src/gromacs/mdlib/tests/settle.cpp

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