#include <gromacs/analysisdata/modules/displacement.h>

Inheritance diagram for gmx::AnalysisDataDisplacementModule:

Collaboration diagram for gmx::AnalysisDataDisplacementModule:

Description

Data module for calculating displacements.

Output data contains a frame for each frame in the input data except the first one. For each frame, there can be multiple points, each of which describes displacement for a certain time difference ending that that frame. The first column contains the time difference (backwards from the current frame), and the remaining columns the sizes of the displacements.

Current implementation is not very generic, but should be easy to extend.

Classes
class	Impl
	Private implementation class for AnalysisDataDisplacementModule. More...

Public Member Functions
void	setMaxTime (real tmax)
	Sets the largest displacement time to be calculated.

void	setMSDHistogram (const std::shared_ptr< AnalysisDataBinAverageModule > &histm)
	Sets an histogram module that will receive a MSD histogram. More...

int	flags () const override
	Returns properties supported by the module. More...

void	dataStarted (AbstractAnalysisData *data) override
	Called (once) when the data has been set up properly. More...

void	frameStarted (const AnalysisDataFrameHeader &header) override
	Called at the start of each data frame. More...

void	pointsAdded (const AnalysisDataPointSetRef &points) override
	Called one or more times during each data frame. More...

void	frameFinished (const AnalysisDataFrameHeader &header) override
	Called when a data frame is finished. More...

void	dataFinished () override
	Called (once) when no more data is available. More...

Public Member Functions inherited from gmx::AbstractAnalysisData
bool	isMultipoint () const
	Whether the data can have multiple points in the same column in the same frame. More...

int	dataSetCount () const
	Returns the number of data sets in the data object. More...

int	columnCount (int dataSet) const
	Returns the number of columns in a data set. More...

int	columnCount () const
	Returns the number of columns in the data. More...

virtual int	frameCount () const =0
	Returns the total number of frames in the data. More...

AnalysisDataFrameRef	tryGetDataFrame (int index) const
	Access stored data. More...

AnalysisDataFrameRef	getDataFrame (int index) const
	Access stored data. More...

bool	requestStorage (int nframes)
	Request storage of frames. More...

void	addModule (const AnalysisDataModulePointer &module)
	Adds a module to process the data. More...

void	addColumnModule (int col, int span, const AnalysisDataModulePointer &module)
	Adds a module that processes only a subset of the columns. More...

void	applyModule (IAnalysisDataModule *module)
	Applies a module to process data that is ready. More...

Additional Inherited Members
Public Types inherited from gmx::IAnalysisDataModule
enum	Flag { efAllowMultipoint = 1 << 0, efOnlyMultipoint = 1 << 1, efAllowMulticolumn = 1 << 2, efAllowMissing = 1 << 3, efAllowMultipleDataSets = 1 << 4 }
	Possible flags for flags(). More...

Protected Member Functions inherited from gmx::AbstractAnalysisData
	AbstractAnalysisData ()
	Initializes a new analysis data object. More...

void	setDataSetCount (int dataSetCount)
	Sets the number of data sets. More...

void	setColumnCount (int dataSet, int columnCount)
	Sets the number of columns for a data set. More...

void	setMultipoint (bool bMultipoint)
	Sets whether the data has multiple points per column in a frame. More...

AnalysisDataModuleManager &	moduleManager ()
	Returns the module manager to use for calling notification methods.

const AnalysisDataModuleManager &	moduleManager () const
	Returns the module manager to use for calling notification methods.

Member Function Documentation

void gmx::AnalysisDataDisplacementModule::dataFinished ( )

overridevirtual

Called (once) when no more data is available.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataDisplacementModule::dataStarted ( AbstractAnalysisData * data )

overridevirtual

Called (once) when the data has been set up properly.

Parameters

[in] data Data object to which the module is added.

Exceptions

APIError	if the provided data is not compatible.
unspecified	Can throw any exception required by the implementing class to report errors.

When the data is ready, either this method or parallelDataStarted() is called, depending on the nature of the input data. If this method is called, the input data will always present the frames in sequential order.

The data to which the module is attached is passed as an argument to provide access to properties of the data for initialization and/or validation. The module can also call AbstractAnalysisData::requestStorage() if needed.

This is the only place where the module gets access to the data; if properties of the data are required later, the module should store them internally. It is guaranteed that the data properties (column count, whether it's multipoint) do not change once this method has been called.

Notice that data will be a proxy object if the module is added as a column module, not the data object for which AbstractAnalysisData::addColumnModule() was called.

Implements gmx::AnalysisDataModuleSerial.

int gmx::AnalysisDataDisplacementModule::flags ( ) const

overridevirtual

Returns properties supported by the module.

The return value of this method should not change after the module has been added to a data (this responsibility can, and in most cases must, be delegated to the user of the module).

The purpose of this method is to remove the need for common checks for data compatibility in the classes that implement the interface. Instead, AbstractAnalysisData performs these checks based on the flags provided.

Does not throw.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataDisplacementModule::frameFinished ( const AnalysisDataFrameHeader & header )

overridevirtual

Called when a data frame is finished.

Parameters

[in] header Header information for the frame that is ending.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataDisplacementModule::frameStarted ( const AnalysisDataFrameHeader & frame )

overridevirtual

Called at the start of each data frame.

Parameters

[in] frame Header information for the frame that is starting.

Exceptions

unspecified Can throw any exception required by the implementing class to report errors.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataDisplacementModule::pointsAdded ( const AnalysisDataPointSetRef & points )

overridevirtual

Called one or more times during each data frame.

Parameters

[in] points Set of points added (also provides access to frame-level data).

Exceptions

APIError	if the provided data is not compatible.
unspecified	Can throw any exception required by the implementing class to report errors.

Can be called once or multiple times for a frame. For all data objects currently implemented in the library (and all objects that will use AnalysisDataStorage for internal implementation), it is called exactly once for each frame if the data is not multipoint, but currently this restriction is not enforced.

Implements gmx::AnalysisDataModuleSerial.

void gmx::AnalysisDataDisplacementModule::setMSDHistogram ( const std::shared_ptr< AnalysisDataBinAverageModule > & histm )

Sets an histogram module that will receive a MSD histogram.

If this function is not called, no histogram is calculated.

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

api/legacy/include/gromacs/analysisdata/modules/displacement.h
src/gromacs/analysisdata/modules/displacement.cpp

Description

Classes

Public Member Functions

Additional Inherited Members

Member Function Documentation