src/gromacs/selection/tests/selectioncollection.cpp

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  35 /*! \internal \file
  36  * \brief
  37  * Tests selection parsing and compilation.
  38  *
  39  * \author Teemu Murtola <teemu.murtola@gmail.com>
  40  * \ingroup module_selection
  41  */
  42 #include <gtest/gtest.h>
  43
  44 #include "gromacs/options/basicoptions.h"
  45 #include "gromacs/options/options.h"
  46 #include "gromacs/selection/indexutil.h"
  47 #include "gromacs/selection/selectioncollection.h"
  48 #include "gromacs/selection/selection.h"
  49 #include "gromacs/utility/arrayref.h"
  50 #include "gromacs/utility/exceptions.h"
  51 #include "gromacs/utility/flags.h"
  52 #include "gromacs/utility/gmxregex.h"
  53 #include "gromacs/utility/stringutil.h"
  54
  55 #include "testutils/refdata.h"
  56 #include "testutils/testasserts.h"
  57 #include "testutils/testfilemanager.h"
  58 #include "testutils/testoptions.h"
  59
  60 #include "toputils.h"
  61
  62 namespace
  63 {
  64
  65 /********************************************************************
  66  * Test fixture for selection testing
  67  */
  68
  69 class SelectionCollectionTest : public ::testing::Test
  70 {
  71     public:
  72         static int               s_debugLevel;
  73
  74         SelectionCollectionTest();
  75         ~SelectionCollectionTest();
  76
  77         void setAtomCount(int natoms)
  78         {
  79             ASSERT_NO_THROW_GMX(sc_.setTopology(NULL, natoms));
  80         }
  81         void loadTopology(const char *filename);
  82         void setTopology();
  83         void loadIndexGroups(const char *filename);
  84
  85         gmx::test::TopologyManager  topManager_;
  86         gmx::SelectionCollection    sc_;
  87         gmx::SelectionList          sel_;
  88         t_topology                 *top_;
  89         t_trxframe                 *frame_;
  90         gmx_ana_indexgrps_t        *grps_;
  91 };
  92
  93 int SelectionCollectionTest::s_debugLevel = 0;
  94
  95 // \cond/\endcond do not seem to work here with Doxygen 1.8.5 parser.
  96 #ifndef DOXYGEN
  97 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
  98 {
  99     options->addOption(gmx::IntegerOption("seldebug")
 100                            .store(&SelectionCollectionTest::s_debugLevel)
 101                            .description("Set selection debug level"));
 102 }
 103 #endif
 104
 105 SelectionCollectionTest::SelectionCollectionTest()
 106     : top_(NULL), frame_(NULL), grps_(NULL)
 107 {
 108     topManager_.requestFrame();
 109     sc_.setDebugLevel(s_debugLevel);
 110     sc_.setReferencePosType("atom");
 111     sc_.setOutputPosType("atom");
 112 }
 113
 114 SelectionCollectionTest::~SelectionCollectionTest()
 115 {
 116     if (grps_ != NULL)
 117     {
 118         gmx_ana_indexgrps_free(grps_);
 119     }
 120 }
 121
 122 void
 123 SelectionCollectionTest::loadTopology(const char *filename)
 124 {
 125     topManager_.loadTopology(filename);
 126     setTopology();
 127 }
 128
 129 void
 130 SelectionCollectionTest::setTopology()
 131 {
 132     top_   = topManager_.topology();
 133     frame_ = topManager_.frame();
 134
 135     ASSERT_NO_THROW_GMX(sc_.setTopology(top_, -1));
 136 }
 137
 138 void
 139 SelectionCollectionTest::loadIndexGroups(const char *filename)
 140 {
 141     GMX_RELEASE_ASSERT(grps_ == NULL,
 142                        "External groups can only be loaded once");
 143     std::string fullpath =
 144         gmx::test::TestFileManager::getInputFilePath(filename);
 145     gmx_ana_indexgrps_init(&grps_, NULL, fullpath.c_str());
 146     sc_.setIndexGroups(grps_);
 147 }
 148
 149
 150 /********************************************************************
 151  * Test fixture for selection testing with reference data
 152  */
 153
 154 class SelectionCollectionDataTest : public SelectionCollectionTest
 155 {
 156     public:
 157         enum TestFlag
 158         {
 159             efTestEvaluation            = 1<<0,
 160             efTestPositionAtoms         = 1<<1,
 161             efTestPositionCoordinates   = 1<<2,
 162             efTestPositionMapping       = 1<<3,
 163             efTestPositionMasses        = 1<<4,
 164             efTestPositionCharges       = 1<<5,
 165             efTestSelectionNames        = 1<<6,
 166             efDontTestCompiledAtoms     = 1<<8
 167         };
 168         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 169
 170         SelectionCollectionDataTest()
 171             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 172         {
 173         }
 174
 175         void setFlags(TestFlags flags) { flags_ = flags; }
 176
 177         void runParser(const gmx::ConstArrayRef<const char *> &selections);
 178         void runCompiler();
 179         void runEvaluate();
 180         void runEvaluateFinal();
 181
 182         void runTest(int                                     natoms,
 183                      const gmx::ConstArrayRef<const char *> &selections);
 184         void runTest(const char                             *filename,
 185                      const gmx::ConstArrayRef<const char *> &selections);
 186
 187     private:
 188         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 189                                    const gmx::Selection &sel, TestFlags flags);
 190
 191         void checkCompiled();
 192
 193         gmx::test::TestReferenceData    data_;
 194         gmx::test::TestReferenceChecker checker_;
 195         size_t                          count_;
 196         int                             framenr_;
 197         TestFlags                       flags_;
 198 };
 199
 200
 201 void
 202 SelectionCollectionDataTest::checkSelection(
 203         gmx::test::TestReferenceChecker *checker,
 204         const gmx::Selection &sel, TestFlags flags)
 205 {
 206     using gmx::test::TestReferenceChecker;
 207
 208     {
 209         gmx::ConstArrayRef<int> atoms = sel.atomIndices();
 210         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 211     }
 212     if (flags.test(efTestPositionAtoms)
 213         || flags.test(efTestPositionCoordinates)
 214         || flags.test(efTestPositionMapping)
 215         || flags.test(efTestPositionMasses)
 216         || flags.test(efTestPositionCharges))
 217     {
 218         TestReferenceChecker compound(
 219                 checker->checkSequenceCompound("Positions", sel.posCount()));
 220         for (int i = 0; i < sel.posCount(); ++i)
 221         {
 222             TestReferenceChecker          poscompound(compound.checkCompound("Position", NULL));
 223             const gmx::SelectionPosition &p = sel.position(i);
 224             if (flags.test(efTestPositionAtoms))
 225             {
 226                 gmx::ConstArrayRef<int> atoms = p.atomIndices();
 227                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 228             }
 229             if (flags.test(efTestPositionCoordinates))
 230             {
 231                 poscompound.checkVector(p.x(), "Coordinates");
 232             }
 233             if (flags.test(efTestPositionMapping))
 234             {
 235                 poscompound.checkInteger(p.refId(), "RefId");
 236                 poscompound.checkInteger(p.mappedId(), "MappedId");
 237             }
 238             if (flags.test(efTestPositionMasses))
 239             {
 240                 poscompound.checkReal(p.mass(), "Mass");
 241             }
 242             if (flags.test(efTestPositionCharges))
 243             {
 244                 poscompound.checkReal(p.charge(), "Charge");
 245             }
 246         }
 247     }
 248 }
 249
 250
 251 void
 252 SelectionCollectionDataTest::runParser(
 253         const gmx::ConstArrayRef<const char *> &selections)
 254 {
 255     using gmx::test::TestReferenceChecker;
 256
 257     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 258     size_t               varcount = 0;
 259     count_ = 0;
 260     for (size_t i = 0; i < selections.size(); ++i)
 261     {
 262         SCOPED_TRACE(std::string("Parsing selection \"")
 263                      + selections[i] + "\"");
 264         gmx::SelectionList result;
 265         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 266         sel_.insert(sel_.end(), result.begin(), result.end());
 267         if (sel_.size() == count_)
 268         {
 269             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 270             TestReferenceChecker varcompound(
 271                     compound.checkCompound("ParsedVariable", id.c_str()));
 272             varcompound.checkString(selections[i], "Input");
 273             ++varcount;
 274         }
 275         else
 276         {
 277             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 278             TestReferenceChecker selcompound(
 279                     compound.checkCompound("ParsedSelection", id.c_str()));
 280             selcompound.checkString(selections[i], "Input");
 281             if (flags_.test(efTestSelectionNames))
 282             {
 283                 selcompound.checkString(sel_[count_].name(), "Name");
 284             }
 285             selcompound.checkString(sel_[count_].selectionText(), "Text");
 286             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 287             ++count_;
 288         }
 289     }
 290 }
 291
 292
 293 void
 294 SelectionCollectionDataTest::runCompiler()
 295 {
 296     ASSERT_NO_THROW_GMX(sc_.compile());
 297     ASSERT_EQ(count_, sel_.size());
 298     checkCompiled();
 299 }
 300
 301
 302 void
 303 SelectionCollectionDataTest::checkCompiled()
 304 {
 305     using gmx::test::TestReferenceChecker;
 306     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 307
 308     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 309     for (size_t i = 0; i < count_; ++i)
 310     {
 311         SCOPED_TRACE(std::string("Checking selection \"") +
 312                      sel_[i].selectionText() + "\"");
 313         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 314         TestReferenceChecker selcompound(
 315                 compound.checkCompound("Selection", id.c_str()));
 316         if (flags_.test(efTestSelectionNames))
 317         {
 318             selcompound.checkString(sel_[i].name(), "Name");
 319         }
 320         if (!flags_.test(efDontTestCompiledAtoms))
 321         {
 322             checkSelection(&selcompound, sel_[i], flags_ & mask);
 323         }
 324     }
 325 }
 326
 327
 328 void
 329 SelectionCollectionDataTest::runEvaluate()
 330 {
 331     using gmx::test::TestReferenceChecker;
 332
 333     ++framenr_;
 334     ASSERT_NO_THROW_GMX(sc_.evaluate(frame_, NULL));
 335     std::string          frame = gmx::formatString("Frame%d", framenr_);
 336     TestReferenceChecker compound(
 337             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 338     for (size_t i = 0; i < count_; ++i)
 339     {
 340         SCOPED_TRACE(std::string("Checking selection \"") +
 341                      sel_[i].selectionText() + "\"");
 342         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 343         TestReferenceChecker selcompound(
 344                 compound.checkCompound("Selection", id.c_str()));
 345         checkSelection(&selcompound, sel_[i], flags_);
 346     }
 347 }
 348
 349
 350 void
 351 SelectionCollectionDataTest::runEvaluateFinal()
 352 {
 353     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 354     checkCompiled();
 355 }
 356
 357
 358 void
 359 SelectionCollectionDataTest::runTest(
 360         int natoms, const gmx::ConstArrayRef<const char *> &selections)
 361 {
 362     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 363     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 364     ASSERT_NO_FATAL_FAILURE(runCompiler());
 365 }
 366
 367
 368 void
 369 SelectionCollectionDataTest::runTest(
 370         const char *filename, const gmx::ConstArrayRef<const char *> &selections)
 371 {
 372     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 373     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 374     ASSERT_NO_FATAL_FAILURE(runCompiler());
 375     if (flags_.test(efTestEvaluation))
 376     {
 377         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 378         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 379     }
 380 }
 381
 382
 383 /********************************************************************
 384  * Tests for SelectionCollection functionality without reference data
 385  */
 386
 387 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 388 {
 389     EXPECT_FALSE(sc_.requiresTopology());
 390     EXPECT_NO_THROW_GMX(sc_.compile());
 391 }
 392
 393 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 394 {
 395     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 396     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 397     ASSERT_EQ(2U, sel_.size());
 398     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 399     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 400     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 401     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 402     ASSERT_NO_THROW_GMX(sc_.compile());
 403     EXPECT_TRUE(sel_[0].hasVelocities());
 404     EXPECT_TRUE(sel_[1].hasVelocities());
 405     EXPECT_TRUE(sel_[0].hasForces());
 406     EXPECT_TRUE(sel_[1].hasForces());
 407 }
 408
 409 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 410 {
 411     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 412                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 413     // These should match the contents of selfile.dat
 414     ASSERT_EQ(2U, sel_.size());
 415     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 416     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 417 }
 418
 419 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 420 {
 421     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 422     EXPECT_THROW_GMX({
 423                          sc_.parseFromString("resname ~ \"R[A\"");
 424                          sc_.compile();
 425                      }, gmx::InvalidInputError);
 426 }
 427
 428 TEST_F(SelectionCollectionTest, HandlesUnsupportedRegularExpressions)
 429 {
 430     if (!gmx::Regex::isSupported())
 431     {
 432         ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 433         EXPECT_THROW_GMX({
 434                              sc_.parseFromString("resname \"R[AD]\"");
 435                              sc_.compile();
 436                          }, gmx::InvalidInputError);
 437     }
 438 }
 439
 440 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 441 {
 442     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 443                      gmx::InvalidInputError);
 444 }
 445
 446 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 447 {
 448     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 449                      gmx::InvalidInputError);
 450 }
 451
 452 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 453 {
 454     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 455                      gmx::InvalidInputError);
 456 }
 457
 458 TEST_F(SelectionCollectionTest, HandlesHelpKeywordInInvalidContext)
 459 {
 460     EXPECT_THROW_GMX(sc_.parseFromString("resname help"),
 461                      gmx::InvalidInputError);
 462 }
 463
 464 // TODO: Tests for more parser errors
 465
 466 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 467 {
 468     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 469     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 470     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 471 }
 472
 473 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 474 {
 475     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 476     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 477     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 478 }
 479
 480 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 481 {
 482     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 483     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 484     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 485     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 486 }
 487
 488 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 489 {
 490     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 491     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 492     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 493     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 494 }
 495
 496 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 497 {
 498     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 499     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpUnsorted\""),
 500                      gmx::InconsistentInputError);
 501     EXPECT_THROW_GMX(sc_.parseFromString("2"), gmx::InconsistentInputError);
 502 }
 503
 504 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 505 {
 506     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 2; group \"GrpUnsorted\""));
 507     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 508     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 509 }
 510
 511 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 512 {
 513     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 514     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 515     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 516 }
 517
 518 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 519 {
 520     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 521     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 522     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 523 }
 524
 525 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 526 {
 527     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 528     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 529     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 530 }
 531
 532 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 533 {
 534     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 535     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 536     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 537 }
 538
 539 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 540 {
 541     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 542     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 543     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 544 }
 545
 546 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 547 {
 548     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 549     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 550     ASSERT_NO_THROW_GMX(sc_.compile());
 551     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 552 }
 553
 554 // TODO: Tests for evaluation errors
 555
 556
 557 /********************************************************************
 558  * Tests for selection keywords
 559  */
 560
 561 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 562 {
 563     static const char * const selections[] = {
 564         "all",
 565         "none"
 566     };
 567     runTest(10, selections);
 568 }
 569
 570 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 571 {
 572     static const char * const selections[] = {
 573         "atomnr 1 to 3 6 to 8",
 574         "atomnr 4 2 5 to 7",
 575         "atomnr <= 5"
 576     };
 577     runTest(10, selections);
 578 }
 579
 580 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 581 {
 582     static const char * const selections[] = {
 583         "resnr 1 2 5",
 584         "resid 4 to 3"
 585     };
 586     runTest("simple.gro", selections);
 587 }
 588
 589 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 590 {
 591     static const char * const selections[] = {
 592         "resindex 1 4",
 593         "residue 1 3"
 594     };
 595     runTest("simple.pdb", selections);
 596 }
 597
 598 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 599 {
 600     static const char * const selections[] = {
 601         "molindex 1 4",
 602         "molecule 2 3 5"
 603     };
 604     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 605     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 606     topManager_.initUniformMolecules(3);
 607     ASSERT_NO_FATAL_FAILURE(runCompiler());
 608 }
 609
 610 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 611 {
 612     static const char * const selections[] = {
 613         "name CB",
 614         "atomname S1 S2"
 615     };
 616     runTest("simple.gro", selections);
 617 }
 618
 619 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 620 {
 621     static const char * const selections[] = {
 622         "name HG21",
 623         "name 1HG2",
 624         "pdbname HG21 CB",
 625         "pdbatomname 1HG2"
 626     };
 627     runTest("simple.pdb", selections);
 628 }
 629
 630
 631 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 632 {
 633     static const char * const selections[] = {
 634         "atomtype CA"
 635     };
 636     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 637     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 638     const char *const types[] = { "CA", "SA", "SB" };
 639     topManager_.initAtomTypes(types);
 640     ASSERT_NO_FATAL_FAILURE(runCompiler());
 641 }
 642
 643 TEST_F(SelectionCollectionDataTest, HandlesChain)
 644 {
 645     static const char * const selections[] = {
 646         "chain A",
 647         "chain B"
 648     };
 649     runTest("simple.pdb", selections);
 650 }
 651
 652 TEST_F(SelectionCollectionDataTest, HandlesMass)
 653 {
 654     static const char * const selections[] = {
 655         "mass > 5"
 656     };
 657     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 658     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 659     for (int i = 0; i < top_->atoms.nr; ++i)
 660     {
 661         top_->atoms.atom[i].m = 1.0 + i;
 662     }
 663     ASSERT_NO_FATAL_FAILURE(runCompiler());
 664 }
 665
 666 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 667 {
 668     static const char * const selections[] = {
 669         "charge < 0.5"
 670     };
 671     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 672     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 673     for (int i = 0; i < top_->atoms.nr; ++i)
 674     {
 675         top_->atoms.atom[i].q = i / 10.0;
 676     }
 677     ASSERT_NO_FATAL_FAILURE(runCompiler());
 678 }
 679
 680 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 681 {
 682     static const char * const selections[] = {
 683         "altloc \" \"",
 684         "altloc A"
 685     };
 686     runTest("simple.pdb", selections);
 687 }
 688
 689 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 690 {
 691     static const char * const selections[] = {
 692         "insertcode \" \"",
 693         "insertcode A"
 694     };
 695     runTest("simple.pdb", selections);
 696 }
 697
 698 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 699 {
 700     static const char * const selections[] = {
 701         "occupancy 1",
 702         "occupancy < .5"
 703     };
 704     runTest("simple.pdb", selections);
 705 }
 706
 707 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 708 {
 709     static const char * const selections[] = {
 710         "beta 0",
 711         "beta >= 0.3"
 712     };
 713     runTest("simple.pdb", selections);
 714 }
 715
 716 TEST_F(SelectionCollectionDataTest, HandlesResname)
 717 {
 718     static const char * const selections[] = {
 719         "resname RA",
 720         "resname RB RC"
 721     };
 722     runTest("simple.gro", selections);
 723 }
 724
 725 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 726 {
 727     static const char * const selections[] = {
 728         "x < 3",
 729         "y >= 3",
 730         "x {-1 to 2}"
 731     };
 732     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 733     runTest("simple.gro", selections);
 734 }
 735
 736
 737 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 738 {
 739     static const char * const selections[] = {
 740         "same residue as atomnr 1 4 12"
 741     };
 742     runTest("simple.gro", selections);
 743 }
 744
 745
 746 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 747 {
 748     static const char * const selections[] = {
 749         "same resname as atomnr 1 14"
 750     };
 751     runTest("simple.gro", selections);
 752 }
 753
 754
 755 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 756 {
 757     static const char * const selections[] = {
 758         "cog of resnr 1 3",
 759         "res_cog of name CB and resnr 1 3",
 760         "whole_res_cog of name CB and resnr 1 3",
 761         "part_res_cog of x < 3",
 762         "dyn_res_cog of x < 3"
 763     };
 764     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 765              | efTestPositionAtoms);
 766     runTest("simple.gro", selections);
 767 }
 768
 769
 770 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 771 {
 772     static const char * const selections[] = {
 773         "distance from cog of resnr 1 < 2"
 774     };
 775     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 776     runTest("simple.gro", selections);
 777 }
 778
 779
 780 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 781 {
 782     static const char * const selections[] = {
 783         "mindistance from resnr 1 < 2"
 784     };
 785     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 786     runTest("simple.gro", selections);
 787 }
 788
 789
 790 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 791 {
 792     static const char * const selections[] = {
 793         "within 1 of resnr 2"
 794     };
 795     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 796     runTest("simple.gro", selections);
 797 }
 798
 799
 800 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 801 {
 802     // Both of these should evaluate to empty on a correct implementation.
 803     static const char * const selections[] = {
 804         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 805         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 806     };
 807     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 808     runTest("sphere.gro", selections);
 809 }
 810
 811
 812 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 813 {
 814     static const char * const selections[] = {
 815         "all permute 3 1 2",
 816         "res_cog of resnr 1 to 4 permute 2 1",
 817         "name CB S1 and res_cog x < 3 permute 2 1"
 818     };
 819     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 820              | efTestPositionAtoms | efTestPositionMapping);
 821     runTest("simple.gro", selections);
 822 }
 823
 824
 825 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 826 {
 827     static const char * const selections[] = {
 828         "name S2 plus name S1",
 829         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 830         "name S1 and y < 3 plus res_cog of x < 2.5"
 831     };
 832     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 833              | efTestPositionAtoms | efTestPositionMapping);
 834     runTest("simple.gro", selections);
 835 }
 836
 837
 838 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 839 {
 840     static const char * const selections[] = {
 841         "name S2 merge name S1",
 842         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 843         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 844     };
 845     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 846              | efTestPositionAtoms | efTestPositionMapping);
 847     runTest("simple.gro", selections);
 848 }
 849
 850
 851 /********************************************************************
 852  * Tests for generic selection evaluation
 853  */
 854
 855 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 856 {
 857     static const char * const selections[] = {
 858         "name CB",
 859         "y > 2",
 860         "res_cog of y > 2"
 861     };
 862     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 863              | efTestPositionMasses | efTestPositionCharges);
 864     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 865     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 866     for (int i = 0; i < top_->atoms.nr; ++i)
 867     {
 868         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 869         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 870     }
 871     ASSERT_NO_FATAL_FAILURE(runCompiler());
 872     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 873     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 874 }
 875
 876 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 877 {
 878     static const char * const selections[] = {
 879         "atomnr 1 to 3 8 to 9",
 880         "y > 2",
 881         "cog of (y > 2)"
 882     };
 883     setFlags(TestFlags() | efTestPositionAtoms
 884              | efTestPositionMasses | efTestPositionCharges);
 885     runTest(10, selections);
 886 }
 887
 888
 889 /********************************************************************
 890  * Tests for selection syntactic constructs
 891  */
 892
 893 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 894 {
 895     static const char * const selections[] = {
 896         "\"GroupSelection\" group \"GrpA\"",
 897         "\"DynamicSelection\" x < 5",
 898         "y < 3"
 899     };
 900     setFlags(TestFlags() | efTestSelectionNames);
 901     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 902     runTest(10, selections);
 903 }
 904
 905 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 906 {
 907     static const char * const selections[] = {
 908         "group \"GrpA\"",
 909         "GrpB",
 910         "1",
 911         "group \"GrpB\" and resname RB"
 912     };
 913     setFlags(TestFlags() | efTestSelectionNames);
 914     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 915     runTest("simple.gro", selections);
 916 }
 917
 918 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 919 {
 920     static const char * const selections[] = {
 921         "group \"GrpA\"",
 922         "GrpB",
 923         "1",
 924         "group \"GrpB\" and resname RB"
 925     };
 926     setFlags(TestFlags() | efTestSelectionNames);
 927     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 928     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 929     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 930     ASSERT_NO_FATAL_FAILURE(runCompiler());
 931 }
 932
 933 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 934 {
 935     static const char * const selections[] = {
 936         "[1, -2, 3.5]"
 937     };
 938     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 939     runTest("simple.gro", selections);
 940 }
 941
 942
 943 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 944 {
 945     static const char * const selections[] = {
 946         "within 1 of [2, 1, 0]"
 947     };
 948     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 949     runTest("simple.gro", selections);
 950 }
 951
 952
 953 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 954 {
 955     static const char * const selections[] = {
 956         "name = S1 \"C?\"",
 957         "name ? S1 \"C?\""
 958     };
 959     runTest("simple.gro", selections);
 960 }
 961
 962
 963 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 964 {
 965     static const char * const selections[] = {
 966         "name \"S?\"",
 967         "name ? \"S?\""
 968     };
 969     runTest("simple.gro", selections);
 970 }
 971
 972
 973 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
 974 {
 975     static const char * const selections[] = {
 976         "resname \"R[BD]\"",
 977         "resname ~ \"R[BD]\""
 978     };
 979     if (gmx::Regex::isSupported())
 980     {
 981         runTest("simple.gro", selections);
 982     }
 983 }
 984
 985
 986 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
 987 {
 988     static const char * const selections[] = {
 989         "atomnr 1 to 5 and atomnr 2 to 7",
 990         "atomnr 1 to 5 or not atomnr 3 to 8",
 991         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
 992         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
 993         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
 994     };
 995     runTest(10, selections);
 996 }
 997
 998
 999 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1000 {
1001     static const char * const selections[] = {
1002         "same residue as (atomnr 3 5 13 or y > 5)",
1003         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1004     };
1005     setFlags(TestFlags() | efTestEvaluation);
1006     runTest("simple.gro", selections);
1007 }
1008
1009
1010 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1011 {
1012     static const char * const selections[] = {
1013         "none and x > 2",
1014         "none and same resname as resnr 2"
1015     };
1016     runTest("simple.gro", selections);
1017 }
1018
1019
1020 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1021 {
1022     static const char * const selections[] = {
1023         "x > 2",
1024         "2 < x",
1025         "y > resnr",
1026         "resnr < 2.5",
1027         "2.5 > resnr"
1028     };
1029     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1030     runTest("simple.gro", selections);
1031 }
1032
1033
1034 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1035 {
1036     static const char * const selections[] = {
1037         "x+1 > 3",
1038         "(y-1)^2 <= 1",
1039         "x+--1 > 3",
1040         "-x+-1 < -3"
1041     };
1042     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1043     runTest("simple.gro", selections);
1044 }
1045
1046
1047 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1048 {
1049     static const char * const selections[] = {
1050         "value = x + y",
1051         "value <= 4",
1052         "index = resnr",
1053         "index < 3"
1054     };
1055     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1056     runTest("simple.gro", selections);
1057 }
1058
1059
1060 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1061 {
1062     static const char * const selections[] = {
1063         "value = x + y",
1064         "resname RA and value <= 4",
1065         "resname RA RB and x < 3 and value <= 4",
1066         "index = atomnr",
1067         "resname RA and index < 3",
1068         "resname RB and y < 3 and index < 6"
1069     };
1070     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1071     runTest("simple.gro", selections);
1072 }
1073
1074
1075 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1076 {
1077     static const char * const selections[] = {
1078         "foo = res_cog of resname RA",
1079         "foo",
1080         "within 1 of foo",
1081         "bar = cog of resname RA",
1082         "bar",
1083         "within 1 of bar"
1084     };
1085     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1086     runTest("simple.gro", selections);
1087 }
1088
1089
1090 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1091 {
1092     static const char * const selections[] = {
1093         "constpos = [1.0, 2.5, 0.5]",
1094         "constpos",
1095         "within 2 of constpos"
1096     };
1097     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1098              | efTestPositionAtoms);
1099     runTest("simple.gro", selections);
1100 }
1101
1102
1103 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1104 {
1105     static const char * const selections[] = {
1106         "constint = 4",
1107         "constreal1 = 0.5",
1108         "constreal2 = 2.7",
1109         "resnr < constint",
1110         "x + constreal1 < constreal2"
1111     };
1112     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1113     runTest("simple.gro", selections);
1114 }
1115
1116
1117 /********************************************************************
1118  * Tests for complex boolean syntax
1119  */
1120
1121 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1122 {
1123     static const char * const selections[] = {
1124         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1125         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1126         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1127         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1128         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1129     };
1130     runTest(10, selections);
1131 }
1132
1133
1134 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1135 {
1136     static const char * const selections[] = {
1137         "foo = atomnr 4 to 7 or x < 2",
1138         "atomnr 1 to 4 and foo",
1139         "atomnr 2 to 6 and y < 3 and foo",
1140         "atomnr 6 to 10 and not foo"
1141     };
1142     runTest(10, selections);
1143 }
1144
1145
1146 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1147 {
1148     static const char * const selections[] = {
1149         "foo = atomnr 4 to 7",
1150         "bar = foo and x < 2",
1151         "bar2 = foo and y < 2",
1152         "atomnr 1 to 4 and bar",
1153         "atomnr 2 to 6 and y < 3 and bar2",
1154         "atomnr 6 to 10 and not foo"
1155     };
1156     runTest(10, selections);
1157 }
1158
1159
1160 /********************************************************************
1161  * Tests for complex subexpression cases
1162  *
1163  * These tests use some knowledge of the implementation to trigger different
1164  * paths in the code.
1165  */
1166
1167 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1168 {
1169     static const char * const selections[] = {
1170         "unused1 = atomnr 1 to 3",
1171         "foo = atomnr 4 to 7",
1172         "atomnr 1 to 6 and foo",
1173         "unused2 = atomnr 3 to 5"
1174     };
1175     runTest(10, selections);
1176 }
1177
1178
1179 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1180 {
1181     static const char * const selections[] = {
1182         "foo = atomnr 4 to 7 and x < 2",
1183         "atomnr 1 to 5 and foo",
1184         "atomnr 3 to 7 and foo"
1185     };
1186     runTest(10, selections);
1187 }
1188
1189
1190 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1191 {
1192     static const char * const selections[] = {
1193         "foo = atomnr 4 to 7 and x < 2",
1194         "atomnr 1 to 6 and foo",
1195         "within 1 of foo",
1196         "foo"
1197     };
1198     runTest(10, selections);
1199 }
1200
1201
1202 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1203 {
1204     static const char * const selections[] = {
1205         "foo = atomnr 1 to 8 and x < 10",
1206         "atomnr 1 to 5 and y < 10 and foo",
1207         "foo"
1208     };
1209     setFlags(TestFlags() | efTestEvaluation);
1210     runTest("simple.gro", selections);
1211 }
1212
1213
1214 } // namespace