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40 #include "gromacs/utility/enumerationhelpers.h"
51 #include "gromacs/applied_forces/awh/read_params.h"
52 #include "gromacs/math/veccompare.h"
53 #include "gromacs/math/vecdump.h"
54 #include "gromacs/mdtypes/awh_params.h"
55 #include "gromacs/mdtypes/md_enums.h"
56 #include "gromacs/mdtypes/multipletimestepping.h"
57 #include "gromacs/mdtypes/pull_params.h"
58 #include "gromacs/pbcutil/pbc.h"
59 #include "gromacs/utility/compare.h"
60 #include "gromacs/utility/cstringutil.h"
61 #include "gromacs/utility/fatalerror.h"
62 #include "gromacs/utility/keyvaluetree.h"
63 #include "gromacs/utility/smalloc.h"
64 #include "gromacs/utility/snprintf.h"
65 #include "gromacs/utility/strconvert.h"
66 #include "gromacs/utility/stringutil.h"
67 #include "gromacs/utility/textwriter.h"
68 #include "gromacs/utility/txtdump.h"
70 //! Macro to select a bool name
71 #define EBOOL(e) gmx::boolToString(e)
73 /* Default values for nstcalcenergy, used when the are no other restrictions. */
74 constexpr int c_defaultNstCalcEnergy = 10;
76 /* The minimum number of integration steps required for reasonably accurate
77 * integration of first and second order coupling algorithms.
79 const int nstmin_berendsen_tcouple = 5;
80 const int nstmin_berendsen_pcouple = 10;
81 const int nstmin_harmonic = 20;
83 /* Default values for T- and P- coupling intervals, used when the are no other
86 constexpr int c_defaultNstTCouple = 10;
87 constexpr int c_defaultNstPCouple = 10;
89 t_inputrec::t_inputrec()
91 // TODO When this memset is removed, remove the suppression of
92 // gcc -Wno-class-memaccess in a CMakeLists.txt file.
93 std::memset(this, 0, sizeof(*this)); // NOLINT(bugprone-undefined-memory-manipulation)
94 fepvals = std::make_unique<t_lambda>();
95 expandedvals = std::make_unique<t_expanded>();
96 simtempvals = std::make_unique<t_simtemp>();
99 t_inputrec::~t_inputrec()
104 int ir_optimal_nstcalcenergy(const t_inputrec* ir)
114 nst = c_defaultNstCalcEnergy;
119 nst = std::lcm(nst, ir->mtsLevels.back().stepFactor);
125 int tcouple_min_integration_steps(TemperatureCoupling etc)
131 case TemperatureCoupling::No: n = 0; break;
132 case TemperatureCoupling::Berendsen:
133 case TemperatureCoupling::Yes: n = nstmin_berendsen_tcouple; break;
134 case TemperatureCoupling::VRescale:
135 /* V-rescale supports instantaneous rescaling */
138 case TemperatureCoupling::NoseHoover: n = nstmin_harmonic; break;
139 case TemperatureCoupling::Andersen:
140 case TemperatureCoupling::AndersenMassive: n = 1; break;
141 default: gmx_incons("Unknown etc value");
147 int ir_optimal_nsttcouple(const t_inputrec* ir)
149 int nmin, nwanted, n;
153 nmin = tcouple_min_integration_steps(ir->etc);
155 nwanted = c_defaultNstTCouple;
158 if (ir->etc != TemperatureCoupling::No)
160 for (g = 0; g < ir->opts.ngtc; g++)
162 if (ir->opts.tau_t[g] > 0)
164 tau_min = std::min(tau_min, ir->opts.tau_t[g]);
169 if (nmin == 0 || ir->delta_t * nwanted <= tau_min)
175 n = static_cast<int>(tau_min / (ir->delta_t * nmin) + 0.001);
180 while (nwanted % n != 0)
189 int pcouple_min_integration_steps(PressureCoupling epc)
195 case PressureCoupling::No: n = 0; break;
196 case PressureCoupling::Berendsen:
197 case PressureCoupling::CRescale:
198 case PressureCoupling::Isotropic: n = nstmin_berendsen_pcouple; break;
199 case PressureCoupling::ParrinelloRahman:
200 case PressureCoupling::Mttk: n = nstmin_harmonic; break;
201 default: gmx_incons("Unknown epc value");
207 int ir_optimal_nstpcouple(const t_inputrec* ir)
209 const int minIntegrationSteps = pcouple_min_integration_steps(ir->epc);
211 const int nwanted = c_defaultNstPCouple;
213 // With multiple time-stepping we can only compute the pressure at slowest steps
214 const int minNstPCouple = (ir->useMts ? ir->mtsLevels.back().stepFactor : 1);
217 if (minIntegrationSteps == 0 || ir->delta_t * nwanted <= ir->tau_p)
223 n = static_cast<int>(ir->tau_p / (ir->delta_t * minIntegrationSteps) + 0.001);
224 if (n < minNstPCouple)
228 // Without MTS we try to make nstpcouple a "nice" number
231 while (nwanted % n != 0)
238 // With MTS, nstpcouple should be a multiple of the slowest MTS interval
241 n = n - (n % minNstPCouple);
247 gmx_bool ir_coulomb_switched(const t_inputrec* ir)
249 return (ir->coulombtype == CoulombInteractionType::Switch
250 || ir->coulombtype == CoulombInteractionType::Shift
251 || ir->coulombtype == CoulombInteractionType::PmeSwitch
252 || ir->coulombtype == CoulombInteractionType::PmeUserSwitch
253 || ir->coulomb_modifier == InteractionModifiers::PotSwitch
254 || ir->coulomb_modifier == InteractionModifiers::ForceSwitch);
257 gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec* ir)
259 return (ir->cutoff_scheme == CutoffScheme::Verlet || ir_coulomb_switched(ir)
260 || ir->coulomb_modifier != InteractionModifiers::None
261 || ir->coulombtype == CoulombInteractionType::RFZero);
264 gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec* ir)
266 return (ir_coulomb_is_zero_at_cutoff(ir) || ir->coulombtype == CoulombInteractionType::User
267 || ir->coulombtype == CoulombInteractionType::PmeUser);
270 gmx_bool ir_vdw_switched(const t_inputrec* ir)
272 return (ir->vdwtype == VanDerWaalsType::Switch || ir->vdwtype == VanDerWaalsType::Shift
273 || ir->vdw_modifier == InteractionModifiers::PotSwitch
274 || ir->vdw_modifier == InteractionModifiers::ForceSwitch);
277 gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec* ir)
279 return (ir->cutoff_scheme == CutoffScheme::Verlet || ir_vdw_switched(ir)
280 || ir->vdw_modifier != InteractionModifiers::None);
283 gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec* ir)
285 return (ir_vdw_is_zero_at_cutoff(ir) || ir->vdwtype == VanDerWaalsType::User);
288 static void done_t_rot(t_rot* rot)
294 if (rot->grp != nullptr)
296 for (int i = 0; i < rot->ngrp; i++)
298 sfree(rot->grp[i].ind);
299 sfree(rot->grp[i].x_ref);
306 static void done_t_swapCoords(t_swapcoords* swapCoords)
308 if (swapCoords == nullptr)
312 for (int i = 0; i < swapCoords->ngrp; i++)
314 sfree(swapCoords->grp[i].ind);
315 sfree(swapCoords->grp[i].molname);
317 sfree(swapCoords->grp);
321 void done_inputrec(t_inputrec* ir)
323 sfree(ir->opts.nrdf);
324 sfree(ir->opts.ref_t);
325 for (int i = 0; i < ir->opts.ngtc; i++)
327 sfree(ir->opts.anneal_time[i]);
328 sfree(ir->opts.anneal_temp[i]);
330 sfree(ir->opts.annealing);
331 sfree(ir->opts.anneal_npoints);
332 sfree(ir->opts.anneal_time);
333 sfree(ir->opts.anneal_temp);
334 sfree(ir->opts.tau_t);
335 sfree(ir->opts.nFreeze);
336 sfree(ir->opts.egp_flags);
338 done_t_swapCoords(ir->swap);
343 static void pr_grp_opts(FILE* out, int indent, const char* title, const t_grpopts* opts, gmx_bool bMDPformat)
349 fprintf(out, "%s:\n", title);
352 pr_indent(out, indent);
353 fprintf(out, "nrdf%s", bMDPformat ? " = " : ":");
354 for (i = 0; (i < opts->ngtc); i++)
356 fprintf(out, " %10g", opts->nrdf[i]);
360 pr_indent(out, indent);
361 fprintf(out, "ref-t%s", bMDPformat ? " = " : ":");
362 for (i = 0; (i < opts->ngtc); i++)
364 fprintf(out, " %10g", opts->ref_t[i]);
368 pr_indent(out, indent);
369 fprintf(out, "tau-t%s", bMDPformat ? " = " : ":");
370 for (i = 0; (i < opts->ngtc); i++)
372 fprintf(out, " %10g", opts->tau_t[i]);
376 /* Pretty-print the simulated annealing info */
377 fprintf(out, "annealing%s", bMDPformat ? " = " : ":");
378 for (i = 0; (i < opts->ngtc); i++)
380 fprintf(out, " %10s", enumValueToString(opts->annealing[i]));
384 fprintf(out, "annealing-npoints%s", bMDPformat ? " = " : ":");
385 for (i = 0; (i < opts->ngtc); i++)
387 fprintf(out, " %10d", opts->anneal_npoints[i]);
391 for (i = 0; (i < opts->ngtc); i++)
393 if (opts->anneal_npoints[i] > 0)
395 fprintf(out, "annealing-time [%d]:\t", i);
396 for (j = 0; (j < opts->anneal_npoints[i]); j++)
398 fprintf(out, " %10.1f", opts->anneal_time[i][j]);
401 fprintf(out, "annealing-temp [%d]:\t", i);
402 for (j = 0; (j < opts->anneal_npoints[i]); j++)
404 fprintf(out, " %10.1f", opts->anneal_temp[i][j]);
410 pr_indent(out, indent);
411 fprintf(out, "nfreeze:");
412 for (i = 0; (i < opts->ngfrz); i++)
414 for (m = 0; (m < DIM); m++)
416 fprintf(out, " %10s", opts->nFreeze[i][m] ? "Y" : "N");
422 for (i = 0; (i < opts->ngener); i++)
424 pr_indent(out, indent);
425 fprintf(out, "energygrp-flags[%3d]:", i);
426 for (m = 0; (m < opts->ngener); m++)
428 fprintf(out, " %d", opts->egp_flags[opts->ngener * i + m]);
436 static void pr_matrix(FILE* fp, int indent, const char* title, const rvec* m, gmx_bool bMDPformat)
441 "%-10s = %g %g %g %g %g %g\n",
452 pr_rvecs(fp, indent, title, m, DIM);
456 #define PS(t, s) pr_str(fp, indent, t, s)
457 #define PI(t, s) pr_int(fp, indent, t, s)
458 #define PSTEP(t, s) pr_int64(fp, indent, t, s)
459 #define PR(t, s) pr_real(fp, indent, t, s)
460 #define PD(t, s) pr_double(fp, indent, t, s)
462 static void pr_pull_group(FILE* fp, int indent, int g, const t_pull_group* pgrp)
464 pr_indent(fp, indent);
465 fprintf(fp, "pull-group %d:\n", g);
467 pr_ivec_block(fp, indent, "atom", pgrp->ind.data(), pgrp->ind.size(), TRUE);
468 pr_rvec(fp, indent, "weight", pgrp->weight.data(), pgrp->weight.size(), TRUE);
469 PI("pbcatom", pgrp->pbcatom);
472 static void pr_pull_coord(FILE* fp, int indent, int c, const t_pull_coord* pcrd)
476 pr_indent(fp, indent);
477 fprintf(fp, "pull-coord %d:\n", c);
478 PS("type", enumValueToString(pcrd->eType));
479 if (pcrd->eType == PullingAlgorithm::External)
481 PS("potential-provider", pcrd->externalPotentialProvider.c_str());
483 PS("geometry", enumValueToString(pcrd->eGeom));
484 for (g = 0; g < pcrd->ngroup; g++)
488 sprintf(buf, "group[%d]", g);
489 PI(buf, pcrd->group[g]);
491 pr_ivec(fp, indent, "dim", pcrd->dim, DIM, TRUE);
492 pr_rvec(fp, indent, "origin", pcrd->origin, DIM, TRUE);
493 pr_rvec(fp, indent, "vec", pcrd->vec, DIM, TRUE);
494 PS("start", EBOOL(pcrd->bStart));
495 PR("init", pcrd->init);
496 PR("rate", pcrd->rate);
501 static void pr_simtempvals(FILE* fp, int indent, const t_simtemp* simtemp, int n_lambda)
503 PS("simulated-tempering-scaling", enumValueToString(simtemp->eSimTempScale));
504 PR("sim-temp-low", simtemp->simtemp_low);
505 PR("sim-temp-high", simtemp->simtemp_high);
506 pr_rvec(fp, indent, "simulated tempering temperatures", simtemp->temperatures.data(), n_lambda, TRUE);
509 static void pr_expandedvals(FILE* fp, int indent, const t_expanded* expand, int n_lambda)
512 PI("nstexpanded", expand->nstexpanded);
513 PS("lmc-stats", enumValueToString(expand->elamstats));
514 PS("lmc-move", enumValueToString(expand->elmcmove));
515 PS("lmc-weights-equil", enumValueToString(expand->elmceq));
516 if (expand->elmceq == LambdaWeightWillReachEquilibrium::NumAtLambda)
518 PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
520 if (expand->elmceq == LambdaWeightWillReachEquilibrium::Samples)
522 PI("weight-equil-number-samples", expand->equil_samples);
524 if (expand->elmceq == LambdaWeightWillReachEquilibrium::Steps)
526 PI("weight-equil-number-steps", expand->equil_steps);
528 if (expand->elmceq == LambdaWeightWillReachEquilibrium::WLDelta)
530 PR("weight-equil-wl-delta", expand->equil_wl_delta);
532 if (expand->elmceq == LambdaWeightWillReachEquilibrium::Ratio)
534 PR("weight-equil-count-ratio", expand->equil_ratio);
536 PI("lmc-seed", expand->lmc_seed);
537 PR("mc-temperature", expand->mc_temp);
538 PI("lmc-repeats", expand->lmc_repeats);
539 PI("lmc-gibbsdelta", expand->gibbsdeltalam);
540 PI("lmc-forced-nstart", expand->lmc_forced_nstart);
541 PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix));
542 PI("nst-transition-matrix", expand->nstTij);
543 PI("mininum-var-min", expand->minvarmin); /*default is reasonable */
544 PI("weight-c-range", expand->c_range); /* default is just C=0 */
545 PR("wl-scale", expand->wl_scale);
546 PR("wl-ratio", expand->wl_ratio);
547 PR("init-wl-delta", expand->init_wl_delta);
548 PS("wl-oneovert", EBOOL(expand->bWLoneovert));
550 pr_indent(fp, indent);
551 pr_rvec(fp, indent, "init-lambda-weights", expand->init_lambda_weights.data(), n_lambda, TRUE);
552 PS("init-weights", EBOOL(expand->bInit_weights));
555 static void pr_fepvals(FILE* fp, int indent, const t_lambda* fep, gmx_bool bMDPformat)
559 PR("init-lambda", fep->init_lambda);
560 PI("init-lambda-state", fep->init_fep_state);
561 PR("delta-lambda", fep->delta_lambda);
562 PI("nstdhdl", fep->nstdhdl);
566 PI("n-lambdas", fep->n_lambda);
568 if (fep->n_lambda > 0)
570 pr_indent(fp, indent);
571 fprintf(fp, "separate-dvdl%s\n", bMDPformat ? " = " : ":");
572 for (auto i : gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool>::keys())
574 fprintf(fp, "%18s = ", enumValueToString(i));
575 if (fep->separate_dvdl[i])
577 fprintf(fp, " TRUE");
581 fprintf(fp, " FALSE");
585 fprintf(fp, "all-lambdas%s\n", bMDPformat ? " = " : ":");
586 for (auto key : gmx::EnumerationArray<FreeEnergyPerturbationCouplingType, bool>::keys())
588 fprintf(fp, "%18s = ", enumValueToString(key));
589 int i = static_cast<int>(key);
590 for (j = 0; j < fep->n_lambda; j++)
592 fprintf(fp, " %10g", fep->all_lambda[i][j]);
597 PI("calc-lambda-neighbors", fep->lambda_neighbors);
598 PS("dhdl-print-energy", enumValueToString(fep->edHdLPrintEnergy));
599 PR("sc-alpha", fep->sc_alpha);
600 PI("sc-power", fep->sc_power);
601 PR("sc-r-power", fep->sc_r_power);
602 PR("sc-sigma", fep->sc_sigma);
603 PR("sc-sigma-min", fep->sc_sigma_min);
604 PS("sc-coul", EBOOL(fep->bScCoul));
605 PI("dh-hist-size", fep->dh_hist_size);
606 PD("dh-hist-spacing", fep->dh_hist_spacing);
607 PS("separate-dhdl-file", enumValueToString(fep->separate_dhdl_file));
608 PS("dhdl-derivatives", enumValueToString(fep->dhdl_derivatives));
611 static void pr_pull(FILE* fp, int indent, const pull_params_t& pull)
615 PR("pull-cylinder-r", pull.cylinder_r);
616 PR("pull-constr-tol", pull.constr_tol);
617 PS("pull-print-COM", EBOOL(pull.bPrintCOM));
618 PS("pull-print-ref-value", EBOOL(pull.bPrintRefValue));
619 PS("pull-print-components", EBOOL(pull.bPrintComp));
620 PI("pull-nstxout", pull.nstxout);
621 PI("pull-nstfout", pull.nstfout);
622 PS("pull-pbc-ref-prev-step-com", EBOOL(pull.bSetPbcRefToPrevStepCOM));
623 PS("pull-xout-average", EBOOL(pull.bXOutAverage));
624 PS("pull-fout-average", EBOOL(pull.bFOutAverage));
625 PI("pull-ngroups", pull.ngroup);
626 for (g = 0; g < pull.ngroup; g++)
628 pr_pull_group(fp, indent, g, &pull.group[g]);
630 PI("pull-ncoords", pull.ncoord);
631 for (g = 0; g < pull.ncoord; g++)
633 pr_pull_coord(fp, indent, g, &pull.coord[g]);
637 static void pr_awh_bias_dim(FILE* fp, int indent, const gmx::AwhDimParams& awhDimParams, const char* prefix)
639 pr_indent(fp, indent);
641 fprintf(fp, "%s:\n", prefix);
642 PS("coord-provider", enumValueToString(awhDimParams.coordinateProvider()));
643 PI("coord-index", awhDimParams.coordinateIndex() + 1);
644 PR("start", awhDimParams.origin());
645 PR("end", awhDimParams.end());
646 PR("period", awhDimParams.period());
647 PR("force-constant", awhDimParams.forceConstant());
648 PR("diffusion", awhDimParams.diffusion());
649 PR("cover-diameter", awhDimParams.coverDiameter());
652 static void pr_awh_bias(FILE* fp, int indent, const gmx::AwhBiasParams& awhBiasParams, const char* prefix)
656 sprintf(opt, "%s-error-init", prefix);
657 PR(opt, awhBiasParams.initialErrorEstimate());
658 sprintf(opt, "%s-growth", prefix);
659 PS(opt, enumValueToString(awhBiasParams.growthType()));
660 sprintf(opt, "%s-target", prefix);
661 PS(opt, enumValueToString(awhBiasParams.targetDistribution()));
662 sprintf(opt, "%s-target-beta-scalng", prefix);
663 PR(opt, awhBiasParams.targetBetaScaling());
664 sprintf(opt, "%s-target-cutoff", prefix);
665 PR(opt, awhBiasParams.targetCutoff());
666 sprintf(opt, "%s-user-data", prefix);
667 PS(opt, EBOOL(awhBiasParams.userPMFEstimate()));
668 sprintf(opt, "%s-share-group", prefix);
669 PI(opt, awhBiasParams.shareGroup());
670 sprintf(opt, "%s-equilibrate-histogram", prefix);
671 PS(opt, EBOOL(awhBiasParams.equilibrateHistogram()));
672 sprintf(opt, "%s-ndim", prefix);
673 PI(opt, awhBiasParams.ndim());
676 for (const auto& dimParam : awhBiasParams.dimParams())
678 char prefixdim[STRLEN];
679 sprintf(prefixdim, "%s-dim%d", prefix, d + 1);
680 pr_awh_bias_dim(fp, indent, dimParam, prefixdim);
685 static void pr_awh(FILE* fp, int indent, gmx::AwhParams* awhParams)
687 PS("awh-potential", enumValueToString(awhParams->potential()));
688 PI("awh-seed", awhParams->seed());
689 PI("awh-nstout", awhParams->nstout());
690 PI("awh-nstsample", awhParams->nstSampleCoord());
691 PI("awh-nsamples-update", awhParams->numSamplesUpdateFreeEnergy());
692 PS("awh-share-bias-multisim", EBOOL(awhParams->shareBiasMultisim()));
693 PI("awh-nbias", awhParams->numBias());
696 for (const auto& awhBiasParam : awhParams->awhBiasParams())
698 auto prefix = gmx::formatString("awh%d", k + 1);
699 pr_awh_bias(fp, indent, awhBiasParam, prefix.c_str());
704 static void pr_rotgrp(FILE* fp, int indent, int g, const t_rotgrp* rotg)
706 pr_indent(fp, indent);
707 fprintf(fp, "rot-group %d:\n", g);
709 PS("rot-type", enumValueToString(rotg->eType));
710 PS("rot-massw", EBOOL(rotg->bMassW));
711 pr_ivec_block(fp, indent, "atom", rotg->ind, rotg->nat, TRUE);
712 pr_rvecs(fp, indent, "x-ref", rotg->x_ref, rotg->nat);
713 pr_rvec(fp, indent, "rot-vec", rotg->inputVec, DIM, TRUE);
714 pr_rvec(fp, indent, "rot-pivot", rotg->pivot, DIM, TRUE);
715 PR("rot-rate", rotg->rate);
716 PR("rot-k", rotg->k);
717 PR("rot-slab-dist", rotg->slab_dist);
718 PR("rot-min-gauss", rotg->min_gaussian);
719 PR("rot-eps", rotg->eps);
720 PS("rot-fit-method", enumValueToString(rotg->eFittype));
721 PI("rot-potfit-nstep", rotg->PotAngle_nstep);
722 PR("rot-potfit-step", rotg->PotAngle_step);
725 static void pr_rot(FILE* fp, int indent, const t_rot* rot)
729 PI("rot-nstrout", rot->nstrout);
730 PI("rot-nstsout", rot->nstsout);
731 PI("rot-ngroups", rot->ngrp);
732 for (g = 0; g < rot->ngrp; g++)
734 pr_rotgrp(fp, indent, g, &rot->grp[g]);
739 static void pr_swap(FILE* fp, int indent, const t_swapcoords* swap)
743 /* Enums for better readability of the code */
751 PI("swap-frequency", swap->nstswap);
753 /* The split groups that define the compartments */
754 for (int j = 0; j < 2; j++)
756 snprintf(str, STRLEN, "massw_split%d", j);
757 PS(str, EBOOL(swap->massw_split[j]));
758 snprintf(str, STRLEN, "split atoms group %d", j);
759 pr_ivec_block(fp, indent, str, swap->grp[j].ind, swap->grp[j].nat, TRUE);
762 /* The solvent group */
766 swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].molname);
770 swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].ind,
771 swap->grp[static_cast<int>(SwapGroupSplittingType::Solvent)].nat,
774 /* Now print the indices for all the ion groups: */
775 for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < swap->ngrp; ig++)
777 snprintf(str, STRLEN, "ion group %s", swap->grp[ig].molname);
778 pr_ivec_block(fp, indent, str, swap->grp[ig].ind, swap->grp[ig].nat, TRUE);
781 PR("cyl0-r", swap->cyl0r);
782 PR("cyl0-up", swap->cyl0u);
783 PR("cyl0-down", swap->cyl0l);
784 PR("cyl1-r", swap->cyl1r);
785 PR("cyl1-up", swap->cyl1u);
786 PR("cyl1-down", swap->cyl1l);
787 PI("coupl-steps", swap->nAverage);
789 /* Print the requested ion counts for both compartments */
790 for (int ic = eCompA; ic <= eCompB; ic++)
792 for (int ig = static_cast<int>(SwapGroupSplittingType::Count); ig < swap->ngrp; ig++)
794 snprintf(str, STRLEN, "%s-in-%c", swap->grp[ig].molname, 'A' + ic);
795 PI(str, swap->grp[ig].nmolReq[ic]);
799 PR("threshold", swap->threshold);
800 PR("bulk-offsetA", swap->bulkOffset[eCompA]);
801 PR("bulk-offsetB", swap->bulkOffset[eCompB]);
805 static void pr_imd(FILE* fp, int indent, const t_IMD* imd)
807 PI("IMD-atoms", imd->nat);
808 pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE);
812 void pr_inputrec(FILE* fp, int indent, const char* title, const t_inputrec* ir, gmx_bool bMDPformat)
814 const char* infbuf = "inf";
816 if (available(fp, ir, indent, title))
820 indent = pr_title(fp, indent, title);
822 /* Try to make this list appear in the same order as the
823 * options are written in the default mdout.mdp, and with
824 * the same user-exposed names to facilitate debugging.
826 PS("integrator", enumValueToString(ir->eI));
827 PR("tinit", ir->init_t);
828 PR("dt", ir->delta_t);
829 PSTEP("nsteps", ir->nsteps);
830 PSTEP("init-step", ir->init_step);
831 PI("simulation-part", ir->simulation_part);
832 PS("mts", EBOOL(ir->useMts));
835 for (int mtsIndex = 1; mtsIndex < static_cast<int>(ir->mtsLevels.size()); mtsIndex++)
837 const auto& mtsLevel = ir->mtsLevels[mtsIndex];
838 const std::string forceKey = gmx::formatString("mts-level%d-forces", mtsIndex + 1);
839 std::string forceGroups;
840 for (int i = 0; i < static_cast<int>(gmx::MtsForceGroups::Count); i++)
842 if (mtsLevel.forceGroups[i])
844 if (!forceGroups.empty())
848 forceGroups += gmx::mtsForceGroupNames[i];
851 PS(forceKey.c_str(), forceGroups.c_str());
852 const std::string factorKey = gmx::formatString("mts-level%d-factor", mtsIndex + 1);
853 PI(factorKey.c_str(), mtsLevel.stepFactor);
856 PS("comm-mode", enumValueToString(ir->comm_mode));
857 PI("nstcomm", ir->nstcomm);
859 /* Langevin dynamics */
860 PR("bd-fric", ir->bd_fric);
861 PSTEP("ld-seed", ir->ld_seed);
863 /* Energy minimization */
864 PR("emtol", ir->em_tol);
865 PR("emstep", ir->em_stepsize);
866 PI("niter", ir->niter);
867 PR("fcstep", ir->fc_stepsize);
868 PI("nstcgsteep", ir->nstcgsteep);
869 PI("nbfgscorr", ir->nbfgscorr);
871 /* Test particle insertion */
872 PR("rtpi", ir->rtpi);
875 PI("nstxout", ir->nstxout);
876 PI("nstvout", ir->nstvout);
877 PI("nstfout", ir->nstfout);
878 PI("nstlog", ir->nstlog);
879 PI("nstcalcenergy", ir->nstcalcenergy);
880 PI("nstenergy", ir->nstenergy);
881 PI("nstxout-compressed", ir->nstxout_compressed);
882 PR("compressed-x-precision", ir->x_compression_precision);
884 /* Neighborsearching parameters */
885 PS("cutoff-scheme", enumValueToString(ir->cutoff_scheme));
886 PI("nstlist", ir->nstlist);
887 PS("pbc", c_pbcTypeNames[ir->pbcType].c_str());
888 PS("periodic-molecules", EBOOL(ir->bPeriodicMols));
889 PR("verlet-buffer-tolerance", ir->verletbuf_tol);
890 PR("rlist", ir->rlist);
892 /* Options for electrostatics and VdW */
893 PS("coulombtype", enumValueToString(ir->coulombtype));
894 PS("coulomb-modifier", enumValueToString(ir->coulomb_modifier));
895 PR("rcoulomb-switch", ir->rcoulomb_switch);
896 PR("rcoulomb", ir->rcoulomb);
897 if (ir->epsilon_r != 0)
899 PR("epsilon-r", ir->epsilon_r);
903 PS("epsilon-r", infbuf);
905 if (ir->epsilon_rf != 0)
907 PR("epsilon-rf", ir->epsilon_rf);
911 PS("epsilon-rf", infbuf);
913 PS("vdw-type", enumValueToString(ir->vdwtype));
914 PS("vdw-modifier", enumValueToString(ir->vdw_modifier));
915 PR("rvdw-switch", ir->rvdw_switch);
916 PR("rvdw", ir->rvdw);
917 PS("DispCorr", enumValueToString(ir->eDispCorr));
918 PR("table-extension", ir->tabext);
920 PR("fourierspacing", ir->fourier_spacing);
921 PI("fourier-nx", ir->nkx);
922 PI("fourier-ny", ir->nky);
923 PI("fourier-nz", ir->nkz);
924 PI("pme-order", ir->pme_order);
925 PR("ewald-rtol", ir->ewald_rtol);
926 PR("ewald-rtol-lj", ir->ewald_rtol_lj);
927 PS("lj-pme-comb-rule", enumValueToString(ir->ljpme_combination_rule));
928 PS("ewald-geometry", enumValueToString(ir->ewald_geometry));
929 PR("epsilon-surface", ir->epsilon_surface);
931 /* Options for weak coupling algorithms */
932 PS("tcoupl", enumValueToString(ir->etc));
933 PI("nsttcouple", ir->nsttcouple);
934 PI("nh-chain-length", ir->opts.nhchainlength);
935 PS("print-nose-hoover-chain-variables", EBOOL(ir->bPrintNHChains));
937 PS("pcoupl", enumValueToString(ir->epc));
938 PS("pcoupltype", enumValueToString(ir->epct));
939 PI("nstpcouple", ir->nstpcouple);
940 PR("tau-p", ir->tau_p);
941 pr_matrix(fp, indent, "compressibility", ir->compress, bMDPformat);
942 pr_matrix(fp, indent, "ref-p", ir->ref_p, bMDPformat);
943 PS("refcoord-scaling", enumValueToString(ir->refcoord_scaling));
947 fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX], ir->posres_com[YY], ir->posres_com[ZZ]);
948 fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX], ir->posres_comB[YY], ir->posres_comB[ZZ]);
952 pr_rvec(fp, indent, "posres-com", ir->posres_com, DIM, TRUE);
953 pr_rvec(fp, indent, "posres-comB", ir->posres_comB, DIM, TRUE);
957 PS("QMMM", EBOOL(ir->bQMMM));
958 fprintf(fp, "%s:\n", "qm-opts");
959 pr_int(fp, indent, "ngQM", ir->opts.ngQM);
961 /* CONSTRAINT OPTIONS */
962 PS("constraint-algorithm", enumValueToString(ir->eConstrAlg));
963 PS("continuation", EBOOL(ir->bContinuation));
965 PS("Shake-SOR", EBOOL(ir->bShakeSOR));
966 PR("shake-tol", ir->shake_tol);
967 PI("lincs-order", ir->nProjOrder);
968 PI("lincs-iter", ir->nLincsIter);
969 PR("lincs-warnangle", ir->LincsWarnAngle);
972 PI("nwall", ir->nwall);
973 PS("wall-type", enumValueToString(ir->wall_type));
974 PR("wall-r-linpot", ir->wall_r_linpot);
976 PI("wall-atomtype[0]", ir->wall_atomtype[0]);
977 PI("wall-atomtype[1]", ir->wall_atomtype[1]);
979 PR("wall-density[0]", ir->wall_density[0]);
980 PR("wall-density[1]", ir->wall_density[1]);
981 PR("wall-ewald-zfac", ir->wall_ewald_zfac);
984 PS("pull", EBOOL(ir->bPull));
987 pr_pull(fp, indent, *ir->pull);
991 PS("awh", EBOOL(ir->bDoAwh));
994 pr_awh(fp, indent, ir->awhParams.get());
997 /* ENFORCED ROTATION */
998 PS("rotation", EBOOL(ir->bRot));
1001 pr_rot(fp, indent, ir->rot);
1004 /* INTERACTIVE MD */
1005 PS("interactiveMD", EBOOL(ir->bIMD));
1008 pr_imd(fp, indent, ir->imd);
1011 /* NMR refinement stuff */
1012 PS("disre", enumValueToString(ir->eDisre));
1013 PS("disre-weighting", enumValueToString(ir->eDisreWeighting));
1014 PS("disre-mixed", EBOOL(ir->bDisreMixed));
1015 PR("dr-fc", ir->dr_fc);
1016 PR("dr-tau", ir->dr_tau);
1017 PR("nstdisreout", ir->nstdisreout);
1019 PR("orire-fc", ir->orires_fc);
1020 PR("orire-tau", ir->orires_tau);
1021 PR("nstorireout", ir->nstorireout);
1023 /* FREE ENERGY VARIABLES */
1024 PS("free-energy", enumValueToString(ir->efep));
1025 if (ir->efep != FreeEnergyPerturbationType::No || ir->bSimTemp)
1027 pr_fepvals(fp, indent, ir->fepvals.get(), bMDPformat);
1031 pr_expandedvals(fp, indent, ir->expandedvals.get(), ir->fepvals->n_lambda);
1034 /* NON-equilibrium MD stuff */
1035 PR("cos-acceleration", ir->cos_accel);
1036 pr_matrix(fp, indent, "deform", ir->deform, bMDPformat);
1038 /* SIMULATED TEMPERING */
1039 PS("simulated-tempering", EBOOL(ir->bSimTemp));
1042 pr_simtempvals(fp, indent, ir->simtempvals.get(), ir->fepvals->n_lambda);
1045 /* ION/WATER SWAPPING FOR COMPUTATIONAL ELECTROPHYSIOLOGY */
1046 PS("swapcoords", enumValueToString(ir->eSwapCoords));
1047 if (ir->eSwapCoords != SwapType::No)
1049 pr_swap(fp, indent, ir->swap);
1052 /* USER-DEFINED THINGIES */
1053 PI("userint1", ir->userint1);
1054 PI("userint2", ir->userint2);
1055 PI("userint3", ir->userint3);
1056 PI("userint4", ir->userint4);
1057 PR("userreal1", ir->userreal1);
1058 PR("userreal2", ir->userreal2);
1059 PR("userreal3", ir->userreal3);
1060 PR("userreal4", ir->userreal4);
1064 gmx::TextWriter writer(fp);
1065 writer.wrapperSettings().setIndent(indent);
1066 gmx::dumpKeyValueTree(&writer, *ir->params);
1069 pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat);
1076 static void cmp_grpopts(FILE* fp, const t_grpopts* opt1, const t_grpopts* opt2, real ftol, real abstol)
1079 char buf1[256], buf2[256];
1081 cmp_int(fp, "inputrec->grpopts.ngtc", -1, opt1->ngtc, opt2->ngtc);
1082 cmp_int(fp, "inputrec->grpopts.ngfrz", -1, opt1->ngfrz, opt2->ngfrz);
1083 cmp_int(fp, "inputrec->grpopts.ngener", -1, opt1->ngener, opt2->ngener);
1084 for (i = 0; (i < std::min(opt1->ngtc, opt2->ngtc)); i++)
1086 cmp_real(fp, "inputrec->grpopts.nrdf", i, opt1->nrdf[i], opt2->nrdf[i], ftol, abstol);
1087 cmp_real(fp, "inputrec->grpopts.ref_t", i, opt1->ref_t[i], opt2->ref_t[i], ftol, abstol);
1088 cmp_real(fp, "inputrec->grpopts.tau_t", i, opt1->tau_t[i], opt2->tau_t[i], ftol, abstol);
1089 cmpEnum(fp, "inputrec->grpopts.annealing", opt1->annealing[i], opt2->annealing[i]);
1090 cmp_int(fp, "inputrec->grpopts.anneal_npoints", i, opt1->anneal_npoints[i], opt2->anneal_npoints[i]);
1091 if (opt1->anneal_npoints[i] == opt2->anneal_npoints[i])
1093 sprintf(buf1, "inputrec->grpopts.anneal_time[%d]", i);
1094 sprintf(buf2, "inputrec->grpopts.anneal_temp[%d]", i);
1095 for (j = 0; j < opt1->anneal_npoints[i]; j++)
1097 cmp_real(fp, buf1, j, opt1->anneal_time[i][j], opt2->anneal_time[i][j], ftol, abstol);
1098 cmp_real(fp, buf2, j, opt1->anneal_temp[i][j], opt2->anneal_temp[i][j], ftol, abstol);
1102 if (opt1->ngener == opt2->ngener)
1104 for (i = 0; i < opt1->ngener; i++)
1106 for (j = i; j < opt1->ngener; j++)
1108 sprintf(buf1, "inputrec->grpopts.egp_flags[%d]", i);
1109 cmp_int(fp, buf1, j, opt1->egp_flags[opt1->ngener * i + j], opt2->egp_flags[opt1->ngener * i + j]);
1113 for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++)
1115 cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]);
1119 static void cmp_pull(FILE* fp)
1122 "WARNING: Both files use COM pulling, but comparing of the pull struct is not "
1123 "implemented (yet). The pull parameters could be the same or different.\n");
1126 static void cmp_awhDimParams(FILE* fp,
1127 const gmx::AwhDimParams& dimp1,
1128 const gmx::AwhDimParams& dimp2,
1133 /* Note that we have double index here, but the compare functions only
1134 * support one index, so here we only print the dim index and not the bias.
1137 "inputrec.awhParams->bias?->dim->coord_index",
1139 dimp1.coordinateIndex(),
1140 dimp2.coordinateIndex());
1141 cmp_double(fp, "inputrec->awhParams->bias?->dim->period", dimIndex, dimp1.period(), dimp2.period(), ftol, abstol);
1143 "inputrec->awhParams->bias?->dim->diffusion",
1149 cmp_double(fp, "inputrec->awhParams->bias?->dim->origin", dimIndex, dimp1.origin(), dimp2.origin(), ftol, abstol);
1150 cmp_double(fp, "inputrec->awhParams->bias?->dim->end", dimIndex, dimp1.end(), dimp2.end(), ftol, abstol);
1152 "inputrec->awhParams->bias?->dim->coord_value_init",
1154 dimp1.initialCoordinate(),
1155 dimp2.initialCoordinate(),
1159 "inputrec->awhParams->bias?->dim->coverDiameter",
1161 dimp1.coverDiameter(),
1162 dimp2.coverDiameter(),
1167 static void cmp_awhBiasParams(FILE* fp,
1168 const gmx::AwhBiasParams& bias1,
1169 const gmx::AwhBiasParams& bias2,
1174 cmp_int(fp, "inputrec->awhParams->ndim", biasIndex, bias1.ndim(), bias2.ndim());
1175 cmpEnum<gmx::AwhTargetType>(
1176 fp, "inputrec->awhParams->biaseTarget", bias1.targetDistribution(), bias2.targetDistribution());
1178 "inputrec->awhParams->biastargetBetaScaling",
1180 bias1.targetBetaScaling(),
1181 bias2.targetBetaScaling(),
1185 "inputrec->awhParams->biastargetCutoff",
1187 bias1.targetCutoff(),
1188 bias2.targetCutoff(),
1191 cmpEnum<gmx::AwhHistogramGrowthType>(
1192 fp, "inputrec->awhParams->biaseGrowth", bias1.growthType(), bias2.growthType());
1193 cmp_bool(fp, "inputrec->awhParams->biasbUserData", biasIndex, bias1.userPMFEstimate(), bias2.userPMFEstimate());
1195 "inputrec->awhParams->biaserror_initial",
1197 bias1.initialErrorEstimate(),
1198 bias2.initialErrorEstimate(),
1201 cmp_int(fp, "inputrec->awhParams->biasShareGroup", biasIndex, bias1.shareGroup(), bias2.shareGroup());
1203 const auto dimParams1 = bias1.dimParams();
1204 const auto dimParams2 = bias2.dimParams();
1205 for (int dim = 0; dim < std::min(bias1.ndim(), bias2.ndim()); dim++)
1207 cmp_awhDimParams(fp, dimParams1[dim], dimParams2[dim], dim, ftol, abstol);
1211 static void cmp_awhParams(FILE* fp, const gmx::AwhParams& awh1, const gmx::AwhParams& awh2, real ftol, real abstol)
1213 cmp_int(fp, "inputrec->awhParams->nbias", -1, awh1.numBias(), awh2.numBias());
1214 cmp_int64(fp, "inputrec->awhParams->seed", awh1.seed(), awh2.seed());
1215 cmp_int(fp, "inputrec->awhParams->nstout", -1, awh1.nstout(), awh2.nstout());
1216 cmp_int(fp, "inputrec->awhParams->nstsample_coord", -1, awh1.nstSampleCoord(), awh2.nstSampleCoord());
1218 "inputrec->awhParams->nsamples_update_free_energy",
1220 awh1.numSamplesUpdateFreeEnergy(),
1221 awh2.numSamplesUpdateFreeEnergy());
1222 cmpEnum<gmx::AwhPotentialType>(
1223 fp, "inputrec->awhParams->ePotential", awh1.potential(), awh2.potential());
1224 cmp_bool(fp, "inputrec->awhParams->shareBiasMultisim", -1, awh1.shareBiasMultisim(), awh2.shareBiasMultisim());
1226 if (awh1.numBias() == awh2.numBias())
1228 const auto awhBiasParams1 = awh1.awhBiasParams();
1229 const auto awhBiasParams2 = awh2.awhBiasParams();
1230 for (int bias = 0; bias < awh1.numBias(); bias++)
1232 cmp_awhBiasParams(fp, awhBiasParams1[bias], awhBiasParams2[bias], bias, ftol, abstol);
1237 static void cmp_simtempvals(FILE* fp,
1238 const t_simtemp* simtemp1,
1239 const t_simtemp* simtemp2,
1245 cmpEnum(fp, "inputrec->simtempvals->eSimTempScale", simtemp1->eSimTempScale, simtemp2->eSimTempScale);
1246 cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high, simtemp2->simtemp_high, ftol, abstol);
1247 cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low, simtemp2->simtemp_low, ftol, abstol);
1248 for (i = 0; i < n_lambda; i++)
1251 "inputrec->simtempvals->temperatures",
1253 simtemp1->temperatures[i],
1254 simtemp2->temperatures[i],
1260 static void cmp_expandedvals(FILE* fp,
1261 const t_expanded* expand1,
1262 const t_expanded* expand2,
1269 cmp_bool(fp, "inputrec->fepvals->bInit_weights", -1, expand1->bInit_weights, expand2->bInit_weights);
1270 cmp_bool(fp, "inputrec->fepvals->bWLoneovert", -1, expand1->bWLoneovert, expand2->bWLoneovert);
1272 for (i = 0; i < n_lambda; i++)
1275 "inputrec->expandedvals->init_lambda_weights",
1277 expand1->init_lambda_weights[i],
1278 expand2->init_lambda_weights[i],
1283 cmpEnum(fp, "inputrec->expandedvals->lambda-stats", expand1->elamstats, expand2->elamstats);
1284 cmpEnum(fp, "inputrec->expandedvals->lambda-mc-move", expand1->elmcmove, expand2->elmcmove);
1285 cmp_int(fp, "inputrec->expandedvals->lmc-repeats", -1, expand1->lmc_repeats, expand2->lmc_repeats);
1286 cmp_int(fp, "inputrec->expandedvals->lmc-gibbsdelta", -1, expand1->gibbsdeltalam, expand2->gibbsdeltalam);
1287 cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart, expand2->lmc_forced_nstart);
1288 cmpEnum(fp, "inputrec->expandedvals->lambda-weights-equil", expand1->elmceq, expand2->elmceq);
1290 "inputrec->expandedvals->,weight-equil-number-all-lambda",
1292 expand1->equil_n_at_lam,
1293 expand2->equil_n_at_lam);
1294 cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples, expand2->equil_samples);
1295 cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps, expand2->equil_steps);
1297 "inputrec->expandedvals->weight-equil-wl-delta",
1299 expand1->equil_wl_delta,
1300 expand2->equil_wl_delta,
1304 "inputrec->expandedvals->weight-equil-count-ratio",
1306 expand1->equil_ratio,
1307 expand2->equil_ratio,
1311 "inputrec->expandedvals->symmetrized-transition-matrix",
1313 expand1->bSymmetrizedTMatrix,
1314 expand2->bSymmetrizedTMatrix);
1315 cmp_int(fp, "inputrec->expandedvals->nstTij", -1, expand1->nstTij, expand2->nstTij);
1316 cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin, expand2->minvarmin); /*default is reasonable */
1317 cmp_int(fp, "inputrec->expandedvals->weight-c-range", -1, expand1->c_range, expand2->c_range); /* default is just C=0 */
1318 cmp_real(fp, "inputrec->expandedvals->wl-scale", -1, expand1->wl_scale, expand2->wl_scale, ftol, abstol);
1319 cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta, expand2->init_wl_delta, ftol, abstol);
1320 cmp_real(fp, "inputrec->expandedvals->wl-ratio", -1, expand1->wl_ratio, expand2->wl_ratio, ftol, abstol);
1321 cmp_int(fp, "inputrec->expandedvals->nstexpanded", -1, expand1->nstexpanded, expand2->nstexpanded);
1322 cmp_int(fp, "inputrec->expandedvals->lmc-seed", -1, expand1->lmc_seed, expand2->lmc_seed);
1323 cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp, ftol, abstol);
1326 static void cmp_fepvals(FILE* fp, const t_lambda* fep1, const t_lambda* fep2, real ftol, real abstol)
1329 cmp_int(fp, "inputrec->nstdhdl", -1, fep1->nstdhdl, fep2->nstdhdl);
1330 cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state, fep2->init_fep_state, ftol, abstol);
1331 cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda, ftol, abstol);
1332 cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda);
1333 for (i = 0; i < static_cast<int>(FreeEnergyPerturbationCouplingType::Count); i++)
1335 for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++)
1338 "inputrec->fepvals->all_lambda",
1340 fep1->all_lambda[i][j],
1341 fep2->all_lambda[i][j],
1346 cmp_int(fp, "inputrec->fepvals->lambda_neighbors", 1, fep1->lambda_neighbors, fep2->lambda_neighbors);
1347 cmp_real(fp, "inputrec->fepvals->sc_alpha", -1, fep1->sc_alpha, fep2->sc_alpha, ftol, abstol);
1348 cmp_int(fp, "inputrec->fepvals->sc_power", -1, fep1->sc_power, fep2->sc_power);
1349 cmp_real(fp, "inputrec->fepvals->sc_r_power", -1, fep1->sc_r_power, fep2->sc_r_power, ftol, abstol);
1350 cmp_real(fp, "inputrec->fepvals->sc_sigma", -1, fep1->sc_sigma, fep2->sc_sigma, ftol, abstol);
1351 cmpEnum(fp, "inputrec->fepvals->edHdLPrintEnergy", fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy);
1352 cmp_bool(fp, "inputrec->fepvals->bScCoul", -1, fep1->bScCoul, fep1->bScCoul);
1353 cmpEnum(fp, "inputrec->separate_dhdl_file", fep1->separate_dhdl_file, fep2->separate_dhdl_file);
1354 cmpEnum(fp, "inputrec->dhdl_derivatives", fep1->dhdl_derivatives, fep2->dhdl_derivatives);
1355 cmp_int(fp, "inputrec->dh_hist_size", -1, fep1->dh_hist_size, fep2->dh_hist_size);
1356 cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing, ftol, abstol);
1359 void cmp_inputrec(FILE* fp, const t_inputrec* ir1, const t_inputrec* ir2, real ftol, real abstol)
1361 fprintf(fp, "comparing inputrec\n");
1363 /* gcc 2.96 doesnt like these defines at all, but issues a huge list
1364 * of warnings. Maybe it will change in future versions, but for the
1365 * moment I've spelled them out instead. /EL 000820
1366 * #define CIB(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
1367 * #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
1368 * #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol)
1370 cmpEnum(fp, "inputrec->eI", ir1->eI, ir2->eI);
1371 cmp_int64(fp, "inputrec->nsteps", ir1->nsteps, ir2->nsteps);
1372 cmp_int64(fp, "inputrec->init_step", ir1->init_step, ir2->init_step);
1373 cmp_int(fp, "inputrec->simulation_part", -1, ir1->simulation_part, ir2->simulation_part);
1374 cmp_int(fp, "inputrec->mts", -1, static_cast<int>(ir1->useMts), static_cast<int>(ir2->useMts));
1375 if (ir1->useMts && ir2->useMts)
1377 cmp_int(fp, "inputrec->mts-levels", -1, ir1->mtsLevels.size(), ir2->mtsLevels.size());
1379 "inputrec->mts-level2-forces",
1381 ir1->mtsLevels[1].forceGroups.to_ulong(),
1382 ir2->mtsLevels[1].forceGroups.to_ulong());
1384 "inputrec->mts-level2-factor",
1386 ir1->mtsLevels[1].stepFactor,
1387 ir2->mtsLevels[1].stepFactor);
1389 cmp_int(fp, "inputrec->pbcType", -1, static_cast<int>(ir1->pbcType), static_cast<int>(ir2->pbcType));
1390 cmp_bool(fp, "inputrec->bPeriodicMols", -1, ir1->bPeriodicMols, ir2->bPeriodicMols);
1391 cmpEnum(fp, "inputrec->cutoff_scheme", ir1->cutoff_scheme, ir2->cutoff_scheme);
1392 cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist);
1393 cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm);
1394 cmpEnum(fp, "inputrec->comm_mode", ir1->comm_mode, ir2->comm_mode);
1395 cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog);
1396 cmp_int(fp, "inputrec->nstxout", -1, ir1->nstxout, ir2->nstxout);
1397 cmp_int(fp, "inputrec->nstvout", -1, ir1->nstvout, ir2->nstvout);
1398 cmp_int(fp, "inputrec->nstfout", -1, ir1->nstfout, ir2->nstfout);
1399 cmp_int(fp, "inputrec->nstcalcenergy", -1, ir1->nstcalcenergy, ir2->nstcalcenergy);
1400 cmp_int(fp, "inputrec->nstenergy", -1, ir1->nstenergy, ir2->nstenergy);
1401 cmp_int(fp, "inputrec->nstxout_compressed", -1, ir1->nstxout_compressed, ir2->nstxout_compressed);
1402 cmp_double(fp, "inputrec->init_t", -1, ir1->init_t, ir2->init_t, ftol, abstol);
1403 cmp_double(fp, "inputrec->delta_t", -1, ir1->delta_t, ir2->delta_t, ftol, abstol);
1405 "inputrec->x_compression_precision",
1407 ir1->x_compression_precision,
1408 ir2->x_compression_precision,
1411 cmp_real(fp, "inputrec->fourierspacing", -1, ir1->fourier_spacing, ir2->fourier_spacing, ftol, abstol);
1412 cmp_int(fp, "inputrec->nkx", -1, ir1->nkx, ir2->nkx);
1413 cmp_int(fp, "inputrec->nky", -1, ir1->nky, ir2->nky);
1414 cmp_int(fp, "inputrec->nkz", -1, ir1->nkz, ir2->nkz);
1415 cmp_int(fp, "inputrec->pme_order", -1, ir1->pme_order, ir2->pme_order);
1416 cmp_real(fp, "inputrec->ewald_rtol", -1, ir1->ewald_rtol, ir2->ewald_rtol, ftol, abstol);
1417 cmpEnum(fp, "inputrec->ewald_geometry", ir1->ewald_geometry, ir2->ewald_geometry);
1418 cmp_real(fp, "inputrec->epsilon_surface", -1, ir1->epsilon_surface, ir2->epsilon_surface, ftol, abstol);
1420 "inputrec->bContinuation",
1422 static_cast<int>(ir1->bContinuation),
1423 static_cast<int>(ir2->bContinuation));
1424 cmp_int(fp, "inputrec->bShakeSOR", -1, static_cast<int>(ir1->bShakeSOR), static_cast<int>(ir2->bShakeSOR));
1425 cmpEnum(fp, "inputrec->etc", ir1->etc, ir2->etc);
1427 "inputrec->bPrintNHChains",
1429 static_cast<int>(ir1->bPrintNHChains),
1430 static_cast<int>(ir2->bPrintNHChains));
1431 cmpEnum(fp, "inputrec->epc", ir1->epc, ir2->epc);
1432 cmpEnum(fp, "inputrec->epct", ir1->epct, ir2->epct);
1433 cmp_real(fp, "inputrec->tau_p", -1, ir1->tau_p, ir2->tau_p, ftol, abstol);
1434 cmp_rvec(fp, "inputrec->ref_p(x)", -1, ir1->ref_p[XX], ir2->ref_p[XX], ftol, abstol);
1435 cmp_rvec(fp, "inputrec->ref_p(y)", -1, ir1->ref_p[YY], ir2->ref_p[YY], ftol, abstol);
1436 cmp_rvec(fp, "inputrec->ref_p(z)", -1, ir1->ref_p[ZZ], ir2->ref_p[ZZ], ftol, abstol);
1437 cmp_rvec(fp, "inputrec->compress(x)", -1, ir1->compress[XX], ir2->compress[XX], ftol, abstol);
1438 cmp_rvec(fp, "inputrec->compress(y)", -1, ir1->compress[YY], ir2->compress[YY], ftol, abstol);
1439 cmp_rvec(fp, "inputrec->compress(z)", -1, ir1->compress[ZZ], ir2->compress[ZZ], ftol, abstol);
1440 cmpEnum(fp, "refcoord_scaling", ir1->refcoord_scaling, ir2->refcoord_scaling);
1441 cmp_rvec(fp, "inputrec->posres_com", -1, ir1->posres_com, ir2->posres_com, ftol, abstol);
1442 cmp_rvec(fp, "inputrec->posres_comB", -1, ir1->posres_comB, ir2->posres_comB, ftol, abstol);
1443 cmp_real(fp, "inputrec->verletbuf_tol", -1, ir1->verletbuf_tol, ir2->verletbuf_tol, ftol, abstol);
1444 cmp_real(fp, "inputrec->rlist", -1, ir1->rlist, ir2->rlist, ftol, abstol);
1445 cmp_real(fp, "inputrec->rtpi", -1, ir1->rtpi, ir2->rtpi, ftol, abstol);
1446 cmpEnum(fp, "inputrec->coulombtype", ir1->coulombtype, ir2->coulombtype);
1447 cmpEnum(fp, "inputrec->coulomb_modifier", ir1->coulomb_modifier, ir2->coulomb_modifier);
1448 cmp_real(fp, "inputrec->rcoulomb_switch", -1, ir1->rcoulomb_switch, ir2->rcoulomb_switch, ftol, abstol);
1449 cmp_real(fp, "inputrec->rcoulomb", -1, ir1->rcoulomb, ir2->rcoulomb, ftol, abstol);
1450 cmpEnum(fp, "inputrec->vdwtype", ir1->vdwtype, ir2->vdwtype);
1451 cmpEnum(fp, "inputrec->vdw_modifier", ir1->vdw_modifier, ir2->vdw_modifier);
1452 cmp_real(fp, "inputrec->rvdw_switch", -1, ir1->rvdw_switch, ir2->rvdw_switch, ftol, abstol);
1453 cmp_real(fp, "inputrec->rvdw", -1, ir1->rvdw, ir2->rvdw, ftol, abstol);
1454 cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol);
1455 cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol);
1456 cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol);
1458 cmpEnum(fp, "inputrec->eDispCorr", ir1->eDispCorr, ir2->eDispCorr);
1459 cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol);
1460 cmpEnum(fp, "inputrec->efep", ir1->efep, ir2->efep);
1461 cmp_fepvals(fp, ir1->fepvals.get(), ir2->fepvals.get(), ftol, abstol);
1462 cmp_int(fp, "inputrec->bSimTemp", -1, static_cast<int>(ir1->bSimTemp), static_cast<int>(ir2->bSimTemp));
1463 if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp))
1466 ir1->simtempvals.get(),
1467 ir2->simtempvals.get(),
1468 std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda),
1472 cmp_int(fp, "inputrec->bExpanded", -1, static_cast<int>(ir1->bExpanded), static_cast<int>(ir2->bExpanded));
1473 if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded))
1475 cmp_expandedvals(fp,
1476 ir1->expandedvals.get(),
1477 ir2->expandedvals.get(),
1478 std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda),
1482 cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall);
1483 cmpEnum(fp, "inputrec->wall_type", ir1->wall_type, ir2->wall_type);
1484 cmp_int(fp, "inputrec->wall_atomtype[0]", -1, ir1->wall_atomtype[0], ir2->wall_atomtype[0]);
1485 cmp_int(fp, "inputrec->wall_atomtype[1]", -1, ir1->wall_atomtype[1], ir2->wall_atomtype[1]);
1486 cmp_real(fp, "inputrec->wall_density[0]", -1, ir1->wall_density[0], ir2->wall_density[0], ftol, abstol);
1487 cmp_real(fp, "inputrec->wall_density[1]", -1, ir1->wall_density[1], ir2->wall_density[1], ftol, abstol);
1488 cmp_real(fp, "inputrec->wall_ewald_zfac", -1, ir1->wall_ewald_zfac, ir2->wall_ewald_zfac, ftol, abstol);
1490 cmp_bool(fp, "inputrec->bPull", -1, ir1->bPull, ir2->bPull);
1491 if (ir1->bPull && ir2->bPull)
1496 cmp_bool(fp, "inputrec->bDoAwh", -1, ir1->bDoAwh, ir2->bDoAwh);
1497 if (ir1->bDoAwh && ir2->bDoAwh)
1499 cmp_awhParams(fp, *ir1->awhParams, *ir2->awhParams, ftol, abstol);
1502 cmpEnum(fp, "inputrec->eDisre", ir1->eDisre, ir2->eDisre);
1503 cmp_real(fp, "inputrec->dr_fc", -1, ir1->dr_fc, ir2->dr_fc, ftol, abstol);
1504 cmpEnum(fp, "inputrec->eDisreWeighting", ir1->eDisreWeighting, ir2->eDisreWeighting);
1505 cmp_int(fp, "inputrec->bDisreMixed", -1, static_cast<int>(ir1->bDisreMixed), static_cast<int>(ir2->bDisreMixed));
1506 cmp_int(fp, "inputrec->nstdisreout", -1, ir1->nstdisreout, ir2->nstdisreout);
1507 cmp_real(fp, "inputrec->dr_tau", -1, ir1->dr_tau, ir2->dr_tau, ftol, abstol);
1508 cmp_real(fp, "inputrec->orires_fc", -1, ir1->orires_fc, ir2->orires_fc, ftol, abstol);
1509 cmp_real(fp, "inputrec->orires_tau", -1, ir1->orires_tau, ir2->orires_tau, ftol, abstol);
1510 cmp_int(fp, "inputrec->nstorireout", -1, ir1->nstorireout, ir2->nstorireout);
1511 cmp_real(fp, "inputrec->em_stepsize", -1, ir1->em_stepsize, ir2->em_stepsize, ftol, abstol);
1512 cmp_real(fp, "inputrec->em_tol", -1, ir1->em_tol, ir2->em_tol, ftol, abstol);
1513 cmp_int(fp, "inputrec->niter", -1, ir1->niter, ir2->niter);
1514 cmp_real(fp, "inputrec->fc_stepsize", -1, ir1->fc_stepsize, ir2->fc_stepsize, ftol, abstol);
1515 cmp_int(fp, "inputrec->nstcgsteep", -1, ir1->nstcgsteep, ir2->nstcgsteep);
1516 cmp_int(fp, "inputrec->nbfgscorr", 0, ir1->nbfgscorr, ir2->nbfgscorr);
1517 cmpEnum(fp, "inputrec->eConstrAlg", ir1->eConstrAlg, ir2->eConstrAlg);
1518 cmp_int(fp, "inputrec->nProjOrder", -1, ir1->nProjOrder, ir2->nProjOrder);
1519 cmp_real(fp, "inputrec->LincsWarnAngle", -1, ir1->LincsWarnAngle, ir2->LincsWarnAngle, ftol, abstol);
1520 cmp_int(fp, "inputrec->nLincsIter", -1, ir1->nLincsIter, ir2->nLincsIter);
1521 cmp_real(fp, "inputrec->bd_fric", -1, ir1->bd_fric, ir2->bd_fric, ftol, abstol);
1522 cmp_int64(fp, "inputrec->ld_seed", ir1->ld_seed, ir2->ld_seed);
1523 cmp_real(fp, "inputrec->cos_accel", -1, ir1->cos_accel, ir2->cos_accel, ftol, abstol);
1524 cmp_rvec(fp, "inputrec->deform(a)", -1, ir1->deform[XX], ir2->deform[XX], ftol, abstol);
1525 cmp_rvec(fp, "inputrec->deform(b)", -1, ir1->deform[YY], ir2->deform[YY], ftol, abstol);
1526 cmp_rvec(fp, "inputrec->deform(c)", -1, ir1->deform[ZZ], ir2->deform[ZZ], ftol, abstol);
1529 cmp_int(fp, "inputrec->userint1", -1, ir1->userint1, ir2->userint1);
1530 cmp_int(fp, "inputrec->userint2", -1, ir1->userint2, ir2->userint2);
1531 cmp_int(fp, "inputrec->userint3", -1, ir1->userint3, ir2->userint3);
1532 cmp_int(fp, "inputrec->userint4", -1, ir1->userint4, ir2->userint4);
1533 cmp_real(fp, "inputrec->userreal1", -1, ir1->userreal1, ir2->userreal1, ftol, abstol);
1534 cmp_real(fp, "inputrec->userreal2", -1, ir1->userreal2, ir2->userreal2, ftol, abstol);
1535 cmp_real(fp, "inputrec->userreal3", -1, ir1->userreal3, ir2->userreal3, ftol, abstol);
1536 cmp_real(fp, "inputrec->userreal4", -1, ir1->userreal4, ir2->userreal4, ftol, abstol);
1537 cmp_grpopts(fp, &(ir1->opts), &(ir2->opts), ftol, abstol);
1538 gmx::TextWriter writer(fp);
1539 gmx::compareKeyValueTrees(&writer, *ir1->params, *ir2->params, ftol, abstol);
1542 void comp_pull_AB(FILE* fp, const pull_params_t& pull, real ftol, real abstol)
1544 for (int i = 0; i < pull.ncoord; i++)
1546 fprintf(fp, "comparing pull coord %d\n", i);
1547 cmp_real(fp, "pull-coord->k", -1, pull.coord[i].k, pull.coord[i].kB, ftol, abstol);
1551 gmx_bool inputrecDeform(const t_inputrec* ir)
1553 return (ir->deform[XX][XX] != 0 || ir->deform[YY][YY] != 0 || ir->deform[ZZ][ZZ] != 0
1554 || ir->deform[YY][XX] != 0 || ir->deform[ZZ][XX] != 0 || ir->deform[ZZ][YY] != 0);
1557 gmx_bool inputrecDynamicBox(const t_inputrec* ir)
1559 return (ir->epc != PressureCoupling::No || ir->eI == IntegrationAlgorithm::TPI || inputrecDeform(ir));
1562 gmx_bool inputrecPreserveShape(const t_inputrec* ir)
1564 return (ir->epc != PressureCoupling::No && ir->deform[XX][XX] == 0
1565 && (ir->epct == PressureCouplingType::Isotropic
1566 || ir->epct == PressureCouplingType::SemiIsotropic));
1569 gmx_bool inputrecNeedMutot(const t_inputrec* ir)
1571 return ((ir->coulombtype == CoulombInteractionType::Ewald || EEL_PME(ir->coulombtype))
1572 && (ir->ewald_geometry == EwaldGeometry::ThreeDC || ir->epsilon_surface != 0));
1575 gmx_bool inputrecExclForces(const t_inputrec* ir)
1577 return (EEL_FULL(ir->coulombtype) || (EEL_RF(ir->coulombtype)));
1580 gmx_bool inputrecNptTrotter(const t_inputrec* ir)
1582 return (((ir->eI == IntegrationAlgorithm::VV) || (ir->eI == IntegrationAlgorithm::VVAK))
1583 && (ir->epc == PressureCoupling::Mttk) && (ir->etc == TemperatureCoupling::NoseHoover));
1586 gmx_bool inputrecNvtTrotter(const t_inputrec* ir)
1588 return (((ir->eI == IntegrationAlgorithm::VV) || (ir->eI == IntegrationAlgorithm::VVAK))
1589 && (ir->epc != PressureCoupling::Mttk) && (ir->etc == TemperatureCoupling::NoseHoover));
1592 gmx_bool inputrecNphTrotter(const t_inputrec* ir)
1594 return (((ir->eI == IntegrationAlgorithm::VV) || (ir->eI == IntegrationAlgorithm::VVAK))
1595 && (ir->epc == PressureCoupling::Mttk) && (ir->etc != TemperatureCoupling::NoseHoover));
1598 bool inputrecPbcXY2Walls(const t_inputrec* ir)
1600 return (ir->pbcType == PbcType::XY && ir->nwall == 2);
1603 bool inputrecFrozenAtoms(const t_inputrec* ir)
1605 return ((ir->opts.nFreeze != nullptr)
1606 && (ir->opts.ngfrz > 1 || ir->opts.nFreeze[0][XX] != 0 || ir->opts.nFreeze[0][YY] != 0
1607 || ir->opts.nFreeze[0][ZZ] != 0));
1610 bool integratorHasConservedEnergyQuantity(const t_inputrec* ir)
1613 { // NOLINT bugprone-branch-clone
1614 // Energy minimization or stochastic integrator: no conservation
1617 else if (ir->etc == TemperatureCoupling::No && ir->epc == PressureCoupling::No)
1619 // The total energy is conserved, no additional conserved quanitity
1624 // Shear stress with Parrinello-Rahman is not supported (tedious)
1626 ((ir->epc == PressureCoupling::ParrinelloRahman || ir->epc == PressureCoupling::Mttk)
1627 && (ir->ref_p[YY][XX] != 0 || ir->ref_p[ZZ][XX] != 0 || ir->ref_p[ZZ][YY] != 0));
1629 return !ETC_ANDERSEN(ir->etc) && !shearWithPR;
1633 bool integratorHasReferenceTemperature(const t_inputrec* ir)
1635 return ((ir->etc != TemperatureCoupling::No) || EI_SD(ir->eI)
1636 || (ir->eI == IntegrationAlgorithm::BD) || EI_TPI(ir->eI));
1639 int inputrec2nboundeddim(const t_inputrec* ir)
1641 if (inputrecPbcXY2Walls(ir))
1647 return numPbcDimensions(ir->pbcType);
1651 int ndof_com(const t_inputrec* ir)
1655 switch (ir->pbcType)
1658 case PbcType::No: n = 3; break;
1659 case PbcType::XY: n = (ir->nwall == 0 ? 3 : 2); break;
1660 case PbcType::Screw: n = 1; break;
1661 default: gmx_incons("Unknown pbc in calc_nrdf");
1667 real maxReferenceTemperature(const t_inputrec& ir)
1669 if (EI_ENERGY_MINIMIZATION(ir.eI) || ir.eI == IntegrationAlgorithm::NM)
1674 if (EI_MD(ir.eI) && ir.etc == TemperatureCoupling::No)
1679 /* SD and BD also use ref_t and tau_t for setting the reference temperature.
1680 * TPI can be treated as MD, since it needs an ensemble temperature.
1683 real maxTemperature = 0;
1684 for (int i = 0; i < ir.opts.ngtc; i++)
1686 if (ir.opts.tau_t[i] >= 0)
1688 maxTemperature = std::max(maxTemperature, ir.opts.ref_t[i]);
1692 return maxTemperature;
1695 bool haveEwaldSurfaceContribution(const t_inputrec& ir)
1697 return EEL_PME_EWALD(ir.coulombtype)
1698 && (ir.ewald_geometry == EwaldGeometry::ThreeDC || ir.epsilon_surface != 0);
1701 bool haveFreeEnergyType(const t_inputrec& ir, const int fepType)
1703 for (int i = 0; i < ir.fepvals->n_lambda; i++)
1705 if (ir.fepvals->all_lambda[fepType][i] > 0)