Collect the critical non-bonded parameters and masking information for work unit-based evaluation of the systems in an AtomGraphSynthesis. Compared to the abstracts for a single system's AtomGraph, this merges the ImplicitSolventKit and NonbondedKit. For comparison, the SyValenceKit object merges the information for valence interactions, constraints, and virtual sites abstracts from the single topology's set of abstracts. More...

#include <synthesis_abstracts.h>

Collaboration diagram for stormm::trajectory::SyNonbondedKit< T, T2 >:

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Public Member Functions
	SyNonbondedKit (int nsys_in, UnitCellType unit_cell_in, int nnbwu_in, const int nbwu_abstracts_in, const uint2 nbwu_insr_in, const int atom_offsets, const int atom_counts, T coulomb_in, ImplicitSolventModel igb_in, int neck_table_size_in, T dielectric_in, T kappa_in, T saltcon_in, T gb_offset_in, T gb_neckscale_in, T gb_neckcut_in, const T charge_in, const int q_idx_in, const T q_params_in, const int lj_idx_in, const int n_lj_types_in, const int ljabc_offsets_in, const T2 ljab_coeff_in, const T ljc_coeff_in, const T lj_sigma_in, const int neck_gb_idx_in, const T pb_radii_in, const T gb_screen_in, const T gb_alpha_in, const T gb_beta_in, const T gb_gamma_in, const T2 neck_limits_in)
	The constructor takes a straight list of arguments for each member variable.


	SyNonbondedKit (const SyNonbondedKit &original)=default
	The copy and move constructors are taken at their default values for this abstract containing const elements.

	SyNonbondedKit (SyNonbondedKit &&original)=default

Public Attributes
const int	nsys
	The total number of systems in the synthesis.

const UnitCellType	unit_cell
	The type of unit cell for all systems.

const int	nnbwu
	The number of non-bonded work units in the synthesis.

const int *	nbwu_abstracts
	Abstracts for all non-bonded work units.

const uint2 *	nbwu_insr
	Instructions for all non-bonded work units.

const int *	atom_offsets

const int *	atom_counts

const T	coulomb

const ImplicitSolventModel	igb

const int	neck_table_size
	Length of each side of the square "neck" GB limit tables.

const T	dielectric
	Solvent dielectric constant.

const T	kappa
	Inverse of the Debye-Huckel length (based on the dielectic)

const T	saltcon
	The salt concentration to use in GB calculations.

const T	gb_offset

const T	gb_neckscale
	Neck function scaling parameter for neck GB.

const T	gb_neckcut
	Cutoff for the "neck" GB function.

const T *	charge

const int *	q_idx

const T *	q_params

const int *	lj_idx

const int *	n_lj_types
	Lennard-Jones type counts for all systems.

const int *	ljabc_offsets

const T2 *	ljab_coeff
	Lennard-Jones interaction A and B coefficients.

const T *	ljc_coeff
	Lennard-Jones interaction C coefficients.

const T *	lj_sigma
	Lennard-Jones sigma parameters for all atom type pairs.

const int *	neck_gb_idx

const T *	pb_radii
	Atomic PB radii for all atoms in all systems.

const T *	gb_screen
	Generalized Born screening factors for all atoms and systems.

const T *	gb_alpha
	Generalized born alpha parameters (one parameter per atom)

const T *	gb_beta
	Generalized born beta parameters (one parameter per atom)

const T *	gb_gamma
	Generalized born gamma parameters (one parameter per atom)

const T2 *	neck_limits
	Interlaced neck GB maximum separations and values tables.

Detailed Description

template<typename T, typename T2>
struct stormm::trajectory::SyNonbondedKit< T, T2 >

Collect the critical non-bonded parameters and masking information for work unit-based evaluation of the systems in an AtomGraphSynthesis. Compared to the abstracts for a single system's AtomGraph, this merges the ImplicitSolventKit and NonbondedKit. For comparison, the SyValenceKit object merges the information for valence interactions, constraints, and virtual sites abstracts from the single topology's set of abstracts.