Python Poscar Examples

Example #1

File: xdat2pos.py Project: tarbaig/simpy

def main():
    a = Poscar("POSCAR") 
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    conf, steps = parse_XDATCAR()
    toPOSCAR(b, conf, steps)

Example #2

def main():
    a = Poscar("POSCAR") 
    b = a.parser()
    b.assignAtomTypes()
    b.assignEleTypes()
    conf, steps = parse_XDATCAR()
    toPOSCAR(b, conf, steps)

Example #3

File: xdat2pos.py Project: muraligopal/simpy

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)

Example #4

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")

Example #5

    def init_from_vasp(cls, poscar_file, settingsfile, isosurface=False):

        from poscar import Poscar

        pos = Poscar(poscar_file)
        structure = pos.unitcell

        if isosurface:
            data, grid = pos.get_data()

        else:
            data, grid = [], {}

        return cls(data, grid, structure, settingsfile)

Example #6

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)

Example #7

File: scan.py Project: muraligopal/simpy

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)

Example #8

File: scan_distance.py Project: erinshawusc/simpy

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)

Example #9

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 #10

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 #11

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)

Example #12

""" 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)

Example #13

import sys
sys.path.append(r"D:\Desktop\VASP practical\Pymatgen")
from poscar import Poscar

my_lattace = Poscar(r'E:\VASP practical\Input\zwf\jiasuan')  #二水石膏

my_lattace.slab('jiasuan')  #生成吸附结构输入文件

Example #14

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 #15

File: test.py Project: tarbaig/simpy

from mytype import System, Molecule, Atom
from poscar import Poscar
from output_conf import toPoscar

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()

toPoscar(b)

Example #16

elif socket.gethostname() == "zwicky":
    POT_DATA_BASE = "/home/tcheng/Soft/potpaw_PBE"
elif "onyx" in socket.gethostname():
    POT_DATA_BASE = "/p/home/taocheng/src/vasp/vasp.5.3/potcar/potpaw_PBE"
elif socket.gethostname() == "tao-ThinkCentre-M79":
    POT_DATA_BASE = "/home/tao/src/vasp/vasp.5.3.5/potcar/potpaw_PBE"
elif socket.gethostname() == "tao-ThinkCentre-M79":
    POT_DATA_BASE = "/home/tao/src/vasp/vasp.5.3.5/potcar/potpaw_PBE"
elif socket.gethostname() == "tao-Precision-Tower-3420-ubuntu":
    POT_DATA_BASE = "/home/tao/data/soft/vasp/vasp.5.3.5/potcar/potpaw_PBE"
elif socket.gethostname() == "mu05":
    POT_DATA_BASE = "/home/chengtao/soft/vasp/potpaw_PBE"
elif socket.gethostname() == "mu01":
    POT_DATA_BASE = "/opt/software/vasp.5.4.4/potpaw_PBE"
elif "stampede2" in socket.gethostname():
    POT_DATA_BASE = "/home1/04076/tg833760/soft/vasp/potcar/potpaw_PBE"

o = open("POTCAR", "w")
a = Poscar("POSCAR")
for i in a.atomtypes:
    print(i)
    pot = os.path.join(POT_DATA_BASE, POT[i])
    pot = os.path.join(pot, "POTCAR")
    f = open(pot, "r")
    for j in f:
        if j.strip().startswith("VR"):
            print(j)
        o.write(j)
    f.close()
o.close()

Example #17

File: xdat2pos.py Project: erinshawusc/simpy

def main():
    a = Poscar("POSCAR") 
    b = a.parser()
    conf, steps = parse_XDATCAR()
    toPOSCAR(b, conf, steps)