src/gromacs/mdlib/tests/constr.cpp

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 2018,2019, by the GROMACS development team, led by
   5  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
   6  * and including many others, as listed in the AUTHORS file in the
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   8  *
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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
  48 #include "gmxpre.h"
  49
  50 #include "gromacs/mdlib/constr.h"
  51
  52 #include "config.h"
  53
  54 #include <assert.h>
  55
  56 #include <cmath>
  57
  58 #include <algorithm>
  59 #include <unordered_map>
  60 #include <vector>
  61
  62 #include <gtest/gtest.h>
  63
  64 #include "gromacs/fileio/gmxfio.h"
  65 #include "gromacs/gmxlib/nrnb.h"
  66 #include "gromacs/math/paddedvector.h"
  67 #include "gromacs/math/vec.h"
  68 #include "gromacs/math/vectypes.h"
  69 #include "gromacs/mdlib/lincs.h"
  70 #include "gromacs/mdlib/shake.h"
  71 #include "gromacs/mdrunutility/multisim.h"
  72 #include "gromacs/mdtypes/commrec.h"
  73 #include "gromacs/mdtypes/inputrec.h"
  74 #include "gromacs/mdtypes/mdatom.h"
  75 #include "gromacs/pbcutil/pbc.h"
  76 #include "gromacs/topology/block.h"
  77 #include "gromacs/topology/idef.h"
  78 #include "gromacs/topology/ifunc.h"
  79 #include "gromacs/topology/topology.h"
  80 #include "gromacs/utility/smalloc.h"
  81 #include "gromacs/utility/stringutil.h"
  82 #include "gromacs/utility/unique_cptr.h"
  83
  84 #include "testutils/refdata.h"
  85 #include "testutils/testasserts.h"
  86
  87 #include "constr_impl.h"
  88
  89 namespace gmx
  90 {
  91 namespace test
  92 {
  93
  94 ConstraintsTestData::ConstraintsTestData(const std::string &title,
  95                                          int numAtoms, std::vector<real> masses,
  96                                          std::vector<int> constraints, std::vector<real> constraintsR0,
  97                                          bool computeVirial, tensor virialScaledRef,
  98                                          bool compute_dHdLambda, float dHdLambdaRef,
  99                                          real initialTime, real timestep,
 100                                          const std::vector<RVec> &x, const std::vector<RVec> &xPrime, const std::vector<RVec> &v,
 101                                          real shakeTolerance, gmx_bool shakeUseSOR,
 102                                          int lincsNumIterations, int lincsExpansionOrder, real lincsWarnAngle)
 103 {
 104     // This is to trick Gerrit
 105     {
 106         {
 107             title_    = title;    // Human-friendly name of the system
 108             numAtoms_ = numAtoms; // Number of atoms
 109
 110             // Masses of atoms
 111             masses_ = masses;
 112             invmass_.resize(numAtoms); // Vector of inverse masses
 113
 114             for (int i = 0; i < numAtoms; i++)
 115             {
 116                 invmass_[i] = 1.0/masses.at(i);
 117             }
 118
 119             // Saving constraints to check if they are satisfied after algorithm was applied
 120             constraints_   = constraints;   // Constraints indices (in type-i-j format)
 121             constraintsR0_ = constraintsR0; // Equilibrium distances for each type of constraint
 122
 123             invdt_  = 1.0/timestep;         // Inverse timestep
 124
 125             // Communication record
 126             cr_.nnodes = 1;
 127             cr_.dd     = nullptr;
 128
 129             // Multisim data
 130             ms_.sim  = 0;
 131             ms_.nsim = 1;
 132
 133             // Input record - data that usually comes from configuration file (.mdp)
 134             ir_.efep           = 0;
 135             ir_.init_t         = initialTime;
 136             ir_.delta_t        = timestep;
 137             ir_.eI             = 0;
 138
 139             // MD atoms data
 140             md_.nMassPerturbed = 0;
 141             md_.lambda         = 0.0;
 142             md_.invmass        = invmass_.data();
 143             md_.nr             = numAtoms;
 144             md_.homenr         = numAtoms;
 145
 146             // Virial evaluation
 147             computeVirial_ = computeVirial;
 148             if (computeVirial)
 149             {
 150                 for (int i = 0; i < DIM; i++)
 151                 {
 152                     for (int j = 0; j < DIM; j++)
 153                     {
 154                         virialScaled_[i][j]    = 0;
 155                         virialScaledRef_[i][j] = virialScaledRef[i][j];
 156                     }
 157                 }
 158             }
 159
 160
 161             // Free energy evaluation
 162             compute_dHdLambda_ = compute_dHdLambda;
 163             dHdLambda_         = 0;
 164             if (compute_dHdLambda_)
 165             {
 166                 ir_.efep                    = efepYES;
 167                 dHdLambdaRef_               = dHdLambdaRef;
 168             }
 169             else
 170             {
 171                 ir_.efep                    = efepNO;
 172                 dHdLambdaRef_               = 0;
 173             }
 174
 175             // Constraints and their parameters (local topology)
 176             for (int i = 0; i < F_NRE; i++)
 177             {
 178                 idef_.il[i].nr = 0;
 179             }
 180             idef_.il[F_CONSTR].nr   = constraints.size();
 181
 182             snew(idef_.il[F_CONSTR].iatoms, constraints.size());
 183             int maxType = 0;
 184             for (unsigned i = 0; i < constraints.size(); i++)
 185             {
 186                 if (i % 3 == 0)
 187                 {
 188                     if (maxType < constraints.at(i))
 189                     {
 190                         maxType = constraints.at(i);
 191                     }
 192                 }
 193                 idef_.il[F_CONSTR].iatoms[i] = constraints.at(i);
 194             }
 195             snew(idef_.iparams, maxType + 1);
 196             for (unsigned i = 0; i < constraints.size()/3; i++)
 197             {
 198                 idef_.iparams[constraints.at(3*i)].constr.dA = constraintsR0.at(constraints.at(3*i));
 199                 idef_.iparams[constraints.at(3*i)].constr.dB = constraintsR0.at(constraints.at(3*i));
 200             }
 201
 202             // Constraints and their parameters (global topology)
 203             InteractionList interactionList;
 204             interactionList.iatoms.resize(constraints.size());
 205             for (unsigned i = 0; i < constraints.size(); i++)
 206             {
 207                 interactionList.iatoms.at(i) = constraints.at(i);
 208             }
 209             InteractionList interactionListEmpty;
 210             interactionListEmpty.iatoms.resize(0);
 211
 212             gmx_moltype_t molType;
 213             molType.atoms.nr             = numAtoms;
 214             molType.ilist.at(F_CONSTR)   = interactionList;
 215             molType.ilist.at(F_CONSTRNC) = interactionListEmpty;
 216             mtop_.moltype.push_back(molType);
 217
 218             gmx_molblock_t molBlock;
 219             molBlock.type = 0;
 220             molBlock.nmol = 1;
 221             mtop_.molblock.push_back(molBlock);
 222
 223             mtop_.natoms = numAtoms;
 224             mtop_.ffparams.iparams.resize(maxType + 1);
 225             for (int i = 0; i <= maxType; i++)
 226             {
 227                 mtop_.ffparams.iparams.at(i) = idef_.iparams[i];
 228             }
 229             mtop_.bIntermolecularInteractions = false;
 230
 231             // Coordinates and velocities
 232             x_.resizeWithPadding(numAtoms);
 233             xPrime_.resizeWithPadding(numAtoms);
 234             xPrime0_.resizeWithPadding(numAtoms);
 235             xPrime2_.resizeWithPadding(numAtoms);
 236
 237             v_.resizeWithPadding(numAtoms);
 238             v0_.resizeWithPadding(numAtoms);
 239
 240             std::copy(x.begin(), x.end(), x_.begin());
 241             std::copy(xPrime.begin(), xPrime.end(), xPrime_.begin());
 242             std::copy(xPrime.begin(), xPrime.end(), xPrime0_.begin());
 243             std::copy(xPrime.begin(), xPrime.end(), xPrime2_.begin());
 244
 245             std::copy(v.begin(), v.end(), v_.begin());
 246             std::copy(v.begin(), v.end(), v0_.begin());
 247
 248             // SHAKE-specific parameters
 249             ir_.shake_tol            = shakeTolerance;
 250             ir_.bShakeSOR            = shakeUseSOR;
 251
 252             // LINCS-specific parameters
 253             ir_.nLincsIter     = lincsNumIterations;
 254             ir_.nProjOrder     = lincsExpansionOrder;
 255             ir_.LincsWarnAngle = lincsWarnAngle;
 256         }
 257     }
 258 }
 259
 260 /*! \brief
 261  * Reset the data structure so it can be reused.
 262  *
 263  * Set the coordinates and velocities back to their values before
 264  * constraining. The scaled virial tensor and dHdLambda are zeroed.
 265  *
 266  */
 267 void ConstraintsTestData::reset()
 268 {
 269     xPrime_  = xPrime0_;
 270     xPrime2_ = xPrime0_;
 271     v_       = v0_;
 272
 273     if (computeVirial_)
 274     {
 275         for (int i = 0; i < DIM; i++)
 276         {
 277             for (int j = 0; j < DIM; j++)
 278             {
 279                 virialScaled_[i][j] = 0;
 280             }
 281         }
 282     }
 283     dHdLambda_         = 0;
 284 }
 285
 286 /*! \brief
 287  * Cleaning up the memory.
 288  */
 289 ConstraintsTestData::~ConstraintsTestData()
 290 {
 291     sfree(idef_.il[F_CONSTR].iatoms);
 292     sfree(idef_.iparams);
 293 }
 294
 295 namespace
 296 {
 297
 298 /*! \brief The two-dimensional parameter space for test.
 299  *
 300  * The test will run for all possible combinations of accessible
 301  * values of the:
 302  * 1. PBC setup ("PBCNONE" or "PBCXYZ")
 303  * 2. The algorithm ("SHAKE", "LINCS" or "LINCS_GPU").
 304  */
 305 typedef std::tuple<std::string, std::string> ConstraintsTestParameters;
 306
 307 //! Names of all availible algorithms
 308 std::vector<std::string> algorithmsNames;
 309
 310 //! Method that fills and returns algorithmNames to the test macros.
 311 std::vector<std::string> getAlgorithmsNames()
 312 {
 313     algorithmsNames.emplace_back("SHAKE");
 314     algorithmsNames.emplace_back("LINCS");
 315     std::string errorMessage;
 316     if (GMX_GPU == GMX_GPU_CUDA && canDetectGpus(&errorMessage))
 317     {
 318         algorithmsNames.emplace_back("LINCS_CUDA");
 319     }
 320     return algorithmsNames;
 321 }
 322
 323 /*! \brief Test fixture for constraints.
 324  *
 325  * The fixture uses following test systems:
 326  * 1. Two atoms, connected with one constraint (e.g. NH).
 327  * 2. Three atoms, connected consequently with two constraints (e.g. CH2).
 328  * 3. Three atoms, constrained to the fourth atom (e.g. CH3).
 329  * 4. Four atoms, connected by two independent constraints.
 330  * 5. Three atoms, connected by three constraints in a triangle
 331  *      (e.g. H2O with constrained H-O-H angle).
 332  * 6. Four atoms, connected by three consequential constraints.
 333  *
 334  * For all systems, the final lengths of the constraints are tested against the
 335  * reference values, the direction of each constraint is checked.
 336  * Test also verifies that the center of mass has not been
 337  * shifted by the constraints and that its velocity has not changed.
 338  * For some systems, the value for scaled virial tensor is checked against
 339  * pre-computed data.
 340  */
 341 class ConstraintsTest : public ::testing::TestWithParam<ConstraintsTestParameters>
 342 {
 343     public:
 344         //! PBC setups
 345         std::unordered_map <std::string, t_pbc>                                             pbcs_;
 346         //! Algorithms (SHAKE and LINCS)
 347         std::unordered_map <std::string, void(*)(ConstraintsTestData *testData, t_pbc pbc)> algorithms_;
 348
 349         /*! \brief Test setup function.
 350          *
 351          * Setting up the pbcs and algorithms. Note, that corresponding string keywords
 352          * have to be explicitly added at the end of this file when the tests are called.
 353          *
 354          */
 355         void SetUp() override
 356         {
 357
 358             //
 359             // PBC initialization
 360             //
 361             t_pbc pbc;
 362
 363             // Infinitely small box
 364             matrix boxNone = { {0, 0, 0}, {0, 0, 0}, {0, 0, 0} };
 365             set_pbc(&pbc, epbcNONE, boxNone);
 366             pbcs_["PBCNone"] = pbc;
 367
 368             // Rectangular box
 369             matrix boxXyz = { {10.0, 0.0, 0.0}, {0.0, 20.0, 0.0}, {0.0, 0.0, 15.0} };
 370             set_pbc(&pbc, epbcXYZ, boxXyz);
 371             pbcs_["PBCXYZ"] = pbc;
 372
 373             //
 374             // Algorithms
 375             //
 376             // SHAKE
 377             algorithms_["SHAKE"] = applyShake;
 378             // LINCS
 379             algorithms_["LINCS"] = applyLincs;
 380             // LINCS using CUDA (will only be called if CUDA is available)
 381             algorithms_["LINCS_CUDA"] = applyLincsCuda;
 382         }
 383
 384         /*! \brief
 385          * The test on the final length of constrained bonds.
 386          *
 387          * Goes through all the constraints and checks if the final length of all the constraints is equal
 388          * to the target length with provided tolerance.
 389          *
 390          * \param[in] tolerance       Allowed tolerance in final lengths.
 391          * \param[in] testData        Test data structure.
 392          * \param[in] pbc             Periodic boundary data.
 393          */
 394         void checkConstrainsLength(FloatingPointTolerance tolerance, const ConstraintsTestData &testData, t_pbc pbc)
 395         {
 396
 397             // Test if all the constraints are satisfied
 398             for (unsigned c = 0; c < testData.constraints_.size()/3; c++)
 399             {
 400                 real r0 = testData.constraintsR0_.at(testData.constraints_.at(3*c));
 401                 int  i  = testData.constraints_.at(3*c + 1);
 402                 int  j  = testData.constraints_.at(3*c + 2);
 403                 RVec xij0, xij1;
 404                 real d0, d1;
 405                 if (pbc.ePBC == epbcXYZ)
 406                 {
 407                     pbc_dx_aiuc(&pbc, testData.x_[i], testData.x_[j], xij0);
 408                     pbc_dx_aiuc(&pbc, testData.xPrime_[i], testData.xPrime_[j], xij1);
 409                 }
 410                 else
 411                 {
 412                     rvec_sub(testData.x_[i], testData.x_[j], xij0);
 413                     rvec_sub(testData.xPrime_[i], testData.xPrime_[j], xij1);
 414                 }
 415                 d0 = norm(xij0);
 416                 d1 = norm(xij1);
 417                 EXPECT_REAL_EQ_TOL(r0, d1, tolerance) << gmx::formatString(
 418                         "rij = %f, which is not equal to r0 = %f for constraint #%u, between atoms %d and %d"
 419                         " (before constraining rij was %f).", d1, r0, c, i, j, d0);
 420             }
 421         }
 422
 423         /*! \brief
 424          * The test on the final length of constrained bonds.
 425          *
 426          * Goes through all the constraints and checks if the direction of constraint has not changed
 427          * by the algorithm (i.e. the constraints algorithm arrived to the solution that is closest
 428          * to the initial system conformation).
 429          *
 430          * \param[in] testData        Test data structure.
 431          * \param[in] pbc             Periodic boundary data.
 432          */
 433         void checkConstrainsDirection(const ConstraintsTestData &testData, t_pbc pbc)
 434         {
 435
 436             for (unsigned c = 0; c < testData.constraints_.size()/3; c++)
 437             {
 438                 int  i  = testData.constraints_.at(3*c + 1);
 439                 int  j  = testData.constraints_.at(3*c + 2);
 440                 RVec xij0, xij1;
 441                 if (pbc.ePBC == epbcXYZ)
 442                 {
 443                     pbc_dx_aiuc(&pbc, testData.x_[i], testData.x_[j], xij0);
 444                     pbc_dx_aiuc(&pbc, testData.xPrime_[i], testData.xPrime_[j], xij1);
 445                 }
 446                 else
 447                 {
 448                     rvec_sub(testData.x_[i], testData.x_[j], xij0);
 449                     rvec_sub(testData.xPrime_[i], testData.xPrime_[j], xij1);
 450                 }
 451
 452                 real dot = xij0.dot(xij1);
 453
 454                 EXPECT_GE(dot, 0.0) << gmx::formatString(
 455                         "The constraint %u changed direction. Constraining algorithm might have returned the wrong root "
 456                         "of the constraints equation.", c);
 457
 458             }
 459         }
 460
 461         /*! \brief
 462          * The test on the coordinates of the center of the mass (COM) of the system.
 463          *
 464          * Checks if the center of mass has not been shifted by the constraints. Note,
 465          * that this test does not take into account the periodic boundary conditions.
 466          * Hence it will not work should the constraints decide to move atoms across
 467          * PBC borders.
 468          *
 469          * \param[in] tolerance       Allowed tolerance in COM coordinates.
 470          * \param[in] testData        Test data structure.
 471          */
 472         void checkCOMCoordinates(FloatingPointTolerance tolerance, const ConstraintsTestData &testData)
 473         {
 474
 475             RVec comPrime0({0.0, 0.0, 0.0});
 476             RVec comPrime({0.0, 0.0, 0.0});
 477             for (int i = 0; i < testData.numAtoms_; i++)
 478             {
 479                 comPrime0 += testData.masses_[i]*testData.xPrime0_[i];
 480                 comPrime  += testData.masses_[i]*testData.xPrime_[i];
 481             }
 482
 483             comPrime0 /= testData.numAtoms_;
 484             comPrime  /= testData.numAtoms_;
 485
 486             EXPECT_REAL_EQ_TOL(comPrime[XX], comPrime0[XX], tolerance)
 487             << "Center of mass was shifted by constraints in x-direction.";
 488             EXPECT_REAL_EQ_TOL(comPrime[YY], comPrime0[YY], tolerance)
 489             << "Center of mass was shifted by constraints in y-direction.";
 490             EXPECT_REAL_EQ_TOL(comPrime[ZZ], comPrime0[ZZ], tolerance)
 491             << "Center of mass was shifted by constraints in z-direction.";
 492
 493         }
 494
 495         /*! \brief
 496          * The test on the velocity of the center of the mass (COM) of the system.
 497          *
 498          * Checks if the velocity of the center of mass has not changed.
 499          *
 500          * \param[in] tolerance       Allowed tolerance in COM velocity components.
 501          * \param[in] testData        Test data structure.
 502          */
 503         void checkCOMVelocity(FloatingPointTolerance tolerance, const ConstraintsTestData &testData)
 504         {
 505
 506             RVec comV0({0.0, 0.0, 0.0});
 507             RVec comV({0.0, 0.0, 0.0});
 508             for (int i = 0; i < testData.numAtoms_; i++)
 509             {
 510                 comV0 += testData.masses_[i]*testData.v0_[i];
 511                 comV  += testData.masses_[i]*testData.v_[i];
 512             }
 513             comV0 /= testData.numAtoms_;
 514             comV  /= testData.numAtoms_;
 515
 516             EXPECT_REAL_EQ_TOL(comV[XX], comV0[XX], tolerance)
 517             << "Velocity of the center of mass in x-direction has been changed by constraints.";
 518             EXPECT_REAL_EQ_TOL(comV[YY], comV0[YY], tolerance)
 519             << "Velocity of the center of mass in y-direction has been changed by constraints.";
 520             EXPECT_REAL_EQ_TOL(comV[ZZ], comV0[ZZ], tolerance)
 521             << "Velocity of the center of mass in z-direction has been changed by constraints.";
 522         }
 523
 524         /*! \brief
 525          * The test of virial tensor.
 526          *
 527          * Checks if the values in the scaled virial tensor are equal to pre-computed values.
 528          *
 529          * \param[in] tolerance       Tolerance for the tensor values.
 530          * \param[in] testData        Test data structure.
 531          */
 532         void checkVirialTensor(FloatingPointTolerance tolerance, const ConstraintsTestData &testData)
 533         {
 534             for (int i = 0; i < DIM; i++)
 535             {
 536                 for (int j = 0; j < DIM; j++)
 537                 {
 538                     EXPECT_REAL_EQ_TOL(testData.virialScaledRef_[i][j], testData.virialScaled_[i][j],
 539                                        tolerance) << gmx::formatString(
 540                             "Values in virial tensor at [%d][%d] are not within the tolerance from reference value.", i, j);
 541                 }
 542             }
 543         }
 544 };
 545
 546 TEST_P(ConstraintsTest, SingleConstraint){
 547     std::string       title    = "one constraint (e.g. OH)";
 548     int               numAtoms = 2;
 549
 550     std::vector<real> masses        = {1.0, 12.0};
 551     std::vector<int>  constraints   = {0, 0, 1};
 552     std::vector<real> constraintsR0 = {0.1};
 553
 554     real              oneTenthOverSqrtTwo    = 0.1_real / std::sqrt(2.0_real);
 555
 556     std::vector<RVec> x = {{ 0.0, oneTenthOverSqrtTwo, 0.0 },
 557                            { oneTenthOverSqrtTwo, 0.0, 0.0 }};
 558     std::vector<RVec> xPrime = {{ 0.01,  0.08,  0.01 },
 559                                 { 0.06,  0.01, -0.01 }};
 560     std::vector<RVec> v = {{ 1.0, 2.0, 3.0 },
 561                            { 3.0, 2.0, 1.0 }};
 562
 563     tensor            virialScaledRef = {{-5.58e-04,  5.58e-04, 0.00e+00 },
 564                                          { 5.58e-04, -5.58e-04, 0.00e+00 },
 565                                          { 0.00e+00,  0.00e+00, 0.00e+00 }};
 566
 567     real              shakeTolerance         = 0.0001;
 568     gmx_bool          shakeUseSOR            = false;
 569
 570     int               lincsNIter                      = 1;
 571     int               lincslincsExpansionOrder        = 4;
 572     real              lincsWarnAngle                  = 30.0;
 573
 574     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 575             (title, numAtoms, masses,
 576             constraints, constraintsR0,
 577             true, virialScaledRef,
 578             false, 0,
 579             real(0.0), real(0.001),
 580             x, xPrime, v,
 581             shakeTolerance, shakeUseSOR,
 582             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 583     std::string pbcName;
 584     std::string algorithmName;
 585     std::tie(pbcName, algorithmName) = GetParam();
 586     t_pbc                                   pbc       = pbcs_.at(pbcName);
 587
 588     // Apply constraints
 589     algorithms_.at(algorithmName)(testData.get(), pbc);
 590
 591     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 592     checkConstrainsDirection(*testData, pbc);
 593     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 594     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 595
 596     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 597
 598 }
 599
 600 TEST_P(ConstraintsTest, TwoDisjointConstraints){
 601
 602     std::string       title            = "two disjoint constraints";
 603     int               numAtoms         = 4;
 604     std::vector<real> masses           = {0.5, 1.0/3.0, 0.25, 1.0};
 605     std::vector<int>  constraints      = {0, 0, 1, 1, 2, 3};
 606     std::vector<real> constraintsR0    = {2.0, 1.0};
 607
 608
 609     std::vector<RVec> x = {{  2.50, -3.10, 15.70 },
 610                            {  0.51, -3.02, 15.55 },
 611                            { -0.50, -3.00, 15.20 },
 612                            { -1.51, -2.95, 15.05 }};
 613
 614     std::vector<RVec> xPrime = {{  2.50, -3.10, 15.70 },
 615                                 {  0.51, -3.02, 15.55 },
 616                                 { -0.50, -3.00, 15.20 },
 617                                 { -1.51, -2.95, 15.05 }};
 618
 619     std::vector<RVec> v = {{ 0.0, 1.0, 0.0 },
 620                            { 1.0, 0.0, 0.0 },
 621                            { 0.0, 0.0, 1.0 },
 622                            { 0.0, 0.0, 0.0 }};
 623
 624     tensor            virialScaledRef = {{ 3.3e-03, -1.7e-04,  5.6e-04 },
 625                                          {-1.7e-04,  8.9e-06, -2.8e-05 },
 626                                          { 5.6e-04, -2.8e-05,  8.9e-05 }};
 627
 628     real              shakeTolerance         = 0.0001;
 629     gmx_bool          shakeUseSOR            = false;
 630
 631     int               lincsNIter                      = 1;
 632     int               lincslincsExpansionOrder        = 4;
 633     real              lincsWarnAngle                  = 30.0;
 634
 635     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 636             (title, numAtoms, masses,
 637             constraints, constraintsR0,
 638             true, virialScaledRef,
 639             false, 0,
 640             real(0.0), real(0.001),
 641             x, xPrime, v,
 642             shakeTolerance, shakeUseSOR,
 643             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 644
 645     std::string pbcName;
 646     std::string algorithmName;
 647     std::tie(pbcName, algorithmName) = GetParam();
 648     t_pbc                                   pbc       = pbcs_.at(pbcName);
 649
 650     // Apply constraints
 651     algorithms_.at(algorithmName)(testData.get(), pbc);
 652
 653     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 654     checkConstrainsDirection(*testData, pbc);
 655     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 656     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 657
 658     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 659
 660 }
 661
 662 TEST_P(ConstraintsTest, ThreeSequentialConstraints){
 663
 664     std::string       title            = "three atoms, connected longitudinally (e.g. CH2)";
 665     int               numAtoms         = 3;
 666     std::vector<real> masses           = {1.0, 12.0, 16.0 };
 667     std::vector<int>  constraints      = {0, 0, 1, 1, 1, 2};
 668     std::vector<real> constraintsR0    = {0.1, 0.2};
 669
 670     real              oneTenthOverSqrtTwo    = 0.1_real / std::sqrt(2.0_real);
 671     real              twoTenthsOverSqrtThree = 0.2_real / std::sqrt(3.0_real);
 672
 673     std::vector<RVec> x = {{ oneTenthOverSqrtTwo, oneTenthOverSqrtTwo, 0.0 },
 674                            { 0.0, 0.0, 0.0 },
 675                            { twoTenthsOverSqrtThree, twoTenthsOverSqrtThree, twoTenthsOverSqrtThree }};
 676
 677     std::vector<RVec> xPrime = {{  0.08, 0.07,  0.01 },
 678                                 { -0.02, 0.01, -0.02 },
 679                                 {  0.10, 0.12,  0.11 }};
 680
 681     std::vector<RVec> v = {{ 1.0, 0.0, 0.0 },
 682                            { 0.0, 1.0, 0.0 },
 683                            { 0.0, 0.0, 1.0 }};
 684
 685     tensor            virialScaledRef = {{ 4.14e-03, 4.14e-03, 3.31e-03},
 686                                          { 4.14e-03, 4.14e-03, 3.31e-03},
 687                                          { 3.31e-03, 3.31e-03, 3.31e-03}};
 688
 689     real              shakeTolerance         = 0.0001;
 690     gmx_bool          shakeUseSOR            = false;
 691
 692     int               lincsNIter                      = 1;
 693     int               lincslincsExpansionOrder        = 4;
 694     real              lincsWarnAngle                  = 30.0;
 695
 696     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 697             (title, numAtoms, masses,
 698             constraints, constraintsR0,
 699             true, virialScaledRef,
 700             false, 0,
 701             real(0.0), real(0.001),
 702             x, xPrime, v,
 703             shakeTolerance, shakeUseSOR,
 704             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 705
 706     std::string pbcName;
 707     std::string algorithmName;
 708     std::tie(pbcName, algorithmName) = GetParam();
 709     t_pbc                                   pbc       = pbcs_.at(pbcName);
 710
 711     // Apply constraints
 712     algorithms_.at(algorithmName)(testData.get(), pbc);
 713
 714     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 715     checkConstrainsDirection(*testData, pbc);
 716     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 717     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 718
 719     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 720
 721 }
 722
 723 TEST_P(ConstraintsTest, ThreeConstraintsWithCentralAtom){
 724
 725     std::string       title            = "three atoms, connected to the central atom (e.g. CH3)";
 726     int               numAtoms         = 4;
 727     std::vector<real> masses           = {12.0, 1.0, 1.0, 1.0 };
 728     std::vector<int>  constraints      = {0, 0, 1, 0, 0, 2, 0, 0, 3};
 729     std::vector<real> constraintsR0    = {0.1};
 730
 731
 732     std::vector<RVec> x = {{ 0.00,  0.00,  0.00 },
 733                            { 0.10,  0.00,  0.00 },
 734                            { 0.00, -0.10,  0.00 },
 735                            { 0.00,  0.00,  0.10 }};
 736
 737     std::vector<RVec> xPrime = {{ 0.004,  0.009, -0.010 },
 738                                 { 0.110, -0.006,  0.003 },
 739                                 {-0.007, -0.102, -0.007 },
 740                                 {-0.005,  0.011,  0.102 }};
 741
 742     std::vector<RVec> v = {{ 1.0, 0.0, 0.0 },
 743                            { 1.0, 0.0, 0.0 },
 744                            { 1.0, 0.0, 0.0 },
 745                            { 1.0, 0.0, 0.0 }};
 746
 747     tensor            virialScaledRef = {{7.14e-04, 0.00e+00, 0.00e+00},
 748                                          {0.00e+00, 1.08e-03, 0.00e+00},
 749                                          {0.00e+00, 0.00e+00, 1.15e-03}};
 750
 751     real              shakeTolerance         = 0.0001;
 752     gmx_bool          shakeUseSOR            = false;
 753
 754     int               lincsNIter                      = 1;
 755     int               lincslincsExpansionOrder        = 4;
 756     real              lincsWarnAngle                  = 30.0;
 757
 758     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 759             (title, numAtoms, masses,
 760             constraints, constraintsR0,
 761             true, virialScaledRef,
 762             false, 0,
 763             real(0.0), real(0.001),
 764             x, xPrime, v,
 765             shakeTolerance, shakeUseSOR,
 766             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 767
 768     std::string pbcName;
 769     std::string algorithmName;
 770     std::tie(pbcName, algorithmName) = GetParam();
 771     t_pbc                                   pbc       = pbcs_.at(pbcName);
 772
 773     // Apply constraints
 774     algorithms_.at(algorithmName)(testData.get(), pbc);
 775
 776     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 777     checkConstrainsDirection(*testData, pbc);
 778     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 779     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 780
 781     checkVirialTensor(absoluteTolerance(0.0001), *testData);
 782 }
 783
 784 TEST_P(ConstraintsTest, FourSequentialConstraints){
 785
 786     std::string       title            = "four atoms, connected longitudinally";
 787     int               numAtoms         = 4;
 788     std::vector<real> masses           = {0.5, 1.0/3.0, 0.25, 1.0};
 789     std::vector<int>  constraints      = {0, 0, 1, 1, 1, 2, 2, 2, 3};
 790     std::vector<real> constraintsR0    = {2.0, 1.0, 1.0};
 791
 792
 793     std::vector<RVec> x = {{  2.50, -3.10, 15.70 },
 794                            {  0.51, -3.02, 15.55 },
 795                            { -0.50, -3.00, 15.20 },
 796                            { -1.51, -2.95, 15.05 }};
 797
 798     std::vector<RVec> xPrime = {{  2.50, -3.10, 15.70 },
 799                                 {  0.51, -3.02, 15.55 },
 800                                 { -0.50, -3.00, 15.20 },
 801                                 { -1.51, -2.95, 15.05 }};
 802
 803     std::vector<RVec> v = {{ 0.0, 0.0,  2.0 },
 804                            { 0.0, 0.0,  3.0 },
 805                            { 0.0, 0.0, -4.0 },
 806                            { 0.0, 0.0, -1.0 }};
 807
 808     tensor            virialScaledRef = {{ 1.15e-01, -4.20e-03,  2.12e-02},
 809                                          {-4.20e-03,  1.70e-04, -6.41e-04},
 810                                          { 2.12e-02, -6.41e-04,  5.45e-03}};
 811
 812     real              shakeTolerance         = 0.0001;
 813     gmx_bool          shakeUseSOR            = false;
 814
 815     int               lincsNIter                      = 4;
 816     int               lincslincsExpansionOrder        = 8;
 817     real              lincsWarnAngle                  = 30.0;
 818
 819     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 820             (title, numAtoms, masses,
 821             constraints, constraintsR0,
 822             true, virialScaledRef,
 823             false, 0,
 824             real(0.0), real(0.001),
 825             x, xPrime, v,
 826             shakeTolerance, shakeUseSOR,
 827             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 828
 829     std::string pbcName;
 830     std::string algorithmName;
 831     std::tie(pbcName, algorithmName) = GetParam();
 832     t_pbc                                   pbc       = pbcs_.at(pbcName);
 833
 834     // Apply constraints
 835     algorithms_.at(algorithmName)(testData.get(), pbc);
 836
 837     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 838     checkConstrainsDirection(*testData, pbc);
 839     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 840     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 841
 842     checkVirialTensor(absoluteTolerance(0.01), *testData);
 843
 844 }
 845
 846 TEST_P(ConstraintsTest, TriangleOfConstraints){
 847
 848     std::string       title            = "basic triangle (tree atoms, connected to each other)";
 849     int               numAtoms         = 3;
 850     std::vector<real> masses           = {1.0, 1.0, 1.0};
 851     std::vector<int>  constraints      = {0, 0, 1, 2, 0, 2, 1, 1, 2};
 852     std::vector<real> constraintsR0    = {0.1, 0.1, 0.1};
 853
 854     real              oneTenthOverSqrtTwo    = 0.1_real / std::sqrt(2.0_real);
 855
 856     std::vector<RVec> x = {{ oneTenthOverSqrtTwo, 0.0, 0.0 },
 857                            { 0.0, oneTenthOverSqrtTwo, 0.0 },
 858                            { 0.0, 0.0, oneTenthOverSqrtTwo }};
 859
 860     std::vector<RVec> xPrime = {{  0.09, -0.02,  0.01 },
 861                                 { -0.02,  0.10, -0.02 },
 862                                 {  0.03, -0.01,  0.07 }};
 863
 864     std::vector<RVec> v = {{  1.0,  1.0,  1.0 },
 865                            { -2.0, -2.0, -2.0 },
 866                            {  1.0,  1.0,  1.0 }};
 867
 868     tensor            virialScaledRef = {{ 6.00e-04, -1.61e-03,  1.01e-03},
 869                                          {-1.61e-03,  2.53e-03, -9.25e-04},
 870                                          { 1.01e-03, -9.25e-04, -8.05e-05}};
 871
 872     real              shakeTolerance         = 0.0001;
 873     gmx_bool          shakeUseSOR            = false;
 874
 875     int               lincsNIter                      = 1;
 876     int               lincslincsExpansionOrder        = 4;
 877     real              lincsWarnAngle                  = 30.0;
 878
 879     std::unique_ptr<ConstraintsTestData>   testData = std::make_unique<ConstraintsTestData>
 880             (title, numAtoms, masses,
 881             constraints, constraintsR0,
 882             true, virialScaledRef,
 883             false, 0,
 884             real(0.0), real(0.001),
 885             x, xPrime, v,
 886             shakeTolerance, shakeUseSOR,
 887             lincsNIter, lincslincsExpansionOrder, lincsWarnAngle);
 888
 889     std::string pbcName;
 890     std::string algorithmName;
 891     std::tie(pbcName, algorithmName) = GetParam();
 892     t_pbc                                   pbc       = pbcs_.at(pbcName);
 893
 894     // Apply constraints
 895     algorithms_.at(algorithmName)(testData.get(), pbc);
 896
 897     checkConstrainsLength(absoluteTolerance(0.0002), *testData, pbc);
 898     checkConstrainsDirection(*testData, pbc);
 899     checkCOMCoordinates(absoluteTolerance(0.0001), *testData);
 900     checkCOMVelocity(absoluteTolerance(0.0001), *testData);
 901
 902     checkVirialTensor(absoluteTolerance(0.00001), *testData);
 903
 904 }
 905
 906
 907 INSTANTIATE_TEST_CASE_P(WithParameters, ConstraintsTest,
 908                             ::testing::Combine(::testing::Values("PBCNone", "PBCXYZ"),
 909                                                    ::testing::ValuesIn(getAlgorithmsNames())));
 910
 911 } // namespace
 912 } // namespace test
 913 } // namespace gmx