src/gromacs/trajectoryanalysis/tests/surfacearea.cpp

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  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/utilities.h"
  52 #include "gromacs/math/vec.h"
  53 #include "gromacs/pbcutil/pbc.h"
  54 #include "gromacs/random/threefry.h"
  55 #include "gromacs/random/uniformrealdistribution.h"
  56 #include "gromacs/utility/arrayref.h"
  57 #include "gromacs/utility/gmxassert.h"
  58 #include "gromacs/utility/smalloc.h"
  59
  60 #include "testutils/refdata.h"
  61 #include "testutils/testasserts.h"
  62
  63 namespace
  64 {
  65
  66 /********************************************************************
  67  * SurfaceAreaTest
  68  */
  69
  70 class SurfaceAreaTest : public ::testing::Test
  71 {
  72 public:
  73     SurfaceAreaTest() :
  74         box_(),
  75         rng_(12345),
  76         area_(0.0),
  77         volume_(0.0),
  78         atomArea_(nullptr),
  79         dotCount_(0),
  80         dots_(nullptr)
  81     {
  82     }
  83     ~SurfaceAreaTest() override
  84     {
  85         sfree(atomArea_);
  86         sfree(dots_);
  87     }
  88
  89     void addSphere(real x, real y, real z, real radius, bool bAddToIndex = true)
  90     {
  91         if (bAddToIndex)
  92         {
  93             index_.push_back(x_.size());
  94         }
  95         x_.emplace_back(x, y, z);
  96         radius_.push_back(radius);
  97     }
  98
  99     void generateRandomPosition(rvec x, real* radius)
 100     {
 101         rvec                               fx;
 102         gmx::UniformRealDistribution<real> dist;
 103
 104         fx[XX] = dist(rng_);
 105         fx[YY] = dist(rng_);
 106         fx[ZZ] = dist(rng_);
 107         mvmul(box_, fx, x);
 108         *radius = 1.5 * dist(rng_) + 0.5;
 109     }
 110
 111     void generateRandomPositions(int count)
 112     {
 113         x_.reserve(count);
 114         radius_.reserve(count);
 115         index_.reserve(count);
 116         for (int i = 0; i < count; ++i)
 117         {
 118             rvec x;
 119             real radius;
 120             generateRandomPosition(x, &radius);
 121             addSphere(x[XX], x[YY], x[ZZ], radius);
 122         }
 123     }
 124     void translatePoints(real x, real y, real z)
 125     {
 126         for (size_t i = 0; i < x_.size(); ++i)
 127         {
 128             x_[i][XX] += x;
 129             x_[i][YY] += y;
 130             x_[i][ZZ] += z;
 131         }
 132     }
 133
 134     void calculate(int ndots, int flags, bool bPBC)
 135     {
 136         volume_ = 0.0;
 137         sfree(atomArea_);
 138         atomArea_ = nullptr;
 139         dotCount_ = 0;
 140         sfree(dots_);
 141         dots_ = nullptr;
 142         t_pbc pbc;
 143         if (bPBC)
 144         {
 145             set_pbc(&pbc, PbcType::Xyz, box_);
 146         }
 147         gmx::SurfaceAreaCalculator calculator;
 148         calculator.setDotCount(ndots);
 149         calculator.setRadii(radius_);
 150         calculator.calculate(as_rvec_array(x_.data()),
 151                              bPBC ? &pbc : nullptr,
 152                              index_.size(),
 153                              index_.data(),
 154                              flags,
 155                              &area_,
 156                              &volume_,
 157                              &atomArea_,
 158                              &dots_,
 159                              &dotCount_);
 160     }
 161     real resultArea() const { return area_; }
 162     real resultVolume() const { return volume_; }
 163     real atomArea(int index) const { return atomArea_[index]; }
 164
 165     void checkReference(gmx::test::TestReferenceChecker* checker, const char* id, bool checkDotCoordinates)
 166     {
 167         gmx::test::TestReferenceChecker compound(checker->checkCompound("SASA", id));
 168         compound.checkReal(area_, "Area");
 169         if (volume_ > 0.0)
 170         {
 171             compound.checkReal(volume_, "Volume");
 172         }
 173         if (atomArea_ != nullptr)
 174         {
 175             compound.checkSequenceArray(index_.size(), atomArea_, "AtomArea");
 176         }
 177         if (dots_ != nullptr)
 178         {
 179             if (checkDotCoordinates)
 180             {
 181                 // The algorithm may produce the dots in different order in
 182                 // single and double precision due to some internal
 183                 // sorting...
 184                 std::qsort(dots_, dotCount_, sizeof(rvec), &dotComparer);
 185                 compound.checkSequenceArray(3 * dotCount_, dots_, "Dots");
 186             }
 187             else
 188             {
 189                 compound.checkInteger(dotCount_, "DotCount");
 190             }
 191         }
 192     }
 193
 194     gmx::test::TestReferenceData data_;
 195     matrix                       box_;
 196
 197 private:
 198     static int dotComparer(const void* a, const void* b)
 199     {
 200         for (int d = DIM - 1; d >= 0; --d)
 201         {
 202             const real ad = reinterpret_cast<const real*>(a)[d];
 203             const real bd = reinterpret_cast<const real*>(b)[d];
 204             // A fudge factor is needed to get an ordering that is the same
 205             // in single and double precision, since the points are not
 206             // exactly on the same Z plane even though in exact arithmetic
 207             // they probably would be.
 208             if (ad < bd - 0.001)
 209             {
 210                 return -1;
 211             }
 212             else if (ad > bd + 0.001)
 213             {
 214                 return 1;
 215             }
 216         }
 217         return 0;
 218     }
 219
 220     gmx::DefaultRandomEngine rng_;
 221     std::vector<gmx::RVec>   x_;
 222     std::vector<real>        radius_;
 223     std::vector<int>         index_;
 224
 225     real  area_;
 226     real  volume_;
 227     real* atomArea_;
 228     int   dotCount_;
 229     real* dots_;
 230 };
 231
 232 TEST_F(SurfaceAreaTest, ComputesSinglePoint)
 233 {
 234     gmx::test::FloatingPointTolerance tolerance(gmx::test::defaultRealTolerance());
 235     addSphere(1, 1, 1, 1);
 236     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA, false));
 237     EXPECT_REAL_EQ_TOL(4 * M_PI, resultArea(), tolerance);
 238     EXPECT_REAL_EQ_TOL(4 * M_PI, atomArea(0), tolerance);
 239     EXPECT_REAL_EQ_TOL(4 * M_PI / 3, resultVolume(), tolerance);
 240 }
 241
 242 TEST_F(SurfaceAreaTest, ComputesTwoPoints)
 243 {
 244     gmx::test::FloatingPointTolerance tolerance(gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 245     addSphere(1, 1, 1, 1);
 246     addSphere(2, 1, 1, 1);
 247     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 248     EXPECT_REAL_EQ_TOL(2 * 2 * M_PI * 1.5, resultArea(), tolerance);
 249     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(0), tolerance);
 250     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(1), tolerance);
 251 }
 252
 253 TEST_F(SurfaceAreaTest, ComputesTwoPointsOfUnequalRadius)
 254 {
 255     gmx::test::FloatingPointTolerance tolerance(gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 256     // Spheres of radius 1 and 2 with intersection at 1.5
 257     const real dist = 0.5 + sqrt(3.25);
 258     addSphere(1.0, 1.0, 1.0, 1);
 259     addSphere(1.0 + dist, 1.0, 1.0, 2);
 260     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 261     EXPECT_REAL_EQ_TOL(2 * M_PI * (1.5 + (dist - 0.5 + 2) * 2), resultArea(), tolerance);
 262     EXPECT_REAL_EQ_TOL(2 * M_PI * 1.5, atomArea(0), tolerance);
 263     EXPECT_REAL_EQ_TOL(2 * M_PI * (dist - 0.5 + 2) * 2, atomArea(1), tolerance);
 264 }
 265
 266 TEST_F(SurfaceAreaTest, SurfacePoints12)
 267 {
 268     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 269     addSphere(0, 0, 0, 1);
 270     ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
 271     checkReference(&checker, "Surface", true);
 272 }
 273
 274 TEST_F(SurfaceAreaTest, SurfacePoints32)
 275 {
 276     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 277     addSphere(0, 0, 0, 1);
 278     ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
 279     checkReference(&checker, "Surface", true);
 280 }
 281
 282 TEST_F(SurfaceAreaTest, SurfacePoints42)
 283 {
 284     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 285     addSphere(0, 0, 0, 1);
 286     ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
 287     checkReference(&checker, "Surface", true);
 288 }
 289
 290 TEST_F(SurfaceAreaTest, SurfacePoints122)
 291 {
 292     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 293     addSphere(0, 0, 0, 1);
 294     ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
 295     checkReference(&checker, "Surface", true);
 296 }
 297
 298 TEST_F(SurfaceAreaTest, Computes100Points)
 299 {
 300     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 301     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 302     box_[XX][XX] = 10.0;
 303     box_[YY][YY] = 10.0;
 304     box_[ZZ][ZZ] = 10.0;
 305     generateRandomPositions(100);
 306     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, false));
 307     checkReference(&checker, "100Points", false);
 308 }
 309
 310 TEST_F(SurfaceAreaTest, Computes100PointsWithRectangularPBC)
 311 {
 312     // TODO: It would be nice to check that this produces the same result as
 313     // without PBC, without duplicating the reference files.
 314     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 315     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 316     box_[XX][XX] = 10.0;
 317     box_[YY][YY] = 10.0;
 318     box_[ZZ][ZZ] = 10.0;
 319     generateRandomPositions(100);
 320     box_[XX][XX]    = 20.0;
 321     box_[YY][YY]    = 20.0;
 322     box_[ZZ][ZZ]    = 20.0;
 323     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 324     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 325     checkReference(&checker, "100Points", false);
 326
 327     translatePoints(15.0, 0, 0);
 328     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 329     checkReference(&checker, "100Points", false);
 330
 331     translatePoints(-15.0, 15.0, 0);
 332     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 333     checkReference(&checker, "100Points", false);
 334
 335     translatePoints(0, -15.0, 15.0);
 336     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 337     checkReference(&checker, "100Points", false);
 338 }
 339
 340 TEST_F(SurfaceAreaTest, Computes100PointsWithTriclinicPBC)
 341 {
 342     // TODO: It would be nice to check that this produces the same result as
 343     // without PBC, without duplicating the reference files.
 344     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 345     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 346     box_[XX][XX] = 10.0;
 347     box_[YY][YY] = 10.0;
 348     box_[ZZ][ZZ] = 10.0;
 349     generateRandomPositions(100);
 350     box_[XX][XX] = 20.0;
 351     box_[YY][XX] = 10.0;
 352     box_[YY][YY] = 10.0 * sqrt(3.0);
 353     box_[ZZ][XX] = 10.0;
 354     box_[ZZ][YY] = 10.0 * sqrt(1.0 / 3.0);
 355     box_[ZZ][ZZ] = 20.0 * sqrt(2.0 / 3.0);
 356
 357     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 358     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 359     checkReference(&checker, "100Points", false);
 360
 361     translatePoints(15.0, 0, 0);
 362     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 363     checkReference(&checker, "100Points", false);
 364
 365     translatePoints(-15.0, box_[YY][YY] - 5.0, 0);
 366     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 367     checkReference(&checker, "100Points", false);
 368
 369     translatePoints(0, -(box_[YY][YY] - 5.0), 15.0);
 370     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 371     checkReference(&checker, "100Points", false);
 372 }
 373
 374 } // namespace