xyz2poscar

#!/usr/bin/env python


# -------
# Imports
# -------

from argparse import ArgumentParser;

import numpy as np;

from SpectroscoPy.Interfaces.Misc import ReadXYZ;
from SpectroscoPy.Interfaces.VASP import WritePOSCAR;

from SpectroscoPy.Utilities import CartesianToFractionalCoordinates;


# ----
# Main
# ----

if __name__ == "__main__":
    # Parse command-line arguments.

    parser = ArgumentParser("Convert an XYZ-format molecular structure to a VASP 5 POSCAR file");

    parser.add_argument(
        "XYZFile",
        metavar = "<xyz_file>",
        type = str,
        help = "XYZ-format file to convert"
        );

    parser.add_argument(
        "-o", "--output",
        metavar = "<poscar_file>",
        type = str, dest = "POSCARFile",
        default = "POSCAR.vasp",
        help = "Output POSCAR file"
        );

    parser.add_argument(
        "--padding",
        metavar = "<box_padding>",
        type = float, dest = "Padding",
        default = 15.0,
        help = "Padding between periodic images (default: 15 A)"
        );

    parser.add_argument(
        "--title",
        metavar = "<title>",
        type = str, dest = "TitleLine",
        default = None,
        help = "Override the title line (line 1) of the POSCAR file (default: read from XYZ file)"
        );

    args = parser.parse_args();

    # Read XYZ file.

    titleLine, atomicSymbols, atomPositions = ReadXYZ(args.XYZFile);

    # Find minimum and maximum x, y and z coordinates and work out the lattice vectors using the supplied padding.

    minPos = np.min(atomPositions, axis = 0);
    maxPos = np.max(atomPositions, axis = 0);

    latticeVectors = np.diag(
        (maxPos - minPos) + args.Padding
        );

    # Adjust positions to place the atom at the centre of the cell.

    translationVector = (-1.0 * minPos) + args.Padding / 2.0;

    atomPositions = [
        position + translationVector for position in atomPositions
        ];

    # Convert positions from cartesian to fractional coordinates.

    atomPositions = CartesianToFractionalCoordinates(atomPositions, latticeVectors);

    # Write output file.

    WritePOSCAR(
        (latticeVectors, atomicSymbols, atomPositions),
        args.POSCARFile,
        titleLine = args.TitleLine if args.TitleLine != None else titleLine
        );