TissueForge::metrics Namespace Reference

Tissue Forge simulation metrics. More...

Functions
FVector3	relativePosition (const FVector3 &pos, const FVector3 &origin, const bool &comp_bc=true)
	Computes the relative position with respect to an origin while optionally account for boundary conditions.
ParticleList	neighborhoodParticles (const FVector3 &position, const FloatP_t &dist, const bool &comp_bc=true)
HRESULT	calculateVirial (FloatP_t *origin, FloatP_t radius, const std::set< short int > &typeIds, FloatP_t *tensor)
HRESULT	particlesVirial (int32_t *parts, uint16_t nr_parts, uint32_t flags, FloatP_t *tensor)
HRESULT	particlesRadiusOfGyration (int32_t *parts, uint16_t nr_parts, FloatP_t *result)
HRESULT	particlesCenterOfMass (int32_t *parts, uint16_t nr_parts, FloatP_t *result)
HRESULT	particlesCenterOfGeometry (int32_t *parts, uint16_t nr_parts, FloatP_t *result)
HRESULT	particlesMomentOfInertia (int32_t *parts, uint16_t nr_parts, FloatP_t *result)
FVector3	cartesianToSpherical (const FVector3 &postion, const FVector3 &origin)
HRESULT	particleNeighbors (struct Particle *part, FloatP_t radius, const std::set< short int > *typeIds, uint16_t *nr_parts, int32_t **parts)
std::vector< std::vector< std::vector< ParticleList > > >	particleGrid (const iVector3 &shape)
HRESULT	particleGrid (const iVector3 &shape, ParticleList *result)
FVector3	eigenVals (const FMatrix3 &mat, const bool &symmetric=false)
	Compute the eigenvalues of a 3x3 matrix.
FVector4	eigenVals (const FMatrix4 &mat, const bool &symmetric=false)
	Compute the eigenvalues of a 4x4 matrix.
std::pair< FVector3 FMatrix3 >	eigenVecsVals (const FMatrix3 &mat, const bool &symmetric=false)
	Compute the eigenvectors and eigenvalues of a 3x3 matrix.
std::pair< FVector4 FMatrix4 >	eigenVecsVals (const FMatrix4 &mat, const bool &symmetric=false)
	Compute the eigenvectors and eigenvalues of a 4x4 matrix.

Detailed Description

Tissue Forge simulation metrics.

Function Documentation

calculateVirial()

HRESULT TissueForge::metrics::calculateVirial	(	FloatP_t *	origin,
		FloatP_t	radius,
		const std::set< short int > &	typeIds,
		FloatP_t *	tensor )

@origin [in] origin of the sphere where we will comptute the local virial tensor. @radius [in] include all partices a given radius in calculation. @typeIds [in] vector of type ids to indlude in calculation, if empty, includes all particles. @tensor [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.

cartesianToSpherical()

FVector3 TissueForge::metrics::cartesianToSpherical	(	const FVector3 &	postion,
		const FVector3 &	origin )

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

eigenVals() [1/2]

FVector3 TissueForge::metrics::eigenVals	(	const FMatrix3 &	mat,
		const bool &	symmetric = false )

Compute the eigenvalues of a 3x3 matrix.

Parameters

mat	the matrix
symmetric	flag signifying whether the matrix is symmetric

Returns

eigenvalues

eigenVals() [2/2]

FVector4 TissueForge::metrics::eigenVals	(	const FMatrix4 &	mat,
		const bool &	symmetric = false )

Compute the eigenvalues of a 4x4 matrix.

Parameters

mat	the matrix
symmetric	flag signifying whether the matrix is symmetric

Returns

eigenvalues

eigenVecsVals() [1/2]

std::pair< FVector3 FMatrix3 > TissueForge::metrics::eigenVecsVals	(	const FMatrix3 &	mat,
		const bool &	symmetric = false )

Compute the eigenvectors and eigenvalues of a 3x3 matrix.

Parameters

mat	the matrix
symmetric	flag signifying whether the matrix is symmetric

Returns

eigenvalues, eigenvectors

eigenVecsVals() [2/2]

std::pair< FVector4 FMatrix4 > TissueForge::metrics::eigenVecsVals	(	const FMatrix4 &	mat,
		const bool &	symmetric = false )

Compute the eigenvectors and eigenvalues of a 4x4 matrix.

Parameters

mat	the matrix
symmetric	flag signifying whether the matrix is symmetric

Returns

eigenvalues, eigenvectors

neighborhoodParticles()

ParticleList TissueForge::metrics::neighborhoodParticles	(	const FVector3 &	position,
		const FloatP_t &	dist,
		const bool &	comp_bc = true )

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

particleGrid()

std::vector< std::vector< std::vector< ParticleList > > > TissueForge::metrics::particleGrid

(

const iVector3 &

shape

)

Creates an array of ParticleList objects.

particleNeighbors()

HRESULT TissueForge::metrics::particleNeighbors	(	struct Particle *	part,
		FloatP_t	radius,
		const std::set< short int > *	typeIds,
		uint16_t *	nr_parts,
		int32_t **	parts )

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

Allocates a buffer, and stores the results there.

Parameters

part	the particle
radius	[optional] the radius of the neighborhood
typeIds	[optional] set of type ids to include. If not given, gets all other parts within radius.
nr_parts	[out] number of parts
parts	[out] newly allocated buffer of particle ids.

particlesCenterOfGeometry()

HRESULT TissueForge::metrics::particlesCenterOfGeometry	(	int32_t *	parts,
		uint16_t	nr_parts,
		FloatP_t *	result )

Parameters

result

pointer to float[3] to store result.

particlesCenterOfMass()

HRESULT TissueForge::metrics::particlesCenterOfMass	(	int32_t *	parts,
		uint16_t	nr_parts,
		FloatP_t *	result )

Parameters

result

pointer to float[3] to store result

particlesMomentOfInertia()

HRESULT TissueForge::metrics::particlesMomentOfInertia	(	int32_t *	parts,
		uint16_t	nr_parts,
		FloatP_t *	result )

Parameters

result

pointer to float[9] to store result.

particlesRadiusOfGyration()

HRESULT TissueForge::metrics::particlesRadiusOfGyration	(	int32_t *	parts,
		uint16_t	nr_parts,
		FloatP_t *	result )

Parameters

result

pointer to float to store result.

particlesVirial()

HRESULT TissueForge::metrics::particlesVirial	(	int32_t *	parts,
		uint16_t	nr_parts,
		uint32_t	flags,
		FloatP_t *	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.

relativePosition()

FVector3 TissueForge::metrics::relativePosition	(	const FVector3 &	pos,
		const FVector3 &	origin,
		const bool &	comp_bc = true )

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	absolute position
origin	origin
comp_bc	flag to compensate for boundary conditions; default true

Returns

FVector3 relative position with respect to the given origin