void
AbstractPlotModule::dataStarted(AbstractAnalysisData * /* data */)
{
if (!impl_->filename_.empty())
{
if (impl_->bPlain_)
{
impl_->fp_ = gmx_fio_fopen(impl_->filename_.c_str(), "w");
}
else
{
time_unit_t time_unit
= static_cast<time_unit_t>(impl_->settings_.timeUnit() + 1);
xvg_format_t xvg_format
= (impl_->settings_.plotFormat() > 0
? static_cast<xvg_format_t>(impl_->settings_.plotFormat())
: exvgNONE);
output_env_t oenv;
output_env_init(&oenv, getProgramContext(), time_unit, FALSE, xvg_format, 0);
boost::shared_ptr<output_env> oenvGuard(oenv, &output_env_done);
impl_->fp_ = xvgropen(impl_->filename_.c_str(), impl_->title_.c_str(),
impl_->xlabel_.c_str(), impl_->ylabel_.c_str(),
oenv);
const SelectionCollection *selections
= impl_->settings_.selectionCollection();
if (selections != NULL)
{
selections->printXvgrInfo(impl_->fp_, oenv);
}
if (!impl_->subtitle_.empty())
{
xvgr_subtitle(impl_->fp_, impl_->subtitle_.c_str(), oenv);
}
if (output_env_get_print_xvgr_codes(oenv)
&& !impl_->legend_.empty())
{
std::vector<const char *> legend;
legend.reserve(impl_->legend_.size());
for (size_t i = 0; i < impl_->legend_.size(); ++i)
{
legend.push_back(impl_->legend_[i].c_str());
}
xvgr_legend(impl_->fp_, legend.size(), &legend[0], oenv);
}
}
}
}
extern FILE *open_dhdl(const char *filename, const t_inputrec *ir,
const gmx_output_env_t *oenv)
{
FILE *fp;
const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
*lambdastate = "\\lambda state";
char title[STRLEN], label_x[STRLEN], label_y[STRLEN];
int i, nps, nsets, nsets_de, nsetsbegin;
int n_lambda_terms = 0;
t_lambda *fep = ir->fepvals; /* for simplicity */
t_expanded *expand = ir->expandedvals;
char **setname;
char buf[STRLEN], lambda_vec_str[STRLEN], lambda_name_str[STRLEN];
int bufplace = 0;
int nsets_dhdl = 0;
int s = 0;
int nsetsextend;
gmx_bool write_pV = FALSE;
/* count the number of different lambda terms */
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
n_lambda_terms++;
}
}
if (fep->n_lambda == 0)
{
sprintf(title, "%s", dhdl);
sprintf(label_x, "Time (ps)");
sprintf(label_y, "%s (%s %s)",
dhdl, unit_energy, "[\\lambda]\\S-1\\N");
}
else
{
sprintf(title, "%s and %s", dhdl, deltag);
sprintf(label_x, "Time (ps)");
sprintf(label_y, "%s and %s (%s %s)",
dhdl, deltag, unit_energy, "[\\8l\\4]\\S-1\\N");
}
fp = gmx_fio_fopen(filename, "w+");
xvgr_header(fp, title, label_x, label_y, exvggtXNY, oenv);
if (!(ir->bSimTemp))
{
bufplace = sprintf(buf, "T = %g (K) ",
ir->opts.ref_t[0]);
}
if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
{
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* compatibility output */
sprintf(&(buf[bufplace]), "%s = %.4f", lambda, fep->init_lambda);
}
else
{
print_lambda_vector(fep, fep->init_fep_state, TRUE, FALSE,
lambda_vec_str);
print_lambda_vector(fep, fep->init_fep_state, TRUE, TRUE,
lambda_name_str);
sprintf(&(buf[bufplace]), "%s %d: %s = %s",
lambdastate, fep->init_fep_state,
lambda_name_str, lambda_vec_str);
}
}
xvgr_subtitle(fp, buf, oenv);
nsets_dhdl = 0;
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
nsets_dhdl = n_lambda_terms;
}
/* count the number of delta_g states */
nsets_de = fep->lambda_stop_n - fep->lambda_start_n;
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
{
nsets += 1; /*add fep state for expanded ensemble */
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
{
nsetsextend += 1; /* for PV term, other terms possible if required for
the reduced potential (only needed with foreign
lambda, and only output when init_lambda is not
set in order to maintain compatibility of the
dhdl.xvg file) */
write_pV = TRUE;
}
snew(setname, nsetsextend);
if (expand->elmcmove > elmcmoveNO)
{
/* state for the fep_vals, if we have alchemical sampling */
sprintf(buf, "%s", "Thermodynamic state");
setname[s] = gmx_strdup(buf);
s += 1;
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
switch (fep->edHdLPrintEnergy)
{
case edHdLPrintEnergyPOTENTIAL:
sprintf(buf, "%s (%s)", "Potential Energy", unit_energy);
break;
case edHdLPrintEnergyTOTAL:
case edHdLPrintEnergyYES:
default:
sprintf(buf, "%s (%s)", "Total Energy", unit_energy);
}
setname[s] = gmx_strdup(buf);
s += 1;
}
if (fep->dhdl_derivatives == edhdlderivativesYES)
{
for (i = 0; i < efptNR; i++)
{
if (fep->separate_dvdl[i])
{
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* compatibility output */
sprintf(buf, "%s %s %.4f", dhdl, lambda, fep->init_lambda);
}
else
{
double lam = fep->init_lambda;
if (fep->init_lambda < 0)
{
lam = fep->all_lambda[i][fep->init_fep_state];
}
sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
lam);
}
setname[s] = gmx_strdup(buf);
s += 1;
}
}
}
if (fep->n_lambda > 0)
{
/* g_bar has to determine the lambda values used in this simulation
* from this xvg legend.
*/
if (expand->elmcmove > elmcmoveNO)
{
nsetsbegin = 1; /* for including the expanded ensemble */
}
else
{
nsetsbegin = 0;
}
if (fep->edHdLPrintEnergy != edHdLPrintEnergyNO)
{
nsetsbegin += 1;
}
nsetsbegin += nsets_dhdl;
for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
{
print_lambda_vector(fep, i, FALSE, FALSE, lambda_vec_str);
if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
{
/* for compatible dhdl.xvg files */
nps = sprintf(buf, "%s %s %s", deltag, lambda, lambda_vec_str);
}
else
{
nps = sprintf(buf, "%s %s to %s", deltag, lambda, lambda_vec_str);
}
if (ir->bSimTemp)
{
/* print the temperature for this state if doing simulated annealing */
sprintf(&buf[nps], "T = %g (%s)",
ir->simtempvals->temperatures[s-(nsetsbegin)],
unit_temp_K);
}
setname[s] = gmx_strdup(buf);
s++;
}
if (write_pV)
{
sprintf(buf, "pV (%s)", unit_energy);
setname[nsetsextend-1] = gmx_strdup(buf); /* the first entry after
nsets */
}
xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
for (s = 0; s < nsetsextend; s++)
{
sfree(setname[s]);
}
sfree(setname);
}
return fp;
}
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;
}
FILE *open_dhdl(const char *filename,const t_inputrec *ir,
const output_env_t oenv)
{
FILE *fp;
const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda";
char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
char **setname;
char buf[STRLEN];
sprintf(label_x,"%s (%s)","Time",unit_time);
if (ir->n_flambda == 0)
{
sprintf(title,"%s",dhdl);
sprintf(label_y,"%s (%s %s)",
dhdl,unit_energy,"[\\lambda]\\S-1\\N");
}
else
{
sprintf(title,"%s, %s",dhdl,deltag);
sprintf(label_y,"(%s)",unit_energy);
}
fp = gmx_fio_fopen(filename,"w+");
xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
if (ir->delta_lambda == 0)
{
sprintf(buf,"T = %g (K), %s = %g",
ir->opts.ref_t[0],lambda,ir->init_lambda);
}
else
{
sprintf(buf,"T = %g (K)",
ir->opts.ref_t[0]);
}
xvgr_subtitle(fp,buf,oenv);
if (ir->n_flambda > 0)
{
int nsets,s,nsi=0;
/* g_bar has to determine the lambda values used in this simulation
* from this xvg legend. */
nsets = ( (ir->dhdl_derivatives==dhdlderivativesYES) ? 1 : 0) +
ir->n_flambda;
snew(setname,nsets);
if (ir->dhdl_derivatives == dhdlderivativesYES)
{
sprintf(buf,"%s %s %g",dhdl,lambda,ir->init_lambda);
setname[nsi++] = strdup(buf);
}
for(s=0; s<ir->n_flambda; s++)
{
sprintf(buf,"%s %s %g",deltag,lambda,ir->flambda[s]);
setname[nsi++] = strdup(buf);
}
xvgr_legend(fp,nsets,(const char**)setname,oenv);
for(s=0; s<nsets; s++)
{
sfree(setname[s]);
}
sfree(setname);
}
return fp;
}
extern FILE *open_dhdl(const char *filename,const t_inputrec *ir,
const output_env_t oenv)
{
FILE *fp;
const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda",
*lambdastate="\\lambda state",*remain="remaining";
char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
int i,np,nps,nsets,nsets_de,nsetsbegin;
t_lambda *fep;
char **setname;
char buf[STRLEN];
int bufplace=0;
int nsets_dhdl = 0;
int s = 0;
int nsetsextend;
/* for simplicity */
fep = ir->fepvals;
if (fep->n_lambda == 0)
{
sprintf(title,"%s",dhdl);
sprintf(label_x,"Time (ps)");
sprintf(label_y,"%s (%s %s)",
dhdl,unit_energy,"[\\lambda]\\S-1\\N");
}
else
{
sprintf(title,"%s and %s",dhdl,deltag);
sprintf(label_x,"Time (ps)");
sprintf(label_y,"%s and %s (%s %s)",
dhdl,deltag,unit_energy,"[\\8l\\4]\\S-1\\N");
}
fp = gmx_fio_fopen(filename,"w+");
xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
if (!(ir->bSimTemp))
{
bufplace = sprintf(buf,"T = %g (K) ",
ir->opts.ref_t[0]);
}
if (ir->efep != efepSLOWGROWTH)
{
if (fep->n_lambda == 0)
{
sprintf(&(buf[bufplace]),"%s = %g",
lambda,fep->init_lambda);
}
else
{
sprintf(&(buf[bufplace]),"%s = %d",
lambdastate,fep->init_fep_state);
}
}
xvgr_subtitle(fp,buf,oenv);
for (i=0;i<efptNR;i++)
{
if (fep->separate_dvdl[i]) {nsets_dhdl++;}
}
/* count the number of delta_g states */
nsets_de = fep->n_lambda;
nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
if (fep->n_lambda>0 && ir->bExpanded)
{
nsets += 1; /*add fep state for expanded ensemble */
}
if (fep->bPrintEnergy)
{
nsets += 1; /* add energy to the dhdl as well */
}
nsetsextend = nsets;
if ((ir->epc!=epcNO) && (fep->n_lambda>0))
{
nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda) */
}
snew(setname,nsetsextend);
if (ir->bExpanded)
{
/* state for the fep_vals, if we have alchemical sampling */
sprintf(buf,"%s","Thermodynamic state");
setname[s] = strdup(buf);
s+=1;
}
if (fep->bPrintEnergy)
{
sprintf(buf,"%s (%s)","Energy",unit_energy);
setname[s] = strdup(buf);
s+=1;
}
for (i=0;i<efptNR;i++)
{
if (fep->separate_dvdl[i]) {
sprintf(buf,"%s (%s)",dhdl,efpt_names[i]);
setname[s] = strdup(buf);
s+=1;
}
}
if (fep->n_lambda > 0)
{
/* g_bar has to determine the lambda values used in this simulation
* from this xvg legend.
*/
if (ir->bExpanded) {
nsetsbegin = 1; /* for including the expanded ensemble */
} else {
nsetsbegin = 0;
}
if (fep->bPrintEnergy)
{
nsetsbegin += 1;
}
nsetsbegin += nsets_dhdl;
for(s=nsetsbegin; s<nsets; s++)
{
nps = sprintf(buf,"%s %s (",deltag,lambda);
for (i=0;i<efptNR;i++)
{
if (fep->separate_dvdl[i])
{
np = sprintf(&buf[nps],"%g,",fep->all_lambda[i][s-(nsetsbegin)]);
nps += np;
}
}
if (ir->bSimTemp)
{
/* print the temperature for this state if doing simulated annealing */
sprintf(&buf[nps],"T = %g (%s))",ir->simtempvals->temperatures[s-(nsetsbegin)],unit_temp_K);
}
else
{
sprintf(&buf[nps-1],")"); /* -1 to overwrite the last comma */
}
setname[s] = strdup(buf);
}
if (ir->epc!=epcNO) {
np = sprintf(buf,"pV (%s)",unit_energy);
setname[nsetsextend-1] = strdup(buf); /* the first entry after nsets */
}
xvgr_legend(fp,nsetsextend,(const char **)setname,oenv);
for(s=0; s<nsetsextend; s++)
{
sfree(setname[s]);
}
sfree(setname);
}
return fp;
}
