src/gromacs/mdlib/tests/constr.cpp

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  35 /*! \internal \file
  36  * \brief SHAKE and LINCS tests.
  37  *
  38  * \todo Better tests for virial are needed.
  39  * \todo Tests for bigger systems to test threads synchronization,
  40  *       reduction, etc. on the GPU.
  41  * \todo Tests for algorithms for derivatives.
  42  * \todo Free-energy perturbation tests
  43  *
  44  * \author Artem Zhmurov <zhmurov@gmail.com>
  45  * \ingroup module_mdlib
  46  */
  47 #include "gmxpre.h"
  48
  49 #include "config.h"
  50
  51 #include <assert.h>
  52
  53 #include <unordered_map>
  54 #include <vector>
  55
  56 #include <gtest/gtest.h>
  57
  58 #include "gromacs/math/vec.h"
  59 #include "gromacs/math/vectypes.h"
  60 #include "gromacs/pbcutil/pbc.h"
  61 #include "gromacs/utility/stringutil.h"
  62
  63 #include "testutils/testasserts.h"
  64
  65 #include "constrtestdata.h"
  66 #include "constrtestrunners.h"
  67
  68 namespace gmx
  69 {
  70 namespace test
  71 {
  72 namespace
  73 {
  74
  75 /*! \brief The two-dimensional parameter space for test.
  76  *
  77  * The test will run for all possible combinations of accessible
  78  * values of the:
  79  * 1. PBC setup ("PBCNONE" or "PBCXYZ")
  80  * 2. The algorithm ("SHAKE", "LINCS" or "LINCS_GPU").
  81  */
  82 typedef std::tuple<std::string, std::string> ConstraintsTestParameters;
  83
  84 //! Names of all availible runners
  85 std::vector<std::string> runnersNames;
  86
  87 //! Method that fills and returns runnersNames to the test macros.
  88 std::vector<std::string> getRunnersNames()
  89 {
  90     runnersNames.emplace_back("SHAKE");
  91     runnersNames.emplace_back("LINCS");
  92     if (GMX_GPU == GMX_GPU_CUDA && canComputeOnGpu())
  93     {
  94         runnersNames.emplace_back("LINCS_CUDA");
  95     }
  96     return runnersNames;
  97 }
  98
  99 /*! \brief Test fixture for constraints.
 100  *
 101  * The fixture uses following test systems:
 102  * 1. Two atoms, connected with one constraint (e.g. NH).
 103  * 2. Three atoms, connected consequently with two constraints (e.g. CH2).
 104  * 3. Three atoms, constrained to the fourth atom (e.g. CH3).
 105  * 4. Four atoms, connected by two independent constraints.
 106  * 5. Three atoms, connected by three constraints in a triangle
 107  *      (e.g. H2O with constrained H-O-H angle).
 108  * 6. Four atoms, connected by three consequential constraints.
 109  *
 110  * For all systems, the final lengths of the constraints are tested against the
 111  * reference values, the direction of each constraint is checked.
 112  * Test also verifies that the center of mass has not been
 113  * shifted by the constraints and that its velocity has not changed.
 114  * For some systems, the value for scaled virial tensor is checked against
 115  * pre-computed data.
 116  */
 117 class ConstraintsTest : public ::testing::TestWithParam<ConstraintsTestParameters>
 118 {
 119 public:
 120     //! PBC setups
 121     std::unordered_map<std::string, t_pbc> pbcs_;
 122     //! Algorithms (SHAKE and LINCS)
 123     std::unordered_map<std::string, void (*)(ConstraintsTestData* testData, t_pbc pbc)> algorithms_;
 124
 125     /*! \brief Test setup function.
 126      *
 127      * Setting up the pbcs and algorithms. Note, that corresponding string keywords
 128      * have to be explicitly added at the end of this file when the tests are called.
 129      *
 130      */
 131     void SetUp() override
 132     {
 133
 134         //
 135         // PBC initialization
 136         //
 137         t_pbc pbc;
 138
 139         // Infinitely small box
 140         matrix boxNone = { { 0, 0, 0 }, { 0, 0, 0 }, { 0, 0, 0 } };
 141         set_pbc(&pbc, PbcType::No, boxNone);
 142         pbcs_["PBCNone"] = pbc;
 143
 144         // Rectangular box
 145         matrix boxXyz = { { 10.0, 0.0, 0.0 }, { 0.0, 20.0, 0.0 }, { 0.0, 0.0, 15.0 } };
 146         set_pbc(&pbc, PbcType::Xyz, boxXyz);
 147         pbcs_["PBCXYZ"] = pbc;
 148
 149         //
 150         // Algorithms
 151         //
 152         // SHAKE
 153         algorithms_["SHAKE"] = applyShake;
 154         // LINCS
 155         algorithms_["LINCS"] = applyLincs;
 156         // LINCS using CUDA (will only be called if CUDA is available)
 157         algorithms_["LINCS_CUDA"] = applyLincsCuda;
 158     }
 159
 160     /*! \brief
 161      * The test on the final length of constrained bonds.
 162      *
 163      * Goes through all the constraints and checks if the final length of all the constraints is
 164      * equal to the target length with provided tolerance.
 165      *
 166      * \param[in] tolerance       Allowed tolerance in final lengths.
 167      * \param[in] testData        Test data structure.
 168      * \param[in] pbc             Periodic boundary data.
 169      */
 170     void checkConstrainsLength(FloatingPointTolerance tolerance, const ConstraintsTestData& testData, t_pbc pbc)
 171     {
 172
 173         // Test if all the constraints are satisfied
 174         for (index c = 0; c < ssize(testData.constraints_) / 3; c++)
 175         {
 176             real r0 = testData.constraintsR0_.at(testData.constraints_.at(3 * c));
 177             int  i  = testData.constraints_.at(3 * c + 1);
 178             int  j  = testData.constraints_.at(3 * c + 2);
 179             RVec xij0, xij1;
 180             real d0, d1;
 181             if (pbc.pbcType == PbcType::Xyz)
 182             {
 183                 pbc_dx_aiuc(&pbc, testData.x_[i], testData.x_[j], xij0);
 184                 pbc_dx_aiuc(&pbc, testData.xPrime_[i], testData.xPrime_[j], xij1);
 185             }
 186             else
 187             {
 188                 rvec_sub(testData.x_[i], testData.x_[j], xij0);
 189                 rvec_sub(testData.xPrime_[i], testData.xPrime_[j], xij1);
 190             }
 191             d0 = norm(xij0);
 192             d1 = norm(xij1);
 193             EXPECT_REAL_EQ_TOL(r0, d1, tolerance) << gmx::formatString(
 194                     "rij = %f, which is not equal to r0 = %f for constraint #%zd, between atoms %d "
 195                     "and %d"
 196                     " (before constraining rij was %f).",
 197                     d1, r0, c, i, j, d0);
 198         }
 199     }
 200
 201     /*! \brief
 202      * The test on the final length of constrained bonds.
 203      *
 204      * Goes through all the constraints and checks if the direction of constraint has not changed
 205      * by the algorithm (i.e. the constraints algorithm arrived to the solution that is closest
 206      * to the initial system conformation).
 207      *
 208      * \param[in] testData        Test data structure.
 209      * \param[in] pbc             Periodic boundary data.
 210      */
 211     void checkConstrainsDirection(const ConstraintsTestData& testData, t_pbc pbc)
 212     {
 213
 214         for (index c = 0; c < ssize(testData.constraints_) / 3; c++)
 215         {
 216             int  i = testData.constraints_.at(3 * c + 1);
 217             int  j = testData.constraints_.at(3 * c + 2);
 218             RVec xij0, xij1;
 219             if (pbc.pbcType == PbcType::Xyz)
 220             {
 221                 pbc_dx_aiuc(&pbc, testData.x_[i], testData.x_[j], xij0);
 222                 pbc_dx_aiuc(&pbc, testData.xPrime_[i], testData.xPrime_[j], xij1);
 223             }
 224             else
 225             {
 226                 rvec_sub(testData.x_[i], testData.x_[j], xij0);
 227                 rvec_sub(testData.xPrime_[i], testData.xPrime_[j], xij1);
 228             }
 229
 230             real dot = xij0.dot(xij1);
 231
 232             EXPECT_GE(dot, 0.0) << gmx::formatString(
 233                     "The constraint %zd changed direction. Constraining algorithm might have "
 234                     "returned the wrong root "
 235                     "of the constraints equation.",
 236                     c);
 237         }
 238     }
 239
 240     /*! \brief
 241      * The test on the coordinates of the center of the mass (COM) of the system.
 242      *
 243      * Checks if the center of mass has not been shifted by the constraints. Note,
 244      * that this test does not take into account the periodic boundary conditions.
 245      * Hence it will not work should the constraints decide to move atoms across
 246      * PBC borders.
 247      *
 248      * \param[in] tolerance       Allowed tolerance in COM coordinates.
 249      * \param[in] testData        Test data structure.
 250      */
 251     void checkCOMCoordinates(FloatingPointTolerance tolerance, const ConstraintsTestData& testData)
 252     {
 253
 254         RVec comPrime0({ 0.0, 0.0, 0.0 });
 255         RVec comPrime({ 0.0, 0.0, 0.0 });
 256         for (int i = 0; i < testData.numAtoms_; i++)
 257         {
 258             comPrime0 += testData.masses_[i] * testData.xPrime0_[i];
 259             comPrime += testData.masses_[i] * testData.xPrime_[i];
 260         }
 261
 262         comPrime0 /= testData.numAtoms_;
 263         comPrime /= testData.numAtoms_;
 264
 265         EXPECT_REAL_EQ_TOL(comPrime[XX], comPrime0[XX], tolerance)
 266                 << "Center of mass was shifted by constraints in x-direction.";
 267         EXPECT_REAL_EQ_TOL(comPrime[YY], comPrime0[YY], tolerance)
 268                 << "Center of mass was shifted by constraints in y-direction.";
 269         EXPECT_REAL_EQ_TOL(comPrime[ZZ], comPrime0[ZZ], tolerance)
 270                 << "Center of mass was shifted by constraints in z-direction.";
 271     }
 272
 273     /*! \brief
 274      * The test on the velocity of the center of the mass (COM) of the system.
 275      *
 276      * Checks if the velocity of the center of mass has not changed.
 277      *
 278      * \param[in] tolerance       Allowed tolerance in COM velocity components.
 279      * \param[in] testData        Test data structure.
 280      */
 281     void checkCOMVelocity(FloatingPointTolerance tolerance, const ConstraintsTestData& testData)
 282     {
 283
 284         RVec comV0({ 0.0, 0.0, 0.0 });
 285         RVec comV({ 0.0, 0.0, 0.0 });
 286         for (int i = 0; i < testData.numAtoms_; i++)
 287         {
 288             comV0 += testData.masses_[i] * testData.v0_[i];
 289             comV += testData.masses_[i] * testData.v_[i];
 290         }
 291         comV0 /= testData.numAtoms_;
 292         comV /= testData.numAtoms_;
 293
 294         EXPECT_REAL_EQ_TOL(comV[XX], comV0[XX], tolerance)
 295                 << "Velocity of the center of mass in x-direction has been changed by constraints.";
 296         EXPECT_REAL_EQ_TOL(comV[YY], comV0[YY], tolerance)
 297                 << "Velocity of the center of mass in y-direction has been changed by constraints.";
 298         EXPECT_REAL_EQ_TOL(comV[ZZ], comV0[ZZ], tolerance)
 299                 << "Velocity of the center of mass in z-direction has been changed by constraints.";
 300     }
 301
 302     /*! \brief
 303      * The test of virial tensor.
 304      *
 305      * Checks if the values in the scaled virial tensor are equal to pre-computed values.
 306      *
 307      * \param[in] tolerance       Tolerance for the tensor values.
 308      * \param[in] testData        Test data structure.
 309      */
 310     void checkVirialTensor(FloatingPointTolerance tolerance, const ConstraintsTestData& testData)
 311     {
 312         for (int i = 0; i < DIM; i++)
 313         {
 314             for (int j = 0; j < DIM; j++)
 315             {
 316                 EXPECT_REAL_EQ_TOL(testData.virialScaledRef_[i][j], testData.virialScaled_[i][j], tolerance)
 317                         << gmx::formatString(
 318                                    "Values in virial tensor at [%d][%d] are not within the "
 319                                    "tolerance from reference value.",
 320                                    i, j);
 321             }
 322         }
 323     }
 324 };
 325
 326 TEST_P(ConstraintsTest, SingleConstraint)
 327 {
 328     std::string title    = "one constraint (e.g. OH)";
 329     int         numAtoms = 2;
 330
 331     std::vector<real> masses        = { 1.0, 12.0 };
 332     std::vector<int>  constraints   = { 0, 0, 1 };
 333     std::vector<real> constraintsR0 = { 0.1 };
 334
 335     real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
 336
 337     std::vector<RVec> x = { { 0.0, oneTenthOverSqrtTwo, 0.0 }, { oneTenthOverSqrtTwo, 0.0, 0.0 } };
 338     std::vector<RVec> xPrime = { { 0.01, 0.08, 0.01 }, { 0.06, 0.01, -0.01 } };
 339     std::vector<RVec> v      = { { 1.0, 2.0, 3.0 }, { 3.0, 2.0, 1.0 } };
 340
 341     tensor virialScaledRef = { { -5.58e-04, 5.58e-04, 0.00e+00 },
 342                                { 5.58e-04, -5.58e-04, 0.00e+00 },
 343                                { 0.00e+00, 0.00e+00, 0.00e+00 } };
 344
 345     real     shakeTolerance = 0.0001;
 346     gmx_bool shakeUseSOR    = false;
 347
 348     int  lincsNIter               = 1;
 349     int  lincslincsExpansionOrder = 4;
 350     real lincsWarnAngle           = 30.0;
 351
 352     std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
 353             title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
 354             real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
 355             lincslincsExpansionOrder, lincsWarnAngle);
 356     std::string pbcName;
 357     std::string algorithmName;
 358     std::tie(pbcName, algorithmName) = GetParam();
 359     t_pbc pbc                        = pbcs_.at(pbcName);
 360
 361     // Apply constraints
 362     algorithms_.at(algorithmName)(testData.get(), pbc);
 363
 364     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 365     checkConstrainsDirection(*testData, pbc);
 366     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 367     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 368
 369     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 370 }
 371
 372 TEST_P(ConstraintsTest, TwoDisjointConstraints)
 373 {
 374
 375     std::string       title         = "two disjoint constraints";
 376     int               numAtoms      = 4;
 377     std::vector<real> masses        = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
 378     std::vector<int>  constraints   = { 0, 0, 1, 1, 2, 3 };
 379     std::vector<real> constraintsR0 = { 2.0, 1.0 };
 380
 381
 382     std::vector<RVec> x = {
 383         { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
 384     };
 385
 386     std::vector<RVec> xPrime = {
 387         { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
 388     };
 389
 390     std::vector<RVec> v = { { 0.0, 1.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 0.0, 0.0, 1.0 }, { 0.0, 0.0, 0.0 } };
 391
 392     tensor virialScaledRef = { { 3.3e-03, -1.7e-04, 5.6e-04 },
 393                                { -1.7e-04, 8.9e-06, -2.8e-05 },
 394                                { 5.6e-04, -2.8e-05, 8.9e-05 } };
 395
 396     real     shakeTolerance = 0.0001;
 397     gmx_bool shakeUseSOR    = false;
 398
 399     int  lincsNIter               = 1;
 400     int  lincslincsExpansionOrder = 4;
 401     real lincsWarnAngle           = 30.0;
 402
 403     std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
 404             title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
 405             real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
 406             lincslincsExpansionOrder, lincsWarnAngle);
 407
 408     std::string pbcName;
 409     std::string algorithmName;
 410     std::tie(pbcName, algorithmName) = GetParam();
 411     t_pbc pbc                        = pbcs_.at(pbcName);
 412
 413     // Apply constraints
 414     algorithms_.at(algorithmName)(testData.get(), pbc);
 415
 416     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 417     checkConstrainsDirection(*testData, pbc);
 418     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 419     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 420
 421     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 422 }
 423
 424 TEST_P(ConstraintsTest, ThreeSequentialConstraints)
 425 {
 426
 427     std::string       title         = "three atoms, connected longitudinally (e.g. CH2)";
 428     int               numAtoms      = 3;
 429     std::vector<real> masses        = { 1.0, 12.0, 16.0 };
 430     std::vector<int>  constraints   = { 0, 0, 1, 1, 1, 2 };
 431     std::vector<real> constraintsR0 = { 0.1, 0.2 };
 432
 433     real oneTenthOverSqrtTwo    = 0.1_real / std::sqrt(2.0_real);
 434     real twoTenthsOverSqrtThree = 0.2_real / std::sqrt(3.0_real);
 435
 436     std::vector<RVec> x = { { oneTenthOverSqrtTwo, oneTenthOverSqrtTwo, 0.0 },
 437                             { 0.0, 0.0, 0.0 },
 438                             { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree } };
 439
 440     std::vector<RVec> xPrime = { { 0.08, 0.07, 0.01 }, { -0.02, 0.01, -0.02 }, { 0.10, 0.12, 0.11 } };
 441
 442     std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 0.0, 1.0, 0.0 }, { 0.0, 0.0, 1.0 } };
 443
 444     tensor virialScaledRef = { { 4.14e-03, 4.14e-03, 3.31e-03 },
 445                                { 4.14e-03, 4.14e-03, 3.31e-03 },
 446                                { 3.31e-03, 3.31e-03, 3.31e-03 } };
 447
 448     real     shakeTolerance = 0.0001;
 449     gmx_bool shakeUseSOR    = false;
 450
 451     int  lincsNIter               = 1;
 452     int  lincslincsExpansionOrder = 4;
 453     real lincsWarnAngle           = 30.0;
 454
 455     std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
 456             title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
 457             real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
 458             lincslincsExpansionOrder, lincsWarnAngle);
 459
 460     std::string pbcName;
 461     std::string algorithmName;
 462     std::tie(pbcName, algorithmName) = GetParam();
 463     t_pbc pbc                        = pbcs_.at(pbcName);
 464
 465     // Apply constraints
 466     algorithms_.at(algorithmName)(testData.get(), pbc);
 467
 468     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 469     checkConstrainsDirection(*testData, pbc);
 470     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 471     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 472
 473     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 474 }
 475
 476 TEST_P(ConstraintsTest, ThreeConstraintsWithCentralAtom)
 477 {
 478
 479     std::string       title         = "three atoms, connected to the central atom (e.g. CH3)";
 480     int               numAtoms      = 4;
 481     std::vector<real> masses        = { 12.0, 1.0, 1.0, 1.0 };
 482     std::vector<int>  constraints   = { 0, 0, 1, 0, 0, 2, 0, 0, 3 };
 483     std::vector<real> constraintsR0 = { 0.1 };
 484
 485
 486     std::vector<RVec> x = {
 487         { 0.00, 0.00, 0.00 }, { 0.10, 0.00, 0.00 }, { 0.00, -0.10, 0.00 }, { 0.00, 0.00, 0.10 }
 488     };
 489
 490     std::vector<RVec> xPrime = { { 0.004, 0.009, -0.010 },
 491                                  { 0.110, -0.006, 0.003 },
 492                                  { -0.007, -0.102, -0.007 },
 493                                  { -0.005, 0.011, 0.102 } };
 494
 495     std::vector<RVec> v = { { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 }, { 1.0, 0.0, 0.0 } };
 496
 497     tensor virialScaledRef = { { 7.14e-04, 0.00e+00, 0.00e+00 },
 498                                { 0.00e+00, 1.08e-03, 0.00e+00 },
 499                                { 0.00e+00, 0.00e+00, 1.15e-03 } };
 500
 501     real     shakeTolerance = 0.0001;
 502     gmx_bool shakeUseSOR    = false;
 503
 504     int  lincsNIter               = 1;
 505     int  lincslincsExpansionOrder = 4;
 506     real lincsWarnAngle           = 30.0;
 507
 508     std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
 509             title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
 510             real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
 511             lincslincsExpansionOrder, lincsWarnAngle);
 512
 513     std::string pbcName;
 514     std::string algorithmName;
 515     std::tie(pbcName, algorithmName) = GetParam();
 516     t_pbc pbc                        = pbcs_.at(pbcName);
 517
 518     // Apply constraints
 519     algorithms_.at(algorithmName)(testData.get(), pbc);
 520
 521     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 522     checkConstrainsDirection(*testData, pbc);
 523     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 524     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 525
 526     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 527 }
 528
 529 TEST_P(ConstraintsTest, FourSequentialConstraints)
 530 {
 531
 532     std::string       title         = "four atoms, connected longitudinally";
 533     int               numAtoms      = 4;
 534     std::vector<real> masses        = { 0.5, 1.0 / 3.0, 0.25, 1.0 };
 535     std::vector<int>  constraints   = { 0, 0, 1, 1, 1, 2, 2, 2, 3 };
 536     std::vector<real> constraintsR0 = { 2.0, 1.0, 1.0 };
 537
 538
 539     std::vector<RVec> x = {
 540         { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
 541     };
 542
 543     std::vector<RVec> xPrime = {
 544         { 2.50, -3.10, 15.70 }, { 0.51, -3.02, 15.55 }, { -0.50, -3.00, 15.20 }, { -1.51, -2.95, 15.05 }
 545     };
 546
 547     std::vector<RVec> v = { { 0.0, 0.0, 2.0 }, { 0.0, 0.0, 3.0 }, { 0.0, 0.0, -4.0 }, { 0.0, 0.0, -1.0 } };
 548
 549     tensor virialScaledRef = { { 1.15e-01, -4.20e-03, 2.12e-02 },
 550                                { -4.20e-03, 1.70e-04, -6.41e-04 },
 551                                { 2.12e-02, -6.41e-04, 5.45e-03 } };
 552
 553     real     shakeTolerance = 0.0001;
 554     gmx_bool shakeUseSOR    = false;
 555
 556     int  lincsNIter               = 4;
 557     int  lincslincsExpansionOrder = 8;
 558     real lincsWarnAngle           = 30.0;
 559
 560     std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
 561             title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
 562             real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
 563             lincslincsExpansionOrder, lincsWarnAngle);
 564
 565     std::string pbcName;
 566     std::string algorithmName;
 567     std::tie(pbcName, algorithmName) = GetParam();
 568     t_pbc pbc                        = pbcs_.at(pbcName);
 569
 570     // Apply constraints
 571     algorithms_.at(algorithmName)(testData.get(), pbc);
 572
 573     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 574     checkConstrainsDirection(*testData, pbc);
 575     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 576     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 577
 578     checkVirialTensor(absoluteTolerance(0.01), *testData);
 579 }
 580
 581 TEST_P(ConstraintsTest, TriangleOfConstraints)
 582 {
 583
 584     std::string       title         = "basic triangle (tree atoms, connected to each other)";
 585     int               numAtoms      = 3;
 586     std::vector<real> masses        = { 1.0, 1.0, 1.0 };
 587     std::vector<int>  constraints   = { 0, 0, 1, 2, 0, 2, 1, 1, 2 };
 588     std::vector<real> constraintsR0 = { 0.1, 0.1, 0.1 };
 589
 590     real oneTenthOverSqrtTwo = 0.1_real / std::sqrt(2.0_real);
 591
 592     std::vector<RVec> x = { { oneTenthOverSqrtTwo, 0.0, 0.0 },
 593                             { 0.0, oneTenthOverSqrtTwo, 0.0 },
 594                             { 0.0, 0.0, oneTenthOverSqrtTwo } };
 595
 596     std::vector<RVec> xPrime = { { 0.09, -0.02, 0.01 }, { -0.02, 0.10, -0.02 }, { 0.03, -0.01, 0.07 } };
 597
 598     std::vector<RVec> v = { { 1.0, 1.0, 1.0 }, { -2.0, -2.0, -2.0 }, { 1.0, 1.0, 1.0 } };
 599
 600     tensor virialScaledRef = { { 6.00e-04, -1.61e-03, 1.01e-03 },
 601                                { -1.61e-03, 2.53e-03, -9.25e-04 },
 602                                { 1.01e-03, -9.25e-04, -8.05e-05 } };
 603
 604     real     shakeTolerance = 0.0001;
 605     gmx_bool shakeUseSOR    = false;
 606
 607     int  lincsNIter               = 1;
 608     int  lincslincsExpansionOrder = 4;
 609     real lincsWarnAngle           = 30.0;
 610
 611     std::unique_ptr<ConstraintsTestData> testData = std::make_unique<ConstraintsTestData>(
 612             title, numAtoms, masses, constraints, constraintsR0, true, virialScaledRef, false, 0,
 613             real(0.0), real(0.001), x, xPrime, v, shakeTolerance, shakeUseSOR, lincsNIter,
 614             lincslincsExpansionOrder, lincsWarnAngle);
 615
 616     std::string pbcName;
 617     std::string runnerName;
 618     std::tie(pbcName, runnerName) = GetParam();
 619     t_pbc pbc                     = pbcs_.at(pbcName);
 620
 621     // Apply constraints
 622     algorithms_.at(runnerName)(testData.get(), pbc);
 623
 624     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 625     checkConstrainsDirection(*testData, pbc);
 626     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 627     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 628
 629     checkVirialTensor(absoluteTolerance(0.00001), *testData);
 630 }
 631
 632
 633 INSTANTIATE_TEST_CASE_P(WithParameters,
 634                         ConstraintsTest,
 635                         ::testing::Combine(::testing::Values("PBCNone", "PBCXYZ"),
 636                                            ::testing::ValuesIn(getRunnersNames())));
 637
 638 } // namespace
 639 } // namespace test
 640 } // namespace gmx