2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2010, The GROMACS development team.
6 * Copyright (c) 2012,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
47 #include "gromacs/math/veccompare.h"
48 #include "gromacs/math/vecdump.h"
49 #include "gromacs/mdtypes/awh_params.h"
50 #include "gromacs/mdtypes/md_enums.h"
51 #include "gromacs/mdtypes/pull_params.h"
52 #include "gromacs/pbcutil/pbc.h"
53 #include "gromacs/utility/compare.h"
54 #include "gromacs/utility/cstringutil.h"
55 #include "gromacs/utility/fatalerror.h"
56 #include "gromacs/utility/keyvaluetree.h"
57 #include "gromacs/utility/smalloc.h"
58 #include "gromacs/utility/snprintf.h"
59 #include "gromacs/utility/strconvert.h"
60 #include "gromacs/utility/stringutil.h"
61 #include "gromacs/utility/textwriter.h"
62 #include "gromacs/utility/txtdump.h"
64 //! Macro to select a bool name
65 #define EBOOL(e) gmx::boolToString(e)
67 /* The minimum number of integration steps required for reasonably accurate
68 * integration of first and second order coupling algorithms.
70 const int nstmin_berendsen_tcouple = 5;
71 const int nstmin_berendsen_pcouple = 10;
72 const int nstmin_harmonic = 20;
74 t_inputrec::t_inputrec()
76 // TODO When this memset is removed, remove the suppression of
77 // gcc -Wno-class-memaccess in a CMakeLists.txt file.
78 std::memset(this, 0, sizeof(*this)); // NOLINT(bugprone-undefined-memory-manipulation)
80 snew(expandedvals, 1);
84 t_inputrec::~t_inputrec()
89 static int nst_wanted(const t_inputrec *ir)
101 int ir_optimal_nstcalcenergy(const t_inputrec *ir)
103 return nst_wanted(ir);
106 int tcouple_min_integration_steps(int etc)
117 n = nstmin_berendsen_tcouple;
120 /* V-rescale supports instantaneous rescaling */
127 case etcANDERSENMASSIVE:
131 gmx_incons("Unknown etc value");
137 int ir_optimal_nsttcouple(const t_inputrec *ir)
139 int nmin, nwanted, n;
143 nmin = tcouple_min_integration_steps(ir->etc);
145 nwanted = nst_wanted(ir);
148 if (ir->etc != etcNO)
150 for (g = 0; g < ir->opts.ngtc; g++)
152 if (ir->opts.tau_t[g] > 0)
154 tau_min = std::min(tau_min, ir->opts.tau_t[g]);
159 if (nmin == 0 || ir->delta_t*nwanted <= tau_min)
165 n = static_cast<int>(tau_min/(ir->delta_t*nmin) + 0.001);
170 while (nwanted % n != 0)
179 int pcouple_min_integration_steps(int epc)
190 n = nstmin_berendsen_pcouple;
192 case epcPARRINELLORAHMAN:
197 gmx_incons("Unknown epc value");
203 int ir_optimal_nstpcouple(const t_inputrec *ir)
205 int nmin, nwanted, n;
207 nmin = pcouple_min_integration_steps(ir->epc);
209 nwanted = nst_wanted(ir);
211 if (nmin == 0 || ir->delta_t*nwanted <= ir->tau_p)
217 n = static_cast<int>(ir->tau_p/(ir->delta_t*nmin) + 0.001);
222 while (nwanted % n != 0)
231 gmx_bool ir_coulomb_switched(const t_inputrec *ir)
233 return (ir->coulombtype == eelSWITCH ||
234 ir->coulombtype == eelSHIFT ||
235 ir->coulombtype == eelENCADSHIFT ||
236 ir->coulombtype == eelPMESWITCH ||
237 ir->coulombtype == eelPMEUSERSWITCH ||
238 ir->coulomb_modifier == eintmodPOTSWITCH ||
239 ir->coulomb_modifier == eintmodFORCESWITCH);
242 gmx_bool ir_coulomb_is_zero_at_cutoff(const t_inputrec *ir)
244 return (ir->cutoff_scheme == ecutsVERLET ||
245 ir_coulomb_switched(ir) || ir->coulomb_modifier != eintmodNONE ||
246 ir->coulombtype == eelRF_ZERO);
249 gmx_bool ir_coulomb_might_be_zero_at_cutoff(const t_inputrec *ir)
251 return (ir_coulomb_is_zero_at_cutoff(ir) || ir->coulombtype == eelUSER || ir->coulombtype == eelPMEUSER);
254 gmx_bool ir_vdw_switched(const t_inputrec *ir)
256 return (ir->vdwtype == evdwSWITCH ||
257 ir->vdwtype == evdwSHIFT ||
258 ir->vdwtype == evdwENCADSHIFT ||
259 ir->vdw_modifier == eintmodPOTSWITCH ||
260 ir->vdw_modifier == eintmodFORCESWITCH);
263 gmx_bool ir_vdw_is_zero_at_cutoff(const t_inputrec *ir)
265 return (ir->cutoff_scheme == ecutsVERLET ||
266 ir_vdw_switched(ir) || ir->vdw_modifier != eintmodNONE);
269 gmx_bool ir_vdw_might_be_zero_at_cutoff(const t_inputrec *ir)
271 return (ir_vdw_is_zero_at_cutoff(ir) || ir->vdwtype == evdwUSER);
274 static void done_pull_group(t_pull_group *pgrp)
283 static void done_pull_params(pull_params_t *pull)
287 for (i = 0; i < pull->ngroup+1; i++)
289 done_pull_group(pull->group);
296 static void done_lambdas(t_lambda *fep)
298 if (fep->n_lambda > 0)
300 for (int i = 0; i < efptNR; i++)
302 sfree(fep->all_lambda[i]);
305 sfree(fep->all_lambda);
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.QMmethod);
325 sfree(ir->opts.QMbasis);
326 sfree(ir->opts.QMcharge);
327 sfree(ir->opts.QMmult);
329 sfree(ir->opts.CASorbitals);
330 sfree(ir->opts.CASelectrons);
331 sfree(ir->opts.SAon);
332 sfree(ir->opts.SAoff);
333 sfree(ir->opts.SAsteps);
334 sfree(ir->opts.egp_flags);
335 done_lambdas(ir->fepvals);
337 sfree(ir->expandedvals);
338 sfree(ir->simtempvals);
342 done_pull_params(ir->pull);
348 static void pr_qm_opts(FILE *fp, int indent, const char *title, const t_grpopts *opts)
350 fprintf(fp, "%s:\n", title);
352 pr_int(fp, indent, "ngQM", opts->ngQM);
355 pr_ivec(fp, indent, "QMmethod", opts->QMmethod, opts->ngQM, FALSE);
356 pr_ivec(fp, indent, "QMbasis", opts->QMbasis, opts->ngQM, FALSE);
357 pr_ivec(fp, indent, "QMcharge", opts->QMcharge, opts->ngQM, FALSE);
358 pr_ivec(fp, indent, "QMmult", opts->QMmult, opts->ngQM, FALSE);
359 pr_bvec(fp, indent, "SH", opts->bSH, opts->ngQM, FALSE);
360 pr_ivec(fp, indent, "CASorbitals", opts->CASorbitals, opts->ngQM, FALSE);
361 pr_ivec(fp, indent, "CASelectrons", opts->CASelectrons, opts->ngQM, FALSE);
362 pr_rvec(fp, indent, "SAon", opts->SAon, opts->ngQM, FALSE);
363 pr_rvec(fp, indent, "SAoff", opts->SAoff, opts->ngQM, FALSE);
364 pr_ivec(fp, indent, "SAsteps", opts->SAsteps, opts->ngQM, FALSE);
368 static void pr_grp_opts(FILE *out, int indent, const char *title, const t_grpopts *opts,
375 fprintf(out, "%s:\n", title);
378 pr_indent(out, indent);
379 fprintf(out, "nrdf%s", bMDPformat ? " = " : ":");
380 for (i = 0; (i < opts->ngtc); i++)
382 fprintf(out, " %10g", opts->nrdf[i]);
386 pr_indent(out, indent);
387 fprintf(out, "ref-t%s", bMDPformat ? " = " : ":");
388 for (i = 0; (i < opts->ngtc); i++)
390 fprintf(out, " %10g", opts->ref_t[i]);
394 pr_indent(out, indent);
395 fprintf(out, "tau-t%s", bMDPformat ? " = " : ":");
396 for (i = 0; (i < opts->ngtc); i++)
398 fprintf(out, " %10g", opts->tau_t[i]);
402 /* Pretty-print the simulated annealing info */
403 fprintf(out, "annealing%s", bMDPformat ? " = " : ":");
404 for (i = 0; (i < opts->ngtc); i++)
406 fprintf(out, " %10s", EANNEAL(opts->annealing[i]));
410 fprintf(out, "annealing-npoints%s", bMDPformat ? " = " : ":");
411 for (i = 0; (i < opts->ngtc); i++)
413 fprintf(out, " %10d", opts->anneal_npoints[i]);
417 for (i = 0; (i < opts->ngtc); i++)
419 if (opts->anneal_npoints[i] > 0)
421 fprintf(out, "annealing-time [%d]:\t", i);
422 for (j = 0; (j < opts->anneal_npoints[i]); j++)
424 fprintf(out, " %10.1f", opts->anneal_time[i][j]);
427 fprintf(out, "annealing-temp [%d]:\t", i);
428 for (j = 0; (j < opts->anneal_npoints[i]); j++)
430 fprintf(out, " %10.1f", opts->anneal_temp[i][j]);
436 pr_indent(out, indent);
437 fprintf(out, "acc:\t");
438 for (i = 0; (i < opts->ngacc); i++)
440 for (m = 0; (m < DIM); m++)
442 fprintf(out, " %10g", opts->acc[i][m]);
447 pr_indent(out, indent);
448 fprintf(out, "nfreeze:");
449 for (i = 0; (i < opts->ngfrz); i++)
451 for (m = 0; (m < DIM); m++)
453 fprintf(out, " %10s", opts->nFreeze[i][m] ? "Y" : "N");
459 for (i = 0; (i < opts->ngener); i++)
461 pr_indent(out, indent);
462 fprintf(out, "energygrp-flags[%3d]:", i);
463 for (m = 0; (m < opts->ngener); m++)
465 fprintf(out, " %d", opts->egp_flags[opts->ngener*i+m]);
473 static void pr_matrix(FILE *fp, int indent, const char *title, const rvec *m,
478 fprintf(fp, "%-10s = %g %g %g %g %g %g\n", title,
479 m[XX][XX], m[YY][YY], m[ZZ][ZZ], m[XX][YY], m[XX][ZZ], m[YY][ZZ]);
483 pr_rvecs(fp, indent, title, m, DIM);
487 #define PS(t, s) pr_str(fp, indent, t, s)
488 #define PI(t, s) pr_int(fp, indent, t, s)
489 #define PSTEP(t, s) pr_int64(fp, indent, t, s)
490 #define PR(t, s) pr_real(fp, indent, t, s)
491 #define PD(t, s) pr_double(fp, indent, t, s)
493 static void pr_pull_group(FILE *fp, int indent, int g, const t_pull_group *pgrp)
495 pr_indent(fp, indent);
496 fprintf(fp, "pull-group %d:\n", g);
498 pr_ivec_block(fp, indent, "atom", pgrp->ind, pgrp->nat, TRUE);
499 pr_rvec(fp, indent, "weight", pgrp->weight, pgrp->nweight, TRUE);
500 PI("pbcatom", pgrp->pbcatom);
503 static void pr_pull_coord(FILE *fp, int indent, int c, const t_pull_coord *pcrd)
507 pr_indent(fp, indent);
508 fprintf(fp, "pull-coord %d:\n", c);
509 PS("type", EPULLTYPE(pcrd->eType));
510 if (pcrd->eType == epullEXTERNAL)
512 PS("potential-provider", pcrd->externalPotentialProvider);
514 PS("geometry", EPULLGEOM(pcrd->eGeom));
515 for (g = 0; g < pcrd->ngroup; g++)
519 sprintf(buf, "group[%d]", g);
520 PI(buf, pcrd->group[g]);
522 pr_ivec(fp, indent, "dim", pcrd->dim, DIM, TRUE);
523 pr_rvec(fp, indent, "origin", pcrd->origin, DIM, TRUE);
524 pr_rvec(fp, indent, "vec", pcrd->vec, DIM, TRUE);
525 PS("start", EBOOL(pcrd->bStart));
526 PR("init", pcrd->init);
527 PR("rate", pcrd->rate);
532 static void pr_simtempvals(FILE *fp, int indent, const t_simtemp *simtemp, int n_lambda)
534 PS("simulated-tempering-scaling", ESIMTEMP(simtemp->eSimTempScale));
535 PR("sim-temp-low", simtemp->simtemp_low);
536 PR("sim-temp-high", simtemp->simtemp_high);
537 pr_rvec(fp, indent, "simulated tempering temperatures", simtemp->temperatures, n_lambda, TRUE);
540 static void pr_expandedvals(FILE *fp, int indent, const t_expanded *expand, int n_lambda)
543 PI("nstexpanded", expand->nstexpanded);
544 PS("lmc-stats", elamstats_names[expand->elamstats]);
545 PS("lmc-move", elmcmove_names[expand->elmcmove]);
546 PS("lmc-weights-equil", elmceq_names[expand->elmceq]);
547 if (expand->elmceq == elmceqNUMATLAM)
549 PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
551 if (expand->elmceq == elmceqSAMPLES)
553 PI("weight-equil-number-samples", expand->equil_samples);
555 if (expand->elmceq == elmceqSTEPS)
557 PI("weight-equil-number-steps", expand->equil_steps);
559 if (expand->elmceq == elmceqWLDELTA)
561 PR("weight-equil-wl-delta", expand->equil_wl_delta);
563 if (expand->elmceq == elmceqRATIO)
565 PR("weight-equil-count-ratio", expand->equil_ratio);
567 PI("lmc-seed", expand->lmc_seed);
568 PR("mc-temperature", expand->mc_temp);
569 PI("lmc-repeats", expand->lmc_repeats);
570 PI("lmc-gibbsdelta", expand->gibbsdeltalam);
571 PI("lmc-forced-nstart", expand->lmc_forced_nstart);
572 PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix));
573 PI("nst-transition-matrix", expand->nstTij);
574 PI("mininum-var-min", expand->minvarmin); /*default is reasonable */
575 PI("weight-c-range", expand->c_range); /* default is just C=0 */
576 PR("wl-scale", expand->wl_scale);
577 PR("wl-ratio", expand->wl_ratio);
578 PR("init-wl-delta", expand->init_wl_delta);
579 PS("wl-oneovert", EBOOL(expand->bWLoneovert));
581 pr_indent(fp, indent);
582 pr_rvec(fp, indent, "init-lambda-weights", expand->init_lambda_weights, n_lambda, TRUE);
583 PS("init-weights", EBOOL(expand->bInit_weights));
586 static void pr_fepvals(FILE *fp, int indent, const t_lambda *fep, gmx_bool bMDPformat)
590 PR("init-lambda", fep->init_lambda);
591 PI("init-lambda-state", fep->init_fep_state);
592 PR("delta-lambda", fep->delta_lambda);
593 PI("nstdhdl", fep->nstdhdl);
597 PI("n-lambdas", fep->n_lambda);
599 if (fep->n_lambda > 0)
601 pr_indent(fp, indent);
602 fprintf(fp, "separate-dvdl%s\n", bMDPformat ? " = " : ":");
603 for (i = 0; i < efptNR; i++)
605 fprintf(fp, "%18s = ", efpt_names[i]);
606 if (fep->separate_dvdl[i])
608 fprintf(fp, " TRUE");
612 fprintf(fp, " FALSE");
616 fprintf(fp, "all-lambdas%s\n", bMDPformat ? " = " : ":");
617 for (i = 0; i < efptNR; i++)
619 fprintf(fp, "%18s = ", efpt_names[i]);
620 for (j = 0; j < fep->n_lambda; j++)
622 fprintf(fp, " %10g", fep->all_lambda[i][j]);
627 PI("calc-lambda-neighbors", fep->lambda_neighbors);
628 PS("dhdl-print-energy", edHdLPrintEnergy_names[fep->edHdLPrintEnergy]);
629 PR("sc-alpha", fep->sc_alpha);
630 PI("sc-power", fep->sc_power);
631 PR("sc-r-power", fep->sc_r_power);
632 PR("sc-sigma", fep->sc_sigma);
633 PR("sc-sigma-min", fep->sc_sigma_min);
634 PS("sc-coul", EBOOL(fep->bScCoul));
635 PI("dh-hist-size", fep->dh_hist_size);
636 PD("dh-hist-spacing", fep->dh_hist_spacing);
637 PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file));
638 PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives));
641 static void pr_pull(FILE *fp, int indent, const pull_params_t *pull)
645 PR("pull-cylinder-r", pull->cylinder_r);
646 PR("pull-constr-tol", pull->constr_tol);
647 PS("pull-print-COM", EBOOL(pull->bPrintCOM));
648 PS("pull-print-ref-value", EBOOL(pull->bPrintRefValue));
649 PS("pull-print-components", EBOOL(pull->bPrintComp));
650 PI("pull-nstxout", pull->nstxout);
651 PI("pull-nstfout", pull->nstfout);
652 PS("pull-pbc-ref-prev-step-com", EBOOL(pull->bSetPbcRefToPrevStepCOM));
653 PS("pull-xout-average", EBOOL(pull->bXOutAverage));
654 PS("pull-fout-average", EBOOL(pull->bFOutAverage));
655 PI("pull-ngroups", pull->ngroup);
656 for (g = 0; g < pull->ngroup; g++)
658 pr_pull_group(fp, indent, g, &pull->group[g]);
660 PI("pull-ncoords", pull->ncoord);
661 for (g = 0; g < pull->ncoord; g++)
663 pr_pull_coord(fp, indent, g, &pull->coord[g]);
667 static void pr_awh_bias_dim(FILE *fp, int indent, gmx::AwhDimParams *awhDimParams, const char *prefix)
669 pr_indent(fp, indent);
671 fprintf(fp, "%s:\n", prefix);
672 PS("coord-provider", EAWHCOORDPROVIDER(awhDimParams->eCoordProvider));
673 PI("coord-index", awhDimParams->coordIndex + 1);
674 PR("start", awhDimParams->origin);
675 PR("end", awhDimParams->end);
676 PR("period", awhDimParams->period);
677 PR("force-constant", awhDimParams->forceConstant);
678 PR("diffusion", awhDimParams->diffusion);
679 PR("start", awhDimParams->origin);
680 PR("end", awhDimParams->end);
681 PR("cover-diameter", awhDimParams->coverDiameter);
684 static void pr_awh_bias(FILE *fp, int indent, gmx::AwhBiasParams *awhBiasParams, const char *prefix)
688 sprintf(opt, "%s-error-init", prefix);
689 PR(opt, awhBiasParams->errorInitial);
690 sprintf(opt, "%s-growth", prefix);
691 PS(opt, EAWHGROWTH(awhBiasParams->eGrowth));
692 sprintf(opt, "%s-target", prefix);
693 PS(opt, EAWHTARGET(awhBiasParams->eTarget));
694 sprintf(opt, "%s-target-beta-scalng", prefix);
695 PR(opt, awhBiasParams->targetBetaScaling);
696 sprintf(opt, "%s-target-cutoff", prefix);
697 PR(opt, awhBiasParams->targetCutoff);
698 sprintf(opt, "%s-user-data", prefix);
699 PS(opt, EBOOL(awhBiasParams->bUserData));
700 sprintf(opt, "%s-share-group", prefix);
701 PI(opt, awhBiasParams->shareGroup);
702 sprintf(opt, "%s-equilibrate-histogram", prefix);
703 PS(opt, EBOOL(awhBiasParams->equilibrateHistogram));
704 sprintf(opt, "%s-ndim", prefix);
705 PI(opt, awhBiasParams->ndim);
707 for (int d = 0; d < awhBiasParams->ndim; d++)
709 char prefixdim[STRLEN];
710 sprintf(prefixdim, "%s-dim%d", prefix, d + 1);
711 pr_awh_bias_dim(fp, indent, &awhBiasParams->dimParams[d], prefixdim);
715 static void pr_awh(FILE *fp, int indent, gmx::AwhParams *awhParams)
717 PS("awh-potential", EAWHPOTENTIAL(awhParams->ePotential));
718 PI("awh-seed", awhParams->seed);
719 PI("awh-nstout", awhParams->nstOut);
720 PI("awh-nstsample", awhParams->nstSampleCoord);
721 PI("awh-nsamples-update", awhParams->numSamplesUpdateFreeEnergy);
722 PS("awh-share-bias-multisim", EBOOL(awhParams->shareBiasMultisim));
723 PI("awh-nbias", awhParams->numBias);
725 for (int k = 0; k < awhParams->numBias; k++)
727 auto prefix = gmx::formatString("awh%d", k + 1);
728 pr_awh_bias(fp, indent, &awhParams->awhBiasParams[k], prefix.c_str());
732 static void pr_rotgrp(FILE *fp, int indent, int g, const t_rotgrp *rotg)
734 pr_indent(fp, indent);
735 fprintf(fp, "rot-group %d:\n", g);
737 PS("rot-type", EROTGEOM(rotg->eType));
738 PS("rot-massw", EBOOL(rotg->bMassW));
739 pr_ivec_block(fp, indent, "atom", rotg->ind, rotg->nat, TRUE);
740 pr_rvecs(fp, indent, "x-ref", rotg->x_ref, rotg->nat);
741 pr_rvec(fp, indent, "rot-vec", rotg->inputVec, DIM, TRUE);
742 pr_rvec(fp, indent, "rot-pivot", rotg->pivot, DIM, TRUE);
743 PR("rot-rate", rotg->rate);
744 PR("rot-k", rotg->k);
745 PR("rot-slab-dist", rotg->slab_dist);
746 PR("rot-min-gauss", rotg->min_gaussian);
747 PR("rot-eps", rotg->eps);
748 PS("rot-fit-method", EROTFIT(rotg->eFittype));
749 PI("rot-potfit-nstep", rotg->PotAngle_nstep);
750 PR("rot-potfit-step", rotg->PotAngle_step);
753 static void pr_rot(FILE *fp, int indent, const t_rot *rot)
757 PI("rot-nstrout", rot->nstrout);
758 PI("rot-nstsout", rot->nstsout);
759 PI("rot-ngroups", rot->ngrp);
760 for (g = 0; g < rot->ngrp; g++)
762 pr_rotgrp(fp, indent, g, &rot->grp[g]);
767 static void pr_swap(FILE *fp, int indent, const t_swapcoords *swap)
771 /* Enums for better readability of the code */
777 PI("swap-frequency", swap->nstswap);
779 /* The split groups that define the compartments */
780 for (int j = 0; j < 2; j++)
782 snprintf(str, STRLEN, "massw_split%d", j);
783 PS(str, EBOOL(swap->massw_split[j]));
784 snprintf(str, STRLEN, "split atoms group %d", j);
785 pr_ivec_block(fp, indent, str, swap->grp[j].ind, swap->grp[j].nat, TRUE);
788 /* The solvent group */
789 snprintf(str, STRLEN, "solvent group %s", swap->grp[eGrpSolvent].molname);
790 pr_ivec_block(fp, indent, str, swap->grp[eGrpSolvent].ind, swap->grp[eGrpSolvent].nat, TRUE);
792 /* Now print the indices for all the ion groups: */
793 for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
795 snprintf(str, STRLEN, "ion group %s", swap->grp[ig].molname);
796 pr_ivec_block(fp, indent, str, swap->grp[ig].ind, swap->grp[ig].nat, TRUE);
799 PR("cyl0-r", swap->cyl0r);
800 PR("cyl0-up", swap->cyl0u);
801 PR("cyl0-down", swap->cyl0l);
802 PR("cyl1-r", swap->cyl1r);
803 PR("cyl1-up", swap->cyl1u);
804 PR("cyl1-down", swap->cyl1l);
805 PI("coupl-steps", swap->nAverage);
807 /* Print the requested ion counts for both compartments */
808 for (int ic = eCompA; ic <= eCompB; ic++)
810 for (int ig = eSwapFixedGrpNR; ig < swap->ngrp; ig++)
812 snprintf(str, STRLEN, "%s-in-%c", swap->grp[ig].molname, 'A'+ic);
813 PI(str, swap->grp[ig].nmolReq[ic]);
817 PR("threshold", swap->threshold);
818 PR("bulk-offsetA", swap->bulkOffset[eCompA]);
819 PR("bulk-offsetB", swap->bulkOffset[eCompB]);
823 static void pr_imd(FILE *fp, int indent, const t_IMD *imd)
825 PI("IMD-atoms", imd->nat);
826 pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE);
830 void pr_inputrec(FILE *fp, int indent, const char *title, const t_inputrec *ir,
833 const char *infbuf = "inf";
835 if (available(fp, ir, indent, title))
839 indent = pr_title(fp, indent, title);
841 /* Try to make this list appear in the same order as the
842 * options are written in the default mdout.mdp, and with
843 * the same user-exposed names to facilitate debugging.
845 PS("integrator", EI(ir->eI));
846 PR("tinit", ir->init_t);
847 PR("dt", ir->delta_t);
848 PSTEP("nsteps", ir->nsteps);
849 PSTEP("init-step", ir->init_step);
850 PI("simulation-part", ir->simulation_part);
851 PS("comm-mode", ECOM(ir->comm_mode));
852 PI("nstcomm", ir->nstcomm);
854 /* Langevin dynamics */
855 PR("bd-fric", ir->bd_fric);
856 PSTEP("ld-seed", ir->ld_seed);
858 /* Energy minimization */
859 PR("emtol", ir->em_tol);
860 PR("emstep", ir->em_stepsize);
861 PI("niter", ir->niter);
862 PR("fcstep", ir->fc_stepsize);
863 PI("nstcgsteep", ir->nstcgsteep);
864 PI("nbfgscorr", ir->nbfgscorr);
866 /* Test particle insertion */
867 PR("rtpi", ir->rtpi);
870 PI("nstxout", ir->nstxout);
871 PI("nstvout", ir->nstvout);
872 PI("nstfout", ir->nstfout);
873 PI("nstlog", ir->nstlog);
874 PI("nstcalcenergy", ir->nstcalcenergy);
875 PI("nstenergy", ir->nstenergy);
876 PI("nstxout-compressed", ir->nstxout_compressed);
877 PR("compressed-x-precision", ir->x_compression_precision);
879 /* Neighborsearching parameters */
880 PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme));
881 PI("nstlist", ir->nstlist);
882 PS("pbc", epbc_names[ir->ePBC]);
883 PS("periodic-molecules", EBOOL(ir->bPeriodicMols));
884 PR("verlet-buffer-tolerance", ir->verletbuf_tol);
885 PR("rlist", ir->rlist);
887 /* Options for electrostatics and VdW */
888 PS("coulombtype", EELTYPE(ir->coulombtype));
889 PS("coulomb-modifier", INTMODIFIER(ir->coulomb_modifier));
890 PR("rcoulomb-switch", ir->rcoulomb_switch);
891 PR("rcoulomb", ir->rcoulomb);
892 if (ir->epsilon_r != 0)
894 PR("epsilon-r", ir->epsilon_r);
898 PS("epsilon-r", infbuf);
900 if (ir->epsilon_rf != 0)
902 PR("epsilon-rf", ir->epsilon_rf);
906 PS("epsilon-rf", infbuf);
908 PS("vdw-type", EVDWTYPE(ir->vdwtype));
909 PS("vdw-modifier", INTMODIFIER(ir->vdw_modifier));
910 PR("rvdw-switch", ir->rvdw_switch);
911 PR("rvdw", ir->rvdw);
912 PS("DispCorr", EDISPCORR(ir->eDispCorr));
913 PR("table-extension", ir->tabext);
915 PR("fourierspacing", ir->fourier_spacing);
916 PI("fourier-nx", ir->nkx);
917 PI("fourier-ny", ir->nky);
918 PI("fourier-nz", ir->nkz);
919 PI("pme-order", ir->pme_order);
920 PR("ewald-rtol", ir->ewald_rtol);
921 PR("ewald-rtol-lj", ir->ewald_rtol_lj);
922 PS("lj-pme-comb-rule", ELJPMECOMBNAMES(ir->ljpme_combination_rule));
923 PR("ewald-geometry", ir->ewald_geometry);
924 PR("epsilon-surface", ir->epsilon_surface);
926 /* Options for weak coupling algorithms */
927 PS("tcoupl", ETCOUPLTYPE(ir->etc));
928 PI("nsttcouple", ir->nsttcouple);
929 PI("nh-chain-length", ir->opts.nhchainlength);
930 PS("print-nose-hoover-chain-variables", EBOOL(ir->bPrintNHChains));
932 PS("pcoupl", EPCOUPLTYPE(ir->epc));
933 PS("pcoupltype", EPCOUPLTYPETYPE(ir->epct));
934 PI("nstpcouple", ir->nstpcouple);
935 PR("tau-p", ir->tau_p);
936 pr_matrix(fp, indent, "compressibility", ir->compress, bMDPformat);
937 pr_matrix(fp, indent, "ref-p", ir->ref_p, bMDPformat);
938 PS("refcoord-scaling", EREFSCALINGTYPE(ir->refcoord_scaling));
942 fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX],
943 ir->posres_com[YY], ir->posres_com[ZZ]);
944 fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX],
945 ir->posres_comB[YY], ir->posres_comB[ZZ]);
949 pr_rvec(fp, indent, "posres-com", ir->posres_com, DIM, TRUE);
950 pr_rvec(fp, indent, "posres-comB", ir->posres_comB, DIM, TRUE);
954 PS("QMMM", EBOOL(ir->bQMMM));
955 PI("QMconstraints", ir->QMconstraints);
956 PI("QMMMscheme", ir->QMMMscheme);
957 PR("MMChargeScaleFactor", ir->scalefactor);
958 pr_qm_opts(fp, indent, "qm-opts", &(ir->opts));
960 /* CONSTRAINT OPTIONS */
961 PS("constraint-algorithm", ECONSTRTYPE(ir->eConstrAlg));
962 PS("continuation", EBOOL(ir->bContinuation));
964 PS("Shake-SOR", EBOOL(ir->bShakeSOR));
965 PR("shake-tol", ir->shake_tol);
966 PI("lincs-order", ir->nProjOrder);
967 PI("lincs-iter", ir->nLincsIter);
968 PR("lincs-warnangle", ir->LincsWarnAngle);
971 PI("nwall", ir->nwall);
972 PS("wall-type", EWALLTYPE(ir->wall_type));
973 PR("wall-r-linpot", ir->wall_r_linpot);
975 PI("wall-atomtype[0]", ir->wall_atomtype[0]);
976 PI("wall-atomtype[1]", ir->wall_atomtype[1]);
978 PR("wall-density[0]", ir->wall_density[0]);
979 PR("wall-density[1]", ir->wall_density[1]);
980 PR("wall-ewald-zfac", ir->wall_ewald_zfac);
983 PS("pull", EBOOL(ir->bPull));
986 pr_pull(fp, indent, ir->pull);
990 PS("awh", EBOOL(ir->bDoAwh));
993 pr_awh(fp, indent, ir->awhParams);
996 /* ENFORCED ROTATION */
997 PS("rotation", EBOOL(ir->bRot));
1000 pr_rot(fp, indent, ir->rot);
1003 /* INTERACTIVE MD */
1004 PS("interactiveMD", EBOOL(ir->bIMD));
1007 pr_imd(fp, indent, ir->imd);
1010 /* NMR refinement stuff */
1011 PS("disre", EDISRETYPE(ir->eDisre));
1012 PS("disre-weighting", EDISREWEIGHTING(ir->eDisreWeighting));
1013 PS("disre-mixed", EBOOL(ir->bDisreMixed));
1014 PR("dr-fc", ir->dr_fc);
1015 PR("dr-tau", ir->dr_tau);
1016 PR("nstdisreout", ir->nstdisreout);
1018 PR("orire-fc", ir->orires_fc);
1019 PR("orire-tau", ir->orires_tau);
1020 PR("nstorireout", ir->nstorireout);
1022 /* FREE ENERGY VARIABLES */
1023 PS("free-energy", EFEPTYPE(ir->efep));
1024 if (ir->efep != efepNO || ir->bSimTemp)
1026 pr_fepvals(fp, indent, ir->fepvals, bMDPformat);
1030 pr_expandedvals(fp, indent, ir->expandedvals, ir->fepvals->n_lambda);
1033 /* NON-equilibrium MD stuff */
1034 PR("cos-acceleration", ir->cos_accel);
1035 pr_matrix(fp, indent, "deform", ir->deform, bMDPformat);
1037 /* SIMULATED TEMPERING */
1038 PS("simulated-tempering", EBOOL(ir->bSimTemp));
1041 pr_simtempvals(fp, indent, ir->simtempvals, ir->fepvals->n_lambda);
1044 /* ION/WATER SWAPPING FOR COMPUTATIONAL ELECTROPHYSIOLOGY */
1045 PS("swapcoords", ESWAPTYPE(ir->eSwapCoords));
1046 if (ir->eSwapCoords != eswapNO)
1048 pr_swap(fp, indent, ir->swap);
1051 /* USER-DEFINED THINGIES */
1052 PI("userint1", ir->userint1);
1053 PI("userint2", ir->userint2);
1054 PI("userint3", ir->userint3);
1055 PI("userint4", ir->userint4);
1056 PR("userreal1", ir->userreal1);
1057 PR("userreal2", ir->userreal2);
1058 PR("userreal3", ir->userreal3);
1059 PR("userreal4", ir->userreal4);
1063 gmx::TextWriter writer(fp);
1064 writer.wrapperSettings().setIndent(indent);
1065 gmx::dumpKeyValueTree(&writer, *ir->params);
1068 pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat);
1075 static void cmp_grpopts(FILE *fp, const t_grpopts *opt1, const t_grpopts *opt2, real ftol, real abstol)
1078 char buf1[256], buf2[256];
1080 cmp_int(fp, "inputrec->grpopts.ngtc", -1, opt1->ngtc, opt2->ngtc);
1081 cmp_int(fp, "inputrec->grpopts.ngacc", -1, opt1->ngacc, opt2->ngacc);
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 cmp_int(fp, "inputrec->grpopts.annealing", i, opt1->annealing[i], opt2->annealing[i]);
1090 cmp_int(fp, "inputrec->grpopts.anneal_npoints", i,
1091 opt1->anneal_npoints[i], opt2->anneal_npoints[i]);
1092 if (opt1->anneal_npoints[i] == opt2->anneal_npoints[i])
1094 sprintf(buf1, "inputrec->grpopts.anneal_time[%d]", i);
1095 sprintf(buf2, "inputrec->grpopts.anneal_temp[%d]", i);
1096 for (j = 0; j < opt1->anneal_npoints[i]; j++)
1098 cmp_real(fp, buf1, j, opt1->anneal_time[i][j], opt2->anneal_time[i][j], ftol, abstol);
1099 cmp_real(fp, buf2, j, opt1->anneal_temp[i][j], opt2->anneal_temp[i][j], ftol, abstol);
1103 if (opt1->ngener == opt2->ngener)
1105 for (i = 0; i < opt1->ngener; i++)
1107 for (j = i; j < opt1->ngener; j++)
1109 sprintf(buf1, "inputrec->grpopts.egp_flags[%d]", i);
1110 cmp_int(fp, buf1, j,
1111 opt1->egp_flags[opt1->ngener*i+j],
1112 opt2->egp_flags[opt1->ngener*i+j]);
1116 for (i = 0; (i < std::min(opt1->ngacc, opt2->ngacc)); i++)
1118 cmp_rvec(fp, "inputrec->grpopts.acc", i, opt1->acc[i], opt2->acc[i], ftol, abstol);
1120 for (i = 0; (i < std::min(opt1->ngfrz, opt2->ngfrz)); i++)
1122 cmp_ivec(fp, "inputrec->grpopts.nFreeze", i, opt1->nFreeze[i], opt2->nFreeze[i]);
1126 static void cmp_pull(FILE *fp)
1128 fprintf(fp, "WARNING: Both files use COM pulling, but comparing of the pull struct is not implemented (yet). The pull parameters could be the same or different.\n");
1131 static void cmp_awhDimParams(FILE *fp, const gmx::AwhDimParams *dimp1, const gmx::AwhDimParams *dimp2, int dimIndex, real ftol, real abstol)
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.
1136 cmp_int(fp, "inputrec.awhParams->bias?->dim->coord_index", dimIndex, dimp1->coordIndex, dimp2->coordIndex);
1137 cmp_double(fp, "inputrec->awhParams->bias?->dim->period", dimIndex, dimp1->period, dimp2->period, ftol, abstol);
1138 cmp_double(fp, "inputrec->awhParams->bias?->dim->diffusion", dimIndex, dimp1->diffusion, dimp2->diffusion, ftol, abstol);
1139 cmp_double(fp, "inputrec->awhParams->bias?->dim->origin", dimIndex, dimp1->origin, dimp2->origin, ftol, abstol);
1140 cmp_double(fp, "inputrec->awhParams->bias?->dim->end", dimIndex, dimp1->end, dimp2->end, ftol, abstol);
1141 cmp_double(fp, "inputrec->awhParams->bias?->dim->coord_value_init", dimIndex, dimp1->coordValueInit, dimp2->coordValueInit, ftol, abstol);
1142 cmp_double(fp, "inputrec->awhParams->bias?->dim->coverDiameter", dimIndex, dimp1->coverDiameter, dimp2->coverDiameter, ftol, abstol);
1145 static void cmp_awhBiasParams(FILE *fp, const gmx::AwhBiasParams *bias1, const gmx::AwhBiasParams *bias2, int biasIndex, real ftol, real abstol)
1147 cmp_int(fp, "inputrec->awhParams->ndim", biasIndex, bias1->ndim, bias2->ndim);
1148 cmp_int(fp, "inputrec->awhParams->biaseTarget", biasIndex, bias1->eTarget, bias2->eTarget);
1149 cmp_double(fp, "inputrec->awhParams->biastargetBetaScaling", biasIndex, bias1->targetBetaScaling, bias2->targetBetaScaling, ftol, abstol);
1150 cmp_double(fp, "inputrec->awhParams->biastargetCutoff", biasIndex, bias1->targetCutoff, bias2->targetCutoff, ftol, abstol);
1151 cmp_int(fp, "inputrec->awhParams->biaseGrowth", biasIndex, bias1->eGrowth, bias2->eGrowth);
1152 cmp_bool(fp, "inputrec->awhParams->biasbUserData", biasIndex, bias1->bUserData != 0, bias2->bUserData != 0);
1153 cmp_double(fp, "inputrec->awhParams->biaserror_initial", biasIndex, bias1->errorInitial, bias2->errorInitial, ftol, abstol);
1154 cmp_int(fp, "inputrec->awhParams->biasShareGroup", biasIndex, bias1->shareGroup, bias2->shareGroup);
1156 for (int dim = 0; dim < std::min(bias1->ndim, bias2->ndim); dim++)
1158 cmp_awhDimParams(fp, &bias1->dimParams[dim], &bias2->dimParams[dim], dim, ftol, abstol);
1162 static void cmp_awhParams(FILE *fp, const gmx::AwhParams *awh1, const gmx::AwhParams *awh2, real ftol, real abstol)
1164 cmp_int(fp, "inputrec->awhParams->nbias", -1, awh1->numBias, awh2->numBias);
1165 cmp_int64(fp, "inputrec->awhParams->seed", awh1->seed, awh2->seed);
1166 cmp_int(fp, "inputrec->awhParams->nstout", -1, awh1->nstOut, awh2->nstOut);
1167 cmp_int(fp, "inputrec->awhParams->nstsample_coord", -1, awh1->nstSampleCoord, awh2->nstSampleCoord);
1168 cmp_int(fp, "inputrec->awhParams->nsamples_update_free_energy", -1, awh1->numSamplesUpdateFreeEnergy, awh2->numSamplesUpdateFreeEnergy);
1169 cmp_int(fp, "inputrec->awhParams->ePotential", -1, awh1->ePotential, awh2->ePotential);
1170 cmp_bool(fp, "inputrec->awhParams->shareBiasMultisim", -1, awh1->shareBiasMultisim, awh2->shareBiasMultisim);
1172 if (awh1->numBias == awh2->numBias)
1174 for (int bias = 0; bias < awh1->numBias; bias++)
1176 cmp_awhBiasParams(fp, &awh1->awhBiasParams[bias], &awh2->awhBiasParams[bias], bias, ftol, abstol);
1181 static void cmp_simtempvals(FILE *fp, const t_simtemp *simtemp1, const t_simtemp *simtemp2, int n_lambda, real ftol, real abstol)
1184 cmp_int(fp, "inputrec->simtempvals->eSimTempScale", -1, simtemp1->eSimTempScale, simtemp2->eSimTempScale);
1185 cmp_real(fp, "inputrec->simtempvals->simtemp_high", -1, simtemp1->simtemp_high, simtemp2->simtemp_high, ftol, abstol);
1186 cmp_real(fp, "inputrec->simtempvals->simtemp_low", -1, simtemp1->simtemp_low, simtemp2->simtemp_low, ftol, abstol);
1187 for (i = 0; i < n_lambda; i++)
1189 cmp_real(fp, "inputrec->simtempvals->temperatures", -1, simtemp1->temperatures[i], simtemp2->temperatures[i], ftol, abstol);
1193 static void cmp_expandedvals(FILE *fp, const t_expanded *expand1, const t_expanded *expand2, int n_lambda, real ftol, real abstol)
1197 cmp_bool(fp, "inputrec->fepvals->bInit_weights", -1, expand1->bInit_weights, expand2->bInit_weights);
1198 cmp_bool(fp, "inputrec->fepvals->bWLoneovert", -1, expand1->bWLoneovert, expand2->bWLoneovert);
1200 for (i = 0; i < n_lambda; i++)
1202 cmp_real(fp, "inputrec->expandedvals->init_lambda_weights", -1,
1203 expand1->init_lambda_weights[i], expand2->init_lambda_weights[i], ftol, abstol);
1206 cmp_int(fp, "inputrec->expandedvals->lambda-stats", -1, expand1->elamstats, expand2->elamstats);
1207 cmp_int(fp, "inputrec->expandedvals->lambda-mc-move", -1, expand1->elmcmove, expand2->elmcmove);
1208 cmp_int(fp, "inputrec->expandedvals->lmc-repeats", -1, expand1->lmc_repeats, expand2->lmc_repeats);
1209 cmp_int(fp, "inputrec->expandedvals->lmc-gibbsdelta", -1, expand1->gibbsdeltalam, expand2->gibbsdeltalam);
1210 cmp_int(fp, "inputrec->expandedvals->lmc-forced-nstart", -1, expand1->lmc_forced_nstart, expand2->lmc_forced_nstart);
1211 cmp_int(fp, "inputrec->expandedvals->lambda-weights-equil", -1, expand1->elmceq, expand2->elmceq);
1212 cmp_int(fp, "inputrec->expandedvals->,weight-equil-number-all-lambda", -1, expand1->equil_n_at_lam, expand2->equil_n_at_lam);
1213 cmp_int(fp, "inputrec->expandedvals->weight-equil-number-samples", -1, expand1->equil_samples, expand2->equil_samples);
1214 cmp_int(fp, "inputrec->expandedvals->weight-equil-number-steps", -1, expand1->equil_steps, expand2->equil_steps);
1215 cmp_real(fp, "inputrec->expandedvals->weight-equil-wl-delta", -1, expand1->equil_wl_delta, expand2->equil_wl_delta, ftol, abstol);
1216 cmp_real(fp, "inputrec->expandedvals->weight-equil-count-ratio", -1, expand1->equil_ratio, expand2->equil_ratio, ftol, abstol);
1217 cmp_bool(fp, "inputrec->expandedvals->symmetrized-transition-matrix", -1, expand1->bSymmetrizedTMatrix, expand2->bSymmetrizedTMatrix);
1218 cmp_int(fp, "inputrec->expandedvals->nstTij", -1, expand1->nstTij, expand2->nstTij);
1219 cmp_int(fp, "inputrec->expandedvals->mininum-var-min", -1, expand1->minvarmin, expand2->minvarmin); /*default is reasonable */
1220 cmp_int(fp, "inputrec->expandedvals->weight-c-range", -1, expand1->c_range, expand2->c_range); /* default is just C=0 */
1221 cmp_real(fp, "inputrec->expandedvals->wl-scale", -1, expand1->wl_scale, expand2->wl_scale, ftol, abstol);
1222 cmp_real(fp, "inputrec->expandedvals->init-wl-delta", -1, expand1->init_wl_delta, expand2->init_wl_delta, ftol, abstol);
1223 cmp_real(fp, "inputrec->expandedvals->wl-ratio", -1, expand1->wl_ratio, expand2->wl_ratio, ftol, abstol);
1224 cmp_int(fp, "inputrec->expandedvals->nstexpanded", -1, expand1->nstexpanded, expand2->nstexpanded);
1225 cmp_int(fp, "inputrec->expandedvals->lmc-seed", -1, expand1->lmc_seed, expand2->lmc_seed);
1226 cmp_real(fp, "inputrec->expandedvals->mc-temperature", -1, expand1->mc_temp, expand2->mc_temp, ftol, abstol);
1229 static void cmp_fepvals(FILE *fp, const t_lambda *fep1, const t_lambda *fep2, real ftol, real abstol)
1232 cmp_int(fp, "inputrec->nstdhdl", -1, fep1->nstdhdl, fep2->nstdhdl);
1233 cmp_double(fp, "inputrec->fepvals->init_fep_state", -1, fep1->init_fep_state, fep2->init_fep_state, ftol, abstol);
1234 cmp_double(fp, "inputrec->fepvals->delta_lambda", -1, fep1->delta_lambda, fep2->delta_lambda, ftol, abstol);
1235 cmp_int(fp, "inputrec->fepvals->n_lambda", -1, fep1->n_lambda, fep2->n_lambda);
1236 for (i = 0; i < efptNR; i++)
1238 for (j = 0; j < std::min(fep1->n_lambda, fep2->n_lambda); j++)
1240 cmp_double(fp, "inputrec->fepvals->all_lambda", -1, fep1->all_lambda[i][j], fep2->all_lambda[i][j], ftol, abstol);
1243 cmp_int(fp, "inputrec->fepvals->lambda_neighbors", 1, fep1->lambda_neighbors,
1244 fep2->lambda_neighbors);
1245 cmp_real(fp, "inputrec->fepvals->sc_alpha", -1, fep1->sc_alpha, fep2->sc_alpha, ftol, abstol);
1246 cmp_int(fp, "inputrec->fepvals->sc_power", -1, fep1->sc_power, fep2->sc_power);
1247 cmp_real(fp, "inputrec->fepvals->sc_r_power", -1, fep1->sc_r_power, fep2->sc_r_power, ftol, abstol);
1248 cmp_real(fp, "inputrec->fepvals->sc_sigma", -1, fep1->sc_sigma, fep2->sc_sigma, ftol, abstol);
1249 cmp_int(fp, "inputrec->fepvals->edHdLPrintEnergy", -1, fep1->edHdLPrintEnergy, fep1->edHdLPrintEnergy);
1250 cmp_bool(fp, "inputrec->fepvals->bScCoul", -1, fep1->bScCoul, fep1->bScCoul);
1251 cmp_int(fp, "inputrec->separate_dhdl_file", -1, fep1->separate_dhdl_file, fep2->separate_dhdl_file);
1252 cmp_int(fp, "inputrec->dhdl_derivatives", -1, fep1->dhdl_derivatives, fep2->dhdl_derivatives);
1253 cmp_int(fp, "inputrec->dh_hist_size", -1, fep1->dh_hist_size, fep2->dh_hist_size);
1254 cmp_double(fp, "inputrec->dh_hist_spacing", -1, fep1->dh_hist_spacing, fep2->dh_hist_spacing, ftol, abstol);
1257 void cmp_inputrec(FILE *fp, const t_inputrec *ir1, const t_inputrec *ir2, real ftol, real abstol)
1259 fprintf(fp, "comparing inputrec\n");
1261 /* gcc 2.96 doesnt like these defines at all, but issues a huge list
1262 * of warnings. Maybe it will change in future versions, but for the
1263 * moment I've spelled them out instead. /EL 000820
1264 * #define CIB(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
1265 * #define CII(s) cmp_int(fp,"inputrec->"#s,0,ir1->##s,ir2->##s)
1266 * #define CIR(s) cmp_real(fp,"inputrec->"#s,0,ir1->##s,ir2->##s,ftol)
1268 cmp_int(fp, "inputrec->eI", -1, ir1->eI, ir2->eI);
1269 cmp_int64(fp, "inputrec->nsteps", ir1->nsteps, ir2->nsteps);
1270 cmp_int64(fp, "inputrec->init_step", ir1->init_step, ir2->init_step);
1271 cmp_int(fp, "inputrec->simulation_part", -1, ir1->simulation_part, ir2->simulation_part);
1272 cmp_int(fp, "inputrec->ePBC", -1, ir1->ePBC, ir2->ePBC);
1273 cmp_bool(fp, "inputrec->bPeriodicMols", -1, ir1->bPeriodicMols, ir2->bPeriodicMols);
1274 cmp_int(fp, "inputrec->cutoff_scheme", -1, ir1->cutoff_scheme, ir2->cutoff_scheme);
1275 cmp_int(fp, "inputrec->nstlist", -1, ir1->nstlist, ir2->nstlist);
1276 cmp_int(fp, "inputrec->nstcomm", -1, ir1->nstcomm, ir2->nstcomm);
1277 cmp_int(fp, "inputrec->comm_mode", -1, ir1->comm_mode, ir2->comm_mode);
1278 cmp_int(fp, "inputrec->nstlog", -1, ir1->nstlog, ir2->nstlog);
1279 cmp_int(fp, "inputrec->nstxout", -1, ir1->nstxout, ir2->nstxout);
1280 cmp_int(fp, "inputrec->nstvout", -1, ir1->nstvout, ir2->nstvout);
1281 cmp_int(fp, "inputrec->nstfout", -1, ir1->nstfout, ir2->nstfout);
1282 cmp_int(fp, "inputrec->nstcalcenergy", -1, ir1->nstcalcenergy, ir2->nstcalcenergy);
1283 cmp_int(fp, "inputrec->nstenergy", -1, ir1->nstenergy, ir2->nstenergy);
1284 cmp_int(fp, "inputrec->nstxout_compressed", -1, ir1->nstxout_compressed, ir2->nstxout_compressed);
1285 cmp_double(fp, "inputrec->init_t", -1, ir1->init_t, ir2->init_t, ftol, abstol);
1286 cmp_double(fp, "inputrec->delta_t", -1, ir1->delta_t, ir2->delta_t, ftol, abstol);
1287 cmp_real(fp, "inputrec->x_compression_precision", -1, ir1->x_compression_precision, ir2->x_compression_precision, ftol, abstol);
1288 cmp_real(fp, "inputrec->fourierspacing", -1, ir1->fourier_spacing, ir2->fourier_spacing, ftol, abstol);
1289 cmp_int(fp, "inputrec->nkx", -1, ir1->nkx, ir2->nkx);
1290 cmp_int(fp, "inputrec->nky", -1, ir1->nky, ir2->nky);
1291 cmp_int(fp, "inputrec->nkz", -1, ir1->nkz, ir2->nkz);
1292 cmp_int(fp, "inputrec->pme_order", -1, ir1->pme_order, ir2->pme_order);
1293 cmp_real(fp, "inputrec->ewald_rtol", -1, ir1->ewald_rtol, ir2->ewald_rtol, ftol, abstol);
1294 cmp_int(fp, "inputrec->ewald_geometry", -1, ir1->ewald_geometry, ir2->ewald_geometry);
1295 cmp_real(fp, "inputrec->epsilon_surface", -1, ir1->epsilon_surface, ir2->epsilon_surface, ftol, abstol);
1296 cmp_int(fp, "inputrec->bContinuation", -1, static_cast<int>(ir1->bContinuation), static_cast<int>(ir2->bContinuation));
1297 cmp_int(fp, "inputrec->bShakeSOR", -1, static_cast<int>(ir1->bShakeSOR), static_cast<int>(ir2->bShakeSOR));
1298 cmp_int(fp, "inputrec->etc", -1, ir1->etc, ir2->etc);
1299 cmp_int(fp, "inputrec->bPrintNHChains", -1, static_cast<int>(ir1->bPrintNHChains), static_cast<int>(ir2->bPrintNHChains));
1300 cmp_int(fp, "inputrec->epc", -1, ir1->epc, ir2->epc);
1301 cmp_int(fp, "inputrec->epct", -1, ir1->epct, ir2->epct);
1302 cmp_real(fp, "inputrec->tau_p", -1, ir1->tau_p, ir2->tau_p, ftol, abstol);
1303 cmp_rvec(fp, "inputrec->ref_p(x)", -1, ir1->ref_p[XX], ir2->ref_p[XX], ftol, abstol);
1304 cmp_rvec(fp, "inputrec->ref_p(y)", -1, ir1->ref_p[YY], ir2->ref_p[YY], ftol, abstol);
1305 cmp_rvec(fp, "inputrec->ref_p(z)", -1, ir1->ref_p[ZZ], ir2->ref_p[ZZ], ftol, abstol);
1306 cmp_rvec(fp, "inputrec->compress(x)", -1, ir1->compress[XX], ir2->compress[XX], ftol, abstol);
1307 cmp_rvec(fp, "inputrec->compress(y)", -1, ir1->compress[YY], ir2->compress[YY], ftol, abstol);
1308 cmp_rvec(fp, "inputrec->compress(z)", -1, ir1->compress[ZZ], ir2->compress[ZZ], ftol, abstol);
1309 cmp_int(fp, "refcoord_scaling", -1, ir1->refcoord_scaling, ir2->refcoord_scaling);
1310 cmp_rvec(fp, "inputrec->posres_com", -1, ir1->posres_com, ir2->posres_com, ftol, abstol);
1311 cmp_rvec(fp, "inputrec->posres_comB", -1, ir1->posres_comB, ir2->posres_comB, ftol, abstol);
1312 cmp_real(fp, "inputrec->verletbuf_tol", -1, ir1->verletbuf_tol, ir2->verletbuf_tol, ftol, abstol);
1313 cmp_real(fp, "inputrec->rlist", -1, ir1->rlist, ir2->rlist, ftol, abstol);
1314 cmp_real(fp, "inputrec->rtpi", -1, ir1->rtpi, ir2->rtpi, ftol, abstol);
1315 cmp_int(fp, "inputrec->coulombtype", -1, ir1->coulombtype, ir2->coulombtype);
1316 cmp_int(fp, "inputrec->coulomb_modifier", -1, ir1->coulomb_modifier, ir2->coulomb_modifier);
1317 cmp_real(fp, "inputrec->rcoulomb_switch", -1, ir1->rcoulomb_switch, ir2->rcoulomb_switch, ftol, abstol);
1318 cmp_real(fp, "inputrec->rcoulomb", -1, ir1->rcoulomb, ir2->rcoulomb, ftol, abstol);
1319 cmp_int(fp, "inputrec->vdwtype", -1, ir1->vdwtype, ir2->vdwtype);
1320 cmp_int(fp, "inputrec->vdw_modifier", -1, ir1->vdw_modifier, ir2->vdw_modifier); cmp_real(fp, "inputrec->rvdw_switch", -1, ir1->rvdw_switch, ir2->rvdw_switch, ftol, abstol);
1321 cmp_real(fp, "inputrec->rvdw", -1, ir1->rvdw, ir2->rvdw, ftol, abstol);
1322 cmp_real(fp, "inputrec->epsilon_r", -1, ir1->epsilon_r, ir2->epsilon_r, ftol, abstol);
1323 cmp_real(fp, "inputrec->epsilon_rf", -1, ir1->epsilon_rf, ir2->epsilon_rf, ftol, abstol);
1324 cmp_real(fp, "inputrec->tabext", -1, ir1->tabext, ir2->tabext, ftol, abstol);
1326 cmp_int(fp, "inputrec->eDispCorr", -1, ir1->eDispCorr, ir2->eDispCorr);
1327 cmp_real(fp, "inputrec->shake_tol", -1, ir1->shake_tol, ir2->shake_tol, ftol, abstol);
1328 cmp_int(fp, "inputrec->efep", -1, ir1->efep, ir2->efep);
1329 cmp_fepvals(fp, ir1->fepvals, ir2->fepvals, ftol, abstol);
1330 cmp_int(fp, "inputrec->bSimTemp", -1, static_cast<int>(ir1->bSimTemp), static_cast<int>(ir2->bSimTemp));
1331 if ((ir1->bSimTemp == ir2->bSimTemp) && (ir1->bSimTemp))
1333 cmp_simtempvals(fp, ir1->simtempvals, ir2->simtempvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
1335 cmp_int(fp, "inputrec->bExpanded", -1, static_cast<int>(ir1->bExpanded), static_cast<int>(ir2->bExpanded));
1336 if ((ir1->bExpanded == ir2->bExpanded) && (ir1->bExpanded))
1338 cmp_expandedvals(fp, ir1->expandedvals, ir2->expandedvals, std::min(ir1->fepvals->n_lambda, ir2->fepvals->n_lambda), ftol, abstol);
1340 cmp_int(fp, "inputrec->nwall", -1, ir1->nwall, ir2->nwall);
1341 cmp_int(fp, "inputrec->wall_type", -1, ir1->wall_type, ir2->wall_type);
1342 cmp_int(fp, "inputrec->wall_atomtype[0]", -1, ir1->wall_atomtype[0], ir2->wall_atomtype[0]);
1343 cmp_int(fp, "inputrec->wall_atomtype[1]", -1, ir1->wall_atomtype[1], ir2->wall_atomtype[1]);
1344 cmp_real(fp, "inputrec->wall_density[0]", -1, ir1->wall_density[0], ir2->wall_density[0], ftol, abstol);
1345 cmp_real(fp, "inputrec->wall_density[1]", -1, ir1->wall_density[1], ir2->wall_density[1], ftol, abstol);
1346 cmp_real(fp, "inputrec->wall_ewald_zfac", -1, ir1->wall_ewald_zfac, ir2->wall_ewald_zfac, ftol, abstol);
1348 cmp_bool(fp, "inputrec->bPull", -1, ir1->bPull, ir2->bPull);
1349 if (ir1->bPull && ir2->bPull)
1354 cmp_bool(fp, "inputrec->bDoAwh", -1, ir1->bDoAwh, ir2->bDoAwh);
1355 if (ir1->bDoAwh && ir2->bDoAwh)
1357 cmp_awhParams(fp, ir1->awhParams, ir2->awhParams, ftol, abstol);
1360 cmp_int(fp, "inputrec->eDisre", -1, ir1->eDisre, ir2->eDisre);
1361 cmp_real(fp, "inputrec->dr_fc", -1, ir1->dr_fc, ir2->dr_fc, ftol, abstol);
1362 cmp_int(fp, "inputrec->eDisreWeighting", -1, ir1->eDisreWeighting, ir2->eDisreWeighting);
1363 cmp_int(fp, "inputrec->bDisreMixed", -1, static_cast<int>(ir1->bDisreMixed), static_cast<int>(ir2->bDisreMixed));
1364 cmp_int(fp, "inputrec->nstdisreout", -1, ir1->nstdisreout, ir2->nstdisreout);
1365 cmp_real(fp, "inputrec->dr_tau", -1, ir1->dr_tau, ir2->dr_tau, ftol, abstol);
1366 cmp_real(fp, "inputrec->orires_fc", -1, ir1->orires_fc, ir2->orires_fc, ftol, abstol);
1367 cmp_real(fp, "inputrec->orires_tau", -1, ir1->orires_tau, ir2->orires_tau, ftol, abstol);
1368 cmp_int(fp, "inputrec->nstorireout", -1, ir1->nstorireout, ir2->nstorireout);
1369 cmp_real(fp, "inputrec->em_stepsize", -1, ir1->em_stepsize, ir2->em_stepsize, ftol, abstol);
1370 cmp_real(fp, "inputrec->em_tol", -1, ir1->em_tol, ir2->em_tol, ftol, abstol);
1371 cmp_int(fp, "inputrec->niter", -1, ir1->niter, ir2->niter);
1372 cmp_real(fp, "inputrec->fc_stepsize", -1, ir1->fc_stepsize, ir2->fc_stepsize, ftol, abstol);
1373 cmp_int(fp, "inputrec->nstcgsteep", -1, ir1->nstcgsteep, ir2->nstcgsteep);
1374 cmp_int(fp, "inputrec->nbfgscorr", 0, ir1->nbfgscorr, ir2->nbfgscorr);
1375 cmp_int(fp, "inputrec->eConstrAlg", -1, ir1->eConstrAlg, ir2->eConstrAlg);
1376 cmp_int(fp, "inputrec->nProjOrder", -1, ir1->nProjOrder, ir2->nProjOrder);
1377 cmp_real(fp, "inputrec->LincsWarnAngle", -1, ir1->LincsWarnAngle, ir2->LincsWarnAngle, ftol, abstol);
1378 cmp_int(fp, "inputrec->nLincsIter", -1, ir1->nLincsIter, ir2->nLincsIter);
1379 cmp_real(fp, "inputrec->bd_fric", -1, ir1->bd_fric, ir2->bd_fric, ftol, abstol);
1380 cmp_int64(fp, "inputrec->ld_seed", ir1->ld_seed, ir2->ld_seed);
1381 cmp_real(fp, "inputrec->cos_accel", -1, ir1->cos_accel, ir2->cos_accel, ftol, abstol);
1382 cmp_rvec(fp, "inputrec->deform(a)", -1, ir1->deform[XX], ir2->deform[XX], ftol, abstol);
1383 cmp_rvec(fp, "inputrec->deform(b)", -1, ir1->deform[YY], ir2->deform[YY], ftol, abstol);
1384 cmp_rvec(fp, "inputrec->deform(c)", -1, ir1->deform[ZZ], ir2->deform[ZZ], ftol, abstol);
1387 cmp_int(fp, "inputrec->userint1", -1, ir1->userint1, ir2->userint1);
1388 cmp_int(fp, "inputrec->userint2", -1, ir1->userint2, ir2->userint2);
1389 cmp_int(fp, "inputrec->userint3", -1, ir1->userint3, ir2->userint3);
1390 cmp_int(fp, "inputrec->userint4", -1, ir1->userint4, ir2->userint4);
1391 cmp_real(fp, "inputrec->userreal1", -1, ir1->userreal1, ir2->userreal1, ftol, abstol);
1392 cmp_real(fp, "inputrec->userreal2", -1, ir1->userreal2, ir2->userreal2, ftol, abstol);
1393 cmp_real(fp, "inputrec->userreal3", -1, ir1->userreal3, ir2->userreal3, ftol, abstol);
1394 cmp_real(fp, "inputrec->userreal4", -1, ir1->userreal4, ir2->userreal4, ftol, abstol);
1395 cmp_grpopts(fp, &(ir1->opts), &(ir2->opts), ftol, abstol);
1396 gmx::TextWriter writer(fp);
1397 gmx::compareKeyValueTrees(&writer, *ir1->params, *ir2->params, ftol, abstol);
1400 void comp_pull_AB(FILE *fp, pull_params_t *pull, real ftol, real abstol)
1404 for (i = 0; i < pull->ncoord; i++)
1406 fprintf(fp, "comparing pull coord %d\n", i);
1407 cmp_real(fp, "pull-coord->k", -1, pull->coord[i].k, pull->coord[i].kB, ftol, abstol);
1411 gmx_bool inputrecDeform(const t_inputrec *ir)
1413 return (ir->deform[XX][XX] != 0 || ir->deform[YY][YY] != 0 || ir->deform[ZZ][ZZ] != 0 ||
1414 ir->deform[YY][XX] != 0 || ir->deform[ZZ][XX] != 0 || ir->deform[ZZ][YY] != 0);
1417 gmx_bool inputrecDynamicBox(const t_inputrec *ir)
1419 return (ir->epc != epcNO || ir->eI == eiTPI || inputrecDeform(ir));
1422 gmx_bool inputrecPreserveShape(const t_inputrec *ir)
1424 return (ir->epc != epcNO && ir->deform[XX][XX] == 0 &&
1425 (ir->epct == epctISOTROPIC || ir->epct == epctSEMIISOTROPIC));
1428 gmx_bool inputrecNeedMutot(const t_inputrec *ir)
1430 return ((ir->coulombtype == eelEWALD || EEL_PME(ir->coulombtype)) &&
1431 (ir->ewald_geometry == eewg3DC || ir->epsilon_surface != 0));
1434 gmx_bool inputrecExclForces(const t_inputrec *ir)
1436 return (EEL_FULL(ir->coulombtype) || (EEL_RF(ir->coulombtype)));
1439 gmx_bool inputrecNptTrotter(const t_inputrec *ir)
1441 return ( ( (ir->eI == eiVV) || (ir->eI == eiVVAK) ) &&
1442 (ir->epc == epcMTTK) && (ir->etc == etcNOSEHOOVER) );
1445 gmx_bool inputrecNvtTrotter(const t_inputrec *ir)
1447 return ( ( (ir->eI == eiVV) || (ir->eI == eiVVAK) ) &&
1448 (ir->epc != epcMTTK) && (ir->etc == etcNOSEHOOVER) );
1451 gmx_bool inputrecNphTrotter(const t_inputrec *ir)
1453 return ( ( (ir->eI == eiVV) || (ir->eI == eiVVAK) ) &&
1454 (ir->epc == epcMTTK) && (ir->etc != etcNOSEHOOVER) );
1457 bool inputrecPbcXY2Walls(const t_inputrec *ir)
1459 return (ir->ePBC == epbcXY && ir->nwall == 2);
1462 bool integratorHasConservedEnergyQuantity(const t_inputrec *ir)
1466 // Energy minimization or stochastic integrator: no conservation
1469 else if (ir->etc == etcNO && ir->epc == epcNO)
1471 // The total energy is conserved, no additional conserved quanitity
1476 // Shear stress with Parrinello-Rahman is not supported (tedious)
1478 ((ir->epc == epcPARRINELLORAHMAN || ir->epc == epcMTTK) &&
1479 (ir->ref_p[YY][XX] != 0 || ir->ref_p[ZZ][XX] != 0 || ir->ref_p[ZZ][YY] != 0));
1481 return !ETC_ANDERSEN(ir->etc) && !shearWithPR;
1485 bool integratorHasReferenceTemperature(const t_inputrec *ir)
1487 return ((ir->etc != etcNO) || EI_SD(ir->eI) || (ir->eI == eiBD) || EI_TPI(ir->eI));
1490 int inputrec2nboundeddim(const t_inputrec *ir)
1492 if (inputrecPbcXY2Walls(ir))
1498 return ePBC2npbcdim(ir->ePBC);
1502 int ndof_com(const t_inputrec *ir)
1513 n = (ir->nwall == 0 ? 3 : 2);
1519 gmx_incons("Unknown pbc in calc_nrdf");
1525 real maxReferenceTemperature(const t_inputrec &ir)
1527 if (EI_ENERGY_MINIMIZATION(ir.eI) || ir.eI == eiNM)
1532 if (EI_MD(ir.eI) && ir.etc == etcNO)
1537 /* SD and BD also use ref_t and tau_t for setting the reference temperature.
1538 * TPI can be treated as MD, since it needs an ensemble temperature.
1541 real maxTemperature = 0;
1542 for (int i = 0; i < ir.opts.ngtc; i++)
1544 if (ir.opts.tau_t[i] >= 0)
1546 maxTemperature = std::max(maxTemperature, ir.opts.ref_t[i]);
1550 return maxTemperature;