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 #include "gromacs/utility/stringutil.h"
  55
  56 #include "testutils/testasserts.h"
  57
  58 namespace gmx
  59 {
  60 namespace test
  61 {
  62
  63 //! Helper function to obtain resources
  64 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 ===
  86
  87 TrajectoryFrameReader::TrajectoryFrameReader(const std::string &filename)
  88     : filename_(filename),
  89       trajectoryFileGuard_(nullptr),
  90       trxframeGuard_(make_trxframe()),
  91       haveReadFirstFrame_(false),
  92       haveProbedForNextFrame_(false),
  93       nextFrameExists_(false)
  94 {
  95     gmx_output_env_t *oenv;
  96     output_env_init_default(&oenv);
  97     oenvGuard_.reset(oenv);
  98 }
  99
 100 bool
 101 TrajectoryFrameReader::readNextFrame()
 102 {
 103     if (haveProbedForNextFrame_)
 104     {
 105         if (nextFrameExists_)
 106         {
 107             GMX_THROW(APIError("This frame has already been probed for, it should be used before probing again."));
 108         }
 109         else
 110         {
 111             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."));
 112         }
 113     }
 114     haveProbedForNextFrame_ = true;
 115     // If there's a next frame, read it into trxframe_, and report the result.
 116     if (!haveReadFirstFrame_)
 117     {
 118         t_trxstatus *trajectoryFile;
 119         int          flags = TRX_READ_X | TRX_READ_V | TRX_READ_F;
 120         nextFrameExists_ = read_first_frame(oenvGuard_.get(),
 121                                             &trajectoryFile,
 122                                             filename_.c_str(),
 123                                             trxframeGuard_.get(),
 124                                             flags);
 125         if (!trajectoryFile)
 126         {
 127             GMX_THROW(FileIOError("Could not open trajectory file " + filename_ + " for reading"));
 128         }
 129         trajectoryFileGuard_.reset(trajectoryFile);
 130         haveReadFirstFrame_ = true;
 131     }
 132     else
 133     {
 134         nextFrameExists_ = read_next_frame(oenvGuard_.get(),
 135                                            trajectoryFileGuard_.get(),
 136                                            trxframeGuard_.get());
 137     }
 138     return nextFrameExists_;
 139 }
 140
 141 TrajectoryFrame
 142 TrajectoryFrameReader::frame()
 143 {
 144     TrajectoryFrame frame;
 145
 146     if (!haveProbedForNextFrame_)
 147     {
 148         readNextFrame();
 149     }
 150     if (!nextFrameExists_)
 151     {
 152         GMX_THROW(APIError("There is no next frame, so there should have been no attempt to use the data, e.g. by reacting to a call to readNextFrame()."));
 153     }
 154
 155     // Prepare for reading future frames
 156     haveProbedForNextFrame_ = false;
 157     nextFrameExists_        = false;
 158
 159     // The probe filled trxframeGuard_ with new data, so return it
 160     frame.frame_ = trxframeGuard_.get();
 161
 162     if (!frame.frame_->bStep)
 163     {
 164         GMX_THROW(APIError("Cannot handle trajectory frame that lacks a step number"));
 165     }
 166
 167     if (!frame.frame_->bTime)
 168     {
 169         GMX_THROW(APIError("Cannot handle trajectory frame that lacks a time"));
 170     }
 171
 172     return frame;
 173 }
 174
 175 // === TrajectoryFrame ===
 176
 177 TrajectoryFrame::TrajectoryFrame() : frame_(nullptr) {};
 178
 179 std::string TrajectoryFrame::getFrameName() const
 180 {
 181     GMX_RELEASE_ASSERT(frame_, "Cannot get name of invalid frame");
 182     return formatString("Time %f Step %" GMX_PRId64, frame_->time, frame_->step);
 183 }
 184
 185 void compareFrames(const std::pair<TrajectoryFrame, TrajectoryFrame> &frames,
 186                    FloatingPointTolerance tolerance)
 187 {
 188     auto &reference = frames.first;
 189     auto &test      = frames.second;
 190
 191     // NB We checked earlier for both frames that bStep and bTime are set
 192
 193     EXPECT_EQ(reference.frame_->step, test.frame_->step)
 194     << "step didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
 195
 196     EXPECT_EQ(reference.frame_->time, test.frame_->time)
 197     << "time didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
 198
 199     for (int i = 0; i < reference.frame_->natoms && i < test.frame_->natoms; ++i)
 200     {
 201         for (int d = 0; d < DIM; ++d)
 202         {
 203             if (reference.frame_->bX && test.frame_->bX)
 204             {
 205                 EXPECT_REAL_EQ_TOL(reference.frame_->x[i][d], test.frame_->x[i][d], tolerance)
 206                 << " x[" << i << "][" << d <<"] didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
 207             }
 208             if (reference.frame_->bV && test.frame_->bV)
 209             {
 210                 EXPECT_REAL_EQ_TOL(reference.frame_->v[i][d], test.frame_->v[i][d], tolerance)
 211                 << " v[" << i << "][" << d <<"] didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
 212             }
 213             if (reference.frame_->bF && test.frame_->bF)
 214             {
 215                 EXPECT_REAL_EQ_TOL(reference.frame_->f[i][d], test.frame_->f[i][d], tolerance)
 216                 << " f[" << i << "][" << d <<"] didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
 217             }
 218         }
 219     }
 220 }
 221
 222 } // namespace
 223 } // namespace