src/programs/mdrun/tests/initialconstraints.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2017,2018, 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  * This implements basic initial constrains test (using single-rank mdrun)
  38  *
  39  * This test checks that the coordinates from file, which only satisfy
  40  * the constraints up to gro precision, are constrained correctly and that
  41  * the initial velocity of the center of mass does not contribute to the
  42  * kinetic energy at step 0..
  43  * It runs the input system for 1 step (no continuation), and compares the total energy.
  44  *
  45  * \author Aleksei Iupinov <a.yupinov@gmail.com>
  46  * \ingroup module_mdrun_integration_tests
  47  */
  48 #include "gmxpre.h"
  49
  50 #include <string>
  51
  52 #include "gromacs/trajectory/energyframe.h"
  53 #include "gromacs/utility/stringutil.h"
  54
  55 #include "energyreader.h"
  56 #include "moduletest.h"
  57
  58 namespace gmx
  59 {
  60 namespace test
  61 {
  62 namespace
  63 {
  64
  65 //! This type holds input integrators. Now it's holding names, but ei* enum values from md_enums.h could be used instead.
  66 using EnergyIntegratorType = const char *;
  67
  68 //! Test fixture parametrized on integrators
  69 class InitialConstraintsTest : public gmx::test::MdrunTestFixture,
  70                                public ::testing::WithParamInterface<EnergyIntegratorType>
  71 {
  72 };
  73
  74 TEST_P(InitialConstraintsTest, Works)
  75 {
  76     const int         nsteps     = 1;
  77     const float       timestep   = 0.001;
  78     auto              integrator = GetParam();
  79     const std::string integratorName(integrator);
  80     SCOPED_TRACE("Integrating with " + integratorName);
  81     const std::string theMdpFile = formatString("nstcalcenergy           = 1\n"
  82                                                 "nstenergy               = 1\n"
  83                                                 "comm-mode               = linear\n"
  84                                                 "continuation            = no\n"
  85                                                 "constraints             = h-bonds\n"
  86                                                 "lincs_iter              = 2\n"
  87                                                 "verlet-buffer-tolerance = 1e-4\n"
  88                                                 "nsttcouple              = 1\n"    // for md-vv-avek
  89                                                 "nstpcouple              = 1\n"    // for md-vv-avek
  90                                                 "integrator              = %s\n"
  91                                                 "nsteps                  = %d\n"
  92                                                 "dt                      = %f\n",
  93                                                 integratorName.c_str(), nsteps, timestep);
  94
  95     runner_.useStringAsMdpFile(theMdpFile);
  96
  97     const std::string inputFile = "spc-and-methanol";
  98     runner_.useTopGroAndNdxFromDatabase(inputFile.c_str());
  99     EXPECT_EQ(0, runner_.callGrompp());
 100
 101     runner_.edrFileName_ = fileManager_.getTemporaryFilePath(inputFile + ".edr");
 102     ASSERT_EQ(0, runner_.callMdrun());
 103
 104     auto energyReader = openEnergyFileToReadFields(runner_.edrFileName_, {"Total Energy", "Kinetic En."});
 105     real totalEnergy  = 0.0, prevTotalEnergy = 0.0;
 106     auto tolerance    = ulpTolerance(0); // The real value is set below from starting kinetic energy
 107     for (int i = 0; i <= nsteps; i++)
 108     {
 109         EnergyFrame frame = energyReader->frame();
 110         prevTotalEnergy = totalEnergy;
 111         totalEnergy     = frame.at("Total Energy");
 112         if (i == 0)
 113         {
 114             // We set the tolerance for total energy based on magnitude of kinetic energy.
 115             // The reason is that the other total energy component, the potential energy, can in theory have whatever magnitude.
 116             const real startingKineticEnergy = frame.at("Kinetic En.");
 117             tolerance = relativeToleranceAsFloatingPoint(startingKineticEnergy, 1e-5);
 118         }
 119         else
 120         {
 121             EXPECT_REAL_EQ_TOL(totalEnergy, prevTotalEnergy, tolerance);
 122         }
 123     }
 124 }
 125
 126 //! Integrators with energy conservation to test
 127 static const EnergyIntegratorType c_integratorsToTest [] = {"md", "md-vv", "md-vv-avek"};
 128
 129 INSTANTIATE_TEST_CASE_P(Checking, InitialConstraintsTest, ::testing::ValuesIn(c_integratorsToTest));
 130
 131 }
 132 }
 133 }