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             : box_(), rng_(12345), area_(0.0), volume_(0.0),
  74               atomArea_(nullptr), dotCount_(0), dots_(nullptr)
  75         {
  76         }
  77         ~SurfaceAreaTest() override
  78         {
  79             sfree(atomArea_);
  80             sfree(dots_);
  81         }
  82
  83         void addSphere(real x, real y, real z, real radius,
  84                        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;
 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, epbcXYZ, box_);
 141             }
 142             ASSERT_NO_THROW_GMX(
 143                     {
 144                         gmx::SurfaceAreaCalculator calculator;
 145                         calculator.setDotCount(ndots);
 146                         calculator.setRadii(radius_);
 147                         calculator.calculate(as_rvec_array(x_.data()), bPBC ? &pbc : nullptr,
 148                                              index_.size(), index_.data(), flags,
 149                                              &area_, &volume_, &atomArea_,
 150                                              &dots_, &dotCount_);
 151                     });
 152         }
 153         real resultArea() const { return area_; }
 154         real resultVolume() const { return volume_; }
 155         real atomArea(int index) const { return atomArea_[index]; }
 156
 157         void checkReference(gmx::test::TestReferenceChecker *checker, const char *id,
 158                             bool checkDotCoordinates)
 159         {
 160             gmx::test::TestReferenceChecker compound(
 161                     checker->checkCompound("SASA", id));
 162             compound.checkReal(area_, "Area");
 163             if (volume_ > 0.0)
 164             {
 165                 compound.checkReal(volume_, "Volume");
 166             }
 167             if (atomArea_ != nullptr)
 168             {
 169                 compound.checkSequenceArray(index_.size(), atomArea_, "AtomArea");
 170             }
 171             if (dots_ != nullptr)
 172             {
 173                 if (checkDotCoordinates)
 174                 {
 175                     // The algorithm may produce the dots in different order in
 176                     // single and double precision due to some internal
 177                     // sorting...
 178                     std::qsort(dots_, dotCount_, sizeof(rvec), &dotComparer);
 179                     compound.checkSequenceArray(3*dotCount_, dots_, "Dots");
 180                 }
 181                 else
 182                 {
 183                     compound.checkInteger(dotCount_, "DotCount");
 184                 }
 185             }
 186         }
 187
 188         gmx::test::TestReferenceData    data_;
 189         matrix                          box_;
 190
 191     private:
 192         static int dotComparer(const void *a, const void *b)
 193         {
 194             for (int d = DIM - 1; d >= 0; --d)
 195             {
 196                 const real ad = reinterpret_cast<const real *>(a)[d];
 197                 const real bd = reinterpret_cast<const real *>(b)[d];
 198                 // A fudge factor is needed to get an ordering that is the same
 199                 // in single and double precision, since the points are not
 200                 // exactly on the same Z plane even though in exact arithmetic
 201                 // they probably would be.
 202                 if (ad < bd - 0.001)
 203                 {
 204                     return -1;
 205                 }
 206                 else if (ad > bd + 0.001)
 207                 {
 208                     return 1;
 209                 }
 210             }
 211             return 0;
 212         }
 213
 214         gmx::DefaultRandomEngine rng_;
 215         std::vector<gmx::RVec>   x_;
 216         std::vector<real>        radius_;
 217         std::vector<int>         index_;
 218
 219         real                     area_;
 220         real                     volume_;
 221         real                    *atomArea_;
 222         int                      dotCount_;
 223         real                    *dots_;
 224 };
 225
 226 TEST_F(SurfaceAreaTest, ComputesSinglePoint)
 227 {
 228     gmx::test::FloatingPointTolerance tolerance(
 229             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(
 240             gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 241     addSphere(1, 1, 1, 1);
 242     addSphere(2, 1, 1, 1);
 243     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 244     EXPECT_REAL_EQ_TOL(2*2*M_PI*1.5, resultArea(), tolerance);
 245     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
 246     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(1), tolerance);
 247 }
 248
 249 TEST_F(SurfaceAreaTest, ComputesTwoPointsOfUnequalRadius)
 250 {
 251     gmx::test::FloatingPointTolerance tolerance(
 252             gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 253     // Spheres of radius 1 and 2 with intersection at 1.5
 254     const real dist = 0.5 + sqrt(3.25);
 255     addSphere(1.0, 1.0, 1.0, 1);
 256     addSphere(1.0 + dist, 1.0, 1.0, 2);
 257     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 258     EXPECT_REAL_EQ_TOL(2*M_PI*(1.5 + (dist - 0.5 + 2)*2), resultArea(), tolerance);
 259     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
 260     EXPECT_REAL_EQ_TOL(2*M_PI*(dist - 0.5 + 2)*2, atomArea(1), tolerance);
 261 }
 262
 263 TEST_F(SurfaceAreaTest, SurfacePoints12)
 264 {
 265     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 266     addSphere(0, 0, 0, 1);
 267     ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
 268     checkReference(&checker, "Surface", true);
 269 }
 270
 271 TEST_F(SurfaceAreaTest, SurfacePoints32)
 272 {
 273     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 274     addSphere(0, 0, 0, 1);
 275     ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
 276     checkReference(&checker, "Surface", true);
 277 }
 278
 279 TEST_F(SurfaceAreaTest, SurfacePoints42)
 280 {
 281     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 282     addSphere(0, 0, 0, 1);
 283     ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
 284     checkReference(&checker, "Surface", true);
 285 }
 286
 287 TEST_F(SurfaceAreaTest, SurfacePoints122)
 288 {
 289     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 290     addSphere(0, 0, 0, 1);
 291     ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
 292     checkReference(&checker, "Surface", true);
 293 }
 294
 295 TEST_F(SurfaceAreaTest, Computes100Points)
 296 {
 297     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 298     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 299     box_[XX][XX] = 10.0;
 300     box_[YY][YY] = 10.0;
 301     box_[ZZ][ZZ] = 10.0;
 302     generateRandomPositions(100);
 303     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, false));
 304     checkReference(&checker, "100Points", false);
 305 }
 306
 307 TEST_F(SurfaceAreaTest, Computes100PointsWithRectangularPBC)
 308 {
 309     // TODO: It would be nice to check that this produces the same result as
 310     // without PBC, without duplicating the reference files.
 311     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 312     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 313     box_[XX][XX] = 10.0;
 314     box_[YY][YY] = 10.0;
 315     box_[ZZ][ZZ] = 10.0;
 316     generateRandomPositions(100);
 317     box_[XX][XX] = 20.0;
 318     box_[YY][YY] = 20.0;
 319     box_[ZZ][ZZ] = 20.0;
 320     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 321     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 322     checkReference(&checker, "100Points", false);
 323
 324     translatePoints(15.0, 0, 0);
 325     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 326     checkReference(&checker, "100Points", false);
 327
 328     translatePoints(-15.0, 15.0, 0);
 329     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 330     checkReference(&checker, "100Points", false);
 331
 332     translatePoints(0, -15.0, 15.0);
 333     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 334     checkReference(&checker, "100Points", false);
 335 }
 336
 337 TEST_F(SurfaceAreaTest, Computes100PointsWithTriclinicPBC)
 338 {
 339     // TODO: It would be nice to check that this produces the same result as
 340     // without PBC, without duplicating the reference files.
 341     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 342     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 343     box_[XX][XX] = 10.0;
 344     box_[YY][YY] = 10.0;
 345     box_[ZZ][ZZ] = 10.0;
 346     generateRandomPositions(100);
 347     box_[XX][XX] = 20.0;
 348     box_[YY][XX] = 10.0;
 349     box_[YY][YY] = 10.0*sqrt(3.0);
 350     box_[ZZ][XX] = 10.0;
 351     box_[ZZ][YY] = 10.0*sqrt(1.0/3.0);
 352     box_[ZZ][ZZ] = 20.0*sqrt(2.0/3.0);
 353
 354     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 355     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 356     checkReference(&checker, "100Points", false);
 357
 358     translatePoints(15.0, 0, 0);
 359     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 360     checkReference(&checker, "100Points", false);
 361
 362     translatePoints(-15.0, box_[YY][YY] - 5.0, 0);
 363     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 364     checkReference(&checker, "100Points", false);
 365
 366     translatePoints(0, -(box_[YY][YY] - 5.0), 15.0);
 367     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 368     checkReference(&checker, "100Points", false);
 369 }
 370
 371 } // namespace