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 // TODO: Tests for more parser errors
 459
 460 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 461 {
 462     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(NULL));
 463     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 464     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 465 }
 466
 467 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 468 {
 469     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 470     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 471     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 472 }
 473
 474 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 475 {
 476     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 477     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 478     EXPECT_THROW_GMX(sc_.setIndexGroups(NULL), gmx::InconsistentInputError);
 479     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 480 }
 481
 482 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 483 {
 484     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 485     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 486     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 487     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 488 }
 489
 490 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 491 {
 492     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 493     EXPECT_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""),
 494                      gmx::InconsistentInputError);
 495     EXPECT_THROW_GMX(sc_.parseFromString("group 2 or atomnr 2 to 5"),
 496                      gmx::InconsistentInputError);
 497     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of group 2"),
 498                      gmx::InconsistentInputError);
 499 }
 500
 501 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 502 {
 503     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""));
 504     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group 2"));
 505     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 506     // TODO: Add a separate check in the selection compiler for a safer API
 507     // (makes sense in the future if the compiler needs the information for
 508     // other purposes as well).
 509     // EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 510 }
 511
 512 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 513 {
 514     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 515     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 516     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 517 }
 518
 519 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 520 {
 521     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 522     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 523     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 524 }
 525
 526 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 527 {
 528     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 529     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 530     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 531 }
 532
 533 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 534 {
 535     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 536     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 537     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 538 }
 539
 540 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 541 {
 542     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 543     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 544     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 545 }
 546
 547 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 548 {
 549     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 550     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 551     ASSERT_NO_THROW_GMX(sc_.compile());
 552     EXPECT_THROW_GMX(sc_.evaluate(frame_, NULL), gmx::InconsistentInputError);
 553 }
 554
 555 // TODO: Tests for evaluation errors
 556
 557
 558 /********************************************************************
 559  * Tests for selection keywords
 560  */
 561
 562 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 563 {
 564     static const char * const selections[] = {
 565         "all",
 566         "none"
 567     };
 568     runTest(10, selections);
 569 }
 570
 571 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 572 {
 573     static const char * const selections[] = {
 574         "atomnr 1 to 3 6 to 8",
 575         "atomnr 4 2 5 to 7",
 576         "atomnr <= 5"
 577     };
 578     runTest(10, selections);
 579 }
 580
 581 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 582 {
 583     static const char * const selections[] = {
 584         "resnr 1 2 5",
 585         "resid 4 to 3"
 586     };
 587     runTest("simple.gro", selections);
 588 }
 589
 590 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 591 {
 592     static const char * const selections[] = {
 593         "resindex 1 4",
 594         "residue 1 3"
 595     };
 596     runTest("simple.pdb", selections);
 597 }
 598
 599 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 600 {
 601     static const char * const selections[] = {
 602         "molindex 1 4",
 603         "molecule 2 3 5"
 604     };
 605     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 606     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 607     topManager_.initUniformMolecules(3);
 608     ASSERT_NO_FATAL_FAILURE(runCompiler());
 609 }
 610
 611 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 612 {
 613     static const char * const selections[] = {
 614         "name CB",
 615         "atomname S1 S2"
 616     };
 617     runTest("simple.gro", selections);
 618 }
 619
 620 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 621 {
 622     static const char * const selections[] = {
 623         "name HG21",
 624         "name 1HG2",
 625         "pdbname HG21 CB",
 626         "pdbatomname 1HG2"
 627     };
 628     runTest("simple.pdb", selections);
 629 }
 630
 631
 632 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 633 {
 634     static const char * const selections[] = {
 635         "atomtype CA"
 636     };
 637     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 638     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 639     const char *const types[] = { "CA", "SA", "SB" };
 640     topManager_.initAtomTypes(types);
 641     ASSERT_NO_FATAL_FAILURE(runCompiler());
 642 }
 643
 644 TEST_F(SelectionCollectionDataTest, HandlesChain)
 645 {
 646     static const char * const selections[] = {
 647         "chain A",
 648         "chain B"
 649     };
 650     runTest("simple.pdb", selections);
 651 }
 652
 653 TEST_F(SelectionCollectionDataTest, HandlesMass)
 654 {
 655     static const char * const selections[] = {
 656         "mass > 5"
 657     };
 658     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 659     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 660     for (int i = 0; i < top_->atoms.nr; ++i)
 661     {
 662         top_->atoms.atom[i].m = 1.0 + i;
 663     }
 664     ASSERT_NO_FATAL_FAILURE(runCompiler());
 665 }
 666
 667 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 668 {
 669     static const char * const selections[] = {
 670         "charge < 0.5"
 671     };
 672     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 673     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 674     for (int i = 0; i < top_->atoms.nr; ++i)
 675     {
 676         top_->atoms.atom[i].q = i / 10.0;
 677     }
 678     ASSERT_NO_FATAL_FAILURE(runCompiler());
 679 }
 680
 681 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 682 {
 683     static const char * const selections[] = {
 684         "altloc \" \"",
 685         "altloc A"
 686     };
 687     runTest("simple.pdb", selections);
 688 }
 689
 690 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 691 {
 692     static const char * const selections[] = {
 693         "insertcode \" \"",
 694         "insertcode A"
 695     };
 696     runTest("simple.pdb", selections);
 697 }
 698
 699 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 700 {
 701     static const char * const selections[] = {
 702         "occupancy 1",
 703         "occupancy < .5"
 704     };
 705     runTest("simple.pdb", selections);
 706 }
 707
 708 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 709 {
 710     static const char * const selections[] = {
 711         "beta 0",
 712         "beta >= 0.3"
 713     };
 714     runTest("simple.pdb", selections);
 715 }
 716
 717 TEST_F(SelectionCollectionDataTest, HandlesResname)
 718 {
 719     static const char * const selections[] = {
 720         "resname RA",
 721         "resname RB RC"
 722     };
 723     runTest("simple.gro", selections);
 724 }
 725
 726 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
 727 {
 728     static const char * const selections[] = {
 729         "x < 3",
 730         "y >= 3",
 731         "x {-1 to 2}"
 732     };
 733     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 734     runTest("simple.gro", selections);
 735 }
 736
 737
 738 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
 739 {
 740     static const char * const selections[] = {
 741         "same residue as atomnr 1 4 12"
 742     };
 743     runTest("simple.gro", selections);
 744 }
 745
 746
 747 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
 748 {
 749     static const char * const selections[] = {
 750         "same resname as atomnr 1 14"
 751     };
 752     runTest("simple.gro", selections);
 753 }
 754
 755
 756 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
 757 {
 758     static const char * const selections[] = {
 759         "cog of resnr 1 3",
 760         "res_cog of name CB and resnr 1 3",
 761         "whole_res_cog of name CB and resnr 1 3",
 762         "part_res_cog of x < 3",
 763         "dyn_res_cog of x < 3"
 764     };
 765     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 766              | efTestPositionAtoms);
 767     runTest("simple.gro", selections);
 768 }
 769
 770
 771 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
 772 {
 773     static const char * const selections[] = {
 774         "distance from cog of resnr 1 < 2"
 775     };
 776     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 777     runTest("simple.gro", selections);
 778 }
 779
 780
 781 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
 782 {
 783     static const char * const selections[] = {
 784         "mindistance from resnr 1 < 2"
 785     };
 786     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 787     runTest("simple.gro", selections);
 788 }
 789
 790
 791 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
 792 {
 793     static const char * const selections[] = {
 794         "within 1 of resnr 2"
 795     };
 796     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 797     runTest("simple.gro", selections);
 798 }
 799
 800
 801 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
 802 {
 803     // Both of these should evaluate to empty on a correct implementation.
 804     static const char * const selections[] = {
 805         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
 806         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
 807     };
 808     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
 809     runTest("sphere.gro", selections);
 810 }
 811
 812
 813 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
 814 {
 815     static const char * const selections[] = {
 816         "all permute 3 1 2",
 817         "res_cog of resnr 1 to 4 permute 2 1",
 818         "name CB S1 and res_cog x < 3 permute 2 1"
 819     };
 820     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 821              | efTestPositionAtoms | efTestPositionMapping);
 822     runTest("simple.gro", selections);
 823 }
 824
 825
 826 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
 827 {
 828     static const char * const selections[] = {
 829         "name S2 plus name S1",
 830         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
 831         "name S1 and y < 3 plus res_cog of x < 2.5"
 832     };
 833     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 834              | efTestPositionAtoms | efTestPositionMapping);
 835     runTest("simple.gro", selections);
 836 }
 837
 838
 839 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
 840 {
 841     static const char * const selections[] = {
 842         "name S2 merge name S1",
 843         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
 844         "name S1 and x < 2.5 merge res_cog of x < 2.5"
 845     };
 846     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
 847              | efTestPositionAtoms | efTestPositionMapping);
 848     runTest("simple.gro", selections);
 849 }
 850
 851
 852 /********************************************************************
 853  * Tests for generic selection evaluation
 854  */
 855
 856 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
 857 {
 858     static const char * const selections[] = {
 859         "name CB",
 860         "y > 2",
 861         "res_cog of y > 2"
 862     };
 863     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
 864              | efTestPositionMasses | efTestPositionCharges);
 865     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 866     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 867     for (int i = 0; i < top_->atoms.nr; ++i)
 868     {
 869         top_->atoms.atom[i].m =   1.0 + i / 100.0;
 870         top_->atoms.atom[i].q = -(1.0 + i / 100.0);
 871     }
 872     ASSERT_NO_FATAL_FAILURE(runCompiler());
 873     ASSERT_NO_FATAL_FAILURE(runEvaluate());
 874     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 875 }
 876
 877 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
 878 {
 879     static const char * const selections[] = {
 880         "atomnr 1 to 3 8 to 9",
 881         "y > 2",
 882         "cog of (y > 2)"
 883     };
 884     setFlags(TestFlags() | efTestPositionAtoms
 885              | efTestPositionMasses | efTestPositionCharges);
 886     runTest(10, selections);
 887 }
 888
 889
 890 /********************************************************************
 891  * Tests for selection syntactic constructs
 892  */
 893
 894 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
 895 {
 896     static const char * const selections[] = {
 897         "\"GroupSelection\" group \"GrpA\"",
 898         "\"DynamicSelection\" x < 5",
 899         "y < 3"
 900     };
 901     setFlags(TestFlags() | efTestSelectionNames);
 902     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 903     runTest(10, selections);
 904 }
 905
 906 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
 907 {
 908     static const char * const selections[] = {
 909         "group \"GrpA\"",
 910         "GrpB",
 911         "1",
 912         "group \"GrpB\" and resname RB"
 913     };
 914     setFlags(TestFlags() | efTestSelectionNames);
 915     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 916     runTest("simple.gro", selections);
 917 }
 918
 919 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
 920 {
 921     static const char * const selections[] = {
 922         "group \"GrpA\"",
 923         "GrpB",
 924         "1",
 925         "group \"GrpB\" and resname RB"
 926     };
 927     setFlags(TestFlags() | efTestSelectionNames);
 928     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 929     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 930     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 931     ASSERT_NO_FATAL_FAILURE(runCompiler());
 932 }
 933
 934 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
 935 {
 936     static const char * const selections[] = {
 937         "foo = group \"GrpUnsorted\"",
 938         "group \"GrpUnsorted\"",
 939         "GrpUnsorted",
 940         "2",
 941         "res_cog of group \"GrpUnsorted\"",
 942         "group \"GrpUnsorted\" permute 2 1",
 943         "foo"
 944     };
 945     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
 946              | efTestSelectionNames);
 947     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 948     runTest("simple.gro", selections);
 949 }
 950
 951 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelectionsDelayed)
 952 {
 953     static const char * const selections[] = {
 954         "foo = group \"GrpUnsorted\"",
 955         "group \"GrpUnsorted\"",
 956         "GrpUnsorted",
 957         "2",
 958         "res_cog of group \"GrpUnsorted\"",
 959         "group \"GrpUnsorted\" permute 2 1",
 960         "foo"
 961     };
 962     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 963     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 964     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 965     ASSERT_NO_FATAL_FAILURE(runCompiler());
 966 }
 967
 968 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
 969 {
 970     static const char * const selections[] = {
 971         "[1, -2, 3.5]"
 972     };
 973     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 974     runTest("simple.gro", selections);
 975 }
 976
 977
 978 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
 979 {
 980     static const char * const selections[] = {
 981         "within 1 of [2, 1, 0]"
 982     };
 983     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
 984     runTest("simple.gro", selections);
 985 }
 986
 987
 988 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
 989 {
 990     static const char * const selections[] = {
 991         "name = S1 \"C?\"",
 992         "name ? S1 \"C?\""
 993     };
 994     runTest("simple.gro", selections);
 995 }
 996
 997
 998 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
 999 {
1000     static const char * const selections[] = {
1001         "name \"S?\"",
1002         "name ? \"S?\""
1003     };
1004     runTest("simple.gro", selections);
1005 }
1006
1007
1008 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
1009 {
1010     static const char * const selections[] = {
1011         "resname \"R[BD]\"",
1012         "resname ~ \"R[BD]\""
1013     };
1014     if (gmx::Regex::isSupported())
1015     {
1016         runTest("simple.gro", selections);
1017     }
1018 }
1019
1020
1021 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
1022 {
1023     static const char * const selections[] = {
1024         "atomnr 1 to 5 and atomnr 2 to 7",
1025         "atomnr 1 to 5 or not atomnr 3 to 8",
1026         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1027         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1028         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1029     };
1030     runTest(10, selections);
1031 }
1032
1033
1034 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1035 {
1036     static const char * const selections[] = {
1037         "same residue as (atomnr 3 5 13 or y > 5)",
1038         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1039     };
1040     setFlags(TestFlags() | efTestEvaluation);
1041     runTest("simple.gro", selections);
1042 }
1043
1044
1045 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1046 {
1047     static const char * const selections[] = {
1048         "none and x > 2",
1049         "none and same resname as resnr 2"
1050     };
1051     runTest("simple.gro", selections);
1052 }
1053
1054
1055 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1056 {
1057     static const char * const selections[] = {
1058         "x > 2",
1059         "2 < x",
1060         "y > resnr",
1061         "resnr < 2.5",
1062         "2.5 > resnr"
1063     };
1064     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1065     runTest("simple.gro", selections);
1066 }
1067
1068
1069 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1070 {
1071     static const char * const selections[] = {
1072         "x+1 > 3",
1073         "(y-1)^2 <= 1",
1074         "x+--1 > 3",
1075         "-x+-1 < -3"
1076     };
1077     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1078     runTest("simple.gro", selections);
1079 }
1080
1081
1082 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1083 {
1084     static const char * const selections[] = {
1085         "value = x + y",
1086         "value <= 4",
1087         "index = resnr",
1088         "index < 3"
1089     };
1090     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1091     runTest("simple.gro", selections);
1092 }
1093
1094
1095 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1096 {
1097     static const char * const selections[] = {
1098         "value = x + y",
1099         "resname RA and value <= 4",
1100         "resname RA RB and x < 3 and value <= 4",
1101         "index = atomnr",
1102         "resname RA and index < 3",
1103         "resname RB and y < 3 and index < 6"
1104     };
1105     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1106     runTest("simple.gro", selections);
1107 }
1108
1109
1110 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1111 {
1112     static const char * const selections[] = {
1113         "foo = res_cog of resname RA",
1114         "foo",
1115         "within 1 of foo",
1116         "bar = cog of resname RA",
1117         "bar",
1118         "within 1 of bar"
1119     };
1120     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1121     runTest("simple.gro", selections);
1122 }
1123
1124
1125 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1126 {
1127     static const char * const selections[] = {
1128         "constpos = [1.0, 2.5, 0.5]",
1129         "constpos",
1130         "within 2 of constpos"
1131     };
1132     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1133              | efTestPositionAtoms);
1134     runTest("simple.gro", selections);
1135 }
1136
1137
1138 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1139 {
1140     static const char * const selections[] = {
1141         "constint = 4",
1142         "constreal1 = 0.5",
1143         "constreal2 = 2.7",
1144         "resnr < constint",
1145         "x + constreal1 < constreal2"
1146     };
1147     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1148     runTest("simple.gro", selections);
1149 }
1150
1151
1152 /********************************************************************
1153  * Tests for complex boolean syntax
1154  */
1155
1156 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1157 {
1158     static const char * const selections[] = {
1159         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1160         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1161         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1162         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1163         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1164     };
1165     runTest(10, selections);
1166 }
1167
1168
1169 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1170 {
1171     static const char * const selections[] = {
1172         "foo = atomnr 4 to 7 or x < 2",
1173         "atomnr 1 to 4 and foo",
1174         "atomnr 2 to 6 and y < 3 and foo",
1175         "atomnr 6 to 10 and not foo"
1176     };
1177     runTest(10, selections);
1178 }
1179
1180
1181 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1182 {
1183     static const char * const selections[] = {
1184         "foo = atomnr 4 to 7",
1185         "bar = foo and x < 2",
1186         "bar2 = foo and y < 2",
1187         "atomnr 1 to 4 and bar",
1188         "atomnr 2 to 6 and y < 3 and bar2",
1189         "atomnr 6 to 10 and not foo"
1190     };
1191     runTest(10, selections);
1192 }
1193
1194
1195 /********************************************************************
1196  * Tests for complex subexpression cases
1197  *
1198  * These tests use some knowledge of the implementation to trigger different
1199  * paths in the code.
1200  */
1201
1202 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1203 {
1204     static const char * const selections[] = {
1205         "unused1 = atomnr 1 to 3",
1206         "foo = atomnr 4 to 7",
1207         "atomnr 1 to 6 and foo",
1208         "unused2 = atomnr 3 to 5"
1209     };
1210     runTest(10, selections);
1211 }
1212
1213
1214 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1215 {
1216     static const char * const selections[] = {
1217         "foo = atomnr 4 to 7 and x < 2",
1218         "atomnr 1 to 5 and foo",
1219         "atomnr 3 to 7 and foo"
1220     };
1221     runTest(10, selections);
1222 }
1223
1224
1225 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1226 {
1227     static const char * const selections[] = {
1228         "foo = atomnr 4 to 7 and x < 2",
1229         "atomnr 1 to 6 and foo",
1230         "within 1 of foo",
1231         "foo"
1232     };
1233     runTest(10, selections);
1234 }
1235
1236
1237 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1238 {
1239     static const char * const selections[] = {
1240         "foo = atomnr 1 to 8 and x < 10",
1241         "atomnr 1 to 5 and y < 10 and foo",
1242         "foo"
1243     };
1244     setFlags(TestFlags() | efTestEvaluation);
1245     runTest("simple.gro", selections);
1246 }
1247
1248
1249 } // namespace