class for calculating SASA energies calculating SASA of particles based on change object every step More...

#include <energy.h>

Inheritance diagram for Faunus::Energy::SASAEnergy:

Collaboration diagram for Faunus::Energy::SASAEnergy:

Public Member Functions
	SASAEnergy (const Space &spc, double cosolute_molarity, double probe_radius, int slices_per_atom=25, bool dense_container=true)

	SASAEnergy (const json &j, const Space &spc)

double	energy (const Change &change) override
	energy due to change More...

Public Member Functions inherited from Faunus::Energy::SASAEnergyReference
	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

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

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.

Protected Types inherited from Faunus::Energy::SASAEnergyReference
using	index_type = size_t

Protected Member Functions inherited from Faunus::Energy::SASAEnergyReference
auto	indexOf (const Particle &particle) const
	absolute index of particle in space particle vector

Protected Attributes inherited from Faunus::Energy::SASAEnergyReference
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

Detailed Description

class for calculating SASA energies calculating SASA of particles based on change object every step

Constructor & Destructor Documentation

Faunus::Energy::SASAEnergy::SASAEnergy	(	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

double Faunus::Energy::SASAEnergy::energy ( const Change & change )

overridevirtual

energy due to change

update not needed when the state is already accepted

all the active particles will be used for SASA calculation

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