def main():
a = Poscar("POSCAR")
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
conf, steps = parse_XDATCAR()
toPOSCAR(b, conf, steps)
def main():
a = Poscar("POSCAR")
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
conf, steps = parse_XDATCAR()
toPOSCAR(b, conf, steps)
def main():
t0 = 0
if len(sys.argv) > 1:
t0 = int(sys.argv[1])
a = Poscar("POSCAR")
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
conf, steps = parse_XDATCAR(t0)
toPOSCAR(b, conf, steps)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("fname",
default="POSCAR",
nargs="?",
help="geo file name")
parser.add_argument("-n", type=int, help="number of fixed atoms")
parser.add_argument("-r",
action='store_true',
help="reverse the fixing order")
args = parser.parse_args()
if args.n:
n_fixed = int(args.n)
else:
n_fixed = int(input("number of fixed atoms: "))
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
shutil.copy(poscar_file, poscar_file + ".1")
coords = []
for i in range(len(b.atoms)):
coords.append([])
for i in range(len(b.atoms)):
coords[i].append(i)
for j in b.atoms[i].x:
coords[i].append(j)
coords.sort(key=lambda x: x[3])
if args.r:
coords.sort(key=lambda x: x[3], reverse=True)
for i in range(len(coords)):
if i < n_fixed:
coords[i].append("F")
else:
coords[i].append("T")
coords.sort(key=lambda x: x[0])
for i in range(len(b.atoms)):
b.atoms[i].xr = [0, 0, 0]
if coords[i][-1] == "F":
b.atoms[i].xr = [1, 1, 1]
toPoscar(b, "POSCAR_new")
def main():
parser = argparse.ArgumentParser()
parser.add_argument("fname", default="POSCAR", nargs="?", help="geo file name")
parser.add_argument("-xyz", nargs=1, help="xyz, xy, z")
parser.add_argument("-scale", nargs=2, type=float, help="scale factor")
args = parser.parse_args()
#gen_scan(args)
poscar_file = "POSCAR"
a = Poscar(poscar_file)
poscar_file = args.fname
a = Poscar(poscar_file)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
gen_scan(b, args)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("fname", default="POSCAR", nargs="?", help="geo file name")
parser.add_argument("-xyz", nargs=1, help="xyz, xy, z")
parser.add_argument("-scale", nargs=2, type=float, help="scale factor")
args = parser.parse_args()
#gen_scan(args)
poscar_file = "POSCAR"
a = Poscar(poscar_file)
poscar_file = args.fname
a = Poscar(poscar_file)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
gen_scan(b, args)
def main():
parser = argparse.ArgumentParser()
parser.add_argument("fname", default="POSCAR", nargs="?", help="geo file name")
args = parser.parse_args()
scan = Scan()
poscar_file = args.fname
a = Poscar(poscar_file)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
# Read Config
read_conf(scan)
# Generate input
gen_input(scan, b)
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 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")
def main():
parser = argparse.ArgumentParser()
parser.add_argument("fname",
default="POSCAR",
nargs="?",
help="geo file name")
args = parser.parse_args()
scan = Scan()
poscar_file = args.fname
a = Poscar(poscar_file)
b = a.parser()
b.assignAtomTypes()
b.assignEleTypes()
# Read Config
read_conf(scan)
# Generate input
gen_input(scan, b)
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")
def main():
a = Poscar("POSCAR")
b = a.parser()
conf, steps = parse_XDATCAR()
toPOSCAR(b, conf, steps)
""" read the geo file and output to data (LAMMPS), geo and xyz file.
"""
import os
from mytype import System, Molecule, Atom
from poscar import Poscar
from output_conf import toXyz, toGeo
os.chdir("/home/tao/Documents/wag/alpha/opt")
a = Poscar("alpha1.vasp")
b = a.parser()
toXyz(b)
toGeo(b)