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/utility/exceptions.h"
  55 #include "gromacs/utility/stringutil.h"
  56
  57 #include "testutils/testasserts.h"
  58
  59 namespace gmx
  60 {
  61 namespace test
  62 {
  63
  64 EnergyFrameReaderPtr
  65 openEnergyFileToReadFields(const std::string              &filename,
  66                            const std::vector<std::string> &namesOfRequiredEnergyFields)
  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 fields 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> indicesOfEnergyFields;
  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(namesOfRequiredEnergyFields),
  93                                                       std::end(namesOfRequiredEnergyFields),
  94                                                       [name](const std::string &n){
  95                                                           return 0 == n.compare(name);
  96                                                       });
  97             if (requiredEnergy != namesOfRequiredEnergyFields.end())
  98             {
  99                 indicesOfEnergyFields[name] = i;
 100             }
 101         }
 102         // Clean up old data structures
 103         free_enxnms(numEnergyTerms, energyNames);
 104     }
 105
 106     // Throw if we failed to find the fields we need
 107     if (indicesOfEnergyFields.size() != namesOfRequiredEnergyFields.size())
 108     {
 109         std::string requiredEnergiesNotFound = "Did not find the following required energies in mdrun output:\n";
 110         for (auto &name : namesOfRequiredEnergyFields)
 111         {
 112             auto possibleIndex = indicesOfEnergyFields.find(name);
 113             if (possibleIndex == indicesOfEnergyFields.end())
 114             {
 115                 requiredEnergiesNotFound += name + "\n";
 116             }
 117         }
 118         GMX_THROW(APIError(requiredEnergiesNotFound));
 119     }
 120
 121     return EnergyFrameReaderPtr(new EnergyFrameReader(indicesOfEnergyFields, 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> &indicesOfEnergyFields,
 146                                      ener_file *energyFile)
 147     : indicesOfEnergyFields_(indicesOfEnergyFields),
 148       energyFileGuard_(energyFile),
 149       enxframeGuard_(make_enxframe()),
 150       haveProbedForNextFrame_(false),
 151       nextFrameExists_(false)
 152 {
 153 }
 154
 155 bool
 156 EnergyFrameReader::readNextFrame()
 157 {
 158     if (haveProbedForNextFrame_)
 159     {
 160         if (nextFrameExists_)
 161         {
 162             GMX_THROW(APIError("This frame has already been probed for, it should be used before probing again."));
 163         }
 164         else
 165         {
 166             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."));
 167         }
 168     }
 169     haveProbedForNextFrame_ = true;
 170     // If there's a next frame, read it into enxframe_, and report the result.
 171     return nextFrameExists_ = do_enx(energyFileGuard_.get(), enxframeGuard_.get());
 172 }
 173
 174 EnergyFrame
 175 EnergyFrameReader::frame()
 176 {
 177     EnergyFrame energyFrame;
 178
 179     if (!haveProbedForNextFrame_)
 180     {
 181         readNextFrame();
 182     }
 183     if (!nextFrameExists_)
 184     {
 185         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()."));
 186     }
 187
 188     // The probe filled enxframe_ with new data, so now we use that data to fill energyFrame
 189     t_enxframe *enxframe = enxframeGuard_.get();
 190     energyFrame.time_ = enxframe->t;
 191     energyFrame.step_ = enxframe->step;
 192     for (auto &index : indicesOfEnergyFields_)
 193     {
 194         if (index.second >= enxframe->nre)
 195         {
 196             GMX_THROW(InternalError(formatString("Index %d for energy %s not present in energy frame with %d energies",
 197                                                  index.second, index.first.c_str(), enxframe->nre)));
 198         }
 199         energyFrame.values_[index.first] = enxframe->ener[index.second].e;
 200     }
 201
 202     // Prepare for reading future frames
 203     haveProbedForNextFrame_ = false;
 204     nextFrameExists_        = false;
 205
 206     return energyFrame;
 207 }
 208
 209 // === EnergyFrame ===
 210
 211 EnergyFrame::EnergyFrame() : values_(), step_(), time_() {};
 212
 213 std::string EnergyFrame::getFrameName() const
 214 {
 215     return formatString("Time %f Step %" GMX_PRId64, time_, step_);
 216 }
 217
 218 const real &EnergyFrame::at(const std::string &name) const
 219 {
 220     auto valueIterator = values_.find(name);
 221     if (valueIterator == values_.end())
 222     {
 223         GMX_THROW(APIError("Cannot get energy value " + name + " unless previously registered when constructing EnergyFrameReader"));
 224     }
 225     return valueIterator->second;
 226 }
 227
 228 void compareFrames(const std::pair<EnergyFrame, EnergyFrame> &frames,
 229                    FloatingPointTolerance tolerance)
 230 {
 231     auto &reference = frames.first;
 232     auto &test      = frames.second;
 233
 234     for (auto referenceIt = reference.values_.begin(); referenceIt != reference.values_.end(); ++referenceIt)
 235     {
 236         auto testIt = test.values_.find(referenceIt->first);
 237         if (testIt != test.values_.end())
 238         {
 239             auto energyFieldInReference = referenceIt->second;
 240             auto energyFieldInTest      = testIt->second;
 241             EXPECT_REAL_EQ_TOL(energyFieldInReference, energyFieldInTest, tolerance)
 242             << referenceIt->first << " didn't match between reference run " << reference.getFrameName() << " and test run " << test.getFrameName();
 243         }
 244     }
 245 }
 246
 247 } // namespace
 248 } // namespace