src/gromacs/trajectoryanalysis/tests/surfacearea.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2014,2015,2016,2017,2018 by the GROMACS development team.
   5  * Copyright (c) 2019,2020,2021, by the GROMACS development team, led by
   6  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   7  * and including many others, as listed in the AUTHORS file in the
   8  * top-level source directory and at http://www.gromacs.org.
   9  *
  10  * GROMACS is free software; you can redistribute it and/or
  11  * modify it under the terms of the GNU Lesser General Public License
  12  * as published by the Free Software Foundation; either version 2.1
  13  * of the License, or (at your option) any later version.
  14  *
  15  * GROMACS is distributed in the hope that it will be useful,
  16  * but WITHOUT ANY WARRANTY; without even the implied warranty of
  17  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  18  * Lesser General Public License for more details.
  19  *
  20  * You should have received a copy of the GNU Lesser General Public
  21  * License along with GROMACS; if not, see
  22  * http://www.gnu.org/licenses, or write to the Free Software Foundation,
  23  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  24  *
  25  * If you want to redistribute modifications to GROMACS, please
  26  * consider that scientific software is very special. Version
  27  * control is crucial - bugs must be traceable. We will be happy to
  28  * consider code for inclusion in the official distribution, but
  29  * derived work must not be called official GROMACS. Details are found
  30  * in the README & COPYING files - if they are missing, get the
  31  * official version at http://www.gromacs.org.
  32  *
  33  * To help us fund GROMACS development, we humbly ask that you cite
  34  * the research papers on the package. Check out http://www.gromacs.org.
  35  */
  36 /*! \internal \file
  37  * \brief
  38  * Tests for the surface area calculation used by the `sasa` analysis module.
  39  *
  40  * \author Teemu Murtola <teemu.murtola@gmail.com>
  41  * \ingroup module_trajectoryanalysis
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "gromacs/trajectoryanalysis/modules/surfacearea.h"
  46
  47 #include <cstdlib>
  48
  49 #include <gtest/gtest.h>
  50
  51 #include "gromacs/math/units.h"
  52 #include "gromacs/math/utilities.h"
  53 #include "gromacs/math/vec.h"
  54 #include "gromacs/pbcutil/pbc.h"
  55 #include "gromacs/random/threefry.h"
  56 #include "gromacs/random/uniformrealdistribution.h"
  57 #include "gromacs/utility/arrayref.h"
  58 #include "gromacs/utility/gmxassert.h"
  59 #include "gromacs/utility/smalloc.h"
  60
  61 #include "testutils/refdata.h"
  62 #include "testutils/testasserts.h"
  63
  64 namespace
  65 {
  66
  67 /********************************************************************
  68  * SurfaceAreaTest
  69  */
  70
  71 class SurfaceAreaTest : public ::testing::Test
  72 {
  73 public:
  74     SurfaceAreaTest() :
  75         box_(), rng_(12345), area_(0.0), volume_(0.0), atomArea_(nullptr), dotCount_(0), dots_(nullptr)
  76     {
  77     }
  78     ~SurfaceAreaTest() override
  79     {
  80         sfree(atomArea_);
  81         sfree(dots_);
  82     }
  83
  84     void addSphere(real x, real y, real z, real radius, bool bAddToIndex = true)
  85     {
  86         if (bAddToIndex)
  87         {
  88             index_.push_back(x_.size());
  89         }
  90         x_.emplace_back(x, y, z);
  91         radius_.push_back(radius);
  92     }
  93
  94     void generateRandomPosition(rvec x, real* radius)
  95     {
  96         rvec                               fx;
  97         gmx::UniformRealDistribution<real> dist;
  98
  99         fx[XX] = dist(rng_);
 100         fx[YY] = dist(rng_);
 101         fx[ZZ] = dist(rng_);
 102         mvmul(box_, fx, x);
 103         *radius = 1.5 * dist(rng_) + 0.5;
 104     }
 105
 106     void generateRandomPositions(int count)
 107     {
 108         x_.reserve(count);
 109         radius_.reserve(count);
 110         index_.reserve(count);
 111         for (int i = 0; i < count; ++i)
 112         {
 113             rvec x;
 114             real radius = 0;
 115             generateRandomPosition(x, &radius);
 116             addSphere(x[XX], x[YY], x[ZZ], radius);
 117         }
 118     }
 119     void translatePoints(real x, real y, real z)
 120     {
 121         for (size_t i = 0; i < x_.size(); ++i)
 122         {
 123             x_[i][XX] += x;
 124             x_[i][YY] += y;
 125             x_[i][ZZ] += z;
 126         }
 127     }
 128
 129     void calculate(int ndots, int flags, bool bPBC)
 130     {
 131         volume_ = 0.0;
 132         sfree(atomArea_);
 133         atomArea_ = nullptr;
 134         dotCount_ = 0;
 135         sfree(dots_);
 136         dots_ = nullptr;
 137         t_pbc pbc;
 138         if (bPBC)
 139         {
 140             set_pbc(&pbc, PbcType::Xyz, box_);
 141         }
 142         gmx::SurfaceAreaCalculator calculator;
 143         calculator.setDotCount(ndots);
 144         calculator.setRadii(radius_);
 145         calculator.calculate(as_rvec_array(x_.data()),
 146                              bPBC ? &pbc : nullptr,
 147                              index_.size(),
 148                              index_.data(),
 149                              flags,
 150                              &area_,
 151                              &volume_,
 152                              &atomArea_,
 153                              &dots_,
 154                              &dotCount_);
 155     }
 156     real resultArea() const { return area_; }
 157     real resultVolume() const { return volume_; }
 158     real atomArea(int index) const { return atomArea_[index]; }
 159
 160     void checkReference(gmx::test::TestReferenceChecker* checker, const char* id, bool checkDotCoordinates)
 161     {
 162         gmx::test::TestReferenceChecker compound(checker->checkCompound("SASA", id));
 163         compound.checkReal(area_, "Area");
 164         if (volume_ > 0.0)
 165         {
 166             compound.checkReal(volume_, "Volume");
 167         }
 168         if (atomArea_ != nullptr)
 169         {
 170             compound.checkSequenceArray(index_.size(), atomArea_, "AtomArea");
 171         }
 172         if (dots_ != nullptr)
 173         {
 174             if (checkDotCoordinates)
 175             {
 176                 // The algorithm may produce the dots in different order in
 177                 // single and double precision due to some internal
 178                 // sorting...
 179                 std::qsort(dots_, dotCount_, sizeof(rvec), &dotComparer);
 180                 compound.checkSequenceArray(3 * dotCount_, dots_, "Dots");
 181             }
 182             else
 183             {
 184                 compound.checkInteger(dotCount_, "DotCount");
 185             }
 186         }
 187     }
 188
 189     gmx::test::TestReferenceData data_;
 190     matrix                       box_;
 191
 192 private:
 193     static int dotComparer(const void* a, const void* b)
 194     {
 195         for (int d = DIM - 1; d >= 0; --d)
 196         {
 197             const real ad = reinterpret_cast<const real*>(a)[d];
 198             const real bd = reinterpret_cast<const real*>(b)[d];
 199             // A fudge factor is needed to get an ordering that is the same
 200             // in single and double precision, since the points are not
 201             // exactly on the same Z plane even though in exact arithmetic
 202             // they probably would be.
 203             if (ad < bd - 0.001)
 204             {
 205                 return -1;
 206             }
 207             else if (ad > bd + 0.001)
 208             {
 209                 return 1;
 210             }
 211         }
 212         return 0;
 213     }
 214
 215     gmx::DefaultRandomEngine rng_;
 216     std::vector<gmx::RVec>   x_;
 217     std::vector<real>        radius_;
 218     std::vector<int>         index_;
 219
 220     real  area_;
 221     real  volume_;
 222     real* atomArea_;
 223     int   dotCount_;
 224     real* dots_;
 225 };
 226
 227 TEST_F(SurfaceAreaTest, ComputesSinglePoint)
 228 {
 229     gmx::test::FloatingPointTolerance tolerance(gmx::test::defaultRealTolerance());
 230     addSphere(1, 1, 1, 1);
 231     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA, false));
 232     EXPECT_REAL_EQ_TOL(4 * M_PI, resultArea(), tolerance);
 233     EXPECT_REAL_EQ_TOL(4 * M_PI, atomArea(0), tolerance);
 234     EXPECT_REAL_EQ_TOL(4 * M_PI / 3, resultVolume(), tolerance);
 235 }
 236
 237 TEST_F(SurfaceAreaTest, ComputesTwoPoints)
 238 {
 239     gmx::test::FloatingPointTolerance tolerance(gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 240     addSphere(1, 1, 1, 1);
 241     addSphere(2, 1, 1, 1);
 242     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 243     EXPECT_REAL_EQ_TOL(2 * 2 * M_PI * 1.5, resultArea(), tolerance);
 244     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(0), tolerance);
 245     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(1), tolerance);
 246 }
 247
 248 TEST_F(SurfaceAreaTest, ComputesTwoPointsOfUnequalRadius)
 249 {
 250     gmx::test::FloatingPointTolerance tolerance(gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 251     // Spheres of radius 1 and 2 with intersection at 1.5
 252     const real dist = 0.5 + sqrt(3.25);
 253     addSphere(1.0, 1.0, 1.0, 1);
 254     addSphere(1.0 + dist, 1.0, 1.0, 2);
 255     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 256     EXPECT_REAL_EQ_TOL(2 * M_PI * (1.5 + (dist - 0.5 + 2) * 2), resultArea(), tolerance);
 257     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(0), tolerance);
 258     EXPECT_REAL_EQ_TOL(2 * M_PI * (dist - 0.5 + 2) * 2, atomArea(1), tolerance);
 259 }
 260
 261 TEST_F(SurfaceAreaTest, SurfacePoints12)
 262 {
 263     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 264     addSphere(0, 0, 0, 1);
 265     ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
 266     checkReference(&checker, "Surface", true);
 267 }
 268
 269 TEST_F(SurfaceAreaTest, SurfacePoints32)
 270 {
 271     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 272     addSphere(0, 0, 0, 1);
 273     ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
 274     checkReference(&checker, "Surface", true);
 275 }
 276
 277 TEST_F(SurfaceAreaTest, SurfacePoints42)
 278 {
 279     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 280     addSphere(0, 0, 0, 1);
 281     ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
 282     checkReference(&checker, "Surface", true);
 283 }
 284
 285 TEST_F(SurfaceAreaTest, SurfacePoints122)
 286 {
 287     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 288     addSphere(0, 0, 0, 1);
 289     ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
 290     checkReference(&checker, "Surface", true);
 291 }
 292
 293 TEST_F(SurfaceAreaTest, Computes100Points)
 294 {
 295     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 296     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 297     box_[XX][XX] = 10.0;
 298     box_[YY][YY] = 10.0;
 299     box_[ZZ][ZZ] = 10.0;
 300     generateRandomPositions(100);
 301     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, false));
 302     checkReference(&checker, "100Points", false);
 303 }
 304
 305 TEST_F(SurfaceAreaTest, Computes100PointsWithRectangularPBC)
 306 {
 307     // TODO: It would be nice to check that this produces the same result as
 308     // without PBC, without duplicating the reference files.
 309     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 310     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 311     box_[XX][XX] = 10.0;
 312     box_[YY][YY] = 10.0;
 313     box_[ZZ][ZZ] = 10.0;
 314     generateRandomPositions(100);
 315     box_[XX][XX]    = 20.0;
 316     box_[YY][YY]    = 20.0;
 317     box_[ZZ][ZZ]    = 20.0;
 318     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 319     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 320     checkReference(&checker, "100Points", false);
 321
 322     translatePoints(15.0, 0, 0);
 323     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 324     checkReference(&checker, "100Points", false);
 325
 326     translatePoints(-15.0, 15.0, 0);
 327     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 328     checkReference(&checker, "100Points", false);
 329
 330     translatePoints(0, -15.0, 15.0);
 331     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 332     checkReference(&checker, "100Points", false);
 333 }
 334
 335 TEST_F(SurfaceAreaTest, Computes100PointsWithTriclinicPBC)
 336 {
 337     // TODO: It would be nice to check that this produces the same result as
 338     // without PBC, without duplicating the reference files.
 339     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 340     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 341     box_[XX][XX] = 10.0;
 342     box_[YY][YY] = 10.0;
 343     box_[ZZ][ZZ] = 10.0;
 344     generateRandomPositions(100);
 345     box_[XX][XX] = 20.0;
 346     box_[YY][XX] = 10.0;
 347     box_[YY][YY] = 10.0 * sqrt(3.0);
 348     box_[ZZ][XX] = 10.0;
 349     box_[ZZ][YY] = 10.0 * sqrt(1.0 / 3.0);
 350     box_[ZZ][ZZ] = 20.0 * sqrt(2.0 / 3.0);
 351
 352     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 353     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 354     checkReference(&checker, "100Points", false);
 355
 356     translatePoints(15.0, 0, 0);
 357     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 358     checkReference(&checker, "100Points", false);
 359
 360     translatePoints(-15.0, box_[YY][YY] - 5.0, 0);
 361     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 362     checkReference(&checker, "100Points", false);
 363
 364     translatePoints(0, -(box_[YY][YY] - 5.0), 15.0);
 365     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 366     checkReference(&checker, "100Points", false);
 367 }
 368
 369 } // namespace