src/programs/mdrun/tests/energyreader.cpp

   1 /*
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   4  * Copyright (c) 2016, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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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/utility/exceptions.h"
  55 #include "gromacs/utility/scoped_cptr.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
  66 openEnergyFileToReadFields(const std::string              &filename,
  67                            const std::vector<std::string> &namesOfRequiredEnergyFields)
  68 {
  69     ener_file_ptr energyFile(open_enx(filename.c_str(), "r"));
  70
  71     if (!energyFile)
  72     {
  73         GMX_THROW(FileIOError("Could not open energy file " + filename + " for reading"));
  74     }
  75
  76     /* Read in the names of energy fields used in this file. The
  77      * resulting data structure would leak if an exception was thrown,
  78      * so transfer the contents that we actually need to a map we can
  79      * keep.
  80      *
  81      * TODO Technically, the insertions into the map could throw
  82      * std::bad_alloc and we could leak memory allocated by
  83      * do_enxnms(), but there's nothing we can do about this right
  84      * now. */
  85     std::map<std::string, int> indicesOfEnergyFields;
  86     {
  87         int          numEnergyTerms;
  88         gmx_enxnm_t *energyNames = nullptr;
  89         do_enxnms(energyFile.get(), &numEnergyTerms, &energyNames);
  90         for (int i = 0; i != numEnergyTerms; ++i)
  91         {
  92             const char *name           = energyNames[i].name;
  93             auto        requiredEnergy = std::find_if(std::begin(namesOfRequiredEnergyFields),
  94                                                       std::end(namesOfRequiredEnergyFields),
  95                                                       [name](const std::string &n){
  96                                                           return 0 == n.compare(name);
  97                                                       });
  98             if (requiredEnergy != namesOfRequiredEnergyFields.end())
  99             {
 100                 indicesOfEnergyFields[name] = i;
 101             }
 102         }
 103         // Clean up old data structures
 104         free_enxnms(numEnergyTerms, energyNames);
 105     }
 106
 107     // Throw if we failed to find the fields we need
 108     if (indicesOfEnergyFields.size() != namesOfRequiredEnergyFields.size())
 109     {
 110         std::string requiredEnergiesNotFound = "Did not find the following required energies in mdrun output:\n";
 111         for (auto &name : namesOfRequiredEnergyFields)
 112         {
 113             auto possibleIndex = indicesOfEnergyFields.find(name);
 114             if (possibleIndex == indicesOfEnergyFields.end())
 115             {
 116                 requiredEnergiesNotFound += name + "\n";
 117             }
 118         }
 119         GMX_THROW(APIError(requiredEnergiesNotFound));
 120     }
 121
 122     return EnergyFrameReaderPtr(new EnergyFrameReader(indicesOfEnergyFields, energyFile.release()));
 123 }
 124
 125 //! Helper function to obtain resources
 126 t_enxframe *make_enxframe()
 127 {
 128     t_enxframe *frame;
 129
 130     snew(frame, 1);
 131     init_enxframe(frame);
 132
 133     return frame;
 134 }
 135
 136 //! Helper function to clean up resources
 137 void done_enxframe(t_enxframe *fr)
 138 {
 139     // Free the contents, then the pointer itself
 140     free_enxframe(fr);
 141     sfree(fr);
 142 }
 143
 144 // === EnergyFrameReader ===
 145
 146 EnergyFrameReader::EnergyFrameReader(const std::map<std::string, int> &indicesOfEnergyFields,
 147                                      ener_file *energyFile)
 148     : indicesOfEnergyFields_(indicesOfEnergyFields),
 149       energyFileGuard_(energyFile),
 150       enxframeGuard_(make_enxframe()),
 151       haveProbedForNextFrame_(false),
 152       nextFrameExists_(false)
 153 {
 154 }
 155
 156 bool
 157 EnergyFrameReader::readNextFrame()
 158 {
 159     if (haveProbedForNextFrame_)
 160     {
 161         if (nextFrameExists_)
 162         {
 163             GMX_THROW(APIError("This frame has already been probed for, it should be used before probing again."));
 164         }
 165         else
 166         {
 167             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."));
 168         }
 169     }
 170     haveProbedForNextFrame_ = true;
 171     // If there's a next frame, read it into enxframe_, and report the result.
 172     return nextFrameExists_ = do_enx(energyFileGuard_.get(), enxframeGuard_.get());
 173 }
 174
 175 EnergyFrame
 176 EnergyFrameReader::frame()
 177 {
 178     EnergyFrame energyFrame;
 179
 180     if (!haveProbedForNextFrame_)
 181     {
 182         readNextFrame();
 183     }
 184     if (!nextFrameExists_)
 185     {
 186         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()."));
 187     }
 188
 189     // The probe filled enxframe_ with new data, so now we use that data to fill energyFrame
 190     t_enxframe *enxframe = enxframeGuard_.get();
 191     energyFrame.time_ = enxframe->t;
 192     energyFrame.step_ = enxframe->step;
 193     for (auto &index : indicesOfEnergyFields_)
 194     {
 195         if (index.second >= enxframe->nre)
 196         {
 197             GMX_THROW(InternalError(formatString("Index %d for energy %s not present in energy frame with %d energies",
 198                                                  index.second, index.first.c_str(), enxframe->nre)));
 199         }
 200         energyFrame.values_[index.first] = enxframe->ener[index.second].e;
 201     }
 202
 203     // Prepare for reading future frames
 204     haveProbedForNextFrame_ = false;
 205     nextFrameExists_        = false;
 206
 207     return energyFrame;
 208 }
 209
 210 // === EnergyFrame ===
 211
 212 EnergyFrame::EnergyFrame() : values_(), step_(), time_() {};
 213
 214 std::string EnergyFrame::getFrameName() const
 215 {
 216     return formatString("Time %f Step %" GMX_PRId64, time_, step_);
 217 }
 218
 219 const real &EnergyFrame::at(const std::string &name) const
 220 {
 221     auto valueIterator = values_.find(name);
 222     if (valueIterator == values_.end())
 223     {
 224         GMX_THROW(APIError("Cannot get energy value " + name + " unless previously registered when constructing EnergyFrameReader"));
 225     }
 226     return valueIterator->second;
 227 }
 228
 229 void compareFrames(const std::pair<EnergyFrame, EnergyFrame> &frames,
 230                    FloatingPointTolerance tolerance)
 231 {
 232     auto &reference = frames.first;
 233     auto &test      = frames.second;
 234
 235     for (auto referenceIt = reference.values_.begin(); referenceIt != reference.values_.end(); ++referenceIt)
 236     {
 237         auto testIt = test.values_.find(referenceIt->first);
 238         if (testIt != test.values_.end())
 239         {
 240             auto energyFieldInReference = referenceIt->second;
 241             auto energyFieldInTest      = testIt->second;
 242             EXPECT_REAL_EQ_TOL(energyFieldInReference, energyFieldInTest, tolerance)
 243             << referenceIt->first << " didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
 244         }
 245     }
 246 }
 247
 248 } // namespace
 249 } // namespace