src/gromacs/mimic/communicator.cpp

   1 /*
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  35 #include "gmxpre.h"
  36
  37 #include "communicator.h"
  38
  39 #include "config.h"
  40
  41 #include <unordered_set>
  42
  43 #include "gromacs/math/units.h"
  44 #include "gromacs/utility/fatalerror.h"
  45
  46 #if GMX_MIMIC
  47 #include <DataTypes.h>
  48 #include <MessageApi.h>
  49 #endif
  50
  51 // When not built in a configuration with QMMM support, much of this
  52 // code is unreachable by design. Tell clang not to warn about it.
  53 #pragma GCC diagnostic push
  54 #pragma GCC diagnostic ignored "-Wmissing-noreturn"
  55
  56 #if !GMX_MIMIC
  57 //! \brief Definitions to stub the ones defined in DataTypes.h
  58 constexpr int TYPE_INT = 0, TYPE_DOUBLE = 0;
  59
  60 /*! \brief Stub communication library function to call in case if
  61  * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
  62  */
  63 static void MCL_init_client(const char *) // NOLINT(readability-named-parameter)
  64 {
  65     GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  66 }
  67
  68 /*! \brief Stub communication library function to call in case if
  69  * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
  70  */
  71 static void MCL_send(void *, int, int, int) // NOLINT(readability-named-parameter)
  72 {
  73     GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  74 }
  75
  76 /*! \brief Stub communication library function to call in case if
  77  * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
  78  */
  79 static void MCL_receive(void *, int, int, int) // NOLINT(readability-named-parameter)
  80 {
  81     GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  82 }
  83
  84 /*! \brief Stub communication library function to call in case if
  85  * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
  86  */
  87 static void MCL_destroy()
  88 {
  89     GMX_RELEASE_ASSERT(GMX_MIMIC, "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  90 }
  91 #endif
  92
  93 void gmx::MimicCommunicator::init()
  94 {
  95     char path[GMX_PATH_MAX];
  96     gmx_getcwd(path, GMX_PATH_MAX);
  97     return MCL_init_client(path);
  98 }
  99
 100 void gmx::MimicCommunicator::sendInitData(gmx_mtop_t                  *mtop,
 101                                           PaddedHostVector<gmx::RVec>  coords)
 102 {
 103     MCL_send(&mtop->natoms, 1, TYPE_INT, 0);
 104     MCL_send(&mtop->atomtypes.nr, 1, TYPE_INT, 0);
 105
 106     std::vector<int>        atomTypes;
 107     std::vector<int>        nAtomsMol;
 108     std::vector<int>        idOrder;
 109     std::vector<double>     charges;
 110     std::vector<double>     masses(mtop->atomtypes.nr, -1);
 111     std::vector<int>        elements(mtop->atomtypes.nr, -1);
 112     std::vector<int>        bonds;
 113     std::vector<double>     bondLengths;
 114     std::unordered_set<int> existingTypes;
 115
 116     atomTypes.reserve(static_cast<size_t>(mtop->natoms));
 117     charges.reserve(static_cast<size_t>(mtop->natoms));
 118
 119     int offset = 0;
 120     for (const gmx_molblock_t &molblock : mtop->molblock)
 121     {
 122         gmx_moltype_t  *type     = &mtop->moltype[molblock.type];
 123         for (int mol = 0; mol < molblock.nmol; ++mol)
 124         {
 125             int      nconstr  = type->ilist[F_CONSTR].size() / 3;
 126             int      nconstrc = type->ilist[F_CONSTRNC].size() / 3;
 127             int      nsettle  = type->ilist[F_SETTLE].size() / 4;
 128
 129             for (int ncon = 0; ncon < nconstr + nconstrc; ++ncon)
 130             {
 131                 int      contype = type->ilist[F_CONSTR].iatoms[0];
 132                 int      at1     = type->ilist[F_CONSTR].iatoms[1];
 133                 int      at2     = type->ilist[F_CONSTR].iatoms[2];
 134                 bonds.push_back(offset + at1 + 1);
 135                 bonds.push_back(offset + at2 + 1);
 136                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA) / BOHR2NM);
 137             }
 138
 139             for (int ncon = 0; ncon < nsettle; ++ncon)
 140             {
 141                 t_iatom ox;
 142                 t_iatom h1;
 143                 t_iatom h2;
 144
 145                 int     contype = type->ilist[F_SETTLE].iatoms[0];
 146
 147                 ox = type->ilist[F_SETTLE].iatoms[1];
 148                 h1 = type->ilist[F_SETTLE].iatoms[2];
 149                 h2 = type->ilist[F_SETTLE].iatoms[3];
 150
 151                 bonds.push_back(offset + ox + 1);
 152                 bonds.push_back(offset + h1 + 1);
 153
 154                 bonds.push_back(offset + ox + 1);
 155                 bonds.push_back(offset + h2 + 1);
 156
 157                 bonds.push_back(offset + h1 + 1);
 158                 bonds.push_back(offset + h2 + 1);
 159                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA) / BOHR2NM);
 160                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA) / BOHR2NM);
 161                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dB) / BOHR2NM);
 162             }
 163
 164             nAtomsMol.push_back(type->atoms.nr);
 165             for (int at = 0; at < type->atoms.nr; ++at)
 166             {
 167                 int  atomtype = type->atoms.atom[at].type;
 168                 auto charge   = static_cast<double>(type->atoms.atom[at].q);
 169                 idOrder.push_back(offset + 1);
 170                 offset++;
 171                 atomTypes.push_back(atomtype + 1);
 172                 charges.push_back(charge);
 173                 if (existingTypes.insert(atomtype).second)
 174                 {
 175                     masses[atomtype]   = type->atoms.atom[at].m;
 176                     elements[atomtype] = type->atoms.atom[at].atomnumber;
 177                 }
 178             }
 179         }
 180     }
 181     // sending atom types
 182     MCL_send(&*atomTypes.begin(), mtop->natoms, TYPE_INT, 0);
 183
 184     int max_multipole_order = 0;
 185     // sending multipole orders
 186     MCL_send(&max_multipole_order, 1, TYPE_INT, 0);
 187
 188     int nMolecules = nAtomsMol.size();
 189     // sending molecule number
 190     MCL_send(&nMolecules, 1, TYPE_INT, 0);
 191
 192     // sending number of atoms per molecules
 193     MCL_send(&*nAtomsMol.begin(), nAtomsMol.size(), TYPE_INT, 0);
 194
 195     int nBonds = bonds.size() / 2;
 196     // sending number of bond constraints
 197     MCL_send(&nBonds, 1, TYPE_INT, 0);
 198
 199     // sending number of angle constraints
 200     MCL_send(&max_multipole_order, 1, TYPE_INT, 0);
 201
 202     if (nBonds > 0)
 203     {
 204         // sending bonded atoms indices
 205         MCL_send(&*bonds.begin(), bonds.size(), TYPE_INT, 0);
 206
 207         // sending bond lengths
 208         MCL_send(&*bondLengths.begin(), bondLengths.size(), TYPE_DOUBLE, 0);
 209     }
 210
 211     // sending array of atomic charges
 212     MCL_send(&*charges.begin(), mtop->natoms, TYPE_DOUBLE, 0);
 213
 214     // sending array of atomic masses
 215     MCL_send(&*masses.begin(), mtop->atomtypes.nr, TYPE_DOUBLE, 0);
 216
 217     // sending ids of atoms per molecule
 218     MCL_send(&*idOrder.begin(), idOrder.size(), TYPE_INT, 0);
 219
 220     // sending list of elements
 221     MCL_send(&*elements.begin(), mtop->atomtypes.nr, TYPE_INT, 0);
 222
 223     std::vector<double> convertedCoords;
 224     for (auto &coord : coords)
 225     {
 226         convertedCoords.push_back(static_cast<double>(coord[0]) / BOHR2NM);
 227         convertedCoords.push_back(static_cast<double>(coord[1]) / BOHR2NM);
 228         convertedCoords.push_back(static_cast<double>(coord[2]) / BOHR2NM);
 229     }
 230
 231     // sending array of coordinates
 232     MCL_send(&*convertedCoords.begin(), 3 * mtop->natoms, TYPE_DOUBLE, 0);
 233 }
 234
 235 int64_t gmx::MimicCommunicator::getStepNumber()
 236 {
 237     int steps;
 238     MCL_receive(&steps, 1, TYPE_INT, 0);
 239     return steps;
 240 }
 241
 242 void gmx::MimicCommunicator::getCoords(PaddedHostVector<RVec> *x, const int natoms)
 243 {
 244     std::vector<double> coords(natoms * 3);
 245     MCL_receive(&*coords.begin(), 3 * natoms, TYPE_DOUBLE, 0);
 246     for (int j = 0; j < natoms; ++j)
 247     {
 248         (*x)[j][0] = static_cast<real>(coords[j * 3] * BOHR2NM);
 249         (*x)[j][1] = static_cast<real>(coords[j * 3 + 1] * BOHR2NM);
 250         (*x)[j][2] = static_cast<real>(coords[j * 3 + 2] * BOHR2NM);
 251     }
 252 }
 253
 254 void gmx::MimicCommunicator::sendEnergies(real energy)
 255 {
 256     double convertedEnergy = energy / (HARTREE2KJ * AVOGADRO);
 257     MCL_send(&convertedEnergy, 1, TYPE_DOUBLE, 0);
 258 }
 259
 260 void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
 261 {
 262     std::vector<double> convertedForce;
 263     for (int j = 0; j < natoms; ++j)
 264     {
 265         convertedForce.push_back(static_cast<real>(forces[j][0]) / HARTREE_BOHR2MD);
 266         convertedForce.push_back(static_cast<real>(forces[j][1]) / HARTREE_BOHR2MD);
 267         convertedForce.push_back(static_cast<real>(forces[j][2]) / HARTREE_BOHR2MD);
 268     }
 269     MCL_send(&*convertedForce.begin(), convertedForce.size(), TYPE_DOUBLE, 0);
 270 }
 271
 272 void gmx::MimicCommunicator::finalize()
 273 {
 274     MCL_destroy();
 275 }
 276
 277 #pragma GCC diagnostic pop