densityfittingoptions.cpp File Reference

#include "gmxpre.h"
#include "densityfittingoptions.h"
#include "gromacs/applied_forces/densityfitting/densityfitting.h"
#include "gromacs/math/densityfit.h"
#include "gromacs/mdrunutility/mdmodulesnotifiers.h"
#include "gromacs/mdtypes/imdpoptionprovider_helpers.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/optionsection.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "densityfittingamplitudelookup.h"

Include dependency graph for densityfittingoptions.cpp:

Description

Implements force provider for density fitting.

Author

Christian Blau blau@.nosp@m.kth..nosp@m.se

Functions
std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::moduleName ()
	Helper function to make a std::string containing the module name.

Variables
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_activeTag = "active"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_groupTag = "group"
	Denote the .mdp option that defines the group of fit atoms. More...
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_similarityMeasureTag = "similarity-measure"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_amplitudeMethodTag = "atom-spreading-weight"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_forceConstantTag = "force-constant"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_gaussianTransformSpreadingWidthTag = "gaussian-transform-spreading-width"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_gaussianTransformSpreadingRangeInMultiplesOfWidthTag
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_referenceDensityFileNameTag = "reference-density-filename"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_everyNStepsTag = "nst"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_normalizeDensitiesTag = "normalize-densities"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_adaptiveForceScalingTag = "adaptive-force-scaling"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_adaptiveForceScalingTimeConstantTag = "adaptive-force-scaling-time-constant"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_translationTag = "shift-vector"
const std::string	gmx::anonymous_namespace{densityfittingoptions.cpp}::c_transformationMatrixTag = "transformation-matrix"
static const EnumerationArray < DensitySimilarityMeasureMethod, const char * >	gmx::c_densitySimilarityMeasureMethodNames
	Name the methods that may be used to evaluate similarity between densities. More...
static const EnumerationArray < DensityFittingAmplitudeMethod, const char * >	gmx::c_densityFittingAmplitudeMethodNames
	The names of the methods to determine the amplitude of the atoms to be spread on a grid. More...