src/gromacs/selection/tests/nbsearch.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests selection neighborhood searching.
  38  *
  39  * \todo
  40  * Increase coverage of these tests for different corner cases: other PBC cases
  41  * than full 3D, large cutoffs (larger than half the box size), etc.
  42  * At least some of these probably don't work correctly.
  43  *
  44  * \author Teemu Murtola <teemu.murtola@gmail.com>
  45  * \ingroup module_selection
  46  */
  47 #include <gtest/gtest.h>
  48
  49 #include <cmath>
  50
  51 #include <limits>
  52 #include <set>
  53
  54 #include "gromacs/legacyheaders/gmx_random.h"
  55 #include "gromacs/legacyheaders/pbc.h"
  56 #include "gromacs/legacyheaders/smalloc.h"
  57 #include "gromacs/legacyheaders/vec.h"
  58
  59 #include "gromacs/selection/nbsearch.h"
  60
  61 #include "testutils/testasserts.h"
  62
  63 namespace
  64 {
  65
  66 /********************************************************************
  67  * NeighborhoodSearchTestData
  68  */
  69
  70 class NeighborhoodSearchTestData
  71 {
  72     public:
  73         struct TestPosition
  74         {
  75             TestPosition() : refMinDist(0.0), refNearestPoint(-1)
  76             {
  77                 clear_rvec(x);
  78             }
  79             explicit TestPosition(const rvec x)
  80                 : refMinDist(0.0), refNearestPoint(-1)
  81             {
  82                 copy_rvec(x, this->x);
  83             }
  84
  85             rvec                x;
  86             real                refMinDist;
  87             int                 refNearestPoint;
  88             std::set<int>       refPairs;
  89         };
  90         typedef std::vector<TestPosition> TestPositionList;
  91
  92         NeighborhoodSearchTestData(int seed, real cutoff);
  93         ~NeighborhoodSearchTestData();
  94
  95         void addTestPosition(const rvec x)
  96         {
  97             testPositions_.push_back(TestPosition(x));
  98         }
  99         void generateRandomPosition(rvec x);
 100         void generateRandomRefPositions(int count);
 101         void generateRandomTestPositions(int count);
 102         void computeReferences(t_pbc *pbc);
 103
 104         gmx_rng_t                        rng_;
 105         real                             cutoff_;
 106         matrix                           box_;
 107         t_pbc                            pbc_;
 108         int                              refPosCount_;
 109         rvec                            *refPos_;
 110         TestPositionList                 testPositions_;
 111 };
 112
 113 NeighborhoodSearchTestData::NeighborhoodSearchTestData(int seed, real cutoff)
 114     : rng_(NULL), cutoff_(cutoff), refPosCount_(0), refPos_(NULL)
 115 {
 116     // TODO: Handle errors.
 117     rng_ = gmx_rng_init(seed);
 118     clear_mat(box_);
 119     set_pbc(&pbc_, epbcNONE, box_);
 120 }
 121
 122 NeighborhoodSearchTestData::~NeighborhoodSearchTestData()
 123 {
 124     if (rng_ != NULL)
 125     {
 126         gmx_rng_destroy(rng_);
 127     }
 128     sfree(refPos_);
 129 }
 130
 131 void NeighborhoodSearchTestData::generateRandomPosition(rvec x)
 132 {
 133     rvec fx;
 134     fx[XX] = gmx_rng_uniform_real(rng_);
 135     fx[YY] = gmx_rng_uniform_real(rng_);
 136     fx[ZZ] = gmx_rng_uniform_real(rng_);
 137     mvmul(box_, fx, x);
 138     // Add a small displacement to allow positions outside the box
 139     x[XX] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
 140     x[YY] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
 141     x[ZZ] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
 142 }
 143
 144 void NeighborhoodSearchTestData::generateRandomRefPositions(int count)
 145 {
 146     refPosCount_ = count;
 147     snew(refPos_, refPosCount_);
 148     for (int i = 0; i < refPosCount_; ++i)
 149     {
 150         generateRandomPosition(refPos_[i]);
 151     }
 152 }
 153
 154 void NeighborhoodSearchTestData::generateRandomTestPositions(int count)
 155 {
 156     testPositions_.reserve(count);
 157     for (int i = 0; i < count; ++i)
 158     {
 159         rvec x;
 160         generateRandomPosition(x);
 161         addTestPosition(x);
 162     }
 163 }
 164
 165 void NeighborhoodSearchTestData::computeReferences(t_pbc *pbc)
 166 {
 167     real cutoff = cutoff_;
 168     if (cutoff <= 0)
 169     {
 170         cutoff = std::numeric_limits<real>::max();
 171     }
 172     TestPositionList::iterator i;
 173     for (i = testPositions_.begin(); i != testPositions_.end(); ++i)
 174     {
 175         i->refMinDist      = cutoff;
 176         i->refNearestPoint = -1;
 177         i->refPairs.clear();
 178         for (int j = 0; j < refPosCount_; ++j)
 179         {
 180             rvec dx;
 181             if (pbc != NULL)
 182             {
 183                 pbc_dx(pbc, i->x, refPos_[j], dx);
 184             }
 185             else
 186             {
 187                 rvec_sub(i->x, refPos_[j], dx);
 188             }
 189             const real dist = norm(dx);
 190             if (dist < i->refMinDist)
 191             {
 192                 i->refMinDist      = dist;
 193                 i->refNearestPoint = j;
 194             }
 195             if (dist <= cutoff)
 196             {
 197                 i->refPairs.insert(j);
 198             }
 199         }
 200     }
 201 }
 202
 203 /********************************************************************
 204  * NeighborhoodSearchTest
 205  */
 206
 207 class NeighborhoodSearchTest : public ::testing::Test
 208 {
 209     public:
 210         void testIsWithin(gmx::AnalysisNeighborhoodSearch  *search,
 211                           const NeighborhoodSearchTestData &data);
 212         void testMinimumDistance(gmx::AnalysisNeighborhoodSearch  *search,
 213                                  const NeighborhoodSearchTestData &data);
 214         void testNearestPoint(gmx::AnalysisNeighborhoodSearch  *search,
 215                               const NeighborhoodSearchTestData &data);
 216         void testPairSearch(gmx::AnalysisNeighborhoodSearch  *search,
 217                             const NeighborhoodSearchTestData &data);
 218
 219         gmx::AnalysisNeighborhood        nb_;
 220 };
 221
 222 void NeighborhoodSearchTest::testIsWithin(
 223         gmx::AnalysisNeighborhoodSearch  *search,
 224         const NeighborhoodSearchTestData &data)
 225 {
 226     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 227     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 228     {
 229         const bool bWithin = (i->refMinDist <= data.cutoff_);
 230         EXPECT_EQ(bWithin, search->isWithin(i->x))
 231         << "Distance is " << i->refMinDist;
 232     }
 233 }
 234
 235 void NeighborhoodSearchTest::testMinimumDistance(
 236         gmx::AnalysisNeighborhoodSearch  *search,
 237         const NeighborhoodSearchTestData &data)
 238 {
 239     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 240     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 241     {
 242         const real refDist = i->refMinDist;
 243         EXPECT_NEAR_REL(refDist, search->minimumDistance(i->x), 20*GMX_REAL_EPS);
 244     }
 245 }
 246
 247 void NeighborhoodSearchTest::testNearestPoint(
 248         gmx::AnalysisNeighborhoodSearch  *search,
 249         const NeighborhoodSearchTestData &data)
 250 {
 251     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 252     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 253     {
 254         const gmx::AnalysisNeighborhoodPair pair = search->nearestPoint(i->x);
 255         if (pair.isValid())
 256         {
 257             EXPECT_EQ(i->refNearestPoint, pair.refIndex());
 258             EXPECT_EQ(0, pair.testIndex());
 259         }
 260         else
 261         {
 262             EXPECT_EQ(i->refNearestPoint, -1);
 263         }
 264     }
 265 }
 266
 267 void NeighborhoodSearchTest::testPairSearch(
 268         gmx::AnalysisNeighborhoodSearch  *search,
 269         const NeighborhoodSearchTestData &data)
 270 {
 271     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 272     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 273     {
 274         std::set<int> checkSet                         = i->refPairs;
 275         gmx::AnalysisNeighborhoodPairSearch pairSearch =
 276             search->startPairSearch(i->x);
 277         gmx::AnalysisNeighborhoodPair       pair;
 278         while (pairSearch.findNextPair(&pair))
 279         {
 280             EXPECT_EQ(0, pair.testIndex());
 281             if (checkSet.erase(pair.refIndex()) == 0)
 282             {
 283                 // TODO: Check whether the same pair was returned more than
 284                 // once and give a better error message if so.
 285                 ADD_FAILURE()
 286                 << "Expected: Position " << pair.refIndex()
 287                 << " is within cutoff.\n"
 288                 << "  Actual: It is not.";
 289             }
 290         }
 291         EXPECT_TRUE(checkSet.empty()) << "Some positions were not returned by the pair search.";
 292     }
 293 }
 294
 295 /********************************************************************
 296  * Test data generation
 297  */
 298
 299 class TrivialTestData
 300 {
 301     public:
 302         static const NeighborhoodSearchTestData &get()
 303         {
 304             static TrivialTestData singleton;
 305             return singleton.data_;
 306         }
 307
 308         TrivialTestData() : data_(12345, 1.0)
 309         {
 310             data_.box_[XX][XX] = 5.0;
 311             data_.box_[YY][YY] = 5.0;
 312             data_.box_[ZZ][ZZ] = 5.0;
 313             data_.generateRandomRefPositions(10);
 314             data_.generateRandomTestPositions(5);
 315             set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
 316             data_.computeReferences(&data_.pbc_);
 317         }
 318
 319     private:
 320         NeighborhoodSearchTestData data_;
 321 };
 322
 323 class RandomBoxFullPBCData
 324 {
 325     public:
 326         static const NeighborhoodSearchTestData &get()
 327         {
 328             static RandomBoxFullPBCData singleton;
 329             return singleton.data_;
 330         }
 331
 332         RandomBoxFullPBCData() : data_(12345, 1.0)
 333         {
 334             data_.box_[XX][XX] = 10.0;
 335             data_.box_[YY][YY] = 5.0;
 336             data_.box_[ZZ][ZZ] = 7.0;
 337             // TODO: Consider whether manually picking some positions would give better
 338             // test coverage.
 339             data_.generateRandomRefPositions(1000);
 340             data_.generateRandomTestPositions(100);
 341             set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
 342             data_.computeReferences(&data_.pbc_);
 343         }
 344
 345     private:
 346         NeighborhoodSearchTestData data_;
 347 };
 348
 349 class RandomTriclinicFullPBCData
 350 {
 351     public:
 352         static const NeighborhoodSearchTestData &get()
 353         {
 354             static RandomTriclinicFullPBCData singleton;
 355             return singleton.data_;
 356         }
 357
 358         RandomTriclinicFullPBCData() : data_(12345, 1.0)
 359         {
 360             data_.box_[XX][XX] = 5.0;
 361             data_.box_[YY][XX] = 2.5;
 362             data_.box_[YY][YY] = 2.5*sqrt(3.0);
 363             data_.box_[ZZ][XX] = 2.5;
 364             data_.box_[ZZ][YY] = 2.5*sqrt(1.0/3.0);
 365             data_.box_[ZZ][ZZ] = 5.0*sqrt(2.0/3.0);
 366             // TODO: Consider whether manually picking some positions would give better
 367             // test coverage.
 368             data_.generateRandomRefPositions(1000);
 369             data_.generateRandomTestPositions(100);
 370             set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
 371             data_.computeReferences(&data_.pbc_);
 372         }
 373
 374     private:
 375         NeighborhoodSearchTestData data_;
 376 };
 377
 378 class RandomBox2DPBCData
 379 {
 380     public:
 381         static const NeighborhoodSearchTestData &get()
 382         {
 383             static RandomBox2DPBCData singleton;
 384             return singleton.data_;
 385         }
 386
 387         RandomBox2DPBCData() : data_(12345, 1.0)
 388         {
 389             data_.box_[XX][XX] = 10.0;
 390             data_.box_[YY][YY] = 7.0;
 391             data_.box_[ZZ][ZZ] = 5.0;
 392             // TODO: Consider whether manually picking some positions would give better
 393             // test coverage.
 394             data_.generateRandomRefPositions(1000);
 395             data_.generateRandomTestPositions(100);
 396             set_pbc(&data_.pbc_, epbcXY, data_.box_);
 397             data_.computeReferences(&data_.pbc_);
 398         }
 399
 400     private:
 401         NeighborhoodSearchTestData data_;
 402 };
 403
 404 /********************************************************************
 405  * Actual tests
 406  */
 407
 408 TEST_F(NeighborhoodSearchTest, SimpleSearch)
 409 {
 410     const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
 411
 412     nb_.setCutoff(data.cutoff_);
 413     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Simple);
 414     gmx::AnalysisNeighborhoodSearch search =
 415         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 416     ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
 417
 418     testIsWithin(&search, data);
 419     testMinimumDistance(&search, data);
 420     testNearestPoint(&search, data);
 421     testPairSearch(&search, data);
 422 }
 423
 424 TEST_F(NeighborhoodSearchTest, GridSearchBox)
 425 {
 426     const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
 427
 428     nb_.setCutoff(data.cutoff_);
 429     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
 430     gmx::AnalysisNeighborhoodSearch search =
 431         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 432     ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
 433
 434     testIsWithin(&search, data);
 435     testMinimumDistance(&search, data);
 436     testNearestPoint(&search, data);
 437     testPairSearch(&search, data);
 438 }
 439
 440 TEST_F(NeighborhoodSearchTest, GridSearchTriclinic)
 441 {
 442     const NeighborhoodSearchTestData &data = RandomTriclinicFullPBCData::get();
 443
 444     nb_.setCutoff(data.cutoff_);
 445     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
 446     gmx::AnalysisNeighborhoodSearch search =
 447         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 448     ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
 449
 450     testPairSearch(&search, data);
 451 }
 452
 453 TEST_F(NeighborhoodSearchTest, GridSearch2DPBC)
 454 {
 455     const NeighborhoodSearchTestData &data = RandomBox2DPBCData::get();
 456
 457     nb_.setCutoff(data.cutoff_);
 458     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
 459     gmx::AnalysisNeighborhoodSearch search =
 460         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 461     // Currently, grid searching not supported with 2D PBC.
 462     //ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
 463
 464     testIsWithin(&search, data);
 465     testMinimumDistance(&search, data);
 466     testNearestPoint(&search, data);
 467     testPairSearch(&search, data);
 468 }
 469
 470 TEST_F(NeighborhoodSearchTest, HandlesConcurrentSearches)
 471 {
 472     const NeighborhoodSearchTestData &data = TrivialTestData::get();
 473
 474     nb_.setCutoff(data.cutoff_);
 475     gmx::AnalysisNeighborhoodSearch search1 =
 476         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 477     gmx::AnalysisNeighborhoodSearch search2 =
 478         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 479
 480     testPairSearch(&search1, data);
 481     testPairSearch(&search2, data);
 482 }
 483
 484 } // namespace