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Symmetry Representation

symel

Referenced by:

Symel dataclass 

Symel(symbol: str, vector: ndarray | None, rrep: ndarray, m: int | None = None, n: int | None = None, O: str | None = None)

Symmetry element (SymEl): Symmetry operation with its symbol, representative axis, matrix representation and metadata.

Parameters:

  • symbol (str) –

    Schoenflies symbol of the symmetry element (e.g. "C_3", "sigma_h", "i").

  • vector (ndarray | None) –

    Axis vector for Cn and Sn; plane normal vector for sigma; None for E and i.

  • rrep (ndarray) –

    3x3 real-space matrix representation of the operation.

  • m (int | None, default: None ) –

    Power of the generator (e.g. m=2 for C_3^2).

  • n (int | None, default: None ) –

    Order of the principal axis of the generating cycle.

  • O (str | None, default: None ) –

    Origin class of the element. Options: "E", "sigma_v", "C_2'", "i", "sigma_h".

Returned by: Used by:

symtext

symtext.py — Full symmetry characterization of a molecule (Symtext class).

Dependencies: pg_detect — find_point_group point_group — PointGroup symel_gen — pg_to_symels mol_orient — rotate_mol_to_symels atom_mapping — _get_atom_mapping, _get_linear_atom_mapping

Referenced by:

Symtext 

Symtext(mol, rotate_to_std, reverse_rotate, pg, symels, atom_map)

Full symmetry characterization of a molecule.

Holds the point group, list of symmetry elements, atom permutation map, and the rotation matrices that relate the molecule to the canonical orientation defined by the symmetry elements.

Returned by: Used by:
Source code in minimalsym/core/symtext.py 
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def __init__(self, mol, rotate_to_std, reverse_rotate, pg, symels, atom_map):
    self.mol = mol
    self.rotate_to_std = rotate_to_std
    self.reverse_rotate = reverse_rotate
    self.pg = pg
    self.symels = symels
    self.atom_map = atom_map
    if pg.is_linear:
        # Linear groups have infinitely many symmetry elements; the finite
        # atom_map covers only the operations that actually permute atoms.
        self.order = atom_map.shape[1]
    else:
        self.order = len(symels)

from_molecule classmethod 

from_molecule(mol)

Build a Symtext from an ase.Atoms object.

Parameters:

  • mol (Atoms) –

Returns:

Source code in minimalsym/core/symtext.py 
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@classmethod
def from_molecule(cls, mol):
    """
    Build a Symtext from an ase.Atoms object.

    Parameters
    ----------
    mol : ase.Atoms

    Returns
    -------
    Symtext
    """
    mol.translate(-mol.get_center_of_mass())
    pgr = find_point_group(mol)
    pg = PointGroup.from_string(pgr.pg)
    mol, reverse_rotate, rotate_to_std = rotate_mol_to_symels(mol, pgr.paxis, pgr.saxis)
    mol.info["pg"] = pgr.pg
    symels = pg_to_symels(pg.str)
    if pg.is_linear:
        atom_map = _get_linear_atom_mapping(mol, pg)
    else:
        atom_map = _get_atom_mapping(mol, symels)
    return Symtext(mol, rotate_to_std, reverse_rotate, pg, symels, atom_map)

from_PointGroupResult classmethod 

from_PointGroupResult(mol, pgr, is_linear: bool = False)

Build a Symtext from a PointGroupResult object.

Parameters:

  • mol (Atoms) –
  • pgr (PointGroupResult) –

Returns:

Source code in minimalsym/core/symtext.py 
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@classmethod
def from_PointGroupResult(cls, mol, pgr, is_linear:bool=False):
    """
    Build a Symtext from a PointGroupResult object.

    Parameters
    ----------
    mol : ase.Atoms
    pgr : PointGroupResult

    Returns
    -------
    Symtext
    """
    pg = PointGroup.from_string(pgr.pg)
    mol, reverse_rotate, rotate_to_std = rotate_mol_to_symels(mol, pgr.paxis, pgr.saxis)
    mol.info["pg"] = pgr.pg
    symels = pg_to_symels(pg.str)
    if pg.is_linear:
        atom_map = _get_linear_atom_mapping(mol, pg)
    else:
        atom_map = _get_atom_mapping(mol, symels)
    return Symtext(mol, rotate_to_std, reverse_rotate, pg, symels, atom_map)

point_group

Referenced by:

PointGroup 

PointGroup(s, family, n, subfamily)

Schoenflies point group descriptor.

Parses and validates a point group string into its family, order, and subfamily.

Used by:
Source code in minimalsym/core/point_group.py 
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def __init__(self, s, family, n, subfamily):
    self.str = s
    self.family = family
    self.n = n
    if self.n == 0:
        self.is_linear = True
    else:
        self.is_linear = False
    self.subfamily = subfamily
    self.dumb_pg()