src/gromacs/analysisdata/modules/displacement.h

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  35 /*! \file
  36  * \brief
  37  * Declares gmx::AnalysisDataDisplacementModule.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \inpublicapi
  41  * \ingroup module_analysisdata
  42  */
  43 #ifndef GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
  44 #define GMX_ANALYSISDATA_MODULES_DISPLACEMENT_H
  45
  46 #include "gromacs/analysisdata/abstractdata.h"
  47 #include "gromacs/analysisdata/datamodule.h"
  48 #include "gromacs/utility/real.h"
  49
  50 namespace gmx
  51 {
  52
  53 class AnalysisDataBinAverageModule;
  54
  55 /*! \brief
  56  * Data module for calculating displacements.
  57  *
  58  * Output data contains a frame for each frame in the input data except the
  59  * first one.  For each frame, there can be multiple points, each of which
  60  * describes displacement for a certain time difference ending that that frame.
  61  * The first column contains the time difference (backwards from the current
  62  * frame), and the remaining columns the sizes of the displacements.
  63  *
  64  * Current implementation is not very generic, but should be easy to extend.
  65  *
  66  * \inpublicapi
  67  * \ingroup module_analysisdata
  68  */
  69 class AnalysisDataDisplacementModule : public AbstractAnalysisData,
  70                                        public AnalysisDataModuleSerial
  71 {
  72     public:
  73         AnalysisDataDisplacementModule();
  74         ~AnalysisDataDisplacementModule() override;
  75
  76         /*! \brief
  77          * Sets the largest displacement time to be calculated.
  78          */
  79         void setMaxTime(real tmax);
  80         /*! \brief
  81          * Sets an histogram module that will receive a MSD histogram.
  82          *
  83          * If this function is not called, no histogram is calculated.
  84          */
  85         void setMSDHistogram(const std::shared_ptr<AnalysisDataBinAverageModule> &histm);
  86
  87         int flags() const override;
  88
  89         void dataStarted(AbstractAnalysisData *data) override;
  90         void frameStarted(const AnalysisDataFrameHeader &header) override;
  91         void pointsAdded(const AnalysisDataPointSetRef &points) override;
  92         void frameFinished(const AnalysisDataFrameHeader &header) override;
  93         void dataFinished() override;
  94
  95     private:
  96         AnalysisDataFrameRef tryGetDataFrameInternal(int index) const override;
  97         bool requestStorageInternal(int nframes) override;
  98
  99         class Impl;
 100
 101         PrivateImplPointer<Impl> _impl;
 102 };
 103
 104 //! Smart pointer to manage an AnalysisDataDisplacementModule object.
 105 typedef std::shared_ptr<AnalysisDataDisplacementModule>
 106     AnalysisDataDisplacementModulePointer;
 107
 108 } // namespace gmx
 109
 110 #endif