msd.cpp File Reference

#include "gmxpre.h"
#include "msd.h"
#include <cinttypes>
#include <cmath>
#include <cstdlib>
#include <algorithm>
#include <functional>
#include <limits>
#include <memory>
#include <numeric>
#include <optional>
#include <string>
#include <vector>
#include "gromacs/analysisdata/analysisdata.h"
#include "gromacs/analysisdata/modules/average.h"
#include "gromacs/analysisdata/modules/plot.h"
#include "gromacs/analysisdata/paralleloptions.h"
#include "gromacs/fileio/oenv.h"
#include "gromacs/fileio/trxio.h"
#include "gromacs/math/functions.h"
#include "gromacs/options/basicoptions.h"
#include "gromacs/options/filenameoption.h"
#include "gromacs/options/ioptionscontainer.h"
#include "gromacs/options/optionfiletype.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/selection/indexutil.h"
#include "gromacs/selection/selection.h"
#include "gromacs/selection/selectionoption.h"
#include "gromacs/statistics/statistics.h"
#include "gromacs/trajectory/trajectoryframe.h"
#include "gromacs/trajectoryanalysis/analysissettings.h"
#include "gromacs/trajectoryanalysis/topologyinformation.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/enumerationhelpers.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/stringutil.h"
#include "gromacs/utility/vectypes.h"

Include dependency graph for msd.cpp:

Description

Defines the trajectory analysis module for mean squared displacement calculations.

Author

Kevin Boyd kevin.nosp@m.44bo.nosp@m.yd@gm.nosp@m.ail..nosp@m.com

Classes
class	gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData
	Mean Squared Displacement data accumulator. More...
class	gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdData::MsdColumnProxy
	Proxy to a MsdData tau column vector. Supports only push_back. More...
struct	gmx::analysismodules::anonymous_namespace{msd.cpp}::MoleculeData
	Holds data needed for MSD calculations for a single molecule, if requested. More...
class	gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdCoordinateManager
	Handles coordinate operations for MSD calculations. More...
struct	gmx::analysismodules::anonymous_namespace{msd.cpp}::MsdGroupData
	Holds per-group coordinates, analysis, and results. More...
class	gmx::analysismodules::Msd
	Implements the gmx msd module. More...

Enumerations
enum	gmx::analysismodules::anonymous_namespace{msd.cpp}::SingleDimDiffType : int {   X = 0, Y, Z, Unused,   Count }
	Describes 1D MSDs, in the given dimension.
enum	gmx::analysismodules::anonymous_namespace{msd.cpp}::TwoDimDiffType : int {   NormalToX = 0, NormalToY, NormalToZ, Unused,   Count }
	Describes 2D MSDs, in the plane normal to the given dimension.

Functions
template<bool x, bool y, bool z>
double	gmx::analysismodules::anonymous_namespace{msd.cpp}::calcSingleSquaredDistance (const DVec &firstCoords, const DVec &secondCoords)
	Calculates 1,2, or 3D distance for two vectors. More...
template<bool x, bool y, bool z>
double	gmx::analysismodules::anonymous_namespace{msd.cpp}::calcAverageDisplacement (ArrayRef< const DVec > c1, ArrayRef< const DVec > c2)
	Calculate average displacement between sets of points. More...
void	gmx::analysismodules::anonymous_namespace{msd.cpp}::removePbcJumps (ArrayRef< DVec > currentCoords, ArrayRef< const DVec > previousCoords, t_pbc *pbc)
	Removes jumps across periodic boundaries for currentFrame, based on the positions in previousFrame. Updates currentCoords in place.
static size_t	gmx::analysismodules::calculateFitIndex (const int userFitTau, const double defaultTauFraction, const int numTaus, const double dt)
	Calculate the tau index for fitting. If userFitTau < 0, uses the default fraction of max tau.

Variables
constexpr double	gmx::analysismodules::anonymous_namespace{msd.cpp}::c_diffusionConversionFactor = 1000.0
	Convert nm^2/ps to 10e-5 cm^2/s.
constexpr double	gmx::analysismodules::anonymous_namespace{msd.cpp}::c_3DdiffusionDimensionFactor = 6.0
	Three dimensional diffusion coefficient multiplication constant.
constexpr double	gmx::analysismodules::anonymous_namespace{msd.cpp}::c_2DdiffusionDimensionFactor = 4.0
	Two dimensional diffusion coefficient multiplication constant.
constexpr double	gmx::analysismodules::anonymous_namespace{msd.cpp}::c_1DdiffusionDimensionFactor = 2.0
	One dimensional diffusion coefficient multiplication constant.