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CustomHbondForceImpl Class Reference

This is the internal implementation of CustomHbondForce. More...

#include <CustomHbondForceImpl.h>

+ Inheritance diagram for CustomHbondForceImpl:

Public Member Functions

 CustomHbondForceImpl (const CustomHbondForce &owner)
 
 ~CustomHbondForceImpl ()
 
void initialize (ContextImpl &context)
 This is called after the ForceImpl is created and before updateContextState(), calcForces(), or calcEnergy() is called on it.
 
const CustomHbondForce & getOwner () const
 Get the Force object from which this ForceImpl was created.
 
void updateContextState (ContextImpl &context)
 This method is called at the beginning of each time step.
 
double calcForcesAndEnergy (ContextImpl &context, bool includeForces, bool includeEnergy, int groups)
 Calculate the force on each particle generated by this ForceImpl and/or this ForceImpl's contribution to the potential energy of the system.
 
std::map< std::string, double > getDefaultParameters ()
 Get a map containing the default values for all adjustable parameters defined by this ForceImpl.
 
std::vector< std::string > getKernelNames ()
 Get the names of all Kernels used by this Force.
 
void updateParametersInContext (ContextImpl &context)
 
- Public Member Functions inherited from ForceImpl
virtual ~ForceImpl ()
 
virtual std::vector< std::pair
< int, int > > 		getBondedParticles () const
 Get pairs of particles connected by bonds by this force.
 

Static Public Member Functions

static Lepton::ParsedExpression prepareExpression (const CustomHbondForce &force, const std::map< std::string, Lepton::CustomFunction * > &functions, std::map< std::string, std::vector< int > > &distances, std::map< std::string, std::vector< int > > &angles, std::map< std::string, std::vector< int > > &dihedrals)
 This is a utility routine that parses the energy expression, identifies the angles and dihedrals in it, and replaces them with variables.
 

Detailed Description

This is the internal implementation of CustomHbondForce.

Constructor & Destructor Documentation

CustomHbondForceImpl ( const CustomHbondForce &  owner)
~CustomHbondForceImpl ( )

Member Function Documentation

double calcForcesAndEnergy ( ContextImpl &  context,
bool  includeForces,
bool  includeEnergy,
int  groups 
)
virtual

Calculate the force on each particle generated by this ForceImpl and/or this ForceImpl's contribution to the potential energy of the system.

Parameters
contextthe context in which the system is being simulated
includeForcestrue if forces should be calculated
includeEnergytrue if the energy should be calculated
groupsa set of bit flags for which force groups to include. Group i should be included if (groups&(1<<i)) != 0.
Returns
this force's contribution to the potential energy of the system, or 0 if this force does not contribute to potential energy (or if includeEnergy is false)

Implements ForceImpl.

std::map<std::string, double> getDefaultParameters ( )
virtual

Get a map containing the default values for all adjustable parameters defined by this ForceImpl.

These parameters and their default values will automatically be added to the Context.

Implements ForceImpl.

std::vector<std::string> getKernelNames ( )
virtual

Get the names of all Kernels used by this Force.

Implements ForceImpl.

const CustomHbondForce& getOwner ( ) const
inlinevirtual

Get the Force object from which this ForceImpl was created.

Implements ForceImpl.

void initialize ( ContextImpl &  context)
virtual

This is called after the ForceImpl is created and before updateContextState(), calcForces(), or calcEnergy() is called on it.

This allows it to do any necessary initialization.

Implements ForceImpl.

static Lepton::ParsedExpression prepareExpression ( const CustomHbondForce &  force,
const std::map< std::string, Lepton::CustomFunction * > &  functions,
std::map< std::string, std::vector< int > > &  distances,
std::map< std::string, std::vector< int > > &  angles,
std::map< std::string, std::vector< int > > &  dihedrals 
)
static

This is a utility routine that parses the energy expression, identifies the angles and dihedrals in it, and replaces them with variables.

The particle indices returned in the maps are defined as follows: 0=a1, 1=a2, 2=a3, 3=d1, 4=d2, 5=d3.

Parameters
forcethe CustomHbondForce to process
functionsdefinitions of custom function that may appear in the expression
distanceson exit, this will contain an entry for each distance used in the expression. The key is the name of the corresponding variable, and the value is the list of particle indices.
angleson exit, this will contain an entry for each angle used in the expression. The key is the name of the corresponding variable, and the value is the list of particle indices.
dihedralson exit, this will contain an entry for each dihedral used in the expression. The key is the name of the corresponding variable, and the value is the list of particle indices.
Returns
a Parsed expression for the energy
void updateContextState ( ContextImpl &  context)
inlinevirtual

This method is called at the beginning of each time step.

It give the ForceImpl a chance to modify the state variables (positions, velocities, and parameters) stored in the Context in arbitrary ways before integration is performed.

Parameters
contextthe context in which the system is being simulated

Implements ForceImpl.

void updateParametersInContext ( ContextImpl &  context)
The documentation for this class was generated from the following file: