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;
}
/*
* Routine:
* Purpose:
* Algorithm:
* Data Structures:
*
* Params:
* Returns:
* Called By:
* Calls:
* Assumptions:
* Side Effects:
* TODO: None
*/
int
pr_s_customer (void *pSrc)
{
struct S_CUSTOMER_TBL *r;
char szTemp[6];
if (pSrc == NULL)
r = &g_s_customer;
else
r = pSrc;
print_start (S_CUSTOMER);
print_id (S_CUST_ID, r->kID, 1);
print_varchar (S_CUST_SALUTATION, r->pSalutation, 1);
print_varchar (S_CUST_LAST_NAME, r->pLastName, 1);
print_varchar (S_CUST_FIRST_NAME, r->pFirstName, 1);
print_boolean (S_CUST_PREFERRED_FLAG, r->bPreferredFlag, 1);
print_date (S_CUST_BIRTH_DATE, r->dtBirthDate.julian, 1);
print_varchar (S_CUST_BIRTH_COUNTRY, r->pBirthCountry, 1);
print_varchar (S_CUST_LOGIN, r->szLogin, 1);
print_varchar (S_CUST_EMAIL, r->szEmail, 1);
print_date (S_CUST_LAST_LOGIN, r->dtLastLogin.julian, 1);
print_date (S_CUST_FIRST_SHIPTO_DATE, r->dtFirstShipToDate.julian, 1);
print_date (S_CUST_FIRST_PURCHASE_DATE, r->dtFirstPurchaseDate.julian, 1);
print_date (S_CUST_LAST_REVIEW, r->dtReview.julian, 1);
print_varchar (S_CUST_PRIMARY_MACHINE, r->szPrimaryMachine, 1);
print_varchar (S_CUST_SECONDARY_MACHINE, r->szSecondaryMachine, 1);
print_integer (S_CUST_ADDRESS_STREET_NUM,
g_w_customer_address.ca_address.street_num, 1);
print_varchar (S_CUST_ADDRESS_SUITE_NUM,
g_w_customer_address.ca_address.suite_num, 1);
print_varchar (S_CUST_ADDRESS_STREET_NAME1,
g_w_customer_address.ca_address.street_name1, 1);
print_varchar (S_CUST_ADDRESS_STREET_NAME2,
g_w_customer_address.ca_address.street_name2, 1);
print_varchar (S_CUST_ADDRESS_STREET_TYPE,
g_w_customer_address.ca_address.street_type, 1);
print_varchar (S_CUST_ADDRESS_CITY, g_w_customer_address.ca_address.city,
1);
sprintf (szTemp, "%05d", g_w_customer_address.ca_address.zip);
print_varchar (S_CUST_ADDRESS_ZIP, szTemp, 1);
print_varchar (S_CUST_ADDRESS_COUNTY,
g_w_customer_address.ca_address.county, 1);
print_varchar (S_CUST_ADDRESS_STATE, g_w_customer_address.ca_address.state,
1);
print_varchar (S_CUST_ADDRESS_COUNTRY,
g_w_customer_address.ca_address.country, 1);
print_varchar (S_CUST_LOCATION_TYPE, r->pLocationType, 1);
print_varchar (S_CUST_GENDER, r->sGender, 1);
print_varchar (S_CUST_MARITAL_STATUS, r->pMaritalStatus, 1);
print_varchar (S_CUST_EDUCATION, r->pEducation, 1);
print_varchar (S_CUST_CREDIT_RATING, r->pCreditRating, 1);
print_integer (S_CUST_PURCHASE_ESTIMATE, r->nPurchaseEstimate, 1);
print_varchar (S_CUST_BUY_POTENTIAL, r->pBuyPotential, 1);
print_integer (S_CUST_DEPENDENT_CNT, r->nDependents, 1);
print_integer (S_CUST_EMPLOYED_CNT, r->nEmployed, 1);
print_integer (S_CUST_COLLEGE_CNT, r->nCollege, 1);
print_integer (S_CUST_VEHICLE_CNT, r->nVehicle, 1);
print_decimal (S_CUST_INCOME, &r->dIncome, 0);
print_end (S_CUSTOMER);
return (0);
}
END_TEST
/* char *iter_map_2 = */
/* "cluster=1\n" */
/* "part=0 : 1 132.65.174.100 1\n" */
/* "part=0 : 2 132.65.34.139 2\n" */
/* "cluster=2\n" */
/* "part=0 : 1 132.65.34.135 4"; */
/* START_TEST (test_map_iter_2) */
/* { */
/* mapper_t map; */
/* int res; */
/* mapper_iter_t iter; */
/* mapper_node_info_t ni; */
/* int n, cn, pn, a; */
/* print_start("test_map_iter_2"); */
/* map = mapper_init(300); */
/* fail_unless(map != NULL, "Cant create a map object"); */
/* // The local node will be placed in partition 2 of cluster 1 */
/* // mapper_set_my_pe(map, PE_SET(6, 15)); */
/* res = mapper_set_from_mem(map, iter_map_2, strlen(iter_map_2)); */
/* fail_unless(res, "set_from_mem returend 0 for a valid map"); */
/* n = mapperTotalNodeNum(map); */
/* fail_unless(n == 7, "Failed to get total nodes"); */
/* cn = mapperClusterNodeNum(map); */
/* fail_unless(cn == 3, "Failed to get total cluster nodes"); */
/* pn = mapper_get_partition_node_num(map); */
/* fail_unless(pn == 3, "Failed to get total partition nodes"); */
/* // All iteratror */
/* iter = mapper_iter_init(map, MAP_ITER_ALL); */
/* fail_unless(res, "Failed to create iterator"); */
/* a = 0; */
/* while(mapper_next(iter, &ni)) */
/* a++; */
/* fail_unless(a == n, "Number of iterations is not the number of nodes"); */
/* mapper_iter_done(iter); */
/* // Cluster iteratror */
/* iter = mapper_iter_init(map, MAP_ITER_CLUSTER); */
/* fail_unless(res, "Failed to create iterator"); */
/* a = 0; */
/* while(mapper_next(iter, &ni)) */
/* a++; */
/* fail_unless(a == cn, "Number of iterations is not the number of cluster nodes"); */
/* mapper_iter_done(iter); */
/* // Partition iteratror */
/* iter = mapper_iter_init(map, MAP_ITER_PARTITION); */
/* fail_unless(res, "Failed to create iterator"); */
/* a = 0; */
/* while(mapper_next(iter, &ni)) */
/* a++; */
/* fail_unless(a == pn, "Number of iterations is not the number of partition nodes"); */
/* mapper_iter_done(iter); */
/* mapper_done(map); */
/* print_end(); */
/* } */
/* END_TEST */
START_TEST (test_mem_leak)
{
mapper_t map;
int res;
mapper_iter_t iter;
mapper_node_info_t ni;
int a;
print_start("test_mem_leak");
//msx_set_debug(MAP_DEBUG);
unsigned long beforeMemSize = getMyMemSize();
fail_unless(beforeMemSize > 0 , "Failed to get memory size");
for(int i=0 ; i<1000 ; i++) {
map = BuildMosixMap(good_mosixmap_map_3,
strlen(good_mosixmap_map_3) + 1, INPUT_MEM);
fail_unless(map != NULL, "Failed to build map object from good_mosixmap_map_3");
iter = mapperIter(map, MAP_ITER_ALL);
fail_unless(res, "Failed to create iterator");
a = 0;
while(mapperNext(iter, &ni))
a++;
mapperIterDone(iter);
mapperDone(map);
}
unsigned long afterMemSize = getMyMemSize();
fail_unless(afterMemSize > 0 , "Failed to get memory size");
if(debug)
fprintf(stderr, "before %lu after %lu\n", beforeMemSize, afterMemSize);
fail_unless( beforeMemSize == afterMemSize);
msx_set_debug(0);
print_end();
}
void print_human(const struct params *prm, const struct usbmon_packet_1 *ep,
const unsigned char *data, uint64_t start_sec)
{
struct print_cursor pcur;
char udir, utype;
int data_len, i;
int ndesc; /* Display this many */
const struct usbmon_isodesc *dp;
int cnt;
ssize_t rc;
print_start(&pcur, prm->print_buf, prm->print_size);
if ((data_len = ep->len_cap) < 0) { /* Overflow */
data_len = 0;
}
#if 0
enum { TAG_BUF_SIZE = 17 };
char tag_buf[TAG_BUF_SIZE];
print_human_tag(tag_buf, TAG_BUF_SIZE, prm->tagp, ep);
#endif
/*
* We cast into a truncated type for readability.
* The danger of collisions is negligible.
*/
print_safe(&pcur, "%08x", (unsigned int) ep->id);
udir = ((ep->epnum & 0x80) != 0) ? 'i' : 'o';
switch (ep->xfer_type & 0x3) {
case PIPE_ISOCHRONOUS: utype = 'Z'; break;
case PIPE_INTERRUPT: utype = 'I'; break;
case PIPE_CONTROL: utype = 'C'; break;
default: /* PIPE_BULK */ utype = 'B';
}
print_safe(&pcur,
" %u.%06u %c %c%c:%u:%03u:%u",
(unsigned int)(ep->ts_sec - start_sec), ep->ts_usec,
ep->type,
utype, udir, ep->busnum, ep->devnum, ep->epnum & 0x7f);
if (ep->type == 'E') {
print_safe(&pcur, " %d", ep->status);
} else {
if (ep->flag_setup == 0) {
/* Setup packet is present and captured */
print_safe(&pcur,
" s %02x %02x %04x %04x %04x",
ep->s.setup[0],
ep->s.setup[1],
(ep->s.setup[3] << 8) | ep->s.setup[2],
(ep->s.setup[5] << 8) | ep->s.setup[4],
(ep->s.setup[7] << 8) | ep->s.setup[6]);
} else if (ep->flag_setup != '-') {
/* Unable to capture setup packet */
print_safe(&pcur,
" %c __ __ ____ ____ ____", ep->flag_setup);
} else {
/* No setup for this kind of URB */
if (ep->type == 'S' && ep->status == -EINPROGRESS) {
print_safe(&pcur, " -");
} else {
print_safe(&pcur, " %d", ep->status);
}
if (usb_typeisoc(ep->xfer_type) ||
usb_typeint(ep->xfer_type)) {
print_safe(&pcur, ":%d", ep->interval);
}
if (usb_typeisoc(ep->xfer_type)) {
print_safe(&pcur, ":%d", ep->start_frame);
if (ep->type == 'C') {
print_safe(&pcur,
":%d", ep->s.iso.error_count);
}
}
}
if (usb_typeisoc(ep->xfer_type)) {
/*
* This is the number of descriptors used by HC.
*/
print_safe(&pcur, " %d", ep->s.iso.numdesc);
/*
* This is the number of descriptors which we print.
*/
ndesc = ep->ndesc;
if (ndesc > ISODESC_MAX)
ndesc = ISODESC_MAX;
if (ndesc * sizeof(struct usbmon_isodesc) > data_len) {
ndesc = data_len / sizeof(struct usbmon_isodesc);
}
/* This is aligned by malloc */
dp = (struct usbmon_isodesc *) data;
for (i = 0; i < ndesc; i++) {
print_safe(&pcur,
" %d:%u:%u",
dp->iso_stat, dp->iso_off, dp->iso_len);
dp++;
}
/*
* The number of descriptors captured is used to
* find where the data starts.
*/
ndesc = ep->ndesc;
if (ndesc * sizeof(struct usbmon_isodesc) > data_len) {
data_len = 0;
} else {
data += ndesc * sizeof(struct usbmon_isodesc);
data_len -= ndesc * sizeof(struct usbmon_isodesc);
}
}
}
print_safe(&pcur, " %d", ep->length);
if (ep->length > 0) {
if (ep->flag_data == 0) {
print_safe(&pcur, " =\n");
if (data_len >= prm->data_max)
data_len = prm->data_max;
print_human_data(&pcur, ep, data, data_len);
} else {
print_safe(&pcur, " %c\n", ep->flag_data);
}
} else {
print_safe(&pcur, "\n");
}
cnt = print_done(&pcur);
if ((rc = write(1, prm->print_buf, cnt)) < cnt) {
if (rc < 0) {
fprintf(stderr, TAG ": Write error: %s\n",
strerror(errno));
} else {
fprintf(stderr, TAG ": Short write\n");
}
exit(1);
}
}
void print_48(const struct params *prm, const struct usbmon_packet *ep,
const unsigned char *data)
{
struct print_cursor pcur;
char udir, utype;
int data_len, i;
int cnt;
ssize_t rc;
print_start(&pcur, prm->print_buf, prm->print_size);
udir = ((ep->epnum & 0x80) != 0) ? 'i' : 'o';
switch (ep->xfer_type & 0x3) {
case PIPE_ISOCHRONOUS: utype = 'Z'; break;
case PIPE_INTERRUPT: utype = 'I'; break;
case PIPE_CONTROL: utype = 'C'; break;
default: /* PIPE_BULK */ utype = 'B';
}
print_safe(&pcur,
"%llx %u %c %c%c:%03u:%02u",
(long long) ep->id,
(unsigned int)(ep->ts_sec & 0xFFF) * 1000000 + ep->ts_usec,
ep->type,
utype, udir, ep->devnum, ep->epnum & 0x7f);
if (ep->flag_setup == 0) { /* Setup packet is present and captured */
print_safe(&pcur,
" s %02x %02x %04x %04x %04x",
ep->setup[0],
ep->setup[1],
(ep->setup[3] << 8) | ep->setup[2],
(ep->setup[5] << 8) | ep->setup[4],
(ep->setup[7] << 8) | ep->setup[6]);
} else if (ep->flag_setup != '-') { /* Unable to capture setup packet */
print_safe(&pcur,
" %c __ __ ____ ____ ____", ep->flag_setup);
} else { /* No setup for this kind of URB */
print_safe(&pcur, " %d", ep->status);
}
print_safe(&pcur, " %d", ep->length);
if (ep->length > 0) {
if (ep->flag_data == 0) {
print_safe(&pcur, " =");
if ((data_len = ep->len_cap) >= DATA_MAX)
data_len = DATA_MAX;
for (i = 0; i < data_len; i++) {
if (i % 4 == 0) {
print_safe(&pcur, " ");
}
print_safe(&pcur, "%02x", data[i]);
}
print_safe(&pcur, "\n");
} else {
print_safe(&pcur, " %c\n", ep->flag_data);
}
} else {
print_safe(&pcur, "\n");
}
cnt = print_done(&pcur);
if ((rc = write(1, prm->print_buf, cnt)) < cnt) {
if (rc < 0) {
fprintf(stderr, TAG ": Write error: %s\n",
strerror(errno));
} else {
fprintf(stderr, TAG ": Short write\n");
}
exit(1);
}
}
int main (int argc, char **argv)
{
print_start();
print_debug = 0;
load_from_file = 0;
char *dvalue = NULL;
char *evalue = NULL;
char *fvalue = NULL;
char *uvalue = NULL;
char *wvalue = NULL;
int hflag = 0;
int Fflag = 0;
int Xflag = 0;
int Eflag = 0;
int Aflag = 0;
int index;
int c;
opterr = 0;
// compute the options
while ((c = getopt (argc, argv, "d:e:f:u:w:lphFXEA")) != -1)
switch (c)
{
case 'd':
dvalue = optarg;
break;
case 'e':
evalue = optarg;
break;
case 'l':
load_from_file = 1;
break;
case 'f':
fvalue = optarg;
break;
case 'u':
uvalue = optarg;
break;
case 'w':
wvalue = optarg;
break;
case 'h':
hflag = 1;
break;
case 'F':
Fflag = 1;
break;
case 'X':
Xflag = 1;
break;
case 'E':
Eflag = 1;
break;
case 'A':
Aflag = 1;
break;
case 'p':
print_debug = 1;
break;
case '?':
if (optopt == 'd')
fprintf (stderr, "Option -%c requires an argument.\n", optopt);
else if (optopt == 'e')
fprintf (stderr, "Option -%c requires an argument.\n", optopt);
else if (optopt == 'f')
fprintf (stderr, "Option -%c requires an argument.\n", optopt);
else if (optopt == 'u')
fprintf (stderr, "Option -%c requires an argument.\n", optopt);
else if (optopt == 'w')
fprintf (stderr, "Option -%w requires an argument.\n", optopt);
else if (isprint (optopt))
fprintf (stderr, "Unknown option `-%c'.\n", optopt);
else
fprintf (stderr, "Unknown option character `\\x%x'.\n", optopt);
return 1;
default:
abort ();
}
// print help
if (hflag)
print_help();
else if (load_from_file)
{
//write LVALUE to defs.h
FILE *file_def;
file_def = fopen ("defs.h","w");
if (file_def == NULL)
{
printf ("Error open defs.h\n");
return -1;
}
//fseek (file_def, 0, SEEK_END);
fprintf (file_def, "#define LVALUE\n");
fclose(file_def);
}
// write shellcode from a given file to defs.h
else if (fvalue)
{
printf ("write shellcode from %s to defs.h\n", fvalue);
FILE *file_def;
file_def = fopen ("defs.h","w");
if (file_def == NULL)
{
printf ("Error open defs.h\n");
return -1;
}
fseek (file_def, 0, SEEK_END);
// read the shellcode file, write to defs.h
FILE *file_sh = fopen ( fvalue, "r" );
if ( file_sh != NULL )
{
if(Eflag)
fprintf (file_def, "#define FVALUE \"");
else
fprintf (file_def, "#define FVALUE \"\"\n");
char line [ 5000 ];
while ( fgets ( line, sizeof line, file_sh ) != NULL )
fprintf (file_def, "%s", line);
if(Eflag)
fprintf (file_def, "\"\n");
//fprintf (file_def, "\\n");
fclose ( file_sh );
}
else
printf ("Error open %s\n", fvalue);
fclose (file_def);
}
// exec from url
else if (uvalue)
{
printf ("write url %s to defs.h\n", uvalue);
FILE *file_def;
file_def = fopen ("defs.h","w");
if (file_def == NULL)
{
printf ("Error open defs.h\n");
return -1;
}
fseek (file_def, 0, SEEK_END);
fprintf (file_def, "#define UVALUE \"%s\"\n", uvalue);
fclose (file_def);
}
//write flags to defs.h
FILE *file_def;
file_def = fopen ("defs.h","a");
if (file_def == NULL)
{
printf ("Error open defs.h\n");
return -1;
}
//write LVALUE to defs.h
if(print_debug)
fprintf (file_def, "#define PRINT_DEBUG\n");
//write SANDBOX_FOPEN to defs.h
if(Fflag)
fprintf (file_def, "#define SANDBOX_FOPEN\n");
//write X64 to defs.h
if(Xflag)
fprintf (file_def, "#define X64\n");
//write ENCRYPT to defs.h
if(Eflag)
fprintf (file_def, "#define ENCRYPT\n");
//write ASCIIMSF to defs.h
if(Aflag)
fprintf (file_def, "#define ASCIIMSF\n");
fclose(file_def);
} //main
int main(int argc, char *argv[])
{
int freelist = 0, ret = 0;
alpm_errno_t err;
const char *target_name;
alpm_pkg_t *pkg;
alpm_list_t *dblist = NULL;
if(parse_options(argc, argv) != 0) {
usage();
ret = 1;
goto finish;
}
handle = alpm_initialize(ROOTDIR, dbpath, &err);
if(!handle) {
fprintf(stderr, "error: cannot initialize alpm: %s\n",
alpm_strerror(err));
ret = 1;
goto finish;
}
if(searchsyncs) {
if(register_syncs() != 0) {
ret = 1;
goto finish;
}
dblist = alpm_get_syncdbs(handle);
} else {
dblist = alpm_list_add(dblist, alpm_get_localdb(handle));
freelist = 1;
}
/* we only care about the first non option arg for walking */
target_name = argv[optind];
pkg = alpm_find_dbs_satisfier(handle, dblist, target_name);
if(!pkg) {
fprintf(stderr, "error: package '%s' not found\n", target_name);
ret = 1;
goto finish;
}
print_start(alpm_pkg_get_name(pkg), target_name);
tdepth d = {
NULL,
NULL,
1
};
walk_deps(dblist, pkg, &d, reverse);
print_end();
if(freelist) {
alpm_list_free(dblist);
}
finish:
cleanup();
return ret;
}
