class to calculate distribution functions and cross correlations for inverse monte carlo More...

#include <rdf_calculator.h>

Collaboration diagram for votca::csg::RDFCalculator:

[legend]

Classes
struct	group_t
	struct to store collected information for groups (e.g. crosscorrelations) More...

struct	interaction_t
	struct to store collected information for interactions More...

struct	pair_t

class	Worker

Public Member Functions
	RDFCalculator ()

	~RDFCalculator ()

void	Initialize (void)

void	LoadOptions (const std::string &file)
	load cg definitions file

void	BeginEvaluate (Topology top, Topology top_atom)
	begin coarse graining a trajectory

void	EndEvaluate ()
	end coarse graining a trajectory

void	WriteEvery (Index write_every)

void	DoBlocks (bool do_blocks)

void	DoVolumeCorrection (bool do_vol_corr)

void	SetSubvolRadius (double r)

double	AnalyticVolumeCorrection (double t)

std::unique_ptr< CsgApplication::Worker >	ForkWorker ()

void	MergeWorker (CsgApplication::Worker *worker_)

Protected Types
using	group_matrix = Eigen::MatrixXd

using	pair_matrix = Eigen::Block< group_matrix >

Protected Member Functions
interaction_t *	AddInteraction (Property *p)
	create a new interaction entry based on given options

group_t *	getGroup (const std::string &name)
	get group by name, creates one if it doesn't exist

void	WriteDist (const std::string &suffix="")

void	ClearAverages ()

void	DoCorrelations (RDFCalculator::Worker *worker)
	update the correlations after interations were processed

Protected Attributes
Average< double >	avg_vol_

Property	options_
	the options parsed from cg definition file

Index	write_every_

bool	do_blocks_

Index	nframes_

Index	nblock_

double	subvol_rad_

Eigen::Vector3d	boxc_

bool	do_vol_corr_

std::vector< Property * >	bonded_
	list of bonded interactions

std::vector< Property * >	nonbonded_
	list of non-bonded interactions

std::map< std::string, std::unique_ptr< interaction_t > >	interactions_
	std::map ineteractionm-name to interaction

std::map< std::string, std::unique_ptr< group_t > >	groups_
	std::map group-name to group

bool	processed_some_frames_

Detailed Description

class to calculate distribution functions and cross correlations for inverse monte carlo

This class calculates distribution functions as well as cross-correlations for specific groups of interactions based on a given trajectory.

Definition at line 53 of file rdf_calculator.h.

Member Typedef Documentation

◆ group_matrix

using votca::csg::RDFCalculator::group_matrix = Eigen::MatrixXd

protected

Definition at line 85 of file rdf_calculator.h.

◆ pair_matrix

using votca::csg::RDFCalculator::pair_matrix = Eigen::Block<group_matrix>

protected

Definition at line 86 of file rdf_calculator.h.

Constructor & Destructor Documentation

◆ RDFCalculator()

votca::csg::RDFCalculator::RDFCalculator ( )

Definition at line 41 of file rdf_calculator.cc.

◆ ~RDFCalculator()

votca::csg::RDFCalculator::~RDFCalculator ( )

default

Member Function Documentation

◆ AddInteraction()

RDFCalculator::interaction_t * votca::csg::RDFCalculator::AddInteraction ( Property * p )

protected

create a new interaction entry based on given options

Definition at line 120 of file rdf_calculator.cc.

◆ AnalyticVolumeCorrection()

double votca::csg::RDFCalculator::AnalyticVolumeCorrection ( double t )

inline

Definition at line 73 of file rdf_calculator.h.

◆ BeginEvaluate()

void votca::csg::RDFCalculator::BeginEvaluate	(	Topology *	top,
		Topology *	top_atom
	)

begin coarse graining a trajectory

Definition at line 72 of file rdf_calculator.cc.

◆ ClearAverages()

void votca::csg::RDFCalculator::ClearAverages ( )

protected

Definition at line 179 of file rdf_calculator.cc.

◆ DoBlocks()

void votca::csg::RDFCalculator::DoBlocks ( bool do_blocks )

inline

Definition at line 70 of file rdf_calculator.h.

◆ DoCorrelations()

void votca::csg::RDFCalculator::DoCorrelations ( RDFCalculator::Worker * worker )

protected

update the correlations after interations were processed

◆ DoVolumeCorrection()

void votca::csg::RDFCalculator::DoVolumeCorrection ( bool do_vol_corr )

inline

Definition at line 71 of file rdf_calculator.h.

◆ EndEvaluate()

void votca::csg::RDFCalculator::EndEvaluate ( )

end coarse graining a trajectory

Definition at line 147 of file rdf_calculator.cc.

◆ ForkWorker()

std::unique_ptr< CsgApplication::Worker > votca::csg::RDFCalculator::ForkWorker ( )

Definition at line 362 of file rdf_calculator.cc.

◆ getGroup()

RDFCalculator::group_t * votca::csg::RDFCalculator::getGroup ( const std::string & name )

protected

get group by name, creates one if it doesn't exist

Definition at line 321 of file rdf_calculator.cc.

◆ Initialize()

void votca::csg::RDFCalculator::Initialize ( void )

Definition at line 53 of file rdf_calculator.cc.

◆ LoadOptions()

void votca::csg::RDFCalculator::LoadOptions ( const std::string & file )

load cg definitions file

Definition at line 163 of file rdf_calculator.cc.

◆ MergeWorker()

void votca::csg::RDFCalculator::MergeWorker ( CsgApplication::Worker * worker_ )

Definition at line 376 of file rdf_calculator.cc.

◆ SetSubvolRadius()

void votca::csg::RDFCalculator::SetSubvolRadius ( double r )

inline

Definition at line 72 of file rdf_calculator.h.

◆ WriteDist()

void votca::csg::RDFCalculator::WriteDist ( const std::string & suffix = "" )

protected

Definition at line 331 of file rdf_calculator.cc.

◆ WriteEvery()

void votca::csg::RDFCalculator::WriteEvery ( Index write_every )

inline

Definition at line 69 of file rdf_calculator.h.

Member Data Documentation

◆ avg_vol_

Average<double> votca::csg::RDFCalculator::avg_vol_

protected

Definition at line 83 of file rdf_calculator.h.

◆ bonded_

std::vector<Property *> votca::csg::RDFCalculator::bonded_

protected

list of bonded interactions

Definition at line 132 of file rdf_calculator.h.

◆ boxc_

Eigen::Vector3d votca::csg::RDFCalculator::boxc_

protected

Definition at line 128 of file rdf_calculator.h.

◆ do_blocks_

bool votca::csg::RDFCalculator::do_blocks_

protected

Definition at line 122 of file rdf_calculator.h.

◆ do_vol_corr_

bool votca::csg::RDFCalculator::do_vol_corr_

protected

Definition at line 129 of file rdf_calculator.h.

◆ groups_

std::map<std::string, std::unique_ptr<group_t> > votca::csg::RDFCalculator::groups_

protected

std::map group-name to group

Definition at line 139 of file rdf_calculator.h.

◆ interactions_

std::map<std::string, std::unique_ptr<interaction_t> > votca::csg::RDFCalculator::interactions_

protected

std::map ineteractionm-name to interaction

Definition at line 137 of file rdf_calculator.h.

◆ nblock_

Index votca::csg::RDFCalculator::nblock_

protected

Definition at line 126 of file rdf_calculator.h.

◆ nframes_

Index votca::csg::RDFCalculator::nframes_

protected

Definition at line 125 of file rdf_calculator.h.

◆ nonbonded_

std::vector<Property *> votca::csg::RDFCalculator::nonbonded_

protected

list of non-bonded interactions

Definition at line 134 of file rdf_calculator.h.

◆ options_

Property votca::csg::RDFCalculator::options_

protected

the options parsed from cg definition file

Definition at line 118 of file rdf_calculator.h.

◆ processed_some_frames_

bool votca::csg::RDFCalculator::processed_some_frames_

protected

Definition at line 170 of file rdf_calculator.h.

◆ subvol_rad_

double votca::csg::RDFCalculator::subvol_rad_

protected

Definition at line 127 of file rdf_calculator.h.

◆ write_every_

Index votca::csg::RDFCalculator::write_every_

protected

Definition at line 120 of file rdf_calculator.h.

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

csg/src/csgapps/partial_rdf/rdf_calculator.h
csg/src/csgapps/partial_rdf/rdf_calculator.cc

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ group_matrix

◆ pair_matrix

Constructor & Destructor Documentation

◆ RDFCalculator()

◆ ~RDFCalculator()

Member Function Documentation

◆ AddInteraction()

◆ AnalyticVolumeCorrection()

◆ BeginEvaluate()

◆ ClearAverages()

◆ DoBlocks()

◆ DoCorrelations()

◆ DoVolumeCorrection()

◆ EndEvaluate()

◆ ForkWorker()

◆ getGroup()

◆ Initialize()

◆ LoadOptions()

◆ MergeWorker()

◆ SetSubvolRadius()

◆ WriteDist()

◆ WriteEvery()

Member Data Documentation

◆ avg_vol_

◆ bonded_

◆ boxc_

◆ do_blocks_

◆ do_vol_corr_

◆ groups_

◆ interactions_

◆ nblock_

◆ nframes_

◆ nonbonded_

◆ options_

◆ processed_some_frames_

◆ subvol_rad_

◆ write_every_