Sample_class module

class Sample_class.Sample(type_sample)

Bases: object

make_atom(STL, lattice_str, lattice_par, material, orien_x, orien_y, orien_z, vertices, out_pre, ext_ato)

Creates an atom position file sample_with_atoms.lmp. This requires a .stl file with rough surfaces used as a stencil over a larger block of atoms from which out-of-the-mesh atoms are removed

Parameters:

type_sample (str) – Sample type
STL (str) – The stl file with an object that has surface roughness applied to it
lattice_str (str) – The lattice structure of the crystal
lattice_par (float) – The lattice parameter of the crystal in Angstrom
material (str) – The chemical symbol of the desired element
orien_x (list) – The orientation of the crystal in the x direction
orien_y (list) – The orientation of the crystal in the y direction
orien_z (list) – The orientation of the crystal in the z direction
vertices (array) – List of nodes
out_pre (str) – Prefix of the output files

make_atom_matrix(STL, length_x, length_y, length_z, lattice_str, lattice_par, material, orien_x, orien_y, orien_z)

Creates an orthogonal matrix made of atoms.

Parameters:

length_x (float) – Sample dimension
length_y (float) – Sample dimension
length_z (float) – Sample dimension
lattice_str (str) – The lattice structure of the crystal
lattice_par (float) – The lattice parameter of the crystal in Angstrom
material (str) – The chemical symbol of the desired element
orien_x (list) – The orientation of the crystal in the x direction
orien_y (list) – The orientation of the crystal in the y direction
orien_z (list) – The orientation of the crystal in the z direction
out_pre (str) – Prefix of the output files

make_precipitate(STL, lattice_str, lattice_par, material, orien_x, orien_y, orien_z, dim_mat_x, dim_mat_y, dim_mat_z)

Creates an atom position file sample_with_atoms.lmp. This requires a .stl file with rough surfaces used as a stencil over a larger block of atoms from which out-of-the-mesh atoms are removed

Parameters:

type_sample (str) – Sample type
STL (str) – The stl file with an object that has surface roughness applied to it
lattice_str (str) – The lattice structure of the crystal
lattice_par (float) – The lattice parameter of the crystal in Angstrom
material (str) – The chemical symbol of the desired element
orien_x (list) – The orientation of the crystal in the x direction
orien_y (list) – The orientation of the crystal in the y direction
orien_z (list) – The orientation of the crystal in the z direction
out_pre (str) – Prefix of the output files
dim_mat_x (float) – Dimensions of the matrix

make_stl(type_sample, eta, C1, RMS, N, M, radius, length, height, width, ns, alpha, raw_stl, nfaces, surfaces, energies, n_at, lattice_structure, lattice_parameter, material, orien_x, orien_z, out_pre, ext_fem)

Creates an stl file based on the parameters chosen by the user. Based on the type of sample entered, the code will sort through the options of type of samples and if true then the code under the type of sample will be executed. The type of sample affects the type of stl file returned. The code executed requires the parameters to create the object stl and to apply surface roughness onto the object. …; In continuation will add that a separate files will be stored if they want to redo the code.

Parameters:

type_sample (str) – Type of the sample
eta (float) – Roughness exponent
C1 (float) – Roughness normalization factor
RMS (float) – RMS
N (int) – Length of the random numbers matrix
M (int) – Length of the random numbers matrix
radius (float) – The radius of the nanowire or the sphere
length (float) – The length of the box
height (float) – The height of the box
width (float) – The width of the box
ns (float) – Mesh size
alpha (float) – Refine mesh factor
raw_stl (stl) – Input STL file
nfaces (int) – Number of faces in the case of a faceted wire
surfaces (list) – List of surfaces used for Wulff theory
energies (list) – List of energies for each associated surface
n_at (int) – Number of atoms in the case of a faceted NP
lattice_structure (str) – Crystallographic structure of the material
lattice_parameter (float) – Lattice parameter of the material
material (str) – Type of material
orien_x (list) – Orientation along x-axis
orien_z (list) – Orientation along z-axis
out_pre (str) – Prefix of the output files
ext_fem (list) – Output FEM formats list

Returns:

List of nodes and stl file name

put_prec_in_matrix(out_pre, ext_ato)

Introduce a cube/sphere/wulff precipitate into a matrix

Parameters:

out_pre_matrix (str) – Matrix sample
STL (str) – The stl file with an object that has surface roughness
out_pre (str) – Prefix of the output files

Sample_class.make_atom_grain(STL, lattice_structure1, lattice_parameter1, material1, orien_x1, orien_y1, orien_z1, lattice_structure2, lattice_parameter2, material2, orien_x2, orien_y2, orien_z2, vertices, out_pre, ext_ato)

Generates an atomic positions file for the grain object.

Parameters:

STL (str) – The stl file with an object that has surface roughness applied to it
lattice_structure1 (str) – The lattice structure of the crystal 1
lattice_parameter1 (float) – The lattice parameter of the crystal 1 in Angstrom
material1 (str) – The chemical symbol of the desired element 1
orien_x1 (list) – The orientation of the crystal 1 in the x direction
orien_y1 (list) – The orientation of the crystal 1 in the y direction
orien_z1 (list) – The orientation of the crystal 1 in the z direction
lattice_structure2 (str) – The lattice structure of the crystal 2
lattice_parameter2 (float) – The lattice parameter of the crystal 2 in Angstrom
material2 (str) – The chemical symbol of the desired element 2
orien_x2 (list) – The orientation of the crystal 2 in the x direction
orien_y2 (list) – The orientation of the crystal 2 in the y direction
orien_z2 (list) – The orientation of the crystal 2 in the z direction
vertices (array) – List of nodes
out_pre (str) – Prefix of output file
ext_ato (list) – Atomic position file format list

Returns:

Sample_class.make_box(type_sample, B, C1, RMS, N, M, length, height, width, ns, alpha, raw_stl, out_pre, ext_fem)

Creates an stl file of a rough box

Parameters:

type_sample (str) – The name of the sample
B (float) – The degree the roughness is dependent on
C1 (float) – Roughness normalization factor
RMS (float) – RMS
N (int) – Scaling cartesian position
M (int) – Scaling cartesian position
length (float) – Length of the box
height (float) – Height of the box
width (float) – Width of the box
ns (int) – The number of segments desired
alpha (float) – Refine mesh factor
raw_stl (str) – Name of the input stl file
out_pre (str) – Prefix of the output files
ext_fem (list) – List of FEM extension files

Returns: