crystallography

crystallography

apply_atom_site_aniso_symmetry_constraints(atom_site_aniso, name_hm, coord_code, _wyckoff_letter, site_fract)

Apply symmetry constraints to anisotropic ADP tensor components.

Uses the Peterse-Palm probe technique to determine which tensor components are constrained by the site symmetry, then delegates to cryspy's vibration_constraints to enforce them.

Parameters:

Name	Type	Description	Default
atom_site_aniso	dict[str, float]	Dictionary with keys 'adp_11' … 'adp_23'. Modified in place.	required
name_hm	str	Hermann-Mauguin symbol of the space group.	required
coord_code	str | None	IT coordinate system code.	required
_wyckoff_letter	str	Wyckoff position letter (unused, reserved).	required
site_fract	tuple[float, float, float]	Fractional coordinates of the atom site.	required

Returns:

Type	Description
tuple[dict[str, float], tuple[bool, ...]]	The atom_site_aniso dictionary with constrained values, and a 6-tuple of booleans indicating which components remain free for refinement (True = free, False = fixed by symmetry).

Source code in src/easydiffraction/crystallography/crystallography.py

def apply_atom_site_aniso_symmetry_constraints(
    atom_site_aniso: dict[str, float],
    name_hm: str,
    coord_code: str | None,
    _wyckoff_letter: str,
    site_fract: tuple[float, float, float],
) -> tuple[dict[str, float], tuple[bool, ...]]:
    """
    Apply symmetry constraints to anisotropic ADP tensor components.

    Uses the Peterse-Palm probe technique to determine which tensor
    components are constrained by the site symmetry, then delegates to
    cryspy's ``vibration_constraints`` to enforce them.

    Parameters
    ----------
    atom_site_aniso : dict[str, float]
        Dictionary with keys ``'adp_11'`` … ``'adp_23'``.  Modified in
        place.
    name_hm : str
        Hermann-Mauguin symbol of the space group.
    coord_code : str | None
        IT coordinate system code.
    _wyckoff_letter : str
        Wyckoff position letter (unused, reserved).
    site_fract : tuple[float, float, float]
        Fractional coordinates of the atom site.

    Returns
    -------
    tuple[dict[str, float], tuple[bool, ...]]
        The *atom_site_aniso* dictionary with constrained values, and a
        6-tuple of booleans indicating which components remain free for
        refinement (``True`` = free, ``False`` = fixed by symmetry).
    """
    all_free = (True, True, True, True, True, True)

    it_number = get_it_number_by_name_hm_short(name_hm)
    if it_number is None:
        log.error(f"Failed to get IT_number for name_H-M '{name_hm}'")
        return atom_site_aniso, all_free

    ops = _get_general_position_ops(it_number, coord_code)
    if ops is None:
        return atom_site_aniso, all_free

    stabiliser = _site_stabilizer_rotations(ops, site_fract)
    if len(stabiliser) <= 1:
        # Identity only — no ADP constraints
        return atom_site_aniso, all_free

    numb = _calc_adp_constraint_number(stabiliser)
    if numb == 0:
        return atom_site_aniso, all_free

    param_i = (
        atom_site_aniso['adp_11'],
        atom_site_aniso['adp_22'],
        atom_site_aniso['adp_33'],
        atom_site_aniso['adp_12'],
        atom_site_aniso['adp_13'],
        atom_site_aniso['adp_23'],
    )
    sigma_i = (0.0, 0.0, 0.0, 0.0, 0.0, 0.0)
    ref_i = (True, True, True, True, True, True)

    param_i, _sigma_i, ref_i, _constr_i = vibration_constraints(
        numb,
        param_i,
        sigma_i,
        ref_i,
    )

    keys = ('adp_11', 'adp_22', 'adp_33', 'adp_12', 'adp_13', 'adp_23')
    atom_site_aniso.update(dict(zip(keys, param_i, strict=False)))

    return atom_site_aniso, ref_i

apply_atom_site_symmetry_constraints(atom_site, name_hm, coord_code, wyckoff_letter)

Apply symmetry constraints to atom site coordinates.

Parameters:

Name	Type	Description	Default
atom_site	dict[str, Any]	Dictionary containing atom position data.	required
name_hm	str	Hermann-Mauguin symbol of the space group.	required
coord_code	int	Coordinate system code.	required
wyckoff_letter	str	Wyckoff position letter.	required

Returns:

Type	Description
dict[str, Any]	The atom_site dictionary with applied symmetry constraints.

Source code in src/easydiffraction/crystallography/crystallography.py

def apply_atom_site_symmetry_constraints(
    atom_site: dict[str, Any],
    name_hm: str,
    coord_code: int,
    wyckoff_letter: str,
) -> dict[str, Any]:
    """
    Apply symmetry constraints to atom site coordinates.

    Parameters
    ----------
    atom_site : dict[str, Any]
        Dictionary containing atom position data.
    name_hm : str
        Hermann-Mauguin symbol of the space group.
    coord_code : int
        Coordinate system code.
    wyckoff_letter : str
        Wyckoff position letter.

    Returns
    -------
    dict[str, Any]
        The atom_site dictionary with applied symmetry constraints.
    """
    parsed_exprs = _get_wyckoff_exprs(name_hm, coord_code, wyckoff_letter)
    if parsed_exprs is None:
        return atom_site

    _apply_fract_constraints(atom_site, parsed_exprs)
    return atom_site

apply_cell_symmetry_constraints(cell, name_hm)

Apply symmetry constraints to unit cell parameters.

Parameters:

Name	Type	Description	Default
cell	dict[str, float]	Dictionary containing lattice parameters.	required
name_hm	str	Hermann-Mauguin symbol of the space group.	required

Returns:

Type	Description
dict[str, float]	The cell dictionary with applied symmetry constraints.

Source code in src/easydiffraction/crystallography/crystallography.py

def apply_cell_symmetry_constraints(
    cell: dict[str, float],
    name_hm: str,
) -> dict[str, float]:
    """
    Apply symmetry constraints to unit cell parameters.

    Parameters
    ----------
    cell : dict[str, float]
        Dictionary containing lattice parameters.
    name_hm : str
        Hermann-Mauguin symbol of the space group.

    Returns
    -------
    dict[str, float]
        The cell dictionary with applied symmetry constraints.
    """
    it_number = get_it_number_by_name_hm_short(name_hm)
    if it_number is None:
        error_msg = f"Failed to get IT_number for name_H-M '{name_hm}'"
        log.error(error_msg)  # TODO: ValueError? Diagnostics?
        return cell

    crystal_system = get_crystal_system_by_it_number(it_number)
    if crystal_system is None:
        error_msg = f"Failed to get crystal system for IT_number '{it_number}'"
        log.error(error_msg)  # TODO: ValueError? Diagnostics?
        return cell

    if crystal_system == 'cubic':
        a = cell['lattice_a']
        cell['lattice_b'] = a
        cell['lattice_c'] = a
        cell['angle_alpha'] = 90.0
        cell['angle_beta'] = 90.0
        cell['angle_gamma'] = 90.0

    elif crystal_system == 'tetragonal':
        a = cell['lattice_a']
        cell['lattice_b'] = a
        cell['angle_alpha'] = 90.0
        cell['angle_beta'] = 90.0
        cell['angle_gamma'] = 90.0

    elif crystal_system == 'orthorhombic':
        cell['angle_alpha'] = 90.0
        cell['angle_beta'] = 90.0
        cell['angle_gamma'] = 90.0

    elif crystal_system in {'hexagonal', 'trigonal'}:
        a = cell['lattice_a']
        cell['lattice_b'] = a
        cell['angle_alpha'] = 90.0
        cell['angle_beta'] = 90.0
        cell['angle_gamma'] = 120.0

    elif crystal_system == 'monoclinic':
        cell['angle_alpha'] = 90.0
        cell['angle_gamma'] = 90.0

    elif crystal_system == 'triclinic':
        pass  # No constraints to apply

    else:
        error_msg = f'Unknown or unsupported crystal system: {crystal_system}'
        log.error(error_msg)  # TODO: ValueError? Diagnostics?

    return cell

space_groups

Space group reference data.

Loads a gzipped, packaged pickle with crystallographic space-group information. The file is part of the distribution; user input is not involved.