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

#include <csg_stat_imc.h>

Collaboration diagram for votca::csg::Imc:

[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
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	BlockLength (votca::Index length)

void	DoImc (bool do_imc)

void	IncludeIntra (bool include_intra)

void	Extension (std::string ext)

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 (tools::Property *p, bool is_bonded)
	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	InitializeGroups ()
	initializes the group structs after interactions were added

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

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

void	WriteIMCBlock (const std::string &suffix)

void	CalcDeltaS (interaction_t *interaction, Eigen::VectorBlock< Eigen::VectorXd > &dS)

void	ClearAverages ()

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

Protected Attributes
tools::Average< double >	avg_vol_

tools::Property	options_
	the options parsed from cg definition file

votca::Index	block_length_ = 0

bool	do_imc_ = false

bool	include_intra_ = false

std::string	extension_

votca::Index	nframes_

votca::Index	nblock_

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

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

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

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

bool	processed_some_frames_ = false

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 39 of file csg_stat_imc.h.

Member Typedef Documentation

◆ group_matrix

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

protected

Definition at line 60 of file csg_stat_imc.h.

◆ pair_matrix

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

protected

Definition at line 61 of file csg_stat_imc.h.

Member Function Documentation

◆ AddInteraction()

Imc::interaction_t * votca::csg::Imc::AddInteraction	(	tools::Property *	p,
		bool	is_bonded
	)

protected

create a new interaction entry based on given options

Definition at line 185 of file csg_stat_imc.cc.

◆ BeginEvaluate()

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

begin coarse graining a trajectory

Definition at line 83 of file csg_stat_imc.cc.

◆ BlockLength()

void votca::csg::Imc::BlockLength ( votca::Index length )

inline

Definition at line 52 of file csg_stat_imc.h.

◆ CalcDeltaS()

void votca::csg::Imc::CalcDeltaS	(	interaction_t *	interaction,
		Eigen::VectorBlock< Eigen::VectorXd > &	dS
	)

protected

Definition at line 715 of file csg_stat_imc.cc.

◆ ClearAverages()

void votca::csg::Imc::ClearAverages ( )

protected

Definition at line 274 of file csg_stat_imc.cc.

◆ DoCorrelations()

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

protected

update the correlations after interations were processed

Definition at line 522 of file csg_stat_imc.cc.

◆ DoImc()

void votca::csg::Imc::DoImc ( bool do_imc )

inline

Definition at line 53 of file csg_stat_imc.h.

◆ EndEvaluate()

void votca::csg::Imc::EndEvaluate ( )

end coarse graining a trajectory

Definition at line 238 of file csg_stat_imc.cc.

◆ Extension()

void votca::csg::Imc::Extension ( std::string ext )

inline

Definition at line 55 of file csg_stat_imc.h.

◆ ForkWorker()

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

Definition at line 829 of file csg_stat_imc.cc.

◆ getGroup()

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

protected

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

Definition at line 462 of file csg_stat_imc.cc.

◆ IncludeIntra()

void votca::csg::Imc::IncludeIntra ( bool include_intra )

inline

Definition at line 54 of file csg_stat_imc.h.

◆ Initialize()

void votca::csg::Imc::Initialize ( void )

Definition at line 47 of file csg_stat_imc.cc.

◆ InitializeGroups()

void votca::csg::Imc::InitializeGroups ( )

protected

initializes the group structs after interactions were added

Definition at line 474 of file csg_stat_imc.cc.

◆ LoadOptions()

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

load cg definitions file

Definition at line 258 of file csg_stat_imc.cc.

◆ MergeWorker()

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

Definition at line 850 of file csg_stat_imc.cc.

◆ WriteDist()

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

protected

Definition at line 542 of file csg_stat_imc.cc.

◆ WriteIMCBlock()

void votca::csg::Imc::WriteIMCBlock ( const std::string & suffix )

protected

Definition at line 744 of file csg_stat_imc.cc.

◆ WriteIMCData()

void votca::csg::Imc::WriteIMCData ( const std::string & suffix = "" )

protected

Here the inverse monte carlo matrix is calculated and written out

steps:

calculate th

Definition at line 628 of file csg_stat_imc.cc.

Member Data Documentation

◆ avg_vol_

tools::Average<double> votca::csg::Imc::avg_vol_

protected

Definition at line 58 of file csg_stat_imc.h.

◆ block_length_

votca::Index votca::csg::Imc::block_length_ = 0

protected

Definition at line 97 of file csg_stat_imc.h.

◆ bonded_

std::vector<tools::Property *> votca::csg::Imc::bonded_

protected

list of bonded interactions

Definition at line 111 of file csg_stat_imc.h.

◆ do_imc_

bool votca::csg::Imc::do_imc_ = false

protected

Definition at line 99 of file csg_stat_imc.h.

◆ extension_

std::string votca::csg::Imc::extension_

protected

Definition at line 104 of file csg_stat_imc.h.

◆ groups_

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

protected

map group-name to group

Definition at line 118 of file csg_stat_imc.h.

◆ include_intra_

bool votca::csg::Imc::include_intra_ = false

protected

Definition at line 101 of file csg_stat_imc.h.

◆ interactions_

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

protected

map interaction-name to interaction

Definition at line 116 of file csg_stat_imc.h.

◆ nblock_

votca::Index votca::csg::Imc::nblock_

protected

Definition at line 108 of file csg_stat_imc.h.

◆ nframes_

votca::Index votca::csg::Imc::nframes_

protected

Definition at line 107 of file csg_stat_imc.h.

◆ nonbonded_

std::vector<tools::Property *> votca::csg::Imc::nonbonded_

protected

list of non-bonded interactions

Definition at line 113 of file csg_stat_imc.h.

◆ options_

tools::Property votca::csg::Imc::options_

protected

the options parsed from cg definition file

Definition at line 95 of file csg_stat_imc.h.

◆ processed_some_frames_

bool votca::csg::Imc::processed_some_frames_ = false

protected

Definition at line 155 of file csg_stat_imc.h.

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

csg/src/tools/csg_stat_imc.h
csg/src/tools/csg_stat_imc.cc

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ group_matrix

◆ pair_matrix

Member Function Documentation

◆ AddInteraction()

◆ BeginEvaluate()

◆ BlockLength()

◆ CalcDeltaS()

◆ ClearAverages()

◆ DoCorrelations()

◆ DoImc()

◆ EndEvaluate()

◆ Extension()

◆ ForkWorker()

◆ getGroup()

◆ IncludeIntra()

◆ Initialize()

◆ InitializeGroups()

◆ LoadOptions()

◆ MergeWorker()

◆ WriteDist()

◆ WriteIMCBlock()

◆ WriteIMCData()

Member Data Documentation

◆ avg_vol_

◆ block_length_

◆ bonded_

◆ do_imc_

◆ extension_

◆ groups_

◆ include_intra_

◆ interactions_

◆ nblock_

◆ nframes_

◆ nonbonded_

◆ options_

◆ processed_some_frames_