Implements force matching algorithm using cubic spline basis set. More...

#include <csg_fmatch.h>

Inheritance diagram for CGForceMatching:

[legend]

Collaboration diagram for CGForceMatching:

[legend]

Classes
struct	SplineInfo
	structure, which contains CubicSpline object with related parameters More...

Public Member Functions
string	ProgramName () override
	program name

void	HelpText (ostream &out) override
	help text of application without version information

bool	DoTrajectory () override
	overload and return true to enable trajectory command line options

bool	DoMapping () override
	overload and return true to enable mapping command line options

void	Initialize (void) override
	Initialize application data.

bool	EvaluateOptions () override
	Process command line options.

void	BeginEvaluate (Topology top, Topology top_atom) override
	called before the first frame

void	EndEvaluate () override
	called after the last frame

void	EvalConfiguration (Topology conf, Topology conf_atom=nullptr) override
	called for each frame which is mapped

void	LoadOptions (const string &file)
	load options from the input file

Public Member Functions inherited from votca::csg::CsgApplication
	CsgApplication ()=default

	~CsgApplication () override=default

void	Initialize () override
	Initialize application data.

bool	EvaluateOptions () override
	Process command line options.

void	Run (void) override
	Main body of application.

void	ShowHelpText (std::ostream &out) override

virtual bool	DoMappingDefault (void)
	if DoMapping is true, will by default require mapping or not

virtual bool	DoThreaded (void)

virtual bool	SynchronizeThreads (void)

virtual bool	NeedsTopology (void)
	if topology is always needed

virtual bool	EvaluateTopology (Topology , Topology =nullptr)
	called after topology was loaded

void	AddObserver (CGObserver *observer)

bool	ProcessData (Worker *worker)
	Gets frames from TrajectoryReader in an ordered way and, if successful, calls Worker::EvalConfiguration for that frame.

virtual std::unique_ptr< Worker >	ForkWorker (void)

virtual void	MergeWorker (Worker *worker)

Public Member Functions inherited from votca::tools::Application
	Application ()

virtual	~Application ()

int	Exec (int argc, char **argv)
	executes the program

virtual std::string	VersionString ()
	version string of application

void	CheckRequired (const std::string &option_name, const std::string &error_msg="")
	Check weather required option is set.

boost::program_options::options_description_easy_init	AddProgramOptions (const std::string &group="")
	add option for command line

boost::program_options::variables_map &	OptionsMap ()
	get available program options & descriptions

boost::program_options::options_description &	OptionsDesc ()

boost::program_options::options_description &	VisibleOptions ()
	filters out the Hidden group from the options descriptions

void	StopExecution ()
	call StopExecution after EvaluateOptions

Protected Types
using	SplineContainer = vector<SplineInfo>

Protected Member Functions
void	FmatchAccumulateData ()
	Solves FM equations for one block and stores the results for further processing.

void	FmatchAssignSmoothCondsToMatrix (Eigen::MatrixXd &Matrix)
	Assigns smoothing conditions to matrices A_ and B_constr_.

void	EvalBonded (Topology conf, SplineInfo sinfo)
	For each trajectory frame writes equations for bonded interactions to matrix A_.

void	EvalNonbonded (Topology conf, SplineInfo sinfo)
	For each trajectory frame writes equations for non-bonded interactions to matrix A_.

void	EvalNonbonded_Threebody (Topology conf, SplineInfo sinfo)
	For each trajectory frame writes equations for non-bonded threebody interactions to matrix A_.

void	WriteOutFiles ()
	Write results to output files.

void	OpenForcesTrajectory ()

Protected Member Functions inherited from votca::tools::Application

Protected Attributes
votca::tools::Property	options_
	Property object to handle input options.

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

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

SplineContainer	splines_
	vector of SplineInfo * for all interactions

Eigen::MatrixXd	A_
	matrix used to store force matching equations

Eigen::VectorXd	b_
	vector used to store reference forces on CG beads (from atomistic simulations)

Eigen::VectorXd	x_
	Solution of matrix equation A_ * x_ = b_ : CG force-field parameters.

Eigen::MatrixXd	B_constr_
	Additional matrix to handle constrained least squares fit contains constraints, which allow to get a real (smooth) spline (see VOTCA paper)

votca::Index	frame_counter_
	Counter for trajectory frames.

votca::Index	nbeads_
	Number of CG beads.

double	dist_
	accuracy for evaluating the difference in bead positions

bool	constr_least_sq_
	Flag: true for constrained least squares, false for simple least squares.

votca::Index	least_sq_offset_
	used in EvalConf to distinguish constrained and simple least squares

votca::Index	nframes_
	Number of frames used in one block for block averaging.

votca::Index	nblocks_
	Current number of blocks.

votca::Index	line_cntr_
	Counters for lines and columns in B_constr_.

votca::Index	col_cntr_

bool	has_existing_forces_

Topology	top_force_

std::unique_ptr< TrajectoryReader >	trjreader_force_

Protected Attributes inherited from votca::csg::CsgApplication
std::list< CGObserver * >	observers_

bool	do_mapping_

std::vector< std::unique_ptr< Worker > >	myWorkers_

Index	nframes_

bool	is_first_frame_

Index	nthreads_

tools::Mutex	nframesMutex_

tools::Mutex	traj_readerMutex_

std::vector< std::unique_ptr< tools::Mutex > >	threadsMutexesIn_
	stores Mutexes used to impose order for input

std::vector< std::unique_ptr< tools::Mutex > >	threadsMutexesOut_
	stores Mutexes used to impose order for output

std::unique_ptr< TrajectoryReader >	traj_reader_

Protected Attributes inherited from votca::tools::Application
std::map< std::string, boost::program_options::options_description >	op_groups_

bool	continue_execution_ = true

Detailed Description

Implements force matching algorithm using cubic spline basis set.

Force matching method to obtain a coarse-grained force field is implemented using cubic spline basis set. Block averaging over trajectory blocks is used for calculating CG forces and their errors.

Todo: force matching needs a big cleanup!

Definition at line 43 of file csg_fmatch.h.

Member Typedef Documentation

◆ SplineContainer

using CGForceMatching::SplineContainer = vector<SplineInfo>

protected

Definition at line 142 of file csg_fmatch.h.

Member Function Documentation

◆ BeginEvaluate()

void CGForceMatching::BeginEvaluate	(	Topology *	top,
		Topology *	top_atom )

overridevirtual

called before the first frame

Reimplemented from votca::csg::CsgApplication.

Definition at line 66 of file csg_fmatch.cc.

◆ DoMapping()

bool CGForceMatching::DoMapping ( void )

inlineoverridevirtual

overload and return true to enable mapping command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 51 of file csg_fmatch.h.

◆ DoTrajectory()

bool CGForceMatching::DoTrajectory ( void )

inlineoverridevirtual

overload and return true to enable trajectory command line options

Reimplemented from votca::csg::CsgApplication.

Definition at line 50 of file csg_fmatch.h.

◆ EndEvaluate()

void CGForceMatching::EndEvaluate ( )

overridevirtual

called after the last frame

Reimplemented from votca::csg::CsgApplication.

Definition at line 267 of file csg_fmatch.cc.

◆ EvalBonded()

void CGForceMatching::EvalBonded	(	Topology *	conf,
		SplineInfo *	sinfo )

protected

For each trajectory frame writes equations for bonded interactions to matrix A_.

Definition at line 571 of file csg_fmatch.cc.

◆ EvalConfiguration()

void CGForceMatching::EvalConfiguration	(	Topology *	conf,
		Topology *	conf_atom = nullptr )

overridevirtual

called for each frame which is mapped

Reimplemented from votca::csg::CsgApplication.

Definition at line 383 of file csg_fmatch.cc.

◆ EvalNonbonded()

void CGForceMatching::EvalNonbonded	(	Topology *	conf,
		SplineInfo *	sinfo )

protected

For each trajectory frame writes equations for non-bonded interactions to matrix A_.

Definition at line 607 of file csg_fmatch.cc.

◆ EvalNonbonded_Threebody()

void CGForceMatching::EvalNonbonded_Threebody	(	Topology *	conf,
		SplineInfo *	sinfo )

protected

For each trajectory frame writes equations for non-bonded threebody interactions to matrix A_.

Definition at line 686 of file csg_fmatch.cc.

◆ EvaluateOptions()

bool CGForceMatching::EvaluateOptions ( )

overridevirtual

Process command line options.

Returns: true to continue, false to stop

EvaluateOptions is called by Run after parsing the command line. return true if everything is ok, false to stop and show help text.

Implements votca::tools::Application.

Definition at line 53 of file csg_fmatch.cc.

◆ FmatchAccumulateData()

void CGForceMatching::FmatchAccumulateData ( )

protected

Solves FM equations for one block and stores the results for further processing.

Definition at line 469 of file csg_fmatch.cc.

◆ FmatchAssignSmoothCondsToMatrix()

void CGForceMatching::FmatchAssignSmoothCondsToMatrix ( Eigen::MatrixXd & Matrix )

protected

Assigns smoothing conditions to matrices A_ and B_constr_.

Definition at line 539 of file csg_fmatch.cc.

◆ HelpText()

void CGForceMatching::HelpText ( ostream & out )

inlineoverridevirtual

help text of application without version information

Parameters

out	ostream for output

Implements votca::tools::Application.

Definition at line 46 of file csg_fmatch.h.

◆ Initialize()

void CGForceMatching::Initialize ( void )

overridevirtual

Initialize application data.

Initialize is called by run before parsing the command line. All necessary command line arguments can be added here

Implements votca::tools::Application.

Definition at line 44 of file csg_fmatch.cc.

◆ LoadOptions()

void CGForceMatching::LoadOptions ( const string & file )

load options from the input file

Definition at line 565 of file csg_fmatch.cc.

◆ OpenForcesTrajectory()

void CGForceMatching::OpenForcesTrajectory ( )

protected

◆ ProgramName()

string CGForceMatching::ProgramName ( )

inlineoverridevirtual

program name

Returns: string with program name

overload this function to set the program name

Implements votca::tools::Application.

Definition at line 45 of file csg_fmatch.h.

◆ WriteOutFiles()

void CGForceMatching::WriteOutFiles ( )

protected

Write results to output files.

Definition at line 286 of file csg_fmatch.cc.

Member Data Documentation

◆ A_

Eigen::MatrixXd CGForceMatching::A_

protected

matrix used to store force matching equations

Definition at line 147 of file csg_fmatch.h.

◆ b_

Eigen::VectorXd CGForceMatching::b_

protected

vector used to store reference forces on CG beads (from atomistic simulations)

Definition at line 150 of file csg_fmatch.h.

◆ B_constr_

Eigen::MatrixXd CGForceMatching::B_constr_

protected

Additional matrix to handle constrained least squares fit contains constraints, which allow to get a real (smooth) spline (see VOTCA paper)

Definition at line 157 of file csg_fmatch.h.

◆ bonded_

std::vector<votca::tools::Property *> CGForceMatching::bonded_

protected

list of bonded interactions

Definition at line 138 of file csg_fmatch.h.

◆ col_cntr_

votca::Index CGForceMatching::col_cntr_

protected

Definition at line 179 of file csg_fmatch.h.

◆ constr_least_sq_

bool CGForceMatching::constr_least_sq_

protected

Flag: true for constrained least squares, false for simple least squares.

Definition at line 169 of file csg_fmatch.h.

◆ dist_

double CGForceMatching::dist_

protected

accuracy for evaluating the difference in bead positions

Definition at line 165 of file csg_fmatch.h.

◆ frame_counter_

votca::Index CGForceMatching::frame_counter_

protected

Counter for trajectory frames.

Definition at line 160 of file csg_fmatch.h.

◆ has_existing_forces_

bool CGForceMatching::has_existing_forces_

protected

Definition at line 181 of file csg_fmatch.h.

◆ least_sq_offset_

votca::Index CGForceMatching::least_sq_offset_

protected

used in EvalConf to distinguish constrained and simple least squares

Definition at line 172 of file csg_fmatch.h.

◆ line_cntr_

votca::Index CGForceMatching::line_cntr_

protected

Counters for lines and columns in B_constr_.

Definition at line 179 of file csg_fmatch.h.

◆ nbeads_

votca::Index CGForceMatching::nbeads_

protected

Number of CG beads.

Definition at line 162 of file csg_fmatch.h.

◆ nblocks_

votca::Index CGForceMatching::nblocks_

protected

Current number of blocks.

Definition at line 176 of file csg_fmatch.h.

◆ nframes_

votca::Index CGForceMatching::nframes_

protected

Number of frames used in one block for block averaging.

Definition at line 174 of file csg_fmatch.h.

◆ nonbonded_

std::vector<votca::tools::Property *> CGForceMatching::nonbonded_

protected

list of non-bonded interactions

Definition at line 140 of file csg_fmatch.h.

◆ options_

votca::tools::Property CGForceMatching::options_

protected

Property object to handle input options.

Definition at line 136 of file csg_fmatch.h.

◆ splines_

SplineContainer CGForceMatching::splines_

protected

vector of SplineInfo * for all interactions

Definition at line 144 of file csg_fmatch.h.

◆ top_force_

Topology CGForceMatching::top_force_

protected

Definition at line 202 of file csg_fmatch.h.

◆ trjreader_force_

std::unique_ptr<TrajectoryReader> CGForceMatching::trjreader_force_

protected

Definition at line 203 of file csg_fmatch.h.

◆ x_

Eigen::VectorXd CGForceMatching::x_

protected

Solution of matrix equation A_ * x_ = b_ : CG force-field parameters.

Definition at line 153 of file csg_fmatch.h.

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

csg/src/tools/csg_fmatch.h
csg/src/tools/csg_fmatch.cc

Classes

Public Member Functions

Protected Types

Protected Member Functions

Protected Attributes

Detailed Description

Member Typedef Documentation

◆ SplineContainer

Member Function Documentation

◆ BeginEvaluate()

◆ DoMapping()

◆ DoTrajectory()

◆ EndEvaluate()

◆ EvalBonded()

◆ EvalConfiguration()

◆ EvalNonbonded()

◆ EvalNonbonded_Threebody()

◆ EvaluateOptions()

◆ FmatchAccumulateData()

◆ FmatchAssignSmoothCondsToMatrix()

◆ HelpText()

◆ Initialize()

◆ LoadOptions()

◆ OpenForcesTrajectory()

◆ ProgramName()

◆ WriteOutFiles()

Member Data Documentation

◆ A_

◆ b_

◆ B_constr_

◆ bonded_

◆ col_cntr_

◆ constr_least_sq_

◆ dist_

◆ frame_counter_

◆ has_existing_forces_

◆ least_sq_offset_

◆ line_cntr_

◆ nbeads_

◆ nblocks_

◆ nframes_

◆ nonbonded_

◆ options_

◆ splines_

◆ top_force_

◆ trjreader_force_

◆ x_