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(
  66             GMX_MIMIC,
  67             "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  68 }
  69
  70 /*! \brief Stub communication library function to call in case if
  71  * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
  72  */
  73 static void MCL_send(void*, int, int, int) // NOLINT(readability-named-parameter)
  74 {
  75     GMX_RELEASE_ASSERT(
  76             GMX_MIMIC,
  77             "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  78 }
  79
  80 /*! \brief Stub communication library function to call in case if
  81  * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
  82  */
  83 static void MCL_receive(void*, int, int, int) // NOLINT(readability-named-parameter)
  84 {
  85     GMX_RELEASE_ASSERT(
  86             GMX_MIMIC,
  87             "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  88 }
  89
  90 /*! \brief Stub communication library function to call in case if
  91  * GROMACS is compiled without MiMiC. Calling causes GROMACS to exit!
  92  */
  93 static void MCL_destroy()
  94 {
  95     GMX_RELEASE_ASSERT(
  96             GMX_MIMIC,
  97             "GROMACS is compiled without MiMiC support! Please, recompile with -DGMX_MIMIC=ON");
  98 }
  99 #endif
 100
 101 void gmx::MimicCommunicator::init()
 102 {
 103     char path[GMX_PATH_MAX];
 104     gmx_getcwd(path, GMX_PATH_MAX);
 105     MCL_init_client(path);
 106 }
 107
 108 void gmx::MimicCommunicator::sendInitData(gmx_mtop_t* mtop, PaddedHostVector<gmx::RVec> coords)
 109 {
 110     MCL_send(&mtop->natoms, 1, TYPE_INT, 0);
 111     MCL_send(&mtop->atomtypes.nr, 1, TYPE_INT, 0);
 112
 113     std::vector<int>        atomTypes;
 114     std::vector<int>        nAtomsMol;
 115     std::vector<int>        idOrder;
 116     std::vector<double>     charges;
 117     std::vector<double>     masses(mtop->atomtypes.nr, -1);
 118     std::vector<int>        elements(mtop->atomtypes.nr, -1);
 119     std::vector<int>        bonds;
 120     std::vector<double>     bondLengths;
 121     std::unordered_set<int> existingTypes;
 122
 123     atomTypes.reserve(static_cast<size_t>(mtop->natoms));
 124     charges.reserve(static_cast<size_t>(mtop->natoms));
 125
 126     int offset = 0;
 127     for (const gmx_molblock_t& molblock : mtop->molblock)
 128     {
 129         gmx_moltype_t* type = &mtop->moltype[molblock.type];
 130         for (int mol = 0; mol < molblock.nmol; ++mol)
 131         {
 132             int nconstr  = type->ilist[F_CONSTR].size() / 3;
 133             int nconstrc = type->ilist[F_CONSTRNC].size() / 3;
 134             int nsettle  = type->ilist[F_SETTLE].size() / 4;
 135
 136             for (int ncon = 0; ncon < nconstr + nconstrc; ++ncon)
 137             {
 138                 int contype = type->ilist[F_CONSTR].iatoms[0];
 139                 int at1     = type->ilist[F_CONSTR].iatoms[1];
 140                 int at2     = type->ilist[F_CONSTR].iatoms[2];
 141                 bonds.push_back(offset + at1 + 1);
 142                 bonds.push_back(offset + at2 + 1);
 143                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA)
 144                                       / BOHR2NM);
 145             }
 146
 147             for (int ncon = 0; ncon < nsettle; ++ncon)
 148             {
 149                 t_iatom ox;
 150                 t_iatom h1;
 151                 t_iatom h2;
 152
 153                 int contype = type->ilist[F_SETTLE].iatoms[0];
 154
 155                 ox = type->ilist[F_SETTLE].iatoms[1];
 156                 h1 = type->ilist[F_SETTLE].iatoms[2];
 157                 h2 = type->ilist[F_SETTLE].iatoms[3];
 158
 159                 bonds.push_back(offset + ox + 1);
 160                 bonds.push_back(offset + h1 + 1);
 161
 162                 bonds.push_back(offset + ox + 1);
 163                 bonds.push_back(offset + h2 + 1);
 164
 165                 bonds.push_back(offset + h1 + 1);
 166                 bonds.push_back(offset + h2 + 1);
 167                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA)
 168                                       / BOHR2NM);
 169                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dA)
 170                                       / BOHR2NM);
 171                 bondLengths.push_back(static_cast<double>(mtop->ffparams.iparams[contype].constr.dB)
 172                                       / BOHR2NM);
 173             }
 174
 175             nAtomsMol.push_back(type->atoms.nr);
 176             for (int at = 0; at < type->atoms.nr; ++at)
 177             {
 178                 int  atomtype = type->atoms.atom[at].type;
 179                 auto charge   = static_cast<double>(type->atoms.atom[at].q);
 180                 idOrder.push_back(offset + 1);
 181                 offset++;
 182                 atomTypes.push_back(atomtype + 1);
 183                 charges.push_back(charge);
 184                 if (existingTypes.insert(atomtype).second)
 185                 {
 186                     masses[atomtype]   = type->atoms.atom[at].m;
 187                     elements[atomtype] = type->atoms.atom[at].atomnumber;
 188                 }
 189             }
 190         }
 191     }
 192     // sending atom types
 193     MCL_send(&*atomTypes.begin(), mtop->natoms, TYPE_INT, 0);
 194
 195     int max_multipole_order = 0;
 196     // sending multipole orders
 197     MCL_send(&max_multipole_order, 1, TYPE_INT, 0);
 198
 199     int nMolecules = nAtomsMol.size();
 200     // sending molecule number
 201     MCL_send(&nMolecules, 1, TYPE_INT, 0);
 202
 203     // sending number of atoms per molecules
 204     MCL_send(&*nAtomsMol.begin(), nAtomsMol.size(), TYPE_INT, 0);
 205
 206     int nBonds = bonds.size() / 2;
 207     // sending number of bond constraints
 208     MCL_send(&nBonds, 1, TYPE_INT, 0);
 209
 210     // sending number of angle constraints
 211     MCL_send(&max_multipole_order, 1, TYPE_INT, 0);
 212
 213     if (nBonds > 0)
 214     {
 215         // sending bonded atoms indices
 216         MCL_send(&*bonds.begin(), bonds.size(), TYPE_INT, 0);
 217
 218         // sending bond lengths
 219         MCL_send(&*bondLengths.begin(), bondLengths.size(), TYPE_DOUBLE, 0);
 220     }
 221
 222     // sending array of atomic charges
 223     MCL_send(&*charges.begin(), mtop->natoms, TYPE_DOUBLE, 0);
 224
 225     // sending array of atomic masses
 226     MCL_send(&*masses.begin(), mtop->atomtypes.nr, TYPE_DOUBLE, 0);
 227
 228     // sending ids of atoms per molecule
 229     MCL_send(&*idOrder.begin(), idOrder.size(), TYPE_INT, 0);
 230
 231     // sending list of elements
 232     MCL_send(&*elements.begin(), mtop->atomtypes.nr, TYPE_INT, 0);
 233
 234     std::vector<double> convertedCoords;
 235     for (auto& coord : coords)
 236     {
 237         convertedCoords.push_back(static_cast<double>(coord[0]) / BOHR2NM);
 238         convertedCoords.push_back(static_cast<double>(coord[1]) / BOHR2NM);
 239         convertedCoords.push_back(static_cast<double>(coord[2]) / BOHR2NM);
 240     }
 241
 242     // sending array of coordinates
 243     MCL_send(&*convertedCoords.begin(), 3 * mtop->natoms, TYPE_DOUBLE, 0);
 244 }
 245
 246 int64_t gmx::MimicCommunicator::getStepNumber()
 247 {
 248     int steps;
 249     MCL_receive(&steps, 1, TYPE_INT, 0);
 250     return steps;
 251 }
 252
 253 void gmx::MimicCommunicator::getCoords(PaddedHostVector<RVec>* x, const int natoms)
 254 {
 255     std::vector<double> coords(natoms * 3);
 256     MCL_receive(&*coords.begin(), 3 * natoms, TYPE_DOUBLE, 0);
 257     for (int j = 0; j < natoms; ++j)
 258     {
 259         (*x)[j][0] = static_cast<real>(coords[j * 3] * BOHR2NM);
 260         (*x)[j][1] = static_cast<real>(coords[j * 3 + 1] * BOHR2NM);
 261         (*x)[j][2] = static_cast<real>(coords[j * 3 + 2] * BOHR2NM);
 262     }
 263 }
 264
 265 void gmx::MimicCommunicator::sendEnergies(real energy)
 266 {
 267     double convertedEnergy = energy / (HARTREE2KJ * AVOGADRO);
 268     MCL_send(&convertedEnergy, 1, TYPE_DOUBLE, 0);
 269 }
 270
 271 void gmx::MimicCommunicator::sendForces(gmx::ArrayRef<gmx::RVec> forces, int natoms)
 272 {
 273     std::vector<double> convertedForce;
 274     for (int j = 0; j < natoms; ++j)
 275     {
 276         convertedForce.push_back(static_cast<real>(forces[j][0]) / HARTREE_BOHR2MD);
 277         convertedForce.push_back(static_cast<real>(forces[j][1]) / HARTREE_BOHR2MD);
 278         convertedForce.push_back(static_cast<real>(forces[j][2]) / HARTREE_BOHR2MD);
 279     }
 280     MCL_send(&*convertedForce.begin(), convertedForce.size(), TYPE_DOUBLE, 0);
 281 }
 282
 283 void gmx::MimicCommunicator::finalize()
 284 {
 285     MCL_destroy();
 286 }
 287
 288 #pragma GCC diagnostic pop