API Reference¶

Cosymlib¶

class cosymlib.Cosymlib(structures, ignore_atoms_labels=False, ignore_connectivity=False, connectivity=None, connectivity_thresh=None)[source]¶

Main cosymlib class

Parameters:

structures (list) – List of Geometry or Molecule
ignore_atoms_labels (bool) – Ignore atomic element labels is symmetry calculations
ignore_connectivity (bool) – Ignore connectivity in symmetry calculations
connectivity (list) – List of pairs if atom indices that are considered connected
connectivity_thresh (bool) – Connectivity threshold (Ionic radius is used as reference)

get_geometries()[source]¶

Get the geometries

Returns:	List of `Geometry` objects
Return type:	list

get_molecule_path_deviation(shape_label1, shape_label2, central_atom=0)[source]¶

Get molecule path deviation

Parameters:	shape_label1 (str) – First shape reference label shape_label2 (str) – Second shape reference label central_atom (int) – Position of the central atom

get_n_atoms()[source]¶

Get the number of atoms if all structures contains the same number of atoms, else raise exception.

Returns:	Number of atoms
Return type:	int

get_point_group(tol=0.01)[source]¶

Get the point group of all structures

Parameters:	tol (float) – Tolerance
Returns:	a list of point group labels
Return type:	list

get_shape_measure(label, kind, central_atom=0, fix_permutation=False)[source]¶

Get shape measure

Parameters:	label (str) – Reference shape label kind (str) – function name suffix central_atom (int) – Position of the central atom fix_permutation (bool) – Do not permute atoms during shape calculations
Returns:	Shape measures
Return type:	list

molecules¶

Get the molecules

Returns:	List of `Molecule` objects
Return type:	list

print_esym_orientation(group, axis=None, axis2=None, center=None, output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Prints down an xyz file of the molecule with the orientation_axis

Parameters:	group (string) – Symmetry group axis (list) – Main symmetry axis of group axis2 (list) – Secondary symmetry axis of group center (list) – Center output (hook) – Display hook

print_geometric_measure_info(label, multi=1, central_atom=0, center=None, output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Prints geometric symmetry measure verbose

Parameters:	label (str) – Symmetry point group label multi (int) – Number of symmetry axis to find central_atom (int) – Position of the central atom center (list) – Center of symmetry in Cartesian coordinates. If None center is optimized output – Display hook
Type:	hook

print_geometric_symmetry_measure(label, central_atom=0, center=None, output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Prints geometric symmetry measure in format

Parameters:	label (str) – Symmetry point group label central_atom (int) – Position of the central atom center (list) – Center of symmetry in Cartesian coordinates. If None center is optimized output (hook) – Display hook

print_info()[source]¶: Prints general information about the structures

print_minimum_distortion_path_shape(shape_label1, shape_label2, central_atom=0, min_dev=None, max_dev=None, min_gco=None, max_gco=None, num_points=20, output=None)[source]¶

Print the minimum distortion path

Parameters:	shape_label1 (str) – First reference shape label shape_label2 (str) – Second reference shape label central_atom (int) – Position of the central atom min_dev (float) – max_dev (float) – min_gco (float) – max_gco (float) – num_points (int) – Number of points output1 (hook) – Display hook

print_shape_measure(shape_reference, central_atom=0, fix_permutation=False, output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Prints the shape measure of all structures in format

Parameters:	shape_reference (list) – List of references and/or geometries central_atom (int) – Position of the central atom fix_permutation (bool) – Do not permute atoms during shape calculations output (hook) – Display hook

print_shape_structure(shape_reference, central_atom=0, fix_permutation=False, output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Prints the nearest shape structure in format

Parameters:	shape_reference (list) – List of references and/or geometries central_atom (int) – Position of the central atom fix_permutation (bool) – Do not permute atoms during shape calculations output (hook) – Display hook

print_symmetry_nearest_structure(label, central_atom=0, center=None, output=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='UTF-8'>)[source]¶

Prints the nearest structure to ideal symmetric structure

Parameters:	label (str) – Symmetry point group label central_atom (int) – Position of the central atom center (int) – Center of symmetry in Cartesian coordinates. If None center is optimized output (hook) – Display hook

Symmetry¶

class cosymlib.symmetry.Symmetry(structure, central_atom=0, center=None, connect_thresh=1.2, multi=1, axis=None, axis2=None)[source]¶

Symmetry main class

Parameters:

structure (Geometry, Molecule, np.array) – a geometry, molecule or array type object
central_atom (int) – central atom position
center (list) – center of symmetry in Cartesian coordinates. By default center is optimized
connect_thresh (float) – Connectivity threshold (Ionic radius is used as reference)
multi (int) – Number of symmetry axis to find
axis (list) – Main symmetry axis (If None, then optimize)
axis2 (list) – secondary symmetry axis (If None, then optimize)

axis_multi(label, multi=1)[source]¶

Get the optimum N axis

Parameters:	label (str) – point group label multi (int) – number of axis
Returns:	List of axis
Return type:	list

csm_multi(label, multi=1)[source]¶

Get symmetry measure of the optimum N axis

Parameters:	label (str) – point group label multi (int) – number of axis
Returns:	The measures
Return type:	list

measure(label)[source]¶

Get symmetry measure

Parameters:	label (str) – Point group label
Returns:	The measure
Return type:	float

nearest_structure(label)[source]¶

Get nearest structure

Parameters:	label (str) – Point group label
Returns:	The structure
Return type:	Structure

optimum_axis(label)[source]¶

Get the optimum main symmetry axis

Parameters:	label (str) – Point group label
Returns:	The axis
Return type:	list

optimum_permutation(label)[source]¶

Get the optimum atoms permutation

Parameters:	label – point group label
Returns:	The permutation
Return type:	list

reference_axis(label)[source]¶

Get reference axis

Parameters:	label (str) – point group label
Returns:	The axis
Return type:	list

set_parameters(parameters_dict)[source]¶

Set symmetry calculation related parameters

Parameters:	parameters_dict (dict) – parameters in dictionary

Shape¶

class cosymlib.shape.Shape(structure)[source]

Shape main class

Parameters:	structure (Geometry, Molecule, np.array) – a geometry, molecule or array type object

generalized_coordinate(shape_label1, shape_label2, central_atom=0)[source]

Get the generalized coordinate

Parameters:	shape_label1 (str, Geometry) – First shape reference label or Geometry object shape_label2 (str, Geometry) – Second shape reference label or Geometry object central_atom (int) – Central atom position
Returns:	The generalized coordinate

measure(reference, central_atom=0, fix_permutation=False)[source]

Get shape measure

Parameters:	reference (str) – Reference shape label or Geometry object central_atom (int) – Central atom position fix_permutation (bool) – Do not permute atoms during shape calculations
Returns:	The measure
Return type:	float

path_deviation(shape_label1, shape_label2, central_atom=0)[source]

Get the path deviation

Parameters:	shape_label1 (str, Geometry) – First shape reference label or Geometry object shape_label2 (str, Geometry) – Second shape reference label or Geometry object central_atom (int) – Central atom position
Returns:	The path deviation
Return type:	float

structure(reference, central_atom=0, fix_permutation=False)[source]

Get the nearest structure to reference

Parameters:	reference (str, Geometry) – Reference shape label or Geometry object central_atom (int, Geometry) – Central atom position fix_permutation (bool) – Do not permute atoms during shape calculations
Returns:	The structure
Return type:	Structure

Molecule¶

class cosymlib.molecule.Molecule(geometry, electronic_structure=None, name=None)[source]¶

Main molecule class

Parameters:	geometry (Geometry) – The geometry electronic_structure (ElectronicStructure) – The electronic structure name (str) – Molecule name

electronic_structure¶

Get the electronic structure

Returns:	The electronic structure
Return type:	ElectronicStructure

geometry¶

Get the geometry

Returns:	The geometry
Return type:	Geometry

get_charge()[source]¶: Get the charge of the molecule

get_n_atoms()[source]¶

Get the number of atoms

Returns:	number of atoms
Return type:	int

get_pointgroup(tol=0.01)[source]¶

Get the symmetry point group

Parameters:	tol (float) – The tolerance
Returns:	The point group
Return type:	str

get_positions()[source]¶

Get the positions in Cartesian coordinates

Returns:	the coordinates
Return type:	list

get_symbols()[source]¶

Get the atomic elements symbols

Returns:	the symbols
Return type:	list

Geometry¶

class cosymlib.molecule.geometry.Geometry(positions, symbols=(), name='', connectivity=None, connectivity_thresh=1.2)[source]¶

Main geometry class

Parameters:	positions (list) – Cartesian coordinates symbols (list) – Atomic elements symbols name (str) – Geometry name connectivity (list) – Connectivity list connectivity_thresh (float) – Connectivity threshold
Example:

water = Geometry(positions=[[0.0, 0.0, 0.0],
                            [0.0, 1.0, 0.0],
                            [0.0, 0.0, 1.0],
                 symbols=['O', 'H', 'H'],
                 name='water molecule',
                 connectivity=[[1, 2], [1, 3]])

get_connectivity()[source]¶

Get connectivity as a list of pairs of connected atoms

Returns:	The connectivity
Return type:	list

get_n_atoms()[source]¶

Get the number of atoms

Returns:	number of atoms
Return type:	int

get_pointgroup(tol=0.01)[source]¶: Get the symmetry point group :param tol: The tolerance :type tol: float :return: The point group :rtype: str

get_positions()[source]¶

Get the positions in Cartesian coordinates

Returns:	the coordinates
Return type:	list

get_shape_measure(shape_label, central_atom=0, fix_permutation=False)[source]¶

Get the Shape measure

Parameters:	shape_label (str) – Reference shape label central_atom (int) – the central atom position fix_permutation (bool) – Do not permute atoms
Returns:	The measure
Return type:	float

get_symbols()[source]¶

Get the atomic elements symbols

Returns:	the symbols
Return type:	list

get_symmetry_measure(label, central_atom=0, center=None, multi=1)[source]¶

Get the symmetry measure

Parameters:	label (str) – Symmetry point group central_atom (int) – central atom position (0 if no central atom) center (list) – center of the measure in Cartesian coordinates
Returns:	The symmetry measure
Return type:	float

get_symmetry_nearest_structure(label, central_atom=0, center=None, multi=1)[source]¶

Returns the nearest ideal structure

Parameters:	label (str) – symmetry point group central_atom (int) – central atom position (0 if no central atom) center (list) – center of the measure in Cartesian coordinates
Returns:	The structure
Return type:	Geometry

Electronic structure¶

class cosymlib.molecule.electronic_structure.ElectronicStructure(basis, orbital_coefficients, multiplicity=None, alpha_energies=None, beta_energies=None, alpha_occupancy=None, beta_occupancy=None)[source]¶

Main Electronic structure class

Parameters:

basis (dict) – The basis set
orbital_coefficients (list) – Molecular orbital coefficients
multiplicity (int) – The multiplicity
alpha_energies (list) – Alpha molecular orbital energies in Hartree
beta_energies (list) – Beta molecular orbital energies in Hartree
alpha_occupancy (list) – Occupancy of alpha orbitals
beta_occupancy (list) – Occupancy of beta orbitals