src/gromacs/trajectoryanalysis/tests/surfacearea.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests for the surface area calculation used by the `sasa` analysis module.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_trajectoryanalysis
  41  */
  42 #include "gmxpre.h"
  43
  44 #include "gromacs/trajectoryanalysis/modules/surfacearea.h"
  45
  46 #include <cstdlib>
  47
  48 #include <gtest/gtest.h>
  49
  50 #include "gromacs/math/utilities.h"
  51 #include "gromacs/math/vec.h"
  52 #include "gromacs/pbcutil/pbc.h"
  53 #include "gromacs/random/threefry.h"
  54 #include "gromacs/random/uniformrealdistribution.h"
  55 #include "gromacs/utility/arrayref.h"
  56 #include "gromacs/utility/gmxassert.h"
  57 #include "gromacs/utility/smalloc.h"
  58
  59 #include "testutils/refdata.h"
  60 #include "testutils/testasserts.h"
  61
  62 namespace
  63 {
  64
  65 /********************************************************************
  66  * SurfaceAreaTest
  67  */
  68
  69 class SurfaceAreaTest : public ::testing::Test
  70 {
  71     public:
  72         SurfaceAreaTest()
  73             : rng_(12345), area_(0.0), volume_(0.0),
  74               atomArea_(nullptr), dotCount_(0), dots_(nullptr)
  75         {
  76             clear_mat(box_);
  77         }
  78         ~SurfaceAreaTest()
  79         {
  80             sfree(atomArea_);
  81             sfree(dots_);
  82         }
  83
  84         void addSphere(real x, real y, real z, real radius,
  85                        bool bAddToIndex = true)
  86         {
  87             if (bAddToIndex)
  88             {
  89                 index_.push_back(x_.size());
  90             }
  91             x_.emplace_back(x, y, z);
  92             radius_.push_back(radius);
  93         }
  94
  95         void generateRandomPosition(rvec x, real *radius)
  96         {
  97             rvec fx;
  98             gmx::UniformRealDistribution<real> dist;
  99
 100             fx[XX]  = dist(rng_);
 101             fx[YY]  = dist(rng_);
 102             fx[ZZ]  = dist(rng_);
 103             mvmul(box_, fx, x);
 104             *radius = 1.5*dist(rng_) + 0.5;
 105         }
 106
 107         void addDummySpheres(int count)
 108         {
 109             for (int i = 0; i < count; ++i)
 110             {
 111                 rvec x;
 112                 real radius;
 113                 generateRandomPosition(x, &radius);
 114                 addSphere(x[XX], x[YY], x[ZZ], radius, false);
 115             }
 116         }
 117
 118         void generateRandomPositions(int count)
 119         {
 120             x_.reserve(count);
 121             radius_.reserve(count);
 122             index_.reserve(count);
 123             for (int i = 0; i < count; ++i)
 124             {
 125                 rvec x;
 126                 real radius;
 127                 generateRandomPosition(x, &radius);
 128                 addSphere(x[XX], x[YY], x[ZZ], radius);
 129             }
 130         }
 131         void translatePoints(real x, real y, real z)
 132         {
 133             for (size_t i = 0; i < x_.size(); ++i)
 134             {
 135                 x_[i][XX] += x;
 136                 x_[i][YY] += y;
 137                 x_[i][ZZ] += z;
 138             }
 139         }
 140
 141         void calculate(int ndots, int flags, bool bPBC)
 142         {
 143             volume_   = 0.0;
 144             sfree(atomArea_);
 145             atomArea_ = nullptr;
 146             dotCount_ = 0;
 147             sfree(dots_);
 148             dots_     = nullptr;
 149             t_pbc       pbc;
 150             if (bPBC)
 151             {
 152                 set_pbc(&pbc, epbcXYZ, box_);
 153             }
 154             ASSERT_NO_THROW_GMX(
 155                     {
 156                         gmx::SurfaceAreaCalculator calculator;
 157                         calculator.setDotCount(ndots);
 158                         calculator.setRadii(radius_);
 159                         calculator.calculate(as_rvec_array(x_.data()), bPBC ? &pbc : nullptr,
 160                                              index_.size(), index_.data(), flags,
 161                                              &area_, &volume_, &atomArea_,
 162                                              &dots_, &dotCount_);
 163                     });
 164         }
 165         real resultArea() const { return area_; }
 166         real resultVolume() const { return volume_; }
 167         real atomArea(int index) const { return atomArea_[index]; }
 168
 169         void checkReference(gmx::test::TestReferenceChecker *checker, const char *id,
 170                             bool checkDotCoordinates)
 171         {
 172             gmx::test::TestReferenceChecker compound(
 173                     checker->checkCompound("SASA", id));
 174             compound.checkReal(area_, "Area");
 175             if (volume_ > 0.0)
 176             {
 177                 compound.checkReal(volume_, "Volume");
 178             }
 179             if (atomArea_ != nullptr)
 180             {
 181                 compound.checkSequenceArray(index_.size(), atomArea_, "AtomArea");
 182             }
 183             if (dots_ != nullptr)
 184             {
 185                 if (checkDotCoordinates)
 186                 {
 187                     // The algorithm may produce the dots in different order in
 188                     // single and double precision due to some internal
 189                     // sorting...
 190                     std::qsort(dots_, dotCount_, sizeof(rvec), &dotComparer);
 191                     compound.checkSequenceArray(3*dotCount_, dots_, "Dots");
 192                 }
 193                 else
 194                 {
 195                     compound.checkInteger(dotCount_, "DotCount");
 196                 }
 197             }
 198         }
 199
 200         gmx::test::TestReferenceData    data_;
 201         matrix                          box_;
 202
 203     private:
 204         static int dotComparer(const void *a, const void *b)
 205         {
 206             for (int d = DIM - 1; d >= 0; --d)
 207             {
 208                 const real ad = reinterpret_cast<const real *>(a)[d];
 209                 const real bd = reinterpret_cast<const real *>(b)[d];
 210                 // A fudge factor is needed to get an ordering that is the same
 211                 // in single and double precision, since the points are not
 212                 // exactly on the same Z plane even though in exact arithmetic
 213                 // they probably would be.
 214                 if (ad < bd - 0.001)
 215                 {
 216                     return -1;
 217                 }
 218                 else if (ad > bd + 0.001)
 219                 {
 220                     return 1;
 221                 }
 222             }
 223             return 0;
 224         }
 225
 226         gmx::DefaultRandomEngine rng_;
 227         std::vector<gmx::RVec>   x_;
 228         std::vector<real>        radius_;
 229         std::vector<int>         index_;
 230
 231         real                     area_;
 232         real                     volume_;
 233         real                    *atomArea_;
 234         int                      dotCount_;
 235         real                    *dots_;
 236 };
 237
 238 TEST_F(SurfaceAreaTest, ComputesSinglePoint)
 239 {
 240     gmx::test::FloatingPointTolerance tolerance(
 241             gmx::test::defaultRealTolerance());
 242     addSphere(1, 1, 1, 1);
 243     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA, false));
 244     EXPECT_REAL_EQ_TOL(4*M_PI, resultArea(), tolerance);
 245     EXPECT_REAL_EQ_TOL(4*M_PI, atomArea(0), tolerance);
 246     EXPECT_REAL_EQ_TOL(4*M_PI/3, resultVolume(), tolerance);
 247 }
 248
 249 TEST_F(SurfaceAreaTest, ComputesTwoPoints)
 250 {
 251     gmx::test::FloatingPointTolerance tolerance(
 252             gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 253     addSphere(1, 1, 1, 1);
 254     addSphere(2, 1, 1, 1);
 255     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 256     EXPECT_REAL_EQ_TOL(2*2*M_PI*1.5, resultArea(), tolerance);
 257     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
 258     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(1), tolerance);
 259 }
 260
 261 TEST_F(SurfaceAreaTest, ComputesTwoPointsOfUnequalRadius)
 262 {
 263     gmx::test::FloatingPointTolerance tolerance(
 264             gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 265     // Spheres of radius 1 and 2 with intersection at 1.5
 266     const real dist = 0.5 + sqrt(3.25);
 267     addSphere(1.0, 1.0, 1.0, 1);
 268     addSphere(1.0 + dist, 1.0, 1.0, 2);
 269     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 270     EXPECT_REAL_EQ_TOL(2*M_PI*(1.5 + (dist - 0.5 + 2)*2), resultArea(), tolerance);
 271     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
 272     EXPECT_REAL_EQ_TOL(2*M_PI*(dist - 0.5 + 2)*2, atomArea(1), tolerance);
 273 }
 274
 275 TEST_F(SurfaceAreaTest, SurfacePoints12)
 276 {
 277     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 278     addSphere(0, 0, 0, 1);
 279     ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
 280     checkReference(&checker, "Surface", true);
 281 }
 282
 283 TEST_F(SurfaceAreaTest, SurfacePoints32)
 284 {
 285     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 286     addSphere(0, 0, 0, 1);
 287     ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
 288     checkReference(&checker, "Surface", true);
 289 }
 290
 291 TEST_F(SurfaceAreaTest, SurfacePoints42)
 292 {
 293     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 294     addSphere(0, 0, 0, 1);
 295     ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
 296     checkReference(&checker, "Surface", true);
 297 }
 298
 299 TEST_F(SurfaceAreaTest, SurfacePoints122)
 300 {
 301     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 302     addSphere(0, 0, 0, 1);
 303     ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
 304     checkReference(&checker, "Surface", true);
 305 }
 306
 307 TEST_F(SurfaceAreaTest, Computes100Points)
 308 {
 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     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, false));
 316     checkReference(&checker, "100Points", false);
 317 }
 318
 319 TEST_F(SurfaceAreaTest, Computes100PointsWithRectangularPBC)
 320 {
 321     // TODO: It would be nice to check that this produces the same result as
 322     // without PBC, without duplicating the reference files.
 323     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 324     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 325     box_[XX][XX] = 10.0;
 326     box_[YY][YY] = 10.0;
 327     box_[ZZ][ZZ] = 10.0;
 328     generateRandomPositions(100);
 329     box_[XX][XX] = 20.0;
 330     box_[YY][YY] = 20.0;
 331     box_[ZZ][ZZ] = 20.0;
 332     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 333     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 334     checkReference(&checker, "100Points", false);
 335
 336     translatePoints(15.0, 0, 0);
 337     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 338     checkReference(&checker, "100Points", false);
 339
 340     translatePoints(-15.0, 15.0, 0);
 341     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 342     checkReference(&checker, "100Points", false);
 343
 344     translatePoints(0, -15.0, 15.0);
 345     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 346     checkReference(&checker, "100Points", false);
 347 }
 348
 349 TEST_F(SurfaceAreaTest, Computes100PointsWithTriclinicPBC)
 350 {
 351     // TODO: It would be nice to check that this produces the same result as
 352     // without PBC, without duplicating the reference files.
 353     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 354     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 355     box_[XX][XX] = 10.0;
 356     box_[YY][YY] = 10.0;
 357     box_[ZZ][ZZ] = 10.0;
 358     generateRandomPositions(100);
 359     box_[XX][XX] = 20.0;
 360     box_[YY][XX] = 10.0;
 361     box_[YY][YY] = 10.0*sqrt(3.0);
 362     box_[ZZ][XX] = 10.0;
 363     box_[ZZ][YY] = 10.0*sqrt(1.0/3.0);
 364     box_[ZZ][ZZ] = 20.0*sqrt(2.0/3.0);
 365
 366     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 367     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 368     checkReference(&checker, "100Points", false);
 369
 370     translatePoints(15.0, 0, 0);
 371     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 372     checkReference(&checker, "100Points", false);
 373
 374     translatePoints(-15.0, box_[YY][YY] - 5.0, 0);
 375     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 376     checkReference(&checker, "100Points", false);
 377
 378     translatePoints(0, -(box_[YY][YY] - 5.0), 15.0);
 379     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 380     checkReference(&checker, "100Points", false);
 381 }
 382
 383 } // namespace