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 generateRandomPositions(int count)
 108         {
 109             x_.reserve(count);
 110             radius_.reserve(count);
 111             index_.reserve(count);
 112             for (int i = 0; i < count; ++i)
 113             {
 114                 rvec x;
 115                 real radius;
 116                 generateRandomPosition(x, &radius);
 117                 addSphere(x[XX], x[YY], x[ZZ], radius);
 118             }
 119         }
 120         void translatePoints(real x, real y, real z)
 121         {
 122             for (size_t i = 0; i < x_.size(); ++i)
 123             {
 124                 x_[i][XX] += x;
 125                 x_[i][YY] += y;
 126                 x_[i][ZZ] += z;
 127             }
 128         }
 129
 130         void calculate(int ndots, int flags, bool bPBC)
 131         {
 132             volume_   = 0.0;
 133             sfree(atomArea_);
 134             atomArea_ = nullptr;
 135             dotCount_ = 0;
 136             sfree(dots_);
 137             dots_     = nullptr;
 138             t_pbc       pbc;
 139             if (bPBC)
 140             {
 141                 set_pbc(&pbc, epbcXYZ, box_);
 142             }
 143             ASSERT_NO_THROW_GMX(
 144                     {
 145                         gmx::SurfaceAreaCalculator calculator;
 146                         calculator.setDotCount(ndots);
 147                         calculator.setRadii(radius_);
 148                         calculator.calculate(as_rvec_array(x_.data()), bPBC ? &pbc : nullptr,
 149                                              index_.size(), index_.data(), flags,
 150                                              &area_, &volume_, &atomArea_,
 151                                              &dots_, &dotCount_);
 152                     });
 153         }
 154         real resultArea() const { return area_; }
 155         real resultVolume() const { return volume_; }
 156         real atomArea(int index) const { return atomArea_[index]; }
 157
 158         void checkReference(gmx::test::TestReferenceChecker *checker, const char *id,
 159                             bool checkDotCoordinates)
 160         {
 161             gmx::test::TestReferenceChecker compound(
 162                     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(
 230             gmx::test::defaultRealTolerance());
 231     addSphere(1, 1, 1, 1);
 232     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA, false));
 233     EXPECT_REAL_EQ_TOL(4*M_PI, resultArea(), tolerance);
 234     EXPECT_REAL_EQ_TOL(4*M_PI, atomArea(0), tolerance);
 235     EXPECT_REAL_EQ_TOL(4*M_PI/3, resultVolume(), tolerance);
 236 }
 237
 238 TEST_F(SurfaceAreaTest, ComputesTwoPoints)
 239 {
 240     gmx::test::FloatingPointTolerance tolerance(
 241             gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 242     addSphere(1, 1, 1, 1);
 243     addSphere(2, 1, 1, 1);
 244     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 245     EXPECT_REAL_EQ_TOL(2*2*M_PI*1.5, resultArea(), tolerance);
 246     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
 247     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(1), tolerance);
 248 }
 249
 250 TEST_F(SurfaceAreaTest, ComputesTwoPointsOfUnequalRadius)
 251 {
 252     gmx::test::FloatingPointTolerance tolerance(
 253             gmx::test::relativeToleranceAsFloatingPoint(1.0, 0.005));
 254     // Spheres of radius 1 and 2 with intersection at 1.5
 255     const real dist = 0.5 + sqrt(3.25);
 256     addSphere(1.0, 1.0, 1.0, 1);
 257     addSphere(1.0 + dist, 1.0, 1.0, 2);
 258     ASSERT_NO_FATAL_FAILURE(calculate(1000, FLAG_ATOM_AREA, false));
 259     EXPECT_REAL_EQ_TOL(2*M_PI*(1.5 + (dist - 0.5 + 2)*2), resultArea(), tolerance);
 260     EXPECT_REAL_EQ_TOL(2*M_PI*1.5, atomArea(0), tolerance);
 261     EXPECT_REAL_EQ_TOL(2*M_PI*(dist - 0.5 + 2)*2, atomArea(1), tolerance);
 262 }
 263
 264 TEST_F(SurfaceAreaTest, SurfacePoints12)
 265 {
 266     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 267     addSphere(0, 0, 0, 1);
 268     ASSERT_NO_FATAL_FAILURE(calculate(12, FLAG_DOTS, false));
 269     checkReference(&checker, "Surface", true);
 270 }
 271
 272 TEST_F(SurfaceAreaTest, SurfacePoints32)
 273 {
 274     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 275     addSphere(0, 0, 0, 1);
 276     ASSERT_NO_FATAL_FAILURE(calculate(32, FLAG_DOTS, false));
 277     checkReference(&checker, "Surface", true);
 278 }
 279
 280 TEST_F(SurfaceAreaTest, SurfacePoints42)
 281 {
 282     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 283     addSphere(0, 0, 0, 1);
 284     ASSERT_NO_FATAL_FAILURE(calculate(42, FLAG_DOTS, false));
 285     checkReference(&checker, "Surface", true);
 286 }
 287
 288 TEST_F(SurfaceAreaTest, SurfacePoints122)
 289 {
 290     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 291     addSphere(0, 0, 0, 1);
 292     ASSERT_NO_FATAL_FAILURE(calculate(122, FLAG_DOTS, false));
 293     checkReference(&checker, "Surface", true);
 294 }
 295
 296 TEST_F(SurfaceAreaTest, Computes100Points)
 297 {
 298     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 299     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 300     box_[XX][XX] = 10.0;
 301     box_[YY][YY] = 10.0;
 302     box_[ZZ][ZZ] = 10.0;
 303     generateRandomPositions(100);
 304     ASSERT_NO_FATAL_FAILURE(calculate(24, FLAG_VOLUME | FLAG_ATOM_AREA | FLAG_DOTS, false));
 305     checkReference(&checker, "100Points", false);
 306 }
 307
 308 TEST_F(SurfaceAreaTest, Computes100PointsWithRectangularPBC)
 309 {
 310     // TODO: It would be nice to check that this produces the same result as
 311     // without PBC, without duplicating the reference files.
 312     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 313     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 314     box_[XX][XX] = 10.0;
 315     box_[YY][YY] = 10.0;
 316     box_[ZZ][ZZ] = 10.0;
 317     generateRandomPositions(100);
 318     box_[XX][XX] = 20.0;
 319     box_[YY][YY] = 20.0;
 320     box_[ZZ][ZZ] = 20.0;
 321     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 322     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 323     checkReference(&checker, "100Points", false);
 324
 325     translatePoints(15.0, 0, 0);
 326     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 327     checkReference(&checker, "100Points", false);
 328
 329     translatePoints(-15.0, 15.0, 0);
 330     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 331     checkReference(&checker, "100Points", false);
 332
 333     translatePoints(0, -15.0, 15.0);
 334     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 335     checkReference(&checker, "100Points", false);
 336 }
 337
 338 TEST_F(SurfaceAreaTest, Computes100PointsWithTriclinicPBC)
 339 {
 340     // TODO: It would be nice to check that this produces the same result as
 341     // without PBC, without duplicating the reference files.
 342     gmx::test::TestReferenceChecker checker(data_.rootChecker());
 343     checker.setDefaultTolerance(gmx::test::absoluteTolerance(0.001));
 344     box_[XX][XX] = 10.0;
 345     box_[YY][YY] = 10.0;
 346     box_[ZZ][ZZ] = 10.0;
 347     generateRandomPositions(100);
 348     box_[XX][XX] = 20.0;
 349     box_[YY][XX] = 10.0;
 350     box_[YY][YY] = 10.0*sqrt(3.0);
 351     box_[ZZ][XX] = 10.0;
 352     box_[ZZ][YY] = 10.0*sqrt(1.0/3.0);
 353     box_[ZZ][ZZ] = 20.0*sqrt(2.0/3.0);
 354
 355     const int flags = FLAG_ATOM_AREA | FLAG_VOLUME | FLAG_DOTS;
 356     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 357     checkReference(&checker, "100Points", false);
 358
 359     translatePoints(15.0, 0, 0);
 360     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 361     checkReference(&checker, "100Points", false);
 362
 363     translatePoints(-15.0, box_[YY][YY] - 5.0, 0);
 364     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 365     checkReference(&checker, "100Points", false);
 366
 367     translatePoints(0, -(box_[YY][YY] - 5.0), 15.0);
 368     ASSERT_NO_FATAL_FAILURE(calculate(24, flags, true));
 369     checkReference(&checker, "100Points", false);
 370 }
 371
 372 } // namespace