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 "gmxpre.h"
  43
  44 #include "gromacs/selection/selectioncollection.h"
  45
  46 #include <gtest/gtest.h>
  47
  48 #include "gromacs/options/basicoptions.h"
  49 #include "gromacs/options/ioptionscontainer.h"
  50 #include "gromacs/selection/indexutil.h"
  51 #include "gromacs/selection/selection.h"
  52 #include "gromacs/topology/topology.h"
  53 #include "gromacs/trajectory/trajectoryframe.h"
  54 #include "gromacs/utility/arrayref.h"
  55 #include "gromacs/utility/exceptions.h"
  56 #include "gromacs/utility/flags.h"
  57 #include "gromacs/utility/gmxregex.h"
  58 #include "gromacs/utility/stringutil.h"
  59
  60 #include "testutils/interactivetest.h"
  61 #include "testutils/refdata.h"
  62 #include "testutils/testasserts.h"
  63 #include "testutils/testfilemanager.h"
  64 #include "testutils/testoptions.h"
  65
  66 #include "toputils.h"
  67
  68 namespace
  69 {
  70
  71 /********************************************************************
  72  * Test fixture for selection testing
  73  */
  74
  75 class SelectionCollectionTest : public ::testing::Test
  76 {
  77     public:
  78         static int               s_debugLevel;
  79
  80         SelectionCollectionTest();
  81         ~SelectionCollectionTest() override;
  82
  83         void setAtomCount(int natoms)
  84         {
  85             ASSERT_NO_THROW_GMX(sc_.setTopology(nullptr, natoms));
  86         }
  87         void loadTopology(const char *filename);
  88         void setTopology();
  89         void loadIndexGroups(const char *filename);
  90
  91         gmx::test::TopologyManager  topManager_;
  92         gmx::SelectionCollection    sc_;
  93         gmx::SelectionList          sel_;
  94         gmx_ana_indexgrps_t        *grps_;
  95 };
  96
  97 int SelectionCollectionTest::s_debugLevel = 0;
  98
  99 // cond/endcond do not seem to work here with Doxygen 1.8.5 parser.
 100 #ifndef DOXYGEN
 101 GMX_TEST_OPTIONS(SelectionCollectionTestOptions, options)
 102 {
 103     options->addOption(gmx::IntegerOption("seldebug")
 104                            .store(&SelectionCollectionTest::s_debugLevel)
 105                            .description("Set selection debug level"));
 106 }
 107 #endif
 108
 109 SelectionCollectionTest::SelectionCollectionTest()
 110     : grps_(nullptr)
 111 {
 112     topManager_.requestFrame();
 113     sc_.setDebugLevel(s_debugLevel);
 114     sc_.setReferencePosType("atom");
 115     sc_.setOutputPosType("atom");
 116 }
 117
 118 SelectionCollectionTest::~SelectionCollectionTest()
 119 {
 120     if (grps_ != nullptr)
 121     {
 122         gmx_ana_indexgrps_free(grps_);
 123     }
 124 }
 125
 126 void
 127 SelectionCollectionTest::loadTopology(const char *filename)
 128 {
 129     topManager_.loadTopology(filename);
 130     setTopology();
 131 }
 132
 133 void
 134 SelectionCollectionTest::setTopology()
 135 {
 136     ASSERT_NO_THROW_GMX(sc_.setTopology(topManager_.topology(), -1));
 137 }
 138
 139 void
 140 SelectionCollectionTest::loadIndexGroups(const char *filename)
 141 {
 142     GMX_RELEASE_ASSERT(grps_ == nullptr,
 143                        "External groups can only be loaded once");
 144     std::string fullpath =
 145         gmx::test::TestFileManager::getInputFilePath(filename);
 146     gmx_ana_indexgrps_init(&grps_, nullptr, fullpath.c_str());
 147     sc_.setIndexGroups(grps_);
 148 }
 149
 150
 151 /********************************************************************
 152  * Test fixture for interactive SelectionCollection tests
 153  */
 154
 155 class SelectionCollectionInteractiveTest : public SelectionCollectionTest
 156 {
 157     public:
 158         SelectionCollectionInteractiveTest()
 159             : helper_(data_.rootChecker())
 160         {
 161         }
 162
 163         void runTest(int count, bool bInteractive,
 164                      const gmx::ArrayRef<const char *const> &input);
 165
 166         gmx::test::TestReferenceData      data_;
 167         gmx::test::InteractiveTestHelper  helper_;
 168 };
 169
 170 void SelectionCollectionInteractiveTest::runTest(
 171         int count, bool bInteractive,
 172         const gmx::ArrayRef<const char *const> &inputLines)
 173 {
 174     helper_.setInputLines(inputLines);
 175     // TODO: Check something about the returned selections as well.
 176     ASSERT_NO_THROW_GMX(sc_.parseInteractive(
 177                                 count, &helper_.inputStream(),
 178                                 bInteractive ? &helper_.outputStream() : nullptr,
 179                                 "for test context"));
 180     helper_.checkSession();
 181 }
 182
 183
 184 /********************************************************************
 185  * Test fixture for selection testing with reference data
 186  */
 187
 188 class SelectionCollectionDataTest : public SelectionCollectionTest
 189 {
 190     public:
 191         enum TestFlag
 192         {
 193             efTestEvaluation            = 1<<0,
 194             efTestPositionAtoms         = 1<<1,
 195             efTestPositionCoordinates   = 1<<2,
 196             efTestPositionMapping       = 1<<3,
 197             efTestPositionMasses        = 1<<4,
 198             efTestPositionCharges       = 1<<5,
 199             efTestSelectionNames        = 1<<6,
 200             efDontTestCompiledAtoms     = 1<<8
 201         };
 202         typedef gmx::FlagsTemplate<TestFlag> TestFlags;
 203
 204         SelectionCollectionDataTest()
 205             : checker_(data_.rootChecker()), count_(0), framenr_(0)
 206         {
 207         }
 208
 209         void setFlags(TestFlags flags) { flags_ = flags; }
 210
 211         void runParser(const gmx::ArrayRef<const char *const> &selections);
 212         void runCompiler();
 213         void runEvaluate();
 214         void runEvaluateFinal();
 215
 216         void runTest(int                                     natoms,
 217                      const gmx::ArrayRef<const char *const> &selections);
 218         void runTest(const char                             *filename,
 219                      const gmx::ArrayRef<const char *const> &selections);
 220
 221     private:
 222         static void checkSelection(gmx::test::TestReferenceChecker *checker,
 223                                    const gmx::Selection &sel, TestFlags flags);
 224
 225         void checkCompiled();
 226
 227         gmx::test::TestReferenceData    data_;
 228         gmx::test::TestReferenceChecker checker_;
 229         size_t                          count_;
 230         int                             framenr_;
 231         TestFlags                       flags_;
 232 };
 233
 234
 235 void
 236 SelectionCollectionDataTest::checkSelection(
 237         gmx::test::TestReferenceChecker *checker,
 238         const gmx::Selection &sel, TestFlags flags)
 239 {
 240     using gmx::test::TestReferenceChecker;
 241
 242     {
 243         gmx::ArrayRef<const int> atoms = sel.atomIndices();
 244         checker->checkSequence(atoms.begin(), atoms.end(), "Atoms");
 245     }
 246     if (flags.test(efTestPositionAtoms)
 247         || flags.test(efTestPositionCoordinates)
 248         || flags.test(efTestPositionMapping)
 249         || flags.test(efTestPositionMasses)
 250         || flags.test(efTestPositionCharges))
 251     {
 252         TestReferenceChecker compound(
 253                 checker->checkSequenceCompound("Positions", sel.posCount()));
 254         for (int i = 0; i < sel.posCount(); ++i)
 255         {
 256             TestReferenceChecker          poscompound(compound.checkCompound("Position", nullptr));
 257             const gmx::SelectionPosition &p = sel.position(i);
 258             if (flags.test(efTestPositionAtoms))
 259             {
 260                 gmx::ArrayRef<const int> atoms = p.atomIndices();
 261                 poscompound.checkSequence(atoms.begin(), atoms.end(), "Atoms");
 262             }
 263             if (flags.test(efTestPositionCoordinates))
 264             {
 265                 poscompound.checkVector(p.x(), "Coordinates");
 266             }
 267             if (flags.test(efTestPositionMapping))
 268             {
 269                 poscompound.checkInteger(p.refId(), "RefId");
 270                 poscompound.checkInteger(p.mappedId(), "MappedId");
 271             }
 272             if (flags.test(efTestPositionMasses))
 273             {
 274                 poscompound.checkReal(p.mass(), "Mass");
 275             }
 276             if (flags.test(efTestPositionCharges))
 277             {
 278                 poscompound.checkReal(p.charge(), "Charge");
 279             }
 280         }
 281     }
 282 }
 283
 284
 285 void
 286 SelectionCollectionDataTest::runParser(
 287         const gmx::ArrayRef<const char *const> &selections)
 288 {
 289     using gmx::test::TestReferenceChecker;
 290
 291     TestReferenceChecker compound(checker_.checkCompound("ParsedSelections", "Parsed"));
 292     size_t               varcount = 0;
 293     count_ = 0;
 294     for (gmx::index i = 0; i < selections.ssize(); ++i)
 295     {
 296         SCOPED_TRACE(std::string("Parsing selection \"")
 297                      + selections[i] + "\"");
 298         gmx::SelectionList result;
 299         ASSERT_NO_THROW_GMX(result = sc_.parseFromString(selections[i]));
 300         sel_.insert(sel_.end(), result.begin(), result.end());
 301         if (sel_.size() == count_)
 302         {
 303             std::string          id = gmx::formatString("Variable%d", static_cast<int>(varcount + 1));
 304             TestReferenceChecker varcompound(
 305                     compound.checkCompound("ParsedVariable", id.c_str()));
 306             varcompound.checkString(selections[i], "Input");
 307             ++varcount;
 308         }
 309         else
 310         {
 311             std::string          id = gmx::formatString("Selection%d", static_cast<int>(count_ + 1));
 312             TestReferenceChecker selcompound(
 313                     compound.checkCompound("ParsedSelection", id.c_str()));
 314             selcompound.checkString(selections[i], "Input");
 315             if (flags_.test(efTestSelectionNames))
 316             {
 317                 selcompound.checkString(sel_[count_].name(), "Name");
 318             }
 319             selcompound.checkString(sel_[count_].selectionText(), "Text");
 320             selcompound.checkBoolean(sel_[count_].isDynamic(), "Dynamic");
 321             ++count_;
 322         }
 323     }
 324 }
 325
 326
 327 void
 328 SelectionCollectionDataTest::runCompiler()
 329 {
 330     ASSERT_NO_THROW_GMX(sc_.compile());
 331     ASSERT_EQ(count_, sel_.size());
 332     checkCompiled();
 333 }
 334
 335
 336 void
 337 SelectionCollectionDataTest::checkCompiled()
 338 {
 339     using gmx::test::TestReferenceChecker;
 340     const TestFlags      mask = ~TestFlags(efTestPositionCoordinates);
 341
 342     TestReferenceChecker compound(checker_.checkCompound("CompiledSelections", "Compiled"));
 343     for (size_t i = 0; i < count_; ++i)
 344     {
 345         SCOPED_TRACE(std::string("Checking selection \"") +
 346                      sel_[i].selectionText() + "\"");
 347         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 348         TestReferenceChecker selcompound(
 349                 compound.checkCompound("Selection", id.c_str()));
 350         if (flags_.test(efTestSelectionNames))
 351         {
 352             selcompound.checkString(sel_[i].name(), "Name");
 353         }
 354         if (!flags_.test(efDontTestCompiledAtoms))
 355         {
 356             checkSelection(&selcompound, sel_[i], flags_ & mask);
 357         }
 358     }
 359 }
 360
 361
 362 void
 363 SelectionCollectionDataTest::runEvaluate()
 364 {
 365     using gmx::test::TestReferenceChecker;
 366
 367     ++framenr_;
 368     ASSERT_NO_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr));
 369     std::string          frame = gmx::formatString("Frame%d", framenr_);
 370     TestReferenceChecker compound(
 371             checker_.checkCompound("EvaluatedSelections", frame.c_str()));
 372     for (size_t i = 0; i < count_; ++i)
 373     {
 374         SCOPED_TRACE(std::string("Checking selection \"") +
 375                      sel_[i].selectionText() + "\"");
 376         std::string          id = gmx::formatString("Selection%d", static_cast<int>(i + 1));
 377         TestReferenceChecker selcompound(
 378                 compound.checkCompound("Selection", id.c_str()));
 379         checkSelection(&selcompound, sel_[i], flags_);
 380     }
 381 }
 382
 383
 384 void
 385 SelectionCollectionDataTest::runEvaluateFinal()
 386 {
 387     ASSERT_NO_THROW_GMX(sc_.evaluateFinal(framenr_));
 388     checkCompiled();
 389 }
 390
 391
 392 void
 393 SelectionCollectionDataTest::runTest(
 394         int natoms, const gmx::ArrayRef<const char *const> &selections)
 395 {
 396     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 397     ASSERT_NO_FATAL_FAILURE(setAtomCount(natoms));
 398     ASSERT_NO_FATAL_FAILURE(runCompiler());
 399 }
 400
 401
 402 void
 403 SelectionCollectionDataTest::runTest(
 404         const char *filename, const gmx::ArrayRef<const char *const> &selections)
 405 {
 406     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 407     ASSERT_NO_FATAL_FAILURE(loadTopology(filename));
 408     ASSERT_NO_FATAL_FAILURE(runCompiler());
 409     if (flags_.test(efTestEvaluation))
 410     {
 411         ASSERT_NO_FATAL_FAILURE(runEvaluate());
 412         ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
 413     }
 414 }
 415
 416
 417 /********************************************************************
 418  * Tests for SelectionCollection functionality without reference data
 419  */
 420
 421 TEST_F(SelectionCollectionTest, HandlesNoSelections)
 422 {
 423     EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
 424     EXPECT_NO_THROW_GMX(sc_.compile());
 425     EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
 426 }
 427
 428 TEST_F(SelectionCollectionTest, HandlesNoSelectionsWithDefaultPositionType)
 429 {
 430     EXPECT_NO_THROW_GMX(sc_.setOutputPosType("res_com"));
 431     EXPECT_TRUE(sc_.requiredTopologyProperties().needsTopology);
 432     EXPECT_TRUE(sc_.requiredTopologyProperties().needsMasses);
 433     EXPECT_NO_THROW_GMX(sc_.setOutputPosType("res_cog"));
 434     EXPECT_TRUE(sc_.requiredTopologyProperties().needsTopology);
 435     EXPECT_FALSE(sc_.requiredTopologyProperties().needsMasses);
 436     ASSERT_NO_THROW_GMX(sc_.parseFromString("atom of atomnr 1 to 10"));
 437     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 438     ASSERT_NO_THROW_GMX(sc_.compile());
 439     EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
 440 }
 441
 442 TEST_F(SelectionCollectionTest, HandlesVelocityAndForceRequests)
 443 {
 444     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr 1 to 10; none"));
 445     EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
 446     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 447     ASSERT_EQ(2U, sel_.size());
 448     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateVelocities(true));
 449     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateVelocities(true));
 450     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 451     ASSERT_NO_THROW_GMX(sel_[1].setEvaluateForces(true));
 452     EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
 453     ASSERT_NO_THROW_GMX(sc_.compile());
 454     EXPECT_FALSE(sc_.requiredTopologyProperties().hasAny());
 455     EXPECT_TRUE(sel_[0].hasVelocities());
 456     EXPECT_TRUE(sel_[1].hasVelocities());
 457     EXPECT_TRUE(sel_[0].hasForces());
 458     EXPECT_TRUE(sel_[1].hasForces());
 459 }
 460
 461 TEST_F(SelectionCollectionTest, HandlesForceRequestForCenterOfGeometry)
 462 {
 463     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("res_cog of atomnr 1 to 10"));
 464     EXPECT_TRUE(sc_.requiredTopologyProperties().needsTopology);
 465     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 466     ASSERT_EQ(1U, sel_.size());
 467     ASSERT_NO_THROW_GMX(sel_[0].setEvaluateForces(true));
 468     // In principle, the code could know here that the masses are required, but
 469     // currently it only knows this after compilation.
 470     ASSERT_NO_THROW_GMX(sc_.compile());
 471     EXPECT_TRUE(sc_.requiredTopologyProperties().needsMasses);
 472     EXPECT_TRUE(sel_[0].hasForces());
 473 }
 474
 475 TEST_F(SelectionCollectionTest, ParsesSelectionsFromFile)
 476 {
 477     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromFile(
 478                                     gmx::test::TestFileManager::getInputFilePath("selfile.dat")));
 479     // These should match the contents of selfile.dat
 480     ASSERT_EQ(2U, sel_.size());
 481     EXPECT_STREQ("resname RA RB", sel_[0].selectionText());
 482     EXPECT_STREQ("resname RB RC", sel_[1].selectionText());
 483 }
 484
 485 TEST_F(SelectionCollectionTest, HandlesAtypicalWhitespace)
 486 {
 487     ASSERT_NO_THROW_GMX(sel_ = sc_.parseFromString("atomnr\n1\r\nto\t10;\vatomnr 3\f to 14\r"));
 488     ASSERT_EQ(2U, sel_.size());
 489     EXPECT_STREQ("atomnr 1 to 10", sel_[0].selectionText());
 490     // TODO: Get rid of the trailing whitespace.
 491     EXPECT_STREQ("atomnr 3 to 14 ", sel_[1].selectionText());
 492 }
 493
 494 TEST_F(SelectionCollectionTest, HandlesInvalidRegularExpressions)
 495 {
 496     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 497     EXPECT_THROW_GMX({
 498                          sc_.parseFromString("resname ~ \"R[A\"");
 499                          sc_.compile();
 500                      }, gmx::InvalidInputError);
 501 }
 502
 503 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue)
 504 {
 505     EXPECT_THROW_GMX(sc_.parseFromString("mindist from atomnr 1 cutoff"),
 506                      gmx::InvalidInputError);
 507 }
 508
 509 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue2)
 510 {
 511     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of"),
 512                      gmx::InvalidInputError);
 513 }
 514
 515 TEST_F(SelectionCollectionTest, HandlesMissingMethodParamValue3)
 516 {
 517     EXPECT_THROW_GMX(sc_.parseFromString("within of atomnr 1"),
 518                      gmx::InvalidInputError);
 519 }
 520
 521 // TODO: Tests for more parser errors
 522
 523 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser1)
 524 {
 525     ASSERT_NO_THROW_GMX(sc_.setIndexGroups(nullptr));
 526     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 527     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 528 }
 529
 530 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceParser2)
 531 {
 532     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 533     EXPECT_THROW_GMX(sc_.parseFromString("group \"foo\""), gmx::InconsistentInputError);
 534     EXPECT_THROW_GMX(sc_.parseFromString("4"), gmx::InconsistentInputError);
 535 }
 536
 537 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed1)
 538 {
 539     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"foo\""));
 540     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 541     EXPECT_THROW_GMX(sc_.setIndexGroups(nullptr), gmx::InconsistentInputError);
 542     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 543 }
 544
 545 TEST_F(SelectionCollectionTest, HandlesUnknownGroupReferenceDelayed2)
 546 {
 547     ASSERT_NO_THROW_GMX(sc_.parseFromString("group 4; group \"foo\""));
 548     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 549     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 550     EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 551 }
 552
 553 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReference)
 554 {
 555     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 556     EXPECT_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""),
 557                      gmx::InconsistentInputError);
 558     EXPECT_THROW_GMX(sc_.parseFromString("group 2 or atomnr 2 to 5"),
 559                      gmx::InconsistentInputError);
 560     EXPECT_THROW_GMX(sc_.parseFromString("within 1 of group 2"),
 561                      gmx::InconsistentInputError);
 562 }
 563
 564 TEST_F(SelectionCollectionTest, HandlesUnsortedGroupReferenceDelayed)
 565 {
 566     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group \"GrpUnsorted\""));
 567     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 1 to 3 and group 2"));
 568     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 569     // TODO: Add a separate check in the selection compiler for a safer API
 570     // (makes sense in the future if the compiler needs the information for
 571     // other purposes as well).
 572     // EXPECT_THROW_GMX(sc_.compile(), gmx::APIError);
 573 }
 574
 575 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroup)
 576 {
 577     ASSERT_NO_THROW_GMX(sc_.setTopology(nullptr, 5));
 578     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 579     EXPECT_THROW_GMX(sc_.parseFromString("group \"GrpB\""), gmx::InconsistentInputError);
 580 }
 581
 582 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed)
 583 {
 584     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
 585     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
 586     EXPECT_THROW_GMX(sc_.setTopology(nullptr, 5), gmx::InconsistentInputError);
 587 }
 588
 589 TEST_F(SelectionCollectionTest, HandlesOutOfRangeAtomIndexInGroupDelayed2)
 590 {
 591     ASSERT_NO_THROW_GMX(sc_.setTopology(nullptr, 5));
 592     ASSERT_NO_THROW_GMX(sc_.parseFromString("group \"GrpB\""));
 593     EXPECT_THROW_GMX(loadIndexGroups("simple.ndx"), gmx::InconsistentInputError);
 594 }
 595
 596 TEST_F(SelectionCollectionTest, RecoversFromMissingMoleculeInfo)
 597 {
 598     ASSERT_NO_THROW_GMX(sc_.parseFromString("molindex 1 to 5"));
 599     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 600     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 601 }
 602
 603 TEST_F(SelectionCollectionTest, RecoversFromMissingAtomTypes)
 604 {
 605     ASSERT_NO_THROW_GMX(sc_.parseFromString("type CA"));
 606     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 607     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 608 }
 609
 610 TEST_F(SelectionCollectionTest, RecoversFromMissingPDBInfo)
 611 {
 612     ASSERT_NO_THROW_GMX(sc_.parseFromString("altloc A"));
 613     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 614     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 615 }
 616
 617 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation)
 618 {
 619     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 1 1"));
 620     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 621     EXPECT_THROW_GMX(sc_.compile(), gmx::InvalidInputError);
 622 }
 623
 624 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation2)
 625 {
 626     ASSERT_NO_THROW_GMX(sc_.parseFromString("all permute 3 2 1"));
 627     ASSERT_NO_FATAL_FAILURE(setAtomCount(10));
 628     EXPECT_THROW_GMX(sc_.compile(), gmx::InconsistentInputError);
 629 }
 630
 631 TEST_F(SelectionCollectionTest, RecoversFromInvalidPermutation3)
 632 {
 633     ASSERT_NO_THROW_GMX(sc_.parseFromString("x < 1.5 permute 3 2 1"));
 634     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 635     ASSERT_NO_THROW_GMX(sc_.compile());
 636     EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
 637 }
 638
 639 TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets)
 640 {
 641     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 3 to 10"));
 642     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 643     ASSERT_NO_THROW_GMX(sc_.compile());
 644     topManager_.frame()->natoms = 8;
 645     EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
 646 }
 647
 648 TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets2)
 649 {
 650     const int index[] = { 1, 2, 3, 9 };
 651     ASSERT_NO_THROW_GMX(sc_.parseFromString("atomnr 3 4 7 10"));
 652     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 653     ASSERT_NO_THROW_GMX(sc_.compile());
 654     topManager_.initFrameIndices(index);
 655     EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
 656 }
 657
 658 TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets3)
 659 {
 660     const int index[] = { 0, 1, 2, 3, 4, 5, 6, 9, 10, 11 };
 661     // Evaluating the positions will require atoms 1-3, 7-12.
 662     ASSERT_NO_THROW_GMX(sc_.parseFromString("whole_res_cog of atomnr 2 7 11"));
 663     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 664     ASSERT_NO_THROW_GMX(sc_.compile());
 665     topManager_.initFrameIndices(index);
 666     EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
 667 }
 668
 669 TEST_F(SelectionCollectionTest, HandlesFramesWithTooSmallAtomSubsets4)
 670 {
 671     ASSERT_NO_THROW_GMX(sc_.parseFromString("mindistance from atomnr 1 to 5 < 2"));
 672     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
 673     ASSERT_NO_THROW_GMX(sc_.compile());
 674     topManager_.frame()->natoms = 10;
 675     EXPECT_THROW_GMX(sc_.evaluate(topManager_.frame(), nullptr), gmx::InconsistentInputError);
 676 }
 677
 678 // TODO: Tests for more evaluation errors
 679
 680 /********************************************************************
 681  * Tests for interactive selection input
 682  */
 683
 684 TEST_F(SelectionCollectionInteractiveTest, HandlesBasicInput)
 685 {
 686     const char *const input[] = {
 687         "foo = resname RA",
 688         "resname RB",
 689         "\"Name\" resname RC"
 690     };
 691     runTest(-1, true, input);
 692 }
 693
 694 TEST_F(SelectionCollectionInteractiveTest, HandlesContinuation)
 695 {
 696     const char *const input[] = {
 697         "resname RB and \\",
 698         "resname RC"
 699     };
 700     runTest(-1, true, input);
 701 }
 702
 703 TEST_F(SelectionCollectionInteractiveTest, HandlesSingleSelectionInput)
 704 {
 705     const char *const input[] = {
 706         "foo = resname RA",
 707         "resname RA"
 708     };
 709     runTest(1, true, input);
 710 }
 711
 712 TEST_F(SelectionCollectionInteractiveTest, HandlesTwoSelectionInput)
 713 {
 714     const char *const input[] = {
 715         "resname RA",
 716         "resname RB"
 717     };
 718     runTest(2, true, input);
 719 }
 720
 721 TEST_F(SelectionCollectionInteractiveTest, HandlesStatusWithGroups)
 722 {
 723     const char *const input[] = {
 724         "resname RA",
 725         ""
 726     };
 727     loadIndexGroups("simple.ndx");
 728     runTest(-1, true, input);
 729 }
 730
 731 TEST_F(SelectionCollectionInteractiveTest, HandlesStatusWithExistingSelections)
 732 {
 733     const char *const input[] = {
 734         "",
 735         "bar = resname RC",
 736         "resname RA",
 737         ""
 738     };
 739     ASSERT_NO_THROW_GMX(sc_.parseFromString("foo = resname RA"));
 740     ASSERT_NO_THROW_GMX(sc_.parseFromString("resname RB"));
 741     runTest(-1, true, input);
 742 }
 743
 744 TEST_F(SelectionCollectionInteractiveTest, HandlesSingleSelectionInputStatus)
 745 {
 746     const char *const input[] = {
 747         "foo = resname RA",
 748         "",
 749         "resname RB"
 750     };
 751     runTest(1, true, input);
 752 }
 753
 754 TEST_F(SelectionCollectionInteractiveTest, HandlesTwoSelectionInputStatus)
 755 {
 756     const char *const input[] = {
 757         "\"Sel\" resname RA",
 758         "",
 759         "resname RB"
 760     };
 761     runTest(2, true, input);
 762 }
 763
 764 TEST_F(SelectionCollectionInteractiveTest, HandlesMultiSelectionInputStatus)
 765 {
 766     const char *const input[] = {
 767         "\"Sel\" resname RA",
 768         "\"Sel2\" resname RB",
 769         ""
 770     };
 771     runTest(-1, true, input);
 772 }
 773
 774 TEST_F(SelectionCollectionInteractiveTest, HandlesNoFinalNewline)
 775 {
 776     // TODO: There is an extra prompt printed after the input is finished; it
 777     // would be cleaner not to have it, but it's only a cosmetic issue.
 778     const char *const input[] = {
 779         "resname RA"
 780     };
 781     helper_.setLastNewline(false);
 782     runTest(-1, true, input);
 783 }
 784
 785 TEST_F(SelectionCollectionInteractiveTest, HandlesEmptySelections)
 786 {
 787     const char *const input[] = {
 788         "resname RA;",
 789         "; resname RB;;",
 790         " ",
 791         ";"
 792     };
 793     runTest(-1, true, input);
 794 }
 795
 796 TEST_F(SelectionCollectionInteractiveTest, HandlesMultipleSelectionsOnLine)
 797 {
 798     const char *const input[] = {
 799         "resname RA; resname RB and \\",
 800         "resname RC"
 801     };
 802     runTest(2, true, input);
 803 }
 804
 805 TEST_F(SelectionCollectionInteractiveTest, HandlesNoninteractiveInput)
 806 {
 807     const char *const input[] = {
 808         "foo = resname RA",
 809         "resname RB",
 810         "\"Name\" resname RC"
 811     };
 812     runTest(-1, false, input);
 813 }
 814
 815 TEST_F(SelectionCollectionInteractiveTest, HandlesSingleSelectionInputNoninteractively)
 816 {
 817     const char *const input[] = {
 818         "foo = resname RA",
 819         "resname RA"
 820     };
 821     runTest(1, false, input);
 822 }
 823
 824
 825 /********************************************************************
 826  * Tests for selection keywords
 827  */
 828
 829 TEST_F(SelectionCollectionDataTest, HandlesAllNone)
 830 {
 831     static const char * const selections[] = {
 832         "all",
 833         "none"
 834     };
 835     runTest(10, selections);
 836 }
 837
 838 TEST_F(SelectionCollectionDataTest, HandlesAtomnr)
 839 {
 840     static const char * const selections[] = {
 841         "atomnr 1 to 3 6 to 8",
 842         "atomnr 4 2 5 to 7",
 843         "atomnr <= 5"
 844     };
 845     runTest(10, selections);
 846 }
 847
 848 TEST_F(SelectionCollectionDataTest, HandlesResnr)
 849 {
 850     static const char * const selections[] = {
 851         "resnr 1 2 5",
 852         "resid 4 to 3"
 853     };
 854     runTest("simple.gro", selections);
 855 }
 856
 857 TEST_F(SelectionCollectionDataTest, HandlesResIndex)
 858 {
 859     static const char * const selections[] = {
 860         "resindex 1 4",
 861         "residue 1 3"
 862     };
 863     runTest("simple.pdb", selections);
 864 }
 865
 866 TEST_F(SelectionCollectionDataTest, HandlesMolIndex)
 867 {
 868     static const char * const selections[] = {
 869         "molindex 1 4",
 870         "molecule 2 3 5"
 871     };
 872     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 873     ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
 874     topManager_.initUniformMolecules(3);
 875     ASSERT_NO_FATAL_FAILURE(setTopology());
 876     ASSERT_NO_FATAL_FAILURE(runCompiler());
 877 }
 878
 879 TEST_F(SelectionCollectionDataTest, HandlesAtomname)
 880 {
 881     static const char * const selections[] = {
 882         "name CB",
 883         "atomname S1 S2"
 884     };
 885     runTest("simple.gro", selections);
 886 }
 887
 888 TEST_F(SelectionCollectionDataTest, HandlesPdbAtomname)
 889 {
 890     static const char * const selections[] = {
 891         "name HG21",
 892         "name 1HG2",
 893         "pdbname HG21 CB",
 894         "pdbatomname 1HG2"
 895     };
 896     runTest("simple.pdb", selections);
 897 }
 898
 899
 900 TEST_F(SelectionCollectionDataTest, HandlesAtomtype)
 901 {
 902     static const char * const selections[] = {
 903         "atomtype CA"
 904     };
 905     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 906     ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
 907     const char *const types[] = { "CA", "SA", "SB" };
 908     topManager_.initAtomTypes(types);
 909     ASSERT_NO_FATAL_FAILURE(setTopology());
 910     ASSERT_NO_FATAL_FAILURE(runCompiler());
 911 }
 912
 913 TEST_F(SelectionCollectionDataTest, HandlesChain)
 914 {
 915     static const char * const selections[] = {
 916         "chain A",
 917         "chain B"
 918     };
 919     runTest("simple.pdb", selections);
 920 }
 921
 922 TEST_F(SelectionCollectionDataTest, HandlesMass)
 923 {
 924     static const char * const selections[] = {
 925         "mass > 5"
 926     };
 927     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 928     EXPECT_TRUE(sc_.requiredTopologyProperties().needsMasses);
 929     ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
 930     t_atoms &atoms = topManager_.atoms();
 931     for (int i = 0; i < atoms.nr; ++i)
 932     {
 933         atoms.atom[i].m = 1.0 + i;
 934     }
 935     atoms.haveMass = TRUE;
 936     ASSERT_NO_FATAL_FAILURE(setTopology());
 937     ASSERT_NO_FATAL_FAILURE(runCompiler());
 938 }
 939
 940 TEST_F(SelectionCollectionDataTest, HandlesCharge)
 941 {
 942     static const char * const selections[] = {
 943         "charge < 0.5"
 944     };
 945     ASSERT_NO_FATAL_FAILURE(runParser(selections));
 946     ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
 947     t_atoms &atoms = topManager_.atoms();
 948     for (int i = 0; i < atoms.nr; ++i)
 949     {
 950         atoms.atom[i].q = i / 10.0;
 951     }
 952     // Ensure exact representation of 0.5 is used, so that the test is
 953     // reproducible.
 954     atoms.atom[5].q  = 0.5;
 955     atoms.haveCharge = TRUE;
 956     ASSERT_NO_FATAL_FAILURE(setTopology());
 957     ASSERT_NO_FATAL_FAILURE(runCompiler());
 958 }
 959
 960 TEST_F(SelectionCollectionDataTest, HandlesAltLoc)
 961 {
 962     static const char * const selections[] = {
 963         "altloc \" \"",
 964         "altloc A"
 965     };
 966     runTest("simple.pdb", selections);
 967 }
 968
 969 TEST_F(SelectionCollectionDataTest, HandlesInsertCode)
 970 {
 971     static const char * const selections[] = {
 972         "insertcode \" \"",
 973         "insertcode A"
 974     };
 975     runTest("simple.pdb", selections);
 976 }
 977
 978 TEST_F(SelectionCollectionDataTest, HandlesOccupancy)
 979 {
 980     static const char * const selections[] = {
 981         "occupancy 1",
 982         "occupancy < .5"
 983     };
 984     runTest("simple.pdb", selections);
 985 }
 986
 987 TEST_F(SelectionCollectionDataTest, HandlesBeta)
 988 {
 989     static const char * const selections[] = {
 990         "beta 0",
 991         "beta >= 0.3"
 992     };
 993     runTest("simple.pdb", selections);
 994 }
 995
 996 TEST_F(SelectionCollectionDataTest, HandlesResname)
 997 {
 998     static const char * const selections[] = {
 999         "resname RA",
1000         "resname RB RC"
1001     };
1002     runTest("simple.gro", selections);
1003 }
1004
1005 TEST_F(SelectionCollectionDataTest, HandlesCoordinateKeywords)
1006 {
1007     static const char * const selections[] = {
1008         "x < 3",
1009         "y >= 3",
1010         "x {-1 to 2}"
1011     };
1012     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1013     runTest("simple.gro", selections);
1014 }
1015
1016
1017 TEST_F(SelectionCollectionDataTest, HandlesSameResidue)
1018 {
1019     static const char * const selections[] = {
1020         "same residue as atomnr 1 4 12"
1021     };
1022     runTest("simple.gro", selections);
1023 }
1024
1025
1026 TEST_F(SelectionCollectionDataTest, HandlesSameResidueName)
1027 {
1028     static const char * const selections[] = {
1029         "same resname as atomnr 1 14"
1030     };
1031     runTest("simple.gro", selections);
1032 }
1033
1034
1035 TEST_F(SelectionCollectionDataTest, HandlesPositionKeywords)
1036 {
1037     static const char * const selections[] = {
1038         "cog of resnr 1 3",
1039         "res_cog of name CB and resnr 1 3",
1040         "whole_res_cog of name CB and resnr 1 3",
1041         "part_res_cog of x < 3",
1042         "dyn_res_cog of x < 3"
1043     };
1044     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1045              | efTestPositionAtoms);
1046     runTest("simple.gro", selections);
1047 }
1048
1049
1050 TEST_F(SelectionCollectionDataTest, HandlesDistanceKeyword)
1051 {
1052     static const char * const selections[] = {
1053         "distance from cog of resnr 1 < 2"
1054     };
1055     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1056     runTest("simple.gro", selections);
1057 }
1058
1059
1060 TEST_F(SelectionCollectionDataTest, HandlesMinDistanceKeyword)
1061 {
1062     static const char * const selections[] = {
1063         "mindistance from resnr 1 < 2"
1064     };
1065     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1066     runTest("simple.gro", selections);
1067 }
1068
1069
1070 TEST_F(SelectionCollectionDataTest, HandlesWithinKeyword)
1071 {
1072     static const char * const selections[] = {
1073         "within 1 of resnr 2"
1074     };
1075     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1076     runTest("simple.gro", selections);
1077 }
1078
1079
1080 TEST_F(SelectionCollectionDataTest, HandlesInSolidAngleKeyword)
1081 {
1082     // Both of these should evaluate to empty on a correct implementation.
1083     static const char * const selections[] = {
1084         "resname TP and not insolidangle center cog of resname C span resname R cutoff 20",
1085         "resname TN and insolidangle center cog of resname C span resname R cutoff 20"
1086     };
1087     setFlags(TestFlags() | efDontTestCompiledAtoms | efTestEvaluation);
1088     runTest("sphere.gro", selections);
1089 }
1090
1091
1092 TEST_F(SelectionCollectionDataTest, HandlesPermuteModifier)
1093 {
1094     static const char * const selections[] = {
1095         "all permute 3 1 2",
1096         "res_cog of resnr 1 to 4 permute 2 1",
1097         "name CB S1 and res_cog x < 3 permute 2 1"
1098     };
1099     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1100              | efTestPositionAtoms | efTestPositionMapping);
1101     runTest("simple.gro", selections);
1102 }
1103
1104
1105 TEST_F(SelectionCollectionDataTest, HandlesPlusModifier)
1106 {
1107     static const char * const selections[] = {
1108         "name S2 plus name S1",
1109         "res_cog of resnr 2 plus res_cog of resnr 1 plus res_cog of resnr 3",
1110         "name S1 and y < 3 plus res_cog of x < 2.5"
1111     };
1112     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1113              | efTestPositionAtoms | efTestPositionMapping);
1114     runTest("simple.gro", selections);
1115 }
1116
1117
1118 TEST_F(SelectionCollectionDataTest, HandlesMergeModifier)
1119 {
1120     static const char * const selections[] = {
1121         "name S2 merge name S1",
1122         "resnr 1 2 and name S2 merge resnr 1 2 and name S1 merge res_cog of resnr 1 2",
1123         "name S1 and x < 2.5 merge res_cog of x < 2.5"
1124     };
1125     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1126              | efTestPositionAtoms | efTestPositionMapping);
1127     runTest("simple.gro", selections);
1128 }
1129
1130
1131 /********************************************************************
1132  * Tests for generic selection evaluation
1133  */
1134
1135 TEST_F(SelectionCollectionDataTest, ComputesMassesAndCharges)
1136 {
1137     static const char * const selections[] = {
1138         "name CB",
1139         "y > 2",
1140         "res_cog of y > 2"
1141     };
1142     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms
1143              | efTestPositionMasses | efTestPositionCharges);
1144     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1145     ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
1146     t_atoms &atoms = topManager_.atoms();
1147     for (int i = 0; i < atoms.nr; ++i)
1148     {
1149         atoms.atom[i].m =   1.0 + i / 100.0;
1150         atoms.atom[i].q = -(1.0 + i / 100.0);
1151     }
1152     atoms.haveMass   = TRUE;
1153     atoms.haveCharge = TRUE;
1154     ASSERT_NO_FATAL_FAILURE(setTopology());
1155     ASSERT_NO_FATAL_FAILURE(runCompiler());
1156     ASSERT_NO_FATAL_FAILURE(runEvaluate());
1157     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
1158 }
1159
1160 TEST_F(SelectionCollectionDataTest, ComputesMassesAndChargesWithoutTopology)
1161 {
1162     static const char * const selections[] = {
1163         "atomnr 1 to 3 8 to 9",
1164         "y > 2",
1165         "cog of (y > 2)"
1166     };
1167     setFlags(TestFlags() | efTestPositionAtoms
1168              | efTestPositionMasses | efTestPositionCharges);
1169     runTest(10, selections);
1170 }
1171
1172 TEST_F(SelectionCollectionDataTest, HandlesFramesWithAtomSubsets)
1173 {
1174     const int          index[]      = { 0, 1, 2, 3, 4, 5, 9, 10, 11 };
1175     const char * const selections[] = {
1176         "resnr 1 4",
1177         "atomnr 1 2 5 11 and y > 2",
1178         "res_cog of atomnr 2 5 11"
1179     };
1180     setFlags(TestFlags() | efTestEvaluation | efTestPositionAtoms);
1181     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1182     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1183     ASSERT_NO_FATAL_FAILURE(runCompiler());
1184     topManager_.initFrameIndices(index);
1185     ASSERT_NO_FATAL_FAILURE(runEvaluate());
1186     ASSERT_NO_FATAL_FAILURE(runEvaluateFinal());
1187 }
1188
1189
1190 /********************************************************************
1191  * Tests for selection syntactic constructs
1192  */
1193
1194 TEST_F(SelectionCollectionDataTest, HandlesSelectionNames)
1195 {
1196     static const char * const selections[] = {
1197         "\"GroupSelection\" group \"GrpA\"",
1198         "\"DynamicSelection\" x < 5",
1199         "y < 3"
1200     };
1201     setFlags(TestFlags() | efTestSelectionNames);
1202     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1203     runTest(10, selections);
1204 }
1205
1206 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelections)
1207 {
1208     static const char * const selections[] = {
1209         "group \"GrpA\"",
1210         "GrpB",
1211         "1",
1212         // These test that the name of the group is not too eagerly promoted to
1213         // the name of the selection.
1214         "group \"GrpB\" and resname RB",
1215         "group \"GrpA\" permute 5 3 2 1 4",
1216         "group \"GrpA\" plus group \"GrpB\"",
1217         "res_cog of group \"GrpA\""
1218     };
1219     setFlags(TestFlags() | efTestSelectionNames);
1220     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1221     runTest("simple.gro", selections);
1222 }
1223
1224 TEST_F(SelectionCollectionDataTest, HandlesIndexGroupsInSelectionsDelayed)
1225 {
1226     static const char * const selections[] = {
1227         "group \"GrpA\"",
1228         "GrpB",
1229         "1",
1230         "group \"GrpB\" and resname RB"
1231     };
1232     setFlags(TestFlags() | efTestSelectionNames);
1233     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1234     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1235     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1236     ASSERT_NO_FATAL_FAILURE(runCompiler());
1237 }
1238
1239 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelections)
1240 {
1241     static const char * const selections[] = {
1242         "foo = group \"GrpUnsorted\"",
1243         "group \"GrpUnsorted\"",
1244         "GrpUnsorted",
1245         "2",
1246         "res_cog of group \"GrpUnsorted\"",
1247         "group \"GrpUnsorted\" permute 2 1",
1248         "foo"
1249     };
1250     setFlags(TestFlags() | efTestPositionAtoms | efTestPositionMapping
1251              | efTestSelectionNames);
1252     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1253     runTest("simple.gro", selections);
1254 }
1255
1256 TEST_F(SelectionCollectionDataTest, HandlesUnsortedIndexGroupsInSelectionsDelayed)
1257 {
1258     static const char * const selections[] = {
1259         "foo = group \"GrpUnsorted\"",
1260         "group \"GrpUnsorted\"",
1261         "GrpUnsorted",
1262         "2",
1263         "res_cog of group \"GrpUnsorted\"",
1264         "group \"GrpUnsorted\" permute 2 1",
1265         "foo"
1266     };
1267     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1268     ASSERT_NO_FATAL_FAILURE(loadTopology("simple.gro"));
1269     ASSERT_NO_THROW_GMX(loadIndexGroups("simple.ndx"));
1270     ASSERT_NO_FATAL_FAILURE(runCompiler());
1271 }
1272
1273
1274 TEST_F(SelectionCollectionDataTest, HandlesConstantPositions)
1275 {
1276     static const char * const selections[] = {
1277         "[1, -2, 3.5]"
1278     };
1279     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1280              | efTestPositionMapping);
1281     runTest("simple.gro", selections);
1282 }
1283
1284
1285 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionsWithModifiers)
1286 {
1287     static const char * const selections[] = {
1288         "[0, 0, 0] plus [0, 1, 0]"
1289     };
1290     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1291              | efTestPositionMapping);
1292     runTest("simple.gro", selections);
1293 }
1294
1295
1296 TEST_F(SelectionCollectionDataTest, HandlesWithinConstantPositions)
1297 {
1298     static const char * const selections[] = {
1299         "within 1 of [2, 1, 0]"
1300     };
1301     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1302     runTest("simple.gro", selections);
1303 }
1304
1305
1306 TEST_F(SelectionCollectionDataTest, HandlesOverlappingIntegerRanges)
1307 {
1308     static const char * const selections[] = {
1309         "atomnr 2 to 4 5 to 8",
1310         "atomnr 2 to 5 4 to 7"
1311     };
1312     ASSERT_NO_FATAL_FAILURE(runTest(10, selections));
1313 }
1314
1315
1316 TEST_F(SelectionCollectionDataTest, HandlesOverlappingRealRanges)
1317 {
1318     static const char * const selections[] = {
1319         "charge {-0.35 to -0.05 0.25 to 0.75}",
1320         "charge {0.05 to -0.3 -0.05 to 0.55}"
1321     };
1322     ASSERT_NO_FATAL_FAILURE(runParser(selections));
1323     ASSERT_NO_FATAL_FAILURE(topManager_.loadTopology("simple.gro"));
1324     t_atoms &atoms = topManager_.atoms();
1325     for (int i = 0; i < atoms.nr; ++i)
1326     {
1327         atoms.atom[i].q = i / 10.0 - 0.5;
1328     }
1329     atoms.haveCharge = TRUE;
1330     ASSERT_NO_FATAL_FAILURE(setTopology());
1331     ASSERT_NO_FATAL_FAILURE(runCompiler());
1332 }
1333
1334
1335 TEST_F(SelectionCollectionDataTest, HandlesForcedStringMatchingMode)
1336 {
1337     static const char * const selections[] = {
1338         "name = S1 \"C?\"",
1339         "name ? S1 \"C?\""
1340     };
1341     runTest("simple.gro", selections);
1342 }
1343
1344
1345 TEST_F(SelectionCollectionDataTest, HandlesWildcardMatching)
1346 {
1347     static const char * const selections[] = {
1348         "name \"S?\"",
1349         "name ? \"S?\""
1350     };
1351     runTest("simple.gro", selections);
1352 }
1353
1354
1355 TEST_F(SelectionCollectionDataTest, HandlesRegexMatching)
1356 {
1357     static const char * const selections[] = {
1358         "resname \"R[BD]\"",
1359         "resname ~ \"R[BD]\""
1360     };
1361     runTest("simple.gro", selections);
1362 }
1363
1364
1365 TEST_F(SelectionCollectionDataTest, HandlesBasicBoolean)
1366 {
1367     static const char * const selections[] = {
1368         "atomnr 1 to 5 and atomnr 2 to 7",
1369         "atomnr 1 to 5 or not atomnr 3 to 8",
1370         "not not atomnr 1 to 5 and atomnr 2 to 6 and not not atomnr 3 to 7",
1371         "atomnr 1 to 5 and (atomnr 2 to 7 and atomnr 3 to 6)",
1372         "x < 5 and atomnr 1 to 5 and y < 3 and atomnr 2 to 4"
1373     };
1374     runTest(10, selections);
1375 }
1376
1377
1378 TEST_F(SelectionCollectionDataTest, HandlesDynamicAtomValuedParameters)
1379 {
1380     static const char * const selections[] = {
1381         "same residue as (atomnr 3 5 13 or y > 5)",
1382         "(resnr 1 3 5 or x > 10) and same residue as (atomnr 3 5 13 or z > 5)"
1383     };
1384     setFlags(TestFlags() | efTestEvaluation);
1385     runTest("simple.gro", selections);
1386 }
1387
1388
1389 TEST_F(SelectionCollectionDataTest, HandlesEmptySelectionWithUnevaluatedExpressions)
1390 {
1391     static const char * const selections[] = {
1392         "none and x > 2",
1393         "none and same resname as resnr 2"
1394     };
1395     runTest("simple.gro", selections);
1396 }
1397
1398
1399 TEST_F(SelectionCollectionDataTest, HandlesEmptyReferenceForSame)
1400 {
1401     static const char * const selections[] = {
1402         "same residue as none",
1403         "same resname as none"
1404     };
1405     runTest("simple.gro", selections);
1406 }
1407
1408
1409 TEST_F(SelectionCollectionDataTest, HandlesPositionModifiersForKeywords)
1410 {
1411     static const char * const selections[] = {
1412         "res_cog x > 2",
1413         "name CB and res_cog y > 2.5"
1414     };
1415     setFlags(TestFlags() | efTestEvaluation);
1416     runTest("simple.gro", selections);
1417 }
1418
1419
1420 TEST_F(SelectionCollectionDataTest, HandlesPositionModifiersForMethods)
1421 {
1422     static const char * const selections[] = {
1423         "res_cog distance from cog of resnr 1 < 2",
1424         "res_cog within 2 of cog of resnr 1"
1425     };
1426     setFlags(TestFlags() | efTestEvaluation);
1427     runTest("simple.gro", selections);
1428 }
1429
1430
1431 TEST_F(SelectionCollectionDataTest, HandlesKeywordOfPositions)
1432 {
1433     static const char * const selections[] = {
1434         "x < y of cog of resnr 2"
1435     };
1436     setFlags(TestFlags() | efTestEvaluation);
1437     runTest("simple.gro", selections);
1438 }
1439
1440 TEST_F(SelectionCollectionDataTest, HandlesKeywordOfPositionsInArithmetic)
1441 {
1442     static const char * const selections[] = {
1443         "x - y of cog of resnr 2 < 0"
1444     };
1445     setFlags(TestFlags() | efTestEvaluation);
1446     runTest("simple.gro", selections);
1447 }
1448
1449
1450 TEST_F(SelectionCollectionDataTest, HandlesNumericComparisons)
1451 {
1452     static const char * const selections[] = {
1453         "x > 2",
1454         "2 < x",
1455         "y > resnr",
1456         "resnr < 2.5",
1457         "2.5 > resnr"
1458     };
1459     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1460     runTest("simple.gro", selections);
1461 }
1462
1463
1464 TEST_F(SelectionCollectionDataTest, HandlesArithmeticExpressions)
1465 {
1466     static const char * const selections[] = {
1467         "x+1 > 3",
1468         "(y-1)^2 <= 1",
1469         "x+--1 > 3",
1470         "-x+-1 < -3"
1471     };
1472     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1473     runTest("simple.gro", selections);
1474 }
1475
1476
1477 TEST_F(SelectionCollectionDataTest, HandlesNumericVariables)
1478 {
1479     static const char * const selections[] = {
1480         "value = x + y",
1481         "value <= 4",
1482         "index = resnr",
1483         "index < 3"
1484     };
1485     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1486     runTest("simple.gro", selections);
1487 }
1488
1489
1490 TEST_F(SelectionCollectionDataTest, HandlesComplexNumericVariables)
1491 {
1492     static const char * const selections[] = {
1493         "value = x + y",
1494         "resname RA and value <= 4",
1495         "resname RA RB and x < 3 and value <= 4",
1496         "index = atomnr",
1497         "resname RA and index < 3",
1498         "resname RB and y < 3 and index < 6"
1499     };
1500     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1501     runTest("simple.gro", selections);
1502 }
1503
1504
1505 TEST_F(SelectionCollectionDataTest, HandlesPositionVariables)
1506 {
1507     static const char * const selections[] = {
1508         "foo = res_cog of resname RA",
1509         "foo",
1510         "within 1 of foo",
1511         "bar = cog of resname RA",
1512         "bar",
1513         "within 1 of bar"
1514     };
1515     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1516     runTest("simple.gro", selections);
1517 }
1518
1519
1520 TEST_F(SelectionCollectionDataTest, HandlesPositionVariableInModifier)
1521 {
1522     static const char * const selections[] = {
1523         "foo = cog of resnr 1",
1524         "cog of resnr 2 plus foo",
1525         "cog of resnr 3 plus foo"
1526     };
1527     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1528     runTest("simple.gro", selections);
1529 }
1530
1531
1532 TEST_F(SelectionCollectionDataTest, HandlesConstantPositionInVariable)
1533 {
1534     static const char * const selections[] = {
1535         "constpos = [1.0, 2.5, 0.5]",
1536         "constpos",
1537         "within 2 of constpos"
1538     };
1539     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates
1540              | efTestPositionAtoms);
1541     runTest("simple.gro", selections);
1542 }
1543
1544
1545 TEST_F(SelectionCollectionDataTest, HandlesNumericConstantsInVariables)
1546 {
1547     static const char * const selections[] = {
1548         "constint = 4",
1549         "constreal1 = 0.5",
1550         "constreal2 = 2.7",
1551         "resnr < constint",
1552         "x + constreal1 < constreal2"
1553     };
1554     setFlags(TestFlags() | efTestEvaluation | efTestPositionCoordinates);
1555     runTest("simple.gro", selections);
1556 }
1557
1558
1559 /********************************************************************
1560  * Tests for complex boolean syntax
1561  */
1562
1563 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysis)
1564 {
1565     static const char * const selections[] = {
1566         "atomnr 1 to 5 and atomnr 2 to 7 and x < 2",
1567         "atomnr 1 to 5 and (atomnr 4 to 7 or x < 2)",
1568         "atomnr 1 to 5 and y < 3 and (atomnr 4 to 7 or x < 2)",
1569         "atomnr 1 to 5 and not (atomnr 4 to 7 or x < 2)",
1570         "atomnr 1 to 5 or (atomnr 4 to 6 and (atomnr 5 to 7 or x < 2))"
1571     };
1572     runTest(10, selections);
1573 }
1574
1575
1576 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithVariables)
1577 {
1578     static const char * const selections[] = {
1579         "foo = atomnr 4 to 7 or x < 2",
1580         "atomnr 1 to 4 and foo",
1581         "atomnr 2 to 6 and y < 3 and foo",
1582         "atomnr 6 to 10 and not foo"
1583     };
1584     runTest(10, selections);
1585 }
1586
1587
1588 TEST_F(SelectionCollectionDataTest, HandlesBooleanStaticAnalysisWithMoreVariables)
1589 {
1590     static const char * const selections[] = {
1591         "foo = atomnr 4 to 7",
1592         "bar = foo and x < 2",
1593         "bar2 = foo and y < 2",
1594         "atomnr 1 to 4 and bar",
1595         "atomnr 2 to 6 and y < 3 and bar2",
1596         "atomnr 6 to 10 and not foo"
1597     };
1598     runTest(10, selections);
1599 }
1600
1601
1602 /********************************************************************
1603  * Tests for complex subexpression cases
1604  *
1605  * These tests use some knowledge of the implementation to trigger different
1606  * paths in the code.
1607  */
1608
1609 TEST_F(SelectionCollectionDataTest, HandlesUnusedVariables)
1610 {
1611     static const char * const selections[] = {
1612         "unused1 = atomnr 1 to 3",
1613         "foo = atomnr 4 to 7",
1614         "atomnr 1 to 6 and foo",
1615         "unused2 = atomnr 3 to 5"
1616     };
1617     runTest(10, selections);
1618 }
1619
1620
1621 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithStaticEvaluationGroups)
1622 {
1623     static const char * const selections[] = {
1624         "foo = atomnr 4 to 7 and x < 2",
1625         "atomnr 1 to 5 and foo",
1626         "atomnr 3 to 7 and foo"
1627     };
1628     runTest(10, selections);
1629 }
1630
1631
1632 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups)
1633 {
1634     static const char * const selections[] = {
1635         "foo = atomnr 4 to 7 and x < 2",
1636         "atomnr 1 to 6 and foo",
1637         "within 1 of foo",
1638         "foo"
1639     };
1640     runTest(10, selections);
1641 }
1642
1643
1644 TEST_F(SelectionCollectionDataTest, HandlesVariablesWithMixedEvaluationGroups2)
1645 {
1646     static const char * const selections[] = {
1647         "foo = atomnr 1 to 8 and x < 10",
1648         "atomnr 1 to 5 and y < 10 and foo",
1649         "foo"
1650     };
1651     setFlags(TestFlags() | efTestEvaluation);
1652     runTest("simple.gro", selections);
1653 }
1654
1655
1656 } // namespace