src/programs/mdrun/tests/trajectoryreader.cpp

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  35
  36 /*! \internal \file
  37  * \brief Implementions of related classes for tests that want to
  38  * inspect trajectories produced by mdrun.
  39  *
  40  * \author Mark Abraham <mark.j.abraham@gmail.com>
  41  * \ingroup module_mdrun_integration_tests
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "trajectoryreader.h"
  46
  47 #include <memory>
  48 #include <string>
  49
  50 #include "gromacs/fileio/oenv.h"
  51 #include "gromacs/fileio/trxio.h"
  52 #include "gromacs/trajectory/trajectoryframe.h"
  53 #include "gromacs/utility/exceptions.h"
  54
  55 #include "testutils/testasserts.h"
  56 #include "testutils/testmatchers.h"
  57
  58 namespace gmx
  59 {
  60 namespace test
  61 {
  62
  63 //! Helper function to obtain resources
  64 static t_trxframe *make_trxframe()
  65 {
  66     t_trxframe *frame;
  67
  68     snew(frame, 1);
  69     clear_trxframe(frame, true);
  70
  71     return frame;
  72 }
  73
  74 //! Helper function to clean up resources
  75 void done_trxframe(t_trxframe *fr)
  76 {
  77     // Free the contents, then the pointer itself
  78     sfree(fr->x);
  79     sfree(fr->v);
  80     sfree(fr->f);
  81     sfree(fr->index);
  82     sfree(fr);
  83 }
  84
  85 TrajectoryFrameReader::TrajectoryFrameReader(const std::string &filename)
  86     : filename_(filename),
  87       trajectoryFileGuard_(nullptr),
  88       trxframeGuard_(make_trxframe()),
  89       haveReadFirstFrame_(false),
  90       haveProbedForNextFrame_(false),
  91       nextFrameExists_(false)
  92 {
  93     gmx_output_env_t *oenv;
  94     output_env_init_default(&oenv);
  95     oenvGuard_.reset(oenv);
  96 }
  97
  98 bool
  99 TrajectoryFrameReader::readNextFrame()
 100 {
 101     if (haveProbedForNextFrame_)
 102     {
 103         if (nextFrameExists_)
 104         {
 105             GMX_THROW(APIError("This frame has already been probed for, it should be used before probing again."));
 106         }
 107         else
 108         {
 109             GMX_THROW(APIError("This frame has already been probed for, it doesn't exist, so there should not be subsequent attempts to probe for it."));
 110         }
 111     }
 112     haveProbedForNextFrame_ = true;
 113     // If there's a next frame, read it into trxframe_, and report the result.
 114     if (!haveReadFirstFrame_)
 115     {
 116         t_trxstatus *trajectoryFile;
 117         int          flags = TRX_READ_X | TRX_READ_V | TRX_READ_F;
 118         nextFrameExists_ = read_first_frame(oenvGuard_.get(),
 119                                             &trajectoryFile,
 120                                             filename_.c_str(),
 121                                             trxframeGuard_.get(),
 122                                             flags);
 123         if (!trajectoryFile)
 124         {
 125             GMX_THROW(FileIOError("Could not open trajectory file " + filename_ + " for reading"));
 126         }
 127         trajectoryFileGuard_.reset(trajectoryFile);
 128         haveReadFirstFrame_ = true;
 129     }
 130     else
 131     {
 132         nextFrameExists_ = read_next_frame(oenvGuard_.get(),
 133                                            trajectoryFileGuard_.get(),
 134                                            trxframeGuard_.get());
 135     }
 136     return nextFrameExists_;
 137 }
 138
 139 TrajectoryFrame
 140 TrajectoryFrameReader::frame()
 141 {
 142     if (!haveProbedForNextFrame_)
 143     {
 144         readNextFrame();
 145     }
 146     if (!nextFrameExists_)
 147     {
 148         GMX_THROW(APIError("There is no next frame, so there should have been no attempt to get it. Perhaps the return value of readNextFrame() was misused."));
 149     }
 150
 151     // Prepare for reading future frames
 152     haveProbedForNextFrame_ = false;
 153     nextFrameExists_        = false;
 154
 155     // The probe filled trxframeGuard_ with new data, so return it
 156     return TrajectoryFrame(*trxframeGuard_.get());
 157 }
 158
 159 }  // namespace test
 160 }  // namespace gmx