pymatgen.core.bonds — pymatgen 2020.7.3 documentation

# Source code for pymatgen.core.bonds

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

    """
    This class implements definitions for various kinds of bonds. Typically used in
    Molecule analysis.
    """

    import os
    import json
    import collections
    import warnings

    from pymatgen.core.periodic_table import Element

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

    def _load_bond_length_data():
        """Loads bond length data from json file"""
        with open(os.path.join(os.path.dirname(__file__),
                               "bond_lengths.json")) as f:
            data = collections.defaultdict(dict)
            for row in json.load(f):
                els = sorted(row['elements'])
                data[tuple(els)][row['bond_order']] = row['length']
            return data

    bond_lengths = _load_bond_length_data()

    class CovalentBond:
        """
        Defines a covalent bond between two sites.
        """

        def __init__(self, site1, site2):
            """
            Initializes a covalent bond between two sites.

            Args:
                site1 (Site): First site.
                site2 (Site): Second site.
            """
            self.site1 = site1
            self.site2 = site2

        @property
        def length(self):
            """
            Length of the bond.
            """
            return self.site1.distance(self.site2)

        def get_bond_order(self, tol=0.2, default_bl=None):
            """
            The bond order according the distance between the two sites
            Args:
                tol (float): Relative tolerance to test.
                    (1 + tol) * the longest bond distance is considered
                    to be the threshold length for a bond to exist.
                    (1 - tol) * the shortest bond distance is considered
                    to be the shortest possible bond length
                    Defaults to 0.2.
                default_bl: If a particular type of bond does not exist,
                    use this bond length as a default value
                    (bond order = 1). If None, a ValueError will be thrown.
            Returns:
                Float value of bond order. For example, for C-C bond in
                benzene, return 1.7.
            """
            sp1 = list(self.site1.species.keys())[0]
            sp2 = list(self.site2.species.keys())[0]
            dist = self.site1.distance(self.site2)
            return get_bond_order(sp1, sp2, dist, tol, default_bl)

        @staticmethod
        def is_bonded(site1, site2, tol=0.2, bond_order=None, default_bl=None):
            """
            Test if two sites are bonded, up to a certain limit.
            Args:
                site1 (Site): First site
                site2 (Site): Second site
                tol (float): Relative tolerance to test. Basically, the code
                    checks if the distance between the sites is less than (1 +
                    tol) * typical bond distances. Defaults to 0.2, i.e.,
                    20% longer.
                bond_order: Bond order to test. If None, the code simply checks
                    against all possible bond data. Defaults to None.
                default_bl: If a particular type of bond does not exist, use this
                    bond length. If None, a ValueError will be thrown.
            Returns:
                Boolean indicating whether two sites are bonded.
            """
            sp1 = list(site1.species.keys())[0]
            sp2 = list(site2.species.keys())[0]
            dist = site1.distance(site2)
            syms = tuple(sorted([sp1.symbol, sp2.symbol]))
            if syms in bond_lengths:
                all_lengths = bond_lengths[syms]
                if bond_order:
                    return dist < (1 + tol) * all_lengths[bond_order]
                for v in all_lengths.values():
                    if dist < (1 + tol) * v:
                        return True
                return False
            if default_bl:
                return dist < (1 + tol) * default_bl
            raise ValueError("No bond data for elements {} - {}".format(*syms))

        def __repr__(self):
            return "Covalent bond between {} and {}".format(self.site1,
                                                            self.site2)

        def __str__(self):
            return self.__repr__()

    def obtain_all_bond_lengths(sp1, sp2, default_bl=None):
        """
        Obtain bond lengths for all bond orders from bond length database

        Args:
            sp1 (Specie): First specie.
            sp2 (Specie): Second specie.
            default_bl: If a particular type of bond does not exist, use this
                bond length as a default value (bond order = 1).
                If None, a ValueError will be thrown.

        Return:
            A dict mapping bond order to bond length in angstrom
        """
        if isinstance(sp1, Element):
            sp1 = sp1.symbol
        if isinstance(sp2, Element):
            sp2 = sp2.symbol
        syms = tuple(sorted([sp1, sp2]))
        if syms in bond_lengths:
            return bond_lengths[syms].copy()
        if default_bl is not None:
            return {1: default_bl}
        raise ValueError("No bond data for elements {} - {}".format(*syms))

    def get_bond_order(sp1, sp2, dist, tol=0.2, default_bl=None):
        """
        Calculate the bond order given the distance of 2 species

        Args:
            sp1 (Specie): First specie.
            sp2 (Specie): Second specie.
            dist: Their distance in angstrom
            tol (float): Relative tolerance to test. Basically, the code
                checks if the distance between the sites is larger than
                (1 + tol) * the longest bond distance or smaller than
                (1 - tol) * the shortest bond distance to determine if
                they are bonded or the distance is too short.
                Defaults to 0.2.
            default_bl: If a particular type of bond does not exist, use this
                bond length (bond order = 1). If None, a ValueError will be thrown.

        Returns:
            Float value of bond order. For example, for C-C bond in benzene,
            return 1.7.
        """
        all_lengths = obtain_all_bond_lengths(sp1, sp2, default_bl)
        # Transform bond lengths dict to list assuming bond data is successive
        # and add an imaginary bond 0 length
        lengths_list = [all_lengths[1] * (1 + tol)] + \
                       [all_lengths[idx + 1] for idx in range(len(all_lengths))]
        trial_bond_order = 0
        while trial_bond_order < len(lengths_list):
            if lengths_list[trial_bond_order] < dist:
                if trial_bond_order == 0:
                    return trial_bond_order
                low_bl = lengths_list[trial_bond_order]
                high_bl = lengths_list[trial_bond_order - 1]
                return trial_bond_order - (dist - low_bl) / (high_bl - low_bl)
            trial_bond_order += 1
        # Distance shorter than the shortest bond length stored,
        # check if the distance is too short
        if dist < lengths_list[-1] * (1 - tol):  # too short
            warnings.warn('%.2f angstrom distance is too short for %s and %s'
                          % (dist, sp1, sp2))
        # return the highest bond order
        return trial_bond_order - 1

    def get_bond_length(sp1, sp2, bond_order=1):
        """
        Get the bond length between two species.

        Args:
            sp1 (Specie): First specie.
            sp2 (Specie): Second specie.
            bond_order: For species with different possible bond orders,
                this allows one to obtain the bond length for a particular bond
                order. For example, to get the C=C bond length instead of the
                C-C bond length, this should be set to 2. Defaults to 1.

        Returns:
            Bond length in Angstrom. If no data is available, the sum of the atomic
            radius is used.
        """
        sp1 = Element(sp1) if isinstance(sp1, str) else sp1
        sp2 = Element(sp2) if isinstance(sp2, str) else sp2
        try:
            all_lengths = obtain_all_bond_lengths(sp1, sp2)
            return all_lengths[bond_order]
        # The ValueError is raised in `obtain_all_bond_lengths` where no bond
        # data for both elements is found. The KeyError is raised in
        # `__getitem__` method of `dict` builtin class where although bond data
        # for both elements is found, the data for specified bond order does
        # not exist. In both cases, sum of atomic radius is returned.
        except (ValueError, KeyError):
            warnings.warn("No order %d bond lengths between %s and %s found in "
                          "database. Returning sum of atomic radius."
                          % (bond_order, sp1, sp2))
            return sp1.atomic_radius + sp2.atomic_radius