STORMM Source Documentation
Loading...
Searching...
No Matches
stormm::energy::ImplicitSolventRecipe< T > Struct Template Reference

Public Member Functions

 ImplicitSolventRecipe (const ImplicitSolventKit< T > &isk, const NeckGeneralizedBornKit< T > &ngbk)
 The constructor takes two abstracts / kits, from the AtomGraph and from an instantiation of the "neck" GB coefficient tables struct. The results are combined into a single struct, which is essentially a combined abstract but called a "recipe" to denote its status as a fusion of multiple abstracts.
 

Public Attributes

const int natom
 Number of atoms in the system.
 
const ImplicitSolventModel igb
 
const int table_size
 Size of the neck Generalized Born tables (if applicable)
 
const T dielectric
 The dielectric constant to use in solvent screening.
 
const T kappa
 Inverse of the Debye-Huckel length (based on the dielectic)
 
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 int * neck_gb_idx
 
const T * pb_radii
 Poisson-Boltzmann (or Generalized Born) baseline radii.
 
const T * gb_screen
 Generalized Born screening factors.
 
const T * gb_alpha
 
const T * gb_beta
 Generalized Born beta parameters.
 
const T * gb_gamma
 Generalized Born gamma parameters.
 
const T * neck_max_sep
 Neck GB maximum separations table.
 
const T * neck_max_val
 Neck GB maximum values table.
 

Constructor & Destructor Documentation

◆ ImplicitSolventRecipe()

template<typename T>
stormm::energy::ImplicitSolventRecipe< T >::ImplicitSolventRecipe ( const ImplicitSolventKit< T > & isk,
const NeckGeneralizedBornKit< T > & ngbk )
explicit

The constructor takes two abstracts / kits, from the AtomGraph and from an instantiation of the "neck" GB coefficient tables struct. The results are combined into a single struct, which is essentially a combined abstract but called a "recipe" to denote its status as a fusion of multiple abstracts.

Parameters
iskImplicit solvent details for the atoms of a specific system, obtained from an AtomGraph object (see Topology/atomgraph.h)
ngbkTables of constants for "neck" Generalized Born implementations–not needed for all GB but essential for a complete solution. Obtained from a NeckGeneralizedBornTable object (see Constants/generalized_born.h).

Member Data Documentation

◆ gb_alpha

template<typename T>
const T* stormm::energy::ImplicitSolventRecipe< T >::gb_alpha

Generalized Born alpha parameters (obtained from the designated model and atomic numbers / elements of each atom)

◆ gb_offset

template<typename T>
const T stormm::energy::ImplicitSolventRecipe< T >::gb_offset

Offset for baseline Generalized Born radii (default 0.9, larger for neck GB model II)

◆ igb

template<typename T>
const ImplicitSolventModel stormm::energy::ImplicitSolventRecipe< T >::igb

Flavor of Generalized Born (see Topology/atomgraph_enumerators.h)

◆ neck_gb_idx

template<typename T>
const int* stormm::energy::ImplicitSolventRecipe< T >::neck_gb_idx

Neck GB indices for each atom (if applicable–not for all GB models)


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