src/gromacs/fileio/tests/confio.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2015,2016,2017,2018,2019,2020,2021, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
   7  * top-level source directory and at http://www.gromacs.org.
   8  *
   9  * GROMACS is free software; you can redistribute it and/or
  10  * modify it under the terms of the GNU Lesser General Public License
  11  * as published by the Free Software Foundation; either version 2.1
  12  * of the License, or (at your option) any later version.
  13  *
  14  * GROMACS is distributed in the hope that it will be useful,
  15  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  16  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  17  * Lesser General Public License for more details.
  18  *
  19  * You should have received a copy of the GNU Lesser General Public
  20  * License along with GROMACS; if not, see
  21  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  22  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  23  *
  24  * If you want to redistribute modifications to GROMACS, please
  25  * consider that scientific software is very special. Version
  26  * control is crucial - bugs must be traceable. We will be happy to
  27  * consider code for inclusion in the official distribution, but
  28  * derived work must not be called official GROMACS. Details are found
  29  * in the README & COPYING files - if they are missing, get the
  30  * official version at http://www.gromacs.org.
  31  *
  32  * To help us fund GROMACS development, we humbly ask that you cite
  33  * the research papers on the package. Check out http://www.gromacs.org.
  34  */
  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/pbcutil/pbc.h"
  56 #include "gromacs/topology/atoms.h"
  57 #include "gromacs/topology/symtab.h"
  58 #include "gromacs/topology/topology.h"
  59 #include "gromacs/utility/cstringutil.h"
  60 #include "gromacs/utility/smalloc.h"
  61
  62 #include "testutils/stringtest.h"
  63 #include "testutils/testfilemanager.h"
  64
  65 // TODO: These should really appear somewhere centralized.
  66 /*! \brief
  67  * Google Test formatter for GromacsFileType values.
  68  */
  69 static void PrintTo(const GromacsFileType& ftp, std::ostream* os)
  70 {
  71     *os << "'" << ftp2ext(ftp) << "'";
  72 }
  73
  74 namespace
  75 {
  76
  77 class StructureIORoundtripTest :
  78     public gmx::test::StringTestBase,
  79     public ::testing::WithParamInterface<GromacsFileType>
  80 {
  81 public:
  82     StructureIORoundtripTest()
  83     {
  84         generateReferenceTopology();
  85         generateReferenceCoordinates();
  86         testTop_ = nullptr;
  87         testX_   = nullptr;
  88         clear_mat(testBox_);
  89         referenceFilename_ = fileManager_.getTemporaryFilePath(getFileSuffix("ref"));
  90         testFilename_      = 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(),
 107                        *refTop_->name,
 108                        &refTop_->atoms,
 109                        as_rvec_array(refX_.data()),
 110                        nullptr,
 111                        PbcType::Unset,
 112                        refBox_);
 113     }
 114
 115     void readReferenceFileTps()
 116     {
 117         snew(testTop_, 1);
 118         PbcType pbcType = PbcType::Unset;
 119         read_tps_conf(referenceFilename_.c_str(), testTop_, &pbcType, &testX_, nullptr, testBox_, FALSE);
 120     }
 121
 122     void testTopologies()
 123     {
 124         // TODO: Compare the topologies.
 125     }
 126
 127     void writeTestFileAndTest()
 128     {
 129         write_sto_conf(
 130                 testFilename_.c_str(), *testTop_->name, &testTop_->atoms, testX_, nullptr, PbcType::Unset, testBox_);
 131         testFilesEqual(referenceFilename_, testFilename_);
 132     }
 133
 134 private:
 135     static std::string getFileSuffix(const char* type)
 136     {
 137         return std::string(type) + "." + ftp2ext(GetParam());
 138     }
 139
 140     void generateReferenceTopology()
 141     {
 142         snew(refTop_, 1);
 143         open_symtab(&refTop_->symtab);
 144         if (GetParam() == efESP)
 145         {
 146             // Titles cannot be read from an .esp file...
 147             refTop_->name = put_symtab(&refTop_->symtab, "");
 148         }
 149         else
 150         {
 151             refTop_->name = put_symtab(&refTop_->symtab, "Test title");
 152         }
 153         const int atomCount = 10;
 154         init_t_atoms(&refTop_->atoms, atomCount, FALSE);
 155         for (int i = 0; i < atomCount; ++i)
 156         {
 157             char name[3];
 158             name[0]                       = 'A';
 159             name[1]                       = 'A' + i % 3;
 160             name[2]                       = '\0';
 161             refTop_->atoms.atomname[i]    = put_symtab(&refTop_->symtab, name);
 162             refTop_->atoms.atom[i].resind = i / 3;
 163             if (i % 3 == 0)
 164             {
 165                 char resname[3];
 166                 resname[0] = 'R';
 167                 resname[1] = 'A' + i / 3;
 168                 resname[2] = '\0';
 169                 t_atoms_set_resinfo(&refTop_->atoms, i, &refTop_->symtab, resname, i / 3 + 1, ' ', 0, ' ');
 170             }
 171         }
 172         refTop_->atoms.nres = 4;
 173         close_symtab(&refTop_->symtab);
 174     }
 175
 176     void generateReferenceCoordinates()
 177     {
 178         clear_mat(refBox_);
 179         refBox_[XX][XX]     = 1;
 180         refBox_[YY][YY]     = 2;
 181         refBox_[ZZ][ZZ]     = 3;
 182         const int atomCount = refTop_->atoms.nr;
 183         refX_.reserve(atomCount);
 184         for (int i = 0; i < atomCount; ++i)
 185         {
 186             refX_.emplace_back(i % 4, i / 4, (i / 2) % 3);
 187         }
 188     }
 189
 190     gmx::test::TestFileManager fileManager_;
 191     std::string                referenceFilename_;
 192     std::string                testFilename_;
 193     t_topology*                refTop_;
 194     std::vector<gmx::RVec>     refX_;
 195     matrix                     refBox_;
 196     t_topology*                testTop_;
 197     rvec*                      testX_;
 198     matrix                     testBox_;
 199 };
 200
 201 TEST_P(StructureIORoundtripTest, ReadWriteTpsConf)
 202 {
 203     writeReferenceFile();
 204     readReferenceFileTps();
 205     testTopologies();
 206     writeTestFileAndTest();
 207 }
 208
 209 INSTANTIATE_TEST_SUITE_P(WithDifferentFormats,
 210                          StructureIORoundtripTest,
 211                          ::testing::Values(efGRO, efG96, efPDB, efESP));
 212
 213 } // namespace