carmm.analyse.meshgrid package

Submodules

carmm.analyse.meshgrid.meshgrid_functions module

carmm.analyse.meshgrid.meshgrid_functions.atom_mesh_build_mask(meshobject, atoms)

Defines meshgrid of based on a radius set by atomic_radius. Uses np.nan as a junk value. :type meshobject: :param meshobject: Mesh Object

Object storing meshgrid and PBC conditions

Parameters:

atoms – Atoms object Contains information (atomic symbols and positions)

Returns:

3D numpy array

Value of x coordinate on {nx,ny,nz} grid.

mol_yy: 3D numpy array

Value of y coordinate on {nx,ny,nz} grid.

mol_yy: 3D numpy array

Value of z coordinate on {nx,ny,nz} grid.

Return type:

mol_xx

carmm.analyse.meshgrid.meshgrid_functions.distance_meshgrid2point(a_xx, a_yy, a_zz, meshobject)

Function finds the distance between a point (defined in cartesian co-ordinates a_xx, a_yy, a_zz) relative to all points on a Numpy meshgrid (defined in the unit_cell_object). :type a_xx: :param a_xx: float

x coordinate of input point.

Parameters:

  • a_yy – float y coordinate of input point.

  • a_zz – float z coordinate of input point.

  • meshobject – Mesh object Object storing meshgrid and PBC conditions

Returns:

Numpy meshgrid of distances from point [a_xx, a_yy, a_zz].

Return type:

mesh_distances

carmm.analyse.meshgrid.meshgrid_functions.distance_point2point(x_1, y_1, z_1, x_2, y_2, z_2, meshobject)

Function finds the distance between two points (defined in cartesian co-ordinates). :type x_1: :param x_1: float

x coordinate of point 1.

Parameters:

  • y_1 – float y coordinate of point 1.

  • z_1 – float z coordinate of point 1.

  • x_2 – float x coordinate of point 2.

  • y_2 – float y coordinate of point 2.

  • z_2 – float2 z coordinate of point 2.

  • meshobject – Mesh object Object storing meshgrid and PBC conditions

Returns:

Distance between points 1 and 2.

Return type:

o_distance

carmm.analyse.meshgrid.meshgrid_functions.midpoint_points(x_1, y_1, z_1, x_2, y_2, z_2, meshobject)

Function finds the distance between two points (defined in cartesian co-ordinates). :type x_1: :param x_1: float

x coordinate of point 1.

Parameters:

  • y_1 – float y coordinate of point 1.

  • z_1 – float z coordinate of point 1.

  • x_2 – float x coordinate of point 2.

  • y_2 – float y coordinate of point 2.

  • z_2 – float2 z coordinate of point 2.

  • meshobject – Mesh object Object storing meshgrid and PBC conditions

Returns:

numpy array (,3)

x, y and z coordinates of the midpoint between points 1 and 2.

Return type:

midpoint

carmm.analyse.meshgrid.meshgrid_functions.mol_mesh_pbc_check(mesh_pbc, atoms_pbc)

Checks whether the mesh and mol pbc values match, and prints a warning if not. :type mesh_pbc: :param mesh_pbc: Object storing meshgrid and PBC conditions :type atoms_pbc: :param atoms_pbc: Contains information (atomic symbols and positions)

carmm.analyse.meshgrid.meshgrid_mesh module

class carmm.analyse.meshgrid.meshgrid_mesh.Mesh(cell_dims, nx=50, ny=50, nz=50, pbc=[True, True, True], pbc_strict_mode=True)

Bases: object

Object which stores and defines the unit cell parameters (number of points and dimensions) and the mesh grid of the underlying unit cell. Primarily used to reduce the number of variables which need to be passed to associated meshgrid functions.

read_cube_file(cube_name)

carmm.analyse.meshgrid.meshgrid_void module

carmm.analyse.meshgrid.meshgrid_void.void_analysis(meshobject, void_centres, void_radii, void_xx)

Prints basic volumentric information of the void. :type meshobject: :param meshobject: Mesh object.

Meshgrid and unit cell information.

Parameters:

  • void_centres – numpy array Coordinates of the void centres.

  • void_radii – numpy array Radius of the void sphere.

  • void_xx – meshgrid numpy array x coordinates of void mesh grid.

Returns:

float

The total volume of the volume accessible to the probe (Ang**3).

Return type:

void_volume

carmm.analyse.meshgrid.meshgrid_void.void_build_mask(meshobject, void_centres, void_radii, min_void=1.0)

Defines meshgrid of voids given by list of void centres and their radii. Uses np.nan as a junk value. :type meshobject: :param meshobject: Mesh object.

Meshgrid and unit cell information.

Parameters:

  • void_centres – numpy array Coordinates of the void centres.

  • void_radii – numpy array Radius of the void sphere.

  • min_void – float Defines the minimum size of void to plot.

Returns:

numpy array

Contains values of (x, y, z) coordinates for each point on axis occupied by atom van der Waals volume. Set to junk value otherwise.

Return type:

void_xx, void_yy, void_zz

carmm.analyse.meshgrid.meshgrid_void.void_find(meshobject, atoms, coarseness=1)

Defines the maximum spherical radius of probes in unoccupied space. Scans through the distance between the probe point and all atoms in the system, and defines the maximum radius of the probe as the smallest value of (probe_position - atom_position - vdw_radii). Coarseness factor reduces number of probe points by skipping over points in the grid. :type meshobject: :param meshobject: Mesh object

Contains meshgrid and associated unit cell information.

Parameters:

  • atoms – Atoms object Supplies coordinates and atomic information.

  • coarseness – integer Skips over an integer number of points

Returns:

numpy array

Atomic coordiantes of the void centres.

void_radii: numpy array

Radius of the void centres

Return type:

void_centres

Module contents