src/gromacs/mdlib/force.cpp

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   8  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
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  38 #include "gmxpre.h"
  39
  40 #include "force.h"
  41
  42 #include <cassert>
  43 #include <cmath>
  44 #include <cstring>
  45
  46 #include "gromacs/domdec/dlbtiming.h"
  47 #include "gromacs/domdec/domdec.h"
  48 #include "gromacs/domdec/domdec_struct.h"
  49 #include "gromacs/ewald/ewald.h"
  50 #include "gromacs/ewald/long_range_correction.h"
  51 #include "gromacs/ewald/pme.h"
  52 #include "gromacs/gmxlib/network.h"
  53 #include "gromacs/gmxlib/nrnb.h"
  54 #include "gromacs/math/vec.h"
  55 #include "gromacs/math/vecdump.h"
  56 #include "gromacs/mdlib/forcerec_threading.h"
  57 #include "gromacs/mdtypes/commrec.h"
  58 #include "gromacs/mdtypes/enerdata.h"
  59 #include "gromacs/mdtypes/forceoutput.h"
  60 #include "gromacs/mdtypes/forcerec.h"
  61 #include "gromacs/mdtypes/inputrec.h"
  62 #include "gromacs/mdtypes/interaction_const.h"
  63 #include "gromacs/mdtypes/md_enums.h"
  64 #include "gromacs/mdtypes/mdatom.h"
  65 #include "gromacs/mdtypes/simulation_workload.h"
  66 #include "gromacs/pbcutil/ishift.h"
  67 #include "gromacs/pbcutil/pbc.h"
  68 #include "gromacs/timing/wallcycle.h"
  69 #include "gromacs/utility/exceptions.h"
  70 #include "gromacs/utility/fatalerror.h"
  71 #include "gromacs/utility/smalloc.h"
  72
  73 using gmx::ArrayRef;
  74 using gmx::RVec;
  75
  76 static void clearEwaldThreadOutput(ewald_corr_thread_t* ewc_t)
  77 {
  78     ewc_t->Vcorr_q                                        = 0;
  79     ewc_t->Vcorr_lj                                       = 0;
  80     ewc_t->dvdl[FreeEnergyPerturbationCouplingType::Coul] = 0;
  81     ewc_t->dvdl[FreeEnergyPerturbationCouplingType::Vdw]  = 0;
  82     clear_mat(ewc_t->vir_q);
  83     clear_mat(ewc_t->vir_lj);
  84 }
  85
  86 static void reduceEwaldThreadOuput(int nthreads, gmx::ArrayRef<ewald_corr_thread_t> ewc_t)
  87 {
  88     ewald_corr_thread_t& dest = ewc_t[0];
  89
  90     for (int t = 1; t < nthreads; t++)
  91     {
  92         dest.Vcorr_q += ewc_t[t].Vcorr_q;
  93         dest.Vcorr_lj += ewc_t[t].Vcorr_lj;
  94         dest.dvdl[FreeEnergyPerturbationCouplingType::Coul] +=
  95                 ewc_t[t].dvdl[FreeEnergyPerturbationCouplingType::Coul];
  96         dest.dvdl[FreeEnergyPerturbationCouplingType::Vdw] +=
  97                 ewc_t[t].dvdl[FreeEnergyPerturbationCouplingType::Vdw];
  98         m_add(dest.vir_q, ewc_t[t].vir_q, dest.vir_q);
  99         m_add(dest.vir_lj, ewc_t[t].vir_lj, dest.vir_lj);
 100     }
 101 }
 102
 103 void calculateLongRangeNonbondeds(t_forcerec*                    fr,
 104                                   const t_inputrec&              ir,
 105                                   const t_commrec*               cr,
 106                                   t_nrnb*                        nrnb,
 107                                   gmx_wallcycle_t                wcycle,
 108                                   const t_mdatoms*               md,
 109                                   gmx::ArrayRef<const RVec>      coordinates,
 110                                   gmx::ForceWithVirial*          forceWithVirial,
 111                                   gmx_enerdata_t*                enerd,
 112                                   const matrix                   box,
 113                                   gmx::ArrayRef<const real>      lambda,
 114                                   gmx::ArrayRef<const gmx::RVec> mu_tot,
 115                                   const gmx::StepWorkload&       stepWork,
 116                                   const DDBalanceRegionHandler&  ddBalanceRegionHandler)
 117 {
 118     const bool computePmeOnCpu = (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
 119                                  && thisRankHasDuty(cr, DUTY_PME)
 120                                  && (pme_run_mode(fr->pmedata) == PmeRunMode::CPU);
 121
 122     const bool haveEwaldSurfaceTerm = haveEwaldSurfaceContribution(ir);
 123
 124     /* Do long-range electrostatics and/or LJ-PME
 125      * and compute PME surface terms when necessary.
 126      */
 127     if ((computePmeOnCpu || fr->ic->eeltype == CoulombInteractionType::Ewald || haveEwaldSurfaceTerm)
 128         && stepWork.computeNonbondedForces)
 129     {
 130         int  status = 0;
 131         real Vlr_q = 0, Vlr_lj = 0;
 132
 133         /* We reduce all virial, dV/dlambda and energy contributions, except
 134          * for the reciprocal energies (Vlr_q, Vlr_lj) into the same struct.
 135          */
 136         ewald_corr_thread_t& ewaldOutput = fr->ewc_t[0];
 137         clearEwaldThreadOutput(&ewaldOutput);
 138
 139         if (EEL_PME_EWALD(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
 140         {
 141             /* Calculate the Ewald surface force and energy contributions, when necessary */
 142             if (haveEwaldSurfaceTerm)
 143             {
 144                 wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
 145
 146                 int nthreads = fr->nthread_ewc;
 147 #pragma omp parallel for num_threads(nthreads) schedule(static)
 148                 for (int t = 0; t < nthreads; t++)
 149                 {
 150                     try
 151                     {
 152                         ewald_corr_thread_t& ewc_t = fr->ewc_t[t];
 153                         if (t > 0)
 154                         {
 155                             clearEwaldThreadOutput(&ewc_t);
 156                         }
 157
 158                         /* Threading is only supported with the Verlet cut-off
 159                          * scheme and then only single particle forces (no
 160                          * exclusion forces) are calculated, so we can store
 161                          * the forces in the normal, single forceWithVirial->force_ array.
 162                          */
 163                         ewald_LRcorrection(
 164                                 md->homenr,
 165                                 cr,
 166                                 nthreads,
 167                                 t,
 168                                 *fr,
 169                                 ir,
 170                                 gmx::constArrayRefFromArray(md->chargeA, md->nr),
 171                                 gmx::constArrayRefFromArray(md->chargeB, md->nr),
 172                                 (md->nChargePerturbed != 0),
 173                                 coordinates,
 174                                 box,
 175                                 mu_tot,
 176                                 forceWithVirial->force_,
 177                                 &ewc_t.Vcorr_q,
 178                                 lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
 179                                 &ewc_t.dvdl[FreeEnergyPerturbationCouplingType::Coul]);
 180                     }
 181                     GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
 182                 }
 183                 if (nthreads > 1)
 184                 {
 185                     reduceEwaldThreadOuput(nthreads, fr->ewc_t);
 186                 }
 187                 wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
 188             }
 189
 190             if (EEL_PME_EWALD(fr->ic->eeltype) && fr->n_tpi == 0)
 191             {
 192                 /* This is not in a subcounter because it takes a
 193                    negligible and constant-sized amount of time */
 194                 ewaldOutput.Vcorr_q += ewald_charge_correction(
 195                         cr,
 196                         fr,
 197                         lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
 198                         box,
 199                         &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul],
 200                         ewaldOutput.vir_q);
 201             }
 202
 203             if (computePmeOnCpu)
 204             {
 205                 /* Do reciprocal PME for Coulomb and/or LJ. */
 206                 assert(fr->n_tpi >= 0);
 207                 if (fr->n_tpi == 0 || stepWork.stateChanged)
 208                 {
 209                     /* With domain decomposition we close the CPU side load
 210                      * balancing region here, because PME does global
 211                      * communication that acts as a global barrier.
 212                      */
 213                     ddBalanceRegionHandler.closeAfterForceComputationCpu();
 214
 215                     wallcycle_start(wcycle, ewcPMEMESH);
 216                     status = gmx_pme_do(
 217                             fr->pmedata,
 218                             gmx::constArrayRefFromArray(coordinates.data(), md->homenr - fr->n_tpi),
 219                             forceWithVirial->force_,
 220                             gmx::constArrayRefFromArray(md->chargeA, md->nr),
 221                             gmx::constArrayRefFromArray(md->chargeB, md->nr),
 222                             gmx::constArrayRefFromArray(md->sqrt_c6A, md->nr),
 223                             gmx::constArrayRefFromArray(md->sqrt_c6B, md->nr),
 224                             gmx::constArrayRefFromArray(md->sigmaA, md->nr),
 225                             gmx::constArrayRefFromArray(md->sigmaB, md->nr),
 226                             box,
 227                             cr,
 228                             DOMAINDECOMP(cr) ? dd_pme_maxshift_x(*cr->dd) : 0,
 229                             DOMAINDECOMP(cr) ? dd_pme_maxshift_y(*cr->dd) : 0,
 230                             nrnb,
 231                             wcycle,
 232                             ewaldOutput.vir_q,
 233                             ewaldOutput.vir_lj,
 234                             &Vlr_q,
 235                             &Vlr_lj,
 236                             lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
 237                             lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Vdw)],
 238                             &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul],
 239                             &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Vdw],
 240                             stepWork);
 241                     wallcycle_stop(wcycle, ewcPMEMESH);
 242                     if (status != 0)
 243                     {
 244                         gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
 245                     }
 246
 247                     /* We should try to do as little computation after
 248                      * this as possible, because parallel PME synchronizes
 249                      * the nodes, so we want all load imbalance of the
 250                      * rest of the force calculation to be before the PME
 251                      * call.  DD load balancing is done on the whole time
 252                      * of the force call (without PME).
 253                      */
 254                 }
 255                 if (fr->n_tpi > 0)
 256                 {
 257                     /* Determine the PME grid energy of the test molecule
 258                      * with the PME grid potential of the other charges.
 259                      */
 260                     gmx_pme_calc_energy(
 261                             fr->pmedata,
 262                             coordinates.subArray(md->homenr - fr->n_tpi, fr->n_tpi),
 263                             gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
 264                             &Vlr_q);
 265                 }
 266             }
 267         }
 268
 269         if (fr->ic->eeltype == CoulombInteractionType::Ewald)
 270         {
 271             Vlr_q = do_ewald(ir,
 272                              coordinates,
 273                              forceWithVirial->force_,
 274                              gmx::arrayRefFromArray(md->chargeA, md->nr),
 275                              gmx::arrayRefFromArray(md->chargeB, md->nr),
 276                              box,
 277                              cr,
 278                              md->homenr,
 279                              ewaldOutput.vir_q,
 280                              fr->ic->ewaldcoeff_q,
 281                              lambda[static_cast<int>(FreeEnergyPerturbationCouplingType::Coul)],
 282                              &ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul],
 283                              fr->ewald_table.get());
 284         }
 285
 286         /* Note that with separate PME nodes we get the real energies later */
 287         // TODO it would be simpler if we just accumulated a single
 288         // long-range virial contribution.
 289         forceWithVirial->addVirialContribution(ewaldOutput.vir_q);
 290         forceWithVirial->addVirialContribution(ewaldOutput.vir_lj);
 291         enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Coul] +=
 292                 ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Coul];
 293         enerd->dvdl_lin[FreeEnergyPerturbationCouplingType::Vdw] +=
 294                 ewaldOutput.dvdl[FreeEnergyPerturbationCouplingType::Vdw];
 295         enerd->term[F_COUL_RECIP] = Vlr_q + ewaldOutput.Vcorr_q;
 296         enerd->term[F_LJ_RECIP]   = Vlr_lj + ewaldOutput.Vcorr_lj;
 297
 298         if (debug)
 299         {
 300             fprintf(debug,
 301                     "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
 302                     Vlr_q,
 303                     ewaldOutput.Vcorr_q,
 304                     enerd->term[F_COUL_RECIP]);
 305             pr_rvecs(debug, 0, "vir_el_recip after corr", ewaldOutput.vir_q, DIM);
 306             fprintf(debug,
 307                     "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
 308                     Vlr_lj,
 309                     ewaldOutput.Vcorr_lj,
 310                     enerd->term[F_LJ_RECIP]);
 311             pr_rvecs(debug, 0, "vir_lj_recip after corr", ewaldOutput.vir_lj, DIM);
 312         }
 313     }
 314
 315     if (debug)
 316     {
 317         print_nrnb(debug, nrnb);
 318     }
 319 }