t_oriresdata Struct Reference

#include <gromacs/mdtypes/fcdata.h>

Collaboration diagram for t_oriresdata:

Description

Orientation restraining stuff.

Public Member Functions
	t_oriresdata (FILE *fplog, const gmx_mtop_t &mtop, const t_inputrec &ir, const gmx_multisim_t *ms, t_state *globalState, gmx::LocalAtomSetManager *localAtomSetManager)
	Constructor. More...
	~t_oriresdata ()
	Destructor.
const gmx::LocalAtomSet &	fitLocalAtomSet () const
	Returns the local atom set for fitting.
gmx::ArrayRef< const gmx::RVec >	referenceCoordinates () const
	Returns the list of reference coordinates.
gmx::ArrayRef< const real >	fitMasses () const
	Returns the list of masses for fitting.
gmx::ArrayRef< gmx::RVec >	xTmp ()
	Returns the list of coordinates for temporary use, size matches referenceCoordinates.
real	timeAveragingInitFactor () const
	Returns the factor for initializing the time averaging.
gmx::ArrayRef< const real >	DTensorsTimeAveragedHistory () const
	Returns a const view on the time averaged D tensor history.
void	updateHistory ()
	Updates the history with the current values.
	GMX_DISALLOW_COPY_AND_ASSIGN (t_oriresdata)

Public Attributes
real	fc
	Force constant for the restraints.
real	edt
	Multiplication factor for time averaging.
real	edt_1
	1 - edt
real	exp_min_t_tau
	Factor for slowly switching on the force.
const int	numRestraints
	The number of orientation restraints.
int	numExperiments
	The number of experiments.
int	typeMin
	The minimum iparam type index for restraints.
matrix	rotationMatrix
	Rotation matrix to rotate to the reference coordinates.
tensor *	orderTensors = nullptr
	Array of order tensors, one for each experiment.
rvec5 *	DTensors = nullptr
	The order tensor D for all restraints.
rvec5 *	DTensorsEnsembleAv = nullptr
	The ensemble averaged D for all restraints.
rvec5 *	DTensorsTimeAndEnsembleAv = nullptr
	The time and ensemble averaged D restraints.
std::vector< real >	orientations
	The calculated instantaneous orientations.
gmx::ArrayRef< real >	orientationsEnsembleAv
	The calculated emsemble averaged orientations.
std::vector< real >	orientationsEnsembleAvBuffer
	Buffer for the calculated emsemble averaged orientations, only used with ensemble averaging.
gmx::ArrayRef< real >	orientationsTimeAndEnsembleAv
	The calculated time and ensemble averaged orientations.
std::vector< real >	orientationsTimeAndEnsembleAvBuffer
	The weighted (using kfac) RMS deviation.
real	rmsdev
	Buffer for the weighted (using kfac) RMS deviation, only used with time averaging.
std::vector< OriresMatEq >	tmpEq
	An temporary array of matrix + rhs.
std::vector< real >	eigenOutput
	Eigenvalues/vectors, for output only (numExperiments x 12)
std::array< gmx::DVec, DIM >	M
	Tensor to diagonalize.
std::array< double, DIM >	eig_diag
	Eigenvalues.
std::array< gmx::DVec, DIM >	v
	Eigenvectors.

Static Public Attributes
static constexpr int	c_numEigenRealsPerExperiment = 12
	The number of eigenvalues + eigenvectors per experiment.

Constructor & Destructor Documentation

t_oriresdata::t_oriresdata	(	FILE *	fplog,
		const gmx_mtop_t &	mtop,
		const t_inputrec &	ir,
		const gmx_multisim_t *	ms,
		t_state *	globalState,
		gmx::LocalAtomSetManager *	localAtomSetManager
	)

Constructor.

Parameters

[in]	fplog	Log file, can be nullptr
[in]	mtop	The global topology
[in]	ir	The input record
[in]	ms	The multisim communicator, pass nullptr to avoid ensemble averaging
[in]	globalState	The global state, references are set to members
[in,out]	localAtomSetManager	The local atom set manager

Exceptions

InvalidInputError

when there is domain decomposition, fewer than 5 restraints, periodic molecules or more than 1 molecule for a moleculetype with restraints.

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

• src/gromacs/mdtypes/fcdata.h
• src/gromacs/listed_forces/orires.cpp