void
do_md_trajectory_writing(FILE *fplog,
t_commrec *cr,
int nfile,
const t_filenm fnm[],
gmx_int64_t step,
gmx_int64_t step_rel,
double t,
t_inputrec *ir,
t_state *state,
t_state *state_global,
gmx_mtop_t *top_global,
t_forcerec *fr,
gmx_mdoutf_t outf,
t_mdebin *mdebin,
gmx_ekindata_t *ekind,
rvec *f,
rvec *f_global,
int *nchkpt,
gmx_bool bCPT,
gmx_bool bRerunMD,
gmx_bool bLastStep,
gmx_bool bDoConfOut,
gmx_bool bSumEkinhOld
)
{
int mdof_flags;
mdof_flags = 0;
if (do_per_step(step, ir->nstxout))
{
mdof_flags |= MDOF_X;
}
if (do_per_step(step, ir->nstvout))
{
mdof_flags |= MDOF_V;
}
if (do_per_step(step, ir->nstfout))
{
mdof_flags |= MDOF_F;
}
if (do_per_step(step, ir->nstxout_compressed))
{
mdof_flags |= MDOF_X_COMPRESSED;
}
if (bCPT)
{
mdof_flags |= MDOF_CPT;
}
;
#if defined(GMX_FAHCORE) || defined(GMX_WRITELASTSTEP)
if (bLastStep)
{
/* Enforce writing positions and velocities at end of run */
mdof_flags |= (MDOF_X | MDOF_V);
}
#endif
#ifdef GMX_FAHCORE
if (MASTER(cr))
{
fcReportProgress( ir->nsteps, step );
}
#if defined(__native_client__)
fcCheckin(MASTER(cr));
#endif
/* sync bCPT and fc record-keeping */
if (bCPT && MASTER(cr))
{
fcRequestCheckPoint();
}
#endif
if (mdof_flags != 0)
{
wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
if (bCPT)
{
if (MASTER(cr))
{
if (bSumEkinhOld)
{
state_global->ekinstate.bUpToDate = FALSE;
}
else
{
update_ekinstate(&state_global->ekinstate, ekind);
state_global->ekinstate.bUpToDate = TRUE;
}
update_energyhistory(&state_global->enerhist, mdebin);
}
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
step, t, state, state_global, f, f_global);
if (bCPT)
{
(*nchkpt)++;
}
debug_gmx();
if (bLastStep && step_rel == ir->nsteps &&
bDoConfOut && MASTER(cr) &&
!bRerunMD)
{
/* x and v have been collected in mdoutf_write_to_trajectory_files,
* because a checkpoint file will always be written
* at the last step.
*/
fprintf(stderr, "\nWriting final coordinates.\n");
if (fr->bMolPBC)
{
/* Make molecules whole only for confout writing */
do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, state_global->x);
}
write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
*top_global->name, top_global,
state_global->x, state_global->v,
ir->ePBC, state->box);
debug_gmx();
}
wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
}
}
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;
}
void
do_md_trajectory_writing(FILE *fplog,
t_commrec *cr,
int nfile,
const t_filenm fnm[],
gmx_int64_t step,
gmx_int64_t step_rel,
double t,
t_inputrec *ir,
t_state *state,
t_state *state_global,
gmx_mtop_t *top_global,
t_forcerec *fr,
gmx_mdoutf_t outf,
t_mdebin *mdebin,
gmx_ekindata_t *ekind,
rvec *f,
rvec *f_global,
int *nchkpt,
gmx_bool bCPT,
gmx_bool bRerunMD,
gmx_bool bLastStep,
gmx_bool bDoConfOut,
gmx_bool bSumEkinhOld
)
{
int mdof_flags;
rvec *x_for_confout = NULL;
mdof_flags = 0;
if (do_per_step(step, ir->nstxout))
{
mdof_flags |= MDOF_X;
}
if (do_per_step(step, ir->nstvout))
{
mdof_flags |= MDOF_V;
}
if (do_per_step(step, ir->nstfout))
{
mdof_flags |= MDOF_F;
}
if (do_per_step(step, ir->nstxout_compressed))
{
mdof_flags |= MDOF_X_COMPRESSED;
}
if (bCPT)
{
mdof_flags |= MDOF_CPT;
}
;
#if defined(GMX_FAHCORE)
if (bLastStep)
{
/* Enforce writing positions and velocities at end of run */
mdof_flags |= (MDOF_X | MDOF_V);
}
if (MASTER(cr))
{
fcReportProgress( ir->nsteps, step );
}
#if defined(__native_client__)
fcCheckin(MASTER(cr));
#endif
/* sync bCPT and fc record-keeping */
if (bCPT && MASTER(cr))
{
fcRequestCheckPoint();
}
#endif
if (mdof_flags != 0)
{
wallcycle_start(mdoutf_get_wcycle(outf), ewcTRAJ);
if (bCPT)
{
if (MASTER(cr))
{
if (bSumEkinhOld)
{
state_global->ekinstate.bUpToDate = FALSE;
}
else
{
update_ekinstate(&state_global->ekinstate, ekind);
state_global->ekinstate.bUpToDate = TRUE;
}
update_energyhistory(state_global->enerhist, mdebin);
}
}
mdoutf_write_to_trajectory_files(fplog, cr, outf, mdof_flags, top_global,
step, t, state, state_global, f, f_global);
if (bCPT)
{
(*nchkpt)++;
}
debug_gmx();
if (bLastStep && step_rel == ir->nsteps &&
bDoConfOut && MASTER(cr) &&
!bRerunMD)
{
if (fr->bMolPBC && state->x == state_global->x)
{
/* This (single-rank) run needs to allocate a
temporary array of size natoms so that any
periodicity removal for mdrun -confout does not
perturb the update and thus the final .edr
output. This makes .cpt restarts look binary
identical, and makes .edr restarts binary
identical. */
snew(x_for_confout, state_global->natoms);
copy_rvecn(state_global->x, x_for_confout, 0, state_global->natoms);
}
else
{
/* With DD, or no bMolPBC, it doesn't matter if
we change state_global->x */
x_for_confout = state_global->x;
}
/* x and v have been collected in mdoutf_write_to_trajectory_files,
* because a checkpoint file will always be written
* at the last step.
*/
fprintf(stderr, "\nWriting final coordinates.\n");
if (fr->bMolPBC)
{
/* Make molecules whole only for confout writing */
do_pbc_mtop(fplog, ir->ePBC, state->box, top_global, x_for_confout);
}
write_sto_conf_mtop(ftp2fn(efSTO, nfile, fnm),
*top_global->name, top_global,
x_for_confout, state_global->v,
ir->ePBC, state->box);
if (fr->bMolPBC && state->x == state_global->x)
{
sfree(x_for_confout);
}
debug_gmx();
}
wallcycle_stop(mdoutf_get_wcycle(outf), ewcTRAJ);
}
}
double do_md_openmm(FILE *fplog,t_commrec *cr,int nfile,const t_filenm fnm[],
const output_env_t oenv, gmx_bool bVerbose,gmx_bool bCompact,
int nstglobalcomm,
gmx_vsite_t *vsite,gmx_constr_t constr,
int stepout,t_inputrec *ir,
gmx_mtop_t *top_global,
t_fcdata *fcd,
t_state *state_global,
t_mdatoms *mdatoms,
t_nrnb *nrnb,gmx_wallcycle_t wcycle,
gmx_edsam_t ed,t_forcerec *fr,
int repl_ex_nst,int repl_ex_seed,
real cpt_period,real max_hours,
const char *deviceOptions,
unsigned long Flags,
gmx_runtime_t *runtime)
{
gmx_mdoutf_t *outf;
gmx_large_int_t step,step_rel;
double run_time;
double t,t0,lam0;
gmx_bool bSimAnn,
bFirstStep,bStateFromTPX,bLastStep,bStartingFromCpt;
gmx_bool bInitStep=TRUE;
gmx_bool do_ene,do_log, do_verbose,
bX,bV,bF,bCPT;
tensor force_vir,shake_vir,total_vir,pres;
int i,m;
int mdof_flags;
rvec mu_tot;
t_vcm *vcm;
int nchkpt=1;
gmx_localtop_t *top;
t_mdebin *mdebin=NULL;
t_state *state=NULL;
rvec *f_global=NULL;
int n_xtc=-1;
rvec *x_xtc=NULL;
gmx_enerdata_t *enerd;
rvec *f=NULL;
gmx_global_stat_t gstat;
gmx_update_t upd=NULL;
t_graph *graph=NULL;
globsig_t gs;
gmx_groups_t *groups;
gmx_ekindata_t *ekind, *ekind_save;
gmx_bool bAppend;
int a0,a1;
matrix lastbox;
real reset_counters=0,reset_counters_now=0;
char sbuf[STEPSTRSIZE],sbuf2[STEPSTRSIZE];
int handled_stop_condition=gmx_stop_cond_none;
const char *ommOptions = NULL;
void *openmmData;
bAppend = (Flags & MD_APPENDFILES);
check_ir_old_tpx_versions(cr,fplog,ir,top_global);
groups = &top_global->groups;
/* Initial values */
init_md(fplog,cr,ir,oenv,&t,&t0,&state_global->lambda,&lam0,
nrnb,top_global,&upd,
nfile,fnm,&outf,&mdebin,
force_vir,shake_vir,mu_tot,&bSimAnn,&vcm,state_global,Flags);
clear_mat(total_vir);
clear_mat(pres);
/* Energy terms and groups */
snew(enerd,1);
init_enerdata(top_global->groups.grps[egcENER].nr,ir->n_flambda,enerd);
snew(f,top_global->natoms);
/* Kinetic energy data */
snew(ekind,1);
init_ekindata(fplog,top_global,&(ir->opts),ekind);
/* needed for iteration of constraints */
snew(ekind_save,1);
init_ekindata(fplog,top_global,&(ir->opts),ekind_save);
/* Copy the cos acceleration to the groups struct */
ekind->cosacc.cos_accel = ir->cos_accel;
gstat = global_stat_init(ir);
debug_gmx();
{
double io = compute_io(ir,top_global->natoms,groups,mdebin->ebin->nener,1);
if ((io > 2000) && MASTER(cr))
fprintf(stderr,
"\nWARNING: This run will generate roughly %.0f Mb of data\n\n",
io);
}
top = gmx_mtop_generate_local_top(top_global,ir);
a0 = 0;
a1 = top_global->natoms;
state = partdec_init_local_state(cr,state_global);
f_global = f;
atoms2md(top_global,ir,0,NULL,a0,a1-a0,mdatoms);
if (vsite)
{
set_vsite_top(vsite,top,mdatoms,cr);
}
if (ir->ePBC != epbcNONE && !ir->bPeriodicMols)
{
graph = mk_graph(fplog,&(top->idef),0,top_global->natoms,FALSE,FALSE);
}
update_mdatoms(mdatoms,state->lambda);
if (deviceOptions[0]=='\0')
{
/* empty options, which should default to OpenMM in this build */
ommOptions=deviceOptions;
}
else
{
if (gmx_strncasecmp(deviceOptions,"OpenMM",6)!=0)
{
gmx_fatal(FARGS, "This Gromacs version currently only works with OpenMM. Use -device \"OpenMM:<options>\"");
}
else
{
ommOptions=strchr(deviceOptions,':');
if (NULL!=ommOptions)
{
/* Increase the pointer to skip the colon */
ommOptions++;
}
}
}
openmmData = openmm_init(fplog, ommOptions, ir, top_global, top, mdatoms, fr, state);
please_cite(fplog,"Friedrichs2009");
if (MASTER(cr))
{
/* Update mdebin with energy history if appending to output files */
if ( Flags & MD_APPENDFILES )
{
restore_energyhistory_from_state(mdebin,&state_global->enerhist);
}
/* Set the initial energy history in state to zero by updating once */
update_energyhistory(&state_global->enerhist,mdebin);
}
if (constr)
{
set_constraints(constr,top,ir,mdatoms,cr);
}
if (!ir->bContinuation)
{
if (mdatoms->cFREEZE && (state->flags & (1<<estV)))
{
/* Set the velocities of frozen particles to zero */
for (i=mdatoms->start; i<mdatoms->start+mdatoms->homenr; i++)
{
for (m=0; m<DIM; m++)
{
if (ir->opts.nFreeze[mdatoms->cFREEZE[i]][m])
{
state->v[i][m] = 0;
}
}
}
}
if (constr)
{
/* Constrain the initial coordinates and velocities */
do_constrain_first(fplog,constr,ir,mdatoms,state,f,
graph,cr,nrnb,fr,top,shake_vir);
}
if (vsite)
{
/* Construct the virtual sites for the initial configuration */
construct_vsites(fplog,vsite,state->x,nrnb,ir->delta_t,NULL,
top->idef.iparams,top->idef.il,
fr->ePBC,fr->bMolPBC,graph,cr,state->box);
}
}
debug_gmx();
if (MASTER(cr))
{
char tbuf[20];
fprintf(fplog,"Initial temperature: %g K\n",enerd->term[F_TEMP]);
fprintf(stderr,"starting mdrun '%s'\n",
*(top_global->name));
if (ir->nsteps >= 0)
{
sprintf(tbuf,"%8.1f",(ir->init_step+ir->nsteps)*ir->delta_t);
}
else
{
sprintf(tbuf,"%s","infinite");
}
if (ir->init_step > 0)
{
fprintf(stderr,"%s steps, %s ps (continuing from step %s, %8.1f ps).\n",
gmx_step_str(ir->init_step+ir->nsteps,sbuf),tbuf,
gmx_step_str(ir->init_step,sbuf2),
ir->init_step*ir->delta_t);
}
else
{
fprintf(stderr,"%s steps, %s ps.\n",
gmx_step_str(ir->nsteps,sbuf),tbuf);
}
}
fprintf(fplog,"\n");
/* Set and write start time */
runtime_start(runtime);
print_date_and_time(fplog,cr->nodeid,"Started mdrun",runtime);
wallcycle_start(wcycle,ewcRUN);
if (fplog)
fprintf(fplog,"\n");
/* safest point to do file checkpointing is here. More general point would be immediately before integrator call */
debug_gmx();
/***********************************************************
*
* Loop over MD steps
*
************************************************************/
/* loop over MD steps or if rerunMD to end of input trajectory */
bFirstStep = TRUE;
/* Skip the first Nose-Hoover integration when we get the state from tpx */
bStateFromTPX = !opt2bSet("-cpi",nfile,fnm);
bInitStep = bFirstStep && bStateFromTPX;
bStartingFromCpt = (Flags & MD_STARTFROMCPT) && bInitStep;
bLastStep = FALSE;
init_global_signals(&gs,cr,ir,repl_ex_nst);
step = ir->init_step;
step_rel = 0;
while (!bLastStep)
{
wallcycle_start(wcycle,ewcSTEP);
GMX_MPE_LOG(ev_timestep1);
bLastStep = (step_rel == ir->nsteps);
t = t0 + step*ir->delta_t;
if (gs.set[eglsSTOPCOND] != 0)
{
bLastStep = TRUE;
}
do_log = do_per_step(step,ir->nstlog) || bFirstStep || bLastStep;
do_verbose = bVerbose &&
(step % stepout == 0 || bFirstStep || bLastStep);
if (MASTER(cr) && do_log)
{
print_ebin_header(fplog,step,t,state->lambda);
}
clear_mat(force_vir);
GMX_MPE_LOG(ev_timestep2);
/* We write a checkpoint at this MD step when:
* either when we signalled through gs (in OpenMM NS works different),
* or at the last step (but not when we do not want confout),
* but never at the first step.
*/
bCPT = ((gs.set[eglsCHKPT] ||
(bLastStep && (Flags & MD_CONFOUT))) &&
step > ir->init_step );
if (bCPT)
{
gs.set[eglsCHKPT] = 0;
}
/* Now we have the energies and forces corresponding to the
* coordinates at time t. We must output all of this before
* the update.
* for RerunMD t is read from input trajectory
*/
GMX_MPE_LOG(ev_output_start);
mdof_flags = 0;
if (do_per_step(step,ir->nstxout))
{
mdof_flags |= MDOF_X;
}
if (do_per_step(step,ir->nstvout))
{
mdof_flags |= MDOF_V;
}
if (do_per_step(step,ir->nstfout))
{
mdof_flags |= MDOF_F;
}
if (do_per_step(step,ir->nstxtcout))
{
mdof_flags |= MDOF_XTC;
}
if (bCPT)
{
mdof_flags |= MDOF_CPT;
};
do_ene = (do_per_step(step,ir->nstenergy) || bLastStep);
if (mdof_flags != 0 || do_ene || do_log)
{
wallcycle_start(wcycle,ewcTRAJ);
bF = (mdof_flags & MDOF_F);
bX = (mdof_flags & (MDOF_X | MDOF_XTC | MDOF_CPT));
bV = (mdof_flags & (MDOF_V | MDOF_CPT));
openmm_copy_state(openmmData, state, &t, f, enerd, bX, bV, bF, do_ene);
upd_mdebin(mdebin, FALSE,TRUE,
t,mdatoms->tmass,enerd,state,lastbox,
shake_vir,force_vir,total_vir,pres,
ekind,mu_tot,constr);
print_ebin(outf->fp_ene,do_ene,FALSE,FALSE,do_log?fplog:NULL,
step,t,
eprNORMAL,bCompact,mdebin,fcd,groups,&(ir->opts));
write_traj(fplog,cr,outf,mdof_flags,top_global,
step,t,state,state_global,f,f_global,&n_xtc,&x_xtc);
if (bCPT)
{
nchkpt++;
bCPT = FALSE;
}
debug_gmx();
if (bLastStep && step_rel == ir->nsteps &&
(Flags & MD_CONFOUT) && MASTER(cr))
{
/* x and v have been collected in write_traj,
* because a checkpoint file will always be written
* at the last step.
*/
fprintf(stderr,"\nWriting final coordinates.\n");
if (ir->ePBC != epbcNONE && !ir->bPeriodicMols)
{
/* Make molecules whole only for confout writing */
do_pbc_mtop(fplog,ir->ePBC,state->box,top_global,state_global->x);
}
write_sto_conf_mtop(ftp2fn(efSTO,nfile,fnm),
*top_global->name,top_global,
state_global->x,state_global->v,
ir->ePBC,state->box);
debug_gmx();
}
wallcycle_stop(wcycle,ewcTRAJ);
}
GMX_MPE_LOG(ev_output_finish);
/* Determine the wallclock run time up till now */
run_time = gmx_gettime() - (double)runtime->real;
/* Check whether everything is still allright */
if (((int)gmx_get_stop_condition() > handled_stop_condition)
#ifdef GMX_THREADS
&& MASTER(cr)
#endif
)
{
/* this is just make gs.sig compatible with the hack
of sending signals around by MPI_Reduce with together with
other floats */
/* NOTE: this only works for serial code. For code that allows
MPI nodes to propagate their condition, see kernel/md.c*/
if ( gmx_get_stop_condition() == gmx_stop_cond_next_ns )
gs.set[eglsSTOPCOND]=1;
if ( gmx_get_stop_condition() == gmx_stop_cond_next )
gs.set[eglsSTOPCOND]=1;
/* < 0 means stop at next step, > 0 means stop at next NS step */
if (fplog)
{
fprintf(fplog,
"\n\nReceived the %s signal, stopping at the next %sstep\n\n",
gmx_get_signal_name(),
gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
fflush(fplog);
}
fprintf(stderr,
"\n\nReceived the %s signal, stopping at the next %sstep\n\n",
gmx_get_signal_name(),
gs.sig[eglsSTOPCOND]==1 ? "NS " : "");
fflush(stderr);
handled_stop_condition=(int)gmx_get_stop_condition();
}
else if (MASTER(cr) &&
(max_hours > 0 && run_time > max_hours*60.0*60.0*0.99) &&
gs.set[eglsSTOPCOND] == 0)
{
/* Signal to terminate the run */
gs.set[eglsSTOPCOND] = 1;
if (fplog)
{
fprintf(fplog,"\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
}
fprintf(stderr, "\nStep %s: Run time exceeded %.3f hours, will terminate the run\n",gmx_step_str(step,sbuf),max_hours*0.99);
}
/* checkpoints */
if (MASTER(cr) && (cpt_period >= 0 &&
(cpt_period == 0 ||
run_time >= nchkpt*cpt_period*60.0)) &&
gs.set[eglsCHKPT] == 0)
{
gs.set[eglsCHKPT] = 1;
}
/* Time for performance */
if (((step % stepout) == 0) || bLastStep)
{
runtime_upd_proc(runtime);
}
if (do_per_step(step,ir->nstlog))
{
if (fflush(fplog) != 0)
{
gmx_fatal(FARGS,"Cannot flush logfile - maybe you are out of quota?");
}
}
/* Remaining runtime */
if (MULTIMASTER(cr) && (do_verbose || gmx_got_usr_signal() ))
{
print_time(stderr,runtime,step,ir,cr);
}
bFirstStep = FALSE;
bInitStep = FALSE;
bStartingFromCpt = FALSE;
step++;
step_rel++;
openmm_take_one_step(openmmData);
}
/* End of main MD loop */
debug_gmx();
/* Stop the time */
runtime_end(runtime);
if (MASTER(cr))
{
if (ir->nstcalcenergy > 0)
{
print_ebin(outf->fp_ene,FALSE,FALSE,FALSE,fplog,step,t,
eprAVER,FALSE,mdebin,fcd,groups,&(ir->opts));
}
}
openmm_cleanup(fplog, openmmData);
done_mdoutf(outf);
debug_gmx();
runtime->nsteps_done = step_rel;
return 0;
}
