src/gromacs/coordinateio/outputadapters/outputselector.h

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  35 /*! \file
  36  * \brief
  37  * Declares gmx::OutputSelector.
  38  *
  39  * \author Paul Bauer <paul.bauer.q@gmail.com>
  40  * \inpublicapi
  41  * \ingroup module_coordinateio
  42  */
  43 #ifndef GMX_COORDINATEIO_OUTPUTSELECTOR_H
  44 #define GMX_COORDINATEIO_OUTPUTSELECTOR_H
  45
  46 #include <algorithm>
  47
  48 #include "gromacs/coordinateio/ioutputadapter.h"
  49 #include "gromacs/selection/selectionoption.h"
  50 #include "gromacs/topology/atoms.h"
  51
  52 namespace gmx
  53 {
  54
  55 /*!\brief
  56  * OutputSelector class controls setting which coordinates are actually written.
  57  *
  58  * This adapter selects a subset of the particles and their data for output.
  59  * The subset is specified via a selection object (see \ref module_selection).
  60  * The corresponding particle data (coordinates, velocities, forces) and
  61  * topology information is copied from as available from the input data.
  62  *
  63  * \inpublicapi
  64  * \ingroup module_coordinateio
  65  *
  66  */
  67 class OutputSelector : public IOutputAdapter
  68 {
  69     public:
  70         /*! \brief
  71          * Construct OutputSelector object with initial selection.
  72          *
  73          * Can be used to initialize OutputSelector from outside of trajectoryanalysis
  74          * framework.
  75          */
  76         explicit OutputSelector(const Selection &sel) :
  77             sel_(sel), selectionAtoms_(nullptr)
  78         {
  79             GMX_RELEASE_ASSERT(sel.isValid() && sel.hasOnlyAtoms(),
  80                                "Need a valid selection out of simple atom indices");
  81         }
  82         /*! \brief
  83          *  Move assignment constructor for OutputSelector.
  84          */
  85         OutputSelector(OutputSelector &&old) noexcept = default;
  86
  87         ~OutputSelector() override {}
  88
  89         /*! \brief
  90          * Change coordinate frame information for output.
  91          *
  92          * Takes the previously internally stored coordinates and saves them again.
  93          * Applies correct number of atoms in this case.
  94          *
  95          * \param[in] input Coordinate frame to be modified later.
  96          */
  97         void processFrame(int /*framenumber*/, t_trxframe *input) override;
  98
  99         void checkAbilityDependencies(unsigned long /* abilities */) const override {}
 100
 101     private:
 102
 103         /*! \brief
 104          * Selection of atoms that will be written to disk.
 105          *
 106          * Internal selection of atoms chosen by the user that will be written
 107          * to disk during processing.
 108          */
 109         const Selection                            &sel_;
 110         /*! \brief
 111          * Local storage of modified atoms.
 112          *
 113          * When selection input information, we might will have to adjust the
 114          * atoms content to match the new output. To perform this, we keep track
 115          * of modified atoms information in this object that is not used by default.
 116          */
 117         AtomsDataPtr      selectionAtoms_;
 118         //! Local storage for coordinates
 119         std::vector<RVec> localX_;
 120         //! Local storage for velocities
 121         std::vector<RVec> localV_;
 122         //! Local storage for forces
 123         std::vector<RVec> localF_;
 124         //! Local storage for atom indices
 125         std::vector<int>  localIndex_;
 126 };
 127
 128 //! Smart pointer to manage the object.
 129 using OutputSelectorPointer = std::unique_ptr<OutputSelector>;
 130
 131 } // namespace gmx
 132
 133 #endif