#include "legacysimulator.h"
//! Global max algorithm
-static void global_max(t_commrec *cr, int *n)
+static void global_max(t_commrec* cr, int* n)
{
int *sum, i;
}
//! Reallocate arrays.
-static void realloc_bins(double **bin, int *nbin, int nbin_new)
+static void realloc_bins(double** bin, int* nbin, int nbin_new)
{
int i;
}
//! Computes and returns the RF exclusion energy for the last molecule starting at \p beginAtom
-static real
-reactionFieldExclusionCorrection(gmx::ArrayRef<const gmx::RVec> x,
- const t_mdatoms &mdatoms,
- const interaction_const_t &ic,
- const int beginAtom)
+static real reactionFieldExclusionCorrection(gmx::ArrayRef<const gmx::RVec> x,
+ const t_mdatoms& mdatoms,
+ const interaction_const_t& ic,
+ const int beginAtom)
{
real energy = 0;
for (int i = beginAtom; i < mdatoms.homenr; i++)
{
const real qi = mdatoms.chargeA[i];
- energy -= 0.5*qi*qi*ic.c_rf;
+ energy -= 0.5 * qi * qi * ic.c_rf;
for (int j = i + 1; j < mdatoms.homenr; j++)
{
const real qj = mdatoms.chargeA[j];
const real rsq = distance2(x[i], x[j]);
- energy += qi*qj*(ic.k_rf*rsq - ic.c_rf);
+ energy += qi * qj * (ic.k_rf * rsq - ic.c_rf);
}
}
- return ic.epsfac*energy;
+ return ic.epsfac * energy;
}
namespace gmx
{
// TODO: Convert to use the nbnxm kernels by putting the system and the teset molecule on two separate search grids
-void
-LegacySimulator::do_tpi()
+void LegacySimulator::do_tpi()
{
GMX_RELEASE_ASSERT(gmx_omp_nthreads_get(emntDefault) == 1, "TPI does not support OpenMP");
gmx_localtop_t top;
- PaddedHostVector<gmx::RVec> f {};
+ PaddedHostVector<gmx::RVec> f{};
real lambda, t, temp, beta, drmax, epot;
double embU, sum_embU, *sum_UgembU, V, V_all, VembU_all;
- t_trxstatus *status;
+ t_trxstatus* status;
t_trxframe rerun_fr;
gmx_bool bDispCorr, bCharge, bRFExcl, bNotLastFrame, bStateChanged, bNS;
tensor force_vir, shake_vir, vir, pres;
int a_tp0, a_tp1, ngid, gid_tp, nener, e;
- rvec *x_mol;
+ rvec* x_mol;
rvec mu_tot, x_init, dx;
int nnodes, frame;
int64_t frame_step_prev, frame_step;
int64_t nsteps, stepblocksize = 0, step;
int64_t seed;
int i;
- FILE *fp_tpi = nullptr;
- char *ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
+ FILE* fp_tpi = nullptr;
+ char * ptr, *dump_pdb, **leg, str[STRLEN], str2[STRLEN];
double dbl, dump_ener;
gmx_bool bCavity;
int nat_cavity = 0, d;
- real *mass_cavity = nullptr, mass_tot;
+ real * mass_cavity = nullptr, mass_tot;
int nbin;
double invbinw, *bin, refvolshift, logV, bUlogV;
gmx_bool bEnergyOutOfBounds;
- const char *tpid_leg[2] = {"direct", "reweighted"};
+ const char* tpid_leg[2] = { "direct", "reweighted" };
auto mdatoms = mdAtoms->mdatoms();
GMX_UNUSED_VALUE(outputProvider);
- GMX_LOG(mdlog.info).asParagraph().
- appendText("Note that it is planned to change the command gmx mdrun -tpi "
- "(and -tpic) to make the functionality available in a different "
- "form in a future version of GROMACS, e.g. gmx test-particle-insertion.");
+ GMX_LOG(mdlog.info)
+ .asParagraph()
+ .appendText(
+ "Note that it is planned to change the command gmx mdrun -tpi "
+ "(and -tpic) to make the functionality available in a different "
+ "form in a future version of GROMACS, e.g. gmx test-particle-insertion.");
/* Since there is no upper limit to the insertion energies,
* we need to set an upper limit for the distribution output.
gmx_mtop_generate_local_top(*top_global, &top, inputrec->efep != efepNO);
- SimulationGroups *groups = &top_global->groups;
+ SimulationGroups* groups = &top_global->groups;
bCavity = (inputrec->eI == eiTPIC);
if (bCavity)
nat_cavity = 0;
while (sscanf(ptr, "%20lf%n", &dbl, &i) > 0)
{
- srenew(mass_cavity, nat_cavity+1);
+ srenew(mass_cavity, nat_cavity + 1);
mass_cavity[nat_cavity] = dbl;
- fprintf(fplog, "mass[%d] = %f\n",
- nat_cavity+1, mass_cavity[nat_cavity]);
+ fprintf(fplog, "mass[%d] = %f\n", nat_cavity + 1, mass_cavity[nat_cavity]);
nat_cavity++;
ptr += 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,
+ "\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);
+ fprintf(fplog, "\n The temperature for test particle insertion is %.3f K\n\n", temp);
}
- beta = 1.0/(BOLTZ*temp);
+ beta = 1.0 / (BOLTZ * temp);
/* Number of insertions per frame */
nsteps = inputrec->nsteps;
print_start(fplog, cr, walltime_accounting, "Test Particle Insertion");
/* The last charge group is the group to be inserted */
- const t_atoms &atomsToInsert = top_global->moltype[top_global->molblock.back().type].atoms;
- a_tp0 = top_global->natoms - atomsToInsert.nr;
- a_tp1 = top_global->natoms;
+ const t_atoms& atomsToInsert = top_global->moltype[top_global->molblock.back().type].atoms;
+ a_tp0 = top_global->natoms - atomsToInsert.nr;
+ a_tp1 = top_global->natoms;
if (debug)
{
fprintf(debug, "TPI atoms %d-%d\n", a_tp0, a_tp1);
}
}
- snew(x_mol, a_tp1-a_tp0);
+ 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(x[i], x_mol[i-a_tp0]);
+ copy_rvec(x[i], x_mol[i - a_tp0]);
/* Check if we need to print electrostatic energies */
- bCharge |= (mdatoms->chargeA[i] != 0 ||
- ((mdatoms->chargeB != nullptr) && mdatoms->chargeB[i] != 0));
+ bCharge |= (mdatoms->chargeA[i] != 0
+ || ((mdatoms->chargeB != nullptr) && mdatoms->chargeB[i] != 0));
}
bRFExcl = (bCharge && EEL_RF(fr->ic->eeltype));
{
rvec_inc(cog, x[a]);
}
- svmul(1.0_real/(a_tp1 - a_tp0), cog, cog);
+ svmul(1.0_real / (a_tp1 - a_tp0), cog, cog);
real molRadius = 0;
for (int a = a_tp0; a < a_tp1; a++)
{
}
molRadius = std::sqrt(molRadius);
- const real maxCutoff = std::max(inputrec->rvdw, inputrec->rcoulomb);
+ const real maxCutoff = std::max(inputrec->rvdw, inputrec->rcoulomb);
if (bCavity)
{
- if (norm(cog) > 0.5*maxCutoff && fplog)
+ if (norm(cog) > 0.5 * maxCutoff && 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++)
+ for (i = 0; i < a_tp1 - a_tp0; i++)
{
rvec_dec(x_mol[i], cog);
}
if (fplog)
{
- fprintf(fplog, "\nWill insert %d atoms %s partial charges\n",
- a_tp1-a_tp0, bCharge ? "with" : "without");
+ fprintf(fplog, "\nWill insert %d atoms %s partial charges\n", a_tp1 - a_tp0,
+ bCharge ? "with" : "without");
- fprintf(fplog, "\nWill insert %" PRId64 " times in each frame of %s\n",
- nsteps, opt2fn("-rerun", nfile, fnm));
+ fprintf(fplog, "\nWill insert %" PRId64 " times in each frame of %s\n", nsteps,
+ opt2fn("-rerun", nfile, fnm));
}
if (!bCavity)
{
/* With the same pair list we insert in a sphere of radius rtpi in different orientations */
- if (drmax == 0 && a_tp1-a_tp0 == 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);
+ 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);
+ fprintf(fplog,
+ "Will use the same neighborlist for %d insertions in a sphere of radius "
+ "%f\n",
+ inputrec->nstlist, drmax);
}
}
}
{
if (fplog)
{
- fprintf(fplog, "Will insert randomly in a sphere of radius %f around the center of the cavity\n", drmax);
+ fprintf(fplog,
+ "Will insert randomly in a sphere of radius %f around the center of the "
+ "cavity\n",
+ drmax);
}
}
* inserted atoms located in the center of the sphere, so we need
* a buffer of size of the sphere and molecule radius.
*/
- inputrec->rlist = maxCutoff + 2*inputrec->rtpi + 2*molRadius;
+ inputrec->rlist = maxCutoff + 2 * inputrec->rtpi + 2 * molRadius;
fr->rlist = inputrec->rlist;
fr->nbv->changePairlistRadii(inputrec->rlist, inputrec->rlist);
break;
}
}
- nener = 1 + ngid;
+ nener = 1 + ngid;
if (bDispCorr)
{
nener += 1;
/* Copy the random seed set by the user */
seed = inputrec->ld_seed;
- gmx::ThreeFry2x64<16> rng(seed, gmx::RandomDomain::TestParticleInsertion); // 16 bits internal counter => 2^16 * 2 = 131072 values per stream
- gmx::UniformRealDistribution<real> dist;
+ gmx::ThreeFry2x64<16> rng(
+ seed, gmx::RandomDomain::TestParticleInsertion); // 16 bits internal counter => 2^16 * 2 = 131072 values per stream
+ gmx::UniformRealDistribution<real> dist;
if (MASTER(cr))
{
- fp_tpi = xvgropen(opt2fn("-tpi", nfile, fnm),
- "TPI energies", "Time (ps)",
+ 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);
+ snew(leg, 4 + nener);
e = 0;
sprintf(str, "-kT log(<Ve\\S-\\betaU\\N>/<V>)");
leg[e++] = gmx_strdup(str);
leg[e++] = gmx_strdup(str);
}
}
- xvgr_legend(fp_tpi, 4+nener, leg, oenv);
- for (i = 0; i < 4+nener; i++)
+ xvgr_legend(fp_tpi, 4 + nener, leg, oenv);
+ for (i = 0; i < 4 + nener; i++)
{
sfree(leg[i]);
}
/* 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;
+ 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))
+ if (rerun_fr.natoms - (bCavity ? nat_cavity : 0) != mdatoms->nr - (a_tp1 - a_tp0))
{
- gmx_fatal(FARGS, "Number of atoms in trajectory (%d)%s "
+ 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);
+ 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]);
+ case eiTPI: stepblocksize = inputrec->nstlist; break;
+ case eiTPIC: stepblocksize = 1; break;
+ default: gmx_fatal(FARGS, "Unknown integrator %s", ei_names[inputrec->eI]);
}
while (bNotLastFrame)
{
- frame_step = rerun_fr.step;
+ frame_step = rerun_fr.step;
if (frame_step <= frame_step_prev)
{
/* We don't have step number in the trajectory file,
* 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 = frame_step_prev + 1;
}
frame_step_prev = frame_step;
copy_rvec(rerun_fr.x[i], x[i]);
}
copy_mat(rerun_fr.box, state_global->box);
- const matrix &box = state_global->box;
+ const matrix& box = state_global->box;
V = det(box);
logV = log(V);
/* Put all atoms except for the inserted ones on the grid */
rvec vzero = { 0, 0, 0 };
rvec boxDiagonal = { box[XX][XX], box[YY][YY], box[ZZ][ZZ] };
- nbnxn_put_on_grid(fr->nbv.get(), box,
- 0, vzero, boxDiagonal,
- nullptr, { 0, a_tp0 }, -1,
- fr->cginfo, x,
- 0, nullptr);
+ nbnxn_put_on_grid(fr->nbv.get(), box, 0, vzero, boxDiagonal, nullptr, { 0, a_tp0 }, -1,
+ fr->cginfo, x, 0, nullptr);
- step = cr->nodeid*stepblocksize;
+ step = cr->nodeid * stepblocksize;
while (step < nsteps)
{
/* Restart random engine using the frame and insertion step
* wrong you will get an exception when the stream is exhausted.
*/
rng.restart(frame_step, step);
- dist.reset(); // erase any memory in the distribution
+ dist.reset(); // erase any memory in the distribution
if (!bCavity)
{
/* Generate a random position in the box */
for (d = 0; d < DIM; d++)
{
- x_init[d] = dist(rng)*state_global->box[d][d];
+ x_init[d] = dist(rng) * state_global->box[d][d];
}
}
}
if (nat_cavity == 1)
{
/* Copy the location of the cavity */
- copy_rvec(rerun_fr.x[rerun_fr.natoms-1], x_init);
+ copy_rvec(rerun_fr.x[rerun_fr.natoms - 1], x_init);
}
else
{
{
for (d = 0; d < DIM; d++)
{
- x_init[d] +=
- mass_cavity[i]*rerun_fr.x[rerun_fr.natoms-nat_cavity+i][d];
+ x_init[d] += mass_cavity[i]
+ * rerun_fr.x[rerun_fr.natoms - nat_cavity + i][d];
}
mass_tot += mass_cavity[i];
}
}
/* Put the inserted molecule on it's own search grid */
- nbnxn_put_on_grid(fr->nbv.get(), box,
- 1, x_init, x_init,
- nullptr, { a_tp0, a_tp1 }, -1,
- fr->cginfo, x,
- 0, nullptr);
+ nbnxn_put_on_grid(fr->nbv.get(), box, 1, x_init, x_init, nullptr, { a_tp0, a_tp1 },
+ -1, fr->cginfo, x, 0, nullptr);
/* TODO: Avoid updating all atoms at every bNS step */
fr->nbv->setAtomProperties(*mdatoms, fr->cginfo);
- fr->nbv->constructPairlist(InteractionLocality::Local,
- &top.excls, step, nrnb);
+ fr->nbv->constructPairlist(InteractionLocality::Local, &top.excls, step, nrnb);
bNS = FALSE;
}
{
for (d = 0; d < DIM; d++)
{
- dx[d] = (2*dist(rng) - 1)*drmax;
+ dx[d] = (2 * dist(rng) - 1) * drmax;
}
- }
- while (norm2(dx) > drmax*drmax);
+ } while (norm2(dx) > drmax * drmax);
rvec_add(x_init, dx, x_tp);
}
else
/* Copy the coordinates from the top file */
for (i = a_tp0; i < a_tp1; i++)
{
- copy_rvec(x_mol[i-a_tp0], x[i]);
+ copy_rvec(x_mol[i - a_tp0], x[i]);
}
/* Rotate the molecule randomly */
- real angleX = 2*M_PI*dist(rng);
- real angleY = 2*M_PI*dist(rng);
- real angleZ = 2*M_PI*dist(rng);
- rotate_conf(a_tp1-a_tp0, state_global->x.rvec_array()+a_tp0, nullptr,
- angleX, angleY, angleZ);
+ real angleX = 2 * M_PI * dist(rng);
+ real angleY = 2 * M_PI * dist(rng);
+ real angleZ = 2 * M_PI * dist(rng);
+ rotate_conf(a_tp1 - a_tp0, state_global->x.rvec_array() + a_tp0, nullptr, angleX,
+ angleY, angleZ);
/* Shift to the insertion location */
for (i = a_tp0; i < a_tp1; i++)
{
// might raise, then restore the old behaviour.
std::fenv_t floatingPointEnvironment;
std::feholdexcept(&floatingPointEnvironment);
- do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession,
- pull_work,
- step, nrnb, wcycle, &top,
- state_global->box, state_global->x.arrayRefWithPadding(), &state_global->hist,
- f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
- state_global->lambda,
- nullptr, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
- GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY |
- (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
+ do_force(fplog, cr, ms, inputrec, nullptr, nullptr, imdSession, pull_work, step, nrnb,
+ wcycle, &top, state_global->box, state_global->x.arrayRefWithPadding(),
+ &state_global->hist, f.arrayRefWithPadding(), force_vir, mdatoms, enerd, fcd,
+ state_global->lambda, nullptr, fr, runScheduleWork, nullptr, mu_tot, t, nullptr,
+ GMX_FORCE_NONBONDED | GMX_FORCE_ENERGY | (bStateChanged ? GMX_FORCE_STATECHANGED : 0),
DDBalanceRegionHandler(nullptr));
std::feclearexcept(FE_DIVBYZERO | FE_INVALID | FE_OVERFLOW);
std::feupdateenv(&floatingPointEnvironment);
{
/* Calculate long range corrections to pressure and energy */
const DispersionCorrection::Correction correction =
- fr->dispersionCorrection->calculate(state_global->box, lambda);
+ fr->dispersionCorrection->calculate(state_global->box, lambda);
/* figure out how to rearrange the next 4 lines MRS 8/4/2009 */
enerd->term[F_DISPCORR] = correction.energy;
- enerd->term[F_EPOT] += correction.energy;
- enerd->term[F_PRES] += correction.pressure;
- enerd->term[F_DVDL] += correction.dvdl;
+ enerd->term[F_EPOT] += correction.energy;
+ enerd->term[F_PRES] += correction.pressure;
+ enerd->term[F_DVDL] += correction.dvdl;
}
else
{
- enerd->term[F_DISPCORR] = 0;
+ enerd->term[F_DISPCORR] = 0;
}
if (EEL_RF(fr->ic->eeltype))
{
- enerd->term[F_EPOT] += rfExclusionEnergy;
+ enerd->term[F_EPOT] += rfExclusionEnergy;
}
epot = enerd->term[F_EPOT];
{
if (debug)
{
- fprintf(debug, "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t, static_cast<int>(step), epot);
+ fprintf(debug,
+ "\n time %.3f, step %d: non-finite energy %f, using exp(-bU)=0\n", t,
+ static_cast<int>(step), epot);
}
embU = 0;
}
else
{
// Exponent argument is fine in SP range, but output can be in DP range
- embU = exp(static_cast<double>(-beta*epot));
+ embU = exp(static_cast<double>(-beta * epot));
sum_embU += embU;
/* Determine the weighted energy contributions of each energy group */
- e = 0;
- sum_UgembU[e++] += epot*embU;
+ 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)]*embU;
+ sum_UgembU[e++] += enerd->grpp.ener[egBHAMSR][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)]*embU;
+ sum_UgembU[e++] += enerd->grpp.ener[egLJSR][GID(i, gid_tp, ngid)] * embU;
}
}
if (bDispCorr)
{
- sum_UgembU[e++] += enerd->term[F_DISPCORR]*embU;
+ sum_UgembU[e++] += enerd->term[F_DISPCORR] * embU;
}
if (bCharge)
{
}
if (bRFExcl)
{
- sum_UgembU[e++] += rfExclusionEnergy*embU;
+ sum_UgembU[e++] += rfExclusionEnergy * embU;
}
if (EEL_FULL(fr->ic->eeltype))
{
- sum_UgembU[e++] += enerd->term[F_COUL_RECIP]*embU;
+ sum_UgembU[e++] += enerd->term[F_COUL_RECIP] * embU;
}
}
}
- if (embU == 0 || beta*epot > bU_bin_limit)
+ if (embU == 0 || beta * epot > bU_bin_limit)
{
bin[0]++;
}
else
{
- i = gmx::roundToInt((bU_logV_bin_limit
- - (beta*epot - logV + refvolshift))*invbinw);
+ i = gmx::roundToInt((bU_logV_bin_limit - (beta * epot - logV + refvolshift)) * invbinw);
if (i < 0)
{
i = 0;
}
if (i >= nbin)
{
- realloc_bins(&bin, &nbin, i+10);
+ realloc_bins(&bin, &nbin, i + 10);
}
bin[i]++;
}
if (debug)
{
- fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n",
- static_cast<int>(step), epot, x_tp[XX], x_tp[YY], x_tp[ZZ]);
+ fprintf(debug, "TPI %7d %12.5e %12.5f %12.5f %12.5f\n", static_cast<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, static_cast<int>(step));
sprintf(str2, "t: %f step %d ener: %f", t, static_cast<int>(step), epot);
- write_sto_conf_mtop(str, str2, top_global, state_global->x.rvec_array(), state_global->v.rvec_array(),
- inputrec->ePBC, state_global->box);
+ write_sto_conf_mtop(str, str2, top_global, state_global->x.rvec_array(),
+ state_global->v.rvec_array(), inputrec->ePBC, state_global->box);
}
step++;
- if ((step/stepblocksize) % cr->nnodes != cr->nodeid)
+ if ((step / stepblocksize) % cr->nnodes != cr->nodeid)
{
/* Skip all steps assigned to the other MPI ranks */
- step += (cr->nnodes - 1)*stepblocksize;
+ 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(1, &sum_embU, cr);
gmx_sumd(nener, sum_UgembU, cr);
}
frame++;
- V_all += V;
- VembU_all += V*sum_embU/nsteps;
+ V_all += V;
+ VembU_all += V * sum_embU / nsteps;
if (fp_tpi)
{
- if (mdrunOptions.verbose || frame%10 == 0 || frame < 10)
+ if (mdrunOptions.verbose || 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(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);
+ 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, " %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 */
+ } /* End of the loop */
walltime_accounting_end_time(walltime_accounting);
close_trx(status);
if (fplog != nullptr)
{
fprintf(fplog, "\n");
- fprintf(fplog, " <V> = %12.5e nm^3\n", V_all/frame);
- const double mu = -log(VembU_all/V_all)/beta;
+ fprintf(fplog, " <V> = %12.5e nm^3\n", V_all / frame);
+ const double mu = -log(VembU_all / V_all) / beta;
fprintf(fplog, " <mu> = %12.5e kJ/mol\n", mu);
if (!std::isfinite(mu))
{
- fprintf(fplog, "\nThe computed chemical potential is not finite - consider increasing the number of steps and/or the number of frames to insert into.\n");
+ fprintf(fplog,
+ "\nThe computed chemical potential is not finite - consider increasing the "
+ "number of steps and/or the number of frames to insert into.\n");
}
}
}
if (MASTER(cr))
{
- fp_tpi = xvgropen(opt2fn("-tpid", nfile, fnm),
- "TPI energy distribution",
+ 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, tpid_leg, oenv);
- for (i = nbin-1; i > 0; i--)
+ 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,
- roundToInt(bin[i]),
- bin[i]*exp(-bUlogV)*V_all/VembU_all);
+ bUlogV = -i / invbinw + bU_logV_bin_limit - refvolshift + log(V_all / frame);
+ fprintf(fp_tpi, "%6.2f %10d %12.5e\n", bUlogV, roundToInt(bin[i]),
+ bin[i] * exp(-bUlogV) * V_all / VembU_all);
}
xvgrclose(fp_tpi);
}
sfree(sum_UgembU);
- walltime_accounting_set_nsteps_done(walltime_accounting, frame*inputrec->nsteps);
+ walltime_accounting_set_nsteps_done(walltime_accounting, frame * inputrec->nsteps);
}
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff