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)
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")
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")
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")
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")
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")
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")
""" 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')
""" 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')
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")
""" 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)
""" 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
""" 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