src/programs/mdrun/tests/trajectorycomparison.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2016,2017,2018,2019, 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
  36 /*! \internal \file
  37  * \brief Implemention of functions for comparing trajectories
  38  * 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 "trajectorycomparison.h"
  46
  47 #include <gmock/gmock.h>
  48
  49 #include "gromacs/pbcutil/pbc.h"
  50 #include "gromacs/trajectory/trajectoryframe.h"
  51
  52 #include "testutils/testasserts.h"
  53 #include "testutils/testmatchers.h"
  54
  55 namespace gmx
  56 {
  57 namespace test
  58 {
  59
  60 using ::testing::Pointwise;
  61
  62 /*! \brief Compares the box from \c reference and \c test
  63  * according to the \c matchSettings and \c tolerance.
  64  *
  65  * \todo This could be streamlined when we have a proper 3D matrix
  66  * class and view. */
  67 static void compareBox(const TrajectoryFrame              &reference,
  68                        const TrajectoryFrame              &test,
  69                        const TrajectoryFrameMatchSettings &matchSettings,
  70                        const FloatingPointTolerance        tolerance)
  71 {
  72     if (!matchSettings.mustCompareBox)
  73     {
  74         return;
  75     }
  76     bool canCompareBox = true;
  77     if (!reference.hasBox())
  78     {
  79         ADD_FAILURE() << "Comparing the box was required, "
  80         "but the reference frame did not have one";
  81         canCompareBox = false;
  82     }
  83     if (!test.hasBox())
  84     {
  85         ADD_FAILURE() << "Comparing the box was required, "
  86         "but the test frame did not have one";
  87         canCompareBox = false;
  88     }
  89     if (!canCompareBox)
  90     {
  91         return;
  92     }
  93
  94     // Do the comparing.
  95     for (int d = 0; d < DIM; ++d)
  96     {
  97         for (int dd = 0; dd < DIM; ++dd)
  98         {
  99             EXPECT_REAL_EQ_TOL(reference.box()[d][dd], test.box()[d][dd], tolerance);
 100         }
 101     }
 102 }
 103
 104 /*! \brief Help put all atom coordinates in \c frame into its box.
 105  *
 106  * This can perhaps go away when frame->x is a container. */
 107 static std::vector<RVec>
 108 putAtomsInBox(const TrajectoryFrame &frame)
 109 {
 110     std::vector<RVec> x(frame.x().begin(), frame.x().end());
 111     matrix            box;
 112     for (int d = 0; d < DIM; ++d)
 113     {
 114         for (int dd = 0; dd < DIM; ++dd)
 115         {
 116             box[d][dd] = frame.box()[d][dd];
 117         }
 118     }
 119     // Note we don't need to compare bPBC because put_atoms_in_box
 120     // implements a fallback if nothing specific was set in the
 121     // trajectory frame.
 122     put_atoms_in_box(frame.pbc(), box, x);
 123     return x;
 124 }
 125
 126 /*! \brief Return whether the \c comparisonConditions and emptiness of
 127  * reference and test frames means that a comparison should be
 128  * attempted.
 129  *
 130  * This allows the framework to determine whether it is an error if a
 131  * comparison cannot be made. */
 132 static bool shouldDoComparison(const ComparisonConditions comparisonConditions,
 133                                const bool                 referenceIsEmpty,
 134                                const bool                 testIsEmpty)
 135 {
 136     if (comparisonConditions == ComparisonConditions::NoComparison)
 137     {
 138         return false;
 139     }
 140
 141     bool doComparison = true;
 142     if (testIsEmpty)
 143     {
 144         if (comparisonConditions == ComparisonConditions::MustCompare ||
 145             comparisonConditions == ComparisonConditions::CompareIfBothFound ||
 146             (!referenceIsEmpty &&
 147              comparisonConditions == ComparisonConditions::CompareIfReferenceFound))
 148         {
 149             ADD_FAILURE() << "Test frame lacked quantitiy for required comparison";
 150         }
 151         doComparison = false;
 152     }
 153     if (referenceIsEmpty)
 154     {
 155         if (comparisonConditions == ComparisonConditions::MustCompare ||
 156             comparisonConditions == ComparisonConditions::CompareIfBothFound ||
 157             (!testIsEmpty &&
 158              comparisonConditions == ComparisonConditions::CompareIfTestFound))
 159         {
 160             ADD_FAILURE() << "Reference frame lacked quantity for required comparison";
 161         }
 162         doComparison = false;
 163     }
 164     return doComparison;
 165 }
 166
 167 /*! \brief Compares the position coordinates from \c reference and \c test
 168  * according to the \c matchSettings and \c tolerance. */
 169 static void compareCoordinates(const TrajectoryFrame              &reference,
 170                                const TrajectoryFrame              &test,
 171                                const TrajectoryFrameMatchSettings &matchSettings,
 172                                const FloatingPointTolerance        tolerance)
 173 {
 174     SCOPED_TRACE("Comparing coordinates");
 175     if (!shouldDoComparison(matchSettings.coordinatesComparison,
 176                             reference.x().empty(),
 177                             test.x().empty()))
 178     {
 179         return;
 180     }
 181
 182     bool canHandlePbc = true;
 183     if (!reference.hasBox())
 184     {
 185         ADD_FAILURE() << "Comparing positions required PBC handling, "
 186         "but the reference frame did not have a box";
 187         canHandlePbc = false;
 188     }
 189     if (!test.hasBox())
 190     {
 191         ADD_FAILURE() << "Comparing positions required PBC handling, "
 192         "but the test frame did not have a box";
 193         canHandlePbc = false;
 194     }
 195
 196     if (matchSettings.requirePbcHandling && !canHandlePbc)
 197     {
 198         ADD_FAILURE() << "Cannot compare positions for the above reason(s)";
 199         return;
 200     }
 201
 202     if ((matchSettings.handlePbcIfPossible || matchSettings.requirePbcHandling) && canHandlePbc)
 203     {
 204         EXPECT_THAT(putAtomsInBox(test), Pointwise(RVecEq(tolerance), putAtomsInBox(reference)));
 205     }
 206     else
 207     {
 208         EXPECT_THAT(test.x(), Pointwise(RVecEq(tolerance), reference.x()));
 209     }
 210 }
 211
 212 /*! \brief Compares the velocities from \c reference and \c test
 213  * according to the \c matchSettings and \c tolerance. */
 214 static void compareVelocities(const TrajectoryFrame              &reference,
 215                               const TrajectoryFrame              &test,
 216                               const TrajectoryFrameMatchSettings &matchSettings,
 217                               const FloatingPointTolerance        tolerance)
 218 {
 219     SCOPED_TRACE("Comparing velocities");
 220     if (!shouldDoComparison(matchSettings.velocitiesComparison,
 221                             reference.v().empty(),
 222                             test.v().empty()))
 223     {
 224         return;
 225     }
 226     EXPECT_THAT(test.v(), Pointwise(RVecEq(tolerance), reference.v()));
 227 }
 228
 229 /*! \brief Compares the forces from \c reference and \c test
 230  * according to the \c matchSettings and \c tolerance. */
 231 static void compareForces(const TrajectoryFrame              &reference,
 232                           const TrajectoryFrame              &test,
 233                           const TrajectoryFrameMatchSettings &matchSettings,
 234                           const FloatingPointTolerance        tolerance)
 235 {
 236     SCOPED_TRACE("Comparing forces");
 237     if (!shouldDoComparison(matchSettings.forcesComparison,
 238                             reference.f().empty(),
 239                             test.f().empty()))
 240     {
 241         return;
 242     }
 243     EXPECT_THAT(test.f(), Pointwise(RVecEq(tolerance), reference.f()));
 244 }
 245
 246
 247 const TrajectoryTolerances TrajectoryComparison::s_defaultTrajectoryTolerances {
 248     defaultRealTolerance(),                                                       // box
 249     relativeToleranceAsFloatingPoint(1.0, 1.0e-3),                                // positions
 250     defaultRealTolerance(),                                                       // velocities
 251     relativeToleranceAsFloatingPoint(100.0, GMX_DOUBLE ? 1.0e-7 : 5.0e-5)         // forces
 252 };
 253
 254
 255 TrajectoryComparison::TrajectoryComparison(const TrajectoryFrameMatchSettings &matchSettings,
 256                                            const TrajectoryTolerances         &tolerances)
 257     : matchSettings_(matchSettings),
 258       tolerances_(tolerances)
 259 {
 260 }
 261
 262 void TrajectoryComparison::operator()(const TrajectoryFrame &reference,
 263                                       const TrajectoryFrame &test) const
 264 {
 265     SCOPED_TRACE("Comparing trajectory reference frame " + reference.frameName() + " and test frame " + test.frameName());
 266     EXPECT_EQ(reference.step(), test.step());
 267     EXPECT_EQ(reference.time(), test.time());
 268     compareBox(reference, test, matchSettings_, tolerances_.box);
 269     compareCoordinates(reference, test, matchSettings_, tolerances_.coordinates);
 270     compareVelocities(reference, test, matchSettings_, tolerances_.velocities);
 271     compareForces(reference, test, matchSettings_, tolerances_.forces);
 272 }
 273
 274 }  // namespace test
 275 }  // namespace gmx