Stores host-side bonded coefficient rows and topology rows. More...

#include <CharmmParameters.h>

Public Member Functions
	BondedParamsAndLists (const std::vector< int > &pSize, const std::vector< std::vector< float > > &pVal, const std::vector< int > &lSize, const std::vector< std::vector< int > > &lVal)
	Constructs packed bonded data by copying all supplied vectors.

Public Attributes
std::vector< int >	paramsSize

std::vector< std::vector< float > >	paramsVal

std::vector< int >	listsSize

std::vector< std::vector< int > >	listVal

Detailed Description

Stores host-side bonded coefficient rows and topology rows.

paramsSize and listsSize each contain six entries in this order: bond, Urey-Bradley, angle, proper dihedral, improper dihedral, and CMAP. paramsVal concatenates the coefficient rows for those categories:

bond: [b0, kb] in [angstrom, kcal mol^-1 angstrom^-2];
Urey-Bradley: [s0, kub] in [angstrom, kcal mol^-1 angstrom^-2];
angle: [theta0_radians, kTheta] in [radian, kcal mol^-1 radian^-2];
proper dihedral: [signed_n, kChi, sin(delta), cos(delta)] in [dimensionless, kcal mol^-1, dimensionless, dimensionless], where nonterminal rows for a multi-term key use a negative multiplicity;
improper dihedral: [psi0_degrees, kPsi, 0, 1] in [degree, kcal mol^-1 radian^-2, dimensionless, dimensionless];
CMAP: no rows in the current implementation.

listVal concatenates zero-based PSF atom-index rows. Bond and Urey-Bradley rows are [i, j, type, 13]; angle rows are [i, j, k, type, 13, 13]; torsion rows are [i, j, k, l, type, 13, 13, 13]. Type indices are local to each category. The shift sentinel 13 denotes the zero periodic image.

All storage is owned host memory. ForceManager later copies these rows to CUDA force objects.

Constructor & Destructor Documentation

◆ BondedParamsAndLists()

BondedParamsAndLists::BondedParamsAndLists	(	const std::vector< int > &	pSize,
		const std::vector< std::vector< float > > &	pVal,
		const std::vector< int > &	lSize,
		const std::vector< std::vector< int > > &	lVal
	)

inline

Constructs packed bonded data by copying all supplied vectors.

Parameters

[in]	pSize	Six coefficient-row counts in bonded-category order.
[in]	pVal	Concatenated host coefficient rows.
[in]	lSize	Six topology-row counts in bonded-category order.
[in]	lVal	Concatenated host topology rows.

Postcondition: The object owns independent copies of all four inputs.

Exceptions

std::bad_alloc If copying the host vectors requires an allocation that fails.

Note: The constructor does not validate sizes, row widths, or indices.

Member Data Documentation

◆ listsSize

std::vector<int> BondedParamsAndLists::listsSize

Stores the six topology-row counts in bonded-category order.

◆ listVal

std::vector<std::vector<int> > BondedParamsAndLists::listVal

Stores the concatenated zero-based PSF topology rows.

◆ paramsSize

std::vector<int> BondedParamsAndLists::paramsSize

Stores the six coefficient-row counts in bonded-category order.

◆ paramsVal

std::vector<std::vector<float> > BondedParamsAndLists::paramsVal

Stores the concatenated host coefficient rows.

Public Member Functions

Public Attributes