A class to sort and hold details of a topology's Lennard-Jones interactions. The Lennard-Jones table is parsed for a combining rule, tables of sigma and epsilon parameters for self-interactions are kept, and a list of pair-specific sigma and epsilon parameters are stored according to the type indices they modify. More...

#include <lennard_jones_analysis.h>

Public Member Functions
int	getLJTypeCount () const
	Get the number of Lennard-Jones indices, the number of distinct Lennard Jones parameter sets which are needed to describe all interactions.

int	getAtomTypeCount () const
	Get the number of atom types, including all types with equivalent Lennard-Jones parameters.

int	getSetCount () const
	Get the number of Lennard-Jones parameter sets that the analysis has compiled within its data members.

VdwCombiningRule	getMostPrevalentCombiningRule () const
	Get the most prevalent Lennard-Jones rule, as judged by the formula that fits the most combinations of distinct sigma and epsilon parameters.

double	getLJSigma (int consensus_index) const
	Get the Lennard-Jones self interaction sigma for a particular interaction index from within the consensus tables.

double	getLJ14Sigma (int consensus_index) const
	Get the Lennard-Jones 1:4 non-bonded self interaction sigma for a particular interaction index from within the consensus tables. Descriptions of input parameters follow from getLJSigma(), above.

double	getLJEpsilon (int consensus_index) const
	Get the Lennard-Jones self interaction epsilon for a particular interaction index from within the consensus tables.

double	getLJ14Epsilon (int consensus_index) const
	Get the Lennard-Jones 1:4 non-bonded self interaction epsilon for a particular interaction index from within the consensus tables. Descriptions of input parameters follow from getLJEpsilon(), above.

double3	getLJCoefficients (int index_i, int index_j) const
	Get the Lennard-Jones A and B coefficients for the general non-bonded interaction of two Lennard-Jones atom types. Overloading and descriptions of input parameters follow from getLJParameters(), above.

double3	getLJCoefficients (const char4 atype_i, const char4 atype_j, ExceptionResponse policy=ExceptionResponse::DIE) const

double3	getLJ14Coefficients (int index_i, int index_j) const
	Get the Lennard-Jones A and B coefficients for the 1:4 non-bonded interaction of two Lennard-Jones atom types. Overloading and descriptions of input parameters follow from getLJParameters(), above.

double3	getLJ14Coefficients (const char4 atype_i, const char4 atype_j, ExceptionResponse policy=ExceptionResponse::DIE) const

int	getCorrespondence (int set_index, int type_index) const
	Obtain the Lennard-Jones type correspondence for an indexed Lennard-Jones type in one of the underlying sets.

const std::vector< int > &	getSetCorrespondence (int set_index) const
	Obtain the Lennard-Jones type correspondence for one of the underlying sets. This can be used to reconfigure the Lennard-Jones type indices of a topology to fit within the consensus set.

const std::vector< int2 > &	getInputInstances (int consensus_index) const
	Get the input sets and Lennard-Jones types to which one of the consensus Lennard-Jones types maps.

void	addSet (const NonbondedKit< double > &nbk, const std::vector< std::vector< char4 > > &othr_type_aliases)
	Add a new set of Lennard-Jones interactions to the list and expand the internal tables with all unique parameters it may contain, as well as new atom type names for existing parameters. The new topology will be checked to ensure that it does not redefine the parameters associated with known atom type names, or contradict the prevailing combining rules of topologies already incorporated into the tables.


	LennardJonesAnalysis (const NonbondedKit< double > &nbk, const std::vector< std::vector< char4 > > &atom_type_aliases_in)
	The constructor accepts a topology. Supplying additional topologies will expand the analysis to cover multiple systems and create a consensus of their respective Lennard-Jones parameters with arrays to index the original topologies' atoms into the unified tables.


	LennardJonesAnalysis (const LennardJonesAnalysis &original)=default

	LennardJonesAnalysis (LennardJonesAnalysis &&original)=default

LennardJonesAnalysis &	operator= (const LennardJonesAnalysis &original)=default

LennardJonesAnalysis &	operator= (LennardJonesAnalysis &&original)=default


const std::vector< char4 > &	getLJAliases (int consensus_index) const
	Get the atom type names associated with a particular Lennard-Jones parameter set, type index in one of the topologies, or aliases of a particular type name.

const std::vector< char4 > &	getLJAliases (double sigma_query, double epsilon_query, double tolerance=1.0e-4) const

const std::vector< char4 > &	getLJAliases (const char4 atom_type_query, ExceptionResponse policy=ExceptionResponse::DIE) const


double2	getLJParameters (int consensus_index) const
	Get the Lennard-Jones sigma and epsilon parameters for the self interaction of a specific interaction index within the consensus tables or atom type name. The sigma parameter appears in the "x" member of the result and the epsilon parameter in the "y" member.

double2	getLJParameters (const char4 atom_type_query, ExceptionResponse policy=ExceptionResponse::DIE) const


double2	getLJ14Parameters (int consensus_index) const
	Get the Lennard-Jones sigma and epsilon parameters for 1:4 self interactions of a specific interaction index within the consensus tables or atom type name. The sigma parameter appears in the "x" member of the result and the epsilon parameter in the "y" member. Overloading and descriptions of input parameters follow from getLJParameters(), above.

double2	getLJ14Parameters (const char4 atom_type_query, ExceptionResponse policy=ExceptionResponse::DIE) const

Detailed Description

A class to sort and hold details of a topology's Lennard-Jones interactions. The Lennard-Jones table is parsed for a combining rule, tables of sigma and epsilon parameters for self-interactions are kept, and a list of pair-specific sigma and epsilon parameters are stored according to the type indices they modify.

Constructor & Destructor Documentation

◆ LennardJonesAnalysis()

stormm::topology::LennardJonesAnalysis::LennardJonesAnalysis ( const LennardJonesAnalysis & original )

default

Composed of Standard Template Library objects with no pointers to repair, the default copy and move constructors are valid for this object, as are the default copy and move assignment operators.

Parameters

original	A pre-existing object to copy or move
other	An object to place on the right hand side of the assignment statement

Member Function Documentation

◆ addSet()

void stormm::topology::LennardJonesAnalysis::addSet	(	const NonbondedKit< double > &	nbk,
		const std::vector< std::vector< char4 > > &	othr_type_aliases )

Add a new set of Lennard-Jones interactions to the list and expand the internal tables with all unique parameters it may contain, as well as new atom type names for existing parameters. The new topology will be checked to ensure that it does not redefine the parameters associated with known atom type names, or contradict the prevailing combining rules of topologies already incorporated into the tables.

Parameters

nbk	The non-bonded abstract of the topology responsible for the new Lennard-Jones parameter set. While this library is included in the AtomGraph library itself and therefore cannot reference the AtomGraph class in any member functions, the abstracts can be passed in much the same way that other information reduced to its basic form can be handled by this library.
othr_sigma	Sigma parameters determined for the new Lennard-Jones parameters
othr_epsilon	Epsilon parameters determined for the new Lennard-Jones parameters
othr_type_aliases	Type aliases for the new set of Lennard-Jones parameters

◆ getCorrespondence()

int stormm::topology::LennardJonesAnalysis::getCorrespondence	(	int	set_index,
		int	type_index ) const

Obtain the Lennard-Jones type correspondence for an indexed Lennard-Jones type in one of the underlying sets.

Parameters

set_index	The underlying set of interest
type_index	The Lennard-Jones atom type index as presented in the underlying set

◆ getInputInstances()

const std::vector< int2 > & stormm::topology::LennardJonesAnalysis::getInputInstances ( int consensus_index ) const

Get the input sets and Lennard-Jones types to which one of the consensus Lennard-Jones types maps.

Parameters

consensus_index The consensus Lennard-Jones atom type

◆ getLJAliases()

const std::vector< char4 > & stormm::topology::LennardJonesAnalysis::getLJAliases ( int consensus_index ) const

Get the atom type names associated with a particular Lennard-Jones parameter set, type index in one of the topologies, or aliases of a particular type name.

Overloaded:

Indicate the index of the Lennard-Jones type within the consensus parameter tables
Indicate the index of the topology and the Lennard-Jones type index within that topology
Indicate the topology by pointer and the Lennard-Jones type index within that topology
Indicate the sigma and epsilon self-interaction parameters, to within 1.0e-4 precision
Indicate the name of one of the atom types so that all aliases can be found

Parameters

consensus_index	Index of the Lennard-Jones interaction type with the consensus table
ag_query_index	Index of the original AtomGraph within the list of referenced topologies (ag_pointers)
lj_type_index	Lennard-Jones interaction index from within the indicated topology
ag_query	The topology to search for within the list of referenced topologies (failing to find such a topology produces a runtime error)
sigma_query	The self-interaction sigma parameter of interest
epsilon_query	The self-interaction epsilon parameter of interest
tolerance	The tolerance for finding a Lennard-Jones parameter match, if supplying sigma and epsilon explicitly
atom_type_query	Name of one of the atom type aliases, provided so that all others can be found

◆ getLJEpsilon()

double stormm::topology::LennardJonesAnalysis::getLJEpsilon ( int consensus_index ) const

Get the Lennard-Jones self interaction epsilon for a particular interaction index from within the consensus tables.

Parameters

consensus_index The interaction type index of interest

◆ getLJParameters()

double2 stormm::topology::LennardJonesAnalysis::getLJParameters ( int consensus_index ) const

Get the Lennard-Jones sigma and epsilon parameters for the self interaction of a specific interaction index within the consensus tables or atom type name. The sigma parameter appears in the "x" member of the result and the epsilon parameter in the "y" member.

Overloaded:

Specify the index from within the consensus tables
Specify one of the names of an atom type alias bearing the parameters of interest

Parameters

consensus_index	The index of the Lennard-Jones type in the consensus set
atom_type_query	The letter code of the atom type to find within all atom type names, leading to a particular Lennard-Jones type
policy	Course of action to take if bad input is encountered

◆ getLJSigma()

double stormm::topology::LennardJonesAnalysis::getLJSigma ( int consensus_index ) const

Get the Lennard-Jones self interaction sigma for a particular interaction index from within the consensus tables.

Parameters

consensus_index The interaction type index of interest. It may not be obvious what this is if the analysis includes more than one topology, but it can still be useful to have an accessor that accepts this sort of input.

◆ getSetCorrespondence()

const std::vector< int > & stormm::topology::LennardJonesAnalysis::getSetCorrespondence ( int set_index ) const

Obtain the Lennard-Jones type correspondence for one of the underlying sets. This can be used to reconfigure the Lennard-Jones type indices of a topology to fit within the consensus set.

Parameters

set_index The set of interest

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

src/Topology/lennard_jones_analysis.h
src/Topology/lennard_jones_analysis.cpp

Public Member Functions

Detailed Description

Constructor & Destructor Documentation

◆ LennardJonesAnalysis()

Member Function Documentation

◆ addSet()

◆ getCorrespondence()

◆ getInputInstances()

◆ getLJAliases()

◆ getLJEpsilon()

◆ getLJParameters()

◆ getLJSigma()

◆ getSetCorrespondence()