args.element:
            toPdb(b, "out.pdb", 1)
    else:
        toPdb(b, "out.pdb")
    toMsd(b, "sim.msd")
    toGeo(b, "sim.geo")
Exemple #19
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def surface_atoms_read(b):
    sur = np.loadtxt("sur_sas.dat")
    b1 = copy.deepcopy(b)
    b2 = copy.deepcopy(b)
    atoms_sur = []
    atoms_bulk = []
    for i in range(len(sur)):
        if int(sur[i]) == 1:
            atoms_sur.append(b.atoms[i])
        else:
            atoms_bulk.append(b.atoms[i])
    b1.atoms = atoms_sur
    b2.atoms = atoms_bulk
    toPdb(b1, "surface_atoms.pdb")
    toXyz(b1, "surface_atoms.xyz")
    toPdb(b2, "bulk_atoms.pdb")
    toXyz(b2, "bulk_atoms.xyz")
Exemple #20
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def surface_atoms_read(b):
    sur = np.loadtxt("sur_sas.dat")
    b1 = copy.deepcopy(b)
    b2 = copy.deepcopy(b)
    atoms_sur = []
    atoms_bulk = []
    for i in range(len(sur)):
        if int(sur[i]) == 1:
            atoms_sur.append(b.atoms[i])
        else:
            atoms_bulk.append(b.atoms[i])
    b1.atoms = atoms_sur
    b2.atoms = atoms_bulk
    toPdb(b1, "surface_atoms.pdb")
    toXyz(b1, "surface_atoms.xyz")
    toPdb(b2, "bulk_atoms.pdb")
    toXyz(b2, "bulk_atoms.xyz")
Exemple #21
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def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("fname", default="POSCAR", nargs="?", help="geo file name")
    args = parser.parse_args()
    
    poscar_file = args.fname
    a = Poscar(poscar_file)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    print b.getVol()
    #print b.pbc
    
    toXyz(b)
    toGeo(b, "geo")
    toPdb(b, "sim.pdb")
    toReaxLammps(b, "lammps.data")
    toJdft(b, "coords")
Exemple #22
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def output_pdb(control, b, ndx):
    """Output the atoms in ndx to pdb file
    """
    c = copy.deepcopy(b)
    c.atoms = []
    sphere = []
    void = []
    for i in range(len(ndx)):
        for j in range(len(ndx[i])):
            sphere.append((ndx[i][j]))
    for i in range(len(b.atoms)):
        if i not in sphere:
            void.append(i)
    if control.void == "yes":
        for i in void:
            c.atoms.append(b.atoms[i])
    else:
        for i in sphere:
            c.atoms.append(b.atoms[i])
    toPdb(c, control.output)
Exemple #23
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def surface_atoms_cut_off(b):
    """
    """
    cn = np.loadtxt("cn.dat")
    o = open("sur.dat", "w")
    n_cut = 10
    sur = np.where(cn <= 10, 1, 0)
    
    b1 = copy.deepcopy(b)
    atoms = []
    for i in range(len(sur)):
        if sur[i] == 1:
            atoms.append(b.atoms[i])
            o.write("1\n")
        else:
            o.write("0\n")
    o.close()
    b1.atoms = atoms
    toPdb(b1, "surface_atoms.pdb")
    toXyz(b1, "surface_atoms.xyz")
Exemple #24
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def surface_atoms_cut_off(b):
    """
    """
    cn = np.loadtxt("cn.dat")
    o = open("sur.dat", "w")
    n_cut = 10
    sur = np.where(cn <= 10, 1, 0)

    b1 = copy.deepcopy(b)
    atoms = []
    for i in range(len(sur)):
        if sur[i] == 1:
            atoms.append(b.atoms[i])
            o.write("1\n")
        else:
            o.write("0\n")
    o.close()
    b1.atoms = atoms
    toPdb(b1, "surface_atoms.pdb")
    toXyz(b1, "surface_atoms.xyz")
Exemple #25
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def withPbc(testfile="supper.pdb", args=''):
    a = Pdb(testfile)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    #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")
    if args:
        if args.element:
            toPdb(b, "out.pdb", 1)
    else:
        toPdb(b, "out.pdb")
Exemple #26
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def main():
    parser = argparse.ArgumentParser()
    parser.add_argument("fname", default="POSCAR", nargs="?", help="geo file name")
    args = parser.parse_args()
    
    poscar_file = args.fname
    a = Poscar(poscar_file)
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    vol = b.getVol()
    mass = b.getMass()
    density = mass/vol*ATOMIC_MASS_CONSTANT*1e27
    print density
    #print b.pbc
    
    toXyz(b, "contcar.xyz")
    toGeo(b, "geo")
    toPdb(b, "sim.pdb")
    toReaxLammps(b, "lammps.data")
    toJdft(b, "coords")
Exemple #27
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def main(counter):
    # Set up
    x = np.linspace(1,32,32)
    delta = 6.0
    miu = 17.0
    
    # get the distribution
    al_natoms, o_natoms = gaussian(x, delta, miu) 
    
    # read pdb
    a = read_pdb()
    
    # build the atoms list
    ca_list, o_list = build_list(a)
    
    # replace
    al_list, ignore_list = replace(ca_list, o_list, al_natoms, o_natoms)
    
    # do the replace
    process(a, al_list, ignore_list)
    
    # output the data
    toPdb(a, "case%02d.pdb"%counter)
Exemple #28
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def main(counter):
    # Set up
    x = np.linspace(1, 32, 32)
    delta = 6.0
    miu = 17.0

    # get the distribution
    al_natoms, o_natoms = gaussian(x, delta, miu)

    # read pdb
    a = read_pdb()

    # build the atoms list
    ca_list, o_list = build_list(a)

    # replace
    al_list, ignore_list = replace(ca_list, o_list, al_natoms, o_natoms)

    # do the replace
    process(a, al_list, ignore_list)

    # output the data
    toPdb(a, "case%02d.pdb" % counter)
Exemple #29
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def add_o(b, centers, cn):
    """add o
    """
    dx = DELTA_X
    zl = b.pbc[2]
    b1 = copy.deepcopy(b)
    n_cut = 10
    for i in range(len(cn)):
        print "processing %d"%(i*1.0/8183*100)
        n = int(cn[i])
        token = random.random()
        if n < n_cut and token > 0.9:
            a = Atom()
            a.name = "O"
            a.element = "O"
            x0 = b.atoms[i].x[0]
            y0 = b.atoms[i].x[1]
            z0 = b.atoms[i].x[2]
            z0 = z0 - int(z0/zl)*zl
            n_sl = int(z0/dx)
            x1 = centers[n_sl][0]
            y1 = centers[n_sl][1]
            z1 = centers[n_sl][2]
            r2 = (x0-x1)*(x0-x1)
            r2 += (y0-y1)*(y0-y1)
            r2 += (z0-z1)*(z0-z1)
            r1 = math.sqrt(r2)
            r = r1 + 2.0
            s = r/r1
            x = s*(x0-x1) + x1 + 1.0
            y = s*(y0-y1) + y1 + 1.0
            z = s*(z0-z1) + z1
            a.x[0] = x 
            a.x[1] = y
            a.x[2] = z
            b1.atoms.append(a)
    toPdb(b1, "add_o.pdb")
Exemple #30
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def fconv(fname):
    a = FullData(fname)
    b = a.parser()
    b.assignAtomTypes()
    toPdb(b)
Exemple #31
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def fconv(fname):
    a = FullData(fname)
    b = a.parser()
    b.assignAtomTypes()
    toPdb(b)
Exemple #32
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def sortXYZ(testfile="input.pdb", axis="z"):
    a = Pdb(testfile)
    b = a.parser()
    atoms = b.atoms
    b.sortXYZ(axis)
    toPdb(b, "out_sorted.pdb")
Exemple #33
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""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
import sys, os
from mytype import System, Molecule, Atom
from g03 import G03LogConf
from output_conf import toXyz, toGeo, toPdb

usage = """gau2xyz g03logfiles"""
if len(sys.argv) < 2:
    print usage
else:
    for i in sys.argv[1:]:
        outfile = i.split(".")[0]
        if os.path.exists(i):
            a = G03LogConf(i)
            b = a.parser()
            b.assignEleTypes()
            b.geotag = "BIOGRF 200"
            toXyz(b, outfile + ".xyz")
            toGeo(b, outfile + ".geo")
            b.pbc = [50, 50, 50, 90.0, 90.0, 90.0]
            toPdb(b, outfile + ".pdb")
        else:
            print "missing file %s" % i
Exemple #34
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""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
import sys, os
from mytype import System, Molecule, Atom
from g03 import G03LogConf
from output_conf import toXyz, toGeo, toPdb

usage = """gau2xyz g03logfiles"""
if len(sys.argv) < 2:
    print usage
else:
    for i in sys.argv[1:]:
        outfile = i.split(".")[0]
        if os.path.exists(i):
            a = G03LogConf(i)
            b = a.parser()
            b.assignEleTypes()
            b.geotag = "BIOGRF 200"
            toXyz(b, outfile+".xyz")
            toGeo(b, outfile+".geo")
            b.pbc = [50, 50, 50, 90.0, 90.0, 90.0]
            toPdb(b, outfile+".pdb")
        else:
            print "missing file %s"%i
Exemple #35
0
def add_oh(b, centers, cn, n_ignore, ndx):
    dx = DELTA_X
    zl = b.pbc[2]
    b1 = copy.deepcopy(b)
    b2 = copy.deepcopy(b)
    
    a = Atom()
    a.name = "O"
    a.element = "O"
    b2.atoms.append(a)
    a = Atom()
    a.name = "H"
    a.element = "H"
    b2.atoms.append(a)
    
    n_cut = 10
    r_pt_oh = 2.0
    r_oh = 1.0
    for i in range(len(cn)):
        #print "processing %d"%(i*1.0/len(cn)*100)
        token = random.random()
        n = int(cn[i])
        if n < n_cut and token >= 0.0:
            a1 = Atom()
            a1.name = "O"
            a1.element = "O"
            x0 = b.atoms[i].x[0]
            y0 = b.atoms[i].x[1]
            z0 = b.atoms[i].x[2]
            z0 = z0 - int(z0/zl)*zl
            n_sl = int(z0/dx)
            x1 = centers[n_sl][0]
            y1 = centers[n_sl][1]
            z1 = centers[n_sl][2]
            r2 = (x0-x1)*(x0-x1)
            r2 += (y0-y1)*(y0-y1)
            r2 += (z0-z1)*(z0-z1)
            r1 = math.sqrt(r2)
            r = r1 + r_pt_oh
            s = r/r1
            x = s*(x0-x1) + x1 
            y = s*(y0-y1) + y1 
            z = s*(z0-z1) + z1
            a1.x[0] = x 
            a1.x[1] = y
            a1.x[2] = z
            b1.atoms.append(a1)
            b2.atoms[-2].x[0] = x
            b2.atoms[-2].x[1] = y
            b2.atoms[-2].x[2] = z

            a2 = Atom()
            a2.name = "H"
            a2.element = "H"
            r = r1 + r_pt_oh + r_oh
            s = r/r1
            x = s*(x0-x1) + x1 
            y = s*(y0-y1) + y1 
            z = s*(z0-z1) + z1
            a2.x[0] = x 
            a2.x[1] = y
            a2.x[2] = z
            b1.atoms.append(a2)
            b2.atoms[-1].x[0] = x
            b2.atoms[-1].x[1] = y
            b2.atoms[-1].x[2] = z
            if i >= n_ignore - 1:
                toPdb(b2, "%05d_%05d.pdb"%(i, ndx[i]))

    toPdb(b1, "add_oh.pdb")
Exemple #36
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from block import dumpBlock
from dump import Dump
from output_conf import toXyz, toPdb

lmpfile = "dump.lammpstrj"
sepfile = "dump.sep"
dt = 1


# parse the dump file with multi configurations into seperated dump files
nframe = dumpBlock(lmpfile, sepfile, dt)
nframe += 1

for i in range(0, nframe, dt):
#for i in range(10):
    a = Dump("%s%05d.dump"%(sepfile,i))
    b = a.parser()
    #toXyz(b, "xyz%05d.xyz"%i)
    #b.sortXYZ("z")
    toPdb(b, "pdb%05d.pdb"%i)




Exemple #37
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def sortXYZ(testfile="input.pdb", axis="z"):
    a = Pdb(testfile)
    b = a.parser()
    atoms = b.atoms
    b.sortXYZ(axis)
    toPdb(b, "out_sorted.pdb")
Exemple #38
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from block import dumpBlock
from dump import Dump
from output_conf import toXyz, toPdb, toPoscar, toReaxLammps

lmpfile = "dump.lammpstrj"
sepfile = "dump.sep"
dt = 1

# parse the dump file with multi configurations into seperated dump files
nframe = dumpBlock(lmpfile, sepfile, dt)
nframe += 1

for i in range(0, nframe, dt):
    #for i in range(10):
    a = Dump("%s%05d.dump" % (sepfile, i))
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    b.toFrac()

    toXyz(b, "xyz%05d.xyz" % i)
    #b.sortXYZ("z")
    toPdb(b, "pdb%05d.pdb" % i)
    toReaxLammps(b, "lammps.data")
    toPoscar(b, )
Exemple #39
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""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
from mytype import System, Molecule, Atom
from data import ReaxData
from output_conf import toPdb

testfile = "e_2_data.data"
a = ReaxData(testfile)
b = a.parser()
b.assignAtomTypes()
toPdb(b)
Exemple #40
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def get_slice(b, id0):
    logfile = "build.log"
    o = open(logfile, "w")
    
    a0 = b.atoms[id0-1]
    id0 = a0.an
    x0, y0, z0 = a0.x

    o.write("Reference atoms is %d.\n"%id0)
    o.write("The coordination of reference atom is %.4f %.4f %.4f.\n"%
            (x0, y0, z0))
    o.write("Cut from z direction.\n")

    zl = b.pbc[2]

    z0 = z0 - int(z0/zl)*zl
    dz1 = DELTA_Z1
    dz2 = DELTA_Z2
    z1 = z0 - dz1
    z2 = z0 + dz1
    z1 = z1 - math.floor(z1/zl)*zl
    z2 = z2 - math.floor(z2/zl)*zl

    b1 = copy.deepcopy(b)

    o.write("Starting from %.4f to %.4f.\n"%(z1, z2))
    o.write("Cut radius is %.4f.\n"%dz1)
    #o.write("Buffer distance is %.4f.\n"%dz2)
    #o.write("Fixed L1 from %.4f to %.4f\n"%(z1, z2))
    #o.write("Fixed L2 from %.4f to %.4f\n"%(z3, z4))
    
    ca = []
    a_ref = []
    
    for i in range(len(b.atoms)):
        id = b.atoms[i].an
        z = b.atoms[i].x[2]
        z = z - math.floor(z/zl)*zl #pbc
        b1.atoms[i].x[2] = z
        if id == id0:
            a_ref.append(b1.atoms[i])
        else:
            if z1 < z2:
                if z >= z1 and z < z2:
                    ca.append(b1.atoms[i])
            else:
                if z >= 0 and z < z2:
                    ca.append(b1.atoms[i])
                elif z >= z1 and z < zl:
                    ca.append(b1.atoms[i])

    # Shift the atoms according to reference atom
    for i in range(len(ca)):
        z = ca[i].x[2] 
        z = z - z1
        z = z - math.floor(z/zl)*zl
        ca[i].x[2] = z

    z = a_ref[0].x[2] 
    z = z - z1
    z = z - math.floor(z/zl)*zl
    a_ref[0].x[2] = z
    o.write("Sort the atom index according to z.\n")
    ca.sort(key=lambda x: x.x[2])

    c1 = []
    c2 = []
    for i in ca:
        z = i.x[2]
        if z <= dz2:
            c1.append(i)
        elif z > 2*dz1 - dz2:
            c1.append(i)
        else:
            c2.append(i)
            
    o.write("Fixed atoms is %d.\n"%(len(c1)))

    ca = ca + a_ref
    o.write("Total number of atoms is %d.\n"%len(ca))

    o.write("Index is as following:\n")
    counter = 0
    for i in ca:
        if counter % 10 == 0:
            o.write("\n")
        o.write("%8d"%i.an)
        counter += 1
    o.write("\n")
    
    b1.atoms = c1 + c2 + a_ref
    b1.pbc[2] = 2*dz1
    
    o.write("Output to pdb.\n")
    toPdb(b1, "input.pdb")
    toReaxLammps(b1)
    o.close()

    return ca, c1, c2, a_ref
Exemple #41
0
from mytype import System, Molecule, Atom
from poscar import Poscar
from output_conf import toXyz, toGeo, toPdb, toReaxLammps

import sys

if len(sys.argv) > 1:
    fname = sys.argv[1]
else:
    fname = "CONTCAR"
a = Poscar(fname)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
print b.getVol()

toXyz(b)
toGeo(b, "geo")
toPdb(b, "sim.pdb")
toReaxLammps(b, "lammps.data")

Exemple #42
0
def add_oh(b, centers, cn, n_ignore, ndx):
    """add oh
    """
    dx = DELTA_X
    zl = b.pbc[2]
    b1 = copy.deepcopy(b)
    b2 = copy.deepcopy(b)
    
    a = Atom()
    a.name = "O"
    a.element = "O"
    b2.atoms.append(a)
    a = Atom()
    a.name = "H"
    a.element = "H"
    b2.atoms.append(a)
    
    n_cut = 10
    r_pt_oh = 2.0
    r_oh = 1.0
    for i in range(len(cn)):
        #print "processing %d"%(i*1.0/len(cn)*100)
        token = random.random()
        n = int(cn[i])
        if n < n_cut and token >= 0.0:
            a1 = Atom()
            a1.name = "O"
            a1.element = "O"
            x0 = b.atoms[i].x[0]
            y0 = b.atoms[i].x[1]
            z0 = b.atoms[i].x[2]
            z0 = z0 - int(z0/zl)*zl
            n_sl = int(z0/dx)
            x1 = centers[n_sl][0]
            y1 = centers[n_sl][1]
            z1 = centers[n_sl][2]
            r2 = (x0-x1)*(x0-x1)
            r2 += (y0-y1)*(y0-y1)
            r2 += (z0-z1)*(z0-z1)
            r1 = math.sqrt(r2)
            r = r1 + r_pt_oh
            s = r/r1
            x = s*(x0-x1) + x1 
            y = s*(y0-y1) + y1 
            z = s*(z0-z1) + z1
            a1.x[0] = x 
            a1.x[1] = y
            a1.x[2] = z
            b1.atoms.append(a1)
            b2.atoms[-2].x[0] = x
            b2.atoms[-2].x[1] = y
            b2.atoms[-2].x[2] = z

            a2 = Atom()
            a2.name = "H"
            a2.element = "H"
            r = r1 + r_pt_oh + r_oh
            s = r/r1
            x = s*(x0-x1) + x1 
            y = s*(y0-y1) + y1 
            z = s*(z0-z1) + z1
            a2.x[0] = x 
            a2.x[1] = y
            a2.x[2] = z
            b1.atoms.append(a2)
            b2.atoms[-1].x[0] = x
            b2.atoms[-1].x[1] = y
            b2.atoms[-1].x[2] = z
            if i >= n_ignore - 1:
                toPdb(b2, "%05d_%05d.pdb"%(i, ndx[i]))

    toPdb(b1, "add_oh.pdb")