src/programs/mdrun/tests/energyreader.cpp

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  35
  36 /*! \internal \file
  37  * \brief Implementions of related classes for tests that want to
  38  * inspect energies 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 "energyreader.h"
  46
  47 #include <algorithm>
  48 #include <map>
  49 #include <memory>
  50 #include <string>
  51 #include <vector>
  52
  53 #include "gromacs/fileio/enxio.h"
  54 #include "gromacs/trajectory/energyframe.h"
  55 #include "gromacs/utility/exceptions.h"
  56 #include "gromacs/utility/stringutil.h"
  57
  58 #include "testutils/testasserts.h"
  59
  60 namespace gmx
  61 {
  62 namespace test
  63 {
  64
  65 EnergyFrameReaderPtr openEnergyFileToReadTerms(const std::string&              filename,
  66                                                const std::vector<std::string>& namesOfRequiredEnergyTerms)
  67 {
  68     ener_file_ptr energyFile(open_enx(filename.c_str(), "r"));
  69
  70     if (!energyFile)
  71     {
  72         GMX_THROW(FileIOError("Could not open energy file " + filename + " for reading"));
  73     }
  74
  75     /* Read in the names of energy terms used in this file. The
  76      * resulting data structure would leak if an exception was thrown,
  77      * so transfer the contents that we actually need to a map we can
  78      * keep.
  79      *
  80      * TODO Technically, the insertions into the map could throw
  81      * std::bad_alloc and we could leak memory allocated by
  82      * do_enxnms(), but there's nothing we can do about this right
  83      * now. */
  84     std::map<std::string, int> indicesOfEnergyTerms;
  85     {
  86         int          numEnergyTerms;
  87         gmx_enxnm_t* energyNames = nullptr;
  88         do_enxnms(energyFile.get(), &numEnergyTerms, &energyNames);
  89         for (int i = 0; i != numEnergyTerms; ++i)
  90         {
  91             const char* name           = energyNames[i].name;
  92             auto        requiredEnergy = std::find_if(std::begin(namesOfRequiredEnergyTerms),
  93                                                std::end(namesOfRequiredEnergyTerms),
  94                                                [name](const std::string& n) { return name == n; });
  95             if (requiredEnergy != namesOfRequiredEnergyTerms.end())
  96             {
  97                 indicesOfEnergyTerms[name] = i;
  98             }
  99         }
 100         // Clean up old data structures
 101         free_enxnms(numEnergyTerms, energyNames);
 102     }
 103
 104     // Throw if we failed to find the terms we need
 105     if (indicesOfEnergyTerms.size() != namesOfRequiredEnergyTerms.size())
 106     {
 107         std::string requiredEnergiesNotFound =
 108                 "Did not find the following required energies in mdrun output:\n";
 109         for (auto& name : namesOfRequiredEnergyTerms)
 110         {
 111             auto possibleIndex = indicesOfEnergyTerms.find(name);
 112             if (possibleIndex == indicesOfEnergyTerms.end())
 113             {
 114                 requiredEnergiesNotFound += name + "\n";
 115             }
 116         }
 117         GMX_THROW(APIError(requiredEnergiesNotFound));
 118     }
 119
 120     return EnergyFrameReaderPtr(
 121             std::make_unique<EnergyFrameReader>(indicesOfEnergyTerms, energyFile.release()));
 122 }
 123
 124 //! Helper function to obtain resources
 125 static t_enxframe* make_enxframe()
 126 {
 127     t_enxframe* frame;
 128
 129     snew(frame, 1);
 130     init_enxframe(frame);
 131
 132     return frame;
 133 }
 134
 135 //! Helper function to clean up resources
 136 void done_enxframe(t_enxframe* fr)
 137 {
 138     // Free the contents, then the pointer itself
 139     free_enxframe(fr);
 140     sfree(fr);
 141 }
 142
 143 // === EnergyFrameReader ===
 144
 145 EnergyFrameReader::EnergyFrameReader(const std::map<std::string, int>& indicesOfEnergyTerms,
 146                                      ener_file*                        energyFile) :
 147     indicesOfEnergyTerms_(indicesOfEnergyTerms),
 148     energyFileGuard_(energyFile),
 149     enxframeGuard_(make_enxframe()),
 150     haveProbedForNextFrame_(false),
 151     nextFrameExists_(false)
 152 {
 153 }
 154
 155 bool EnergyFrameReader::readNextFrame()
 156 {
 157     if (haveProbedForNextFrame_)
 158     {
 159         if (nextFrameExists_)
 160         {
 161             GMX_THROW(
 162                     APIError("This frame has already been probed for, it should be used before "
 163                              "probing again."));
 164         }
 165         else
 166         {
 167             GMX_THROW(
 168                     APIError("This frame has already been probed for, it doesn't exist, so there "
 169                              "should not be subsequent attempts to probe for it."));
 170         }
 171     }
 172     haveProbedForNextFrame_ = true;
 173     // If there's a next frame, read it into enxframe_, and report the result.
 174     return nextFrameExists_ = do_enx(energyFileGuard_.get(), enxframeGuard_.get());
 175 }
 176
 177 EnergyFrame EnergyFrameReader::frame()
 178 {
 179     if (!haveProbedForNextFrame_)
 180     {
 181         readNextFrame();
 182     }
 183     if (!nextFrameExists_)
 184     {
 185         GMX_THROW(
 186                 APIError("There is no next frame, so there should have been no attempt to use the "
 187                          "data, e.g. by reacting to a call to readNextFrame()."));
 188     }
 189
 190     // Prepare for reading future frames
 191     haveProbedForNextFrame_ = false;
 192     nextFrameExists_        = false;
 193
 194     // The probe filled enxframe_ with new data, so now we use that data to fill energyFrame
 195     return EnergyFrame(*enxframeGuard_.get(), indicesOfEnergyTerms_);
 196 }
 197
 198 } // namespace test
 199 } // namespace gmx