Information need for bonded calculations. Templating is used to serve either of two levels of precision: single (which, on almost any machine and HPC accelerator card, will be fp32) or double (fp64). Parameters for bonds, the highest frequency terms in any system by a factor of roughly 5, will always be stored in double precision, as will parameters for bond angles, the next highest frequency group of terms. The precision of other parameters varies according to the template parameter. More...

#include <atomgraph_abstracts.h>

Collaboration diagram for stormm::structure::ValenceKit< T >:

[legend]

Public Member Functions
	ValenceKit (int natom_in, int nbond_in, int nangl_in, int ndihe_in, int nbond_param_in, int nangl_param_in, int ndihe_param_in, int ninfr14_in, int nattn14_param_in, int nubrd_in, int ncimp_in, int ncmap_in, int nubrd_param_in, int ncimp_param_in, int ncmap_surf_in, const T bond_keq_in, const T bond_leq_in, const T angl_keq_in, const T angl_theta_in, const T dihe_amp_in, const T dihe_freq_in, const T dihe_phi_in, const T attn14_elec_in, const T attn14_vdw_in, const int bond_i_atoms_in, const int bond_j_atoms_in, const int bond_param_idx_in, const char4 bond_modifiers_in, const uint bond_relevance_in, const int angl_i_atoms_in, const int angl_j_atoms_in, const int angl_k_atoms_in, const int angl_param_idx_in, const char4 angl_modifiers_in, const uint angl_relevance_in, const int dihe_i_atoms_in, const int dihe_j_atoms_in, const int dihe_k_atoms_in, const int dihe_l_atoms_in, const int dihe_param_idx_in, const int dihe14_param_idx_in, const char4 dihe_modifiers_in, const int infr14_i_atoms_in, const int infr14_l_atoms_in, const int infr14_param_idx_in, const int ubrd_i_atoms_in, const int ubrd_k_atoms_in, const int ubrd_param_idx_in, const int cimp_i_atoms_in, const int cimp_j_atoms_in, const int cimp_k_atoms_in, const int cimp_l_atoms_in, const int cimp_param_idx_in, const int cmap_i_atoms_in, const int cmap_j_atoms_in, const int cmap_k_atoms_in, const int cmap_l_atoms_in, const int cmap_m_atoms_in, const int cmap_dim_in, const int cmap_surf_bounds_in, const int cmap_patch_bounds_in, const int cmap_surf_idx_in, const T ubrd_keq_in, const T ubrd_leq_in, const T cimp_keq_in, const T cimp_phi_in, const T cmap_surf_in, const T cmap_dphi_in, const T cmap_dpsi_in, const T cmap_dphi_dpsi_in, const T cmap_patches_in, const int bond_asgn_atoms_in, const int bond_asgn_index_in, const int bond_asgn_terms_in, const int bond_asgn_bounds_in, const int angl_asgn_atoms_in, const int angl_asgn_index_in, const int angl_asgn_terms_in, const int angl_asgn_bounds_in, const int dihe_asgn_atoms_in, const int dihe_asgn_index_in, const int dihe_asgn_terms_in, const int dihe_asgn_bounds_in, const int ubrd_asgn_atoms_in, const int ubrd_asgn_index_in, const int ubrd_asgn_terms_in, const int ubrd_asgn_bounds_in, const int cimp_asgn_atoms_in, const int cimp_asgn_index_in, const int cimp_asgn_terms_in, const int cimp_asgn_bounds_in, const int cmap_asgn_atoms_in, const int cmap_asgn_index_in, const int cmap_asgn_terms_in, const int cmap_asgn_bounds_in)
	The constructor takes a Fortran77-worthy list of arguments. It would not be any cleaner to make this object a friend of or nested struct within AtomGraph, due to its templated nature.


	ValenceKit (const ValenceKit &original)=default
	Take the default copy and move constructors. The move assignment operator will get implicitly deleted as this is just a collection of constants.

	ValenceKit (ValenceKit &&other)=default

Public Attributes
const int	natom

const int	nbond
	Number of bonds in the system.

const int	nangl
	Number of bond angles in the system.

const int	ndihe

const int	nbond_param
	Number of unique bond parameters.

const int	nangl_param
	Number of unqiue bond angle parameters.

const int	ndihe_param
	Number of unique cosine dihedral parameters.

const int	ninfr14
	The number of inferred 1:4 exclusions.

const int	nattn14_param
	Number of 1:4 attenuation factor pairs (vdW, electrostatic)

const int	nubrd
	Number of Urey-Bradley 1:3 harmonic angle interactions.

const int	ncimp
	Number of CHARMM harmonic improper interactions.

const int	ncmap
	Number of CHARMM CMAP surface spline-based interactions.

const int	nubrd_param
	Number of unique Urey-Bradley parameters.

const int	ncimp_param
	Number of unique CHARMM harmonic improper parameters.

const int	ncmap_surf
	Number of unique CMAP surfaces.

const T *	bond_keq
	Equilibrium stiffness constants for all unique bonds.

const T *	bond_leq
	Equilibrium lengths for all unique bonds.

const T *	angl_keq
	Equilibrium stiffness constants for all unique bond angles.

const T *	angl_theta
	Equilibrium lengths for all unique bond angles.

const T *	dihe_amp
	Amplitudes for all unique cosine-based dihedrals.

const T *	dihe_freq
	Periodicities for cosine-based dihedral / torsion terms.

const T *	dihe_phi
	Phase angles for cosine-based dihedral / torsion terms.

const T *	attn14_elec

const T *	attn14_vdw

const int *	bond_i_atoms
	Array of first atoms in each bond.

const int *	bond_j_atoms
	Array of second atoms in each bond.

const int *	bond_param_idx
	Parameter indices for each bond in the system.

const char4 *	bond_modifiers
	Modifying details of each bond stretching term.

const uint *	bond_relevance

const int *	angl_i_atoms
	Array of first atoms in each bond angle.

const int *	angl_j_atoms
	Array of second atoms in each bond angle.

const int *	angl_k_atoms
	Array of third atoms in each bond angle.

const int *	angl_param_idx
	Parameter indices for each bond angle in the system.

const char4 *	angl_modifiers
	Modifying details of each angle bending term.

const uint *	angl_relevance

const int *	dihe_i_atoms
	Array of first atoms in each cosine-based dihedral.

const int *	dihe_j_atoms
	Array of second atoms in each cosine-based dihedral.

const int *	dihe_k_atoms

const int *	dihe_l_atoms
	Array of fourth atoms in each cosine-based dihedral.

const int *	dihe_param_idx
	Parameter indices for each cosine-based dihedral in the system.

const int *	dihe14_param_idx

const char4 *	dihe_modifiers

const int *	infr14_i_atoms

const int *	infr14_l_atoms
	Inferred 1:4 interactions' J atoms.

const int *	infr14_param_idx

const int *	ubrd_i_atoms
	First atoms in each Urey-Bradley harmonic angle interaction.

const int *	ubrd_k_atoms
	Second atoms in each Urey-Bradley harmonic angle interaction.

const int *	ubrd_param_idx
	Parameter indices for each Urey-Bradley interaction.

const int *	cimp_i_atoms
	First atoms in each CHARMM harmonic improper dihedral.

const int *	cimp_j_atoms
	Second atoms in each CHARMM harmonic improper dihedral.

const int *	cimp_k_atoms
	Third (center) atoms in each CHARMM harmonic improper dihedral.

const int *	cimp_l_atoms
	Fourth atoms in each CHARMM harmonic improper dihedral.

const int *	cimp_param_idx
	Parameter indices for each CHARMM harmonic improper dihedral.

const int *	cmap_i_atoms
	First atoms of the first dihedral in each CHARMM CMAP term.

const int *	cmap_j_atoms

const int *	cmap_k_atoms

const int *	cmap_l_atoms

const int *	cmap_m_atoms
	Fourth atoms of the second dihedral in each CHARMM CMAP term.

const int *	cmap_dim
	Dimension of each CMAP surface (each surface is a square grid)

const int *	cmap_surf_bounds
	Bounds array for individual CMAP surfaces.

const int *	cmap_patch_bounds

const int *	cmap_surf_idx
	Parameter (surface) indices for CHARMM CMAP interactions.

const T *	ubrd_keq
	Array of unique Urey-Bradley 1:3 harmonic stiffnesses.

const T *	ubrd_leq
	Array of unique Urey-Bradley 1:3 harmonic equilibrium lengths.

const T *	cimp_keq
	Array of unique CHARMM harmonic improper dihedral stiffnesses.

const T *	cimp_phi
	Array of unique CHARMM harmonic improper dihedral phase angles.

const T *	cmap_surf
	Array of CHARMM CMAP surface values.

const T *	cmap_dphi
	Array of CHARMM CMAP surface "phi" derivative values.

const T *	cmap_dpsi
	Array of CHARMM CMAP surface "psi" derivative values.

const T *	cmap_dphi_dpsi
	Array of CHARMM CMAP surface cross derivative values.

const T *	cmap_patches
	Array of interlaced CHARMM CMAP patch matrices.

const int *	bond_asgn_atoms
	Other atoms for bond terms (one atom per term)

const int *	bond_asgn_index
	Parameter indices for bond terms.

const int *	bond_asgn_terms

const int *	bond_asgn_bounds
	Bounds for each atom's assigned bond list.

const int *	angl_asgn_atoms
	Other atoms for bond angle terms (two atoms per term)

const int *	angl_asgn_index
	Parameter indices for bond angle terms.

const int *	angl_asgn_terms

const int *	angl_asgn_bounds
	Bounds for each atom's assigned bond angle list.

const int *	dihe_asgn_atoms
	Other atoms for dihedral terms (three atoms per term)

const int *	dihe_asgn_index
	Parameter indices for dihedral terms.

const int *	dihe_asgn_terms

const int *	dihe_asgn_bounds
	Bounds for each atom's assigned dihedral list.

const int *	ubrd_asgn_atoms
	Other atoms for Urey-Bradley terms (one atom per term)

const int *	ubrd_asgn_index
	Parameter indices for Urey-Bradley terms.

const int *	ubrd_asgn_terms
	Urey-Bradley term indices assigned to each atom.

const int *	ubrd_asgn_bounds
	Bounds for each atom's assigned Urey-Bradley list.

const int *	cimp_asgn_atoms
	Other atoms for CHARMM impropers (three atoms per term)

const int *	cimp_asgn_index
	Parameter indices for CHARMM improper dihedral terms.

const int *	cimp_asgn_terms
	CHARMM improper term indices assigned to each atom.

const int *	cimp_asgn_bounds
	Bounds for each atom's assigned CHARMM improper list.

const int *	cmap_asgn_atoms
	Other atoms for CMAP terms (four atoms per term)

const int *	cmap_asgn_index
	Parameter indices for CMAP terms.

const int *	cmap_asgn_terms
	CMAP term indices assigned to each atom.

const int *	cmap_asgn_bounds
	Bounds for each atom's assigned CMAP list.

Detailed Description

template<typename T>
struct stormm::structure::ValenceKit< T >

Information need for bonded calculations. Templating is used to serve either of two levels of precision: single (which, on almost any machine and HPC accelerator card, will be fp32) or double (fp64). Parameters for bonds, the highest frequency terms in any system by a factor of roughly 5, will always be stored in double precision, as will parameters for bond angles, the next highest frequency group of terms. The precision of other parameters varies according to the template parameter.

Constructor & Destructor Documentation

◆ ValenceKit()

template<typename T>

stormm::topology::ValenceKit< T >::ValenceKit	(	int	natom_in,
		int	nbond_in,
		int	nangl_in,
		int	ndihe_in,
		int	nbond_param_in,
		int	nangl_param_in,
		int	ndihe_param_in,
		int	ninfr14_in,
		int	nattn14_param_in,
		int	nubrd_in,
		int	ncimp_in,
		int	ncmap_in,
		int	nubrd_param_in,
		int	ncimp_param_in,
		int	ncmap_surf_in,
		const T *	bond_keq_in,
		const T *	bond_leq_in,
		const T *	angl_keq_in,
		const T *	angl_theta_in,
		const T *	dihe_amp_in,
		const T *	dihe_freq_in,
		const T *	dihe_phi_in,
		const T *	attn14_elec_in,
		const T *	attn14_vdw_in,
		const int *	bond_i_atoms_in,
		const int *	bond_j_atoms_in,
		const int *	bond_param_idx_in,
		const char4 *	bond_modifiers_in,
		const uint *	bond_relevance_in,
		const int *	angl_i_atoms_in,
		const int *	angl_j_atoms_in,
		const int *	angl_k_atoms_in,
		const int *	angl_param_idx_in,
		const char4 *	angl_modifiers_in,
		const uint *	angl_relevance_in,
		const int *	dihe_i_atoms_in,
		const int *	dihe_j_atoms_in,
		const int *	dihe_k_atoms_in,
		const int *	dihe_l_atoms_in,
		const int *	dihe_param_idx_in,
		const int *	dihe14_param_idx_in,
		const char4 *	dihe_modifiers_in,
		const int *	infr14_i_atoms_in,
		const int *	infr14_l_atoms_in,
		const int *	infr14_param_idx_in,
		const int *	ubrd_i_atoms_in,
		const int *	ubrd_k_atoms_in,
		const int *	ubrd_param_idx_in,
		const int *	cimp_i_atoms_in,
		const int *	cimp_j_atoms_in,
		const int *	cimp_k_atoms_in,
		const int *	cimp_l_atoms_in,
		const int *	cimp_param_idx_in,
		const int *	cmap_i_atoms_in,
		const int *	cmap_j_atoms_in,
		const int *	cmap_k_atoms_in,
		const int *	cmap_l_atoms_in,
		const int *	cmap_m_atoms_in,
		const int *	cmap_dim_in,
		const int *	cmap_surf_bounds_in,
		const int *	cmap_patch_bounds_in,
		const int *	cmap_surf_idx_in,
		const T *	ubrd_keq_in,
		const T *	ubrd_leq_in,
		const T *	cimp_keq_in,
		const T *	cimp_phi_in,
		const T *	cmap_surf_in,
		const T *	cmap_dphi_in,
		const T *	cmap_dpsi_in,
		const T *	cmap_dphi_dpsi_in,
		const T *	cmap_patches_in,
		const int *	bond_asgn_atoms_in,
		const int *	bond_asgn_index_in,
		const int *	bond_asgn_terms_in,
		const int *	bond_asgn_bounds_in,
		const int *	angl_asgn_atoms_in,
		const int *	angl_asgn_index_in,
		const int *	angl_asgn_terms_in,
		const int *	angl_asgn_bounds_in,
		const int *	dihe_asgn_atoms_in,
		const int *	dihe_asgn_index_in,
		const int *	dihe_asgn_terms_in,
		const int *	dihe_asgn_bounds_in,
		const int *	ubrd_asgn_atoms_in,
		const int *	ubrd_asgn_index_in,
		const int *	ubrd_asgn_terms_in,
		const int *	ubrd_asgn_bounds_in,
		const int *	cimp_asgn_atoms_in,
		const int *	cimp_asgn_index_in,
		const int *	cimp_asgn_terms_in,
		const int *	cimp_asgn_bounds_in,
		const int *	cmap_asgn_atoms_in,
		const int *	cmap_asgn_index_in,
		const int *	cmap_asgn_terms_in,
		const int *	cmap_asgn_bounds_in )

explicit

The constructor takes a Fortran77-worthy list of arguments. It would not be any cleaner to make this object a friend of or nested struct within AtomGraph, due to its templated nature.

See the descriptions of eponymous member variables (minus _in) within the ValenceKit object for descriptions of each parameter.

Member Data Documentation

◆ angl_asgn_terms

template<typename T>

const int* stormm::topology::ValenceKit< T >::angl_asgn_terms

Angle term indices assigned to each atom (i.e. the 9th atom is assigned angle terms with indices 46, 48, and 50)

◆ angl_relevance

template<typename T>

const uint* stormm::topology::ValenceKit< T >::angl_relevance

Array detailing the relevance of each bond angle interaction, whether it should be evaluated given directives on the rigidity of bonds to hydrogen atoms or virtual sites

◆ attn14_elec

template<typename T>

const T* stormm::topology::ValenceKit< T >::attn14_elec

Electrostatic 1:4 attenuation parameters, including a zero for no 1:4 interaction. The arrays dihe14_param_idx and infr14_param_idx both index into this array.

◆ attn14_vdw

template<typename T>

const T* stormm::topology::ValenceKit< T >::attn14_vdw

van-der Waals 1:4 attenuation parameters, including a zero for no 1:4 interaction. The arrays dihe14_param_idx and infr14_param_idx both index into this array.

◆ bond_asgn_terms

template<typename T>

const int* stormm::topology::ValenceKit< T >::bond_asgn_terms

Bond term indices assigned to each atom (i.e. the 5th atom is assigned bond terms with indices 18, 20, and 21)

◆ bond_relevance

template<typename T>

const uint* stormm::topology::ValenceKit< T >::bond_relevance

Array detailing the relevance of each bonded interaction, whether it should be evaluated given directives on the rigidity of bonds to hydrogen atoms or virtual sites

◆ cmap_j_atoms

template<typename T>

const int* stormm::topology::ValenceKit< T >::cmap_j_atoms

Second atoms of the first dihedral, first atoms of the second dihedral, in each CHARMM CMAP term

◆ cmap_k_atoms

template<typename T>

const int* stormm::topology::ValenceKit< T >::cmap_k_atoms

Third atoms of the first dihedral, second atoms of the second dihedral, in each CHARMM CMAP term

◆ cmap_l_atoms

template<typename T>

const int* stormm::topology::ValenceKit< T >::cmap_l_atoms

Fourth atoms of the first dihedral, third atoms of the second dihedral, in each CHARMM CMAP term

◆ cmap_patch_bounds

template<typename T>

const int* stormm::topology::ValenceKit< T >::cmap_patch_bounds

Bounds array for individual CMAP surfaces composed of patch matrices (this array is basically 16 times cmap_surf_bounds)

◆ dihe14_param_idx

template<typename T>

const int* stormm::topology::ValenceKit< T >::dihe14_param_idx

Parameter indices for 1:4 attenuated interactions handled by each dihedral through their I and L atoms

◆ dihe_asgn_terms

template<typename T>

const int* stormm::topology::ValenceKit< T >::dihe_asgn_terms

Dihedral term indices assigned to each atom (i.e. the 4th atom is assigned dihedral terms with indices 27, 28, and 29)

◆ dihe_k_atoms

template<typename T>

const int* stormm::topology::ValenceKit< T >::dihe_k_atoms

Array of third atoms in each cosine-based dihedral (these are the center atoms if the dihedral describes a cosine-based improper)

◆ dihe_modifiers

template<typename T>

const char4* stormm::topology::ValenceKit< T >::dihe_modifiers

Modifying details of each dihedral term, including whether it is a proper or improper dihedral with or without a 1:4 attenuated interaction

◆ infr14_i_atoms

template<typename T>

const int* stormm::topology::ValenceKit< T >::infr14_i_atoms

Inferred 1:4 interactions' I atoms. These cannot be handled directly by any dihedrals and so must be treated as separate terms.

◆ infr14_param_idx

template<typename T>

const int* stormm::topology::ValenceKit< T >::infr14_param_idx

Indices into the arrays of 1:4 attenuation parameters for the set of 1:4 interactions with inferred parameters

◆ natom

template<typename T>

const int stormm::topology::ValenceKit< T >::natom

The number of atoms in the system (needed for the overall length of bond_asgn_abounds and similar arrays towards the end, if not just for general convenience)

◆ ndihe

template<typename T>

const int stormm::topology::ValenceKit< T >::ndihe

Number of dihedrals or torsions (includes cosine-based improper torsions) in the system

The documentation for this struct was generated from the following file:

src/Topology/atomgraph_abstracts.h

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ ValenceKit()

Member Data Documentation

◆ angl_asgn_terms

◆ angl_relevance

◆ attn14_elec

◆ attn14_vdw

◆ bond_asgn_terms

◆ bond_relevance

◆ cmap_j_atoms

◆ cmap_k_atoms

◆ cmap_l_atoms

◆ cmap_patch_bounds

◆ dihe14_param_idx

◆ dihe_asgn_terms

◆ dihe_k_atoms

◆ dihe_modifiers

◆ infr14_i_atoms

◆ infr14_param_idx

◆ natom

◆ ndihe