Esempio n. 1
0
double do_tpi(FILE *fplog, t_commrec *cr,
              int nfile, const t_filenm fnm[],
              const output_env_t oenv, gmx_bool bVerbose, gmx_bool gmx_unused bCompact,
              int gmx_unused nstglobalcomm,
              gmx_vsite_t gmx_unused *vsite, gmx_constr_t gmx_unused constr,
              int gmx_unused stepout,
              t_inputrec *inputrec,
              gmx_mtop_t *top_global, t_fcdata *fcd,
              t_state *state,
              t_mdatoms *mdatoms,
              t_nrnb *nrnb, gmx_wallcycle_t wcycle,
              gmx_edsam_t gmx_unused ed,
              t_forcerec *fr,
              int gmx_unused repl_ex_nst, int gmx_unused repl_ex_nex, int gmx_unused repl_ex_seed,
              gmx_membed_t gmx_unused membed,
              real gmx_unused cpt_period, real gmx_unused max_hours,
              const char gmx_unused *deviceOptions,
              int gmx_unused imdport,
              unsigned long gmx_unused Flags,
              gmx_walltime_accounting_t walltime_accounting)
{
    const char     *TPI = "Test Particle Insertion";
    gmx_localtop_t *top;
    gmx_groups_t   *groups;
    gmx_enerdata_t *enerd;
    rvec           *f;
    real            lambda, t, temp, beta, drmax, epot;
    double          embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
    t_trxstatus    *status;
    t_trxframe      rerun_fr;
    gmx_bool        bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS;
    tensor          force_vir, shake_vir, vir, pres;
    int             cg_tp, a_tp0, a_tp1, ngid, gid_tp, nener, e;
    rvec           *x_mol;
    rvec            mu_tot, x_init, dx, x_tp;
    int             nnodes, frame;
    gmx_int64_t     frame_step_prev, frame_step;
    gmx_int64_t     nsteps, stepblocksize = 0, step;
    gmx_int64_t     rnd_count_stride, rnd_count;
    gmx_int64_t     seed;
    double          rnd[4];
    int             i, start, end;
    FILE           *fp_tpi = NULL;
    char           *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
    double          dbl, dump_ener;
    gmx_bool        bCavity;
    int             nat_cavity  = 0, d;
    real           *mass_cavity = NULL, mass_tot;
    int             nbin;
    double          invbinw, *bin, refvolshift, logV, bUlogV;
    real            dvdl, prescorr, enercorr, dvdlcorr;
    gmx_bool        bEnergyOutOfBounds;
    const char     *tpid_leg[2] = {"direct", "reweighted"};

    /* Since there is no upper limit to the insertion energies,
     * we need to set an upper limit for the distribution output.
     */
    real bU_bin_limit      = 50;
    real bU_logV_bin_limit = bU_bin_limit + 10;

    nnodes = cr->nnodes;

    top = gmx_mtop_generate_local_top(top_global, inputrec);

    groups = &top_global->groups;

    bCavity = (inputrec->eI == eiTPIC);
    if (bCavity)
    {
        ptr = getenv("GMX_TPIC_MASSES");
        if (ptr == NULL)
        {
            nat_cavity = 1;
        }
        else
        {
            /* Read (multiple) masses from env var GMX_TPIC_MASSES,
             * The center of mass of the last atoms is then used for TPIC.
             */
            nat_cavity = 0;
            while (sscanf(ptr, "%lf%n", &dbl, &i) > 0)
            {
                srenew(mass_cavity, nat_cavity+1);
                mass_cavity[nat_cavity] = dbl;
                fprintf(fplog, "mass[%d] = %f\n",
                        nat_cavity+1, mass_cavity[nat_cavity]);
                nat_cavity++;
                ptr += i;
            }
            if (nat_cavity == 0)
            {
                gmx_fatal(FARGS, "Found %d masses in GMX_TPIC_MASSES", nat_cavity);
            }
        }
    }

    /*
       init_em(fplog,TPI,inputrec,&lambda,nrnb,mu_tot,
       state->box,fr,mdatoms,top,cr,nfile,fnm,NULL,NULL);*/
    /* We never need full pbc for TPI */
    fr->ePBC = epbcXYZ;
    /* Determine the temperature for the Boltzmann weighting */
    temp = inputrec->opts.ref_t[0];
    if (fplog)
    {
        for (i = 1; (i < inputrec->opts.ngtc); i++)
        {
            if (inputrec->opts.ref_t[i] != temp)
            {
                fprintf(fplog, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
                fprintf(stderr, "\nWARNING: The temperatures of the different temperature coupling groups are not identical\n\n");
            }
        }
        fprintf(fplog,
                "\n  The temperature for test particle insertion is %.3f K\n\n",
                temp);
    }
    beta = 1.0/(BOLTZ*temp);

    /* Number of insertions per frame */
    nsteps = inputrec->nsteps;

    /* Use the same neighborlist with more insertions points
     * in a sphere of radius drmax around the initial point
     */
    /* This should be a proper mdp parameter */
    drmax = inputrec->rtpi;

    /* An environment variable can be set to dump all configurations
     * to pdb with an insertion energy <= this value.
     */
    dump_pdb  = getenv("GMX_TPI_DUMP");
    dump_ener = 0;
    if (dump_pdb)
    {
        sscanf(dump_pdb, "%lf", &dump_ener);
    }

    atoms2md(top_global, inputrec, 0, NULL, top_global->natoms, mdatoms);
    update_mdatoms(mdatoms, inputrec->fepvals->init_lambda);

    snew(enerd, 1);
    init_enerdata(groups->grps[egcENER].nr, inputrec->fepvals->n_lambda, enerd);
    snew(f, top_global->natoms);

    /* Print to log file  */
    walltime_accounting_start(walltime_accounting);
    wallcycle_start(wcycle, ewcRUN);
    print_start(fplog, cr, walltime_accounting, "Test Particle Insertion");

    /* The last charge group is the group to be inserted */
    cg_tp = top->cgs.nr - 1;
    a_tp0 = top->cgs.index[cg_tp];
    a_tp1 = top->cgs.index[cg_tp+1];
    if (debug)
    {
        fprintf(debug, "TPI cg %d, atoms %d-%d\n", cg_tp, a_tp0, a_tp1);
    }
    if (a_tp1 - a_tp0 > 1 &&
        (inputrec->rlist < inputrec->rcoulomb ||
         inputrec->rlist < inputrec->rvdw))
    {
        gmx_fatal(FARGS, "Can not do TPI for multi-atom molecule with a twin-range cut-off");
    }
    snew(x_mol, a_tp1-a_tp0);

    bDispCorr = (inputrec->eDispCorr != edispcNO);
    bCharge   = FALSE;
    for (i = a_tp0; i < a_tp1; i++)
    {
        /* Copy the coordinates of the molecule to be insterted */
        copy_rvec(state->x[i], x_mol[i-a_tp0]);
        /* Check if we need to print electrostatic energies */
        bCharge |= (mdatoms->chargeA[i] != 0 ||
                    (mdatoms->chargeB && mdatoms->chargeB[i] != 0));
    }
    bRFExcl = (bCharge && EEL_RF(fr->eeltype) && fr->eeltype != eelRF_NEC);

    calc_cgcm(fplog, cg_tp, cg_tp+1, &(top->cgs), state->x, fr->cg_cm);
    if (bCavity)
    {
        if (norm(fr->cg_cm[cg_tp]) > 0.5*inputrec->rlist && fplog)
        {
            fprintf(fplog, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
            fprintf(stderr, "WARNING: Your TPI molecule is not centered at 0,0,0\n");
        }
    }
    else
    {
        /* Center the molecule to be inserted at zero */
        for (i = 0; i < a_tp1-a_tp0; i++)
        {
            rvec_dec(x_mol[i], fr->cg_cm[cg_tp]);
        }
    }

    if (fplog)
    {
        fprintf(fplog, "\nWill insert %d atoms %s partial charges\n",
                a_tp1-a_tp0, bCharge ? "with" : "without");

        fprintf(fplog, "\nWill insert %d times in each frame of %s\n",
                (int)nsteps, opt2fn("-rerun", nfile, fnm));
    }

    if (!bCavity)
    {
        if (inputrec->nstlist > 1)
        {
            if (drmax == 0 && a_tp1-a_tp0 == 1)
            {
                gmx_fatal(FARGS, "Re-using the neighborlist %d times for insertions of a single atom in a sphere of radius %f does not make sense", inputrec->nstlist, drmax);
            }
            if (fplog)
            {
                fprintf(fplog, "Will use the same neighborlist for %d insertions in a sphere of radius %f\n", inputrec->nstlist, drmax);
            }
        }
    }
    else
    {
        if (fplog)
        {
            fprintf(fplog, "Will insert randomly in a sphere of radius %f around the center of the cavity\n", drmax);
        }
    }

    ngid   = groups->grps[egcENER].nr;
    gid_tp = GET_CGINFO_GID(fr->cginfo[cg_tp]);
    nener  = 1 + ngid;
    if (bDispCorr)
    {
        nener += 1;
    }
    if (bCharge)
    {
        nener += ngid;
        if (bRFExcl)
        {
            nener += 1;
        }
        if (EEL_FULL(fr->eeltype))
        {
            nener += 1;
        }
    }
    snew(sum_UgembU, nener);

    /* Copy the random seed set by the user */
    seed = inputrec->ld_seed;
    /* We use the frame step number as one random counter.
     * The second counter use the insertion (step) count. But we
     * need multiple random numbers per insertion. This number is
     * not fixed, since we generate random locations in a sphere
     * by putting locations in a cube and some of these fail.
     * A count of 20 is already extremely unlikely, so 10000 is
     * a safe margin for random numbers per insertion.
     */
    rnd_count_stride = 10000;

    if (MASTER(cr))
    {
        fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm),
                          "TPI energies", "Time (ps)",
                          "(kJ mol\\S-1\\N) / (nm\\S3\\N)", oenv);
        xvgr_subtitle(fp_tpi, "f. are averages over one frame", oenv);
        snew(leg, 4+nener);
        e = 0;
        sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
        leg[e++] = strdup(str);
        sprintf(str, "f. -kT log<e\\S-\\betaU\\N>");
        leg[e++] = strdup(str);
        sprintf(str, "f. <e\\S-\\betaU\\N>");
        leg[e++] = strdup(str);
        sprintf(str, "f. V");
        leg[e++] = strdup(str);
        sprintf(str, "f. <Ue\\S-\\betaU\\N>");
        leg[e++] = strdup(str);
        for (i = 0; i < ngid; i++)
        {
            sprintf(str, "f. <U\\sVdW %s\\Ne\\S-\\betaU\\N>",
                    *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
            leg[e++] = strdup(str);
        }
        if (bDispCorr)
        {
            sprintf(str, "f. <U\\sdisp c\\Ne\\S-\\betaU\\N>");
            leg[e++] = strdup(str);
        }
        if (bCharge)
        {
            for (i = 0; i < ngid; i++)
            {
                sprintf(str, "f. <U\\sCoul %s\\Ne\\S-\\betaU\\N>",
                        *(groups->grpname[groups->grps[egcENER].nm_ind[i]]));
                leg[e++] = strdup(str);
            }
            if (bRFExcl)
            {
                sprintf(str, "f. <U\\sRF excl\\Ne\\S-\\betaU\\N>");
                leg[e++] = strdup(str);
            }
            if (EEL_FULL(fr->eeltype))
            {
                sprintf(str, "f. <U\\sCoul recip\\Ne\\S-\\betaU\\N>");
                leg[e++] = strdup(str);
            }
        }
        xvgr_legend(fp_tpi, 4+nener, (const char**)leg, oenv);
        for (i = 0; i < 4+nener; i++)
        {
            sfree(leg[i]);
        }
        sfree(leg);
    }
    clear_rvec(x_init);
    V_all     = 0;
    VembU_all = 0;

    invbinw = 10;
    nbin    = 10;
    snew(bin, nbin);

    /* Avoid frame step numbers <= -1 */
    frame_step_prev = -1;

    bNotLastFrame = read_first_frame(oenv, &status, opt2fn("-rerun", nfile, fnm),
                                     &rerun_fr, TRX_NEED_X);
    frame = 0;

    if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) !=
        mdatoms->nr - (a_tp1 - a_tp0))
    {
        gmx_fatal(FARGS, "Number of atoms in trajectory (%d)%s "
                  "is not equal the number in the run input file (%d) "
                  "minus the number of atoms to insert (%d)\n",
                  rerun_fr.natoms, bCavity ? " minus one" : "",
                  mdatoms->nr, a_tp1-a_tp0);
    }

    refvolshift = log(det(rerun_fr.box));

    switch (inputrec->eI)
    {
        case eiTPI:
            stepblocksize = inputrec->nstlist;
            break;
        case eiTPIC:
            stepblocksize = 1;
            break;
        default:
            gmx_fatal(FARGS, "Unknown integrator %s", ei_names[inputrec->eI]);
    }

#ifdef GMX_SIMD
    /* Make sure we don't detect SIMD overflow generated before this point */
    gmx_simd_check_and_reset_overflow();
#endif

    while (bNotLastFrame)
    {
        frame_step      = rerun_fr.step;
        if (frame_step <= frame_step_prev)
        {
            /* We don't have step number in the trajectory file,
             * or we have constant or decreasing step numbers.
             * Ensure we have increasing step numbers, since we use
             * the step numbers as a counter for random numbers.
             */
            frame_step  = frame_step_prev + 1;
        }
        frame_step_prev = frame_step;

        lambda = rerun_fr.lambda;
        t      = rerun_fr.time;

        sum_embU = 0;
        for (e = 0; e < nener; e++)
        {
            sum_UgembU[e] = 0;
        }

        /* Copy the coordinates from the input trajectory */
        for (i = 0; i < rerun_fr.natoms; i++)
        {
            copy_rvec(rerun_fr.x[i], state->x[i]);
        }
        copy_mat(rerun_fr.box, state->box);

        V    = det(state->box);
        logV = log(V);

        bStateChanged = TRUE;
        bNS           = TRUE;

        step = cr->nodeid*stepblocksize;
        while (step < nsteps)
        {
            /* Initialize the second counter for random numbers using
             * the insertion step index. This ensures that we get
             * the same random numbers independently of how many
             * MPI ranks we use. Also for the same seed, we get
             * the same initial random sequence for different nsteps.
             */
            rnd_count = step*rnd_count_stride;

            if (!bCavity)
            {
                /* Random insertion in the whole volume */
                bNS = (step % inputrec->nstlist == 0);
                if (bNS)
                {
                    /* Generate a random position in the box */
                    gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
                    gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
                    for (d = 0; d < DIM; d++)
                    {
                        x_init[d] = rnd[d]*state->box[d][d];
                    }
                }
                if (inputrec->nstlist == 1)
                {
                    copy_rvec(x_init, x_tp);
                }
                else
                {
                    /* Generate coordinates within |dx|=drmax of x_init */
                    do
                    {
                        gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
                        gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
                        for (d = 0; d < DIM; d++)
                        {
                            dx[d] = (2*rnd[d] - 1)*drmax;
                        }
                    }
                    while (norm2(dx) > drmax*drmax);
                    rvec_add(x_init, dx, x_tp);
                }
            }
            else
            {
                /* Random insertion around a cavity location
                 * given by the last coordinate of the trajectory.
                 */
                if (step == 0)
                {
                    if (nat_cavity == 1)
                    {
                        /* Copy the location of the cavity */
                        copy_rvec(rerun_fr.x[rerun_fr.natoms-1], x_init);
                    }
                    else
                    {
                        /* Determine the center of mass of the last molecule */
                        clear_rvec(x_init);
                        mass_tot = 0;
                        for (i = 0; i < nat_cavity; i++)
                        {
                            for (d = 0; d < DIM; d++)
                            {
                                x_init[d] +=
                                    mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
                            }
                            mass_tot += mass_cavity[i];
                        }
                        for (d = 0; d < DIM; d++)
                        {
                            x_init[d] /= mass_tot;
                        }
                    }
                }
                /* Generate coordinates within |dx|=drmax of x_init */
                do
                {
                    gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
                    gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
                    for (d = 0; d < DIM; d++)
                    {
                        dx[d] = (2*rnd[d] - 1)*drmax;
                    }
                }
                while (norm2(dx) > drmax*drmax);
                rvec_add(x_init, dx, x_tp);
            }

            if (a_tp1 - a_tp0 == 1)
            {
                /* Insert a single atom, just copy the insertion location */
                copy_rvec(x_tp, state->x[a_tp0]);
            }
            else
            {
                /* Copy the coordinates from the top file */
                for (i = a_tp0; i < a_tp1; i++)
                {
                    copy_rvec(x_mol[i-a_tp0], state->x[i]);
                }
                /* Rotate the molecule randomly */
                gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd);
                gmx_rng_cycle_2uniform(frame_step, rnd_count++, seed, RND_SEED_TPI, rnd+2);
                rotate_conf(a_tp1-a_tp0, state->x+a_tp0, NULL,
                            2*M_PI*rnd[0],
                            2*M_PI*rnd[1],
                            2*M_PI*rnd[2]);
                /* Shift to the insertion location */
                for (i = a_tp0; i < a_tp1; i++)
                {
                    rvec_inc(state->x[i], x_tp);
                }
            }

            /* Clear some matrix variables  */
            clear_mat(force_vir);
            clear_mat(shake_vir);
            clear_mat(vir);
            clear_mat(pres);

            /* Set the charge group center of mass of the test particle */
            copy_rvec(x_init, fr->cg_cm[top->cgs.nr-1]);

            /* Calc energy (no forces) on new positions.
             * Since we only need the intermolecular energy
             * and the RF exclusion terms of the inserted molecule occur
             * within a single charge group we can pass NULL for the graph.
             * This also avoids shifts that would move charge groups
             * out of the box.
             *
             * Some checks above ensure than we can not have
             * twin-range interactions together with nstlist > 1,
             * therefore we do not need to remember the LR energies.
             */
            /* Make do_force do a single node force calculation */
            cr->nnodes = 1;
            do_force(fplog, cr, inputrec,
                     step, nrnb, wcycle, top, &top_global->groups,
                     state->box, state->x, &state->hist,
                     f, force_vir, mdatoms, enerd, fcd,
                     state->lambda,
                     NULL, fr, NULL, mu_tot, t, NULL, NULL, FALSE,
                     GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
                     (bNS ? GMX_FORCE_DYNAMICBOX | GMX_FORCE_NS | GMX_FORCE_DO_LR : 0) |
                     (bStateChanged ? GMX_FORCE_STATECHANGED : 0));
            cr->nnodes    = nnodes;
            bStateChanged = FALSE;
            bNS           = FALSE;

            /* Calculate long range corrections to pressure and energy */
            calc_dispcorr(fplog, inputrec, fr, step, top_global->natoms, state->box,
                          lambda, pres, vir, &prescorr, &enercorr, &dvdlcorr);
            /* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
            enerd->term[F_DISPCORR]  = enercorr;
            enerd->term[F_EPOT]     += enercorr;
            enerd->term[F_PRES]     += prescorr;
            enerd->term[F_DVDL_VDW] += dvdlcorr;

            epot               = enerd->term[F_EPOT];
            bEnergyOutOfBounds = FALSE;
#ifdef GMX_SIMD_X86_SSE2_OR_HIGHER
            /* With SSE the energy can overflow, check for this */
            if (gmx_mm_check_and_reset_overflow())
            {
                if (debug)
                {
                    fprintf(debug, "Found an SSE overflow, assuming the energy is out of bounds\n");
                }
                bEnergyOutOfBounds = TRUE;
            }
#endif
            /* If the compiler doesn't optimize this check away
             * we catch the NAN energies.
             * The epot>GMX_REAL_MAX check catches inf values,
             * which should nicely result in embU=0 through the exp below,
             * but it does not hurt to check anyhow.
             */
            /* Non-bonded Interaction usually diverge at r=0.
             * With tabulated interaction functions the first few entries
             * should be capped in a consistent fashion between
             * repulsion, dispersion and Coulomb to avoid accidental
             * negative values in the total energy.
             * The table generation code in tables.c does this.
             * With user tbales the user should take care of this.
             */
            if (epot != epot || epot > GMX_REAL_MAX)
            {
                bEnergyOutOfBounds = TRUE;
            }
            if (bEnergyOutOfBounds)
            {
                if (debug)
                {
                    fprintf(debug, "\n  time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t, (int)step, epot);
                }
                embU = 0;
            }
            else
            {
                embU      = exp(-beta*epot);
                sum_embU += embU;
                /* Determine the weighted energy contributions of each energy group */
                e                = 0;
                sum_UgembU[e++] += epot*embU;
                if (fr->bBHAM)
                {
                    for (i = 0; i < ngid; i++)
                    {
                        sum_UgembU[e++] +=
                            (enerd->grpp.ener[egBHAMSR][GID(i, gid_tp, ngid)] +
                             enerd->grpp.ener[egBHAMLR][GID(i, gid_tp, ngid)])*embU;
                    }
                }
                else
                {
                    for (i = 0; i < ngid; i++)
                    {
                        sum_UgembU[e++] +=
                            (enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] +
                             enerd->grpp.ener[egLJLR][GID(i, gid_tp, ngid)])*embU;
                    }
                }
                if (bDispCorr)
                {
                    sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
                }
                if (bCharge)
                {
                    for (i = 0; i < ngid; i++)
                    {
                        sum_UgembU[e++] +=
                            (enerd->grpp.ener[egCOULSR][GID(i, gid_tp, ngid)] +
                             enerd->grpp.ener[egCOULLR][GID(i, gid_tp, ngid)])*embU;
                    }
                    if (bRFExcl)
                    {
                        sum_UgembU[e++] += enerd->term[F_RF_EXCL]*embU;
                    }
                    if (EEL_FULL(fr->eeltype))
                    {
                        sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
                    }
                }
            }

            if (embU == 0 || beta*epot > bU_bin_limit)
            {
                bin[0]++;
            }
            else
            {
                i = (int)((bU_logV_bin_limit
                           - (beta*epot - logV + refvolshift))*invbinw
                          + 0.5);
                if (i < 0)
                {
                    i = 0;
                }
                if (i >= nbin)
                {
                    realloc_bins(&bin, &nbin, i+10);
                }
                bin[i]++;
            }

            if (debug)
            {
                fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
                        (int)step, epot, x_tp[XX], x_tp[YY], x_tp[ZZ]);
            }

            if (dump_pdb && epot <= dump_ener)
            {
                sprintf(str, "t%g_step%d.pdb", t, (int)step);
                sprintf(str2, "t: %f step %d ener: %f", t, (int)step, epot);
                write_sto_conf_mtop(str, str2, top_global, state->x, state->v,
                                    inputrec->ePBC, state->box);
            }

            step++;
            if ((step/stepblocksize) % cr->nnodes != cr->nodeid)
            {
                /* Skip all steps assigned to the other MPI ranks */
                step += (cr->nnodes - 1)*stepblocksize;
            }
        }

        if (PAR(cr))
        {
            /* When running in parallel sum the energies over the processes */
            gmx_sumd(1,    &sum_embU, cr);
            gmx_sumd(nener, sum_UgembU, cr);
        }

        frame++;
        V_all     += V;
        VembU_all += V*sum_embU/nsteps;

        if (fp_tpi)
        {
            if (bVerbose || frame%10 == 0 || frame < 10)
            {
                fprintf(stderr, "mu %10.3e <mu> %10.3e\n",
                        -log(sum_embU/nsteps)/beta, -log(VembU_all/V_all)/beta);
            }

            fprintf(fp_tpi, "%10.3f %12.5e %12.5e %12.5e %12.5e",
                    t,
                    VembU_all == 0 ? 20/beta : -log(VembU_all/V_all)/beta,
                    sum_embU == 0  ? 20/beta : -log(sum_embU/nsteps)/beta,
                    sum_embU/nsteps, V);
            for (e = 0; e < nener; e++)
            {
                fprintf(fp_tpi, " %12.5e", sum_UgembU[e]/nsteps);
            }
            fprintf(fp_tpi, "\n");
            fflush(fp_tpi);
        }

        bNotLastFrame = read_next_frame(oenv, status, &rerun_fr);
    } /* End of the loop  */
    walltime_accounting_end(walltime_accounting);

    close_trj(status);

    if (fp_tpi != NULL)
    {
        gmx_fio_fclose(fp_tpi);
    }

    if (fplog != NULL)
    {
        fprintf(fplog, "\n");
        fprintf(fplog, "  <V>  = %12.5e nm^3\n", V_all/frame);
        fprintf(fplog, "  <mu> = %12.5e kJ/mol\n", -log(VembU_all/V_all)/beta);
    }

    /* Write the Boltzmann factor histogram */
    if (PAR(cr))
    {
        /* When running in parallel sum the bins over the processes */
        i = nbin;
        global_max(cr, &i);
        realloc_bins(&bin, &nbin, i);
        gmx_sumd(nbin, bin, cr);
    }
    if (MASTER(cr))
    {
        fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm),
                          "TPI energy distribution",
                          "\\betaU - log(V/<V>)", "count", oenv);
        sprintf(str, "number \\betaU > %g: %9.3e", bU_bin_limit, bin[0]);
        xvgr_subtitle(fp_tpi, str, oenv);
        xvgr_legend(fp_tpi, 2, (const char **)tpid_leg, oenv);
        for (i = nbin-1; i > 0; i--)
        {
            bUlogV = -i/invbinw + bU_logV_bin_limit - refvolshift + log(V_all/frame);
            fprintf(fp_tpi, "%6.2f %10d %12.5e\n",
                    bUlogV,
                    (int)(bin[i]+0.5),
                    bin[i]*exp(-bUlogV)*V_all/VembU_all);
        }
        gmx_fio_fclose(fp_tpi);
    }
    sfree(bin);

    sfree(sum_UgembU);

    walltime_accounting_set_nsteps_done(walltime_accounting, frame*inputrec->nsteps);

    return 0;
}
Esempio n. 2
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;
    }
}
Esempio n. 3
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;
    }
}