static void tpx2params(FILE *fp, t_inputrec *ir)
{
fprintf(fp, "\\subsection{Simulation settings}\n");
fprintf(fp, "A total of %g ns were simulated with a time step of %g fs.\n",
ir->nsteps*ir->delta_t*0.001, 1000*ir->delta_t);
fprintf(fp, "Neighbor searching was performed every %d steps.\n", ir->nstlist);
fprintf(fp, "The %s algorithm was used for electrostatic interactions.\n",
EELTYPE(ir->coulombtype));
fprintf(fp, "with a cut-off of %g nm.\n", ir->rcoulomb);
if (ir->coulombtype == eelPME)
{
fprintf(fp, "A reciprocal grid of %d x %d x %d cells was used with %dth order B-spline interpolation.\n", ir->nkx, ir->nky, ir->nkz, ir->pme_order);
}
if (ir->rvdw > ir->rlist)
{
fprintf(fp, "A twin-range Van der Waals cut-off (%g/%g nm) was used, where the long range forces were updated during neighborsearching.\n", ir->rlist, ir->rvdw);
}
else
{
fprintf(fp, "A single cut-off of %g was used for Van der Waals interactions.\n", ir->rlist);
}
if (ir->etc != 0)
{
fprintf(fp, "Temperature coupling was done with the %s algorithm.\n",
etcoupl_names[ir->etc]);
}
if (ir->epc != 0)
{
fprintf(fp, "Pressure coupling was done with the %s algorithm.\n",
epcoupl_names[ir->epc]);
}
fprintf(fp, "\n\n");
}
void writeParameterInformation(TextWriter *writer, const t_inputrec &ir, bool writeFormattedText)
{
writeHeader(writer, "Simulation settings", "subsection", writeFormattedText);
writer->writeLine(formatString("A total of %g ns were simulated with a time step of %g fs.",
ir.nsteps*ir.delta_t*0.001, 1000*ir.delta_t));
writer->writeLine(formatString("Neighbor searching was performed every %d steps.", ir.nstlist));
writer->writeLine(formatString("The %s algorithm was used for electrostatic interactions.",
EELTYPE(ir.coulombtype)));
writer->writeLine(formatString("with a cut-off of %g nm.", ir.rcoulomb));
if (ir.coulombtype == eelPME)
{
writer->writeLine(formatString("A reciprocal grid of %d x %d x %d cells was used with %dth order B-spline interpolation.", ir.nkx, ir.nky, ir.nkz, ir.pme_order));
}
writer->writeLine(formatString("A single cut-off of %g nm was used for Van der Waals interactions.", ir.rlist));
if (ir.etc != 0)
{
writer->writeLine(formatString("Temperature coupling was done with the %s algorithm.",
etcoupl_names[ir.etc]));
}
if (ir.epc != 0)
{
writer->writeLine(formatString("Pressure coupling was done with the %s algorithm.",
epcoupl_names[ir.epc]));
}
writer->ensureEmptyLine();
}
void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
gmx_bool bMDPformat)
{
const char *infbuf="inf";
int i;
if (available(fp,ir,indent,title)) {
if (!bMDPformat)
indent=pr_title(fp,indent,title);
PS("integrator",EI(ir->eI));
PSTEP("nsteps",ir->nsteps);
PSTEP("init-step",ir->init_step);
PS("ns-type",ENS(ir->ns_type));
PI("nstlist",ir->nstlist);
PI("ndelta",ir->ndelta);
PI("nstcomm",ir->nstcomm);
PS("comm-mode",ECOM(ir->comm_mode));
PI("nstlog",ir->nstlog);
PI("nstxout",ir->nstxout);
PI("nstvout",ir->nstvout);
PI("nstfout",ir->nstfout);
PI("nstcalcenergy",ir->nstcalcenergy);
PI("nstenergy",ir->nstenergy);
PI("nstxtcout",ir->nstxtcout);
PR("init-t",ir->init_t);
PR("delta-t",ir->delta_t);
PR("xtcprec",ir->xtcprec);
PI("nkx",ir->nkx);
PI("nky",ir->nky);
PI("nkz",ir->nkz);
PI("pme-order",ir->pme_order);
PR("ewald-rtol",ir->ewald_rtol);
PR("ewald-geometry",ir->ewald_geometry);
PR("epsilon-surface",ir->epsilon_surface);
PS("optimize-fft",BOOL(ir->bOptFFT));
PS("ePBC",EPBC(ir->ePBC));
PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
PS("bContinuation",BOOL(ir->bContinuation));
PS("bShakeSOR",BOOL(ir->bShakeSOR));
PS("etc",ETCOUPLTYPE(ir->etc));
PI("nsttcouple",ir->nsttcouple);
PS("epc",EPCOUPLTYPE(ir->epc));
PS("epctype",EPCOUPLTYPETYPE(ir->epct));
PI("nstpcouple",ir->nstpcouple);
PR("tau-p",ir->tau_p);
pr_matrix(fp,indent,"ref-p",ir->ref_p,bMDPformat);
pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
PS("refcoord-scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
if (bMDPformat)
fprintf(fp,"posres-com = %g %g %g\n",ir->posres_com[XX],
ir->posres_com[YY],ir->posres_com[ZZ]);
else
pr_rvec(fp,indent,"posres-com",ir->posres_com,DIM,TRUE);
if (bMDPformat)
fprintf(fp,"posres-comB = %g %g %g\n",ir->posres_comB[XX],
ir->posres_comB[YY],ir->posres_comB[ZZ]);
else
pr_rvec(fp,indent,"posres-comB",ir->posres_comB,DIM,TRUE);
PI("andersen-seed",ir->andersen_seed);
PR("rlist",ir->rlist);
PR("rlistlong",ir->rlistlong);
PR("rtpi",ir->rtpi);
PS("coulombtype",EELTYPE(ir->coulombtype));
PR("rcoulomb-switch",ir->rcoulomb_switch);
PR("rcoulomb",ir->rcoulomb);
PS("vdwtype",EVDWTYPE(ir->vdwtype));
PR("rvdw-switch",ir->rvdw_switch);
PR("rvdw",ir->rvdw);
if (ir->epsilon_r != 0)
PR("epsilon-r",ir->epsilon_r);
else
PS("epsilon-r",infbuf);
if (ir->epsilon_rf != 0)
PR("epsilon-rf",ir->epsilon_rf);
else
PS("epsilon-rf",infbuf);
PR("tabext",ir->tabext);
PS("implicit-solvent",EIMPLICITSOL(ir->implicit_solvent));
PS("gb-algorithm",EGBALGORITHM(ir->gb_algorithm));
PR("gb-epsilon-solvent",ir->gb_epsilon_solvent);
PI("nstgbradii",ir->nstgbradii);
PR("rgbradii",ir->rgbradii);
PR("gb-saltconc",ir->gb_saltconc);
PR("gb-obc-alpha",ir->gb_obc_alpha);
PR("gb-obc-beta",ir->gb_obc_beta);
PR("gb-obc-gamma",ir->gb_obc_gamma);
PR("gb-dielectric-offset",ir->gb_dielectric_offset);
PS("sa-algorithm",ESAALGORITHM(ir->gb_algorithm));
PR("sa-surface-tension",ir->sa_surface_tension);
PS("DispCorr",EDISPCORR(ir->eDispCorr));
PS("free-energy",EFEPTYPE(ir->efep));
PR("init-lambda",ir->init_lambda);
PR("delta-lambda",ir->delta_lambda);
if (!bMDPformat)
{
PI("n-foreign-lambda",ir->n_flambda);
}
if (ir->n_flambda > 0)
{
pr_indent(fp,indent);
fprintf(fp,"foreign-lambda%s",bMDPformat ? " = " : ":");
for(i=0; i<ir->n_flambda; i++)
{
fprintf(fp," %10g",ir->flambda[i]);
}
fprintf(fp,"\n");
}
PR("sc-alpha",ir->sc_alpha);
PI("sc-power",ir->sc_power);
PR("sc-sigma",ir->sc_sigma);
PR("sc-sigma-min",ir->sc_sigma_min);
PI("nstdhdl", ir->nstdhdl);
PS("separate-dhdl-file", SEPDHDLFILETYPE(ir->separate_dhdl_file));
PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(ir->dhdl_derivatives));
PI("dh-hist-size", ir->dh_hist_size);
PD("dh-hist-spacing", ir->dh_hist_spacing);
PI("nwall",ir->nwall);
PS("wall-type",EWALLTYPE(ir->wall_type));
PI("wall-atomtype[0]",ir->wall_atomtype[0]);
PI("wall-atomtype[1]",ir->wall_atomtype[1]);
PR("wall-density[0]",ir->wall_density[0]);
PR("wall-density[1]",ir->wall_density[1]);
PR("wall-ewald-zfac",ir->wall_ewald_zfac);
PS("pull",EPULLTYPE(ir->ePull));
if (ir->ePull != epullNO)
pr_pull(fp,indent,ir->pull);
PS("rotation",BOOL(ir->bRot));
if (ir->bRot)
pr_rot(fp,indent,ir->rot);
PS("disre",EDISRETYPE(ir->eDisre));
PS("disre-weighting",EDISREWEIGHTING(ir->eDisreWeighting));
PS("disre-mixed",BOOL(ir->bDisreMixed));
PR("dr-fc",ir->dr_fc);
PR("dr-tau",ir->dr_tau);
PR("nstdisreout",ir->nstdisreout);
PR("orires-fc",ir->orires_fc);
PR("orires-tau",ir->orires_tau);
PR("nstorireout",ir->nstorireout);
PR("dihre-fc",ir->dihre_fc);
PR("em-stepsize",ir->em_stepsize);
PR("em-tol",ir->em_tol);
PI("niter",ir->niter);
PR("fc-stepsize",ir->fc_stepsize);
PI("nstcgsteep",ir->nstcgsteep);
PI("nbfgscorr",ir->nbfgscorr);
PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
PR("shake-tol",ir->shake_tol);
PI("lincs-order",ir->nProjOrder);
PR("lincs-warnangle",ir->LincsWarnAngle);
PI("lincs-iter",ir->nLincsIter);
PR("bd-fric",ir->bd_fric);
PI("ld-seed",ir->ld_seed);
PR("cos-accel",ir->cos_accel);
pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
PS("adress",BOOL(ir->bAdress));
if (ir->bAdress){
PS("adress_type",EADRESSTYPE(ir->adress->type));
PR("adress_const_wf",ir->adress->const_wf);
PR("adress_ex_width",ir->adress->ex_width);
PR("adress_hy_width",ir->adress->hy_width);
PS("adress_interface_correction",EADRESSICTYPE(ir->adress->icor));
PS("adress_site",EADRESSSITETYPE(ir->adress->site));
PR("adress_ex_force_cap",ir->adress->ex_forcecap);
PS("adress_do_hybridpairs", BOOL(ir->adress->do_hybridpairs));
pr_rvec(fp,indent,"adress_reference_coords",ir->adress->refs,DIM,TRUE);
}
PI("userint1",ir->userint1);
PI("userint2",ir->userint2);
PI("userint3",ir->userint3);
PI("userint4",ir->userint4);
PR("userreal1",ir->userreal1);
PR("userreal2",ir->userreal2);
PR("userreal3",ir->userreal3);
PR("userreal4",ir->userreal4);
pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
PS("bQMMM",BOOL(ir->bQMMM));
PI("QMconstraints",ir->QMconstraints);
PI("QMMMscheme",ir->QMMMscheme);
PR("scalefactor",ir->scalefactor);
pr_qm_opts(fp,indent,"qm-opts",&(ir->opts));
}
}
void do_force_lowlevel(FILE *fplog, gmx_large_int_t step,
t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
t_grpopts *opts,
rvec x[], history_t *hist,
rvec f[],
rvec f_longrange[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_mtop_t *mtop,
gmx_localtop_t *top,
gmx_genborn_t *born,
t_atomtypes *atype,
gmx_bool bBornRadii,
matrix box,
t_lambda *fepvals,
real *lambda,
t_graph *graph,
t_blocka *excl,
rvec mu_tot[],
int flags,
float *cycles_pme)
{
int i, j, status;
int donb_flags;
gmx_bool bDoEpot, bSepDVDL, bSB;
int pme_flags;
matrix boxs;
rvec box_size;
real Vsr, Vlr, Vcorr = 0;
t_pbc pbc;
real dvdgb;
char buf[22];
double clam_i, vlam_i;
real dvdl_dum[efptNR], dvdl, dvdl_nb[efptNR], lam_i[efptNR];
real dvdlsum;
#ifdef GMX_MPI
double t0 = 0.0, t1, t2, t3; /* time measurement for coarse load balancing */
#endif
#define PRINT_SEPDVDL(s, v, dvdlambda) if (bSepDVDL) {fprintf(fplog, sepdvdlformat, s, v, dvdlambda); }
GMX_MPE_LOG(ev_force_start);
set_pbc(&pbc, fr->ePBC, box);
/* reset free energy components */
for (i = 0; i < efptNR; i++)
{
dvdl_nb[i] = 0;
dvdl_dum[i] = 0;
}
/* Reset box */
for (i = 0; (i < DIM); i++)
{
box_size[i] = box[i][i];
}
bSepDVDL = (fr->bSepDVDL && do_per_step(step, ir->nstlog));
debug_gmx();
/* do QMMM first if requested */
if (fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr, x, f, fr, md);
}
if (bSepDVDL)
{
fprintf(fplog, "Step %s: non-bonded V and dVdl for node %d:\n",
gmx_step_str(step, buf), cr->nodeid);
}
/* Call the short range functions all in one go. */
GMX_MPE_LOG(ev_do_fnbf_start);
#ifdef GMX_MPI
/*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
#define TAKETIME FALSE
if (TAKETIME)
{
MPI_Barrier(cr->mpi_comm_mygroup);
t0 = MPI_Wtime();
}
#endif
if (ir->nwall)
{
/* foreign lambda component for walls */
dvdl = do_walls(ir, fr, box, md, x, f, lambda[efptVDW],
enerd->grpp.ener[egLJSR], nrnb);
PRINT_SEPDVDL("Walls", 0.0, dvdl);
enerd->dvdl_lin[efptVDW] += dvdl;
}
/* If doing GB, reset dvda and calculate the Born radii */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsNONBONDED);
for (i = 0; i < born->nr; i++)
{
fr->dvda[i] = 0;
}
if (bBornRadii)
{
calc_gb_rad(cr, fr, ir, top, atype, x, &(fr->gblist), born, md, nrnb);
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
}
where();
/* We only do non-bonded calculation with group scheme here, the verlet
* calls are done from do_force_cutsVERLET(). */
if (fr->cutoff_scheme == ecutsGROUP && (flags & GMX_FORCE_NONBONDED))
{
donb_flags = 0;
/* Add short-range interactions */
donb_flags |= GMX_NONBONDED_DO_SR;
if (flags & GMX_FORCE_FORCES)
{
donb_flags |= GMX_NONBONDED_DO_FORCE;
}
if (flags & GMX_FORCE_ENERGY)
{
donb_flags |= GMX_NONBONDED_DO_POTENTIAL;
}
if (flags & GMX_FORCE_DO_LR)
{
donb_flags |= GMX_NONBONDED_DO_LR;
}
wallcycle_sub_start(wcycle, ewcsNONBONDED);
do_nonbonded(cr, fr, x, f, f_longrange, md, excl,
&enerd->grpp, box_size, nrnb,
lambda, dvdl_nb, -1, -1, donb_flags);
/* If we do foreign lambda and we have soft-core interactions
* we have to recalculate the (non-linear) energies contributions.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) && fepvals->sc_alpha != 0)
{
for (i = 0; i < enerd->n_lambda; i++)
{
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
reset_foreign_enerdata(enerd);
do_nonbonded(cr, fr, x, f, f_longrange, md, excl,
&(enerd->foreign_grpp), box_size, nrnb,
lam_i, dvdl_dum, -1, -1,
(donb_flags & ~GMX_NONBONDED_DO_FORCE) | GMX_NONBONDED_DO_FOREIGNLAMBDA);
sum_epot(&ir->opts, &(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
wallcycle_sub_stop(wcycle, ewcsNONBONDED);
where();
}
/* If we are doing GB, calculate bonded forces and apply corrections
* to the solvation forces */
/* MRS: Eventually, many need to include free energy contribution here! */
if (ir->implicit_solvent)
{
wallcycle_sub_start(wcycle, ewcsBONDED);
calc_gb_forces(cr, md, born, top, atype, x, f, fr, idef,
ir->gb_algorithm, ir->sa_algorithm, nrnb, bBornRadii, &pbc, graph, enerd);
wallcycle_sub_stop(wcycle, ewcsBONDED);
}
#ifdef GMX_MPI
if (TAKETIME)
{
t1 = MPI_Wtime();
fr->t_fnbf += t1-t0;
}
#endif
if (fepvals->sc_alpha != 0)
{
enerd->dvdl_nonlin[efptVDW] += dvdl_nb[efptVDW];
}
else
{
enerd->dvdl_lin[efptVDW] += dvdl_nb[efptVDW];
}
if (fepvals->sc_alpha != 0)
/* even though coulomb part is linear, we already added it, beacuse we
need to go through the vdw calculation anyway */
{
enerd->dvdl_nonlin[efptCOUL] += dvdl_nb[efptCOUL];
}
else
{
enerd->dvdl_lin[efptCOUL] += dvdl_nb[efptCOUL];
}
Vsr = 0;
if (bSepDVDL)
{
for (i = 0; i < enerd->grpp.nener; i++)
{
Vsr +=
(fr->bBHAM ?
enerd->grpp.ener[egBHAMSR][i] :
enerd->grpp.ener[egLJSR][i])
+ enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
}
dvdlsum = dvdl_nb[efptVDW] + dvdl_nb[efptCOUL];
PRINT_SEPDVDL("VdW and Coulomb SR particle-p.", Vsr, dvdlsum);
}
debug_gmx();
GMX_MPE_LOG(ev_do_fnbf_finish);
if (debug)
{
pr_rvecs(debug, 0, "fshift after SR", fr->fshift, SHIFTS);
}
/* Shift the coordinates. Must be done before bonded forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no bonded forces have to be evaluated.
*/
/* Here sometimes we would not need to shift with NBFonly,
* but we do so anyhow for consistency of the returned coordinates.
*/
if (graph)
{
shift_self(graph, box, x);
if (TRICLINIC(box))
{
inc_nrnb(nrnb, eNR_SHIFTX, 2*graph->nnodes);
}
else
{
inc_nrnb(nrnb, eNR_SHIFTX, graph->nnodes);
}
}
/* Check whether we need to do bondeds or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_BONDED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype)))
{
/* Since all atoms are in the rectangular or triclinic unit-cell,
* only single box vector shifts (2 in x) are required.
*/
set_pbc_dd(&pbc, fr->ePBC, cr->dd, TRUE, box);
}
debug_gmx();
if (flags & GMX_FORCE_BONDED)
{
GMX_MPE_LOG(ev_calc_bonds_start);
wallcycle_sub_start(wcycle, ewcsBONDED);
calc_bonds(fplog, cr->ms,
idef, x, hist, f, fr, &pbc, graph, enerd, nrnb, lambda, md, fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
flags,
fr->bSepDVDL && do_per_step(step, ir->nstlog), step);
/* Check if we have to determine energy differences
* at foreign lambda's.
*/
if (fepvals->n_lambda > 0 && (flags & GMX_FORCE_DHDL) &&
idef->ilsort != ilsortNO_FE)
{
if (idef->ilsort != ilsortFE_SORTED)
{
gmx_incons("The bonded interactions are not sorted for free energy");
}
for (i = 0; i < enerd->n_lambda; i++)
{
reset_foreign_enerdata(enerd);
for (j = 0; j < efptNR; j++)
{
lam_i[j] = (i == 0 ? lambda[j] : fepvals->all_lambda[j][i-1]);
}
calc_bonds_lambda(fplog, idef, x, fr, &pbc, graph, &(enerd->foreign_grpp), enerd->foreign_term, nrnb, lam_i, md,
fcd, DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
sum_epot(&ir->opts, &(enerd->foreign_grpp), enerd->foreign_term);
enerd->enerpart_lambda[i] += enerd->foreign_term[F_EPOT];
}
}
debug_gmx();
GMX_MPE_LOG(ev_calc_bonds_finish);
wallcycle_sub_stop(wcycle, ewcsBONDED);
}
where();
*cycles_pme = 0;
if (EEL_FULL(fr->eeltype))
{
bSB = (ir->nwall == 2);
if (bSB)
{
copy_mat(box, boxs);
svmul(ir->wall_ewald_zfac, boxs[ZZ], boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
clear_mat(fr->vir_el_recip);
if (fr->bEwald)
{
Vcorr = 0;
dvdl = 0;
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
*/
/* The TPI molecule does not have exclusions with the rest
* of the system and no intra-molecular PME grid contributions
* will be calculated in gmx_pme_calc_energy.
*/
if ((ir->cutoff_scheme == ecutsGROUP && fr->n_tpi == 0) ||
ir->ewald_geometry != eewg3D ||
ir->epsilon_surface != 0)
{
int nthreads, t;
wallcycle_sub_start(wcycle, ewcsEWALD_CORRECTION);
if (fr->n_tpi > 0)
{
gmx_fatal(FARGS, "TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
}
nthreads = gmx_omp_nthreads_get(emntBonded);
#pragma omp parallel for num_threads(nthreads) schedule(static)
for (t = 0; t < nthreads; t++)
{
int s, e, i;
rvec *fnv;
tensor *vir;
real *Vcorrt, *dvdlt;
if (t == 0)
{
fnv = fr->f_novirsum;
vir = &fr->vir_el_recip;
Vcorrt = &Vcorr;
dvdlt = &dvdl;
}
else
{
fnv = fr->f_t[t].f;
vir = &fr->f_t[t].vir;
Vcorrt = &fr->f_t[t].Vcorr;
dvdlt = &fr->f_t[t].dvdl[efptCOUL];
for (i = 0; i < fr->natoms_force; i++)
{
clear_rvec(fnv[i]);
}
clear_mat(*vir);
}
*dvdlt = 0;
*Vcorrt =
ewald_LRcorrection(fplog,
fr->excl_load[t], fr->excl_load[t+1],
cr, t, fr,
md->chargeA,
md->nChargePerturbed ? md->chargeB : NULL,
ir->cutoff_scheme != ecutsVERLET,
excl, x, bSB ? boxs : box, mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
fnv, *vir,
lambda[efptCOUL], dvdlt);
}
if (nthreads > 1)
{
reduce_thread_forces(fr->natoms_force, fr->f_novirsum,
fr->vir_el_recip,
&Vcorr, efptCOUL, &dvdl,
nthreads, fr->f_t);
}
wallcycle_sub_stop(wcycle, ewcsEWALD_CORRECTION);
}
if (fr->n_tpi == 0)
{
Vcorr += ewald_charge_correction(cr, fr, lambda[efptCOUL], box,
&dvdl, fr->vir_el_recip);
}
PRINT_SEPDVDL("Ewald excl./charge/dip. corr.", Vcorr, dvdl);
enerd->dvdl_lin[efptCOUL] += dvdl;
}
status = 0;
Vlr = 0;
dvdl = 0;
switch (fr->eeltype)
{
case eelPME:
case eelPMESWITCH:
case eelPMEUSER:
case eelPMEUSERSWITCH:
case eelP3M_AD:
if (cr->duty & DUTY_PME)
{
assert(fr->n_tpi >= 0);
if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
{
pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
if (flags & GMX_FORCE_FORCES)
{
pme_flags |= GMX_PME_CALC_F;
}
if (flags & (GMX_FORCE_VIRIAL | GMX_FORCE_ENERGY))
{
pme_flags |= GMX_PME_CALC_ENER_VIR;
}
if (fr->n_tpi > 0)
{
/* We don't calculate f, but we do want the potential */
pme_flags |= GMX_PME_CALC_POT;
}
wallcycle_start(wcycle, ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
md->start, md->homenr - fr->n_tpi,
x, fr->f_novirsum,
md->chargeA, md->chargeB,
bSB ? boxs : box, cr,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb, wcycle,
fr->vir_el_recip, fr->ewaldcoeff,
&Vlr, lambda[efptCOUL], &dvdl,
pme_flags);
*cycles_pme = wallcycle_stop(wcycle, ewcPMEMESH);
/* We should try to do as little computation after
* this as possible, because parallel PME synchronizes
* the nodes, so we want all load imbalance of the rest
* of the force calculation to be before the PME call.
* DD load balancing is done on the whole time of
* the force call (without PME).
*/
}
if (fr->n_tpi > 0)
{
/* Determine the PME grid energy of the test molecule
* with the PME grid potential of the other charges.
*/
gmx_pme_calc_energy(fr->pmedata, fr->n_tpi,
x + md->homenr - fr->n_tpi,
md->chargeA + md->homenr - fr->n_tpi,
&Vlr);
}
PRINT_SEPDVDL("PME mesh", Vlr, dvdl);
}
break;
case eelEWALD:
Vlr = do_ewald(fplog, FALSE, ir, x, fr->f_novirsum,
md->chargeA, md->chargeB,
box_size, cr, md->homenr,
fr->vir_el_recip, fr->ewaldcoeff,
lambda[efptCOUL], &dvdl, fr->ewald_table);
PRINT_SEPDVDL("Ewald long-range", Vlr, dvdl);
break;
default:
gmx_fatal(FARGS, "No such electrostatics method implemented %s",
eel_names[fr->eeltype]);
}
if (status != 0)
{
gmx_fatal(FARGS, "Error %d in long range electrostatics routine %s",
status, EELTYPE(fr->eeltype));
}
/* Note that with separate PME nodes we get the real energies later */
enerd->dvdl_lin[efptCOUL] += dvdl;
enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
if (debug)
{
fprintf(debug, "Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
Vlr, Vcorr, enerd->term[F_COUL_RECIP]);
pr_rvecs(debug, 0, "vir_el_recip after corr", fr->vir_el_recip, DIM);
pr_rvecs(debug, 0, "fshift after LR Corrections", fr->fshift, SHIFTS);
}
}
else
{
if (EEL_RF(fr->eeltype))
{
/* With the Verlet scheme exclusion forces are calculated
* in the non-bonded kernel.
*/
if (ir->cutoff_scheme != ecutsVERLET && fr->eeltype != eelRF_NEC)
{
dvdl = 0;
enerd->term[F_RF_EXCL] =
RF_excl_correction(fplog, fr, graph, md, excl, x, f,
fr->fshift, &pbc, lambda[efptCOUL], &dvdl);
}
enerd->dvdl_lin[efptCOUL] += dvdl;
PRINT_SEPDVDL("RF exclusion correction",
enerd->term[F_RF_EXCL], dvdl);
}
}
where();
debug_gmx();
if (debug)
{
print_nrnb(debug, nrnb);
}
debug_gmx();
#ifdef GMX_MPI
if (TAKETIME)
{
t2 = MPI_Wtime();
MPI_Barrier(cr->mpi_comm_mygroup);
t3 = MPI_Wtime();
fr->t_wait += t3-t2;
if (fr->timesteps == 11)
{
fprintf(stderr, "* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
cr->nodeid, gmx_step_str(fr->timesteps, buf),
100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
(fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
}
fr->timesteps++;
}
#endif
if (debug)
{
pr_rvecs(debug, 0, "fshift after bondeds", fr->fshift, SHIFTS);
}
GMX_MPE_LOG(ev_force_finish);
}
void do_force_lowlevel(FILE *fplog, gmx_large_int_t step,
t_forcerec *fr, t_inputrec *ir,
t_idef *idef, t_commrec *cr,
t_nrnb *nrnb, gmx_wallcycle_t wcycle,
t_mdatoms *md,
t_grpopts *opts,
rvec x[], history_t *hist,
rvec f[],
gmx_enerdata_t *enerd,
t_fcdata *fcd,
gmx_mtop_t *mtop,
gmx_localtop_t *top,
gmx_genborn_t *born,
t_atomtypes *atype,
gmx_bool bBornRadii,
matrix box,
real lambda,
t_graph *graph,
t_blocka *excl,
rvec mu_tot[],
int flags,
float *cycles_pme)
{
int i,status;
int donb_flags;
gmx_bool bDoEpot,bSepDVDL,bSB;
int pme_flags;
matrix boxs;
rvec box_size;
real dvdlambda,Vsr,Vlr,Vcorr=0,vdip,vcharge;
t_pbc pbc;
real dvdgb;
char buf[22];
gmx_enerdata_t ed_lam;
double lam_i;
real dvdl_dum;
#ifdef GMX_MPI
double t0=0.0,t1,t2,t3; /* time measurement for coarse load balancing */
#endif
#define PRINT_SEPDVDL(s,v,dvdl) if (bSepDVDL) fprintf(fplog,sepdvdlformat,s,v,dvdl);
GMX_MPE_LOG(ev_force_start);
set_pbc(&pbc,fr->ePBC,box);
/* Reset box */
for(i=0; (i<DIM); i++)
{
box_size[i]=box[i][i];
}
bSepDVDL=(fr->bSepDVDL && do_per_step(step,ir->nstlog));
debug_gmx();
/* do QMMM first if requested */
if(fr->bQMMM)
{
enerd->term[F_EQM] = calculate_QMMM(cr,x,f,fr,md);
}
if (bSepDVDL)
{
fprintf(fplog,"Step %s: non-bonded V and dVdl for node %d:\n",
gmx_step_str(step,buf),cr->nodeid);
}
/* Call the short range functions all in one go. */
GMX_MPE_LOG(ev_do_fnbf_start);
dvdlambda = 0;
#ifdef GMX_MPI
/*#define TAKETIME ((cr->npmenodes) && (fr->timesteps < 12))*/
#define TAKETIME FALSE
if (TAKETIME)
{
MPI_Barrier(cr->mpi_comm_mygroup);
t0=MPI_Wtime();
}
#endif
if (ir->nwall)
{
dvdlambda = do_walls(ir,fr,box,md,x,f,lambda,
enerd->grpp.ener[egLJSR],nrnb);
PRINT_SEPDVDL("Walls",0.0,dvdlambda);
enerd->dvdl_lin += dvdlambda;
}
/* If doing GB, reset dvda and calculate the Born radii */
if (ir->implicit_solvent)
{
/* wallcycle_start(wcycle,ewcGB); */
for(i=0; i<born->nr; i++)
{
fr->dvda[i]=0;
}
if(bBornRadii)
{
calc_gb_rad(cr,fr,ir,top,atype,x,&(fr->gblist),born,md,nrnb);
}
/* wallcycle_stop(wcycle, ewcGB); */
}
where();
donb_flags = 0;
if (flags & GMX_FORCE_FORCES)
{
donb_flags |= GMX_DONB_FORCES;
}
do_nonbonded(cr,fr,x,f,md,excl,
fr->bBHAM ?
enerd->grpp.ener[egBHAMSR] :
enerd->grpp.ener[egLJSR],
enerd->grpp.ener[egCOULSR],
enerd->grpp.ener[egGB],box_size,nrnb,
lambda,&dvdlambda,-1,-1,donb_flags);
/* If we do foreign lambda and we have soft-core interactions
* we have to recalculate the (non-linear) energies contributions.
*/
if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) && ir->sc_alpha != 0)
{
init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
for(i=0; i<enerd->n_lambda; i++)
{
lam_i = (i==0 ? lambda : ir->flambda[i-1]);
dvdl_dum = 0;
reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
do_nonbonded(cr,fr,x,f,md,excl,
fr->bBHAM ?
ed_lam.grpp.ener[egBHAMSR] :
ed_lam.grpp.ener[egLJSR],
ed_lam.grpp.ener[egCOULSR],
enerd->grpp.ener[egGB], box_size,nrnb,
lam_i,&dvdl_dum,-1,-1,
GMX_DONB_FOREIGNLAMBDA);
sum_epot(&ir->opts,&ed_lam);
enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
}
destroy_enerdata(&ed_lam);
}
where();
/* If we are doing GB, calculate bonded forces and apply corrections
* to the solvation forces */
if (ir->implicit_solvent) {
calc_gb_forces(cr,md,born,top,atype,x,f,fr,idef,
ir->gb_algorithm,ir->sa_algorithm,nrnb,bBornRadii,&pbc,graph,enerd);
}
#ifdef GMX_MPI
if (TAKETIME)
{
t1=MPI_Wtime();
fr->t_fnbf += t1-t0;
}
#endif
if (ir->sc_alpha != 0)
{
enerd->dvdl_nonlin += dvdlambda;
}
else
{
enerd->dvdl_lin += dvdlambda;
}
Vsr = 0;
if (bSepDVDL)
{
for(i=0; i<enerd->grpp.nener; i++)
{
Vsr +=
(fr->bBHAM ?
enerd->grpp.ener[egBHAMSR][i] :
enerd->grpp.ener[egLJSR][i])
+ enerd->grpp.ener[egCOULSR][i] + enerd->grpp.ener[egGB][i];
}
}
PRINT_SEPDVDL("VdW and Coulomb SR particle-p.",Vsr,dvdlambda);
debug_gmx();
GMX_MPE_LOG(ev_do_fnbf_finish);
if (debug)
{
pr_rvecs(debug,0,"fshift after SR",fr->fshift,SHIFTS);
}
/* Shift the coordinates. Must be done before bonded forces and PPPM,
* but is also necessary for SHAKE and update, therefore it can NOT
* go when no bonded forces have to be evaluated.
*/
/* Here sometimes we would not need to shift with NBFonly,
* but we do so anyhow for consistency of the returned coordinates.
*/
if (graph)
{
shift_self(graph,box,x);
if (TRICLINIC(box))
{
inc_nrnb(nrnb,eNR_SHIFTX,2*graph->nnodes);
}
else
{
inc_nrnb(nrnb,eNR_SHIFTX,graph->nnodes);
}
}
/* Check whether we need to do bondeds or correct for exclusions */
if (fr->bMolPBC &&
((flags & GMX_FORCE_BONDED)
|| EEL_RF(fr->eeltype) || EEL_FULL(fr->eeltype)))
{
/* Since all atoms are in the rectangular or triclinic unit-cell,
* only single box vector shifts (2 in x) are required.
*/
set_pbc_dd(&pbc,fr->ePBC,cr->dd,TRUE,box);
}
debug_gmx();
if (flags & GMX_FORCE_BONDED)
{
GMX_MPE_LOG(ev_calc_bonds_start);
calc_bonds(fplog,cr->ms,
idef,x,hist,f,fr,&pbc,graph,enerd,nrnb,lambda,md,fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL, atype, born,
fr->bSepDVDL && do_per_step(step,ir->nstlog),step);
/* Check if we have to determine energy differences
* at foreign lambda's.
*/
if (ir->n_flambda > 0 && (flags & GMX_FORCE_DHDL) &&
idef->ilsort != ilsortNO_FE)
{
if (idef->ilsort != ilsortFE_SORTED)
{
gmx_incons("The bonded interactions are not sorted for free energy");
}
init_enerdata(mtop->groups.grps[egcENER].nr,ir->n_flambda,&ed_lam);
for(i=0; i<enerd->n_lambda; i++)
{
lam_i = (i==0 ? lambda : ir->flambda[i-1]);
dvdl_dum = 0;
reset_enerdata(&ir->opts,fr,TRUE,&ed_lam,FALSE);
calc_bonds_lambda(fplog,
idef,x,fr,&pbc,graph,&ed_lam,nrnb,lam_i,md,
fcd,
DOMAINDECOMP(cr) ? cr->dd->gatindex : NULL);
sum_epot(&ir->opts,&ed_lam);
enerd->enerpart_lambda[i] += ed_lam.term[F_EPOT];
}
destroy_enerdata(&ed_lam);
}
debug_gmx();
GMX_MPE_LOG(ev_calc_bonds_finish);
}
where();
*cycles_pme = 0;
if (EEL_FULL(fr->eeltype))
{
bSB = (ir->nwall == 2);
if (bSB)
{
copy_mat(box,boxs);
svmul(ir->wall_ewald_zfac,boxs[ZZ],boxs[ZZ]);
box_size[ZZ] *= ir->wall_ewald_zfac;
}
clear_mat(fr->vir_el_recip);
if (fr->bEwald)
{
if (fr->n_tpi == 0)
{
dvdlambda = 0;
Vcorr = ewald_LRcorrection(fplog,md->start,md->start+md->homenr,
cr,fr,
md->chargeA,
md->nChargePerturbed ? md->chargeB : NULL,
excl,x,bSB ? boxs : box,mu_tot,
ir->ewald_geometry,
ir->epsilon_surface,
lambda,&dvdlambda,&vdip,&vcharge);
PRINT_SEPDVDL("Ewald excl./charge/dip. corr.",Vcorr,dvdlambda);
enerd->dvdl_lin += dvdlambda;
}
else
{
if (ir->ewald_geometry != eewg3D || ir->epsilon_surface != 0)
{
gmx_fatal(FARGS,"TPI with PME currently only works in a 3D geometry with tin-foil boundary conditions");
}
/* The TPI molecule does not have exclusions with the rest
* of the system and no intra-molecular PME grid contributions
* will be calculated in gmx_pme_calc_energy.
*/
Vcorr = 0;
}
}
else
{
Vcorr = shift_LRcorrection(fplog,md->start,md->homenr,cr,fr,
md->chargeA,excl,x,TRUE,box,
fr->vir_el_recip);
}
dvdlambda = 0;
status = 0;
switch (fr->eeltype)
{
case eelPPPM:
status = gmx_pppm_do(fplog,fr->pmedata,FALSE,x,fr->f_novirsum,
md->chargeA,
box_size,fr->phi,cr,md->start,md->homenr,
nrnb,ir->pme_order,&Vlr);
break;
case eelPME:
case eelPMESWITCH:
case eelPMEUSER:
case eelPMEUSERSWITCH:
if (cr->duty & DUTY_PME)
{
if (fr->n_tpi == 0 || (flags & GMX_FORCE_STATECHANGED))
{
pme_flags = GMX_PME_SPREAD_Q | GMX_PME_SOLVE;
if (flags & GMX_FORCE_FORCES)
{
pme_flags |= GMX_PME_CALC_F;
}
if (flags & GMX_FORCE_VIRIAL)
{
pme_flags |= GMX_PME_CALC_ENER_VIR;
}
if (fr->n_tpi > 0)
{
/* We don't calculate f, but we do want the potential */
pme_flags |= GMX_PME_CALC_POT;
}
wallcycle_start(wcycle,ewcPMEMESH);
status = gmx_pme_do(fr->pmedata,
md->start,md->homenr - fr->n_tpi,
x,fr->f_novirsum,
md->chargeA,md->chargeB,
bSB ? boxs : box,cr,
DOMAINDECOMP(cr) ? dd_pme_maxshift_x(cr->dd) : 0,
DOMAINDECOMP(cr) ? dd_pme_maxshift_y(cr->dd) : 0,
nrnb,wcycle,
fr->vir_el_recip,fr->ewaldcoeff,
&Vlr,lambda,&dvdlambda,
pme_flags);
*cycles_pme = wallcycle_stop(wcycle,ewcPMEMESH);
/* We should try to do as little computation after
* this as possible, because parallel PME synchronizes
* the nodes, so we want all load imbalance of the rest
* of the force calculation to be before the PME call.
* DD load balancing is done on the whole time of
* the force call (without PME).
*/
}
if (fr->n_tpi > 0)
{
/* Determine the PME grid energy of the test molecule
* with the PME grid potential of the other charges.
*/
gmx_pme_calc_energy(fr->pmedata,fr->n_tpi,
x + md->homenr - fr->n_tpi,
md->chargeA + md->homenr - fr->n_tpi,
&Vlr);
}
PRINT_SEPDVDL("PME mesh",Vlr,dvdlambda);
}
else
{
/* Energies and virial are obtained later from the PME nodes */
/* but values have to be zeroed out here */
Vlr=0.0;
}
break;
case eelEWALD:
Vlr = do_ewald(fplog,FALSE,ir,x,fr->f_novirsum,
md->chargeA,md->chargeB,
box_size,cr,md->homenr,
fr->vir_el_recip,fr->ewaldcoeff,
lambda,&dvdlambda,fr->ewald_table);
PRINT_SEPDVDL("Ewald long-range",Vlr,dvdlambda);
break;
default:
Vlr = 0;
gmx_fatal(FARGS,"No such electrostatics method implemented %s",
eel_names[fr->eeltype]);
}
if (status != 0)
{
gmx_fatal(FARGS,"Error %d in long range electrostatics routine %s",
status,EELTYPE(fr->eeltype));
}
enerd->dvdl_lin += dvdlambda;
enerd->term[F_COUL_RECIP] = Vlr + Vcorr;
if (debug)
{
fprintf(debug,"Vlr = %g, Vcorr = %g, Vlr_corr = %g\n",
Vlr,Vcorr,enerd->term[F_COUL_RECIP]);
pr_rvecs(debug,0,"vir_el_recip after corr",fr->vir_el_recip,DIM);
pr_rvecs(debug,0,"fshift after LR Corrections",fr->fshift,SHIFTS);
}
}
else
{
if (EEL_RF(fr->eeltype))
{
dvdlambda = 0;
if (fr->eeltype != eelRF_NEC)
{
enerd->term[F_RF_EXCL] =
RF_excl_correction(fplog,fr,graph,md,excl,x,f,
fr->fshift,&pbc,lambda,&dvdlambda);
}
enerd->dvdl_lin += dvdlambda;
PRINT_SEPDVDL("RF exclusion correction",
enerd->term[F_RF_EXCL],dvdlambda);
}
}
where();
debug_gmx();
if (debug)
{
print_nrnb(debug,nrnb);
}
debug_gmx();
#ifdef GMX_MPI
if (TAKETIME)
{
t2=MPI_Wtime();
MPI_Barrier(cr->mpi_comm_mygroup);
t3=MPI_Wtime();
fr->t_wait += t3-t2;
if (fr->timesteps == 11)
{
fprintf(stderr,"* PP load balancing info: node %d, step %s, rel wait time=%3.0f%% , load string value: %7.2f\n",
cr->nodeid, gmx_step_str(fr->timesteps,buf),
100*fr->t_wait/(fr->t_wait+fr->t_fnbf),
(fr->t_fnbf+fr->t_wait)/fr->t_fnbf);
}
fr->timesteps++;
}
#endif
if (debug)
{
pr_rvecs(debug,0,"fshift after bondeds",fr->fshift,SHIFTS);
}
GMX_MPE_LOG(ev_force_finish);
}
void pr_inputrec(FILE *fp,int indent,char *title,t_inputrec *ir)
{
char *infbuf="inf";
if (available(fp,ir,title)) {
indent=pr_title(fp,indent,title);
#define PS(t,s) pr_str(fp,indent,t,s)
#define PI(t,s) pr_int(fp,indent,t,s)
#define PR(t,s) pr_real(fp,indent,t,s)
PS("integrator",EI(ir->eI));
PI("nsteps",ir->nsteps);
PS("ns_type",ENS(ir->ns_type));
PI("nstlist",ir->nstlist);
PI("ndelta",ir->ndelta);
PS("bDomDecomp",BOOL(ir->bDomDecomp));
PI("decomp_dir",ir->decomp_dir);
PI("nstcomm",ir->nstcomm);
PI("nstlog",ir->nstlog);
PI("nstxout",ir->nstxout);
PI("nstvout",ir->nstvout);
PI("nstfout",ir->nstfout);
PI("nstenergy",ir->nstenergy);
PI("nstxtcout",ir->nstxtcout);
PR("init_t",ir->init_t);
PR("delta_t",ir->delta_t);
PR("xtcprec",ir->xtcprec);
PI("nkx",ir->nkx);
PI("nky",ir->nky);
PI("nkz",ir->nkz);
PI("pme_order",ir->pme_order);
PR("ewald_rtol",ir->ewald_rtol);
PR("ewald_geometry",ir->ewald_geometry);
PR("epsilon_surface",ir->epsilon_surface);
PS("optimize_fft",BOOL(ir->bOptFFT));
PS("ePBC",EPBC(ir->ePBC));
PS("bUncStart",BOOL(ir->bUncStart));
PS("bShakeSOR",BOOL(ir->bShakeSOR));
PS("etc",ETCOUPLTYPE(ir->etc));
PS("epc",EPCOUPLTYPE(ir->epc));
PS("epctype",EPCOUPLTYPETYPE(ir->epct));
PR("tau_p",ir->tau_p);
pr_rvecs(fp,indent,"ref_p",ir->ref_p,DIM);
pr_rvecs(fp,indent,"compress",ir->compress,DIM);
PS("bSimAnn",BOOL(ir->bSimAnn));
PR("zero_temp_time",ir->zero_temp_time);
PR("rlist",ir->rlist);
PS("coulombtype",EELTYPE(ir->coulombtype));
PR("rcoulomb_switch",ir->rcoulomb_switch);
PR("rcoulomb",ir->rcoulomb);
PS("vdwtype",EVDWTYPE(ir->vdwtype));
PR("rvdw_switch",ir->rvdw_switch);
PR("rvdw",ir->rvdw);
if (fabs(ir->epsilon_r) > GMX_REAL_MIN)
PR("epsilon_r",ir->epsilon_r);
else
PS("epsilon_r",infbuf);
PS("DispCorr",EDISPCORR(ir->eDispCorr));
PR("fudgeQQ",ir->fudgeQQ);
PS("free_energy",EFEPTYPE(ir->efep));
PR("init_lambda",ir->init_lambda);
PR("sc_alpha",ir->sc_alpha);
PR("sc_sigma",ir->sc_sigma);
PR("delta_lambda",ir->delta_lambda);
PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
PS("disre_mixed",BOOL(ir->bDisreMixed));
PR("dr_fc",ir->dr_fc);
PR("dr_tau",ir->dr_tau);
PR("nstdisreout",ir->nstdisreout);
PR("orires_fc",ir->orires_fc);
PR("orires_tau",ir->orires_tau);
PR("nstorireout",ir->nstorireout);
PR("em_stepsize",ir->em_stepsize);
PR("em_tol",ir->em_tol);
PI("niter",ir->niter);
PR("fc_stepsize",ir->fc_stepsize);
PI("nstcgsteep",ir->nstcgsteep);
PS("ConstAlg",ESHAKETYPE(ir->eConstrAlg));
PR("shake_tol",ir->shake_tol);
PI("lincs_order",ir->nProjOrder);
PR("lincs_warnangle",ir->LincsWarnAngle);
PR("bd_temp",ir->bd_temp);
PR("bd_fric",ir->bd_fric);
PI("ld_seed",ir->ld_seed);
PR("cos_accel",ir->cos_accel);
PI("userint1",ir->userint1);
PI("userint2",ir->userint2);
PI("userint3",ir->userint3);
PI("userint4",ir->userint4);
PR("userreal1",ir->userreal1);
PR("userreal2",ir->userreal2);
PR("userreal3",ir->userreal3);
PR("userreal4",ir->userreal4);
#undef PS
#undef PR
#undef PI
pr_grp_opts(fp,indent,"grpopts",&(ir->opts));
pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]));
pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]));
pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]));
pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]));
pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]));
pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]));
}
}
void pr_inputrec(FILE *fp,int indent,const char *title,t_inputrec *ir,
bool bMDPformat)
{
char *infbuf="inf";
if (available(fp,ir,indent,title)) {
if (!bMDPformat)
indent=pr_title(fp,indent,title);
PS("integrator",EI(ir->eI));
PI("nsteps",ir->nsteps);
PI("init_step",ir->init_step);
PS("ns_type",ENS(ir->ns_type));
PI("nstlist",ir->nstlist);
PI("ndelta",ir->ndelta);
PI("nstcomm",ir->nstcomm);
PS("comm_mode",ECOM(ir->comm_mode));
PI("nstlog",ir->nstlog);
PI("nstxout",ir->nstxout);
PI("nstvout",ir->nstvout);
PI("nstfout",ir->nstfout);
PI("nstenergy",ir->nstenergy);
PI("nstxtcout",ir->nstxtcout);
PR("init_t",ir->init_t);
PR("delta_t",ir->delta_t);
PR("xtcprec",ir->xtcprec);
PI("nkx",ir->nkx);
PI("nky",ir->nky);
PI("nkz",ir->nkz);
PI("pme_order",ir->pme_order);
PR("ewald_rtol",ir->ewald_rtol);
PR("ewald_geometry",ir->ewald_geometry);
PR("epsilon_surface",ir->epsilon_surface);
PS("optimize_fft",BOOL(ir->bOptFFT));
PS("ePBC",EPBC(ir->ePBC));
PS("bPeriodicMols",BOOL(ir->bPeriodicMols));
PS("bContinuation",BOOL(ir->bContinuation));
PS("bShakeSOR",BOOL(ir->bShakeSOR));
PS("etc",ETCOUPLTYPE(ir->etc));
PS("epc",EPCOUPLTYPE(ir->epc));
PS("epctype",EPCOUPLTYPETYPE(ir->epct));
PR("tau_p",ir->tau_p);
pr_matrix(fp,indent,"ref_p",ir->ref_p,bMDPformat);
pr_matrix(fp,indent,"compress",ir->compress,bMDPformat);
PS("refcoord_scaling",EREFSCALINGTYPE(ir->refcoord_scaling));
if (bMDPformat)
fprintf(fp,"posres_com = %g %g %g\n",ir->posres_com[XX],
ir->posres_com[YY],ir->posres_com[ZZ]);
else
pr_rvec(fp,indent,"posres_com",ir->posres_com,DIM,TRUE);
if (bMDPformat)
fprintf(fp,"posres_comB = %g %g %g\n",ir->posres_comB[XX],
ir->posres_comB[YY],ir->posres_comB[ZZ]);
else
pr_rvec(fp,indent,"posres_comB",ir->posres_comB,DIM,TRUE);
PI("andersen_seed",ir->andersen_seed);
PR("rlist",ir->rlist);
PR("rtpi",ir->rtpi);
PS("coulombtype",EELTYPE(ir->coulombtype));
PR("rcoulomb_switch",ir->rcoulomb_switch);
PR("rcoulomb",ir->rcoulomb);
PS("vdwtype",EVDWTYPE(ir->vdwtype));
PR("rvdw_switch",ir->rvdw_switch);
PR("rvdw",ir->rvdw);
if (ir->epsilon_r != 0)
PR("epsilon_r",ir->epsilon_r);
else
PS("epsilon_r",infbuf);
if (ir->epsilon_rf != 0)
PR("epsilon_rf",ir->epsilon_rf);
else
PS("epsilon_rf",infbuf);
PR("tabext",ir->tabext);
PS("implicit_solvent",EIMPLICITSOL(ir->implicit_solvent));
PS("gb_algorithm",EGBALGORITHM(ir->gb_algorithm));
PR("gb_epsilon_solvent",ir->gb_epsilon_solvent);
PI("nstgbradii",ir->nstgbradii);
PR("rgbradii",ir->rgbradii);
PR("gb_saltconc",ir->gb_saltconc);
PR("gb_obc_alpha",ir->gb_obc_alpha);
PR("gb_obc_beta",ir->gb_obc_beta);
PR("gb_obc_gamma",ir->gb_obc_gamma);
PR("sa_surface_tension",ir->sa_surface_tension);
PS("DispCorr",EDISPCORR(ir->eDispCorr));
PS("free_energy",EFEPTYPE(ir->efep));
PR("init_lambda",ir->init_lambda);
PR("sc_alpha",ir->sc_alpha);
PI("sc_power",ir->sc_power);
PR("sc_sigma",ir->sc_sigma);
PR("delta_lambda",ir->delta_lambda);
PI("nwall",ir->nwall);
PS("wall_type",EWALLTYPE(ir->wall_type));
PI("wall_atomtype[0]",ir->wall_atomtype[0]);
PI("wall_atomtype[1]",ir->wall_atomtype[1]);
PR("wall_density[0]",ir->wall_density[0]);
PR("wall_density[1]",ir->wall_density[1]);
PR("wall_ewald_zfac",ir->wall_ewald_zfac);
PS("pull",EPULLTYPE(ir->ePull));
if (ir->ePull != epullNO)
pr_pull(fp,indent,ir->pull);
PS("disre",EDISRETYPE(ir->eDisre));
PS("disre_weighting",EDISREWEIGHTING(ir->eDisreWeighting));
PS("disre_mixed",BOOL(ir->bDisreMixed));
PR("dr_fc",ir->dr_fc);
PR("dr_tau",ir->dr_tau);
PR("nstdisreout",ir->nstdisreout);
PR("orires_fc",ir->orires_fc);
PR("orires_tau",ir->orires_tau);
PR("nstorireout",ir->nstorireout);
PR("dihre-fc",ir->dihre_fc);
PR("em_stepsize",ir->em_stepsize);
PR("em_tol",ir->em_tol);
PI("niter",ir->niter);
PR("fc_stepsize",ir->fc_stepsize);
PI("nstcgsteep",ir->nstcgsteep);
PI("nbfgscorr",ir->nbfgscorr);
PS("ConstAlg",ECONSTRTYPE(ir->eConstrAlg));
PR("shake_tol",ir->shake_tol);
PI("lincs_order",ir->nProjOrder);
PR("lincs_warnangle",ir->LincsWarnAngle);
PI("lincs_iter",ir->nLincsIter);
PR("bd_fric",ir->bd_fric);
PI("ld_seed",ir->ld_seed);
PR("cos_accel",ir->cos_accel);
pr_matrix(fp,indent,"deform",ir->deform,bMDPformat);
PI("userint1",ir->userint1);
PI("userint2",ir->userint2);
PI("userint3",ir->userint3);
PI("userint4",ir->userint4);
PR("userreal1",ir->userreal1);
PR("userreal2",ir->userreal2);
PR("userreal3",ir->userreal3);
PR("userreal4",ir->userreal4);
pr_grp_opts(fp,indent,"grpopts",&(ir->opts),bMDPformat);
pr_cosine(fp,indent,"efield-x",&(ir->ex[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-xt",&(ir->et[XX]),bMDPformat);
pr_cosine(fp,indent,"efield-y",&(ir->ex[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-yt",&(ir->et[YY]),bMDPformat);
pr_cosine(fp,indent,"efield-z",&(ir->ex[ZZ]),bMDPformat);
pr_cosine(fp,indent,"efield-zt",&(ir->et[ZZ]),bMDPformat);
PS("bQMMM",BOOL(ir->bQMMM));
PI("QMconstraints",ir->QMconstraints);
PI("QMMMscheme",ir->QMMMscheme);
PR("scalefactor",ir->scalefactor);
pr_qm_opts(fp,indent,"qm_opts",&(ir->opts));
}
}
