Faunus::Energy::SASAEnergyReference Class Reference

class for calculating SASA energies calculating SASA of each particle every step More...

#include <energy.h>

Inheritance diagram for Faunus::Energy::SASAEnergyReference:

Collaboration diagram for Faunus::Energy::SASAEnergyReference:

Public Member Functions
	SASAEnergyReference (const Space &spc, double cosolute_molarity, double probe_radius, int slices_per_atom=25, bool dense_container=true)
	SASAEnergyReference (const json &j, const Space &spc)
const std::vector< double > &	getAreas () const
double	energy (const Change &change) override
	energy due to change
Public Member Functions inherited from Faunus::Energy::EnergyTerm
virtual void	updateState (const Change &change)
	Update internal state to reflect change in e.g. Space. More...
virtual void	force (PointVector &forces)
	update forces on all particles

Protected Types
using	index_type = size_t

Protected Member Functions
void	init () override
	reset and initialize
auto	indexOf (const Particle &particle) const
	absolute index of particle in space particle vector

Protected Attributes
const Space &	spc
	Space to operate on.
std::vector< double >	areas
	Target buffer for calculated surface areas.
double	cosolute_molarity = 0.0
	co-solute concentration (mol/l)
std::unique_ptr< SASA::SASABase >	sasa
	performs neighbour searching and subsequent sasa calculation

Additional Inherited Members
Public Types inherited from Faunus::Energy::EnergyTerm
enum	MonteCarloState { ACCEPTED, TRIAL, NONE }
Public Attributes inherited from Faunus::Energy::EnergyTerm
MonteCarloState	state = MonteCarloState::NONE
std::string	name
	Meaningful name.
std::string	citation_information
	Possible reference; may be left empty.
TimeRelativeOfTotal< std::chrono::microseconds >	timer
	Timer for measuring speed.

Detailed Description

class for calculating SASA energies calculating SASA of each particle every step

This calculates SASA for all particles, i.e. the Change object is ignored and a full (and slow) system update is performed on each call to energy(). This class is used as a reference and base class for more clever implementations.

Constructor & Destructor Documentation

SASAEnergyReference()

Faunus::Energy::SASAEnergyReference::SASAEnergyReference	(	const Space &	spc,
		double	cosolute_molarity,
		double	probe_radius,
		int	slices_per_atom = 25,
		bool	dense_container = true
	)

Parameters

spc
cosolute_molarity	in particles per angstrom cubed
probe_radius	in angstrom
slices_per_atom	number of slices of spheres in SASA calculation
dense_container	flag specifying if a fast memory heavy version of cell_list container is used

---

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

• src/energy.h
• src/energy.cpp