src/gromacs/fileio/tests/confio.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests for reading/writing different structure file formats.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_fileio
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/fileio/confio.h"
  45
  46 #include <iostream>
  47 #include <string>
  48 #include <vector>
  49
  50 #include <gtest/gtest.h>
  51
  52 #include "gromacs/fileio/filetypes.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/math/vectypes.h"
  55 #include "gromacs/topology/atoms.h"
  56 #include "gromacs/topology/symtab.h"
  57 #include "gromacs/topology/topology.h"
  58 #include "gromacs/utility/cstringutil.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 #include "testutils/stringtest.h"
  62 #include "testutils/testfilemanager.h"
  63
  64 // TODO: These should really appear somewhere centralized.
  65 /*! \brief
  66  * Google Test formatter for GromacsFileType values.
  67  */
  68 static void PrintTo(const GromacsFileType &ftp, std::ostream *os)
  69 {
  70     *os << "'" << ftp2ext(ftp) << "'";
  71 }
  72
  73 namespace
  74 {
  75
  76 class StructureIORoundtripTest : public gmx::test::StringTestBase,
  77                                  public ::testing::WithParamInterface<GromacsFileType>
  78 {
  79     public:
  80         StructureIORoundtripTest()
  81         {
  82             generateReferenceTopology();
  83             generateReferenceCoordinates();
  84             testTop_ = nullptr;
  85             testX_   = nullptr;
  86             clear_mat(testBox_);
  87             referenceFilename_ =
  88                 fileManager_.getTemporaryFilePath(getFileSuffix("ref"));
  89             testFilename_ =
  90                 fileManager_.getTemporaryFilePath(getFileSuffix("test"));
  91         }
  92         ~StructureIORoundtripTest() override
  93         {
  94             if (testTop_ != nullptr)
  95             {
  96                 done_top(testTop_);
  97                 sfree(testTop_);
  98             }
  99             sfree(testX_);
 100             done_top(refTop_);
 101             sfree(refTop_);
 102         }
 103
 104         void writeReferenceFile()
 105         {
 106             write_sto_conf(referenceFilename_.c_str(), *refTop_->name,
 107                            &refTop_->atoms, as_rvec_array(refX_.data()), nullptr, -1,
 108                            refBox_);
 109         }
 110
 111         void readReferenceFileTps()
 112         {
 113             snew(testTop_, 1);
 114             int  ePBC = -2;
 115             read_tps_conf(referenceFilename_.c_str(), testTop_,
 116                           &ePBC, &testX_, nullptr, testBox_, FALSE);
 117         }
 118
 119         void testTopologies()
 120         {
 121             // TODO: Compare the topologies.
 122         }
 123
 124         void writeTestFileAndTest()
 125         {
 126             write_sto_conf(testFilename_.c_str(), *testTop_->name,
 127                            &testTop_->atoms, testX_, nullptr, -1, testBox_);
 128             testFilesEqual(referenceFilename_, testFilename_);
 129         }
 130
 131     private:
 132         std::string getFileSuffix(const char *type)
 133         {
 134             return std::string(type) + "." + ftp2ext(GetParam());
 135         }
 136
 137         void generateReferenceTopology()
 138         {
 139             snew(refTop_, 1);
 140             open_symtab(&refTop_->symtab);
 141             if (GetParam() == efESP)
 142             {
 143                 // Titles cannot be read from an .esp file...
 144                 refTop_->name = put_symtab(&refTop_->symtab, "");
 145             }
 146             else
 147             {
 148                 refTop_->name = put_symtab(&refTop_->symtab, "Test title");
 149             }
 150             const int atomCount = 10;
 151             init_t_atoms(&refTop_->atoms, atomCount, FALSE);
 152             for (int i = 0; i < atomCount; ++i)
 153             {
 154                 char name[3];
 155                 name[0]                       = 'A';
 156                 name[1]                       = 'A' + i%3;
 157                 name[2]                       = '\0';
 158                 refTop_->atoms.atomname[i]    = put_symtab(&refTop_->symtab, name);
 159                 refTop_->atoms.atom[i].resind = i/3;
 160                 if (i%3 == 0)
 161                 {
 162                     char resname[3];
 163                     resname[0] = 'R';
 164                     resname[1] = 'A' + i/3;
 165                     resname[2] = '\0';
 166                     t_atoms_set_resinfo(&refTop_->atoms, i, &refTop_->symtab,
 167                                         resname, i/3 + 1, ' ', 0, ' ');
 168                 }
 169             }
 170             refTop_->atoms.nres = 4;
 171             close_symtab(&refTop_->symtab);
 172         }
 173
 174         void generateReferenceCoordinates()
 175         {
 176             clear_mat(refBox_);
 177             refBox_[XX][XX] = 1;
 178             refBox_[YY][YY] = 2;
 179             refBox_[ZZ][ZZ] = 3;
 180             const int atomCount = refTop_->atoms.nr;
 181             refX_.reserve(atomCount);
 182             for (int i = 0; i < atomCount; ++i)
 183             {
 184                 refX_.emplace_back(i%4, i/4, (i/2)%3);
 185             }
 186         }
 187
 188         gmx::test::TestFileManager      fileManager_;
 189         std::string                     referenceFilename_;
 190         std::string                     testFilename_;
 191         t_topology                     *refTop_;
 192         std::vector<gmx::RVec>          refX_;
 193         matrix                          refBox_;
 194         t_topology                     *testTop_;
 195         rvec                           *testX_;
 196         matrix                          testBox_;
 197 };
 198
 199 TEST_P(StructureIORoundtripTest, ReadWriteTpsConf)
 200 {
 201     writeReferenceFile();
 202     readReferenceFileTps();
 203     testTopologies();
 204     writeTestFileAndTest();
 205 }
 206
 207 INSTANTIATE_TEST_CASE_P(WithDifferentFormats,
 208                         StructureIORoundtripTest,
 209                             ::testing::Values(efGRO, efG96, efPDB, efESP));
 210
 211 } // namespace