Update testing matrices and fix warnings

[gromacs.git] / src / gromacs / mdlib / force.cpp

/*
 * This file is part of the GROMACS molecular simulation package.
 *
 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
 * Copyright (c) 2001-2004, The GROMACS development team.
 * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
 * and including many others, as listed in the AUTHORS file in the
 * top-level source directory and at http://www.gromacs.org.
 *
 * GROMACS is free software; you can redistribute it and/or
 * modify it under the terms of the GNU Lesser General Public License
 * as published by the Free Software Foundation; either version 2.1
 * of the License, or (at your option) any later version.
 *
 * GROMACS is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * Lesser General Public License for more details.
 *
 * You should have received a copy of the GNU Lesser General Public
 * License along with GROMACS; if not, see
 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
 *
 * If you want to redistribute modifications to GROMACS, please
 * consider that scientific software is very special. Version
 * control is crucial - bugs must be traceable. We will be happy to
 * consider code for inclusion in the official distribution, but
 * derived work must not be called official GROMACS. Details are found
 * in the README & COPYING files - if they are missing, get the
 * official version at http://www.gromacs.org.
 *
 * To help us fund GROMACS development, we humbly ask that you cite
 * the research papers on the package. Check out http://www.gromacs.org.
 */
#include "gmxpre.h"

#include "force.h"

#include <cassert>
#include <cmath>
#include <cstring>

#include "gromacs/domdec/dlbtiming.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/ewald/ewald.h"
#include "gromacs/ewald/long_range_correction.h"
#include "gromacs/ewald/pme.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/gmxlib/nrnb.h"
#include "gromacs/listed_forces/listed_forces.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vecdump.h"
#include "gromacs/mdlib/force_flags.h"
#include "gromacs/mdlib/forcerec_threading.h"
#include "gromacs/mdlib/qmmm.h"
#include "gromacs/mdlib/rf_util.h"
#include "gromacs/mdlib/wall.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/enerdata.h"
#include "gromacs/mdtypes/forceoutput.h"
#include "gromacs/mdtypes/forcerec.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/smalloc.h"

static void clearEwaldThreadOutput(ewald_corr_thread_t *ewc_t)
{
    ewc_t->Vcorr_q        = 0;
    ewc_t->Vcorr_lj       = 0;
    ewc_t->dvdl[efptCOUL] = 0;
    ewc_t->dvdl[efptVDW]  = 0;
    clear_mat(ewc_t->vir_q);
    clear_mat(ewc_t->vir_lj);
}

static void reduceEwaldThreadOuput(int nthreads, ewald_corr_thread_t *ewc_t)
{
    ewald_corr_thread_t &dest = ewc_t[0];

    for (int t = 1; t < nthreads; t++)
    {
        dest.Vcorr_q        += ewc_t[t].Vcorr_q;
        dest.Vcorr_lj       += ewc_t[t].Vcorr_lj;
        dest.dvdl[efptCOUL] += ewc_t[t].dvdl[efptCOUL];
        dest.dvdl[efptVDW]  += ewc_t[t].dvdl[efptVDW];
        m_add(dest.vir_q,  ewc_t[t].vir_q,  dest.vir_q);
        m_add(dest.vir_lj, ewc_t[t].vir_lj, dest.vir_lj);
    }
}

void
do_force_lowlevel(t_forcerec                               *fr,
                  const t_inputrec                         *ir,
                  const t_idef                             *idef,
                  const t_commrec                          *cr,
                  const gmx_multisim_t                     *ms,
                  t_nrnb                                   *nrnb,
                  gmx_wallcycle_t                           wcycle,
                  const t_mdatoms                          *md,
                  gmx::ArrayRefWithPadding<gmx::RVec>       coordinates,
                  history_t                                *hist,
                  gmx::ForceOutputs                        *forceOutputs,
                  gmx_enerdata_t                           *enerd,
                  t_fcdata                                 *fcd,
                  const matrix                              box,
                  const real                               *lambda,
                  const t_graph                            *graph,
                  const rvec                               *mu_tot,
                  const int                                 flags,
                  const DDBalanceRegionHandler             &ddBalanceRegionHandler)
{
    // TODO: Replace all uses of x by const coordinates
    rvec *x = as_rvec_array(coordinates.paddedArrayRef().data());

    // TODO: Add the shift forces to forceOutputs
    rvec *forceForUseWithShiftForces = forceOutputs->f();
    auto &forceWithVirial            = forceOutputs->forceWithVirial();

    /* do QMMM first if requested */
    if (fr->bQMMM)
    {
        enerd->term[F_EQM] = calculate_QMMM(cr, forceForUseWithShiftForces, fr);
    }

    /* Call the short range functions all in one go. */

    if (ir->nwall)
    {
        /* foreign lambda component for walls */
        real dvdl_walls = do_walls(*ir, *fr, box, *md, x,
                                   &forceWithVirial, lambda[efptVDW],
                                   enerd->grpp.ener[egLJSR].data(), nrnb);
        enerd->dvdl_lin[efptVDW] += dvdl_walls;
    }

    /* Shift the coordinates. Must be done before listed forces and PPPM,
     * but is also necessary for SHAKE and update, therefore it can NOT
     * go when no listed forces have to be evaluated.
     *
     * The shifting and PBC code is deliberately not timed, since with
     * the Verlet scheme it only takes non-zero time with triclinic
     * boxes, and even then the time is around a factor of 100 less
     * than the next smallest counter.
     */


    /* Here sometimes we would not need to shift with NBFonly,
     * but we do so anyhow for consistency of the returned coordinates.
     */
    if (graph)
    {
        shift_self(graph, box, x);
        if (TRICLINIC(box))
        {
            inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
        }
        else
        {
            inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
        }
    }

    {
        t_pbc      pbc;

        /* Check whether we need to take into account PBC in listed interactions. */
        const auto needPbcForListedForces = fr->bMolPBC && bool(flags & GMX_FORCE_LISTED) && haveCpuListedForces(*fr, *idef, *fcd);
        if (needPbcForListedForces)
        {
            /* Since all atoms are in the rectangular or triclinic unit-cell,
             * only single box vector shifts (2 in x) are required.
             */
            set_pbc_dd(&pbc, fr->ePBC, DOMAINDECOMP(cr) ? cr->dd->nc : nullptr,
                       TRUE, box);
        }

        do_force_listed(wcycle, box, ir->fepvals, cr, ms,
                        idef, x, hist,
                        forceForUseWithShiftForces, &forceWithVirial,
                        fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
                        DOMAINDECOMP(cr) ? cr->dd->globalAtomIndices.data() : nullptr,
                        flags);
    }

    const bool computePmeOnCpu =
        (EEL_PME(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype)) &&
        thisRankHasDuty(cr, DUTY_PME) &&
        (pme_run_mode(fr->pmedata) == PmeRunMode::CPU);

    const bool haveEwaldSurfaceTerms =
        EEL_PME_EWALD(fr->ic->eeltype) &&
        (ir->ewald_geometry != eewg3D || ir->epsilon_surface != 0);

    /* Do long-range electrostatics and/or LJ-PME
     * and compute PME surface terms when necessary.
     */
    if (computePmeOnCpu ||
        fr->ic->eeltype == eelEWALD ||
        haveEwaldSurfaceTerms)
    {
        int  status            = 0;
        real Vlr_q             = 0, Vlr_lj = 0;

        /* We reduce all virial, dV/dlambda and energy contributions, except
         * for the reciprocal energies (Vlr_q, Vlr_lj) into the same struct.
         */
        ewald_corr_thread_t &ewaldOutput = fr->ewc_t[0];
        clearEwaldThreadOutput(&ewaldOutput);

        if (EEL_PME_EWALD(fr->ic->eeltype) || EVDW_PME(fr->ic->vdwtype))
        {
            /* Calculate Ewald surface terms, when necessary */
            if (haveEwaldSurfaceTerms)
            {
                wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);

                if (fr->n_tpi > 0)
                {
                    gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
                }

                int nthreads = fr->nthread_ewc;
#pragma omp parallel for num_threads(nthreads) schedule(static)
                for (int t = 0; t < nthreads; t++)
                {
                    try
                    {
                        ewald_corr_thread_t &ewc_t = fr->ewc_t[t];
                        if (t > 0)
                        {
                            clearEwaldThreadOutput(&ewc_t);
                        }

                        /* Threading is only supported with the Verlet cut-off
                         * scheme and then only single particle forces (no
                         * exclusion forces) are calculated, so we can store
                         * the forces in the normal, single forceWithVirial->force_ array.
                         */
                        ewald_LRcorrection(md->homenr, cr, nthreads, t, fr, ir,
                                           md->chargeA, md->chargeB,
                                           (md->nChargePerturbed != 0),
                                           x, box, mu_tot,
                                           ir->ewald_geometry,
                                           ir->epsilon_surface,
                                           as_rvec_array(forceWithVirial.force_.data()),
                                           &ewc_t.Vcorr_q,
                                           lambda[efptCOUL],
                                           &ewc_t.dvdl[efptCOUL]);
                    }
                    GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
                }
                if (nthreads > 1)
                {
                    reduceEwaldThreadOuput(nthreads, fr->ewc_t);
                }
                wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
            }

            if (EEL_PME_EWALD(fr->ic->eeltype) && fr->n_tpi == 0)
            {
                /* This is not in a subcounter because it takes a
                   negligible and constant-sized amount of time */
                ewaldOutput.Vcorr_q +=
                    ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
                                            &ewaldOutput.dvdl[efptCOUL],
                                            ewaldOutput.vir_q);
            }

            if (computePmeOnCpu)
            {
                /* Do reciprocal PME for Coulomb and/or LJ. */
                assert(fr->n_tpi >= 0);
                if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
                {
                    int pme_flags = GMX_PME_SPREAD | GMX_PME_SOLVE;

                    if (flags & GMX_FORCE_FORCES)
                    {
                        pme_flags |= GMX_PME_CALC_F;
                    }
                    if (flags & GMX_FORCE_VIRIAL)
                    {
                        pme_flags |= GMX_PME_CALC_ENER_VIR;
                    }
                    if (fr->n_tpi > 0)
                    {
                        /* We don't calculate f, but we do want the potential */
                        pme_flags |= GMX_PME_CALC_POT;
                    }

                    /* With domain decomposition we close the CPU side load
                     * balancing region here, because PME does global
                     * communication that acts as a global barrier.
                     */
                    ddBalanceRegionHandler.closeAfterForceComputationCpu();

                    wallcycle_start(wcycle, ewcPMEMESH);
                    status = gmx_pme_do(fr->pmedata,
                                        gmx::constArrayRefFromArray(coordinates.unpaddedConstArrayRef().data(), md->homenr - fr->n_tpi),
                                        forceWithVirial.force_,
                                        md->chargeA, md->chargeB,
                                        md->sqrt_c6A, md->sqrt_c6B,
                                        md->sigmaA, md->sigmaB,
                                        box, cr,
                                        DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
                                        DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
                                        nrnb, wcycle,
                                        ewaldOutput.vir_q, ewaldOutput.vir_lj,
                                        &Vlr_q, &Vlr_lj,
                                        lambda[efptCOUL], lambda[efptVDW],
                                        &ewaldOutput.dvdl[efptCOUL],
                                        &ewaldOutput.dvdl[efptVDW],
                                        pme_flags);
                    wallcycle_stop(wcycle, ewcPMEMESH);
                    if (status != 0)
                    {
                        gmx_fatal(FARGS, "Error %d in reciprocal PME routine", status);
                    }

                    /* We should try to do as little computation after
                     * this as possible, because parallel PME synchronizes
                     * the nodes, so we want all load imbalance of the
                     * rest of the force calculation to be before the PME
                     * call.  DD load balancing is done on the whole time
                     * of the force call (without PME).
                     */
                }
                if (fr->n_tpi > 0)
                {
                    if (EVDW_PME(ir->vdwtype))
                    {

                        gmx_fatal(FARGS, "Test particle insertion not implemented with LJ-PME");
                    }
                    /* Determine the PME grid energy of the test molecule
                     * with the PME grid potential of the other charges.
                     */
                    gmx_pme_calc_energy(fr->pmedata,
                                        coordinates.unpaddedConstArrayRef().subArray(md->homenr - fr->n_tpi, fr->n_tpi),
                                        gmx::arrayRefFromArray(md->chargeA + md->homenr - fr->n_tpi, fr->n_tpi),
                                        &Vlr_q);
                }
            }
        }

        if (fr->ic->eeltype == eelEWALD)
        {
            Vlr_q = do_ewald(ir, x, as_rvec_array(forceWithVirial.force_.data()),
                             md->chargeA, md->chargeB,
                             box, cr, md->homenr,
                             ewaldOutput.vir_q, fr->ic->ewaldcoeff_q,
                             lambda[efptCOUL], &ewaldOutput.dvdl[efptCOUL],
                             fr->ewald_table);
        }

        /* Note that with separate PME nodes we get the real energies later */
        // TODO it would be simpler if we just accumulated a single
        // long-range virial contribution.
        forceWithVirial.addVirialContribution(ewaldOutput.vir_q);
        forceWithVirial.addVirialContribution(ewaldOutput.vir_lj);
        enerd->dvdl_lin[efptCOUL] += ewaldOutput.dvdl[efptCOUL];
        enerd->dvdl_lin[efptVDW]  += ewaldOutput.dvdl[efptVDW];
        enerd->term[F_COUL_RECIP]  = Vlr_q + ewaldOutput.Vcorr_q;
        enerd->term[F_LJ_RECIP]    = Vlr_lj + ewaldOutput.Vcorr_lj;

        if (debug)
        {
            fprintf(debug, "Vlr_q = %g, Vcorr_q = %g, Vlr_corr_q = %g\n",
                    Vlr_q, ewaldOutput.Vcorr_q, enerd->term[F_COUL_RECIP]);
            pr_rvecs(debug, 0, "vir_el_recip after corr", ewaldOutput.vir_q, DIM);
            pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
            fprintf(debug, "Vlr_lj: %g, Vcorr_lj = %g, Vlr_corr_lj = %g\n",
                    Vlr_lj, ewaldOutput.Vcorr_lj, enerd->term[F_LJ_RECIP]);
            pr_rvecs(debug, 0, "vir_lj_recip after corr", ewaldOutput.vir_lj, DIM);
        }
    }

    if (debug)
    {
        print_nrnb(debug, nrnb);
    }

    if (debug)
    {
        pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
    }

}