Symmetry and shape analysis¶

The symetry and shape analysis is calculated using the external software :program: shape, :program: symop, and :program: symgroup. To use the interfaces to the binaries have to be placed in a directory included in the $PATH environment variable with the name shape, symop, and symgroup, respectively. Note that setting up an alias in .profile or bashrc for these software will not work.

Shape¶

To use shape interface, shape module has to be loaded by

$ module load montemodes.functions.shape as shape

The use of shape module is divided in two parts: First a shape input object is created. This shape object defines the kind of shape calculation to perform

$ input_shape = shape.Shape(code=1,
                            central_atom=0,
                            custom_atom_list=None)

code: corresponds to the shape code available in shape manual. It depends on the number of vertices.
central_atom: defines the atom number that will be used as central atom. Atom number uses the same rule as shape where the first atom is atom number 1. If central_atom is 0 no central atom will be defined.
custom_atom_list: defines a list of atoms of the structure that will be used in the shape calculation. If this value is None all atoms are used.

methods¶

get_shape(structure [type Structure], input_shape [type Shape]):

Return: Float

Get the shape measure of a structure

get_shape_trajectory(trajectory [list of Structure objects], input_shape [type Shape]):

Return: List of Float

Get the shape of a list of structures

get_info(vertices=None):

Return: Null

Get information about available shapes. (equivalent to shape +).

example¶

$ import montemodes.functions.reading as io_monte
$ import montemodes.functions.shape as shape

$ structure = io_monte.reading_from_xyz_file('ch4.xyz')
$ input_shape = shape.Shape(code=2,
                            central_atom=1,
                            custom_atom_list=None)

$ measure = get_shape(structure, input_shape)
$ print ('The T-4 shape measure of CH4 is {}'.format(measure))

Symop¶

To use symop interface, symop module has to be loaded by

$ module load montemodes.functions.symop as symop

Likewise shape module, symop module is divided in two parts: First a symop input object is created. This symop object defines the kind of symmetry calculation to perform

$ input_symop = symop.Symop(symmetry='c 3',
                            label=False,
                            connect=False,
                            central_atom=0,
                            custom_atom_list=None)

symmetry: corresponds to the symmetry operation to be measured.
label : if True adds %label keyword to symop input (check symop manual for further information).
connect : if True adds %connect keyword to symop input (check symop manual for further information).
central_atom: defines the atom number that will be used as central atom. Atom number uses the same rule as symop where the first atom is atom number 1. If central_atom is 0 no central atom will be defined.
custom_atom_list: defines a list of atoms of the structure that will be used in the shape calculation. If this value is None all atoms are used.

methods¶

get_symmetry(structure [type Structure], symop_input [type symop]):

Return: Float

Get the symmetry measure of a structure.

get_symmetry_trajectory(trajectory [type Structure], symop_input [type symop]):

Return: List of Float

Get the symmetry measure of a list of Structure type objects.

example¶

$ import montemodes.functions.reading as io_monte
$ import montemodes.functions.symop as symop

$ structure = io_monte.reading_from_xyz_file('ch4.xyz')

$ input_symop = symop.Symop(symmetry='c 3',
                            label=False,
                            connect=False,
                            central_atom=0,
                            custom_atom_list=[1,2,3,4])

$ measure = get_symmetry(structure, input_symop)
$ print ('The C3 symmetry measure of CH4 is {}'.format(measure))