src/gromacs/coordinateio/coordinatefile.h

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  35 /*! \file
  36  * \brief
  37  * CoordinateFile takes care of opening files and writing output to them.
  38  *
  39  * \author
  40  * \inpublicapi
  41  * \ingroup module_coordinateio
  42  */
  43 #ifndef GMX_COORDINATEIO_COORDINATEFILE_H
  44 #define GMX_COORDINATEIO_COORDINATEFILE_H
  45
  46 #include <string>
  47 #include <utility>
  48
  49 #include "gromacs/coordinateio/ioutputadapter.h"
  50 #include "gromacs/coordinateio/outputadaptercontainer.h"
  51 #include "gromacs/math/vectypes.h"
  52 #include "gromacs/topology/atoms.h"
  53
  54 struct gmx_mtop_t;
  55 struct t_trxstatus;
  56
  57 namespace gmx
  58 {
  59
  60 class Selection;
  61 class TrajectoryFrameWriter;
  62 struct OutputRequirements;
  63
  64 /*! \brief
  65  * Factory function for TrajectoryFrameWriter.
  66  *
  67  * Used to initialize a new instance of TrajectoryFrameWriter with the user supplied information
  68  * for writing trajectory data to disk. Information needed is the file type, file name
  69  * corresponding to the type, if available topology information and selection information.
  70  *
  71  * If supplied, the modules contained within \p adapters are registered on
  72  * the TrajectoryFrameWriter if possible.
  73  *
  74  * The factory function is responsible for the initial santity checks concerning file types and
  75  * availability of topology information, with the registration of modules being the second part.
  76  *
  77  * \param[in] top                    Pointer to full topology or null.
  78  * \param[in] sel                    Reference to global selection used to construct the object.
  79  * \param[in] filename               Name of new output file, used to deduce file type.
  80  * \param[in] atoms                  Smart Pointer to atoms data or null.
  81  * \param[in] requirements           Container for settings obtained to specify which
  82  *                                   OutputAdapters should be registered.
  83  * \throws    InconsistentInputError When user input and requirements don't match.
  84  */
  85 std::unique_ptr<TrajectoryFrameWriter> createTrajectoryFrameWriter(const gmx_mtop_t*  top,
  86                                                                    const Selection&   sel,
  87                                                                    const std::string& filename,
  88                                                                    AtomsDataPtr       atoms,
  89                                                                    OutputRequirements requirements);
  90
  91 /*!\brief
  92  * Low level method to take care of only file opening and closing.
  93  *
  94  * \inpublicapi
  95  * \ingroup module_coordinateio
  96  *
  97  */
  98 class TrajectoryFileOpener
  99 {
 100 public:
 101     /*! \brief
 102      * Constructor, taking all arguments needed to open valid coordinate files of any type.
 103      *
 104      * \param[in] name Name of the file to create.
 105      * \param[in] filetype Internal filetype to know which kind we are going to have.
 106      * \param[in] sel Reference to selection of atoms to write. Needs to be valid for
 107      *                longer than the lifetime of the object created here.
 108      * \param[in] mtop Topology used to create TNG output. Needs to be valid for longer
 109      *                 than the object created here.
 110      */
 111     TrajectoryFileOpener(const std::string& name, int filetype, const Selection& sel, const gmx_mtop_t* mtop) :
 112         outputFileName_(name),
 113         outputFile_(nullptr),
 114         filetype_(filetype),
 115         sel_(sel),
 116         mtop_(mtop)
 117     {
 118     }
 119
 120     /*! \brief
 121      * Closes new trajectory file after finishing the writing to it.
 122      */
 123     ~TrajectoryFileOpener();
 124
 125     /*! \brief
 126      * Get access to initialized output file object.
 127      *
 128      * Performs lazy initialization if needed.
 129      */
 130     t_trxstatus* outputFile();
 131
 132 private:
 133     //! Name for the new coordinate file.
 134     std::string outputFileName_;
 135
 136     //! File pointer to the coordinate file being written.
 137     t_trxstatus* outputFile_;
 138
 139     //! Storage of file type for determing what kind of file will be written to disk.
 140     int filetype_;
 141
 142     /*! \brief
 143      * Selection of atoms to write out.
 144      *
 145      * Currently, CoordinateFile expects that the lifetime of the selection is longer
 146      * than that of itself, and that the selection remains unchanged during this lifetime.
 147      * A better approach will be to pass the selection to it and expect it to
 148      * manage the lifetime instead.
 149      */
 150     const Selection& sel_;
 151
 152     //! Pointer to topology information if available.
 153     const gmx_mtop_t* mtop_;
 154 };
 155
 156 /*!\brief
 157  * Writes coordinate frames to a sink, e.g. a trajectory file.
 158  *
 159  * Writes all frames passed to the trajectory file handle it
 160  * manages. It can use IOutputAdapter modules to transform the
 161  * frame data before writing. If any transform modules are used,
 162  * makes a deep copy of the frame contents.
 163  *
 164  * \inpublicapi
 165  * \ingroup module_coordinateio
 166  *
 167  */
 168 class TrajectoryFrameWriter
 169 {
 170 public:
 171     friend std::unique_ptr<TrajectoryFrameWriter> createTrajectoryFrameWriter(const gmx_mtop_t* top,
 172                                                                               const Selection&  sel,
 173                                                                               const std::string& filename,
 174                                                                               AtomsDataPtr atoms,
 175                                                                               OutputRequirements requirements);
 176
 177     /*! \brief
 178      * Writes the input frame, after applying any IOutputAdapters.
 179      *
 180      * \param[in] framenumber Number of frame being currently processed.
 181      * \param[in] input View of the constant t_trxframe object provided by the
 182      *                  method that calls the output manager.
 183      */
 184     void prepareAndWriteFrame(int framenumber, const t_trxframe& input);
 185
 186 private:
 187     /*! \brief
 188      * Creates fully initialized object.
 189      *
 190      * \param[in] name Name of the file to create.
 191      * \param[in] filetype Internal filetype to know which kind we are going to have.
 192      * \param[in] sel Reference to selection of atoms to write. Needs to be valid for
 193      *                longer than the lifetime of the object created here.
 194      * \param[in] mtop Topology used to create TNG output. Needs to be valid for longer
 195      *                 than the object created here.
 196      * \param[in] adapters Container of methods that can modify the information written
 197      *                     to the new file.
 198      */
 199     TrajectoryFrameWriter(const std::string&     name,
 200                           int                    filetype,
 201                           const Selection&       sel,
 202                           const gmx_mtop_t*      mtop,
 203                           OutputAdapterContainer adapters) :
 204         file_(name, filetype, sel, mtop),
 205         outputAdapters_(std::move(adapters))
 206     {
 207     }
 208
 209     //! Underlying object for open/writing to file.
 210     TrajectoryFileOpener file_;
 211
 212     //! Storage for list of output adapters.
 213     OutputAdapterContainer outputAdapters_;
 214
 215     //! Local storage for modified positions.
 216     std::vector<RVec> localX_;
 217     //! Local storage for modified velocities.
 218     std::vector<RVec> localV_;
 219     //! Local storage for modified forces.
 220     std::vector<RVec> localF_;
 221     //! Local storage for modified indices.
 222     std::vector<int> localIndex_;
 223 };
 224
 225 //! Smart pointer to manage the TrajectoryFrameWriter object.
 226 using TrajectoryFrameWriterPointer = std::unique_ptr<TrajectoryFrameWriter>;
 227
 228 } // namespace gmx
 229
 230 #endif