stormm::review::MeshFoundation Class Reference

A small object to hold the essential descriptors of the molecule. More...

#include <mesh_foundation.h>

Public Member Functions
int	getReadyFrameCount () const
	Get an indication of whether the object has enough information to direct the construction of a mesh.
const AtomGraph *	getTopologyPointer () const
	Get a const pointer to the topology responsible for creating the associated mesh.
const CoordinateFrame *	getCoordinatePointer () const
	Get a const pointer to the coordinates responsible for creating the associated mesh.
template<typename Tcoord>
const CoordinateSeries< Tcoord > *	getEnsemblePointer () const
	Get a const reference to the array of structures (each stored as a CoordinateFrame) reponsible for creating the associated mesh.
size_t	getEnsembleTypeCode () const
	Get the codified data type of the ensemble.
std::vector< uint >	getFrozenAtomMask () const
	Get the frozen atom mask.
int	getCommentCount () const
	Get the number of comments appended to the mesh.
const std::string &	getComment (int comm_index) const
	Get a comment from the list in the mesh.
MeshBasicsKit	data (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get the object's abstract.
void	setTopology (const AtomGraph *ag_in)
	Set the topology that the mesh shall use. This will allocate and populate the Hybrid array pertaining to the frozen atoms mask. All other mesh data is resized as needed by the allocate() member function.
void	computeNeighborLists (const MeshParameters &mps, const MeshRulers &rlrs, const MeshKlManager &launcher=MeshKlManager(), PrecisionModel prec=PrecisionModel::SINGLE, HybridTargetLevel availability=HybridTargetLevel::HOST)
	Compute neighbor lists for each mesh element, if appropriate for the mesh type.
void	addComment (const std::string &verbiage)
	Add a comment to the mesh.
void	clearComments ()
	Clear the list of comments in the mesh.
	MeshFoundation (const CoordinateFrame *cf_in=nullptr, const AtomGraph *ag_in=nullptr, const std::vector< std::string > &comments={1, "Generated by STORMM"})
	The constructor accepts a topology some form of coordinates. It is overloaded to accept various valid coordinate objects.
	MeshFoundation (const CoordinateFrame &cf, const AtomGraph &ag_in, const std::vector< std::string > &comments={1, "Generated by STORMM"})
template<typename T>
	MeshFoundation (const CoordinateSeries< T > *cs, const AtomGraph *ag_in=nullptr, const std::vector< std::string > &comments={1, "Generated by STORMM"})
template<typename T>
	MeshFoundation (const CoordinateSeries< T > &cs, const AtomGraph &ag_in, const std::vector< std::string > &comments={1, "Generated by STORMM"})
void	setCoordinates (const CoordinateFrame *cf_in)
	Set the coordinates that the mesh shall use.
void	setCoordinates (const CoordinateFrame &cf_in)
template<typename Tcoord>
void	setEnsemble (const CoordinateSeries< Tcoord > *cs_in)
	Set the series of coordinates that the mesh shall use.
template<typename Tcoord>
void	setEnsemble (const CoordinateSeries< Tcoord > &cs_in)

Detailed Description

A small object to hold the essential descriptors of the molecule.

Member Function Documentation

addComment()

void stormm::structure::MeshFoundation::addComment

(

const std::string &

verbiage

)

Add a comment to the mesh.

Parameters

verbiage

The comment to include

computeNeighborLists()

void stormm::structure::MeshFoundation::computeNeighborLists	(	const MeshParameters &	mps,
		const MeshRulers &	rlrs,
		const MeshKlManager &	launcher = MeshKlManager(),
		PrecisionModel	prec = PrecisionModel::SINGLE,
		HybridTargetLevel	availability = HybridTargetLevel::HOST )

Compute neighbor lists for each mesh element, if appropriate for the mesh type.

Parameters

mps	Parameters for the mesh of interest, to provide context for the coordinates contained in this object
rlrs	Pre-computed rulers to aid in ascertaining the location of each atom with standardized precision
launcher	Manager for mesh kernels, dispenses launch parameters
prec	Precision model to use in GPU-based mesh construction computations
availability	Level at which the data is expected to be available

data()

MeshBasicsKit stormm::structure::MeshFoundation::data

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get the object's abstract.

Parameters

tier	Indicate whether to target pointers to memory on the CPU host or GPU device

getComment()

const std::string & stormm::structure::MeshFoundation::getComment

(

int

comm_index

)

const

Get a comment from the list in the mesh.

Parameters

comm_index

The index of the comment to retrieve (this will be checked for validity)

setCoordinates()

void stormm::structure::MeshFoundation::setCoordinates

(

const CoordinateFrame *

cf_in

)

Set the coordinates that the mesh shall use.

Overloaded:

• Supply the coordinates by const pointer
• Supply the coordinates by const reference

Parameters

cf_in

Pointer or reference to the coordinates of interest

setEnsemble()

template<typename Tcoord>

void stormm::structure::MeshFoundation::setEnsemble

(

const CoordinateSeries< Tcoord > *

cs_in

)

Set the series of coordinates that the mesh shall use.

Overloaded:

• Supply the coordinates by const pointer
• Supply the coordinates by const reference

Parameters

cs_in

Pointer or reference to the coordinates of interest

setTopology()

void stormm::structure::MeshFoundation::setTopology

(

const AtomGraph *

ag_in

)

Set the topology that the mesh shall use. This will allocate and populate the Hybrid array pertaining to the frozen atoms mask. All other mesh data is resized as needed by the allocate() member function.

Parameters

ag_in

Pointer to the topology of interest

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The documentation for this class was generated from the following files:

• src/Structure/mesh_foundation.h
• src/Structure/mesh_foundation.cpp