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)