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 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 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")
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")
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")
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 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")
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')
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, )
""" 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
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)
""" 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