Python toXyz Examples

Example #1

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")

Example #2

File: e_2_geo.py Project: tarbaig/simpy

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)

Example #3

File: e_2_jag.py Project: erinshawusc/simpy

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")

Example #4

File: e_2_jag.py Project: tarbaig/simpy

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")

Example #5

File: cn_tools.py Project: erinshawusc/simpy

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")

Example #6

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")

Example #7

File: cn_tools.py Project: tarbaig/simpy

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")

Example #8

File: e_2_contcar.py Project: erinshawusc/simpy

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")

Example #9

File: cn_tools.py Project: tarbaig/simpy

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")

Example #10

File: cn_tools.py Project: erinshawusc/simpy

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")

Example #11

File: e_2_pdb.py Project: karthipitt/simpy

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")

Example #12

File: e_2_contcar.py Project: atomsos/simpy

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")

Example #13

""" parse the geo file with multi configuration into
seperated files
"""
import os
from utilities import parseBlock
from mytype import System, Molecule, Atom
from geo import Geo
from output_conf import toGeo
from output_conf import toXyz

os.chdir("/home/tao/Documents/debug/geofile")
parseBlock("geo", 1)
for i in range(204):
    fname = "out%03d" % i
    a = Geo(fname)
    b = a.parser()
    b.assignAtomTypes()
    toGeo(b, b.name + '.geo')
    toXyz(b, b.name + '.xyz')

Example #14

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, )

Example #15

File: e_2_multi_geo.py Project: carlos-salgado/simpy

""" parse the geo file with multi configuration into
seperated files
"""
import os
from utilities import parseBlock
from mytype import System, Molecule, Atom
from geo import Geo
from output_conf import toGeo
from output_conf import toXyz

os.chdir("/home/tao/Documents/debug/geofile")
parseBlock("geo", 1)
for i in range(204):
    fname = "out%03d"%i 
    a = Geo(fname)
    b = a.parser()
    b.assignAtomTypes()
    toGeo(b, b.name+'.geo')
    toXyz(b, b.name+'.xyz')

Example #16

File: e_2_contcar.py Project: carlos-salgado/simpy

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")

Example #17

""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
from mytype import System, Molecule, Atom
from geo import Geo
from output_conf import toData
from output_conf import toGeo
from output_conf import toXyz

testfile = "../../debug/geo"
a = Geo(testfile)
b = a.parser()
b.assignAtomTypes()
toData(b)
toGeo(b)
toXyz(b)

Example #18

""" 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 G03Gjf
from output_conf import toXyz, toGeo, toGjf

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 = G03Gjf(i)
            b = a.parser()
            b.geotag = "BIOGRF 200"
            toXyz(b, outfile + ".xyz")
            toGeo(b, outfile + ".geo")
            toGjf(b, outfile + ".gjf.bak")
        else:
            print "missing file %s" % i

Example #19

File: e_2_dump.py Project: erinshawusc/simpy

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)

Example #20

File: e_2_g03inp.py Project: carlos-salgado/simpy

""" 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 G03Gjf
from output_conf import toXyz, toGeo, toGjf

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 = G03Gjf(i)
            b = a.parser()
            b.geotag = "BIOGRF 200"
            toXyz(b, outfile+".xyz")
            toGeo(b, outfile+".geo")
            toGjf(b, outfile+".gjf.bak")
        else:
            print "missing file %s"%i