Gromacs
2024.4
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Provides functionality for handling and processing output data from analysis.
This module provides functionality to do common processing for tabular data in analysis tools. In addition to providing this common functionality, one major driver for this module is to make it simple to write analysis tools that process frames in parallel: the functionality in this module takes care of necessary synchronization and communication such that output from the frames is collected and output in the correct order. See Analysis output data handling for an overview of the high-level functionality and the terminology used.
This module consists of two main parts. The first is formed by the gmx::AbstractAnalysisData class and classes that derive from it: gmx::AnalysisData and gmx::AnalysisArrayData. These classes are used to process and store raw data as produced by the analysis tool. They also provide an interface to attach data modules that implement gmx::IAnalysisDataModule.
Modules that implement gmx::IAnalysisDataModule form the second part of the module, and they provide functionality to do processing on the data. These modules can also derive from gmx::AbstractAnalysisData, allowing other modules to be attached to them to form a processing chain that best suits the analysis tool. Typically, such a processing chain ends in a plotting module that writes the data into a file, but the final module can also provide direct access to the processed data, allowing the analysis tool to do custom postprocessing outside the module framework.
To use the functionality in this module, you typically declare one or more AnalysisData objects and set its properties. You then create some module objects and set their properties (see the list of classes that implement gmx::IAnalysisDataModule) and attach them to the data objects or to one another using gmx::AbstractAnalysisData::addModule(). Then you add the actual data values to the gmx::AnalysisData object, which automatically passes it on to the modules. After all data is added, you may optionally access some results directly from the module objects or from the gmx::AnalysisData object itself. However, in many cases it is sufficient to initially add a plotting module to the processing chain, which will then automatically write the results into a file.
For simple processing needs with a small amount of data, an gmx::AnalysisArrayData class is also provided, which keeps all the data in an in-memory array and allows you to manipulate the data as you wish before you pass the data to the attached modules.
Modules that derive from gmx::IAnalysisDataModule can operate in two modes:
The figure below shows the sequence of callbacks that the module receives. Arrows show a dependency between callbacks: the event at the start of the arrow always occurs before the event at the end. The events in the box are repeated for each frame. Dashed lines within this box show dependencies between these frames:
If the input data supports parallel mode, it calls parallelDataStarted(). If the module returns true
from this method, then it will process the frames in the parallel mode. If the module returns false
, it will get the frames in serial order. If the input data does not support parallel mode, it calls dataStarted(), and the module will always get the frames in order.
The sequence of when the module methods are called with respect to when data is added to the data object depends on the type of the module and the type of the data. However, generally the modules do not need to know the details of how this happens, as long as they work with the above state diagram.
For parallel processing, the gmx::AnalysisData object itself only provides the infrastructure to support all of the above, including the reordering of the frames for serial processing. However, the caller is still responsible of the actual thread synchronization, and must call gmx::AnalysisData::finishFrameSerial() for each frame from a suitable context where the serial processing for that frame can be done. When using the data objects as part of the trajectory analysis framework (Framework for trajectory analysis) or energy analysis framework (Framework for energy analysis), these calls are handled by the framework.
New data modules can be implemented to perform custom operations that are not supported by the modules provided in this module. This is done by creating a new class that implements gmx::IAnalysisDataModule. If the new module computes values that can be used as input for other modules, the new class should also derive from gmx::AbstractAnalysisData, and preferably use gmx::AnalysisDataStorage internally to implement storage of values. See the documentation of the mentioned classes for more details on how to implement custom modules. When implementing a new module, it should be considered whether it can be of more general use, and if so, it should be added to this module.
It is also possible to implement new data source objects by deriving a class from gmx::AbstractAnalysisData. This should not normally be necessary, since this module provides general data source objects for most typical uses. If the classes in this module are not suitable for some specific use, it should be considered whether a new generic class could be added (or an existing extended) instead of implementing a local custom solution.
Classes | |
class | gmx::AnalysisDataModuleManager |
Encapsulates handling of data modules attached to AbstractAnalysisData. More... | |
class | gmx::AnalysisDataStorageFrame |
Allows assigning values for a data frame in AnalysisDataStorage. More... | |
class | gmx::AnalysisDataStorage |
Helper class that implements storage of data. More... | |
class | gmx::AnalysisDataParallelOptions |
Parallelization options for analysis data objects. More... | |
class | gmx::test::AnalysisDataTestInputPointSet |
Represents a single set of points in AnalysisDataTestInputFrame structure. More... | |
class | gmx::test::AnalysisDataTestInputFrame |
Represents a single frame in AnalysisDataTestInput structure. More... | |
class | gmx::test::AnalysisDataTestInput |
Represents static input data for AbstractAnalysisData tests. More... | |
class | gmx::test::AnalysisDataTestFixture |
Test fixture for AbstractAnalysisData testing. More... | |
class | gmx::AbstractAnalysisData |
Abstract base class for all objects that provide data. More... | |
class | gmx::AnalysisData |
Parallelizable data container for raw data. More... | |
class | gmx::AnalysisDataHandle |
Handle for inserting data into AnalysisData. More... | |
class | gmx::AbstractAnalysisArrayData |
Abstract base class for data objects that present in-memory data. More... | |
class | gmx::AnalysisArrayData |
Simple in-memory data array. More... | |
class | gmx::AnalysisDataValue |
Value type for representing a single value in analysis data objects. More... | |
class | gmx::AnalysisDataFrameHeader |
Value type for storing frame-level information for analysis data. More... | |
class | gmx::AnalysisDataPointSetRef |
Value type wrapper for non-mutable access to a set of data column values. More... | |
class | gmx::AnalysisDataFrameRef |
Value type wrapper for non-mutable access to a data frame. More... | |
class | gmx::IAnalysisDataModule |
Interface for a module that gets notified whenever data is added. More... | |
class | gmx::AnalysisDataModuleSerial |
Convenience base class for serial analysis data modules. More... | |
class | gmx::AnalysisDataModuleParallel |
Convenience base class for parallel analysis data modules. More... | |
class | gmx::AnalysisDataAverageModule |
Data module for independently averaging each column in input data. More... | |
class | gmx::AnalysisDataFrameAverageModule |
Data module for averaging of columns for each frame. More... | |
class | gmx::AnalysisDataDisplacementModule |
Data module for calculating displacements. More... | |
class | gmx::AnalysisHistogramSettingsInitializer |
Provides "named parameter" idiom for constructing histograms. More... | |
class | gmx::AnalysisHistogramSettings |
Contains parameters that specify histogram bin locations. More... | |
class | gmx::AbstractAverageHistogram |
Base class for representing histograms averaged over frames. More... | |
class | gmx::AnalysisDataSimpleHistogramModule |
Data module for per-frame histograms. More... | |
class | gmx::AnalysisDataWeightedHistogramModule |
Data module for per-frame weighted histograms. More... | |
class | gmx::AnalysisDataBinAverageModule |
Data module for bin averages. More... | |
class | gmx::AnalysisDataLifetimeModule |
Data module for computing lifetime histograms for columns in input data. More... | |
class | gmx::AnalysisDataPlotSettings |
Common settings for data plots. More... | |
class | gmx::AbstractPlotModule |
Abstract data module for writing data into a file. More... | |
class | gmx::AnalysisDataPlotModule |
Plotting module for straightforward plotting of data. More... | |
class | gmx::AnalysisDataVectorPlotModule |
Plotting module specifically for data consisting of vectors. More... | |
Directories | |
directory | analysisdata |
Parallelizable Handling of Output Data (analysisdata) | |
directory | tests |
Unit tests for Parallelizable Handling of Output Data (analysisdata). | |