コード例 #1
0
void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inputrec *ir,
                     t_forcerec *fr, gmx_ekindata_t *ekind,
                     t_state *state, t_state *state_global, t_mdatoms *mdatoms,
                     t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
                     gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
                     tensor pres, rvec mu_tot, gmx_constr_t constr,
                     globsig_t *gs, gmx_bool bInterSimGS,
                     matrix box, gmx_mtop_t *top_global,
                     gmx_bool *bSumEkinhOld, int flags)
{
    int      i, gsi;
    real     gs_buf[eglsNR];
    tensor   corr_vir, corr_pres;
    gmx_bool bEner, bPres, bTemp;
    gmx_bool bStopCM, bGStat,
             bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
    real     prescorr, enercorr, dvdlcorr, dvdl_ekin;

    /* translate CGLO flags to gmx_booleans */
    bStopCM       = flags & CGLO_STOPCM;
    bGStat        = flags & CGLO_GSTAT;
    bReadEkin     = (flags & CGLO_READEKIN);
    bScaleEkin    = (flags & CGLO_SCALEEKIN);
    bEner         = flags & CGLO_ENERGY;
    bTemp         = flags & CGLO_TEMPERATURE;
    bPres         = (flags & CGLO_PRESSURE);
    bConstrain    = (flags & CGLO_CONSTRAINT);

    /* we calculate a full state kinetic energy either with full-step velocity verlet
       or half step where we need the pressure */

    bEkinAveVel = (ir->eI == eiVV || (ir->eI == eiVVAK && bPres) || bReadEkin);

    /* in initalization, it sums the shake virial in vv, and to
       sums ekinh_old in leapfrog (or if we are calculating ekinh_old) for other reasons */

    /* ########## Kinetic energy  ############## */

    if (bTemp)
    {
        /* Non-equilibrium MD: this is parallellized, but only does communication
         * when there really is NEMD.
         */

        if (PAR(cr) && (ekind->bNEMD))
        {
            accumulate_u(cr, &(ir->opts), ekind);
        }
        debug_gmx();
        if (bReadEkin)
        {
            restore_ekinstate_from_state(cr, ekind, &state_global->ekinstate);
        }
        else
        {
            calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
        }

        debug_gmx();
    }

    /* Calculate center of mass velocity if necessary, also parallellized */
    if (bStopCM)
    {
        calc_vcm_grp(0, mdatoms->homenr, mdatoms,
                     state->x, state->v, vcm);
    }

    if (bTemp || bStopCM || bPres || bEner || bConstrain)
    {
        if (!bGStat)
        {
            /* We will not sum ekinh_old,
             * so signal that we still have to do it.
             */
            *bSumEkinhOld = TRUE;

        }
        else
        {
            if (gs != NULL)
            {
                for (i = 0; i < eglsNR; i++)
                {
                    gs_buf[i] = gs->sig[i];
                }
            }
            if (PAR(cr))
            {
                wallcycle_start(wcycle, ewcMoveE);
                global_stat(fplog, gstat, cr, enerd, force_vir, shake_vir, mu_tot,
                            ir, ekind, constr, bStopCM ? vcm : NULL,
                            gs != NULL ? eglsNR : 0, gs_buf,
                            top_global, state,
                            *bSumEkinhOld, flags);
                wallcycle_stop(wcycle, ewcMoveE);
            }
            if (gs != NULL)
            {
                if (MULTISIM(cr) && bInterSimGS)
                {
                    if (MASTER(cr))
                    {
                        /* Communicate the signals between the simulations */
                        gmx_sum_sim(eglsNR, gs_buf, cr->ms);
                    }
                    /* Communicate the signals form the master to the others */
                    gmx_bcast(eglsNR*sizeof(gs_buf[0]), gs_buf, cr);
                }
                for (i = 0; i < eglsNR; i++)
                {
                    if (bInterSimGS || gs_simlocal[i])
                    {
                        /* Set the communicated signal only when it is non-zero,
                         * since signals might not be processed at each MD step.
                         */
                        gsi = (gs_buf[i] >= 0 ?
                               (int)(gs_buf[i] + 0.5) :
                               (int)(gs_buf[i] - 0.5));
                        if (gsi != 0)
                        {
                            gs->set[i] = gsi;
                        }
                        /* Turn off the local signal */
                        gs->sig[i] = 0;
                    }
                }
            }
            *bSumEkinhOld = FALSE;
        }
    }

    if (!ekind->bNEMD && debug && bTemp && (vcm->nr > 0))
    {
        correct_ekin(debug,
                     0, mdatoms->homenr,
                     state->v, vcm->group_p[0],
                     mdatoms->massT, mdatoms->tmass, ekind->ekin);
    }

    /* Do center of mass motion removal */
    if (bStopCM)
    {
        check_cm_grp(fplog, vcm, ir, 1);
        do_stopcm_grp(0, mdatoms->homenr, mdatoms->cVCM,
                      state->x, state->v, vcm);
        inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
    }

    if (bEner)
    {
        /* Calculate the amplitude of the cosine velocity profile */
        ekind->cosacc.vcos = ekind->cosacc.mvcos/mdatoms->tmass;
    }

    if (bTemp)
    {
        /* Sum the kinetic energies of the groups & calc temp */
        /* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with IR_NPT_TROTTER */
        /* three maincase:  VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).
           Leap with AveVel is not supported; it's not clear that it will actually work.
           bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
           If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
         */
        enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
                                       bEkinAveVel, bScaleEkin);
        enerd->dvdl_lin[efptMASS] = (double) dvdl_ekin;

        enerd->term[F_EKIN] = trace(ekind->ekin);
    }

    /* ##########  Long range energy information ###### */

    if (bEner || bPres || bConstrain)
    {
        calc_dispcorr(ir, fr, top_global->natoms, box, state->lambda[efptVDW],
                      corr_pres, corr_vir, &prescorr, &enercorr, &dvdlcorr);
    }

    if (bEner)
    {
        enerd->term[F_DISPCORR]  = enercorr;
        enerd->term[F_EPOT]     += enercorr;
        enerd->term[F_DVDL_VDW] += dvdlcorr;
    }

    /* ########## Now pressure ############## */
    if (bPres || bConstrain)
    {

        m_add(force_vir, shake_vir, total_vir);

        /* Calculate pressure and apply LR correction if PPPM is used.
         * Use the box from last timestep since we already called update().
         */

        enerd->term[F_PRES] = calc_pres(fr->ePBC, ir->nwall, box, ekind->ekin, total_vir, pres);

        /* Calculate long range corrections to pressure and energy */
        /* this adds to enerd->term[F_PRES] and enerd->term[F_ETOT],
           and computes enerd->term[F_DISPCORR].  Also modifies the
           total_vir and pres tesors */

        m_add(total_vir, corr_vir, total_vir);
        m_add(pres, corr_pres, pres);
        enerd->term[F_PDISPCORR] = prescorr;
        enerd->term[F_PRES]     += prescorr;
    }
}
コード例 #2
0
/* TODO Specialize this routine into init-time and loop-time versions?
   e.g. bReadEkin is only true when restoring from checkpoint */
void compute_globals(FILE *fplog, gmx_global_stat *gstat, t_commrec *cr, t_inputrec *ir,
                     t_forcerec *fr, gmx_ekindata_t *ekind,
                     t_state *state, t_mdatoms *mdatoms,
                     t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
                     gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
                     tensor pres, rvec mu_tot, gmx_constr_t constr,
                     gmx::SimulationSignaller *signalCoordinator,
                     matrix box, int *totalNumberOfBondedInteractions,
                     gmx_bool *bSumEkinhOld, int flags)
{
    tensor   corr_vir, corr_pres;
    gmx_bool bEner, bPres, bTemp;
    gmx_bool bStopCM, bGStat,
             bReadEkin, bEkinAveVel, bScaleEkin, bConstrain;
    real     prescorr, enercorr, dvdlcorr, dvdl_ekin;

    /* translate CGLO flags to gmx_booleans */
    bStopCM       = flags & CGLO_STOPCM;
    bGStat        = flags & CGLO_GSTAT;
    bReadEkin     = (flags & CGLO_READEKIN);
    bScaleEkin    = (flags & CGLO_SCALEEKIN);
    bEner         = flags & CGLO_ENERGY;
    bTemp         = flags & CGLO_TEMPERATURE;
    bPres         = (flags & CGLO_PRESSURE);
    bConstrain    = (flags & CGLO_CONSTRAINT);

    /* we calculate a full state kinetic energy either with full-step velocity verlet
       or half step where we need the pressure */

    bEkinAveVel = (ir->eI == eiVV || (ir->eI == eiVVAK && bPres) || bReadEkin);

    /* in initalization, it sums the shake virial in vv, and to
       sums ekinh_old in leapfrog (or if we are calculating ekinh_old) for other reasons */

    /* ########## Kinetic energy  ############## */

    if (bTemp)
    {
        /* Non-equilibrium MD: this is parallellized, but only does communication
         * when there really is NEMD.
         */

        if (PAR(cr) && (ekind->bNEMD))
        {
            accumulate_u(cr, &(ir->opts), ekind);
        }
        if (!bReadEkin)
        {
            calc_ke_part(state, &(ir->opts), mdatoms, ekind, nrnb, bEkinAveVel);
        }
    }

    /* Calculate center of mass velocity if necessary, also parallellized */
    if (bStopCM)
    {
        calc_vcm_grp(0, mdatoms->homenr, mdatoms,
                     state->x, state->v, vcm);
    }

    if (bTemp || bStopCM || bPres || bEner || bConstrain)
    {
        if (!bGStat)
        {
            /* We will not sum ekinh_old,
             * so signal that we still have to do it.
             */
            *bSumEkinhOld = TRUE;

        }
        else
        {
            gmx::ArrayRef<real> signalBuffer = signalCoordinator->getCommunicationBuffer();
            if (PAR(cr))
            {
                wallcycle_start(wcycle, ewcMoveE);
                global_stat(gstat, cr, enerd, force_vir, shake_vir, mu_tot,
                            ir, ekind, constr, bStopCM ? vcm : NULL,
                            signalBuffer.size(), signalBuffer.data(),
                            totalNumberOfBondedInteractions,
                            *bSumEkinhOld, flags);
                wallcycle_stop(wcycle, ewcMoveE);
            }
            signalCoordinator->finalizeSignals();
            *bSumEkinhOld = FALSE;
        }
    }

    if (!ekind->bNEMD && debug && bTemp && (vcm->nr > 0))
    {
        correct_ekin(debug,
                     0, mdatoms->homenr,
                     state->v, vcm->group_p[0],
                     mdatoms->massT, mdatoms->tmass, ekind->ekin);
    }

    /* Do center of mass motion removal */
    if (bStopCM)
    {
        check_cm_grp(fplog, vcm, ir, 1);
        do_stopcm_grp(0, mdatoms->homenr, mdatoms->cVCM,
                      state->x, state->v, vcm);
        inc_nrnb(nrnb, eNR_STOPCM, mdatoms->homenr);
    }

    if (bEner)
    {
        /* Calculate the amplitude of the cosine velocity profile */
        ekind->cosacc.vcos = ekind->cosacc.mvcos/mdatoms->tmass;
    }

    if (bTemp)
    {
        /* Sum the kinetic energies of the groups & calc temp */
        /* compute full step kinetic energies if vv, or if vv-avek and we are computing the pressure with inputrecNptTrotter */
        /* three maincase:  VV with AveVel (md-vv), vv with AveEkin (md-vv-avek), leap with AveEkin (md).
           Leap with AveVel is not supported; it's not clear that it will actually work.
           bEkinAveVel: If TRUE, we simply multiply ekin by ekinscale to get a full step kinetic energy.
           If FALSE, we average ekinh_old and ekinh*ekinscale_nhc to get an averaged half step kinetic energy.
         */
        enerd->term[F_TEMP] = sum_ekin(&(ir->opts), ekind, &dvdl_ekin,
                                       bEkinAveVel, bScaleEkin);
        enerd->dvdl_lin[efptMASS] = (double) dvdl_ekin;

        enerd->term[F_EKIN] = trace(ekind->ekin);
    }

    /* ##########  Long range energy information ###### */

    if (bEner || bPres || bConstrain)
    {
        calc_dispcorr(ir, fr, box, state->lambda[efptVDW],
                      corr_pres, corr_vir, &prescorr, &enercorr, &dvdlcorr);
    }

    if (bEner)
    {
        enerd->term[F_DISPCORR]  = enercorr;
        enerd->term[F_EPOT]     += enercorr;
        enerd->term[F_DVDL_VDW] += dvdlcorr;
    }

    /* ########## Now pressure ############## */
    if (bPres || bConstrain)
    {

        m_add(force_vir, shake_vir, total_vir);

        /* Calculate pressure and apply LR correction if PPPM is used.
         * Use the box from last timestep since we already called update().
         */

        enerd->term[F_PRES] = calc_pres(fr->ePBC, ir->nwall, box, ekind->ekin, total_vir, pres);

        /* Calculate long range corrections to pressure and energy */
        /* this adds to enerd->term[F_PRES] and enerd->term[F_ETOT],
           and computes enerd->term[F_DISPCORR].  Also modifies the
           total_vir and pres tesors */

        m_add(total_vir, corr_vir, total_vir);
        m_add(pres, corr_pres, pres);
        enerd->term[F_PDISPCORR] = prescorr;
        enerd->term[F_PRES]     += prescorr;
    }
}