Adding a new analysis requires the following steps: More...

Classes
struct	_analyse
	Example analysis. More...

struct	_analyse< T, std::enable_if< std::is_base_of< Dipole, T >::value >::type >
	Example analysis. More...

class	Analysis
	Base class for all analysis functions. More...

class	AtomDensity
	Analysis of single atom densities. More...

class	AtomDipDipCorr
	Dipole-dipole correlation function, <{}(0){}(r)> More...

class	AtomicDisplacement
	Tracks displacements of particle positions. More...

class	AtomicPolicy
	SASA sampling policy which samples individually atoms selected by atom type name. More...

class	AtomInertia

class	AtomRDF
	Atomic radial distribution function, g(r) More...

class	AtomsInMoleculePolicy
	SASA sampling policy which samples as a whole atom in a selected molecule if multiple atoms are selected (either by atom names or by indices in a selected molecule) it samples sum of their SASAs in a given molecule if single atom name is selected, it samples just the selected atom SASA in a selected molecule. More...

class	ChargeFluctuations

class	CombinedAnalysis
	Aggregator class for storing and selecting multiple analysis instances. More...

class	Density
	Abstract base class for analysing atomic and molecular densities. More...

class	ElectricPotential
	Samples the electric potential at arbitrary positions in the simulation box. More...

class	FileReactionCoordinate
	Sample and save reaction coordinates to a file. More...

class	GroupMatrixAnalysis
	Samples a matrix of group properties. More...

class	InertiaTensor
	Sample and save the eigenvalues of the inertia tensor for a range of indexes within a molecule. More...

class	MassCenterDisplacement
	Tracks displacements of molecular group mass centers. More...

class	MolecularConformationID
	Create histogram of molecule conformation id. More...

class	MolecularPolicy
	SASA sampling policy which samples individually molecules selected by molecules name. More...

class	MoleculeDensity
	Analysis of molecular group densities. More...

class	MoleculeRDF
	Same as `AtomRDF` but for molecules. More...

class	Multipole
	Molecular multipole moments and their fluctuations. More...

class	MultipoleDistribution
	Multipolar decomposition between groups as a function of separation. More...

class	MultipoleMoments

class	PairAngleFunction

class	PairFunction
	Base class for distribution functions etc. More...

class	PairMatrixAnalysis
	Base class for streaming pair properties to a sparse matrix. More...

class	PatchySpheroCylinderTrajectory
	Generate PSCs text trajectory containing. More...

class	PerturbationAnalysis
	Base class for perturbation analysis. More...

class	PolymerShape
	Analysis of polymer shape - radius of gyration, shape etc. More...

class	PotentialCorrelation
	Samples the electric potential correlation as a function of distance, < Φ₁Φ₂>="">(r) More...

class	QRtraj
	Trajectory with charge and radius, only, for all (active, inactive) particles. More...

class	SanityCheck
	Checks if system is sane. More...

class	SASAAnalysis
	Analysis class for sasa calculations. More...

class	SavePenaltyEnergy

class	SaveState
	Save simulation state and particle coordinates to disk. More...

class	ScatteringFunction
	Sample scattering intensity. More...

class	SlicedDensity
	Density of atom along axis. More...

class	SystemEnergy
	Save system energy to disk. More...

class	VirtualTranslate
	Virtual translation move to calculate force. More...

class	VirtualVolumeMove
	Excess pressure using virtual volume move. More...

class	Voronota
	Analysis of Vorononoi tessellation using the Voronota-LT library. More...

class	WidomInsertion
	Excess chemical potential of molecules. More...

class	XTCtraj
	Write XTC trajectory file. More...

Functions
void	to_json (json &j, const Analysis &base)

std::unique_ptr< Analysis >	createAnalysis (const std::string &name, const json &j, Space &spc, Energy::Hamiltonian &pot)
	Factory function for generating analysis based on name. More...

std::function< double(const Group &, const Group &)>	createGroupGroupProperty (const json &j, const Space &spc, Energy::Hamiltonian &hamiltonian)
	Returns a lambda function that calculates a scalar property for a pair of groups. More...

std::function< bool(double)>	createValueFilter (const std::string &name, const json &j, bool throw_on_error)
	Generate lambda to filter values. More...

	NLOHMANN_JSON_SERIALIZE_ENUM (SASAAnalysis::Policies, {{SASAAnalysis::Policies::ATOMIC, "atomic"}, {SASAAnalysis::Policies::MOLECULAR, "molecular"}, {SASAAnalysis::Policies::ATOMS_IN_MOLECULE, "atoms_in_molecule"}, {SASAAnalysis::Policies::INVALID, nullptr}}) class AreaSamplingPolicy
	abstract base class for different SASA sampling policies

voronotalt::PeriodicBox	get_periodic_box_from_space (const Faunus::Space &spc)

Voronota::Modes	get_voronota_mode_from_name (const std::string &name)

std::string	get_name_from_voronota_mode (const Voronota::Modes mode)

Variables
std::function< double(const Group &, const Group &)>	createGroupGroupProperty (const json &j, const Space &spc, Energy::Hamiltonian &hamiltonian)
	Generates lambda to calculate properties between groups. More...

Detailed Description

Adding a new analysis requires the following steps:

Write an analysis class derived from Analysis::Analysisbase
Add the new class to the factory function Analysis::createAnalysis(), see below
Recommended: add the required json input format to docs/schema.yml
Recommended: add documentation to docs/_docs/analysis.md

Function Documentation

◆ createAnalysis()

std::unique_ptr< Analysis > Faunus::analysis::createAnalysis	(	const std::string &	name,
		const json &	j,
		Space &	spc,
		Energy::Hamiltonian &	pot
	)

Factory function for generating analysis based on name.

Function to create an instance of an analysis based on it's name

Parameters

name	name of analysis to create
j	configuration for analysis
spc	space to operate on
pot	Hamiltonian

Returns: shared pointer to created analysis base class

Parameters

name	Name of analysis to create
j	JSON input for analysis
spc	Space the analysis should operate on
pot	Hamiltonian representing the system

Returns: Shared pointer to analysis

After writing a new analysis, it must be added to this function in order to be controlled from the main faunus input.

◆ createGroupGroupProperty()

std::function<double(const Group&, const Group&)> Faunus::analysis::createGroupGroupProperty	(	const json &	j,
		const Space &	spc,
		Energy::Hamiltonian &	hamiltonian
	)

Returns a lambda function that calculates a scalar property for a pair of groups.

This can be their interaction energy; mass-center distance etc.

◆ createValueFilter()

std::function< bool(double)> Faunus::analysis::createValueFilter	(	const std::string &	name,
		const json &	j,
		bool	throw_on_error
	)

Generate lambda to filter values.

Parameters

name	the policy to use: `all`, `smaller_than`, `function`, ...
j	json object with data matching policy
throw_on_error	Throw if key is an unknown criterion

Returns: Unary predicate to determine if a value is selected or not; nullptr or throw if unknown name.

Exceptions

if	unknown name and `throw_on_error` is true

Variable Documentation

◆ createGroupGroupProperty

std::function<double(const Group&, const Group&)> Faunus::analysis::createGroupGroupProperty(const json &j, const Space &spc, Energy::Hamiltonian &hamiltonian)

Generates lambda to calculate properties between groups.

This looks for the property key in the json object. Supported names are energy, com_distance

Classes

Functions

Variables

Detailed Description

Function Documentation

◆ createAnalysis()

◆ createGroupGroupProperty()

◆ createValueFilter()

Variable Documentation

◆ createGroupGroupProperty