pymatgen.io.xr — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.xr

    # coding: utf-8
    # Copyright (c) Pymatgen Development Team.
    # Distributed under the terms of the MIT License.

    """
    This module provides input and output mechanisms
    for the xr file format, which is a modified CSSR
    file format and, for example, used in GULP.
    In particular, the module makes it easy
    to remove shell positions from relaxations
    that employed core-shell models.
    """

    __author__ = "Nils Edvin Richard Zimmermann"
    __copyright__ = "Copyright 2016, The Materials Project"
    __version__ = "0.1"
    __maintainer__ = "Nils Edvin Richard Zimmermann"
    __email__ = "nils.e.r.zimmermann@gmail.com"
    __date__ = "June 23, 2016"

    import re

    import numpy as np

    from monty.io import zopen
    from math import fabs
    from pymatgen.core.lattice import Lattice
    from pymatgen.core.structure import Structure

    class Xr:
        """
        Basic object for working with xr files.
        """

        def __init__(self, structure):
            """
            Args:
                structure (Structure/IStructure): Structure object to create the
                        Xr object.
            """
            if not structure.is_ordered:
                raise ValueError("Xr file can only be constructed from ordered "
                                 "structure")
            self.structure = structure

        def __str__(self):
            output = ["pymatgen   {:.4f} {:.4f} {:.4f}".format(*self.structure.lattice.abc),
                      "{:.3f} {:.3f} {:.3f}".format(*self.structure.lattice.angles),
                      "{} 0".format(len(self.structure)),
                      "0 {}".format(self.structure.formula)]
            # There are actually 10 more fields per site
            # in a typical xr file from GULP, for example.
            for i, site in enumerate(self.structure.sites):
                output.append("{} {} {:.4f} {:.4f} {:.4f}"
                              .format(i + 1, site.specie, site.x, site.y, site.z))
            mat = self.structure.lattice.matrix
            for i in range(2):
                for j in range(3):
                    output.append("{:.4f} {:.4f} {:.4f}".format(
                        mat[j][0], mat[j][1], mat[j][2]))
            return "\n".join(output)

        def write_file(self, filename):
            """
            Write out an xr file.

            Args:
                filename (str): name of the file to write to.
            """
            with zopen(filename, 'wt') as f:
                f.write(str(self) + "\n")

        @staticmethod
        def from_string(string, use_cores=True, thresh=1.e-4):
            """
            Creates an Xr object from a string representation.

            Args:
                string (str): string representation of an Xr object.
                use_cores (bool): use core positions and discard shell
                        positions if set to True (default).  Otherwise,
                        use shell positions and discard core positions.
                thresh (float): relative threshold for consistency check
                        between cell parameters (lengths and angles) from
                        header information and cell vectors, respectively.

            Returns:
                xr (Xr): Xr object corresponding to the input
                        string representation.
            """
            lines = string.split("\n")
            toks = lines[0].split()
            lengths = [float(toks[i]) for i in range(1, len(toks))]
            toks = lines[1].split()
            angles = [float(i) for i in toks[0:3]]
            toks = lines[2].split()
            nsites = int(toks[0])
            mat = np.zeros((3, 3), dtype=float)
            for i in range(3):
                toks = lines[4 + nsites + i].split()
                toks2 = lines[4 + nsites + i + 3].split()
                for j, item in enumerate(toks):
                    if item != toks2[j]:
                        raise RuntimeError("expected both matrices"
                                           " to be the same in xr file")
                mat[i] = np.array([float(w) for w in toks])
            lat = Lattice(mat)
            if (fabs(lat.a - lengths[0]) / fabs(lat.a) > thresh or
                    fabs(lat.b - lengths[1]) / fabs(lat.b) > thresh or
                    fabs(lat.c - lengths[2]) / fabs(lat.c) > thresh or
                    fabs(lat.alpha - angles[0]) / fabs(lat.alpha) > thresh or
                    fabs(lat.beta - angles[1]) / fabs(lat.beta) > thresh or
                    fabs(lat.gamma - angles[2]) / fabs(lat.gamma) > thresh):
                raise RuntimeError("cell parameters in header (" + str(lengths) +
                                   ", " + str(angles) + ") are not consistent with Cartesian" +
                                   " lattice vectors (" + str(lat.abc) + ", " +
                                   str(lat.angles) + ")")
            # Ignore line w/ index 3.
            sp = []
            coords = []
            for j in range(nsites):
                m = re.match(r"\d+\s+(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+" +
                             r"([0-9\-\.]+)", lines[4 + j].strip())
                if m:
                    tmp_sp = m.group(1)
                    if use_cores and tmp_sp[len(tmp_sp) - 2:] == "_s":
                        continue
                    if not use_cores and tmp_sp[len(tmp_sp) - 2:] == "_c":
                        continue
                    if tmp_sp[len(tmp_sp) - 2] == "_":
                        sp.append(tmp_sp[0:len(tmp_sp) - 2])
                    else:
                        sp.append(tmp_sp)
                    coords.append([float(m.group(i)) for i in range(2, 5)])
            return Xr(Structure(lat, sp, coords, coords_are_cartesian=True))

        @staticmethod
        def from_file(filename, use_cores=True, thresh=1.e-4):
            """
            Reads an xr-formatted file to create an Xr object.

            Args:
                filename (str): name of file to read from.
                use_cores (bool): use core positions and discard shell
                        positions if set to True (default).  Otherwise,
                        use shell positions and discard core positions.
                thresh (float): relative threshold for consistency check
                        between cell parameters (lengths and angles) from
                        header information and cell vectors, respectively.

            Returns:
                xr (Xr): Xr object corresponding to the input
                        file.
            """
            with zopen(filename, "rt") as f:
                return Xr.from_string(
                    f.read(), use_cores=use_cores,
                    thresh=thresh)