src/gromacs/mdlib/tests/constr.cpp

   1 /*
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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, epbcNONE, 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, epbcXYZ, 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 equal
 164          * 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 (unsigned c = 0; c < testData.constraints_.size()/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.ePBC == epbcXYZ)
 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 #%u, between atoms %d and %d"
 195                         " (before constraining rij was %f).", d1, r0, c, i, j, d0);
 196             }
 197         }
 198
 199         /*! \brief
 200          * The test on the final length of constrained bonds.
 201          *
 202          * Goes through all the constraints and checks if the direction of constraint has not changed
 203          * by the algorithm (i.e. the constraints algorithm arrived to the solution that is closest
 204          * to the initial system conformation).
 205          *
 206          * \param[in] testData        Test data structure.
 207          * \param[in] pbc             Periodic boundary data.
 208          */
 209         void checkConstrainsDirection(const ConstraintsTestData &testData, t_pbc pbc)
 210         {
 211
 212             for (unsigned c = 0; c < testData.constraints_.size()/3; c++)
 213             {
 214                 int  i  = testData.constraints_.at(3*c + 1);
 215                 int  j  = testData.constraints_.at(3*c + 2);
 216                 RVec xij0, xij1;
 217                 if (pbc.ePBC == epbcXYZ)
 218                 {
 219                     pbc_dx_aiuc(&pbc, testData.x_[i], testData.x_[j], xij0);
 220                     pbc_dx_aiuc(&pbc, testData.xPrime_[i], testData.xPrime_[j], xij1);
 221                 }
 222                 else
 223                 {
 224                     rvec_sub(testData.x_[i], testData.x_[j], xij0);
 225                     rvec_sub(testData.xPrime_[i], testData.xPrime_[j], xij1);
 226                 }
 227
 228                 real dot = xij0.dot(xij1);
 229
 230                 EXPECT_GE(dot, 0.0) << gmx::formatString(
 231                         "The constraint %u changed direction. Constraining algorithm might have returned the wrong root "
 232                         "of the constraints equation.", c);
 233
 234             }
 235         }
 236
 237         /*! \brief
 238          * The test on the coordinates of the center of the mass (COM) of the system.
 239          *
 240          * Checks if the center of mass has not been shifted by the constraints. Note,
 241          * that this test does not take into account the periodic boundary conditions.
 242          * Hence it will not work should the constraints decide to move atoms across
 243          * PBC borders.
 244          *
 245          * \param[in] tolerance       Allowed tolerance in COM coordinates.
 246          * \param[in] testData        Test data structure.
 247          */
 248         void checkCOMCoordinates(FloatingPointTolerance tolerance, const ConstraintsTestData &testData)
 249         {
 250
 251             RVec comPrime0({0.0, 0.0, 0.0});
 252             RVec comPrime({0.0, 0.0, 0.0});
 253             for (int i = 0; i < testData.numAtoms_; i++)
 254             {
 255                 comPrime0 += testData.masses_[i]*testData.xPrime0_[i];
 256                 comPrime  += testData.masses_[i]*testData.xPrime_[i];
 257             }
 258
 259             comPrime0 /= testData.numAtoms_;
 260             comPrime  /= testData.numAtoms_;
 261
 262             EXPECT_REAL_EQ_TOL(comPrime[XX], comPrime0[XX], tolerance)
 263             << "Center of mass was shifted by constraints in x-direction.";
 264             EXPECT_REAL_EQ_TOL(comPrime[YY], comPrime0[YY], tolerance)
 265             << "Center of mass was shifted by constraints in y-direction.";
 266             EXPECT_REAL_EQ_TOL(comPrime[ZZ], comPrime0[ZZ], tolerance)
 267             << "Center of mass was shifted by constraints in z-direction.";
 268
 269         }
 270
 271         /*! \brief
 272          * The test on the velocity of the center of the mass (COM) of the system.
 273          *
 274          * Checks if the velocity of the center of mass has not changed.
 275          *
 276          * \param[in] tolerance       Allowed tolerance in COM velocity components.
 277          * \param[in] testData        Test data structure.
 278          */
 279         void checkCOMVelocity(FloatingPointTolerance tolerance, const ConstraintsTestData &testData)
 280         {
 281
 282             RVec comV0({0.0, 0.0, 0.0});
 283             RVec comV({0.0, 0.0, 0.0});
 284             for (int i = 0; i < testData.numAtoms_; i++)
 285             {
 286                 comV0 += testData.masses_[i]*testData.v0_[i];
 287                 comV  += testData.masses_[i]*testData.v_[i];
 288             }
 289             comV0 /= testData.numAtoms_;
 290             comV  /= testData.numAtoms_;
 291
 292             EXPECT_REAL_EQ_TOL(comV[XX], comV0[XX], tolerance)
 293             << "Velocity of the center of mass in x-direction has been changed by constraints.";
 294             EXPECT_REAL_EQ_TOL(comV[YY], comV0[YY], tolerance)
 295             << "Velocity of the center of mass in y-direction has been changed by constraints.";
 296             EXPECT_REAL_EQ_TOL(comV[ZZ], comV0[ZZ], tolerance)
 297             << "Velocity of the center of mass in z-direction has been changed by constraints.";
 298         }
 299
 300         /*! \brief
 301          * The test of virial tensor.
 302          *
 303          * Checks if the values in the scaled virial tensor are equal to pre-computed values.
 304          *
 305          * \param[in] tolerance       Tolerance for the tensor values.
 306          * \param[in] testData        Test data structure.
 307          */
 308         void checkVirialTensor(FloatingPointTolerance tolerance, const ConstraintsTestData &testData)
 309         {
 310             for (int i = 0; i < DIM; i++)
 311             {
 312                 for (int j = 0; j < DIM; j++)
 313                 {
 314                     EXPECT_REAL_EQ_TOL(testData.virialScaledRef_[i][j], testData.virialScaled_[i][j],
 315                                        tolerance) << gmx::formatString(
 316                             "Values in virial tensor at [%d][%d] are not within the tolerance from reference value.", i, j);
 317                 }
 318             }
 319         }
 320 };
 321
 322 TEST_P(ConstraintsTest, SingleConstraint){
 323     std::string       title    = "one constraint (e.g. OH)";
 324     int               numAtoms = 2;
 325
 326     std::vector<real> masses        = {1.0, 12.0};
 327     std::vector<int>  constraints   = {0, 0, 1};
 328     std::vector<real> constraintsR0 = {0.1};
 329
 330     real              oneTenthOverSqrtTwo    = 0.1_real / std::sqrt(2.0_real);
 331
 332     std::vector<RVec> x = {{ 0.0, oneTenthOverSqrtTwo, 0.0 },
 333                            { oneTenthOverSqrtTwo, 0.0, 0.0 }};
 334     std::vector<RVec> xPrime = {{ 0.01,  0.08,  0.01 },
 335                                 { 0.06,  0.01, -0.01 }};
 336     std::vector<RVec> v = {{ 1.0, 2.0, 3.0 },
 337                            { 3.0, 2.0, 1.0 }};
 338
 339     tensor            virialScaledRef = {{-5.58e-04,  5.58e-04, 0.00e+00 },
 340                                          { 5.58e-04, -5.58e-04, 0.00e+00 },
 341                                          { 0.00e+00,  0.00e+00, 0.00e+00 }};
 342
 343     real              shakeTolerance         = 0.0001;
 344     gmx_bool          shakeUseSOR            = false;
 345
 346     int               lincsNIter                      = 1;
 347     int               lincslincsExpansionOrder        = 4;
 348     real              lincsWarnAngle                  = 30.0;
 349
 350     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 351             (title, numAtoms, masses,
 352             constraints, constraintsR0,
 353             true, virialScaledRef,
 354             false, 0,
 355             real(0.0), real(0.001),
 356             x, xPrime, v,
 357             shakeTolerance, shakeUseSOR,
 358             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 359     std::string pbcName;
 360     std::string algorithmName;
 361     std::tie(pbcName, algorithmName) = GetParam();
 362     t_pbc                                   pbc       = pbcs_.at(pbcName);
 363
 364     // Apply constraints
 365     algorithms_.at(algorithmName)(testData.get(), pbc);
 366
 367     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 368     checkConstrainsDirection(*testData, pbc);
 369     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 370     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 371
 372     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 373
 374 }
 375
 376 TEST_P(ConstraintsTest, TwoDisjointConstraints){
 377
 378     std::string       title            = "two disjoint constraints";
 379     int               numAtoms         = 4;
 380     std::vector<real> masses           = {0.5, 1.0/3.0, 0.25, 1.0};
 381     std::vector<int>  constraints      = {0, 0, 1, 1, 2, 3};
 382     std::vector<real> constraintsR0    = {2.0, 1.0};
 383
 384
 385     std::vector<RVec> x = {{  2.50, -3.10, 15.70 },
 386                            {  0.51, -3.02, 15.55 },
 387                            { -0.50, -3.00, 15.20 },
 388                            { -1.51, -2.95, 15.05 }};
 389
 390     std::vector<RVec> xPrime = {{  2.50, -3.10, 15.70 },
 391                                 {  0.51, -3.02, 15.55 },
 392                                 { -0.50, -3.00, 15.20 },
 393                                 { -1.51, -2.95, 15.05 }};
 394
 395     std::vector<RVec> v = {{ 0.0, 1.0, 0.0 },
 396                            { 1.0, 0.0, 0.0 },
 397                            { 0.0, 0.0, 1.0 },
 398                            { 0.0, 0.0, 0.0 }};
 399
 400     tensor            virialScaledRef = {{ 3.3e-03, -1.7e-04,  5.6e-04 },
 401                                          {-1.7e-04,  8.9e-06, -2.8e-05 },
 402                                          { 5.6e-04, -2.8e-05,  8.9e-05 }};
 403
 404     real              shakeTolerance         = 0.0001;
 405     gmx_bool          shakeUseSOR            = false;
 406
 407     int               lincsNIter                      = 1;
 408     int               lincslincsExpansionOrder        = 4;
 409     real              lincsWarnAngle                  = 30.0;
 410
 411     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 412             (title, numAtoms, masses,
 413             constraints, constraintsR0,
 414             true, virialScaledRef,
 415             false, 0,
 416             real(0.0), real(0.001),
 417             x, xPrime, v,
 418             shakeTolerance, shakeUseSOR,
 419             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 420
 421     std::string pbcName;
 422     std::string algorithmName;
 423     std::tie(pbcName, algorithmName) = GetParam();
 424     t_pbc                                   pbc       = pbcs_.at(pbcName);
 425
 426     // Apply constraints
 427     algorithms_.at(algorithmName)(testData.get(), pbc);
 428
 429     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 430     checkConstrainsDirection(*testData, pbc);
 431     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 432     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 433
 434     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 435
 436 }
 437
 438 TEST_P(ConstraintsTest, ThreeSequentialConstraints){
 439
 440     std::string       title            = "three atoms, connected longitudinally (e.g. CH2)";
 441     int               numAtoms         = 3;
 442     std::vector<real> masses           = {1.0, 12.0, 16.0 };
 443     std::vector<int>  constraints      = {0, 0, 1, 1, 1, 2};
 444     std::vector<real> constraintsR0    = {0.1, 0.2};
 445
 446     real              oneTenthOverSqrtTwo    = 0.1_real / std::sqrt(2.0_real);
 447     real              twoTenthsOverSqrtThree = 0.2_real / std::sqrt(3.0_real);
 448
 449     std::vector<RVec> x = {{ oneTenthOverSqrtTwo, oneTenthOverSqrtTwo, 0.0 },
 450                            { 0.0, 0.0, 0.0 },
 451                            { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree }};
 452
 453     std::vector<RVec> xPrime = {{  0.08, 0.07,  0.01 },
 454                                 { -0.02, 0.01, -0.02 },
 455                                 {  0.10, 0.12,  0.11 }};
 456
 457     std::vector<RVec> v = {{ 1.0, 0.0, 0.0 },
 458                            { 0.0, 1.0, 0.0 },
 459                            { 0.0, 0.0, 1.0 }};
 460
 461     tensor            virialScaledRef = {{ 4.14e-03, 4.14e-03, 3.31e-03},
 462                                          { 4.14e-03, 4.14e-03, 3.31e-03},
 463                                          { 3.31e-03, 3.31e-03, 3.31e-03}};
 464
 465     real              shakeTolerance         = 0.0001;
 466     gmx_bool          shakeUseSOR            = false;
 467
 468     int               lincsNIter                      = 1;
 469     int               lincslincsExpansionOrder        = 4;
 470     real              lincsWarnAngle                  = 30.0;
 471
 472     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 473             (title, numAtoms, masses,
 474             constraints, constraintsR0,
 475             true, virialScaledRef,
 476             false, 0,
 477             real(0.0), real(0.001),
 478             x, xPrime, v,
 479             shakeTolerance, shakeUseSOR,
 480             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 481
 482     std::string pbcName;
 483     std::string algorithmName;
 484     std::tie(pbcName, algorithmName) = GetParam();
 485     t_pbc                                   pbc       = pbcs_.at(pbcName);
 486
 487     // Apply constraints
 488     algorithms_.at(algorithmName)(testData.get(), pbc);
 489
 490     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 491     checkConstrainsDirection(*testData, pbc);
 492     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 493     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 494
 495     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 496
 497 }
 498
 499 TEST_P(ConstraintsTest, ThreeConstraintsWithCentralAtom){
 500
 501     std::string       title            = "three atoms, connected to the central atom (e.g. CH3)";
 502     int               numAtoms         = 4;
 503     std::vector<real> masses           = {12.0, 1.0, 1.0, 1.0 };
 504     std::vector<int>  constraints      = {0, 0, 1, 0, 0, 2, 0, 0, 3};
 505     std::vector<real> constraintsR0    = {0.1};
 506
 507
 508     std::vector<RVec> x = {{ 0.00,  0.00,  0.00 },
 509                            { 0.10,  0.00,  0.00 },
 510                            { 0.00, -0.10,  0.00 },
 511                            { 0.00,  0.00,  0.10 }};
 512
 513     std::vector<RVec> xPrime = {{ 0.004,  0.009, -0.010 },
 514                                 { 0.110, -0.006,  0.003 },
 515                                 {-0.007, -0.102, -0.007 },
 516                                 {-0.005,  0.011,  0.102 }};
 517
 518     std::vector<RVec> v = {{ 1.0, 0.0, 0.0 },
 519                            { 1.0, 0.0, 0.0 },
 520                            { 1.0, 0.0, 0.0 },
 521                            { 1.0, 0.0, 0.0 }};
 522
 523     tensor            virialScaledRef = {{7.14e-04, 0.00e+00, 0.00e+00},
 524                                          {0.00e+00, 1.08e-03, 0.00e+00},
 525                                          {0.00e+00, 0.00e+00, 1.15e-03}};
 526
 527     real              shakeTolerance         = 0.0001;
 528     gmx_bool          shakeUseSOR            = false;
 529
 530     int               lincsNIter                      = 1;
 531     int               lincslincsExpansionOrder        = 4;
 532     real              lincsWarnAngle                  = 30.0;
 533
 534     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 535             (title, numAtoms, masses,
 536             constraints, constraintsR0,
 537             true, virialScaledRef,
 538             false, 0,
 539             real(0.0), real(0.001),
 540             x, xPrime, v,
 541             shakeTolerance, shakeUseSOR,
 542             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 543
 544     std::string pbcName;
 545     std::string algorithmName;
 546     std::tie(pbcName, algorithmName) = GetParam();
 547     t_pbc                                   pbc       = pbcs_.at(pbcName);
 548
 549     // Apply constraints
 550     algorithms_.at(algorithmName)(testData.get(), pbc);
 551
 552     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 553     checkConstrainsDirection(*testData, pbc);
 554     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 555     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 556
 557     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 558 }
 559
 560 TEST_P(ConstraintsTest, FourSequentialConstraints){
 561
 562     std::string       title            = "four atoms, connected longitudinally";
 563     int               numAtoms         = 4;
 564     std::vector<real> masses           = {0.5, 1.0/3.0, 0.25, 1.0};
 565     std::vector<int>  constraints      = {0, 0, 1, 1, 1, 2, 2, 2, 3};
 566     std::vector<real> constraintsR0    = {2.0, 1.0, 1.0};
 567
 568
 569     std::vector<RVec> x = {{  2.50, -3.10, 15.70 },
 570                            {  0.51, -3.02, 15.55 },
 571                            { -0.50, -3.00, 15.20 },
 572                            { -1.51, -2.95, 15.05 }};
 573
 574     std::vector<RVec> xPrime = {{  2.50, -3.10, 15.70 },
 575                                 {  0.51, -3.02, 15.55 },
 576                                 { -0.50, -3.00, 15.20 },
 577                                 { -1.51, -2.95, 15.05 }};
 578
 579     std::vector<RVec> v = {{ 0.0, 0.0,  2.0 },
 580                            { 0.0, 0.0,  3.0 },
 581                            { 0.0, 0.0, -4.0 },
 582                            { 0.0, 0.0, -1.0 }};
 583
 584     tensor            virialScaledRef = {{ 1.15e-01, -4.20e-03,  2.12e-02},
 585                                          {-4.20e-03,  1.70e-04, -6.41e-04},
 586                                          { 2.12e-02, -6.41e-04,  5.45e-03}};
 587
 588     real              shakeTolerance         = 0.0001;
 589     gmx_bool          shakeUseSOR            = false;
 590
 591     int               lincsNIter                      = 4;
 592     int               lincslincsExpansionOrder        = 8;
 593     real              lincsWarnAngle                  = 30.0;
 594
 595     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 596             (title, numAtoms, masses,
 597             constraints, constraintsR0,
 598             true, virialScaledRef,
 599             false, 0,
 600             real(0.0), real(0.001),
 601             x, xPrime, v,
 602             shakeTolerance, shakeUseSOR,
 603             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 604
 605     std::string pbcName;
 606     std::string algorithmName;
 607     std::tie(pbcName, algorithmName) = GetParam();
 608     t_pbc                                   pbc       = pbcs_.at(pbcName);
 609
 610     // Apply constraints
 611     algorithms_.at(algorithmName)(testData.get(), pbc);
 612
 613     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 614     checkConstrainsDirection(*testData, pbc);
 615     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 616     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 617
 618     checkVirialTensor(absoluteTolerance(0.01), *testData);
 619
 620 }
 621
 622 TEST_P(ConstraintsTest, TriangleOfConstraints){
 623
 624     std::string       title            = "basic triangle (tree atoms, connected to each other)";
 625     int               numAtoms         = 3;
 626     std::vector<real> masses           = {1.0, 1.0, 1.0};
 627     std::vector<int>  constraints      = {0, 0, 1, 2, 0, 2, 1, 1, 2};
 628     std::vector<real> constraintsR0    = {0.1, 0.1, 0.1};
 629
 630     real              oneTenthOverSqrtTwo    = 0.1_real / std::sqrt(2.0_real);
 631
 632     std::vector<RVec> x = {{ oneTenthOverSqrtTwo, 0.0, 0.0 },
 633                            { 0.0, oneTenthOverSqrtTwo, 0.0 },
 634                            { 0.0, 0.0, oneTenthOverSqrtTwo }};
 635
 636     std::vector<RVec> xPrime = {{  0.09, -0.02,  0.01 },
 637                                 { -0.02,  0.10, -0.02 },
 638                                 {  0.03, -0.01,  0.07 }};
 639
 640     std::vector<RVec> v = {{  1.0,  1.0,  1.0 },
 641                            { -2.0, -2.0, -2.0 },
 642                            {  1.0,  1.0,  1.0 }};
 643
 644     tensor            virialScaledRef = {{ 6.00e-04, -1.61e-03,  1.01e-03},
 645                                          {-1.61e-03,  2.53e-03, -9.25e-04},
 646                                          { 1.01e-03, -9.25e-04, -8.05e-05}};
 647
 648     real              shakeTolerance         = 0.0001;
 649     gmx_bool          shakeUseSOR            = false;
 650
 651     int               lincsNIter                      = 1;
 652     int               lincslincsExpansionOrder        = 4;
 653     real              lincsWarnAngle                  = 30.0;
 654
 655     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 656             (title, numAtoms, masses,
 657             constraints, constraintsR0,
 658             true, virialScaledRef,
 659             false, 0,
 660             real(0.0), real(0.001),
 661             x, xPrime, v,
 662             shakeTolerance, shakeUseSOR,
 663             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 664
 665     std::string pbcName;
 666     std::string runnerName;
 667     std::tie(pbcName, runnerName) = GetParam();
 668     t_pbc       pbc               = pbcs_.at(pbcName);
 669
 670     // Apply constraints
 671     algorithms_.at(runnerName)(testData.get(), pbc);
 672
 673     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 674     checkConstrainsDirection(*testData, pbc);
 675     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 676     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 677
 678     checkVirialTensor(absoluteTolerance(0.00001), *testData);
 679
 680 }
 681
 682
 683 INSTANTIATE_TEST_CASE_P(WithParameters, ConstraintsTest,
 684                             ::testing::Combine(::testing::Values("PBCNone", "PBCXYZ"),
 685                                                    ::testing::ValuesIn(getRunnersNames())));
 686
 687 } // namespace
 688 } // namespace test
 689 } // namespace gmx