src/gromacs/mdlib/tests/settle.cpp

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  35 #include "gmxpre.h"
  36
  37 #include "gromacs/mdlib/settle.h"
  38
  39 #include <tuple>
  40 #include <vector>
  41
  42 #include <gtest/gtest.h>
  43
  44 #include "gromacs/math/vec.h"
  45 #include "gromacs/math/vectypes.h"
  46 #include "gromacs/mdtypes/mdatom.h"
  47 #include "gromacs/pbcutil/pbc.h"
  48 #include "gromacs/topology/idef.h"
  49 #include "gromacs/topology/ifunc.h"
  50 #include "gromacs/topology/topology.h"
  51 #include "gromacs/utility/smalloc.h"
  52 #include "gromacs/utility/stringutil.h"
  53 #include "gromacs/utility/unique_cptr.h"
  54
  55 #include "testutils/testasserts.h"
  56
  57 namespace gmx
  58 {
  59
  60 namespace test
  61 {
  62
  63 //! Database of 51 water atom input positions (DIM reals per atom, taken from spc216.gro) for use as test inputs.
  64 const double g_positions[] = {
  65     .130, -.041, -.291,
  66     .120, -.056, -.192,
  67     .044, -.005, -.327,
  68     -.854, -.406, .477,
  69     -.900, -.334, .425,
  70     -.858, -.386, .575,
  71     .351, -.061, .853,
  72     .401, -.147, .859,
  73     .416, .016, .850,
  74     -.067, -.796, .873,
  75     -.129, -.811, .797,
  76     -.119, -.785, .958,
  77     -.635, -.312, -.356,
  78     -.629, -.389, -.292,
  79     -.687, -.338, -.436,
  80     .321, -.919, .242,
  81     .403, -.880, .200,
  82     .294, -1.001, .193,
  83     -.404, .735, .728,
  84     -.409, .670, .803,
  85     -.324, .794, .741,
  86     .461, -.596, -.135,
  87     .411, -.595, -.221,
  88     .398, -.614, -.059,
  89     -.751, -.086, .237,
  90     -.811, -.148, .287,
  91     -.720, -.130, .152,
  92     .202, .285, -.364,
  93     .122, .345, -.377,
  94     .192, .236, -.278,
  95     -.230, -.485, .081,
  96     -.262, -.391, .071,
  97     -.306, -.548, .069,
  98     .464, -.119, .323,
  99     .497, -.080, .409,
 100     .540, -.126, .258,
 101     -.462, .107, .426,
 102     -.486, .070, .336,
 103     -.363, .123, .430,
 104     .249, -.077, -.621,
 105     .306, -.142, -.571,
 106     .233, -.110, -.714,
 107     -.922, -.164, .904,
 108     -.842, -.221, .925,
 109     -.971, -.204, .827,
 110     .382, .700, .480,
 111     .427, .610, .477,
 112     .288, .689, .513,
 113     .781, .264, -.113,
 114     .848, .203, -.070,
 115     .708, .283, -.048
 116 };
 117
 118 //! Simple cubic simulation box to use in tests
 119 matrix g_box = {{real(1.86206), 0, 0}, {0, real(1.86206), 0}, {0, 0, real(1.86206)}};
 120
 121 //! Convenience typedef
 122 typedef std::tuple<int, bool, bool, bool> SettleTestParameters;
 123
 124 /*! \brief Test fixture for testing SETTLE position updates
 125  *
 126  * \todo This also tests that if the calling code requires velocities
 127  * and virial updates, that those outputs do change, but does not test
 128  * that those changes are correct.
 129  *
 130  * \todo Only no-PBC and cubic-PBC are tested here, but the correct
 131  * function of the SIMD version of set_pbx_auic in all cases should be
 132  * tested elsewhere.
 133  */
 134 class SettleTest : public ::testing::TestWithParam<SettleTestParameters>
 135 {
 136     public:
 137         //! Updated water atom positions to constrain (DIM reals per atom)
 138         std::vector<real> updatedPositions_;
 139         //! Water atom velocities to constrain (DIM reals per atom)
 140         std::vector<real> velocities_;
 141         //! PBC option to test
 142         t_pbc             pbcNone_;
 143         //! PBC option to test
 144         t_pbc             pbcXYZ_;
 145
 146         //! Constructor
 147         SettleTest() :
 148             updatedPositions_(std::begin(g_positions), std::end(g_positions)),
 149             velocities_(updatedPositions_.size(), 0)
 150         {
 151             set_pbc(&pbcNone_, epbcNONE, g_box);
 152             set_pbc(&pbcXYZ_, epbcXYZ, g_box);
 153
 154             // Perturb the atom positions, to appear like an
 155             // "update," and where there is definitely constraining
 156             // work to do.
 157             for (size_t i = 0; i != updatedPositions_.size(); ++i)
 158             {
 159                 if (i % 4 == 0)
 160                 {
 161                     updatedPositions_[i] += 0.01;
 162                 }
 163                 else if (i % 4 == 1)
 164                 {
 165                     updatedPositions_[i] -= 0.01;
 166                 }
 167                 else if (i % 4 == 2)
 168                 {
 169                     updatedPositions_[i] += 0.02;
 170                 }
 171                 else if (i % 4 == 3)
 172                 {
 173                     updatedPositions_[i] -= 0.02;
 174                 }
 175             }
 176         }
 177 };
 178
 179 TEST_P(SettleTest, SatisfiesConstraints)
 180 {
 181     int  numSettles;
 182     bool usePbc, useVelocities, calcVirial;
 183     // Make some symbolic names for the parameter combination under
 184     // test.
 185     std::tie(numSettles, usePbc, useVelocities, calcVirial) = GetParam();
 186
 187     // Make a string that describes which parameter combination is
 188     // being tested, to help make failing tests comprehensible.
 189     std::string testDescription = formatString("while testing %d SETTLEs, %sPBC, %svelocities and %scalculating the virial",
 190                                                numSettles,
 191                                                usePbc ? "with " : "without ",
 192                                                useVelocities ? "with " : "without ",
 193                                                calcVirial ? "" : "not ");
 194
 195     const int settleType     = 0;
 196     const int atomsPerSettle = NRAL(F_SETTLE);
 197     ASSERT_LE(numSettles, updatedPositions_.size() / (atomsPerSettle * DIM)) << "cannot test that many SETTLEs " << testDescription;
 198
 199     // Set up the topology. We still have to make some raw pointers,
 200     // but they are put into scope guards for automatic cleanup.
 201     gmx_mtop_t                   *mtop;
 202     snew(mtop, 1);
 203     const unique_cptr<gmx_mtop_t> mtopGuard(mtop);
 204     mtop->nmoltype = 1;
 205     snew(mtop->moltype, mtop->nmoltype);
 206     const unique_cptr<gmx_moltype_t> moltypeGuard(mtop->moltype);
 207     mtop->nmolblock = 1;
 208     snew(mtop->molblock, mtop->nmolblock);
 209     const unique_cptr<gmx_molblock_t> molblockGuard(mtop->molblock);
 210     mtop->molblock[0].type = 0;
 211     std::vector<int>                  iatoms;
 212     for (int i = 0; i < numSettles; ++i)
 213     {
 214         iatoms.push_back(settleType);
 215         iatoms.push_back(i*atomsPerSettle+0);
 216         iatoms.push_back(i*atomsPerSettle+1);
 217         iatoms.push_back(i*atomsPerSettle+2);
 218     }
 219     mtop->moltype[0].ilist[F_SETTLE].iatoms = iatoms.data();
 220     mtop->moltype[0].ilist[F_SETTLE].nr     = iatoms.size();
 221
 222     // Set up the SETTLE parameters.
 223     mtop->ffparams.ntypes = 1;
 224     snew(mtop->ffparams.iparams, mtop->ffparams.ntypes);
 225     const unique_cptr<t_iparams> iparamsGuard(mtop->ffparams.iparams);
 226     const real                   dOH = 0.09572;
 227     const real                   dHH = 0.15139;
 228     mtop->ffparams.iparams[settleType].settle.doh = dOH;
 229     mtop->ffparams.iparams[settleType].settle.dhh = dHH;
 230
 231     // Set up the masses.
 232     t_mdatoms         mdatoms;
 233     std::vector<real> mass, massReciprocal;
 234     const real        oxygenMass = 15.9994, hydrogenMass = 1.008;
 235     for (int i = 0; i < numSettles; ++i)
 236     {
 237         mass.push_back(oxygenMass);
 238         mass.push_back(hydrogenMass);
 239         mass.push_back(hydrogenMass);
 240         massReciprocal.push_back(1./oxygenMass);
 241         massReciprocal.push_back(1./hydrogenMass);
 242         massReciprocal.push_back(1./hydrogenMass);
 243     }
 244     mdatoms.massT   = mass.data();
 245     mdatoms.invmass = massReciprocal.data();
 246     mdatoms.homenr  = numSettles * atomsPerSettle;
 247
 248     // Finally make the settle data structures
 249     gmx_settledata_t settled = settle_init(mtop);
 250     settle_set_constraints(settled, &mtop->moltype[0].ilist[F_SETTLE], &mdatoms);
 251
 252     // Copy the original positions from the array of doubles to a vector of reals
 253     std::vector<real> startingPositions(std::begin(g_positions), std::end(g_positions));
 254
 255     // Run the test
 256     bool       errorOccured;
 257     tensor     virial             = {{0, 0, 0}, {0, 0, 0}, {0, 0, 0}};
 258     int        numThreads         = 1, threadIndex = 0;
 259     const real reciprocalTimeStep = 1.0/0.002;
 260     csettle(settled, numThreads, threadIndex,
 261             usePbc ? &pbcXYZ_ : &pbcNone_,
 262             startingPositions.data(), updatedPositions_.data(), reciprocalTimeStep,
 263             useVelocities ? velocities_.data() : nullptr,
 264             calcVirial, virial, &errorOccured);
 265     settle_free(settled);
 266     EXPECT_FALSE(errorOccured) << testDescription;
 267
 268     // The necessary tolerances for the test to pass were determined
 269     // empirically. This isn't nice, but the required behaviour that
 270     // SETTLE produces constrained coordinates consistent with
 271     // sensible sampling needs to be tested at a much higher level.
 272     FloatingPointTolerance tolerance =
 273         relativeToleranceAsPrecisionDependentUlp(dOH*dOH, 80, 380);
 274
 275     // Verify the updated coordinates match the requirements
 276     int positionIndex = 0, velocityIndex = 0;
 277     for (int i = 0; i < numSettles; ++i)
 278     {
 279         rvec positionO  {
 280             updatedPositions_[positionIndex++], updatedPositions_[positionIndex++], updatedPositions_[positionIndex++]
 281         };
 282         rvec positionH1 {
 283             updatedPositions_[positionIndex++], updatedPositions_[positionIndex++], updatedPositions_[positionIndex++]
 284         };
 285         rvec positionH2 {
 286             updatedPositions_[positionIndex++], updatedPositions_[positionIndex++], updatedPositions_[positionIndex++]
 287         };
 288
 289         EXPECT_REAL_EQ_TOL(dOH*dOH, distance2(positionO, positionH1), tolerance) << formatString("for water %d ", i) << testDescription;
 290         EXPECT_REAL_EQ_TOL(dOH*dOH, distance2(positionO, positionH2), tolerance) << formatString("for water %d ", i) << testDescription;
 291         EXPECT_REAL_EQ_TOL(dHH*dHH, distance2(positionH1, positionH2), tolerance) << formatString("for water %d ", i) << testDescription;
 292
 293         // This merely tests whether the velocities were
 294         // updated from the starting values of zero (or not),
 295         // but not whether the update was correct.
 296         for (int j = 0; j < atomsPerSettle * DIM; ++j, ++velocityIndex)
 297         {
 298             EXPECT_TRUE(useVelocities == (0. != velocities_[velocityIndex])) << formatString("for water %d velocity coordinate %d ", i, j) << testDescription;
 299         }
 300     }
 301
 302     // This merely tests whether the viral was updated from
 303     // the starting values of zero (or not), but not whether
 304     // any update was correct.
 305     for (int d = 0; d < DIM; ++d)
 306     {
 307         for (int dd = 0; dd < DIM; ++dd)
 308         {
 309             EXPECT_TRUE(calcVirial == (0. != virial[d][dd])) << formatString("for virial component[%d][%d] ", d, dd) << testDescription;
 310         }
 311     }
 312 }
 313
 314 // Scan the full Cartesian product of numbers of SETTLE interactions
 315 // (4 and 17 are chosen to test cases that do and do not match
 316 // hardware SIMD widths), and whether or not we use PBC, velocities or
 317 // calculate the virial contribution.
 318 INSTANTIATE_TEST_CASE_P(WithParameters, SettleTest,
 319                             ::testing::Combine(::testing::Values(1, 4, 7),
 320                                                    ::testing::Bool(),
 321                                                    ::testing::Bool(),
 322                                                    ::testing::Bool()));
 323
 324 } // namespace
 325 } // namespace