pymatgen.io.cssr — pymatgen 2020.7.3 documentation

# Source code for pymatgen.io.cssr

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

    """
    This module provides input and output from the CSSR file format.
    """

    import re

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

    __author__ = "Shyue Ping Ong"
    __copyright__ = "Copyright 2012, The Materials Project"
    __version__ = "0.1"
    __maintainer__ = "Shyue Ping Ong"
    __email__ = "shyuep@gmail.com"
    __date__ = "Jan 24, 2012"

    class Cssr:
        """
        Basic object for working with Cssr file. Right now, only conversion from
        a Structure to a Cssr file is supported.
        """

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

        def __str__(self):
            output = ["{:.4f} {:.4f} {:.4f}"
                      .format(*self.structure.lattice.abc),
                      "{:.2f} {:.2f} {:.2f} SPGR =  1 P 1    OPT = 1"
                      .format(*self.structure.lattice.angles),
                      "{} 0".format(len(self.structure)),
                      "0 {}".format(self.structure.formula)]
            for i, site in enumerate(self.structure.sites):
                output.append("{} {} {:.4f} {:.4f} {:.4f}"
                              .format(i + 1, site.specie, site.a, site.b, site.c))
            return "\n".join(output)

        def write_file(self, filename):
            """
            Write out a CSSR file.

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

        @staticmethod
        def from_string(string):
            """
            Reads a string representation to a Cssr object.

            Args:
                string (str): A string representation of a CSSR.

            Returns:
                Cssr object.
            """
            lines = string.split("\n")
            toks = lines[0].split()
            lengths = [float(i) for i in toks]
            toks = lines[1].split()
            angles = [float(i) for i in toks[0:3]]
            latt = Lattice.from_parameters(*lengths, *angles)
            sp = []
            coords = []
            for l in lines[4:]:
                m = re.match(
                    r"\d+\s+(\w+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)\s+([0-9\-\.]+)",
                    l.strip())
                if m:
                    sp.append(m.group(1))
                    coords.append([float(m.group(i)) for i in range(2, 5)])
            return Cssr(Structure(latt, sp, coords))

        @staticmethod
        def from_file(filename):
            """
            Reads a CSSR file to a Cssr object.

            Args:
                filename (str): Filename to read from.

            Returns:
                Cssr object.
            """
            with zopen(filename, "rt") as f:
                return Cssr.from_string(f.read())