sagar.molecule.derive 源代码

# -*- coding: utf-8 -*-
import numpy
from itertools import combinations

from sagar.molecule.structure import Molecule
from sagar.toolkit.derivetool import remove_redundant

class ConfigurationGenerator(object):
    '''
    这个类用于产生各种替换原子的需求
    '''

    def __init__(self, mol, symprec=1e-3):
        if not isinstance(mol, Molecule):
            raise TypeError(
                "want sagar.molecule.structure.molecule, got {:}".
                format(type(mol)))
        self.mol = mol
        self.perms = mol.get_symmetry_permutation(symprec)

    def get_configurations(self, sites, e_num):
        '''
        get_configurations output specific molecule
        for specific concentration.

        parameters:
        sites: list of (lists or tuples), represent element disorder of each sites
        e_num: tuple, number of atoms in disorderd sites.

        yield:

        a tuple
        tuple[0]: Cell object, a list of non-redundant configurations of certain volume supercell.
        tuple[1]: int object, degeneracy of the configuration in all configurations of this volume.
        '''
        perms = self.perms
        mol_positions = self.mol.positions
        for pa, d in remove_redundant(mol_positions, sites, perms, e_num=e_num):
            m = Molecule(pa[0], pa[1])
            yield (m, d)