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 #include <vector>
  54
  55 #include "gromacs/legacyheaders/gmx_random.h"
  56 #include "gromacs/legacyheaders/pbc.h"
  57 #include "gromacs/legacyheaders/smalloc.h"
  58 #include "gromacs/legacyheaders/vec.h"
  59
  60 #include "gromacs/selection/nbsearch.h"
  61
  62 #include "testutils/testasserts.h"
  63
  64 namespace
  65 {
  66
  67 /********************************************************************
  68  * NeighborhoodSearchTestData
  69  */
  70
  71 class NeighborhoodSearchTestData
  72 {
  73     public:
  74         struct TestPosition
  75         {
  76             TestPosition() : refMinDist(0.0), refNearestPoint(-1)
  77             {
  78                 clear_rvec(x);
  79             }
  80             explicit TestPosition(const rvec x)
  81                 : refMinDist(0.0), refNearestPoint(-1)
  82             {
  83                 copy_rvec(x, this->x);
  84             }
  85
  86             rvec                x;
  87             real                refMinDist;
  88             int                 refNearestPoint;
  89             std::set<int>       refPairs;
  90         };
  91         typedef std::vector<TestPosition> TestPositionList;
  92
  93         NeighborhoodSearchTestData(int seed, real cutoff);
  94         ~NeighborhoodSearchTestData();
  95
  96         void addTestPosition(const rvec x)
  97         {
  98             testPositions_.push_back(TestPosition(x));
  99         }
 100         void generateRandomPosition(rvec x);
 101         void generateRandomRefPositions(int count);
 102         void generateRandomTestPositions(int count);
 103         void computeReferences(t_pbc *pbc);
 104
 105         gmx_rng_t                        rng_;
 106         real                             cutoff_;
 107         matrix                           box_;
 108         t_pbc                            pbc_;
 109         int                              refPosCount_;
 110         rvec                            *refPos_;
 111         TestPositionList                 testPositions_;
 112 };
 113
 114 NeighborhoodSearchTestData::NeighborhoodSearchTestData(int seed, real cutoff)
 115     : rng_(NULL), cutoff_(cutoff), refPosCount_(0), refPos_(NULL)
 116 {
 117     // TODO: Handle errors.
 118     rng_ = gmx_rng_init(seed);
 119     clear_mat(box_);
 120     set_pbc(&pbc_, epbcNONE, box_);
 121 }
 122
 123 NeighborhoodSearchTestData::~NeighborhoodSearchTestData()
 124 {
 125     if (rng_ != NULL)
 126     {
 127         gmx_rng_destroy(rng_);
 128     }
 129     sfree(refPos_);
 130 }
 131
 132 void NeighborhoodSearchTestData::generateRandomPosition(rvec x)
 133 {
 134     rvec fx;
 135     fx[XX] = gmx_rng_uniform_real(rng_);
 136     fx[YY] = gmx_rng_uniform_real(rng_);
 137     fx[ZZ] = gmx_rng_uniform_real(rng_);
 138     mvmul(box_, fx, x);
 139     // Add a small displacement to allow positions outside the box
 140     x[XX] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
 141     x[YY] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
 142     x[ZZ] += 0.2 * gmx_rng_uniform_real(rng_) - 0.1;
 143 }
 144
 145 void NeighborhoodSearchTestData::generateRandomRefPositions(int count)
 146 {
 147     refPosCount_ = count;
 148     snew(refPos_, refPosCount_);
 149     for (int i = 0; i < refPosCount_; ++i)
 150     {
 151         generateRandomPosition(refPos_[i]);
 152     }
 153 }
 154
 155 void NeighborhoodSearchTestData::generateRandomTestPositions(int count)
 156 {
 157     testPositions_.reserve(count);
 158     for (int i = 0; i < count; ++i)
 159     {
 160         rvec x;
 161         generateRandomPosition(x);
 162         addTestPosition(x);
 163     }
 164 }
 165
 166 void NeighborhoodSearchTestData::computeReferences(t_pbc *pbc)
 167 {
 168     real cutoff = cutoff_;
 169     if (cutoff <= 0)
 170     {
 171         cutoff = std::numeric_limits<real>::max();
 172     }
 173     TestPositionList::iterator i;
 174     for (i = testPositions_.begin(); i != testPositions_.end(); ++i)
 175     {
 176         i->refMinDist      = cutoff;
 177         i->refNearestPoint = -1;
 178         i->refPairs.clear();
 179         for (int j = 0; j < refPosCount_; ++j)
 180         {
 181             rvec dx;
 182             if (pbc != NULL)
 183             {
 184                 pbc_dx(pbc, i->x, refPos_[j], dx);
 185             }
 186             else
 187             {
 188                 rvec_sub(i->x, refPos_[j], dx);
 189             }
 190             const real dist = norm(dx);
 191             if (dist < i->refMinDist)
 192             {
 193                 i->refMinDist      = dist;
 194                 i->refNearestPoint = j;
 195             }
 196             if (dist <= cutoff)
 197             {
 198                 i->refPairs.insert(j);
 199             }
 200         }
 201     }
 202 }
 203
 204 /********************************************************************
 205  * NeighborhoodSearchTest
 206  */
 207
 208 class NeighborhoodSearchTest : public ::testing::Test
 209 {
 210     public:
 211         void testIsWithin(gmx::AnalysisNeighborhoodSearch  *search,
 212                           const NeighborhoodSearchTestData &data);
 213         void testMinimumDistance(gmx::AnalysisNeighborhoodSearch  *search,
 214                                  const NeighborhoodSearchTestData &data);
 215         void testNearestPoint(gmx::AnalysisNeighborhoodSearch  *search,
 216                               const NeighborhoodSearchTestData &data);
 217         void testPairSearch(gmx::AnalysisNeighborhoodSearch  *search,
 218                             const NeighborhoodSearchTestData &data);
 219
 220         gmx::AnalysisNeighborhood        nb_;
 221 };
 222
 223 void NeighborhoodSearchTest::testIsWithin(
 224         gmx::AnalysisNeighborhoodSearch  *search,
 225         const NeighborhoodSearchTestData &data)
 226 {
 227     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 228     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 229     {
 230         const bool bWithin = (i->refMinDist <= data.cutoff_);
 231         EXPECT_EQ(bWithin, search->isWithin(i->x))
 232         << "Distance is " << i->refMinDist;
 233     }
 234 }
 235
 236 void NeighborhoodSearchTest::testMinimumDistance(
 237         gmx::AnalysisNeighborhoodSearch  *search,
 238         const NeighborhoodSearchTestData &data)
 239 {
 240     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 241     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 242     {
 243         const real refDist = i->refMinDist;
 244         EXPECT_NEAR_REL(refDist, search->minimumDistance(i->x), 20*GMX_REAL_EPS);
 245     }
 246 }
 247
 248 void NeighborhoodSearchTest::testNearestPoint(
 249         gmx::AnalysisNeighborhoodSearch  *search,
 250         const NeighborhoodSearchTestData &data)
 251 {
 252     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 253     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 254     {
 255         const gmx::AnalysisNeighborhoodPair pair = search->nearestPoint(i->x);
 256         if (pair.isValid())
 257         {
 258             EXPECT_EQ(i->refNearestPoint, pair.refIndex());
 259             EXPECT_EQ(0, pair.testIndex());
 260         }
 261         else
 262         {
 263             EXPECT_EQ(i->refNearestPoint, -1);
 264         }
 265     }
 266 }
 267
 268 void NeighborhoodSearchTest::testPairSearch(
 269         gmx::AnalysisNeighborhoodSearch  *search,
 270         const NeighborhoodSearchTestData &data)
 271 {
 272     NeighborhoodSearchTestData::TestPositionList::const_iterator i;
 273     for (i = data.testPositions_.begin(); i != data.testPositions_.end(); ++i)
 274     {
 275         std::set<int> checkSet                         = i->refPairs;
 276         gmx::AnalysisNeighborhoodPairSearch pairSearch =
 277             search->startPairSearch(i->x);
 278         gmx::AnalysisNeighborhoodPair       pair;
 279         while (pairSearch.findNextPair(&pair))
 280         {
 281             EXPECT_EQ(0, pair.testIndex());
 282             if (checkSet.erase(pair.refIndex()) == 0)
 283             {
 284                 // TODO: Check whether the same pair was returned more than
 285                 // once and give a better error message if so.
 286                 ADD_FAILURE()
 287                 << "Expected: Position " << pair.refIndex()
 288                 << " is within cutoff.\n"
 289                 << "  Actual: It is not.";
 290             }
 291         }
 292         EXPECT_TRUE(checkSet.empty()) << "Some positions were not returned by the pair search.";
 293     }
 294 }
 295
 296 /********************************************************************
 297  * Test data generation
 298  */
 299
 300 class TrivialTestData
 301 {
 302     public:
 303         static const NeighborhoodSearchTestData &get()
 304         {
 305             static TrivialTestData singleton;
 306             return singleton.data_;
 307         }
 308
 309         TrivialTestData() : data_(12345, 1.0)
 310         {
 311             data_.box_[XX][XX] = 5.0;
 312             data_.box_[YY][YY] = 5.0;
 313             data_.box_[ZZ][ZZ] = 5.0;
 314             data_.generateRandomRefPositions(10);
 315             data_.generateRandomTestPositions(5);
 316             set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
 317             data_.computeReferences(&data_.pbc_);
 318         }
 319
 320     private:
 321         NeighborhoodSearchTestData data_;
 322 };
 323
 324 class RandomBoxFullPBCData
 325 {
 326     public:
 327         static const NeighborhoodSearchTestData &get()
 328         {
 329             static RandomBoxFullPBCData singleton;
 330             return singleton.data_;
 331         }
 332
 333         RandomBoxFullPBCData() : data_(12345, 1.0)
 334         {
 335             data_.box_[XX][XX] = 10.0;
 336             data_.box_[YY][YY] = 5.0;
 337             data_.box_[ZZ][ZZ] = 7.0;
 338             // TODO: Consider whether manually picking some positions would give better
 339             // test coverage.
 340             data_.generateRandomRefPositions(1000);
 341             data_.generateRandomTestPositions(100);
 342             set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
 343             data_.computeReferences(&data_.pbc_);
 344         }
 345
 346     private:
 347         NeighborhoodSearchTestData data_;
 348 };
 349
 350 class RandomTriclinicFullPBCData
 351 {
 352     public:
 353         static const NeighborhoodSearchTestData &get()
 354         {
 355             static RandomTriclinicFullPBCData singleton;
 356             return singleton.data_;
 357         }
 358
 359         RandomTriclinicFullPBCData() : data_(12345, 1.0)
 360         {
 361             data_.box_[XX][XX] = 5.0;
 362             data_.box_[YY][XX] = 2.5;
 363             data_.box_[YY][YY] = 2.5*sqrt(3.0);
 364             data_.box_[ZZ][XX] = 2.5;
 365             data_.box_[ZZ][YY] = 2.5*sqrt(1.0/3.0);
 366             data_.box_[ZZ][ZZ] = 5.0*sqrt(2.0/3.0);
 367             // TODO: Consider whether manually picking some positions would give better
 368             // test coverage.
 369             data_.generateRandomRefPositions(1000);
 370             data_.generateRandomTestPositions(100);
 371             set_pbc(&data_.pbc_, epbcXYZ, data_.box_);
 372             data_.computeReferences(&data_.pbc_);
 373         }
 374
 375     private:
 376         NeighborhoodSearchTestData data_;
 377 };
 378
 379 class RandomBox2DPBCData
 380 {
 381     public:
 382         static const NeighborhoodSearchTestData &get()
 383         {
 384             static RandomBox2DPBCData singleton;
 385             return singleton.data_;
 386         }
 387
 388         RandomBox2DPBCData() : data_(12345, 1.0)
 389         {
 390             data_.box_[XX][XX] = 10.0;
 391             data_.box_[YY][YY] = 7.0;
 392             data_.box_[ZZ][ZZ] = 5.0;
 393             // TODO: Consider whether manually picking some positions would give better
 394             // test coverage.
 395             data_.generateRandomRefPositions(1000);
 396             data_.generateRandomTestPositions(100);
 397             set_pbc(&data_.pbc_, epbcXY, data_.box_);
 398             data_.computeReferences(&data_.pbc_);
 399         }
 400
 401     private:
 402         NeighborhoodSearchTestData data_;
 403 };
 404
 405 /********************************************************************
 406  * Actual tests
 407  */
 408
 409 TEST_F(NeighborhoodSearchTest, SimpleSearch)
 410 {
 411     const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
 412
 413     nb_.setCutoff(data.cutoff_);
 414     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Simple);
 415     gmx::AnalysisNeighborhoodSearch search =
 416         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 417     ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Simple, search.mode());
 418
 419     testIsWithin(&search, data);
 420     testMinimumDistance(&search, data);
 421     testNearestPoint(&search, data);
 422     testPairSearch(&search, data);
 423 }
 424
 425 TEST_F(NeighborhoodSearchTest, GridSearchBox)
 426 {
 427     const NeighborhoodSearchTestData &data = RandomBoxFullPBCData::get();
 428
 429     nb_.setCutoff(data.cutoff_);
 430     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
 431     gmx::AnalysisNeighborhoodSearch search =
 432         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 433     ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
 434
 435     testIsWithin(&search, data);
 436     testMinimumDistance(&search, data);
 437     testNearestPoint(&search, data);
 438     testPairSearch(&search, data);
 439 }
 440
 441 TEST_F(NeighborhoodSearchTest, GridSearchTriclinic)
 442 {
 443     const NeighborhoodSearchTestData &data = RandomTriclinicFullPBCData::get();
 444
 445     nb_.setCutoff(data.cutoff_);
 446     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
 447     gmx::AnalysisNeighborhoodSearch search =
 448         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 449     ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
 450
 451     testPairSearch(&search, data);
 452 }
 453
 454 TEST_F(NeighborhoodSearchTest, GridSearch2DPBC)
 455 {
 456     const NeighborhoodSearchTestData &data = RandomBox2DPBCData::get();
 457
 458     nb_.setCutoff(data.cutoff_);
 459     nb_.setMode(gmx::AnalysisNeighborhood::eSearchMode_Grid);
 460     gmx::AnalysisNeighborhoodSearch search =
 461         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 462     // Currently, grid searching not supported with 2D PBC.
 463     //ASSERT_EQ(gmx::AnalysisNeighborhood::eSearchMode_Grid, search.mode());
 464
 465     testIsWithin(&search, data);
 466     testMinimumDistance(&search, data);
 467     testNearestPoint(&search, data);
 468     testPairSearch(&search, data);
 469 }
 470
 471 TEST_F(NeighborhoodSearchTest, HandlesConcurrentSearches)
 472 {
 473     const NeighborhoodSearchTestData &data = TrivialTestData::get();
 474
 475     nb_.setCutoff(data.cutoff_);
 476     gmx::AnalysisNeighborhoodSearch search1 =
 477         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 478     gmx::AnalysisNeighborhoodSearch search2 =
 479         nb_.initSearch(&data.pbc_, data.refPosCount_, data.refPos_);
 480
 481     gmx::AnalysisNeighborhoodPairSearch pairSearch1 =
 482         search1.startPairSearch(data.testPositions_[0].x);
 483     gmx::AnalysisNeighborhoodPairSearch pairSearch2 =
 484         search1.startPairSearch(data.testPositions_[1].x);
 485
 486     testPairSearch(&search2, data);
 487
 488     gmx::AnalysisNeighborhoodPair pair;
 489     pairSearch1.findNextPair(&pair);
 490     EXPECT_EQ(0, pair.testIndex());
 491     EXPECT_TRUE(data.testPositions_[0].refPairs.count(pair.refIndex()) == 1);
 492
 493     pairSearch2.findNextPair(&pair);
 494     EXPECT_EQ(0, pair.testIndex());
 495     EXPECT_TRUE(data.testPositions_[1].refPairs.count(pair.refIndex()) == 1);
 496 }
 497
 498 } // namespace