src/gromacs/mdlib/tests/settletestdata.cpp

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  35 /*! \internal \file
  36  * \brief Defines the class that accumulates SETTLE test data.
  37  *
  38  * \author Mark Abraham  <mark.j.abraham@gmail.com>
  39  * \author Artem Zhmurov <zhmurov@gmail.com>
  40  *
  41  * \ingroup module_mdlib
  42  */
  43 #include "gmxpre.h"
  44
  45 #include "settletestdata.h"
  46
  47 #include <algorithm>
  48 #include <unordered_map>
  49 #include <vector>
  50
  51 #include <gtest/gtest.h>
  52
  53 #include "gromacs/gpu_utils/gpu_utils.h"
  54 #include "gromacs/math/paddedvector.h"
  55 #include "gromacs/math/vec.h"
  56 #include "gromacs/math/vectypes.h"
  57 #include "gromacs/mdlib/settle.h"
  58 #include "gromacs/mdtypes/mdatom.h"
  59 #include "gromacs/pbcutil/pbc.h"
  60 #include "gromacs/topology/idef.h"
  61 #include "gromacs/topology/ifunc.h"
  62 #include "gromacs/topology/topology.h"
  63 #include "gromacs/utility/smalloc.h"
  64 #include "gromacs/utility/stringutil.h"
  65 #include "gromacs/utility/unique_cptr.h"
  66
  67 #include "gromacs/mdlib/tests/watersystem.h"
  68 #include "testutils/testasserts.h"
  69
  70 namespace gmx
  71 {
  72 namespace test
  73 {
  74
  75 SettleTestData::SettleTestData(int numSettles) :
  76     numSettles_(numSettles),
  77     x_(c_waterPositions.size()),
  78     xPrime_(c_waterPositions.size()),
  79     v_(c_waterPositions.size())
  80 {
  81     // Initialize coordinates and velocities from the constant set of coordinates
  82     std::copy(c_waterPositions.begin(), c_waterPositions.end(), x_.begin());
  83     std::copy(c_waterPositions.begin(), c_waterPositions.end(), xPrime_.begin());
  84
  85     // Perturb the atom positions, to appear like an
  86     // "update," and where there is definitely constraining
  87     // work to do.
  88     const real deltas[] = { 0.01, -0.01, +0.02, -0.02 };
  89     int        i        = 0;
  90     for (auto& xPrime : xPrime_)
  91     {
  92         xPrime[XX] += deltas[i % 4];
  93         ++i;
  94         xPrime[YY] += deltas[i % 4];
  95         ++i;
  96         xPrime[ZZ] += deltas[i % 4];
  97         ++i;
  98     }
  99     std::fill(v_.begin(), v_.end(), RVec{ 0.0, 0.0, 0.0 });
 100
 101     // Set up the topology.
 102     const int settleType = 0;
 103     mtop_.moltype.resize(1);
 104     mtop_.molblock.resize(1);
 105     mtop_.molblock[0].type   = 0;
 106     std::vector<int>& iatoms = mtop_.moltype[0].ilist[F_SETTLE].iatoms;
 107     for (int i = 0; i < numSettles; ++i)
 108     {
 109         iatoms.push_back(settleType);
 110         iatoms.push_back(i * atomsPerSettle_ + 0);
 111         iatoms.push_back(i * atomsPerSettle_ + 1);
 112         iatoms.push_back(i * atomsPerSettle_ + 2);
 113     }
 114
 115     // Set up the SETTLE parameters.
 116     t_iparams iparams;
 117     iparams.settle.doh = dOH_;
 118     iparams.settle.dhh = dHH_;
 119     mtop_.ffparams.iparams.push_back(iparams);
 120
 121     // Set up the masses.
 122     mtop_.moltype[0].atoms.atom =
 123             static_cast<t_atom*>(calloc(numSettles * atomsPerSettle_, sizeof(t_atom)));
 124     numAtoms_ = numSettles * atomsPerSettle_;
 125     masses_.resize(numAtoms_);
 126     inverseMasses_.resize(numAtoms_);
 127     for (int i = 0; i < numSettles; ++i)
 128     {
 129         masses_[i * atomsPerSettle_ + 0] = oxygenMass_;
 130         masses_[i * atomsPerSettle_ + 1] = hydrogenMass_;
 131         masses_[i * atomsPerSettle_ + 2] = hydrogenMass_;
 132
 133         inverseMasses_[i * atomsPerSettle_ + 0] = 1.0 / oxygenMass_;
 134         inverseMasses_[i * atomsPerSettle_ + 1] = 1.0 / hydrogenMass_;
 135         inverseMasses_[i * atomsPerSettle_ + 2] = 1.0 / hydrogenMass_;
 136
 137         mtop_.moltype[0].atoms.atom[i * atomsPerSettle_ + 0].m = oxygenMass_;
 138         mtop_.moltype[0].atoms.atom[i * atomsPerSettle_ + 1].m = hydrogenMass_;
 139         mtop_.moltype[0].atoms.atom[i * atomsPerSettle_ + 2].m = hydrogenMass_;
 140     }
 141
 142     idef_               = std::make_unique<InteractionDefinitions>(mtop_.ffparams);
 143     idef_->il[F_SETTLE] = mtop_.moltype[0].ilist[F_SETTLE];
 144 }
 145
 146 SettleTestData::~SettleTestData() {}
 147
 148 } // namespace test
 149 } // namespace gmx