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49 #include "gromacs/math/veccompare.h"
50 #include "gromacs/math/vecdump.h"
51 #include "gromacs/mdtypes/awh_params.h"
52 #include "gromacs/mdtypes/md_enums.h"
53 #include "gromacs/mdtypes/multipletimestepping.h"
54 #include "gromacs/mdtypes/pull_params.h"
55 #include "gromacs/pbcutil/pbc.h"
56 #include "gromacs/utility/compare.h"
57 #include "gromacs/utility/cstringutil.h"
58 #include "gromacs/utility/fatalerror.h"
59 #include "gromacs/utility/keyvaluetree.h"
60 #include "gromacs/utility/smalloc.h"
61 #include "gromacs/utility/snprintf.h"
62 #include "gromacs/utility/strconvert.h"
63 #include "gromacs/utility/stringutil.h"
64 #include "gromacs/utility/textwriter.h"
65 #include "gromacs/utility/txtdump.h"
67 //! Macro to select a bool name
68 #define EBOOL(e) gmx::boolToString(e)
70 /* Default values for nstcalcenergy, used when the are no other restrictions. */
71 constexpr int c_defaultNstCalcEnergy = 10;
73 /* The minimum number of integration steps required for reasonably accurate
74 * integration of first and second order coupling algorithms.
76 const int nstmin_berendsen_tcouple = 5;
77 const int nstmin_berendsen_pcouple = 10;
78 const int nstmin_harmonic = 20;
80 /* Default values for T- and P- coupling intervals, used when the are no other
83 constexpr int c_defaultNstTCouple = 10;
84 constexpr int c_defaultNstPCouple = 10;
86 t_inputrec::t_inputrec()
88 // TODO When this memset is removed, remove the suppression of
89 // gcc -Wno-class-memaccess in a CMakeLists.txt file.
90 std::memset(this, 0, sizeof(*this)); // NOLINT(bugprone-undefined-memory-manipulation)
92 snew(expandedvals, 1);
96 t_inputrec::~t_inputrec()
101 int ir_optimal_nstcalcenergy(const t_inputrec* ir)
111 nst = c_defaultNstCalcEnergy;
116 nst = std::lcm(nst, ir->mtsLevels.back().stepFactor);
122 int tcouple_min_integration_steps(int etc)
128 case etcNO: n = 0; break;
130 case etcYES: n = nstmin_berendsen_tcouple; break;
132 /* V-rescale supports instantaneous rescaling */
135 case etcNOSEHOOVER: n = nstmin_harmonic; break;
137 case etcANDERSENMASSIVE: n = 1; break;
138 default: gmx_incons("Unknown etc value");
144 int ir_optimal_nsttcouple(const t_inputrec* ir)
146 int nmin, nwanted, n;
150 nmin = tcouple_min_integration_steps(ir->etc);
152 nwanted = c_defaultNstTCouple;
155 if (ir->etc != etcNO)
157 for (g = 0; g < ir->opts.ngtc; g++)
159 if (ir->opts.tau_t[g] > 0)
161 tau_min = std::min(tau_min, ir->opts.tau_t[g]);
166 if (nmin == 0 || ir->delta_t * nwanted <= tau_min)
172 n = static_cast<int>(tau_min / (ir->delta_t * nmin) + 0.001);
177 while (nwanted % n != 0)
186 int pcouple_min_integration_steps(int epc)
192 case epcNO: n = 0; break;
195 case epcISOTROPIC: n = nstmin_berendsen_pcouple; break;
196 case epcPARRINELLORAHMAN:
197 case epcMTTK: n = nstmin_harmonic; break;
198 default: gmx_incons("Unknown epc value");
204 int ir_optimal_nstpcouple(const t_inputrec* ir)
206 const int minIntegrationSteps = pcouple_min_integration_steps(ir->epc);
208 const int nwanted = c_defaultNstPCouple;
210 // With multiple time-stepping we can only compute the pressure at slowest steps
211 const int minNstPCouple = (ir->useMts ? ir->mtsLevels.back().stepFactor : 1);
214 if (minIntegrationSteps == 0 || ir->delta_t * nwanted <= ir->tau_p)
220 n = static_cast<int>(ir->tau_p / (ir->delta_t * minIntegrationSteps) + 0.001);
221 if (n < minNstPCouple)
225 // Without MTS we try to make nstpcouple a "nice" number
228 while (nwanted % n != 0)
235 // With MTS, nstpcouple should be a multiple of the slowest MTS interval
238 n = n - (n % minNstPCouple);
244 gmx_bool ir_coulomb_switched(const t_inputrec* ir)
246 return (ir->coulombtype == eelSWITCH || ir->coulombtype == eelSHIFT
247 || ir->coulombtype == eelPMESWITCH || ir->coulombtype == eelPMEUSERSWITCH
248 || ir->coulomb_modifier == eintmodPOTSWITCH || ir->coulomb_modifier == eintmodFORCESWITCH);
251 gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir)
253 return (ir->cutoff_scheme == ecutsVERLET || ir_coulomb_switched(ir)
254 || ir->coulomb_modifier != eintmodNONE || ir->coulombtype == eelRF_ZERO);
257 gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir)
259 return (ir_coulomb_is_zero_at_cutoff(ir) || ir->coulombtype == eelUSER || ir->coulombtype == eelPMEUSER);
262 gmx_bool ir_vdw_switched(const t_inputrec* ir)
264 return (ir->vdwtype == evdwSWITCH || ir->vdwtype == evdwSHIFT
265 || ir->vdw_modifier == eintmodPOTSWITCH || ir->vdw_modifier == eintmodFORCESWITCH);
268 gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir)
270 return (ir->cutoff_scheme == ecutsVERLET || ir_vdw_switched(ir) || ir->vdw_modifier != eintmodNONE);
273 gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir)
275 return (ir_vdw_is_zero_at_cutoff(ir) || ir->vdwtype == evdwUSER);
278 static void done_lambdas(t_lambda* fep)
280 if (fep->n_lambda > 0)
282 for (int i = 0; i < efptNR; i++)
284 sfree(fep->all_lambda[i]);
287 sfree(fep->all_lambda);
290 static void done_t_rot(t_rot* rot)
296 if (rot->grp != nullptr)
298 for (int i = 0; i < rot->ngrp; i++)
300 sfree(rot->grp[i].ind);
301 sfree(rot->grp[i].x_ref);
308 void done_inputrec(t_inputrec* ir)
310 sfree(ir->opts.nrdf);
311 sfree(ir->opts.ref_t);
312 for (int i = 0; i < ir->opts.ngtc; i++)
314 sfree(ir->opts.anneal_time[i]);
315 sfree(ir->opts.anneal_temp[i]);
317 sfree(ir->opts.annealing);
318 sfree(ir->opts.anneal_npoints);
319 sfree(ir->opts.anneal_time);
320 sfree(ir->opts.anneal_temp);
321 sfree(ir->opts.tau_t);
323 sfree(ir->opts.nFreeze);
324 sfree(ir->opts.egp_flags);
325 done_lambdas(ir->fepvals);
327 sfree(ir->expandedvals);
328 sfree(ir->simtempvals);
334 static void pr_grp_opts(FILE* out, int indent, const char* title, const t_grpopts* opts, gmx_bool bMDPformat)
340 fprintf(out, "%s:\n", title);
343 pr_indent(out, indent);
344 fprintf(out, "nrdf%s", bMDPformat ? " = " : ":");
345 for (i = 0; (i < opts->ngtc); i++)
347 fprintf(out, " %10g", opts->nrdf[i]);
351 pr_indent(out, indent);
352 fprintf(out, "ref-t%s", bMDPformat ? " = " : ":");
353 for (i = 0; (i < opts->ngtc); i++)
355 fprintf(out, " %10g", opts->ref_t[i]);
359 pr_indent(out, indent);
360 fprintf(out, "tau-t%s", bMDPformat ? " = " : ":");
361 for (i = 0; (i < opts->ngtc); i++)
363 fprintf(out, " %10g", opts->tau_t[i]);
367 /* Pretty-print the simulated annealing info */
368 fprintf(out, "annealing%s", bMDPformat ? " = " : ":");
369 for (i = 0; (i < opts->ngtc); i++)
371 fprintf(out, " %10s", EANNEAL(opts->annealing[i]));
375 fprintf(out, "annealing-npoints%s", bMDPformat ? " = " : ":");
376 for (i = 0; (i < opts->ngtc); i++)
378 fprintf(out, " %10d", opts->anneal_npoints[i]);
382 for (i = 0; (i < opts->ngtc); i++)
384 if (opts->anneal_npoints[i] > 0)
386 fprintf(out, "annealing-time [%d]:\t", i);
387 for (j = 0; (j < opts->anneal_npoints[i]); j++)
389 fprintf(out, " %10.1f", opts->anneal_time[i][j]);
392 fprintf(out, "annealing-temp [%d]:\t", i);
393 for (j = 0; (j < opts->anneal_npoints[i]); j++)
395 fprintf(out, " %10.1f", opts->anneal_temp[i][j]);
401 pr_indent(out, indent);
402 fprintf(out, "acc:\t");
403 for (i = 0; (i < opts->ngacc); i++)
405 for (m = 0; (m < DIM); m++)
407 fprintf(out, " %10g", opts->acc[i][m]);
412 pr_indent(out, indent);
413 fprintf(out, "nfreeze:");
414 for (i = 0; (i < opts->ngfrz); i++)
416 for (m = 0; (m < DIM); m++)
418 fprintf(out, " %10s", opts->nFreeze[i][m] ? "Y" : "N");
424 for (i = 0; (i < opts->ngener); i++)
426 pr_indent(out, indent);
427 fprintf(out, "energygrp-flags[%3d]:", i);
428 for (m = 0; (m < opts->ngener); m++)
430 fprintf(out, " %d", opts->egp_flags[opts->ngener * i + m]);
438 static void pr_matrix(FILE* fp, int indent, const char* title, const rvec* m, gmx_bool bMDPformat)
443 "%-10s = %g %g %g %g %g %g\n",
454 pr_rvecs(fp, indent, title, m, DIM);
458 #define PS(t, s) pr_str(fp, indent, t, s)
459 #define PI(t, s) pr_int(fp, indent, t, s)
460 #define PSTEP(t, s) pr_int64(fp, indent, t, s)
461 #define PR(t, s) pr_real(fp, indent, t, s)
462 #define PD(t, s) pr_double(fp, indent, t, s)
464 static void pr_pull_group(FILE* fp, int indent, int g, const t_pull_group* pgrp)
466 pr_indent(fp, indent);
467 fprintf(fp, "pull-group %d:\n", g);
469 pr_ivec_block(fp, indent, "atom", pgrp->ind.data(), pgrp->ind.size(), TRUE);
470 pr_rvec(fp, indent, "weight", pgrp->weight.data(), pgrp->weight.size(), TRUE);
471 PI("pbcatom", pgrp->pbcatom);
474 static void pr_pull_coord(FILE* fp, int indent, int c, const t_pull_coord* pcrd)
478 pr_indent(fp, indent);
479 fprintf(fp, "pull-coord %d:\n", c);
480 PS("type", EPULLTYPE(pcrd->eType));
481 if (pcrd->eType == epullEXTERNAL)
483 PS("potential-provider", pcrd->externalPotentialProvider.c_str());
485 PS("geometry", EPULLGEOM(pcrd->eGeom));
486 for (g = 0; g < pcrd->ngroup; g++)
490 sprintf(buf, "group[%d]", g);
491 PI(buf, pcrd->group[g]);
493 pr_ivec(fp, indent, "dim", pcrd->dim, DIM, TRUE);
494 pr_rvec(fp, indent, "origin", pcrd->origin, DIM, TRUE);
495 pr_rvec(fp, indent, "vec", pcrd->vec, DIM, TRUE);
496 PS("start", EBOOL(pcrd->bStart));
497 PR("init", pcrd->init);
498 PR("rate", pcrd->rate);
503 static void pr_simtempvals(FILE* fp, int indent, const t_simtemp* simtemp, int n_lambda)
505 PS("simulated-tempering-scaling", ESIMTEMP(simtemp->eSimTempScale));
506 PR("sim-temp-low", simtemp->simtemp_low);
507 PR("sim-temp-high", simtemp->simtemp_high);
508 pr_rvec(fp, indent, "simulated tempering temperatures", simtemp->temperatures, n_lambda, TRUE);
511 static void pr_expandedvals(FILE* fp, int indent, const t_expanded* expand, int n_lambda)
514 PI("nstexpanded", expand->nstexpanded);
515 PS("lmc-stats", elamstats_names[expand->elamstats]);
516 PS("lmc-move", elmcmove_names[expand->elmcmove]);
517 PS("lmc-weights-equil", elmceq_names[expand->elmceq]);
518 if (expand->elmceq == elmceqNUMATLAM)
520 PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
522 if (expand->elmceq == elmceqSAMPLES)
524 PI("weight-equil-number-samples", expand->equil_samples);
526 if (expand->elmceq == elmceqSTEPS)
528 PI("weight-equil-number-steps", expand->equil_steps);
530 if (expand->elmceq == elmceqWLDELTA)
532 PR("weight-equil-wl-delta", expand->equil_wl_delta);
534 if (expand->elmceq == elmceqRATIO)
536 PR("weight-equil-count-ratio", expand->equil_ratio);
538 PI("lmc-seed", expand->lmc_seed);
539 PR("mc-temperature", expand->mc_temp);
540 PI("lmc-repeats", expand->lmc_repeats);
541 PI("lmc-gibbsdelta", expand->gibbsdeltalam);
542 PI("lmc-forced-nstart", expand->lmc_forced_nstart);
543 PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix));
544 PI("nst-transition-matrix", expand->nstTij);
545 PI("mininum-var-min", expand->minvarmin); /*default is reasonable */
546 PI("weight-c-range", expand->c_range); /* default is just C=0 */
547 PR("wl-scale", expand->wl_scale);
548 PR("wl-ratio", expand->wl_ratio);
549 PR("init-wl-delta", expand->init_wl_delta);
550 PS("wl-oneovert", EBOOL(expand->bWLoneovert));
552 pr_indent(fp, indent);
553 pr_rvec(fp, indent, "init-lambda-weights", expand->init_lambda_weights, n_lambda, TRUE);
554 PS("init-weights", EBOOL(expand->bInit_weights));
557 static void pr_fepvals(FILE* fp, int indent, const t_lambda* fep, gmx_bool bMDPformat)
561 PR("init-lambda", fep->init_lambda);
562 PI("init-lambda-state", fep->init_fep_state);
563 PR("delta-lambda", fep->delta_lambda);
564 PI("nstdhdl", fep->nstdhdl);
568 PI("n-lambdas", fep->n_lambda);
570 if (fep->n_lambda > 0)
572 pr_indent(fp, indent);
573 fprintf(fp, "separate-dvdl%s\n", bMDPformat ? " = " : ":");
574 for (i = 0; i < efptNR; i++)
576 fprintf(fp, "%18s = ", efpt_names[i]);
577 if (fep->separate_dvdl[i])
579 fprintf(fp, " TRUE");
583 fprintf(fp, " FALSE");
587 fprintf(fp, "all-lambdas%s\n", bMDPformat ? " = " : ":");
588 for (i = 0; i < efptNR; i++)
590 fprintf(fp, "%18s = ", efpt_names[i]);
591 for (j = 0; j < fep->n_lambda; j++)
593 fprintf(fp, " %10g", fep->all_lambda[i][j]);
598 PI("calc-lambda-neighbors", fep->lambda_neighbors);
599 PS("dhdl-print-energy", edHdLPrintEnergy_names[fep->edHdLPrintEnergy]);
600 PR("sc-alpha", fep->sc_alpha);
601 PI("sc-power", fep->sc_power);
602 PR("sc-r-power", fep->sc_r_power);
603 PR("sc-sigma", fep->sc_sigma);
604 PR("sc-sigma-min", fep->sc_sigma_min);
605 PS("sc-coul", EBOOL(fep->bScCoul));
606 PI("dh-hist-size", fep->dh_hist_size);
607 PD("dh-hist-spacing", fep->dh_hist_spacing);
608 PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file));
609 PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives));
612 static void pr_pull(FILE* fp, int indent, const pull_params_t& pull)
616 PR("pull-cylinder-r", pull.cylinder_r);
617 PR("pull-constr-tol", pull.constr_tol);
618 PS("pull-print-COM", EBOOL(pull.bPrintCOM));
619 PS("pull-print-ref-value", EBOOL(pull.bPrintRefValue));
620 PS("pull-print-components", EBOOL(pull.bPrintComp));
621 PI("pull-nstxout", pull.nstxout);
622 PI("pull-nstfout", pull.nstfout);
623 PS("pull-pbc-ref-prev-step-com", EBOOL(pull.bSetPbcRefToPrevStepCOM));
624 PS("pull-xout-average", EBOOL(pull.bXOutAverage));
625 PS("pull-fout-average", EBOOL(pull.bFOutAverage));
626 PI("pull-ngroups", pull.ngroup);
627 for (g = 0; g < pull.ngroup; g++)
629 pr_pull_group(fp, indent, g, &pull.group[g]);
631 PI("pull-ncoords", pull.ncoord);
632 for (g = 0; g < pull.ncoord; g++)
634 pr_pull_coord(fp, indent, g, &pull.coord[g]);
638 static void pr_awh_bias_dim(FILE* fp, int indent, gmx::AwhDimParams* awhDimParams, const char* prefix)
640 pr_indent(fp, indent);
642 fprintf(fp, "%s:\n", prefix);
643 PS("coord-provider", EAWHCOORDPROVIDER(awhDimParams->eCoordProvider));
644 PI("coord-index", awhDimParams->coordIndex + 1);
645 PR("start", awhDimParams->origin);
646 PR("end", awhDimParams->end);
647 PR("period", awhDimParams->period);
648 PR("force-constant", awhDimParams->forceConstant);
649 PR("diffusion", awhDimParams->diffusion);
650 PR("cover-diameter", awhDimParams->coverDiameter);
653 static void pr_awh_bias(FILE* fp, int indent, gmx::AwhBiasParams* awhBiasParams, const char* prefix)
657 sprintf(opt, "%s-error-init", prefix);
658 PR(opt, awhBiasParams->errorInitial);
659 sprintf(opt, "%s-growth", prefix);
660 PS(opt, EAWHGROWTH(awhBiasParams->eGrowth));
661 sprintf(opt, "%s-target", prefix);
662 PS(opt, EAWHTARGET(awhBiasParams->eTarget));
663 sprintf(opt, "%s-target-beta-scalng", prefix);
664 PR(opt, awhBiasParams->targetBetaScaling);
665 sprintf(opt, "%s-target-cutoff", prefix);
666 PR(opt, awhBiasParams->targetCutoff);
667 sprintf(opt, "%s-user-data", prefix);
668 PS(opt, EBOOL(awhBiasParams->bUserData));
669 sprintf(opt, "%s-share-group", prefix);
670 PI(opt, awhBiasParams->shareGroup);
671 sprintf(opt, "%s-equilibrate-histogram", prefix);
672 PS(opt, EBOOL(awhBiasParams->equilibrateHistogram));
673 sprintf(opt, "%s-ndim", prefix);
674 PI(opt, awhBiasParams->ndim);
676 for (int d = 0; d < awhBiasParams->ndim; d++)
678 char prefixdim[STRLEN];
679 sprintf(prefixdim, "%s-dim%d", prefix, d + 1);
680 pr_awh_bias_dim(fp, indent, &awhBiasParams->dimParams[d], prefixdim);
684 static void pr_awh(FILE* fp, int indent, gmx::AwhParams* awhParams)
686 PS("awh-potential", EAWHPOTENTIAL(awhParams->ePotential));
687 PI("awh-seed", awhParams->seed);
688 PI("awh-nstout", awhParams->nstOut);
689 PI("awh-nstsample", awhParams->nstSampleCoord);
690 PI("awh-nsamples-update", awhParams->numSamplesUpdateFreeEnergy);
691 PS("awh-share-bias-multisim", EBOOL(awhParams->shareBiasMultisim));
692 PI("awh-nbias", awhParams->numBias);
694 for (int k = 0; k < awhParams->numBias; k++)
696 auto prefix = gmx::formatString("awh%d", k + 1);
697 pr_awh_bias(fp, indent, &awhParams->awhBiasParams[k], prefix.c_str());
701 static void pr_rotgrp(FILE* fp, int indent, int g, const t_rotgrp* rotg)
703 pr_indent(fp, indent);
704 fprintf(fp, "rot-group %d:\n", g);
706 PS("rot-type", EROTGEOM(rotg->eType));
707 PS("rot-massw", EBOOL(rotg->bMassW));
708 pr_ivec_block(fp, indent, "atom", rotg->ind, rotg->nat, TRUE);
709 pr_rvecs(fp, indent, "x-ref", rotg->x_ref, rotg->nat);
710 pr_rvec(fp, indent, "rot-vec", rotg->inputVec, DIM, TRUE);
711 pr_rvec(fp, indent, "rot-pivot", rotg->pivot, DIM, TRUE);
712 PR("rot-rate", rotg->rate);
713 PR("rot-k", rotg->k);
714 PR("rot-slab-dist", rotg->slab_dist);
715 PR("rot-min-gauss", rotg->min_gaussian);
716 PR("rot-eps", rotg->eps);
717 PS("rot-fit-method", EROTFIT(rotg->eFittype));
718 PI("rot-potfit-nstep", rotg->PotAngle_nstep);
719 PR("rot-potfit-step", rotg->PotAngle_step);
722 static void pr_rot(FILE* fp, int indent, const t_rot* rot)
726 PI("rot-nstrout", rot->nstrout);
727 PI("rot-nstsout", rot->nstsout);
728 PI("rot-ngroups", rot->ngrp);
729 for (g = 0; g < rot->ngrp; g++)
731 pr_rotgrp(fp, indent, g, &rot->grp[g]);
736 static void pr_swap(FILE* fp, int indent, const t_swapcoords* swap)
740 /* Enums for better readability of the code */
748 PI("swap-frequency", swap->nstswap);
750 /* The split groups that define the compartments */
751 for (int j = 0; j < 2; j++)
753 snprintf(str, STRLEN, "massw_split%d", j);
754 PS(str, EBOOL(swap->massw_split[j]));
755 snprintf(str, STRLEN, "split atoms group %d", j);
756 pr_ivec_block(fp, indent, str, swap->grp[j].ind, swap->grp[j].nat, TRUE);
759 /* The solvent group */
760 snprintf(str, STRLEN, "solvent group %s", swap->grp[eGrpSolvent].molname);
761 pr_ivec_block(fp, indent, str, swap->grp[eGrpSolvent].ind, swap->grp[eGrpSolvent].nat, TRUE);
763 /* Now print the indices for all the ion groups: */
764 for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
766 snprintf(str, STRLEN, "ion group %s", swap->grp[ig].molname);
767 pr_ivec_block(fp, indent, str, swap->grp[ig].ind, swap->grp[ig].nat, TRUE);
770 PR("cyl0-r", swap->cyl0r);
771 PR("cyl0-up", swap->cyl0u);
772 PR("cyl0-down", swap->cyl0l);
773 PR("cyl1-r", swap->cyl1r);
774 PR("cyl1-up", swap->cyl1u);
775 PR("cyl1-down", swap->cyl1l);
776 PI("coupl-steps", swap->nAverage);
778 /* Print the requested ion counts for both compartments */
779 for (int ic = eCompA; ic <= eCompB; ic++)
781 for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
783 snprintf(str, STRLEN, "%s-in-%c", swap->grp[ig].molname, 'A' + ic);
784 PI(str, swap->grp[ig].nmolReq[ic]);
788 PR("threshold", swap->threshold);
789 PR("bulk-offsetA", swap->bulkOffset[eCompA]);
790 PR("bulk-offsetB", swap->bulkOffset[eCompB]);
794 static void pr_imd(FILE* fp, int indent, const t_IMD* imd)
796 PI("IMD-atoms", imd->nat);
797 pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE);
801 void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, gmx_bool bMDPformat)
803 const char* infbuf = "inf";
805 if (available(fp, ir, indent, title))
809 indent = pr_title(fp, indent, title);
811 /* Try to make this list appear in the same order as the
812 * options are written in the default mdout.mdp, and with
813 * the same user-exposed names to facilitate debugging.
815 PS("integrator", EI(ir->eI));
816 PR("tinit", ir->init_t);
817 PR("dt", ir->delta_t);
818 PSTEP("nsteps", ir->nsteps);
819 PSTEP("init-step", ir->init_step);
820 PI("simulation-part", ir->simulation_part);
821 PS("mts", EBOOL(ir->useMts));
824 for (int mtsIndex = 1; mtsIndex < static_cast<int>(ir->mtsLevels.size()); mtsIndex++)
826 const auto& mtsLevel = ir->mtsLevels[mtsIndex];
827 const std::string forceKey = gmx::formatString("mts-level%d-forces", mtsIndex + 1);
828 std::string forceGroups;
829 for (int i = 0; i < static_cast<int>(gmx::MtsForceGroups::Count); i++)
831 if (mtsLevel.forceGroups[i])
833 if (!forceGroups.empty())
837 forceGroups += gmx::mtsForceGroupNames[i];
840 PS(forceKey.c_str(), forceGroups.c_str());
841 const std::string factorKey = gmx::formatString("mts-level%d-factor", mtsIndex + 1);
842 PI(factorKey.c_str(), mtsLevel.stepFactor);
845 PS("comm-mode", ECOM(ir->comm_mode));
846 PI("nstcomm", ir->nstcomm);
848 /* Langevin dynamics */
849 PR("bd-fric", ir->bd_fric);
850 PSTEP("ld-seed", ir->ld_seed);
852 /* Energy minimization */
853 PR("emtol", ir->em_tol);
854 PR("emstep", ir->em_stepsize);
855 PI("niter", ir->niter);
856 PR("fcstep", ir->fc_stepsize);
857 PI("nstcgsteep", ir->nstcgsteep);
858 PI("nbfgscorr", ir->nbfgscorr);
860 /* Test particle insertion */
861 PR("rtpi", ir->rtpi);
864 PI("nstxout", ir->nstxout);
865 PI("nstvout", ir->nstvout);
866 PI("nstfout", ir->nstfout);
867 PI("nstlog", ir->nstlog);
868 PI("nstcalcenergy", ir->nstcalcenergy);
869 PI("nstenergy", ir->nstenergy);
870 PI("nstxout-compressed", ir->nstxout_compressed);
871 PR("compressed-x-precision", ir->x_compression_precision);
873 /* Neighborsearching parameters */
874 PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme));
875 PI("nstlist", ir->nstlist);
876 PS("pbc", c_pbcTypeNames[ir->pbcType].c_str());
877 PS("periodic-molecules", EBOOL(ir->bPeriodicMols));
878 PR("verlet-buffer-tolerance", ir->verletbuf_tol);
879 PR("rlist", ir->rlist);
881 /* Options for electrostatics and VdW */
882 PS("coulombtype", EELTYPE(ir->coulombtype));
883 PS("coulomb-modifier", INTMODIFIER(ir->coulomb_modifier));
884 PR("rcoulomb-switch", ir->rcoulomb_switch);
885 PR("rcoulomb", ir->rcoulomb);
886 if (ir->epsilon_r != 0)
888 PR("epsilon-r", ir->epsilon_r);
892 PS("epsilon-r", infbuf);
894 if (ir->epsilon_rf != 0)
896 PR("epsilon-rf", ir->epsilon_rf);
900 PS("epsilon-rf", infbuf);
902 PS("vdw-type", EVDWTYPE(ir->vdwtype));
903 PS("vdw-modifier", INTMODIFIER(ir->vdw_modifier));
904 PR("rvdw-switch", ir->rvdw_switch);
905 PR("rvdw", ir->rvdw);
906 PS("DispCorr", EDISPCORR(ir->eDispCorr));
907 PR("table-extension", ir->tabext);
909 PR("fourierspacing", ir->fourier_spacing);
910 PI("fourier-nx", ir->nkx);
911 PI("fourier-ny", ir->nky);
912 PI("fourier-nz", ir->nkz);
913 PI("pme-order", ir->pme_order);
914 PR("ewald-rtol", ir->ewald_rtol);
915 PR("ewald-rtol-lj", ir->ewald_rtol_lj);
916 PS("lj-pme-comb-rule", ELJPMECOMBNAMES(ir->ljpme_combination_rule));
917 PR("ewald-geometry", ir->ewald_geometry);
918 PR("epsilon-surface", ir->epsilon_surface);
920 /* Options for weak coupling algorithms */
921 PS("tcoupl", ETCOUPLTYPE(ir->etc));
922 PI("nsttcouple", ir->nsttcouple);
923 PI("nh-chain-length", ir->opts.nhchainlength);
924 PS("print-nose-hoover-chain-variables", EBOOL(ir->bPrintNHChains));
926 PS("pcoupl", EPCOUPLTYPE(ir->epc));
927 PS("pcoupltype", EPCOUPLTYPETYPE(ir->epct));
928 PI("nstpcouple", ir->nstpcouple);
929 PR("tau-p", ir->tau_p);
930 pr_matrix(fp, indent, "compressibility", ir->compress, bMDPformat);
931 pr_matrix(fp, indent, "ref-p", ir->ref_p, bMDPformat);
932 PS("refcoord-scaling", EREFSCALINGTYPE(ir->refcoord_scaling));
936 fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX], ir->posres_com[YY], ir->posres_com[ZZ]);
937 fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX], ir->posres_comB[YY], ir->posres_comB[ZZ]);
941 pr_rvec(fp, indent, "posres-com", ir->posres_com, DIM, TRUE);
942 pr_rvec(fp, indent, "posres-comB", ir->posres_comB, DIM, TRUE);
946 PS("QMMM", EBOOL(ir->bQMMM));
947 fprintf(fp, "%s:\n", "qm-opts");
948 pr_int(fp, indent, "ngQM", ir->opts.ngQM);
950 /* CONSTRAINT OPTIONS */
951 PS("constraint-algorithm", ECONSTRTYPE(ir->eConstrAlg));
952 PS("continuation", EBOOL(ir->bContinuation));
954 PS("Shake-SOR", EBOOL(ir->bShakeSOR));
955 PR("shake-tol", ir->shake_tol);
956 PI("lincs-order", ir->nProjOrder);
957 PI("lincs-iter", ir->nLincsIter);
958 PR("lincs-warnangle", ir->LincsWarnAngle);
961 PI("nwall", ir->nwall);
962 PS("wall-type", EWALLTYPE(ir->wall_type));
963 PR("wall-r-linpot", ir->wall_r_linpot);
965 PI("wall-atomtype[0]", ir->wall_atomtype[0]);
966 PI("wall-atomtype[1]", ir->wall_atomtype[1]);
968 PR("wall-density[0]", ir->wall_density[0]);
969 PR("wall-density[1]", ir->wall_density[1]);
970 PR("wall-ewald-zfac", ir->wall_ewald_zfac);
973 PS("pull", EBOOL(ir->bPull));
976 pr_pull(fp, indent, *ir->pull);
980 PS("awh", EBOOL(ir->bDoAwh));
983 pr_awh(fp, indent, ir->awhParams);
986 /* ENFORCED ROTATION */
987 PS("rotation", EBOOL(ir->bRot));
990 pr_rot(fp, indent, ir->rot);
994 PS("interactiveMD", EBOOL(ir->bIMD));
997 pr_imd(fp, indent, ir->imd);
1000 /* NMR refinement stuff */
1001 PS("disre", EDISRETYPE(ir->eDisre));
1002 PS("disre-weighting", EDISREWEIGHTING(ir->eDisreWeighting));
1003 PS("disre-mixed", EBOOL(ir->bDisreMixed));
1004 PR("dr-fc", ir->dr_fc);
1005 PR("dr-tau", ir->dr_tau);
1006 PR("nstdisreout", ir->nstdisreout);
1008 PR("orire-fc", ir->orires_fc);
1009 PR("orire-tau", ir->orires_tau);
1010 PR("nstorireout", ir->nstorireout);
1012 /* FREE ENERGY VARIABLES */
1013 PS("free-energy", EFEPTYPE(ir->efep));
1014 if (ir->efep != efepNO || ir->bSimTemp)
1016 pr_fepvals(fp, indent, ir->fepvals, bMDPformat);
1020 pr_expandedvals(fp, indent, ir->expandedvals, ir->fepvals->n_lambda);
1023 /* NON-equilibrium MD stuff */
1024 PR("cos-acceleration", ir->cos_accel);
1025 pr_matrix(fp, indent, "deform", ir->deform, bMDPformat);
1027 /* SIMULATED TEMPERING */
1028 PS("simulated-tempering", EBOOL(ir->bSimTemp));
1031 pr_simtempvals(fp, indent, ir->simtempvals, ir->fepvals->n_lambda);
1034 /* ION/WATER SWAPPING FOR COMPUTATIONAL ELECTROPHYSIOLOGY */
1035 PS("swapcoords", ESWAPTYPE(ir->eSwapCoords));
1036 if (ir->eSwapCoords != eswapNO)
1038 pr_swap(fp, indent, ir->swap);
1041 /* USER-DEFINED THINGIES */
1042 PI("userint1", ir->userint1);
1043 PI("userint2", ir->userint2);
1044 PI("userint3", ir->userint3);
1045 PI("userint4", ir->userint4);
1046 PR("userreal1", ir->userreal1);
1047 PR("userreal2", ir->userreal2);
1048 PR("userreal3", ir->userreal3);
1049 PR("userreal4", ir->userreal4);
1053 gmx::TextWriter writer(fp);
1054 writer.wrapperSettings().setIndent(indent);
1055 gmx::dumpKeyValueTree(&writer, *ir->params);
1058 pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat);
1065 static void cmp_grpopts(FILE* fp, const t_grpopts* opt1, const t_grpopts* opt2, real ftol, real abstol)
1068 char buf1[256], buf2[256];
1070 cmp_int(fp, "inputrec->grpopts.ngtc", -1, opt1->ngtc, opt2->ngtc);
1071 cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc);
1072 cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz);
1073 cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener);
1074 for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++)
1076 cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol);
1077 cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol);
1078 cmp_real(fp, "inputrec->grpopts.tau_t", i, opt1->tau_t[i], opt2->tau_t[i], ftol, abstol);
1079 cmp_int(fp, "inputrec->grpopts.annealing", i, opt1->annealing[i], opt2->annealing[i]);
1080 cmp_int(fp, "inputrec->grpopts.anneal_npoints", i, opt1->anneal_npoints[i], opt2->anneal_npoints[i]);
1081 if (opt1->anneal_npoints[i] == opt2->anneal_npoints[i])
1083 sprintf(buf1, "inputrec->grpopts.anneal_time[%d]", i);
1084 sprintf(buf2, "inputrec->grpopts.anneal_temp[%d]", i);
1085 for (j = 0; j < opt1->anneal_npoints[i]; j++)
1087 cmp_real(fp, buf1, j, opt1->anneal_time[i][j], opt2->anneal_time[i][j], ftol, abstol);
1088 cmp_real(fp, buf2, j, opt1->anneal_temp[i][j], opt2->anneal_temp[i][j], ftol, abstol);
1092 if (opt1->ngener == opt2->ngener)
1094 for (i = 0; i < opt1->ngener; i++)
1096 for (j = i; j < opt1->ngener; j++)
1098 sprintf(buf1, "inputrec->grpopts.egp_flags[%d]", i);
1099 cmp_int(fp, buf1, j, opt1->egp_flags[opt1->ngener * i + j], opt2->egp_flags[opt1->ngener * i + j]);
1103 for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++)
1105 cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol);
1107 for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++)
1109 cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]);
1113 static void cmp_pull(FILE* fp)
1116 "WARNING: Both files use COM pulling, but comparing of the pull struct is not "
1117 "implemented (yet). The pull parameters could be the same or different.\n");
1120 static void cmp_awhDimParams(FILE* fp,
1121 const gmx::AwhDimParams* dimp1,
1122 const gmx::AwhDimParams* dimp2,
1127 /* Note that we have double index here, but the compare functions only
1128 * support one index, so here we only print the dim index and not the bias.
1130 cmp_int(fp, "inputrec.awhParams->bias?->dim->coord_index", dimIndex, dimp1->coordIndex, dimp2->coordIndex);
1131 cmp_double(fp, "inputrec->awhParams->bias?->dim->period", dimIndex, dimp1->period, dimp2->period, ftol, abstol);
1132 cmp_double(fp, "inputrec->awhParams->bias?->dim->diffusion", dimIndex, dimp1->diffusion, dimp2->diffusion, ftol, abstol);
1133 cmp_double(fp, "inputrec->awhParams->bias?->dim->origin", dimIndex, dimp1->origin, dimp2->origin, ftol, abstol);
1134 cmp_double(fp, "inputrec->awhParams->bias?->dim->end", dimIndex, dimp1->end, dimp2->end, ftol, abstol);
1136 "inputrec->awhParams->bias?->dim->coord_value_init",
1138 dimp1->coordValueInit,
1139 dimp2->coordValueInit,
1143 "inputrec->awhParams->bias?->dim->coverDiameter",
1145 dimp1->coverDiameter,
1146 dimp2->coverDiameter,
1151 static void cmp_awhBiasParams(FILE* fp,
1152 const gmx::AwhBiasParams* bias1,
1153 const gmx::AwhBiasParams* bias2,
1158 cmp_int(fp, "inputrec->awhParams->ndim", biasIndex, bias1->ndim, bias2->ndim);
1159 cmp_int(fp, "inputrec->awhParams->biaseTarget", biasIndex, bias1->eTarget, bias2->eTarget);
1161 "inputrec->awhParams->biastargetBetaScaling",
1163 bias1->targetBetaScaling,
1164 bias2->targetBetaScaling,
1168 "inputrec->awhParams->biastargetCutoff",
1170 bias1->targetCutoff,
1171 bias2->targetCutoff,
1174 cmp_int(fp, "inputrec->awhParams->biaseGrowth", biasIndex, bias1->eGrowth, bias2->eGrowth);
1175 cmp_bool(fp, "inputrec->awhParams->biasbUserData", biasIndex, bias1->bUserData != 0, bias2->bUserData != 0);
1177 "inputrec->awhParams->biaserror_initial",
1179 bias1->errorInitial,
1180 bias2->errorInitial,
1183 cmp_int(fp, "inputrec->awhParams->biasShareGroup", biasIndex, bias1->shareGroup, bias2->shareGroup);
1185 for (int dim = 0; dim < std::min(bias1->ndim, bias2->ndim); dim++)
1187 cmp_awhDimParams(fp, &bias1->dimParams[dim], &bias2->dimParams[dim], dim, ftol, abstol);
1191 static void cmp_awhParams(FILE* fp, const gmx::AwhParams* awh1, const gmx::AwhParams* awh2, real ftol, real abstol)
1193 cmp_int(fp, "inputrec->awhParams->nbias", -1, awh1->numBias, awh2->numBias);
1194 cmp_int64(fp, "inputrec->awhParams->seed", awh1->seed, awh2->seed);
1195 cmp_int(fp, "inputrec->awhParams->nstout", -1, awh1->nstOut, awh2->nstOut);
1196 cmp_int(fp, "inputrec->awhParams->nstsample_coord", -1, awh1->nstSampleCoord, awh2->nstSampleCoord);
1198 "inputrec->awhParams->nsamples_update_free_energy",
1200 awh1->numSamplesUpdateFreeEnergy,
1201 awh2->numSamplesUpdateFreeEnergy);
1202 cmp_int(fp, "inputrec->awhParams->ePotential", -1, awh1->ePotential, awh2->ePotential);
1203 cmp_bool(fp, "inputrec->awhParams->shareBiasMultisim", -1, awh1->shareBiasMultisim, awh2->shareBiasMultisim);
1205 if (awh1->numBias == awh2->numBias)
1207 for (int bias = 0; bias < awh1->numBias; bias++)
1209 cmp_awhBiasParams(fp, &awh1->awhBiasParams[bias], &awh2->awhBiasParams[bias], bias, ftol, abstol);
1214 static void cmp_simtempvals(FILE* fp,
1215 const t_simtemp* simtemp1,
1216 const t_simtemp* simtemp2,
1222 cmp_int(fp, "inputrec->simtempvals->eSimTempScale", -1, simtemp1->eSimTempScale, simtemp2->eSimTempScale);
1223 cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high, simtemp2->simtemp_high, ftol, abstol);
1224 cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low, simtemp2->simtemp_low, ftol, abstol);
1225 for (i = 0; i < n_lambda; i++)
1228 "inputrec->simtempvals->temperatures",
1230 simtemp1->temperatures[i],
1231 simtemp2->temperatures[i],
1237 static void cmp_expandedvals(FILE* fp,
1238 const t_expanded* expand1,
1239 const t_expanded* expand2,
1246 cmp_bool(fp, "inputrec->fepvals->bInit_weights", -1, expand1->bInit_weights, expand2->bInit_weights);
1247 cmp_bool(fp, "inputrec->fepvals->bWLoneovert", -1, expand1->bWLoneovert, expand2->bWLoneovert);
1249 for (i = 0; i < n_lambda; i++)
1252 "inputrec->expandedvals->init_lambda_weights",
1254 expand1->init_lambda_weights[i],
1255 expand2->init_lambda_weights[i],
1260 cmp_int(fp, "inputrec->expandedvals->lambda-stats", -1, expand1->elamstats, expand2->elamstats);
1261 cmp_int(fp, "inputrec->expandedvals->lambda-mc-move", -1, expand1->elmcmove, expand2->elmcmove);
1262 cmp_int(fp, "inputrec->expandedvals->lmc-repeats", -1, expand1->lmc_repeats, expand2->lmc_repeats);
1263 cmp_int(fp, "inputrec->expandedvals->lmc-gibbsdelta", -1, expand1->gibbsdeltalam, expand2->gibbsdeltalam);
1264 cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart, expand2->lmc_forced_nstart);
1265 cmp_int(fp, "inputrec->expandedvals->lambda-weights-equil", -1, expand1->elmceq, expand2->elmceq);
1267 "inputrec->expandedvals->,weight-equil-number-all-lambda",
1269 expand1->equil_n_at_lam,
1270 expand2->equil_n_at_lam);
1271 cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples, expand2->equil_samples);
1272 cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps, expand2->equil_steps);
1274 "inputrec->expandedvals->weight-equil-wl-delta",
1276 expand1->equil_wl_delta,
1277 expand2->equil_wl_delta,
1281 "inputrec->expandedvals->weight-equil-count-ratio",
1283 expand1->equil_ratio,
1284 expand2->equil_ratio,
1288 "inputrec->expandedvals->symmetrized-transition-matrix",
1290 expand1->bSymmetrizedTMatrix,
1291 expand2->bSymmetrizedTMatrix);
1292 cmp_int(fp, "inputrec->expandedvals->nstTij", -1, expand1->nstTij, expand2->nstTij);
1293 cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin, expand2->minvarmin); /*default is reasonable */
1294 cmp_int(fp, "inputrec->expandedvals->weight-c-range", -1, expand1->c_range, expand2->c_range); /* default is just C=0 */
1295 cmp_real(fp, "inputrec->expandedvals->wl-scale", -1, expand1->wl_scale, expand2->wl_scale, ftol, abstol);
1296 cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta, expand2->init_wl_delta, ftol, abstol);
1297 cmp_real(fp, "inputrec->expandedvals->wl-ratio", -1, expand1->wl_ratio, expand2->wl_ratio, ftol, abstol);
1298 cmp_int(fp, "inputrec->expandedvals->nstexpanded", -1, expand1->nstexpanded, expand2->nstexpanded);
1299 cmp_int(fp, "inputrec->expandedvals->lmc-seed", -1, expand1->lmc_seed, expand2->lmc_seed);
1300 cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp, ftol, abstol);
1303 static void cmp_fepvals(FILE* fp, const t_lambda* fep1, const t_lambda* fep2, real ftol, real abstol)
1306 cmp_int(fp, "inputrec->nstdhdl", -1, fep1->nstdhdl, fep2->nstdhdl);
1307 cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state, fep2->init_fep_state, ftol, abstol);
1308 cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda, ftol, abstol);
1309 cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda);
1310 for (i = 0; i < efptNR; i++)
1312 for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++)
1315 "inputrec->fepvals->all_lambda",
1317 fep1->all_lambda[i][j],
1318 fep2->all_lambda[i][j],
1323 cmp_int(fp, "inputrec->fepvals->lambda_neighbors", 1, fep1->lambda_neighbors, fep2->lambda_neighbors);
1324 cmp_real(fp, "inputrec->fepvals->sc_alpha", -1, fep1->sc_alpha, fep2->sc_alpha, ftol, abstol);
1325 cmp_int(fp, "inputrec->fepvals->sc_power", -1, fep1->sc_power, fep2->sc_power);
1326 cmp_real(fp, "inputrec->fepvals->sc_r_power", -1, fep1->sc_r_power, fep2->sc_r_power, ftol, abstol);
1327 cmp_real(fp, "inputrec->fepvals->sc_sigma", -1, fep1->sc_sigma, fep2->sc_sigma, ftol, abstol);
1328 cmp_int(fp, "inputrec->fepvals->edHdLPrintEnergy", -1, fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy);
1329 cmp_bool(fp, "inputrec->fepvals->bScCoul", -1, fep1->bScCoul, fep1->bScCoul);
1330 cmp_int(fp, "inputrec->separate_dhdl_file", -1, fep1->separate_dhdl_file, fep2->separate_dhdl_file);
1331 cmp_int(fp, "inputrec->dhdl_derivatives", -1, fep1->dhdl_derivatives, fep2->dhdl_derivatives);
1332 cmp_int(fp, "inputrec->dh_hist_size", -1, fep1->dh_hist_size, fep2->dh_hist_size);
1333 cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing, ftol, abstol);
1336 void cmp_inputrec(FILE* fp, const t_inputrec* ir1, const t_inputrec* ir2, real ftol, real abstol)
1338 fprintf(fp, "comparing inputrec\n");
1340 /* gcc 2.96 doesnt like these defines at all, but issues a huge list
1341 * of warnings. Maybe it will change in future versions, but for the
1342 * moment I've spelled them out instead. /EL 000820
1343 * #define CIB(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
1344 * #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
1345 * #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol)
1347 cmp_int(fp, "inputrec->eI", -1, ir1->eI, ir2->eI);
1348 cmp_int64(fp, "inputrec->nsteps", ir1->nsteps, ir2->nsteps);
1349 cmp_int64(fp, "inputrec->init_step", ir1->init_step, ir2->init_step);
1350 cmp_int(fp, "inputrec->simulation_part", -1, ir1->simulation_part, ir2->simulation_part);
1351 cmp_int(fp, "inputrec->mts", -1, static_cast<int>(ir1->useMts), static_cast<int>(ir2->useMts));
1352 if (ir1->useMts && ir2->useMts)
1354 cmp_int(fp, "inputrec->mts-levels", -1, ir1->mtsLevels.size(), ir2->mtsLevels.size());
1356 "inputrec->mts-level2-forces",
1358 ir1->mtsLevels[1].forceGroups.to_ulong(),
1359 ir2->mtsLevels[1].forceGroups.to_ulong());
1361 "inputrec->mts-level2-factor",
1363 ir1->mtsLevels[1].stepFactor,
1364 ir2->mtsLevels[1].stepFactor);
1366 cmp_int(fp, "inputrec->pbcType", -1, static_cast<int>(ir1->pbcType), static_cast<int>(ir2->pbcType));
1367 cmp_bool(fp, "inputrec->bPeriodicMols", -1, ir1->bPeriodicMols, ir2->bPeriodicMols);
1368 cmp_int(fp, "inputrec->cutoff_scheme", -1, ir1->cutoff_scheme, ir2->cutoff_scheme);
1369 cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist);
1370 cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm);
1371 cmp_int(fp, "inputrec->comm_mode", -1, ir1->comm_mode, ir2->comm_mode);
1372 cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog);
1373 cmp_int(fp, "inputrec->nstxout", -1, ir1->nstxout, ir2->nstxout);
1374 cmp_int(fp, "inputrec->nstvout", -1, ir1->nstvout, ir2->nstvout);
1375 cmp_int(fp, "inputrec->nstfout", -1, ir1->nstfout, ir2->nstfout);
1376 cmp_int(fp, "inputrec->nstcalcenergy", -1, ir1->nstcalcenergy, ir2->nstcalcenergy);
1377 cmp_int(fp, "inputrec->nstenergy", -1, ir1->nstenergy, ir2->nstenergy);
1378 cmp_int(fp, "inputrec->nstxout_compressed", -1, ir1->nstxout_compressed, ir2->nstxout_compressed);
1379 cmp_double(fp, "inputrec->init_t", -1, ir1->init_t, ir2->init_t, ftol, abstol);
1380 cmp_double(fp, "inputrec->delta_t", -1, ir1->delta_t, ir2->delta_t, ftol, abstol);
1382 "inputrec->x_compression_precision",
1384 ir1->x_compression_precision,
1385 ir2->x_compression_precision,
1388 cmp_real(fp, "inputrec->fourierspacing", -1, ir1->fourier_spacing, ir2->fourier_spacing, ftol, abstol);
1389 cmp_int(fp, "inputrec->nkx", -1, ir1->nkx, ir2->nkx);
1390 cmp_int(fp, "inputrec->nky", -1, ir1->nky, ir2->nky);
1391 cmp_int(fp, "inputrec->nkz", -1, ir1->nkz, ir2->nkz);
1392 cmp_int(fp, "inputrec->pme_order", -1, ir1->pme_order, ir2->pme_order);
1393 cmp_real(fp, "inputrec->ewald_rtol", -1, ir1->ewald_rtol, ir2->ewald_rtol, ftol, abstol);
1394 cmp_int(fp, "inputrec->ewald_geometry", -1, ir1->ewald_geometry, ir2->ewald_geometry);
1395 cmp_real(fp, "inputrec->epsilon_surface", -1, ir1->epsilon_surface, ir2->epsilon_surface, ftol, abstol);
1397 "inputrec->bContinuation",
1399 static_cast<int>(ir1->bContinuation),
1400 static_cast<int>(ir2->bContinuation));
1401 cmp_int(fp, "inputrec->bShakeSOR", -1, static_cast<int>(ir1->bShakeSOR), static_cast<int>(ir2->bShakeSOR));
1402 cmp_int(fp, "inputrec->etc", -1, ir1->etc, ir2->etc);
1404 "inputrec->bPrintNHChains",
1406 static_cast<int>(ir1->bPrintNHChains),
1407 static_cast<int>(ir2->bPrintNHChains));
1408 cmp_int(fp, "inputrec->epc", -1, ir1->epc, ir2->epc);
1409 cmp_int(fp, "inputrec->epct", -1, ir1->epct, ir2->epct);
1410 cmp_real(fp, "inputrec->tau_p", -1, ir1->tau_p, ir2->tau_p, ftol, abstol);
1411 cmp_rvec(fp, "inputrec->ref_p(x)", -1, ir1->ref_p[XX], ir2->ref_p[XX], ftol, abstol);
1412 cmp_rvec(fp, "inputrec->ref_p(y)", -1, ir1->ref_p[YY], ir2->ref_p[YY], ftol, abstol);
1413 cmp_rvec(fp, "inputrec->ref_p(z)", -1, ir1->ref_p[ZZ], ir2->ref_p[ZZ], ftol, abstol);
1414 cmp_rvec(fp, "inputrec->compress(x)", -1, ir1->compress[XX], ir2->compress[XX], ftol, abstol);
1415 cmp_rvec(fp, "inputrec->compress(y)", -1, ir1->compress[YY], ir2->compress[YY], ftol, abstol);
1416 cmp_rvec(fp, "inputrec->compress(z)", -1, ir1->compress[ZZ], ir2->compress[ZZ], ftol, abstol);
1417 cmp_int(fp, "refcoord_scaling", -1, ir1->refcoord_scaling, ir2->refcoord_scaling);
1418 cmp_rvec(fp, "inputrec->posres_com", -1, ir1->posres_com, ir2->posres_com, ftol, abstol);
1419 cmp_rvec(fp, "inputrec->posres_comB", -1, ir1->posres_comB, ir2->posres_comB, ftol, abstol);
1420 cmp_real(fp, "inputrec->verletbuf_tol", -1, ir1->verletbuf_tol, ir2->verletbuf_tol, ftol, abstol);
1421 cmp_real(fp, "inputrec->rlist", -1, ir1->rlist, ir2->rlist, ftol, abstol);
1422 cmp_real(fp, "inputrec->rtpi", -1, ir1->rtpi, ir2->rtpi, ftol, abstol);
1423 cmp_int(fp, "inputrec->coulombtype", -1, ir1->coulombtype, ir2->coulombtype);
1424 cmp_int(fp, "inputrec->coulomb_modifier", -1, ir1->coulomb_modifier, ir2->coulomb_modifier);
1425 cmp_real(fp, "inputrec->rcoulomb_switch", -1, ir1->rcoulomb_switch, ir2->rcoulomb_switch, ftol, abstol);
1426 cmp_real(fp, "inputrec->rcoulomb", -1, ir1->rcoulomb, ir2->rcoulomb, ftol, abstol);
1427 cmp_int(fp, "inputrec->vdwtype", -1, ir1->vdwtype, ir2->vdwtype);
1428 cmp_int(fp, "inputrec->vdw_modifier", -1, ir1->vdw_modifier, ir2->vdw_modifier);
1429 cmp_real(fp, "inputrec->rvdw_switch", -1, ir1->rvdw_switch, ir2->rvdw_switch, ftol, abstol);
1430 cmp_real(fp, "inputrec->rvdw", -1, ir1->rvdw, ir2->rvdw, ftol, abstol);
1431 cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol);
1432 cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol);
1433 cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol);
1435 cmp_int(fp, "inputrec->eDispCorr", -1, ir1->eDispCorr, ir2->eDispCorr);
1436 cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol);
1437 cmp_int(fp, "inputrec->efep", -1, ir1->efep, ir2->efep);
1438 cmp_fepvals(fp, ir1->fepvals, ir2->fepvals, ftol, abstol);
1439 cmp_int(fp, "inputrec->bSimTemp", -1, static_cast<int>(ir1->bSimTemp), static_cast<int>(ir2->bSimTemp));
1440 if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp))
1445 std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda),
1449 cmp_int(fp, "inputrec->bExpanded", -1, static_cast<int>(ir1->bExpanded), static_cast<int>(ir2->bExpanded));
1450 if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded))
1452 cmp_expandedvals(fp,
1455 std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda),
1459 cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall);
1460 cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type);
1461 cmp_int(fp, "inputrec->wall_atomtype[0]", -1, ir1->wall_atomtype[0], ir2->wall_atomtype[0]);
1462 cmp_int(fp, "inputrec->wall_atomtype[1]", -1, ir1->wall_atomtype[1], ir2->wall_atomtype[1]);
1463 cmp_real(fp, "inputrec->wall_density[0]", -1, ir1->wall_density[0], ir2->wall_density[0], ftol, abstol);
1464 cmp_real(fp, "inputrec->wall_density[1]", -1, ir1->wall_density[1], ir2->wall_density[1], ftol, abstol);
1465 cmp_real(fp, "inputrec->wall_ewald_zfac", -1, ir1->wall_ewald_zfac, ir2->wall_ewald_zfac, ftol, abstol);
1467 cmp_bool(fp, "inputrec->bPull", -1, ir1->bPull, ir2->bPull);
1468 if (ir1->bPull && ir2->bPull)
1473 cmp_bool(fp, "inputrec->bDoAwh", -1, ir1->bDoAwh, ir2->bDoAwh);
1474 if (ir1->bDoAwh && ir2->bDoAwh)
1476 cmp_awhParams(fp, ir1->awhParams, ir2->awhParams, ftol, abstol);
1479 cmp_int(fp, "inputrec->eDisre", -1, ir1->eDisre, ir2->eDisre);
1480 cmp_real(fp, "inputrec->dr_fc", -1, ir1->dr_fc, ir2->dr_fc, ftol, abstol);
1481 cmp_int(fp, "inputrec->eDisreWeighting", -1, ir1->eDisreWeighting, ir2->eDisreWeighting);
1482 cmp_int(fp, "inputrec->bDisreMixed", -1, static_cast<int>(ir1->bDisreMixed), static_cast<int>(ir2->bDisreMixed));
1483 cmp_int(fp, "inputrec->nstdisreout", -1, ir1->nstdisreout, ir2->nstdisreout);
1484 cmp_real(fp, "inputrec->dr_tau", -1, ir1->dr_tau, ir2->dr_tau, ftol, abstol);
1485 cmp_real(fp, "inputrec->orires_fc", -1, ir1->orires_fc, ir2->orires_fc, ftol, abstol);
1486 cmp_real(fp, "inputrec->orires_tau", -1, ir1->orires_tau, ir2->orires_tau, ftol, abstol);
1487 cmp_int(fp, "inputrec->nstorireout", -1, ir1->nstorireout, ir2->nstorireout);
1488 cmp_real(fp, "inputrec->em_stepsize", -1, ir1->em_stepsize, ir2->em_stepsize, ftol, abstol);
1489 cmp_real(fp, "inputrec->em_tol", -1, ir1->em_tol, ir2->em_tol, ftol, abstol);
1490 cmp_int(fp, "inputrec->niter", -1, ir1->niter, ir2->niter);
1491 cmp_real(fp, "inputrec->fc_stepsize", -1, ir1->fc_stepsize, ir2->fc_stepsize, ftol, abstol);
1492 cmp_int(fp, "inputrec->nstcgsteep", -1, ir1->nstcgsteep, ir2->nstcgsteep);
1493 cmp_int(fp, "inputrec->nbfgscorr", 0, ir1->nbfgscorr, ir2->nbfgscorr);
1494 cmp_int(fp, "inputrec->eConstrAlg", -1, ir1->eConstrAlg, ir2->eConstrAlg);
1495 cmp_int(fp, "inputrec->nProjOrder", -1, ir1->nProjOrder, ir2->nProjOrder);
1496 cmp_real(fp, "inputrec->LincsWarnAngle", -1, ir1->LincsWarnAngle, ir2->LincsWarnAngle, ftol, abstol);
1497 cmp_int(fp, "inputrec->nLincsIter", -1, ir1->nLincsIter, ir2->nLincsIter);
1498 cmp_real(fp, "inputrec->bd_fric", -1, ir1->bd_fric, ir2->bd_fric, ftol, abstol);
1499 cmp_int64(fp, "inputrec->ld_seed", ir1->ld_seed, ir2->ld_seed);
1500 cmp_real(fp, "inputrec->cos_accel", -1, ir1->cos_accel, ir2->cos_accel, ftol, abstol);
1501 cmp_rvec(fp, "inputrec->deform(a)", -1, ir1->deform[XX], ir2->deform[XX], ftol, abstol);
1502 cmp_rvec(fp, "inputrec->deform(b)", -1, ir1->deform[YY], ir2->deform[YY], ftol, abstol);
1503 cmp_rvec(fp, "inputrec->deform(c)", -1, ir1->deform[ZZ], ir2->deform[ZZ], ftol, abstol);
1506 cmp_int(fp, "inputrec->userint1", -1, ir1->userint1, ir2->userint1);
1507 cmp_int(fp, "inputrec->userint2", -1, ir1->userint2, ir2->userint2);
1508 cmp_int(fp, "inputrec->userint3", -1, ir1->userint3, ir2->userint3);
1509 cmp_int(fp, "inputrec->userint4", -1, ir1->userint4, ir2->userint4);
1510 cmp_real(fp, "inputrec->userreal1", -1, ir1->userreal1, ir2->userreal1, ftol, abstol);
1511 cmp_real(fp, "inputrec->userreal2", -1, ir1->userreal2, ir2->userreal2, ftol, abstol);
1512 cmp_real(fp, "inputrec->userreal3", -1, ir1->userreal3, ir2->userreal3, ftol, abstol);
1513 cmp_real(fp, "inputrec->userreal4", -1, ir1->userreal4, ir2->userreal4, ftol, abstol);
1514 cmp_grpopts(fp, &(ir1->opts), &(ir2->opts), ftol, abstol);
1515 gmx::TextWriter writer(fp);
1516 gmx::compareKeyValueTrees(&writer, *ir1->params, *ir2->params, ftol, abstol);
1519 void comp_pull_AB(FILE* fp, const pull_params_t& pull, real ftol, real abstol)
1521 for (int i = 0; i < pull.ncoord; i++)
1523 fprintf(fp, "comparing pull coord %d\n", i);
1524 cmp_real(fp, "pull-coord->k", -1, pull.coord[i].k, pull.coord[i].kB, ftol, abstol);
1528 gmx_bool inputrecDeform(const t_inputrec* ir)
1530 return (ir->deform[XX][XX] != 0 || ir->deform[YY][YY] != 0 || ir->deform[ZZ][ZZ] != 0
1531 || ir->deform[YY][XX] != 0 || ir->deform[ZZ][XX] != 0 || ir->deform[ZZ][YY] != 0);
1534 gmx_bool inputrecDynamicBox(const t_inputrec* ir)
1536 return (ir->epc != epcNO || ir->eI == eiTPI || inputrecDeform(ir));
1539 gmx_bool inputrecPreserveShape(const t_inputrec* ir)
1541 return (ir->epc != epcNO && ir->deform[XX][XX] == 0
1542 && (ir->epct == epctISOTROPIC || ir->epct == epctSEMIISOTROPIC));
1545 gmx_bool inputrecNeedMutot(const t_inputrec* ir)
1547 return ((ir->coulombtype == eelEWALD || EEL_PME(ir->coulombtype))
1548 && (ir->ewald_geometry == eewg3DC || ir->epsilon_surface != 0));
1551 gmx_bool inputrecExclForces(const t_inputrec* ir)
1553 return (EEL_FULL(ir->coulombtype) || (EEL_RF(ir->coulombtype)));
1556 gmx_bool inputrecNptTrotter(const t_inputrec* ir)
1558 return (((ir->eI == eiVV) || (ir->eI == eiVVAK)) && (ir->epc == epcMTTK) && (ir->etc == etcNOSEHOOVER));
1561 gmx_bool inputrecNvtTrotter(const t_inputrec* ir)
1563 return (((ir->eI == eiVV) || (ir->eI == eiVVAK)) && (ir->epc != epcMTTK) && (ir->etc == etcNOSEHOOVER));
1566 gmx_bool inputrecNphTrotter(const t_inputrec* ir)
1568 return (((ir->eI == eiVV) || (ir->eI == eiVVAK)) && (ir->epc == epcMTTK) && (ir->etc != etcNOSEHOOVER));
1571 bool inputrecPbcXY2Walls(const t_inputrec* ir)
1573 return (ir->pbcType == PbcType::XY && ir->nwall == 2);
1576 bool integratorHasConservedEnergyQuantity(const t_inputrec* ir)
1579 { // NOLINT bugprone-branch-clone
1580 // Energy minimization or stochastic integrator: no conservation
1583 else if (ir->etc == etcNO && ir->epc == epcNO)
1585 // The total energy is conserved, no additional conserved quanitity
1590 // Shear stress with Parrinello-Rahman is not supported (tedious)
1592 ((ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK)
1593 && (ir->ref_p[YY][XX] != 0 || ir->ref_p[ZZ][XX] != 0 || ir->ref_p[ZZ][YY] != 0));
1595 return !ETC_ANDERSEN(ir->etc) && !shearWithPR;
1599 bool integratorHasReferenceTemperature(const t_inputrec* ir)
1601 return ((ir->etc != etcNO) || EI_SD(ir->eI) || (ir->eI == eiBD) || EI_TPI(ir->eI));
1604 int inputrec2nboundeddim(const t_inputrec* ir)
1606 if (inputrecPbcXY2Walls(ir))
1612 return numPbcDimensions(ir->pbcType);
1616 int ndof_com(const t_inputrec* ir)
1620 switch (ir->pbcType)
1623 case PbcType::No: n = 3; break;
1624 case PbcType::XY: n = (ir->nwall == 0 ? 3 : 2); break;
1625 case PbcType::Screw: n = 1; break;
1626 default: gmx_incons("Unknown pbc in calc_nrdf");
1632 real maxReferenceTemperature(const t_inputrec& ir)
1634 if (EI_ENERGY_MINIMIZATION(ir.eI) || ir.eI == eiNM)
1639 if (EI_MD(ir.eI) && ir.etc == etcNO)
1644 /* SD and BD also use ref_t and tau_t for setting the reference temperature.
1645 * TPI can be treated as MD, since it needs an ensemble temperature.
1648 real maxTemperature = 0;
1649 for (int i = 0; i < ir.opts.ngtc; i++)
1651 if (ir.opts.tau_t[i] >= 0)
1653 maxTemperature = std::max(maxTemperature, ir.opts.ref_t[i]);
1657 return maxTemperature;
1660 bool haveEwaldSurfaceContribution(const t_inputrec& ir)
1662 return EEL_PME_EWALD(ir.coulombtype) && (ir.ewald_geometry == eewg3DC || ir.epsilon_surface != 0);
1665 bool haveFreeEnergyType(const t_inputrec& ir, const int fepType)
1667 for (int i = 0; i < ir.fepvals->n_lambda; i++)
1669 if (ir.fepvals->all_lambda[fepType][i] > 0)