Metrics

tissue_forge.metrics.relative_position(pos, origin, comp_bc=1)

Computes the relative position with respect to an origin while optionally account for boundary conditions.

If boundaries along a dimension are periodic, then this chooses the relative coordinate closest to the origin.

Parameters:

  • pos (FVector3) – absolute position

  • origin (FVector3) – origin

  • comp_bc (boolean, optional) – flag to compensate for boundary conditions; default true

Return type:

FVector3

Returns:

FVector3 relative position with respect to the given origin

tissue_forge.metrics.neighborhood_particles(position, dist, comp_bc=1)

find all particles in a neighborhood defined by a point and distance

tissue_forge.metrics.calculate_virial(origin, radius, typeIds, tensor)

[in] origin of the sphere where we will comptute the local virial tensor. [in] include all partices a given radius in calculation. [in] vector of type ids to indlude in calculation, if empty, includes all particles. [out] result vector, writes a 3x3 matrix in a row-major in the given location.

If periodoc, we don’t include the periodic image cells, because we only calculate the forces within the simulation volume.

tissue_forge.metrics.particles_virial(parts, nr_parts, flags, tensor)

calculate the virial tensor for a specific list of particles. currently uses center of mass as origin, may change in the future with different flags.

flags currently ignored.

tissue_forge.metrics.particles_radius_of_gyration(parts, nr_parts, result)
Parameters:

result: – pointer to float to store result.

tissue_forge.metrics.particles_center_of_mass(parts, nr_parts, result)
Parameters:

result: – pointer to float[3] to store result

tissue_forge.metrics.particles_center_of_geometry(parts, nr_parts, result)
Parameters:

result: – pointer to float[3] to store result.

tissue_forge.metrics.particles_moment_of_inertia(parts, nr_parts, result)
Parameters:

result: – pointer to float[9] to store result.

tissue_forge.metrics.cartesian_to_spherical(postion, origin)

converts cartesian to spherical, writes spherical coords in to result array. return FVector3{radius, theta, phi};

tissue_forge.metrics.particle_neighbors(part, radius, typeIds, nr_parts, parts)

Searches and enumerates a location of space for all particles there.

Allocates a buffer, and stores the results there.

Parameters:

  • part (Particle) – the particle

  • radius (float) – [optional] the radius of the neighborhood

  • typeIds (std::set< short,std::less< short >,std::allocator< short > >) – [optional] set of type ids to include. If not given, gets all other parts within radius.

  • nr_parts (int) – [out] number of parts

  • parts (int) – [out] newly allocated buffer of particle ids.

tissue_forge.metrics.eigenvals(*args)

Overload 1:

Compute the eigenvalues of a 3x3 matrix

Parameters:

  • mat (FMatrix3) – the matrix

  • symmetric (boolean, optional) – flag signifying whether the matrix is symmetric

Return type:

FVector3

Returns:

eigenvalues


Overload 2:

Compute the eigenvalues of a 4x4 matrix

Parameters:

  • mat (FMatrix4) – the matrix

  • symmetric (boolean, optional) – flag signifying whether the matrix is symmetric

Return type:

FVector4

Returns:

eigenvalues

tissue_forge.metrics.eigenvecs_vals(*args)

Overload 1:

Compute the eigenvectors and eigenvalues of a 3x3 matrix

Parameters:

  • mat (FMatrix3) – the matrix

  • symmetric (boolean, optional) – flag signifying whether the matrix is symmetric

Return type:

std::pair< TissueForge::FVector3,TissueForge::FMatrix3 >

Returns:

eigenvalues, eigenvectors


Overload 2:

Compute the eigenvectors and eigenvalues of a 4x4 matrix

Parameters:

  • mat (FMatrix4) – the matrix

  • symmetric (boolean, optional) – flag signifying whether the matrix is symmetric

Return type:

std::pair< TissueForge::FVector4,TissueForge::FMatrix4 >

Returns:

eigenvalues, eigenvectors