Func_pyrough module

Func_pyrough.G_hex(latt_param, latt_param_z)

Generate the direct metric tensor for Miller-Bravais indices for hcp structure

Parameters:

  • latt_param – lattice parameter along a

  • latt_param_z – lattice parameter along c

Returns:

The direct metric tensor

Func_pyrough.Vector4to3(orien)

Convert a 4-indices vector into a normalized 3-indices vector

Parameters:

orien (array) – [h,k,l,m] vector

Returns:

an

Func_pyrough.align_poly(vertices, angles)

Aligns the first facet with x-axis

Parameters:

  • vertices (array) – List of nodes

  • angles (array) – List of angles

Returns:

Rotated nodes

Func_pyrough.base(radius, nfaces)

Creates the base of the faceted wire from radius and number of faces.

Parameters:

  • radius (float) – Radius of the wire

  • nfaces (int) – Number of faces

Returns:

Points forming the base of the wire and angles associated to each face

Func_pyrough.box(width, length, height, ns)

Creates the box mesh

Parameters:

  • width (float) – Width of the box

  • length (float) – Length of the box

  • height (float) – Height of the box

  • ns (float) – Mesh size

Returns:

vertices and faces of box mesh

Func_pyrough.cart2cyl(matrix)

Calculates cylindrical coordinates from cartesian ones.

Parameters:

matrix (array) – List of cartesian coordinates

Returns:

Cylindrical coordinates

Func_pyrough.center_3d_dataset(dataset)
Parameters:

dataset (array) – Array of positions

Returns:

Centered position dataset

Func_pyrough.concatenate_list_data(a_list)

Combines the elements of a list into one element in the form of a string.

Parameters:

a_list (list) – List with elements of type int

Returns:

A string

Func_pyrough.convert_in_list_of_string(lattice_parameter)

Rewrite the json lattice_parameter in the correct format i.e., a list of string

Parameters:

lattice_parameter (float or list of floats) – input from the json file

Returns:

lattice_parameter (list of strings)

Func_pyrough.coord_cart_sphere(C1, C2, r, vertices, t, z, y, x)

Creates a new matrix with x, y, z in cartesian coordinates

Parameters:

  • C1 (float) – Roughness normalization factor

  • C2 (float) – Roughness normalization factor constant for sphere

  • r (int) – Roughness height matrix

  • vertices (array) – List of nodes

  • t (array) – x y z coordinates

  • z (array) – z coordinates

  • y (array) – y coordinates

  • x (array) – x coordinates

Returns:

Cartesian coordinates

Func_pyrough.coord_sphere(vertices)

Creates a matrix with the columns that correspond to the coordinates of either x, y, z and t which contains x y z coordinates in an array

Parameters:

vertices (array) – List of nodes

Returns:

Coordinates

Func_pyrough.cube(length, ns)

Creates cube object mesh

Parameters:

  • length (float) – Length of the cube

  • ns (float) – Mesh size

Returns:

vertices and faces of cube mesh

Func_pyrough.cube_faces(length)

Generates the points and faces of a cube

Parameters:

length (float) – Size of the cube

Returns:

Points and faces of the cube

Func_pyrough.cyl2cart(matrix)

Calculates cartesian coordinates from cylindrical ones.

Parameters:

matrix (array) – List of cylindrical coordinates

Returns:

Cartesian coordinates

Func_pyrough.cylinder(length, r, ns)

Creates the mesh of a cylinder

Parameters:

  • length (float) – Length of the cylinder

  • r (float) – Radius of the cylinder

  • ns (float) – Mesh size

Returns:

vertices and faces of cylinder mesh

Func_pyrough.dotprod(orien1, orien2, lattice_parameter) → float

Run the dot product between two vectors. Works for cubic and hexagonal basis.

Parameters:

  • orien1 (list) – [h,k,l] or [h,k,i,l] vector

  • orien2 (list) – [h,k,l] or [h,k,i,l] vector

Returns:

the float result of the dot product

Func_pyrough.duplicate(side_length, orien, lattice_par, cristallo)

Takes in a length and an crystal orientation to calculate the duplication factor for atomsk.

Parameters:

  • side_length (float) – Length of one of the sides of the object

  • orien (list) – Crystal orientation

  • lattice_par (string) – Lattice parameter

  • cristallo – cristal structure

Returns:

Duplication factor and string of orientations

Func_pyrough.error_quit(error_mess)

Print error message before quiting the code.

Parameters:

error_mess (str) – error message

Returns:

print error and quit

Func_pyrough.faces_normals(obj_points, obj_faces)

Calculates each face’s normals.

Parameters:

  • obj_points (array) – List of points

  • obj_faces (array) – List of faces

Returns:

List of normals

Func_pyrough.make_obj(surfaces, energies, n_at, lattice_structure, lattice_parameter, material, orien_x, orien_z, out_pre)

Creates an OBJ file of a faceted NP. Stores the points and faces from this file.

Parameters:

  • surfaces (list) – List of surfaces for Wulff theory

  • energies (list) – List of energies associated to surfaces for Wulff theory

  • n_at (int) – Number of atoms

  • lattice_structure (str) – Atomic structure of the sample

  • lattice_parameter (float) – Lattice parameter

  • material (str) – Type of atom

  • orien_x (list) – Orientation along x-axis

  • orien_y (list) – Orientation along y-axis

  • orien_z (list) – Orientation along z-axis

  • out_pre (str) – Prefix for output files

Returns:

List of points and faces of OBJ file

Func_pyrough.make_rough(type_sample, z, nodesurf, vertices, angles)

Applies roughness to the sample.

Parameters:

  • type_sample (str) – The type of the sample

  • z (array) – Surface roughness to apply on the sample

  • nodesurf (array) – List of nodes to be moved

  • vertices (array) – Nodes of the sample

  • angles (array) – List of angles to be followed by roughness (Only in the case of a faceted wire)

Returns:

Rough sample

Func_pyrough.make_rough_wulff(vertices, B, C1, RMS, N, M, nodesurf, node_edge, node_corner, list_n)

Applies roughness to the sample in the case of a Wulff-shaped nanoparticle.

Parameters:

  • vertices (array) – Nodes of the sample

  • B (float) – The degree of the roughness

  • C1 (float) – Roughness normalization factor

  • RMS (float) – Root Mean Square

  • N (int) – Scaling cartesian position

  • M (int) – Scaling cartesian position

  • nodesurf (array) – List of surface nodes

  • node_edge (array) – List of nodes located on edges

  • node_corner (array) – List of nodes located on corners

  • list_n (list) – List of face’s normals

Returns:

Rough Wulff sample

Func_pyrough.needs_triple_correction(orien) → bool

Check if a 4-indices hcp orientation vector needs the 1/3 normalization factor.

Parameters:

orien (array) – orientation vector

Func_pyrough.node_corner(nodesurf)

From surface nodes, finds all nodes located on edges and corners.

Parameters:

nodesurf (array) – List of surface nodes

Returns:

List of nodes located on edges and list of nodes located on corners

Func_pyrough.node_indexing(vertices)

Creates a column that has an assigned index number for each row in vertices and also the nodenumbers which is an array file from 0 - length of the vertices

Parameters:

vertices (array) – Vector for the points

Returns:

Numbered vertices and raw numbers column.

Func_pyrough.node_surface(sample_type, vertices, nodenumber, points, faces)

Finds the nodes at the surface of the object. These nodes will have the surface roughness applied to it.

Parameters:

  • sample_type (str) – The name of the sample

  • vertices (array) – List of nodes

  • nodenumber (array) – Number of the corresponding node

  • points (array) – Polygon shape (Faceted wire case)

  • faces (array) – Facets list (Wulff case)

Returns:

Surface nodes

Func_pyrough.norm(vec, lattparam) → float

Returns the norm of a 3- or 4-indices vector vector.

Parameters:

  • vec (array) – [h,k,l] or [h,k,i,l] vector

  • lattparam (array) – lattice parameter(s)

Returns:

the norm (float) of the vector vec

Func_pyrough.normalize(surf)

Normalizes the coordinates of points composing the surface.

Parameters:

surf (array) – List of nodes of the surface

Returns:

Normalized surface

Func_pyrough.phi(t, z)

Calculates the arctan2 of an array filled with vector norms and an array filled with z coordinates which are the same size.

Parameters:

  • t (array) – Coordinates x y in a list

  • z (array) – Z coordinates

Returns:

An array of angles in radians

Func_pyrough.physical_norm(self, uvtw)

Returns the physically correct length of a crystallographic vector.

Func_pyrough.poly(length, base_points, ns)
Parameters:

  • length (float) – Length of the faceted wire

  • base_points (list) – Shape of the base

  • ns (float) – Mesh size

Returns:

vertices and faces of faceted wire mesh

Func_pyrough.radius(v)

Calculates the vector norm for the axis 1 of the values in the given array.

Parameters:

v (array) – The vertices of the sphere

Returns:

A vector norm

Func_pyrough.random_numbers(sfrN, sfrM)

Generates the G and U matrices for the mathematical formulation of rough surfaces.

Parameters:

  • sfrN (array) – Vector for the N decomposition

  • sfrM (array) – Vector for the M decomposition

Returns:

G and U matrices

Func_pyrough.random_surf2(sample_type, m, n, N, M, B, xv, yv, sfrM, sfrN, C1, RMS, out_pre)

Returns an array with the Z values representing the surface roughness.

Parameters:

  • sample_type (str) – The type of the sample

  • m (array) – Wavenumbers

  • n (array) – Wavenumbers

  • N (int) – Scaling cartesian position

  • M (int) – Scaling cartesian position

  • B (float) – The degree of the roughness

  • xv (array) – Unique x coordinate values from the objects vertices

  • yv (array) – Unique y coordinate values from the objects vertices

  • sfrN (array) – Vector for the N decomposition

  • sfrM (array) – Vector for the M decomposition

  • C1 (float) – Roughness normalization factor

  • RMS (float) – Root Mean Square

  • out_pre (str) – Prefix of output files

Returns:

Surface roughness

Func_pyrough.rdnsurf(m, n, B, xv, yv, sfrM, sfrN)

Generates random surface roughness that will replace the previous z values in the vertices matrix.

Parameters:

  • m (array) – Wavenumber

  • n (array) – Wavenumber

  • B (float) – The degree the roughness is dependent on

  • xv (array) – Unique x coordinate values from the objects vertices

  • yv (array) – Unique y coordinate values from the objects vertices

  • sfrM (array) – Matrix of random numbers that range from 1 to 2N

  • sfrN (array) – Matrix of random numbers that range from 1 to 2N

Returns:

Roughness height matrix

Func_pyrough.rdnsurf_2(m, n, B, xv, yv, sfrM, sfrN)

Generates random surface roughness that will replace the previous z values in the vertices matrix.

Parameters:

  • m (array) – Wavenumber

  • n (array) – Wavenumber

  • B (float) – The degree the roughness is dependent on

  • xv (array) – Unique x coordinate values from the objects vertices

  • yv (array) – Unique y coordinate values from the objects vertices

  • sfrM (array) – Matrix of random numbers that range from 1 to 2N

  • sfrN (array) – Matrix of random numbers that range from 1 to 2N

Returns:

Roughness height matrix

Func_pyrough.read_stl(sample_type, raw_stl, width, length, height, radius, ns, points)

Reads an input stl file or creates a new one if no input

Parameters:

  • sample_type (str) – Name of the sample

  • raw_stl (str) – Name of the input stl file

  • width (float) – Width of the box

  • length (float) – Length of the box/wire

  • height (float) – Height of the box

  • radius (float) – Radius of the wire/sphere

  • ns (int) – The number of segments desired

  • points (list) – List of points constituting the base (in case of faceted wire)

Returns:

List of points and faces

Func_pyrough.read_stl_wulff(raw_stl, obj_points, obj_faces, ns)

Reads an input stl file or creates a new one if no input (Wulff case).

Parameters:

  • raw_stl (str) – Name of the input stl file

  • obj_points (list) – List of points from OBJ file

  • obj_faces (list) – List of faces from OBJ file

  • ns (float) – Mesh size

Returns:

List of points and faces

Func_pyrough.rebox(file_lmp, eps)

Fits the box dimensions to the sample.

Parameters:

file_lmp (str) – .lmp file containing the atom positions

Returns:

Reboxed position file

Func_pyrough.refine_3Dmesh(type_sample, out_pre, ns, alpha, ext_fem)
Parameters:

  • type_sample (str) – Type of object

  • out_pre (str) – Outfit file name

  • ns (float) – Mesh size

  • alpha (float) – Refine mesh factor

  • ext_fem (list) – FEM extensions list

Returns:

Refined 3D meshs for all required formats

Func_pyrough.refine_box(out_pre, ns, alpha, angle, ext_fem)
Parameters:

  • out_pre (str) – Outfit file name

  • ns (float) – Mesh size

  • alpha (float) – Refine mesh factor

  • angle (float) – Angle value for facets detection

  • ext_fem (list) – FEM extensions list

Returns:

Refined box mesh

Func_pyrough.refine_sphere(out_pre, ns, alpha, angle, ext_fem)
Parameters:

  • out_pre (str) – Outfit file name

  • ns (float) – Mesh size

  • alpha (float) – Refine mesh factor

  • angle (float) – Angle value for facets detection

  • ext_fem (list) – FEM extensions list

Returns:

Refined sphere mesh

Func_pyrough.refine_wire(out_pre, ns, alpha, angle, ext_fem)
Parameters:

  • out_pre (str) – Outfit file name

  • ns (float) – Mesh size

  • alpha (float) – Refine mesh factor

  • angle (float) – Angle value for facets detection

  • ext_fem (list) – FEM extensions list

Returns:

Refined wire mesh

Func_pyrough.remove_duplicates_2d_ordered(data)
Parameters:

data (list) – Initial list

Returns:

List with no duplicates

Func_pyrough.rho(x, y)

The Pythagorean theorem equation is used to obtain a value for a side of a triangle.

Parameters:

  • x (int) – Represents the length of a side in the triangle

  • y (int) – Represents the length of a side in the triangle

Returns:

The length of hypotenuse

Func_pyrough.rms_calc(Z)

Calculates the RMS of a height distribution

Parameters:

z (array) – height matrix

Returns:

RMS

Func_pyrough.rot(surf, n1)

Rotates a surface oriented along n1 axis in order to be oriented along z-axis.

Parameters:

  • surf (array) – List of nodes from the surface

  • n1 (array) – Surface normal

Returns:

Rotated surface

Func_pyrough.rot_matrix(n, theta)

Generates the rotation matrix. Initial orientation is n, and the angle of rotation is theta. Final orientation is the z-axis.

Parameters:

  • n (list) – Initial orientation

  • theta (float) – Rotation angle

Returns:

Rotation matrix

Func_pyrough.rotate_obj_wulff(obj_points, orien_x, orien_z)
Parameters:

  • obj_points (array) – Points describing the facets of the wulff-shape

  • orien_x (list) – Orientation along x-axis

  • orien_z (list) – Orientation along z-axis

Returns:

Points respecting the desired orientation

Func_pyrough.rough_matrix_sphere(nbPoint, B, thetaa, phii, vert_phi_theta, r)

Creates the displacement values of the nodes on the surface of the sphere

Parameters:

  • nbPoint (int) – Number of points on the sphere

  • B (float) – The degree the roughness is dependent on

  • thetaa (array) – Arctan2 of x and y coordinates

  • phii (array) – Arctan2 of vector norms and z coordinates

  • vert_phi_theta (array) – Array filled with two elements that are the angles corresponding to the position of the node on the sphere.

  • r (int) – Roughness height matrix

Returns:

Rough matrix

Func_pyrough.segment_intersects_plane(S, P, a, b, c, d)
Parameters:

  • S (list) – Point defining segment with the origin

  • P (list) – Plane normal

  • a (float) – Plane equation (ax + by + cz + d = 0)

  • b (float) – Plane equation (ax + by + cz + d = 0)

  • c (float) – Plane equation (ax + by + cz + d = 0)

  • d (float) – Plane equation (ax + by + cz + d = 0)

Returns:

Boolean value for plane intersection or not

Func_pyrough.sphere(r, ns)
Parameters:

  • r (float) – Radius of the sphere

  • ns (float) – Mesh size

Returns:

vertices and faces of sphere mesh

Func_pyrough.stat_analysis(z, N, M, C1, B, sample_type, out_pre)

Displays the statistical analysis of the surface roughness generator

Parameters:

  • z (float) – Roughness height matrix

  • N (int) – Scaling cartesian position

  • M (int) – Scaling cartesian position

  • C1 (float) – Roughness normalization factor

  • B (float) – The degree the roughness is dependent on

  • sample_type (str) – The name of the sample

  • out_pre (str) – Prefix of output files

Func_pyrough.stl_file(vertices, faces, out_pre)

Creates an stl file from the vertices and faces of the desired object.

Parameters:

  • vertices (array) – The coordinates obtained from the mesh

  • faces – The faces of the triangles generated from the mesh

  • out_pre (str) – Prefix of the output files

Func_pyrough.strain_file1_to_file2(file1, file2)

Strain file1 to match file2 dimensions

Parameters:

  • file1

  • file2

Returns:

reprocessed file1

Func_pyrough.test_pyrough_execution(dir)

Check if all .json files in examples/ folder can be computed without error

Parameters:

dir (str) – examples/ folder

Func_pyrough.theta(x, y)

Calculates the arctan2 of two given arrays whose size are the same.

Parameters:

  • x (array) – x coordinates

  • y (array) – y coordinates

Returns:

An array of angles in radians

Func_pyrough.two_odd_one_even(orien)

Test if 2 indices amongst [h,k,l] are odd

Parameters:

orien (array) – [h,k,l] vector

Returns:

True or False

Func_pyrough.vectors(N, M)

Creates vector of integers between -N and N. Same for M

Parameters:

  • N (int) – Scaling cartesian position

  • M (int) – Scaling cartesian position

Returns:

2 vectors

Func_pyrough.vertex_tp(x, y, t, z)

Creates an array filled with two elements that are the angles corresponding to the position of the node on the sphere.

Parameters:

  • x (array) – X coordinates

  • y (array) – Y coordinates

  • t (array) – x & y coordinates stored in a list

  • z (array) – Z coordinates

Returns:

An array with angles as elements

Func_pyrough.write_stl(filename, vertices, face_list)

Creates an STL file from faces and vertices.

Parameters:

  • filename (str) – name of the STL file

  • vertices (array) – list of vertices

  • face_list (array) – list of faces

Func_pyrough.wulff(points, faces, ns)
Parameters:

  • points (list) – Vertices of Wulff-shape

  • faces (list) – Facets of Wulff-shape

  • ns (float) – Mesh size

Returns:

vertices and faces of Wulff mesh