Bug Summary

File:gromacs/gmxlib/txtdump.c
Location:line 1558, column 21
Description:Value stored to 'size' is never read

Annotated Source Code

1/*
2 * This file is part of the GROMACS molecular simulation package.
3 *
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, 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.
10 *
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.
15 *
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.
20 *
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.
25 *
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.
33 *
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.
36 */
37#ifdef HAVE_CONFIG_H1
38#include <config.h>
39#endif
40
41/* This file is completely threadsafe - please keep it that way! */
42
43#include <stdio.h>
44#include <stdlib.h>
45
46#include "typedefs.h"
47#include "types/commrec.h"
48#include "names.h"
49#include "txtdump.h"
50#include "gromacs/math/vec.h"
51#include "macros.h"
52
53#include "gromacs/utility/fatalerror.h"
54#include "gromacs/utility/smalloc.h"
55
56int pr_indent(FILE *fp, int n)
57{
58 int i;
59
60 for (i = 0; i < n; i++)
61 {
62 (void) fprintf(fp, " ");
63 }
64 return n;
65}
66
67int available(FILE *fp, void *p, int indent, const char *title)
68{
69 if (!p)
70 {
71 if (indent > 0)
72 {
73 pr_indent(fp, indent);
74 }
75 (void) fprintf(fp, "%s: not available\n", title);
76 }
77 return (p != NULL((void*)0));
78}
79
80int pr_title(FILE *fp, int indent, const char *title)
81{
82 (void) pr_indent(fp, indent);
83 (void) fprintf(fp, "%s:\n", title);
84 return (indent+INDENT3);
85}
86
87int pr_title_n(FILE *fp, int indent, const char *title, int n)
88{
89 (void) pr_indent(fp, indent);
90 (void) fprintf(fp, "%s (%d):\n", title, n);
91 return (indent+INDENT3);
92}
93
94int pr_title_nxn(FILE *fp, int indent, const char *title, int n1, int n2)
95{
96 (void) pr_indent(fp, indent);
97 (void) fprintf(fp, "%s (%dx%d):\n", title, n1, n2);
98 return (indent+INDENT3);
99}
100
101void pr_ivec(FILE *fp, int indent, const char *title, int vec[], int n, gmx_bool bShowNumbers)
102{
103 int i;
104
105 if (available(fp, vec, indent, title))
106 {
107 indent = pr_title_n(fp, indent, title, n);
108 for (i = 0; i < n; i++)
109 {
110 (void) pr_indent(fp, indent);
111 (void) fprintf(fp, "%s[%d]=%d\n", title, bShowNumbers ? i : -1, vec[i]);
112 }
113 }
114}
115
116void pr_ivec_block(FILE *fp, int indent, const char *title, int vec[], int n, gmx_bool bShowNumbers)
117{
118 int i, j;
119
120 if (available(fp, vec, indent, title))
121 {
122 indent = pr_title_n(fp, indent, title, n);
123 i = 0;
124 while (i < n)
125 {
126 j = i+1;
127 while (j < n && vec[j] == vec[j-1]+1)
128 {
129 j++;
130 }
131 /* Print consecutive groups of 3 or more as blocks */
132 if (j - i < 3)
133 {
134 while (i < j)
135 {
136 (void) pr_indent(fp, indent);
137 (void) fprintf(fp, "%s[%d]=%d\n",
138 title, bShowNumbers ? i : -1, vec[i]);
139 i++;
140 }
141 }
142 else
143 {
144 (void) pr_indent(fp, indent);
145 (void) fprintf(fp, "%s[%d,...,%d] = {%d,...,%d}\n",
146 title,
147 bShowNumbers ? i : -1,
148 bShowNumbers ? j-1 : -1,
149 vec[i], vec[j-1]);
150 i = j;
151 }
152 }
153 }
154}
155
156void pr_bvec(FILE *fp, int indent, const char *title, gmx_bool vec[], int n, gmx_bool bShowNumbers)
157{
158 int i;
159
160 if (available(fp, vec, indent, title))
161 {
162 indent = pr_title_n(fp, indent, title, n);
163 for (i = 0; i < n; i++)
164 {
165 (void) pr_indent(fp, indent);
166 (void) fprintf(fp, "%s[%d]=%s\n", title, bShowNumbers ? i : -1,
167 EBOOL(vec[i])((((vec[i]) < 0) || ((vec[i]) >= (2))) ? "UNDEFINED" : (
bool_names)[vec[i]]));
168 }
169 }
170}
171
172void pr_ivecs(FILE *fp, int indent, const char *title, ivec vec[], int n, gmx_bool bShowNumbers)
173{
174 int i, j;
175
176 if (available(fp, vec, indent, title))
177 {
178 indent = pr_title_nxn(fp, indent, title, n, DIM3);
179 for (i = 0; i < n; i++)
180 {
181 (void) pr_indent(fp, indent);
182 (void) fprintf(fp, "%s[%d]={", title, bShowNumbers ? i : -1);
183 for (j = 0; j < DIM3; j++)
184 {
185 if (j != 0)
186 {
187 (void) fprintf(fp, ", ");
188 }
189 fprintf(fp, "%d", vec[i][j]);
190 }
191 (void) fprintf(fp, "}\n");
192 }
193 }
194}
195
196void pr_rvec(FILE *fp, int indent, const char *title, real vec[], int n, gmx_bool bShowNumbers)
197{
198 int i;
199
200 if (available(fp, vec, indent, title))
201 {
202 indent = pr_title_n(fp, indent, title, n);
203 for (i = 0; i < n; i++)
204 {
205 pr_indent(fp, indent);
206 fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
207 }
208 }
209}
210
211void pr_dvec(FILE *fp, int indent, const char *title, double vec[], int n, gmx_bool bShowNumbers)
212{
213 int i;
214
215 if (available(fp, vec, indent, title))
216 {
217 indent = pr_title_n(fp, indent, title, n);
218 for (i = 0; i < n; i++)
219 {
220 pr_indent(fp, indent);
221 fprintf(fp, "%s[%d]=%12.5e\n", title, bShowNumbers ? i : -1, vec[i]);
222 }
223 }
224}
225
226
227/*
228 void pr_mat(FILE *fp,int indent,char *title,matrix m)
229 {
230 int i,j;
231
232 if (available(fp,m,indent,title)) {
233 indent=pr_title_n(fp,indent,title,n);
234 for(i=0; i<n; i++) {
235 pr_indent(fp,indent);
236 fprintf(fp,"%s[%d]=%12.5e %12.5e %12.5e\n",
237 title,bShowNumbers?i:-1,m[i][XX],m[i][YY],m[i][ZZ]);
238 }
239 }
240 }
241 */
242
243void pr_rvecs_len(FILE *fp, int indent, const char *title, rvec vec[], int n)
244{
245 int i, j;
246
247 if (available(fp, vec, indent, title))
248 {
249 indent = pr_title_nxn(fp, indent, title, n, DIM3);
250 for (i = 0; i < n; i++)
251 {
252 (void) pr_indent(fp, indent);
253 (void) fprintf(fp, "%s[%5d]={", title, i);
254 for (j = 0; j < DIM3; j++)
255 {
256 if (j != 0)
257 {
258 (void) fprintf(fp, ", ");
259 }
260 (void) fprintf(fp, "%12.5e", vec[i][j]);
261 }
262 (void) fprintf(fp, "} len=%12.5e\n", norm(vec[i]));
263 }
264 }
265}
266
267void pr_rvecs(FILE *fp, int indent, const char *title, rvec vec[], int n)
268{
269 const char *fshort = "%12.5e";
270 const char *flong = "%15.8e";
271 const char *format;
272 int i, j;
273
274 if (getenv("LONGFORMAT") != NULL((void*)0))
275 {
276 format = flong;
277 }
278 else
279 {
280 format = fshort;
281 }
282
283 if (available(fp, vec, indent, title))
284 {
285 indent = pr_title_nxn(fp, indent, title, n, DIM3);
286 for (i = 0; i < n; i++)
287 {
288 (void) pr_indent(fp, indent);
289 (void) fprintf(fp, "%s[%5d]={", title, i);
290 for (j = 0; j < DIM3; j++)
291 {
292 if (j != 0)
293 {
294 (void) fprintf(fp, ", ");
295 }
296 (void) fprintf(fp, format, vec[i][j]);
297 }
298 (void) fprintf(fp, "}\n");
299 }
300 }
301}
302
303
304void pr_rvecs_of_dim(FILE *fp, int indent, const char *title, rvec vec[], int n, int dim)
305{
306 const char *fshort = "%12.5e";
307 const char *flong = "%15.8e";
308 const char *format;
309 int i, j;
310
311 if (getenv("LONGFORMAT") != NULL((void*)0))
312 {
313 format = flong;
314 }
315 else
316 {
317 format = fshort;
318 }
319
320 if (available(fp, vec, indent, title))
321 {
322 indent = pr_title_nxn(fp, indent, title, n, dim);
323 for (i = 0; i < n; i++)
324 {
325 (void) pr_indent(fp, indent);
326 (void) fprintf(fp, "%s[%5d]={", title, i);
327 for (j = 0; j < dim; j++)
328 {
329 if (j != 0)
330 {
331 (void) fprintf(fp, ", ");
332 }
333 (void) fprintf(fp, format, vec[i][j]);
334 }
335 (void) fprintf(fp, "}\n");
336 }
337 }
338}
339
340void pr_reals(FILE *fp, int indent, const char *title, real *vec, int n)
341{
342 int i;
343
344 if (available(fp, vec, indent, title))
345 {
346 (void) pr_indent(fp, indent);
347 (void) fprintf(fp, "%s:\t", title);
348 for (i = 0; i < n; i++)
349 {
350 fprintf(fp, " %10g", vec[i]);
351 }
352 (void) fprintf(fp, "\n");
353 }
354}
355
356void pr_doubles(FILE *fp, int indent, const char *title, double *vec, int n)
357{
358 int i;
359
360 if (available(fp, vec, indent, title))
361 {
362 (void) pr_indent(fp, indent);
363 (void) fprintf(fp, "%s:\t", title);
364 for (i = 0; i < n; i++)
365 {
366 fprintf(fp, " %10g", vec[i]);
367 }
368 (void) fprintf(fp, "\n");
369 }
370}
371
372void pr_reals_of_dim(FILE *fp, int indent, const char *title, real *vec, int n, int dim)
373{
374 int i, j;
375 const char *fshort = "%12.5e";
376 const char *flong = "%15.8e";
377 const char *format;
378
379 if (getenv("LONGFORMAT") != NULL((void*)0))
380 {
381 format = flong;
382 }
383 else
384 {
385 format = fshort;
386 }
387
388 if (available(fp, vec, indent, title))
389 {
390 indent = pr_title_nxn(fp, indent, title, n, dim);
391 for (i = 0; i < n; i++)
392 {
393 (void) pr_indent(fp, indent);
394 (void) fprintf(fp, "%s[%5d]={", title, i);
395 for (j = 0; j < dim; j++)
396 {
397 if (j != 0)
398 {
399 (void) fprintf(fp, ", ");
400 }
401 (void) fprintf(fp, format, vec[i * dim + j]);
402 }
403 (void) fprintf(fp, "}\n");
404 }
405 }
406}
407
408static void pr_int(FILE *fp, int indent, const char *title, int i)
409{
410 pr_indent(fp, indent);
411 fprintf(fp, "%-20s = %d\n", title, i);
412}
413
414static void pr_int64(FILE *fp, int indent, const char *title, gmx_int64_t i)
415{
416 char buf[STEPSTRSIZE22];
417
418 pr_indent(fp, indent);
419 fprintf(fp, "%-20s = %s\n", title, gmx_step_str(i, buf));
420}
421
422static void pr_real(FILE *fp, int indent, const char *title, real r)
423{
424 pr_indent(fp, indent);
425 fprintf(fp, "%-20s = %g\n", title, r);
426}
427
428static void pr_double(FILE *fp, int indent, const char *title, double d)
429{
430 pr_indent(fp, indent);
431 fprintf(fp, "%-20s = %g\n", title, d);
432}
433
434static void pr_str(FILE *fp, int indent, const char *title, const char *s)
435{
436 pr_indent(fp, indent);
437 fprintf(fp, "%-30s = %s\n", title, s);
438}
439
440void pr_qm_opts(FILE *fp, int indent, const char *title, t_grpopts *opts)
441{
442 int i, m, j;
443
444 fprintf(fp, "%s:\n", title);
445
446 pr_int(fp, indent, "ngQM", opts->ngQM);
447 if (opts->ngQM > 0)
448 {
449 pr_ivec(fp, indent, "QMmethod", opts->QMmethod, opts->ngQM, FALSE0);
450 pr_ivec(fp, indent, "QMbasis", opts->QMbasis, opts->ngQM, FALSE0);
451 pr_ivec(fp, indent, "QMcharge", opts->QMcharge, opts->ngQM, FALSE0);
452 pr_ivec(fp, indent, "QMmult", opts->QMmult, opts->ngQM, FALSE0);
453 pr_bvec(fp, indent, "bSH", opts->bSH, opts->ngQM, FALSE0);
454 pr_ivec(fp, indent, "CASorbitals", opts->CASorbitals, opts->ngQM, FALSE0);
455 pr_ivec(fp, indent, "CASelectrons", opts->CASelectrons, opts->ngQM, FALSE0);
456 pr_rvec(fp, indent, "SAon", opts->SAon, opts->ngQM, FALSE0);
457 pr_rvec(fp, indent, "SAon", opts->SAon, opts->ngQM, FALSE0);
458 pr_ivec(fp, indent, "SAsteps", opts->SAsteps, opts->ngQM, FALSE0);
459 pr_bvec(fp, indent, "bOPT", opts->bOPT, opts->ngQM, FALSE0);
460 pr_bvec(fp, indent, "bTS", opts->bTS, opts->ngQM, FALSE0);
461 }
462}
463
464static void pr_grp_opts(FILE *out, int indent, const char *title, t_grpopts *opts,
465 gmx_bool bMDPformat)
466{
467 int i, m, j;
468
469 if (!bMDPformat)
470 {
471 fprintf(out, "%s:\n", title);
472 }
473
474 pr_indent(out, indent);
475 fprintf(out, "nrdf%s", bMDPformat ? " = " : ":");
476 for (i = 0; (i < opts->ngtc); i++)
477 {
478 fprintf(out, " %10g", opts->nrdf[i]);
479 }
480 fprintf(out, "\n");
481
482 pr_indent(out, indent);
483 fprintf(out, "ref-t%s", bMDPformat ? " = " : ":");
484 for (i = 0; (i < opts->ngtc); i++)
485 {
486 fprintf(out, " %10g", opts->ref_t[i]);
487 }
488 fprintf(out, "\n");
489
490 pr_indent(out, indent);
491 fprintf(out, "tau-t%s", bMDPformat ? " = " : ":");
492 for (i = 0; (i < opts->ngtc); i++)
493 {
494 fprintf(out, " %10g", opts->tau_t[i]);
495 }
496 fprintf(out, "\n");
497
498 /* Pretty-print the simulated annealing info */
499 fprintf(out, "anneal%s", bMDPformat ? " = " : ":");
500 for (i = 0; (i < opts->ngtc); i++)
501 {
502 fprintf(out, " %10s", EANNEAL(opts->annealing[i])((((opts->annealing[i]) < 0) || ((opts->annealing[i]
) >= (eannNR))) ? "UNDEFINED" : (eann_names)[opts->annealing
[i]]));
503 }
504 fprintf(out, "\n");
505
506 fprintf(out, "ann-npoints%s", bMDPformat ? " = " : ":");
507 for (i = 0; (i < opts->ngtc); i++)
508 {
509 fprintf(out, " %10d", opts->anneal_npoints[i]);
510 }
511 fprintf(out, "\n");
512
513 for (i = 0; (i < opts->ngtc); i++)
514 {
515 if (opts->anneal_npoints[i] > 0)
516 {
517 fprintf(out, "ann. times [%d]:\t", i);
518 for (j = 0; (j < opts->anneal_npoints[i]); j++)
519 {
520 fprintf(out, " %10.1f", opts->anneal_time[i][j]);
521 }
522 fprintf(out, "\n");
523 fprintf(out, "ann. temps [%d]:\t", i);
524 for (j = 0; (j < opts->anneal_npoints[i]); j++)
525 {
526 fprintf(out, " %10.1f", opts->anneal_temp[i][j]);
527 }
528 fprintf(out, "\n");
529 }
530 }
531
532 pr_indent(out, indent);
533 fprintf(out, "acc:\t");
534 for (i = 0; (i < opts->ngacc); i++)
535 {
536 for (m = 0; (m < DIM3); m++)
537 {
538 fprintf(out, " %10g", opts->acc[i][m]);
539 }
540 }
541 fprintf(out, "\n");
542
543 pr_indent(out, indent);
544 fprintf(out, "nfreeze:");
545 for (i = 0; (i < opts->ngfrz); i++)
546 {
547 for (m = 0; (m < DIM3); m++)
548 {
549 fprintf(out, " %10s", opts->nFreeze[i][m] ? "Y" : "N");
550 }
551 }
552 fprintf(out, "\n");
553
554
555 for (i = 0; (i < opts->ngener); i++)
556 {
557 pr_indent(out, indent);
558 fprintf(out, "energygrp-flags[%3d]:", i);
559 for (m = 0; (m < opts->ngener); m++)
560 {
561 fprintf(out, " %d", opts->egp_flags[opts->ngener*i+m]);
562 }
563 fprintf(out, "\n");
564 }
565
566 fflush(out);
567}
568
569static void pr_matrix(FILE *fp, int indent, const char *title, rvec *m,
570 gmx_bool bMDPformat)
571{
572 if (bMDPformat)
573 {
574 fprintf(fp, "%-10s = %g %g %g %g %g %g\n", title,
575 m[XX0][XX0], m[YY1][YY1], m[ZZ2][ZZ2], m[XX0][YY1], m[XX0][ZZ2], m[YY1][ZZ2]);
576 }
577 else
578 {
579 pr_rvecs(fp, indent, title, m, DIM3);
580 }
581}
582
583static void pr_cosine(FILE *fp, int indent, const char *title, t_cosines *cos,
584 gmx_bool bMDPformat)
585{
586 int j;
587
588 if (bMDPformat)
589 {
590 fprintf(fp, "%s = %d\n", title, cos->n);
591 }
592 else
593 {
594 indent = pr_title(fp, indent, title);
595 (void) pr_indent(fp, indent);
596 fprintf(fp, "n = %d\n", cos->n);
597 if (cos->n > 0)
598 {
599 (void) pr_indent(fp, indent+2);
600 fprintf(fp, "a =");
601 for (j = 0; (j < cos->n); j++)
602 {
603 fprintf(fp, " %e", cos->a[j]);
604 }
605 fprintf(fp, "\n");
606 (void) pr_indent(fp, indent+2);
607 fprintf(fp, "phi =");
608 for (j = 0; (j < cos->n); j++)
609 {
610 fprintf(fp, " %e", cos->phi[j]);
611 }
612 fprintf(fp, "\n");
613 }
614 }
615}
616
617#define PS(t, s) pr_str(fp, indent, t, s)
618#define PI(t, s) pr_int(fp, indent, t, s)
619#define PSTEP(t, s)pr_int64(fp, indent, t, s) pr_int64(fp, indent, t, s)
620#define PR(t, s) pr_real(fp, indent, t, s)
621#define PD(t, s)pr_double(fp, indent, t, s) pr_double(fp, indent, t, s)
622
623static void pr_pull_group(FILE *fp, int indent, int g, t_pull_group *pgrp)
624{
625 pr_indent(fp, indent);
626 fprintf(fp, "pull-group %d:\n", g);
627 indent += 2;
628 pr_ivec_block(fp, indent, "atom", pgrp->ind, pgrp->nat, TRUE1);
629 pr_rvec(fp, indent, "weight", pgrp->weight, pgrp->nweight, TRUE1);
630 PI("pbcatom", pgrp->pbcatom);
631}
632
633static void pr_pull_coord(FILE *fp, int indent, int c, t_pull_coord *pcrd)
634{
635 pr_indent(fp, indent);
636 fprintf(fp, "pull-coord %d:\n", c);
637 PI("group[0]", pcrd->group[0]);
638 PI("group[1]", pcrd->group[1]);
639 pr_rvec(fp, indent, "origin", pcrd->origin, DIM3, TRUE1);
640 pr_rvec(fp, indent, "vec", pcrd->vec, DIM3, TRUE1);
641 PR("init", pcrd->init);
642 PR("rate", pcrd->rate);
643 PR("k", pcrd->k);
644 PR("kB", pcrd->kB);
645}
646
647static void pr_simtempvals(FILE *fp, int indent, t_simtemp *simtemp, int n_lambda)
648{
649 PR("simtemp_low", simtemp->simtemp_low);
650 PR("simtemp_high", simtemp->simtemp_high);
651 PS("simulated-tempering-scaling", ESIMTEMP(simtemp->eSimTempScale)((((simtemp->eSimTempScale) < 0) || ((simtemp->eSimTempScale
) >= (esimtempNR))) ? "UNDEFINED" : (esimtemp_names)[simtemp
->eSimTempScale]));
652 pr_rvec(fp, indent, "simulated tempering temperatures", simtemp->temperatures, n_lambda, TRUE1);
653}
654
655static void pr_expandedvals(FILE *fp, int indent, t_expanded *expand, int n_lambda)
656{
657
658 PI("nstexpanded", expand->nstexpanded);
659 PS("lambda-stats", elamstats_names[expand->elamstats]);
660 PS("lambda-mc-move", elmcmove_names[expand->elmcmove]);
661 PI("lmc-repeats", expand->lmc_repeats);
662 PI("lmc-gibbsdelta", expand->gibbsdeltalam);
663 PI("lmc-nstart", expand->lmc_forced_nstart);
664 PS("symmetrized-transition-matrix", EBOOL(expand->bSymmetrizedTMatrix)((((expand->bSymmetrizedTMatrix) < 0) || ((expand->bSymmetrizedTMatrix
) >= (2))) ? "UNDEFINED" : (bool_names)[expand->bSymmetrizedTMatrix
]));
665 PI("nst-transition-matrix", expand->nstTij);
666 PI("mininum-var-min", expand->minvarmin); /*default is reasonable */
667 PI("weight-c-range", expand->c_range); /* default is just C=0 */
668 PR("wl-scale", expand->wl_scale);
669 PR("init-wl-delta", expand->init_wl_delta);
670 PR("wl-ratio", expand->wl_ratio);
671 PS("bWLoneovert", EBOOL(expand->bWLoneovert)((((expand->bWLoneovert) < 0) || ((expand->bWLoneovert
) >= (2))) ? "UNDEFINED" : (bool_names)[expand->bWLoneovert
]));
672 PI("lmc-seed", expand->lmc_seed);
673 PR("mc-temperature", expand->mc_temp);
674 PS("lmc-weights-equil", elmceq_names[expand->elmceq]);
675 if (expand->elmceq == elmceqNUMATLAM)
676 {
677 PI("weight-equil-number-all-lambda", expand->equil_n_at_lam);
678 }
679 if (expand->elmceq == elmceqSAMPLES)
680 {
681 PI("weight-equil-number-samples", expand->equil_samples);
682 }
683 if (expand->elmceq == elmceqSTEPS)
684 {
685 PI("weight-equil-number-steps", expand->equil_steps);
686 }
687 if (expand->elmceq == elmceqWLDELTA)
688 {
689 PR("weight-equil-wl-delta", expand->equil_wl_delta);
690 }
691 if (expand->elmceq == elmceqRATIO)
692 {
693 PR("weight-equil-count-ratio", expand->equil_ratio);
694 }
695
696 pr_indent(fp, indent);
697 pr_rvec(fp, indent, "init-lambda-weights", expand->init_lambda_weights, n_lambda, TRUE1);
698 PS("init-weights", EBOOL(expand->bInit_weights)((((expand->bInit_weights) < 0) || ((expand->bInit_weights
) >= (2))) ? "UNDEFINED" : (bool_names)[expand->bInit_weights
]));
699}
700
701static void pr_fepvals(FILE *fp, int indent, t_lambda *fep, gmx_bool bMDPformat)
702{
703 int i, j;
704
705 PI("nstdhdl", fep->nstdhdl);
706 PI("init-lambda-state", fep->init_fep_state);
707 PR("init-lambda", fep->init_lambda);
708 PR("delta-lambda", fep->delta_lambda);
709 if (!bMDPformat)
710 {
711 PI("n-lambdas", fep->n_lambda);
712 }
713 if (fep->n_lambda > 0)
714 {
715 pr_indent(fp, indent);
716 fprintf(fp, "separate-dvdl%s\n", bMDPformat ? " = " : ":");
717 for (i = 0; i < efptNR; i++)
718 {
719 fprintf(fp, "%18s = ", efpt_names[i]);
720 if (fep->separate_dvdl[i])
721 {
722 fprintf(fp, " TRUE");
723 }
724 else
725 {
726 fprintf(fp, " FALSE");
727 }
728 fprintf(fp, "\n");
729 }
730 fprintf(fp, "all-lambdas%s\n", bMDPformat ? " = " : ":");
731 for (i = 0; i < efptNR; i++)
732 {
733 fprintf(fp, "%18s = ", efpt_names[i]);
734 for (j = 0; j < fep->n_lambda; j++)
735 {
736 fprintf(fp, " %10g", fep->all_lambda[i][j]);
737 }
738 fprintf(fp, "\n");
739 }
740 }
741 PI("calc-lambda-neighbors", fep->lambda_neighbors);
742
743 PR("sc-alpha", fep->sc_alpha);
744 PS("bScCoul", EBOOL(fep->bScCoul)((((fep->bScCoul) < 0) || ((fep->bScCoul) >= (2))
) ? "UNDEFINED" : (bool_names)[fep->bScCoul]));
745 PS("bScPrintEnergy", EBOOL(fep->bPrintEnergy)((((fep->bPrintEnergy) < 0) || ((fep->bPrintEnergy) >=
(2))) ? "UNDEFINED" : (bool_names)[fep->bPrintEnergy]));
746 PI("sc-power", fep->sc_power);
747 PR("sc-r-power", fep->sc_r_power);
748 PR("sc-sigma", fep->sc_sigma);
749 PR("sc-sigma-min", fep->sc_sigma_min);
750 PS("separate-dhdl-file", SEPDHDLFILETYPE(fep->separate_dhdl_file)((((fep->separate_dhdl_file) < 0) || ((fep->separate_dhdl_file
) >= (esepdhdlfileNR))) ? "UNDEFINED" : (separate_dhdl_file_names
)[fep->separate_dhdl_file]));
751 PS("dhdl-derivatives", DHDLDERIVATIVESTYPE(fep->dhdl_derivatives)((((fep->dhdl_derivatives) < 0) || ((fep->dhdl_derivatives
) >= (edhdlderivativesNR))) ? "UNDEFINED" : (dhdl_derivatives_names
)[fep->dhdl_derivatives]));
752 PI("dh-hist-size", fep->dh_hist_size);
753 PD("dh-hist-spacing", fep->dh_hist_spacing)pr_double(fp, indent, "dh-hist-spacing", fep->dh_hist_spacing
);
754};
755
756static void pr_pull(FILE *fp, int indent, t_pull *pull)
757{
758 int g;
759
760 PS("pull-geometry", EPULLGEOM(pull->eGeom)((((pull->eGeom) < 0) || ((pull->eGeom) >= (epullgNR
))) ? "UNDEFINED" : (epullg_names)[pull->eGeom]));
761 pr_ivec(fp, indent, "pull-dim", pull->dim, DIM3, TRUE1);
762 PR("pull-r1", pull->cyl_r1);
763 PR("pull-r0", pull->cyl_r0);
764 PR("pull-constr-tol", pull->constr_tol);
765 PS("pull-bPrintRef", EBOOL(pull->bPrintRef)((((pull->bPrintRef) < 0) || ((pull->bPrintRef) >=
(2))) ? "UNDEFINED" : (bool_names)[pull->bPrintRef]));
766 PI("pull-nstxout", pull->nstxout);
767 PI("pull-nstfout", pull->nstfout);
768 PI("pull-ngroup", pull->ngroup);
769 for (g = 0; g < pull->ngroup; g++)
770 {
771 pr_pull_group(fp, indent, g, &pull->group[g]);
772 }
773 PI("pull-ncoord", pull->ncoord);
774 for (g = 0; g < pull->ncoord; g++)
775 {
776 pr_pull_coord(fp, indent, g, &pull->coord[g]);
777 }
778}
779
780static void pr_rotgrp(FILE *fp, int indent, int g, t_rotgrp *rotg)
781{
782 pr_indent(fp, indent);
783 fprintf(fp, "rotation_group %d:\n", g);
784 indent += 2;
785 PS("type", EROTGEOM(rotg->eType)((((rotg->eType) < 0) || ((rotg->eType) >= (erotgNR
))) ? "UNDEFINED" : (erotg_names)[rotg->eType]));
786 PS("massw", EBOOL(rotg->bMassW)((((rotg->bMassW) < 0) || ((rotg->bMassW) >= (2))
) ? "UNDEFINED" : (bool_names)[rotg->bMassW]));
787 pr_ivec_block(fp, indent, "atom", rotg->ind, rotg->nat, TRUE1);
788 pr_rvecs(fp, indent, "x_ref", rotg->x_ref, rotg->nat);
789 pr_rvec(fp, indent, "vec", rotg->vec, DIM3, TRUE1);
790 pr_rvec(fp, indent, "pivot", rotg->pivot, DIM3, TRUE1);
791 PR("rate", rotg->rate);
792 PR("k", rotg->k);
793 PR("slab_dist", rotg->slab_dist);
794 PR("min_gaussian", rotg->min_gaussian);
795 PR("epsilon", rotg->eps);
796 PS("fit_method", EROTFIT(rotg->eFittype)((((rotg->eFittype) < 0) || ((rotg->eFittype) >= (
erotgFitNR))) ? "UNDEFINED" : (erotg_fitnames)[rotg->eFittype
]));
797 PI("potfitangle_nstep", rotg->PotAngle_nstep);
798 PR("potfitangle_step", rotg->PotAngle_step);
799}
800
801static void pr_rot(FILE *fp, int indent, t_rot *rot)
802{
803 int g;
804
805 PI("rot_nstrout", rot->nstrout);
806 PI("rot_nstsout", rot->nstsout);
807 PI("rot_ngrp", rot->ngrp);
808 for (g = 0; g < rot->ngrp; g++)
809 {
810 pr_rotgrp(fp, indent, g, &rot->grp[g]);
811 }
812}
813
814
815static void pr_swap(FILE *fp, int indent, t_swapcoords *swap)
816{
817 int i, j;
818 char str[STRLEN4096];
819
820
821 PI("frequency", swap->nstswap);
822 for (j = 0; j < 2; j++)
823 {
824 sprintf(str, "nanions%c", j+'A');
825 PI(str, swap->nanions[j]);
826 sprintf(str, "ncations%c", j+'A');
827 PI(str, swap->ncations[j]);
828 }
829 PI("coupling_steps", swap->nAverage);
830 PR("threshold", swap->threshold);
831 for (j = 0; j < 2; j++)
832 {
833 sprintf(str, "splitgroup%d_massw", j);
834 PS(str, EBOOL(swap->massw_split[j])((((swap->massw_split[j]) < 0) || ((swap->massw_split
[j]) >= (2))) ? "UNDEFINED" : (bool_names)[swap->massw_split
[j]]));
835 sprintf(str, "split atoms group %d", j);
836 pr_ivec_block(fp, indent, str, swap->ind_split[j], swap->nat_split[j], TRUE1);
837 }
838 pr_ivec_block(fp, indent, "swap atoms", swap->ind, swap->nat, TRUE1);
839 pr_ivec_block(fp, indent, "solvent atoms", swap->ind_sol, swap->nat_sol, TRUE1);
840 PR("cyl0_radius", swap->cyl0r);
841 PR("cyl0_upper", swap->cyl0u);
842 PR("cyl0_lower", swap->cyl0l);
843 PR("cyl1_radius", swap->cyl1r);
844 PR("cyl1_upper", swap->cyl1u);
845 PR("cyl1_lower", swap->cyl1l);
846}
847
848
849static void pr_imd(FILE *fp, int indent, t_IMD *imd)
850{
851 PI("IMD_atoms", imd->nat);
852 pr_ivec_block(fp, indent, "atom", imd->ind, imd->nat, TRUE1);
853}
854
855
856void pr_inputrec(FILE *fp, int indent, const char *title, t_inputrec *ir,
857 gmx_bool bMDPformat)
858{
859 const char *infbuf = "inf";
860 int i;
861
862 if (available(fp, ir, indent, title))
863 {
864 if (!bMDPformat)
865 {
866 indent = pr_title(fp, indent, title);
867 }
868 /* This strings do not all have a direct correspondence to
869 .mdp entries, but we should follow the same convention of
870 using hyphens in the names users read and write. */
871 PS("integrator", EI(ir->eI)((((ir->eI) < 0) || ((ir->eI) >= (eiNR))) ? "UNDEFINED"
: (ei_names)[ir->eI]));
872 PSTEP("nsteps", ir->nsteps)pr_int64(fp, indent, "nsteps", ir->nsteps);
873 PSTEP("init-step", ir->init_step)pr_int64(fp, indent, "init-step", ir->init_step);
874 PS("cutoff-scheme", ECUTSCHEME(ir->cutoff_scheme)((((ir->cutoff_scheme) < 0) || ((ir->cutoff_scheme) >=
(ecutsNR))) ? "UNDEFINED" : (ecutscheme_names)[ir->cutoff_scheme
]));
875 PS("ns-type", ENS(ir->ns_type)((((ir->ns_type) < 0) || ((ir->ns_type) >= (ensNR
))) ? "UNDEFINED" : (ens_names)[ir->ns_type]));
876 PI("nstlist", ir->nstlist);
877 PI("ndelta", ir->ndelta);
878 PI("nstcomm", ir->nstcomm);
879 PS("comm-mode", ECOM(ir->comm_mode)((((ir->comm_mode) < 0) || ((ir->comm_mode) >= (ecmNR
))) ? "UNDEFINED" : (ecm_names)[ir->comm_mode]));
880 PI("nstlog", ir->nstlog);
881 PI("nstxout", ir->nstxout);
882 PI("nstvout", ir->nstvout);
883 PI("nstfout", ir->nstfout);
884 PI("nstcalcenergy", ir->nstcalcenergy);
885 PI("nstenergy", ir->nstenergy);
886 PI("nstxout-compressed", ir->nstxout_compressed);
887 PR("init-t", ir->init_t);
888 PR("delta-t", ir->delta_t);
889
890 PR("x-compression-precision", ir->x_compression_precision);
891 PR("fourierspacing", ir->fourier_spacing);
892 PI("nkx", ir->nkx);
893 PI("nky", ir->nky);
894 PI("nkz", ir->nkz);
895 PI("pme-order", ir->pme_order);
896 PR("ewald-rtol", ir->ewald_rtol);
897 PR("ewald-rtol-lj", ir->ewald_rtol_lj);
898 PR("ewald-geometry", ir->ewald_geometry);
899 PR("epsilon-surface", ir->epsilon_surface);
900 PS("optimize-fft", EBOOL(ir->bOptFFT)((((ir->bOptFFT) < 0) || ((ir->bOptFFT) >= (2))) ?
"UNDEFINED" : (bool_names)[ir->bOptFFT]));
901 PS("lj-pme-comb-rule", ELJPMECOMBNAMES(ir->ljpme_combination_rule)((((ir->ljpme_combination_rule) < 0) || ((ir->ljpme_combination_rule
) >= (eljpmeNR))) ? "UNDEFINED" : (eljpme_names)[ir->ljpme_combination_rule
]));
902 PS("ePBC", EPBC(ir->ePBC)((((ir->ePBC) < 0) || ((ir->ePBC) >= (epbcNR))) ?
"UNDEFINED" : (epbc_names)[ir->ePBC]));
903 PS("bPeriodicMols", EBOOL(ir->bPeriodicMols)((((ir->bPeriodicMols) < 0) || ((ir->bPeriodicMols) >=
(2))) ? "UNDEFINED" : (bool_names)[ir->bPeriodicMols]));
904 PS("bContinuation", EBOOL(ir->bContinuation)((((ir->bContinuation) < 0) || ((ir->bContinuation) >=
(2))) ? "UNDEFINED" : (bool_names)[ir->bContinuation]));
905 PS("bShakeSOR", EBOOL(ir->bShakeSOR)((((ir->bShakeSOR) < 0) || ((ir->bShakeSOR) >= (2
))) ? "UNDEFINED" : (bool_names)[ir->bShakeSOR]));
906 PS("etc", ETCOUPLTYPE(ir->etc)((((ir->etc) < 0) || ((ir->etc) >= (etcNR))) ? "UNDEFINED"
: (etcoupl_names)[ir->etc]));
907 PS("bPrintNHChains", EBOOL(ir->bPrintNHChains)((((ir->bPrintNHChains) < 0) || ((ir->bPrintNHChains
) >= (2))) ? "UNDEFINED" : (bool_names)[ir->bPrintNHChains
]));
908 PI("nsttcouple", ir->nsttcouple);
909 PS("epc", EPCOUPLTYPE(ir->epc)((((ir->epc) < 0) || ((ir->epc) >= (epcNR))) ? "UNDEFINED"
: (epcoupl_names)[ir->epc]));
910 PS("epctype", EPCOUPLTYPETYPE(ir->epct)((((ir->epct) < 0) || ((ir->epct) >= (epctNR))) ?
"UNDEFINED" : (epcoupltype_names)[ir->epct]));
911 PI("nstpcouple", ir->nstpcouple);
912 PR("tau-p", ir->tau_p);
913 pr_matrix(fp, indent, "ref-p", ir->ref_p, bMDPformat);
914 pr_matrix(fp, indent, "compress", ir->compress, bMDPformat);
915 PS("refcoord-scaling", EREFSCALINGTYPE(ir->refcoord_scaling)((((ir->refcoord_scaling) < 0) || ((ir->refcoord_scaling
) >= (erscNR))) ? "UNDEFINED" : (erefscaling_names)[ir->
refcoord_scaling]));
916 if (bMDPformat)
917 {
918 fprintf(fp, "posres-com = %g %g %g\n", ir->posres_com[XX0],
919 ir->posres_com[YY1], ir->posres_com[ZZ2]);
920 }
921 else
922 {
923 pr_rvec(fp, indent, "posres-com", ir->posres_com, DIM3, TRUE1);
924 }
925 if (bMDPformat)
926 {
927 fprintf(fp, "posres-comB = %g %g %g\n", ir->posres_comB[XX0],
928 ir->posres_comB[YY1], ir->posres_comB[ZZ2]);
929 }
930 else
931 {
932 pr_rvec(fp, indent, "posres-comB", ir->posres_comB, DIM3, TRUE1);
933 }
934 PR("verlet-buffer-tolerance", ir->verletbuf_tol);
935 PR("rlist", ir->rlist);
936 PR("rlistlong", ir->rlistlong);
937 PR("nstcalclr", ir->nstcalclr);
938 PR("rtpi", ir->rtpi);
939 PS("coulombtype", EELTYPE(ir->coulombtype)((((ir->coulombtype) < 0) || ((ir->coulombtype) >=
(eelNR))) ? "UNDEFINED" : (eel_names)[ir->coulombtype]));
940 PS("coulomb-modifier", INTMODIFIER(ir->coulomb_modifier)((((ir->coulomb_modifier) < 0) || ((ir->coulomb_modifier
) >= (eintmodNR))) ? "UNDEFINED" : (eintmod_names)[ir->
coulomb_modifier]));
941 PR("rcoulomb-switch", ir->rcoulomb_switch);
942 PR("rcoulomb", ir->rcoulomb);
943 PS("vdwtype", EVDWTYPE(ir->vdwtype)((((ir->vdwtype) < 0) || ((ir->vdwtype) >= (evdwNR
))) ? "UNDEFINED" : (evdw_names)[ir->vdwtype]));
944 PS("vdw-modifier", INTMODIFIER(ir->vdw_modifier)((((ir->vdw_modifier) < 0) || ((ir->vdw_modifier) >=
(eintmodNR))) ? "UNDEFINED" : (eintmod_names)[ir->vdw_modifier
]));
945 PR("rvdw-switch", ir->rvdw_switch);
946 PR("rvdw", ir->rvdw);
947 if (ir->epsilon_r != 0)
948 {
949 PR("epsilon-r", ir->epsilon_r);
950 }
951 else
952 {
953 PS("epsilon-r", infbuf);
954 }
955 if (ir->epsilon_rf != 0)
956 {
957 PR("epsilon-rf", ir->epsilon_rf);
958 }
959 else
960 {
961 PS("epsilon-rf", infbuf);
962 }
963 PR("tabext", ir->tabext);
964 PS("implicit-solvent", EIMPLICITSOL(ir->implicit_solvent)((((ir->implicit_solvent) < 0) || ((ir->implicit_solvent
) >= (eisNR))) ? "UNDEFINED" : (eis_names)[ir->implicit_solvent
]));
965 PS("gb-algorithm", EGBALGORITHM(ir->gb_algorithm)((((ir->gb_algorithm) < 0) || ((ir->gb_algorithm) >=
(egbNR))) ? "UNDEFINED" : (egb_names)[ir->gb_algorithm]));
966 PR("gb-epsilon-solvent", ir->gb_epsilon_solvent);
967 PI("nstgbradii", ir->nstgbradii);
968 PR("rgbradii", ir->rgbradii);
969 PR("gb-saltconc", ir->gb_saltconc);
970 PR("gb-obc-alpha", ir->gb_obc_alpha);
971 PR("gb-obc-beta", ir->gb_obc_beta);
972 PR("gb-obc-gamma", ir->gb_obc_gamma);
973 PR("gb-dielectric-offset", ir->gb_dielectric_offset);
974 PS("sa-algorithm", ESAALGORITHM(ir->gb_algorithm)((((ir->gb_algorithm) < 0) || ((ir->gb_algorithm) >=
(esaNR))) ? "UNDEFINED" : (esa_names)[ir->gb_algorithm]));
975 PR("sa-surface-tension", ir->sa_surface_tension);
976 PS("DispCorr", EDISPCORR(ir->eDispCorr)((((ir->eDispCorr) < 0) || ((ir->eDispCorr) >= (edispcNR
))) ? "UNDEFINED" : (edispc_names)[ir->eDispCorr]));
977 PS("bSimTemp", EBOOL(ir->bSimTemp)((((ir->bSimTemp) < 0) || ((ir->bSimTemp) >= (2))
) ? "UNDEFINED" : (bool_names)[ir->bSimTemp]));
978 if (ir->bSimTemp)
979 {
980 pr_simtempvals(fp, indent, ir->simtempvals, ir->fepvals->n_lambda);
981 }
982 PS("free-energy", EFEPTYPE(ir->efep)((((ir->efep) < 0) || ((ir->efep) >= (efepNR))) ?
"UNDEFINED" : (efep_names)[ir->efep]));
983 if (ir->efep != efepNO || ir->bSimTemp)
984 {
985 pr_fepvals(fp, indent, ir->fepvals, bMDPformat);
986 }
987 if (ir->bExpanded)
988 {
989 pr_expandedvals(fp, indent, ir->expandedvals, ir->fepvals->n_lambda);
990 }
991
992 PI("nwall", ir->nwall);
993 PS("wall-type", EWALLTYPE(ir->wall_type)((((ir->wall_type) < 0) || ((ir->wall_type) >= (ewtNR
))) ? "UNDEFINED" : (ewt_names)[ir->wall_type]));
994 PI("wall-atomtype[0]", ir->wall_atomtype[0]);
995 PI("wall-atomtype[1]", ir->wall_atomtype[1]);
996 PR("wall-density[0]", ir->wall_density[0]);
997 PR("wall-density[1]", ir->wall_density[1]);
998 PR("wall-ewald-zfac", ir->wall_ewald_zfac);
999
1000 PS("pull", EPULLTYPE(ir->ePull)((((ir->ePull) < 0) || ((ir->ePull) >= (epullNR))
) ? "UNDEFINED" : (epull_names)[ir->ePull]));
1001 if (ir->ePull != epullNO)
1002 {
1003 pr_pull(fp, indent, ir->pull);
1004 }
1005
1006 PS("rotation", EBOOL(ir->bRot)((((ir->bRot) < 0) || ((ir->bRot) >= (2))) ? "UNDEFINED"
: (bool_names)[ir->bRot]));
1007 if (ir->bRot)
1008 {
1009 pr_rot(fp, indent, ir->rot);
1010 }
1011
1012 PS("interactiveMD", EBOOL(ir->bIMD)((((ir->bIMD) < 0) || ((ir->bIMD) >= (2))) ? "UNDEFINED"
: (bool_names)[ir->bIMD]));
1013 if (ir->bIMD)
1014 {
1015 pr_imd(fp, indent, ir->imd);
1016 }
1017
1018 PS("disre", EDISRETYPE(ir->eDisre)((((ir->eDisre) < 0) || ((ir->eDisre) >= (edrNR))
) ? "UNDEFINED" : (edisre_names)[ir->eDisre]));
1019 PS("disre-weighting", EDISREWEIGHTING(ir->eDisreWeighting)((((ir->eDisreWeighting) < 0) || ((ir->eDisreWeighting
) >= (edrwNR))) ? "UNDEFINED" : (edisreweighting_names)[ir
->eDisreWeighting]));
1020 PS("disre-mixed", EBOOL(ir->bDisreMixed)((((ir->bDisreMixed) < 0) || ((ir->bDisreMixed) >=
(2))) ? "UNDEFINED" : (bool_names)[ir->bDisreMixed]));
1021 PR("dr-fc", ir->dr_fc);
1022 PR("dr-tau", ir->dr_tau);
1023 PR("nstdisreout", ir->nstdisreout);
1024 PR("orires-fc", ir->orires_fc);
1025 PR("orires-tau", ir->orires_tau);
1026 PR("nstorireout", ir->nstorireout);
1027
1028 PR("dihre-fc", ir->dihre_fc);
1029
1030 PR("em-stepsize", ir->em_stepsize);
1031 PR("em-tol", ir->em_tol);
1032 PI("niter", ir->niter);
1033 PR("fc-stepsize", ir->fc_stepsize);
1034 PI("nstcgsteep", ir->nstcgsteep);
1035 PI("nbfgscorr", ir->nbfgscorr);
1036
1037 PS("ConstAlg", ECONSTRTYPE(ir->eConstrAlg)((((ir->eConstrAlg) < 0) || ((ir->eConstrAlg) >= (
econtNR))) ? "UNDEFINED" : (econstr_names)[ir->eConstrAlg]
));
1038 PR("shake-tol", ir->shake_tol);
1039 PI("lincs-order", ir->nProjOrder);
1040 PR("lincs-warnangle", ir->LincsWarnAngle);
1041 PI("lincs-iter", ir->nLincsIter);
1042 PR("bd-fric", ir->bd_fric);
1043 PSTEP("ld-seed", ir->ld_seed)pr_int64(fp, indent, "ld-seed", ir->ld_seed);
1044 PR("cos-accel", ir->cos_accel);
1045 pr_matrix(fp, indent, "deform", ir->deform, bMDPformat);
1046
1047 PS("adress", EBOOL(ir->bAdress)((((ir->bAdress) < 0) || ((ir->bAdress) >= (2))) ?
"UNDEFINED" : (bool_names)[ir->bAdress]));
1048 if (ir->bAdress)
1049 {
1050 PS("adress-type", EADRESSTYPE(ir->adress->type)((((ir->adress->type) < 0) || ((ir->adress->type
) >= (eAdressNR))) ? "UNDEFINED" : (eAdresstype_names)[ir->
adress->type]));
1051 PR("adress-const-wf", ir->adress->const_wf);
1052 PR("adress-ex-width", ir->adress->ex_width);
1053 PR("adress-hy-width", ir->adress->hy_width);
1054 PS("adress-interface-correction", EADRESSICTYPE(ir->adress->icor)((((ir->adress->icor) < 0) || ((ir->adress->icor
) >= (eAdressICNR))) ? "UNDEFINED" : (eAdressICtype_names)
[ir->adress->icor]));
1055 PS("adress-site", EADRESSSITETYPE(ir->adress->site)((((ir->adress->site) < 0) || ((ir->adress->site
) >= (eAdressSITENR))) ? "UNDEFINED" : (eAdressSITEtype_names
)[ir->adress->site]));
1056 PR("adress-ex-force-cap", ir->adress->ex_forcecap);
1057 PS("adress-do-hybridpairs", EBOOL(ir->adress->do_hybridpairs)((((ir->adress->do_hybridpairs) < 0) || ((ir->adress
->do_hybridpairs) >= (2))) ? "UNDEFINED" : (bool_names)
[ir->adress->do_hybridpairs]));
1058
1059 pr_rvec(fp, indent, "adress-reference-coords", ir->adress->refs, DIM3, TRUE1);
1060 }
1061 PI("userint1", ir->userint1);
1062 PI("userint2", ir->userint2);
1063 PI("userint3", ir->userint3);
1064 PI("userint4", ir->userint4);
1065 PR("userreal1", ir->userreal1);
1066 PR("userreal2", ir->userreal2);
1067 PR("userreal3", ir->userreal3);
1068 PR("userreal4", ir->userreal4);
1069 pr_grp_opts(fp, indent, "grpopts", &(ir->opts), bMDPformat);
1070 pr_cosine(fp, indent, "efield-x", &(ir->ex[XX0]), bMDPformat);
1071 pr_cosine(fp, indent, "efield-xt", &(ir->et[XX0]), bMDPformat);
1072 pr_cosine(fp, indent, "efield-y", &(ir->ex[YY1]), bMDPformat);
1073 pr_cosine(fp, indent, "efield-yt", &(ir->et[YY1]), bMDPformat);
1074 pr_cosine(fp, indent, "efield-z", &(ir->ex[ZZ2]), bMDPformat);
1075 pr_cosine(fp, indent, "efield-zt", &(ir->et[ZZ2]), bMDPformat);
1076 PS("eSwapCoords", ESWAPTYPE(ir->eSwapCoords)((((ir->eSwapCoords) < 0) || ((ir->eSwapCoords) >=
(eSwapTypesNR))) ? "UNDEFINED" : (eSwapTypes_names)[ir->eSwapCoords
]));
1077 if (ir->eSwapCoords != eswapNO)
1078 {
1079 pr_swap(fp, indent, ir->swap);
1080 }
1081 PS("bQMMM", EBOOL(ir->bQMMM)((((ir->bQMMM) < 0) || ((ir->bQMMM) >= (2))) ? "UNDEFINED"
: (bool_names)[ir->bQMMM]));
1082 PI("QMconstraints", ir->QMconstraints);
1083 PI("QMMMscheme", ir->QMMMscheme);
1084 PR("scalefactor", ir->scalefactor);
1085 pr_qm_opts(fp, indent, "qm-opts", &(ir->opts));
1086 }
1087}
1088#undef PS
1089#undef PR
1090#undef PI
1091
1092static void pr_harm(FILE *fp, t_iparams *iparams, const char *r, const char *kr)
1093{
1094 fprintf(fp, "%sA=%12.5e, %sA=%12.5e, %sB=%12.5e, %sB=%12.5e\n",
1095 r, iparams->harmonic.rA, kr, iparams->harmonic.krA,
1096 r, iparams->harmonic.rB, kr, iparams->harmonic.krB);
1097}
1098
1099void pr_iparams(FILE *fp, t_functype ftype, t_iparams *iparams)
1100{
1101 int i;
1102 real VA[4], VB[4], *rbcA, *rbcB;
1103
1104 switch (ftype)
1105 {
1106 case F_ANGLES:
1107 case F_G96ANGLES:
1108 pr_harm(fp, iparams, "th", "ct");
1109 break;
1110 case F_CROSS_BOND_BONDS:
1111 fprintf(fp, "r1e=%15.8e, r2e=%15.8e, krr=%15.8e\n",
1112 iparams->cross_bb.r1e, iparams->cross_bb.r2e,
1113 iparams->cross_bb.krr);
1114 break;
1115 case F_CROSS_BOND_ANGLES:
1116 fprintf(fp, "r1e=%15.8e, r1e=%15.8e, r3e=%15.8e, krt=%15.8e\n",
1117 iparams->cross_ba.r1e, iparams->cross_ba.r2e,
1118 iparams->cross_ba.r3e, iparams->cross_ba.krt);
1119 break;
1120 case F_LINEAR_ANGLES:
1121 fprintf(fp, "klinA=%15.8e, aA=%15.8e, klinB=%15.8e, aB=%15.8e\n",
1122 iparams->linangle.klinA, iparams->linangle.aA,
1123 iparams->linangle.klinB, iparams->linangle.aB);
1124 break;
1125 case F_UREY_BRADLEY:
1126 fprintf(fp, "thetaA=%15.8e, kthetaA=%15.8e, r13A=%15.8e, kUBA=%15.8e, thetaB=%15.8e, kthetaB=%15.8e, r13B=%15.8e, kUBB=%15.8e\n", iparams->u_b.thetaA, iparams->u_b.kthetaA, iparams->u_b.r13A, iparams->u_b.kUBA, iparams->u_b.thetaB, iparams->u_b.kthetaB, iparams->u_b.r13B, iparams->u_b.kUBB);
1127 break;
1128 case F_QUARTIC_ANGLES:
1129 fprintf(fp, "theta=%15.8e", iparams->qangle.theta);
1130 for (i = 0; i < 5; i++)
1131 {
1132 fprintf(fp, ", c%c=%15.8e", '0'+i, iparams->qangle.c[i]);
1133 }
1134 fprintf(fp, "\n");
1135 break;
1136 case F_BHAM:
1137 fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
1138 iparams->bham.a, iparams->bham.b, iparams->bham.c);
1139 break;
1140 case F_BONDS:
1141 case F_G96BONDS:
1142 case F_HARMONIC:
1143 pr_harm(fp, iparams, "b0", "cb");
1144 break;
1145 case F_IDIHS:
1146 pr_harm(fp, iparams, "xi", "cx");
1147 break;
1148 case F_MORSE:
1149 fprintf(fp, "b0A=%15.8e, cbA=%15.8e, betaA=%15.8e, b0B=%15.8e, cbB=%15.8e, betaB=%15.8e\n",
1150 iparams->morse.b0A, iparams->morse.cbA, iparams->morse.betaA,
1151 iparams->morse.b0B, iparams->morse.cbB, iparams->morse.betaB);
1152 break;
1153 case F_CUBICBONDS:
1154 fprintf(fp, "b0=%15.8e, kb=%15.8e, kcub=%15.8e\n",
1155 iparams->cubic.b0, iparams->cubic.kb, iparams->cubic.kcub);
1156 break;
1157 case F_CONNBONDS:
1158 fprintf(fp, "\n");
1159 break;
1160 case F_FENEBONDS:
1161 fprintf(fp, "bm=%15.8e, kb=%15.8e\n", iparams->fene.bm, iparams->fene.kb);
1162 break;
1163 case F_RESTRBONDS:
1164 fprintf(fp, "lowA=%15.8e, up1A=%15.8e, up2A=%15.8e, kA=%15.8e, lowB=%15.8e, up1B=%15.8e, up2B=%15.8e, kB=%15.8e,\n",
1165 iparams->restraint.lowA, iparams->restraint.up1A,
1166 iparams->restraint.up2A, iparams->restraint.kA,
1167 iparams->restraint.lowB, iparams->restraint.up1B,
1168 iparams->restraint.up2B, iparams->restraint.kB);
1169 break;
1170 case F_TABBONDS:
1171 case F_TABBONDSNC:
1172 case F_TABANGLES:
1173 case F_TABDIHS:
1174 fprintf(fp, "tab=%d, kA=%15.8e, kB=%15.8e\n",
1175 iparams->tab.table, iparams->tab.kA, iparams->tab.kB);
1176 break;
1177 case F_POLARIZATION:
1178 fprintf(fp, "alpha=%15.8e\n", iparams->polarize.alpha);
1179 break;
1180 case F_ANHARM_POL:
1181 fprintf(fp, "alpha=%15.8e drcut=%15.8e khyp=%15.8e\n",
1182 iparams->anharm_polarize.alpha,
1183 iparams->anharm_polarize.drcut,
1184 iparams->anharm_polarize.khyp);
1185 break;
1186 case F_THOLE_POL:
1187 fprintf(fp, "a=%15.8e, alpha1=%15.8e, alpha2=%15.8e, rfac=%15.8e\n",
1188 iparams->thole.a, iparams->thole.alpha1, iparams->thole.alpha2,
1189 iparams->thole.rfac);
1190 break;
1191 case F_WATER_POL:
1192 fprintf(fp, "al_x=%15.8e, al_y=%15.8e, al_z=%15.8e, rOH=%9.6f, rHH=%9.6f, rOD=%9.6f\n",
1193 iparams->wpol.al_x, iparams->wpol.al_y, iparams->wpol.al_z,
1194 iparams->wpol.rOH, iparams->wpol.rHH, iparams->wpol.rOD);
1195 break;
1196 case F_LJ:
1197 fprintf(fp, "c6=%15.8e, c12=%15.8e\n", iparams->lj.c6, iparams->lj.c12);
1198 break;
1199 case F_LJ14:
1200 fprintf(fp, "c6A=%15.8e, c12A=%15.8e, c6B=%15.8e, c12B=%15.8e\n",
1201 iparams->lj14.c6A, iparams->lj14.c12A,
1202 iparams->lj14.c6B, iparams->lj14.c12B);
1203 break;
1204 case F_LJC14_Q:
1205 fprintf(fp, "fqq=%15.8e, qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
1206 iparams->ljc14.fqq,
1207 iparams->ljc14.qi, iparams->ljc14.qj,
1208 iparams->ljc14.c6, iparams->ljc14.c12);
1209 break;
1210 case F_LJC_PAIRS_NB:
1211 fprintf(fp, "qi=%15.8e, qj=%15.8e, c6=%15.8e, c12=%15.8e\n",
1212 iparams->ljcnb.qi, iparams->ljcnb.qj,
1213 iparams->ljcnb.c6, iparams->ljcnb.c12);
1214 break;
1215 case F_PDIHS:
1216 case F_PIDIHS:
1217 case F_ANGRES:
1218 case F_ANGRESZ:
1219 fprintf(fp, "phiA=%15.8e, cpA=%15.8e, phiB=%15.8e, cpB=%15.8e, mult=%d\n",
1220 iparams->pdihs.phiA, iparams->pdihs.cpA,
1221 iparams->pdihs.phiB, iparams->pdihs.cpB,
1222 iparams->pdihs.mult);
1223 break;
1224 case F_DISRES:
1225 fprintf(fp, "label=%4d, type=%1d, low=%15.8e, up1=%15.8e, up2=%15.8e, fac=%15.8e)\n",
1226 iparams->disres.label, iparams->disres.type,
1227 iparams->disres.low, iparams->disres.up1,
1228 iparams->disres.up2, iparams->disres.kfac);
1229 break;
1230 case F_ORIRES:
1231 fprintf(fp, "ex=%4d, label=%d, power=%4d, c=%15.8e, obs=%15.8e, kfac=%15.8e)\n",
1232 iparams->orires.ex, iparams->orires.label, iparams->orires.power,
1233 iparams->orires.c, iparams->orires.obs, iparams->orires.kfac);
1234 break;
1235 case F_DIHRES:
1236 fprintf(fp, "phiA=%15.8e, dphiA=%15.8e, kfacA=%15.8e, phiB=%15.8e, dphiB=%15.8e, kfacB=%15.8e\n",
1237 iparams->dihres.phiA, iparams->dihres.dphiA, iparams->dihres.kfacA,
1238 iparams->dihres.phiB, iparams->dihres.dphiB, iparams->dihres.kfacB);
1239 break;
1240 case F_POSRES:
1241 fprintf(fp, "pos0A=(%15.8e,%15.8e,%15.8e), fcA=(%15.8e,%15.8e,%15.8e), pos0B=(%15.8e,%15.8e,%15.8e), fcB=(%15.8e,%15.8e,%15.8e)\n",
1242 iparams->posres.pos0A[XX0], iparams->posres.pos0A[YY1],
1243 iparams->posres.pos0A[ZZ2], iparams->posres.fcA[XX0],
1244 iparams->posres.fcA[YY1], iparams->posres.fcA[ZZ2],
1245 iparams->posres.pos0B[XX0], iparams->posres.pos0B[YY1],
1246 iparams->posres.pos0B[ZZ2], iparams->posres.fcB[XX0],
1247 iparams->posres.fcB[YY1], iparams->posres.fcB[ZZ2]);
1248 break;
1249 case F_FBPOSRES:
1250 fprintf(fp, "pos0=(%15.8e,%15.8e,%15.8e), geometry=%d, r=%15.8e, k=%15.8e\n",
1251 iparams->fbposres.pos0[XX0], iparams->fbposres.pos0[YY1],
1252 iparams->fbposres.pos0[ZZ2], iparams->fbposres.geom,
1253 iparams->fbposres.r, iparams->fbposres.k);
1254 break;
1255 case F_RBDIHS:
1256 for (i = 0; i < NR_RBDIHS6; i++)
1257 {
1258 fprintf(fp, "%srbcA[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcA[i]);
1259 }
1260 fprintf(fp, "\n");
1261 for (i = 0; i < NR_RBDIHS6; i++)
1262 {
1263 fprintf(fp, "%srbcB[%d]=%15.8e", i == 0 ? "" : ", ", i, iparams->rbdihs.rbcB[i]);
1264 }
1265 fprintf(fp, "\n");
1266 break;
1267 case F_FOURDIHS:
1268 /* Use the OPLS -> Ryckaert-Bellemans formula backwards to get the
1269 * OPLS potential constants back.
1270 */
1271 rbcA = iparams->rbdihs.rbcA;
1272 rbcB = iparams->rbdihs.rbcB;
1273
1274 VA[3] = -0.25*rbcA[4];
1275 VA[2] = -0.5*rbcA[3];
1276 VA[1] = 4.0*VA[3]-rbcA[2];
1277 VA[0] = 3.0*VA[2]-2.0*rbcA[1];
1278
1279 VB[3] = -0.25*rbcB[4];
1280 VB[2] = -0.5*rbcB[3];
1281 VB[1] = 4.0*VB[3]-rbcB[2];
1282 VB[0] = 3.0*VB[2]-2.0*rbcB[1];
1283
1284 for (i = 0; i < NR_FOURDIHS4; i++)
1285 {
1286 fprintf(fp, "%sFourA[%d]=%15.8e", i == 0 ? "" : ", ", i, VA[i]);
1287 }
1288 fprintf(fp, "\n");
1289 for (i = 0; i < NR_FOURDIHS4; i++)
1290 {
1291 fprintf(fp, "%sFourB[%d]=%15.8e", i == 0 ? "" : ", ", i, VB[i]);
1292 }
1293 fprintf(fp, "\n");
1294 break;
1295
1296 case F_CONSTR:
1297 case F_CONSTRNC:
1298 fprintf(fp, "dA=%15.8e, dB=%15.8e\n", iparams->constr.dA, iparams->constr.dB);
1299 break;
1300 case F_SETTLE:
1301 fprintf(fp, "doh=%15.8e, dhh=%15.8e\n", iparams->settle.doh,
1302 iparams->settle.dhh);
1303 break;
1304 case F_VSITE2:
1305 fprintf(fp, "a=%15.8e\n", iparams->vsite.a);
1306 break;
1307 case F_VSITE3:
1308 case F_VSITE3FD:
1309 case F_VSITE3FAD:
1310 fprintf(fp, "a=%15.8e, b=%15.8e\n", iparams->vsite.a, iparams->vsite.b);
1311 break;
1312 case F_VSITE3OUT:
1313 case F_VSITE4FD:
1314 case F_VSITE4FDN:
1315 fprintf(fp, "a=%15.8e, b=%15.8e, c=%15.8e\n",
1316 iparams->vsite.a, iparams->vsite.b, iparams->vsite.c);
1317 break;
1318 case F_VSITEN:
1319 fprintf(fp, "n=%2d, a=%15.8e\n", iparams->vsiten.n, iparams->vsiten.a);
1320 break;
1321 case F_GB12:
1322 case F_GB13:
1323 case F_GB14:
1324 fprintf(fp, "sar=%15.8e, st=%15.8e, pi=%15.8e, gbr=%15.8e, bmlt=%15.8e\n", iparams->gb.sar, iparams->gb.st, iparams->gb.pi, iparams->gb.gbr, iparams->gb.bmlt);
1325 break;
1326 case F_CMAP:
1327 fprintf(fp, "cmapA=%1d, cmapB=%1d\n", iparams->cmap.cmapA, iparams->cmap.cmapB);
1328 break;
1329 case F_RESTRANGLES:
1330 pr_harm(fp, iparams, "ktheta", "costheta0");
1331 break;
1332 case F_RESTRDIHS:
1333 fprintf(fp, "phiA=%15.8e, cpA=%15.8e",
1334 iparams->pdihs.phiA, iparams->pdihs.cpA);
1335 break;
1336 case F_CBTDIHS:
1337 fprintf(fp, "kphi=%15.8e", iparams->cbtdihs.cbtcA[0]);
1338 for (i = 1; i < NR_CBTDIHS6; i++)
1339 {
1340 fprintf(fp, ", cbtcA[%d]=%15.8e", i-1, iparams->cbtdihs.cbtcA[i]);
1341 }
1342 fprintf(fp, "\n");
1343 break;
1344 default:
1345 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/txtdump.c"
, 1345, "unknown function type %d (%s) in %s line %d",
1346 ftype, interaction_function[ftype].name, __FILE__"/home/alexxy/Develop/gromacs/src/gromacs/gmxlib/txtdump.c", __LINE__1346);
1347 }
1348}
1349
1350void pr_ilist(FILE *fp, int indent, const char *title,
1351 t_functype *functype, t_ilist *ilist, gmx_bool bShowNumbers)
1352{
1353 int i, j, k, type, ftype;
1354 t_iatom *iatoms;
1355
1356 if (available(fp, ilist, indent, title) && ilist->nr > 0)
1357 {
1358 indent = pr_title(fp, indent, title);
1359 (void) pr_indent(fp, indent);
1360 fprintf(fp, "nr: %d\n", ilist->nr);
1361 if (ilist->nr > 0)
1362 {
1363 (void) pr_indent(fp, indent);
1364 fprintf(fp, "iatoms:\n");
1365 iatoms = ilist->iatoms;
1366 for (i = j = 0; i < ilist->nr; )
1367 {
1368#ifndef DEBUG
1369 (void) pr_indent(fp, indent+INDENT3);
1370 type = *(iatoms++);
1371 ftype = functype[type];
1372 (void) fprintf(fp, "%d type=%d (%s)",
1373 bShowNumbers ? j : -1, bShowNumbers ? type : -1,
1374 interaction_function[ftype].name);
1375 j++;
1376 for (k = 0; k < interaction_function[ftype].nratoms; k++)
1377 {
1378 (void) fprintf(fp, " %u", *(iatoms++));
1379 }
1380 (void) fprintf(fp, "\n");
1381 i += 1+interaction_function[ftype].nratoms;
1382#else
1383 fprintf(fp, "%5d%5d\n", i, iatoms[i]);
1384 i++;
1385#endif
1386 }
1387 }
1388 }
1389}
1390
1391static void pr_cmap(FILE *fp, int indent, const char *title,
1392 gmx_cmap_t *cmap_grid, gmx_bool bShowNumbers)
1393{
1394 int i, j, nelem;
1395 real dx, idx;
1396
1397 dx = 360.0 / cmap_grid->grid_spacing;
1398 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1399
1400 if (available(fp, cmap_grid, indent, title))
1401 {
1402 fprintf(fp, "%s\n", title);
1403
1404 for (i = 0; i < cmap_grid->ngrid; i++)
1405 {
1406 idx = -180.0;
1407 fprintf(fp, "%8s %8s %8s %8s\n", "V", "dVdx", "dVdy", "d2dV");
1408
1409 fprintf(fp, "grid[%3d]={\n", bShowNumbers ? i : -1);
1410
1411 for (j = 0; j < nelem; j++)
1412 {
1413 if ( (j%cmap_grid->grid_spacing) == 0)
1414 {
1415 fprintf(fp, "%8.1f\n", idx);
1416 idx += dx;
1417 }
1418
1419 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4]);
1420 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+1]);
1421 fprintf(fp, "%8.3f ", cmap_grid->cmapdata[i].cmap[j*4+2]);
1422 fprintf(fp, "%8.3f\n", cmap_grid->cmapdata[i].cmap[j*4+3]);
1423 }
1424 fprintf(fp, "\n");
1425 }
1426 }
1427
1428}
1429
1430void pr_ffparams(FILE *fp, int indent, const char *title,
1431 gmx_ffparams_t *ffparams,
1432 gmx_bool bShowNumbers)
1433{
1434 int i, j;
1435
1436 indent = pr_title(fp, indent, title);
1437 (void) pr_indent(fp, indent);
1438 (void) fprintf(fp, "atnr=%d\n", ffparams->atnr);
1439 (void) pr_indent(fp, indent);
1440 (void) fprintf(fp, "ntypes=%d\n", ffparams->ntypes);
1441 for (i = 0; i < ffparams->ntypes; i++)
1442 {
1443 (void) pr_indent(fp, indent+INDENT3);
1444 (void) fprintf(fp, "functype[%d]=%s, ",
1445 bShowNumbers ? i : -1,
1446 interaction_function[ffparams->functype[i]].name);
1447 pr_iparams(fp, ffparams->functype[i], &ffparams->iparams[i]);
1448 }
1449 (void) pr_double(fp, indent, "reppow", ffparams->reppow);
1450 (void) pr_real(fp, indent, "fudgeQQ", ffparams->fudgeQQ);
1451 pr_cmap(fp, indent, "cmap", &ffparams->cmap_grid, bShowNumbers);
1452}
1453
1454void pr_idef(FILE *fp, int indent, const char *title, t_idef *idef, gmx_bool bShowNumbers)
1455{
1456 int i, j;
1457
1458 if (available(fp, idef, indent, title))
1459 {
1460 indent = pr_title(fp, indent, title);
1461 (void) pr_indent(fp, indent);
1462 (void) fprintf(fp, "atnr=%d\n", idef->atnr);
1463 (void) pr_indent(fp, indent);
1464 (void) fprintf(fp, "ntypes=%d\n", idef->ntypes);
1465 for (i = 0; i < idef->ntypes; i++)
1466 {
1467 (void) pr_indent(fp, indent+INDENT3);
1468 (void) fprintf(fp, "functype[%d]=%s, ",
1469 bShowNumbers ? i : -1,
1470 interaction_function[idef->functype[i]].name);
1471 pr_iparams(fp, idef->functype[i], &idef->iparams[i]);
1472 }
1473 (void) pr_real(fp, indent, "fudgeQQ", idef->fudgeQQ);
1474
1475 for (j = 0; (j < F_NRE); j++)
1476 {
1477 pr_ilist(fp, indent, interaction_function[j].longname,
1478 idef->functype, &idef->il[j], bShowNumbers);
1479 }
1480 }
1481}
1482
1483static int pr_block_title(FILE *fp, int indent, const char *title, t_block *block)
1484{
1485 int i;
1486
1487 if (available(fp, block, indent, title))
1488 {
1489 indent = pr_title(fp, indent, title);
1490 (void) pr_indent(fp, indent);
1491 (void) fprintf(fp, "nr=%d\n", block->nr);
1492 }
1493 return indent;
1494}
1495
1496static int pr_blocka_title(FILE *fp, int indent, const char *title, t_blocka *block)
1497{
1498 int i;
1499
1500 if (available(fp, block, indent, title))
1501 {
1502 indent = pr_title(fp, indent, title);
1503 (void) pr_indent(fp, indent);
1504 (void) fprintf(fp, "nr=%d\n", block->nr);
1505 (void) pr_indent(fp, indent);
1506 (void) fprintf(fp, "nra=%d\n", block->nra);
1507 }
1508 return indent;
1509}
1510
1511static void low_pr_blocka(FILE *fp, int indent, const char *title, t_blocka *block, gmx_bool bShowNumbers)
1512{
1513 int i;
1514
1515 if (available(fp, block, indent, title))
1516 {
1517 indent = pr_blocka_title(fp, indent, title, block);
1518 for (i = 0; i <= block->nr; i++)
1519 {
1520 (void) pr_indent(fp, indent+INDENT3);
1521 (void) fprintf(fp, "%s->index[%d]=%u\n",
1522 title, bShowNumbers ? i : -1, block->index[i]);
1523 }
1524 for (i = 0; i < block->nra; i++)
1525 {
1526 (void) pr_indent(fp, indent+INDENT3);
1527 (void) fprintf(fp, "%s->a[%d]=%u\n",
1528 title, bShowNumbers ? i : -1, block->a[i]);
1529 }
1530 }
1531}
1532
1533void pr_block(FILE *fp, int indent, const char *title, t_block *block, gmx_bool bShowNumbers)
1534{
1535 int i, j, ok, size, start, end;
1536
1537 if (available(fp, block, indent, title))
1538 {
1539 indent = pr_block_title(fp, indent, title, block);
1540 start = 0;
1541 end = start;
1542 if ((ok = (block->index[start] == 0)) == 0)
1543 {
1544 (void) fprintf(fp, "block->index[%d] should be 0\n", start);
1545 }
1546 else
1547 {
1548 for (i = 0; i < block->nr; i++)
1549 {
1550 end = block->index[i+1];
1551 size = pr_indent(fp, indent);
1552 if (end <= start)
1553 {
1554 size += fprintf(fp, "%s[%d]={}\n", title, i);
1555 }
1556 else
1557 {
1558 size += fprintf(fp, "%s[%d]={%d..%d}\n",
Value stored to 'size' is never read
1559 title, bShowNumbers ? i : -1,
1560 bShowNumbers ? start : -1, bShowNumbers ? end-1 : -1);
1561 }
1562 start = end;
1563 }
1564 }
1565 }
1566}
1567
1568void pr_blocka(FILE *fp, int indent, const char *title, t_blocka *block, gmx_bool bShowNumbers)
1569{
1570 int i, j, ok, size, start, end;
1571
1572 if (available(fp, block, indent, title))
1573 {
1574 indent = pr_blocka_title(fp, indent, title, block);
1575 start = 0;
1576 end = start;
1577 if ((ok = (block->index[start] == 0)) == 0)
1578 {
1579 (void) fprintf(fp, "block->index[%d] should be 0\n", start);
1580 }
1581 else
1582 {
1583 for (i = 0; i < block->nr; i++)
1584 {
1585 end = block->index[i+1];
1586 size = pr_indent(fp, indent);
1587 if (end <= start)
1588 {
1589 size += fprintf(fp, "%s[%d]={", title, i);
1590 }
1591 else
1592 {
1593 size += fprintf(fp, "%s[%d][%d..%d]={",
1594 title, bShowNumbers ? i : -1,
1595 bShowNumbers ? start : -1, bShowNumbers ? end-1 : -1);
1596 }
1597 for (j = start; j < end; j++)
1598 {
1599 if (j > start)
1600 {
1601 size += fprintf(fp, ", ");
1602 }
1603 if ((size) > (USE_WIDTH((80)-(10))))
1604 {
1605 (void) fprintf(fp, "\n");
1606 size = pr_indent(fp, indent+INDENT3);
1607 }
1608 size += fprintf(fp, "%u", block->a[j]);
1609 }
1610 (void) fprintf(fp, "}\n");
1611 start = end;
1612 }
1613 }
1614 if ((end != block->nra) || (!ok))
1615 {
1616 (void) pr_indent(fp, indent);
1617 (void) fprintf(fp, "tables inconsistent, dumping complete tables:\n");
1618 low_pr_blocka(fp, indent, title, block, bShowNumbers);
1619 }
1620 }
1621}
1622
1623static void pr_strings(FILE *fp, int indent, const char *title, char ***nm, int n, gmx_bool bShowNumbers)
1624{
1625 int i;
1626
1627 if (available(fp, nm, indent, title))
1628 {
1629 indent = pr_title_n(fp, indent, title, n);
1630 for (i = 0; i < n; i++)
1631 {
1632 (void) pr_indent(fp, indent);
1633 (void) fprintf(fp, "%s[%d]={name=\"%s\"}\n",
1634 title, bShowNumbers ? i : -1, *(nm[i]));
1635 }
1636 }
1637}
1638
1639static void pr_strings2(FILE *fp, int indent, const char *title,
1640 char ***nm, char ***nmB, int n, gmx_bool bShowNumbers)
1641{
1642 int i;
1643
1644 if (available(fp, nm, indent, title))
1645 {
1646 indent = pr_title_n(fp, indent, title, n);
1647 for (i = 0; i < n; i++)
1648 {
1649 (void) pr_indent(fp, indent);
1650 (void) fprintf(fp, "%s[%d]={name=\"%s\",nameB=\"%s\"}\n",
1651 title, bShowNumbers ? i : -1, *(nm[i]), *(nmB[i]));
1652 }
1653 }
1654}
1655
1656static void pr_resinfo(FILE *fp, int indent, const char *title, t_resinfo *resinfo, int n, gmx_bool bShowNumbers)
1657{
1658 int i;
1659
1660 if (available(fp, resinfo, indent, title))
1661 {
1662 indent = pr_title_n(fp, indent, title, n);
1663 for (i = 0; i < n; i++)
1664 {
1665 (void) pr_indent(fp, indent);
1666 (void) fprintf(fp, "%s[%d]={name=\"%s\", nr=%d, ic='%c'}\n",
1667 title, bShowNumbers ? i : -1,
1668 *(resinfo[i].name), resinfo[i].nr,
1669 (resinfo[i].ic == '\0') ? ' ' : resinfo[i].ic);
1670 }
1671 }
1672}
1673
1674static void pr_atom(FILE *fp, int indent, const char *title, t_atom *atom, int n)
1675{
1676 int i, j;
1677
1678 if (available(fp, atom, indent, title))
1679 {
1680 indent = pr_title_n(fp, indent, title, n);
1681 for (i = 0; i < n; i++)
1682 {
1683 (void) pr_indent(fp, indent);
1684 fprintf(fp, "%s[%6d]={type=%3d, typeB=%3d, ptype=%8s, m=%12.5e, "
1685 "q=%12.5e, mB=%12.5e, qB=%12.5e, resind=%5d, atomnumber=%3d}\n",
1686 title, i, atom[i].type, atom[i].typeB, ptype_str[atom[i].ptype],
1687 atom[i].m, atom[i].q, atom[i].mB, atom[i].qB,
1688 atom[i].resind, atom[i].atomnumber);
1689 }
1690 }
1691}
1692
1693static void pr_grps(FILE *fp, const char *title, t_grps grps[], char **grpname[])
1694{
1695 int i, j;
1696
1697 for (i = 0; (i < egcNR); i++)
1698 {
1699 fprintf(fp, "%s[%-12s] nr=%d, name=[", title, gtypes[i], grps[i].nr);
1700 for (j = 0; (j < grps[i].nr); j++)
1701 {
1702 fprintf(fp, " %s", *(grpname[grps[i].nm_ind[j]]));
1703 }
1704 fprintf(fp, "]\n");
1705 }
1706}
1707
1708static void pr_groups(FILE *fp, int indent,
1709 gmx_groups_t *groups,
1710 gmx_bool bShowNumbers)
1711{
1712 int grpnr[egcNR];
1713 int nat_max, i, g;
1714
1715 pr_grps(fp, "grp", groups->grps, groups->grpname);
1716 pr_strings(fp, indent, "grpname", groups->grpname, groups->ngrpname, bShowNumbers);
1717
1718 (void) pr_indent(fp, indent);
1719 fprintf(fp, "groups ");
1720 for (g = 0; g < egcNR; g++)
1721 {
1722 printf(" %5.5s", gtypes[g]);
1723 }
1724 printf("\n");
1725
1726 (void) pr_indent(fp, indent);
1727 fprintf(fp, "allocated ");
1728 nat_max = 0;
1729 for (g = 0; g < egcNR; g++)
1730 {
1731 printf(" %5d", groups->ngrpnr[g]);
1732 nat_max = max(nat_max, groups->ngrpnr[g])(((nat_max) > (groups->ngrpnr[g])) ? (nat_max) : (groups
->ngrpnr[g]) );
1733 }
1734 printf("\n");
1735
1736 if (nat_max == 0)
1737 {
1738 (void) pr_indent(fp, indent);
1739 fprintf(fp, "groupnr[%5s] =", "*");
1740 for (g = 0; g < egcNR; g++)
1741 {
1742 fprintf(fp, " %3d ", 0);
1743 }
1744 fprintf(fp, "\n");
1745 }
1746 else
1747 {
1748 for (i = 0; i < nat_max; i++)
1749 {
1750 (void) pr_indent(fp, indent);
1751 fprintf(fp, "groupnr[%5d] =", i);
1752 for (g = 0; g < egcNR; g++)
1753 {
1754 fprintf(fp, " %3d ",
1755 groups->grpnr[g] ? groups->grpnr[g][i] : 0);
1756 }
1757 fprintf(fp, "\n");
1758 }
1759 }
1760}
1761
1762void pr_atoms(FILE *fp, int indent, const char *title, t_atoms *atoms,
1763 gmx_bool bShownumbers)
1764{
1765 if (available(fp, atoms, indent, title))
1766 {
1767 indent = pr_title(fp, indent, title);
1768 pr_atom(fp, indent, "atom", atoms->atom, atoms->nr);
1769 pr_strings(fp, indent, "atom", atoms->atomname, atoms->nr, bShownumbers);
1770 pr_strings2(fp, indent, "type", atoms->atomtype, atoms->atomtypeB, atoms->nr, bShownumbers);
1771 pr_resinfo(fp, indent, "residue", atoms->resinfo, atoms->nres, bShownumbers);
1772 }
1773}
1774
1775
1776void pr_atomtypes(FILE *fp, int indent, const char *title, t_atomtypes *atomtypes,
1777 gmx_bool bShowNumbers)
1778{
1779 int i;
1780 if (available(fp, atomtypes, indent, title))
1781 {
1782 indent = pr_title(fp, indent, title);
1783 for (i = 0; i < atomtypes->nr; i++)
1784 {
1785 pr_indent(fp, indent);
1786 fprintf(fp,
1787 "atomtype[%3d]={radius=%12.5e, volume=%12.5e, gb_radius=%12.5e, surftens=%12.5e, atomnumber=%4d, S_hct=%12.5e)}\n",
1788 bShowNumbers ? i : -1, atomtypes->radius[i], atomtypes->vol[i],
1789 atomtypes->gb_radius[i],
1790 atomtypes->surftens[i], atomtypes->atomnumber[i], atomtypes->S_hct[i]);
1791 }
1792 }
1793}
1794
1795static void pr_moltype(FILE *fp, int indent, const char *title,
1796 gmx_moltype_t *molt, int n,
1797 gmx_ffparams_t *ffparams,
1798 gmx_bool bShowNumbers)
1799{
1800 int j;
1801
1802 indent = pr_title_n(fp, indent, title, n);
1803 (void) pr_indent(fp, indent);
1804 (void) fprintf(fp, "name=\"%s\"\n", *(molt->name));
1805 pr_atoms(fp, indent, "atoms", &(molt->atoms), bShowNumbers);
1806 pr_block(fp, indent, "cgs", &molt->cgs, bShowNumbers);
1807 pr_blocka(fp, indent, "excls", &molt->excls, bShowNumbers);
1808 for (j = 0; (j < F_NRE); j++)
1809 {
1810 pr_ilist(fp, indent, interaction_function[j].longname,
1811 ffparams->functype, &molt->ilist[j], bShowNumbers);
1812 }
1813}
1814
1815static void pr_molblock(FILE *fp, int indent, const char *title,
1816 gmx_molblock_t *molb, int n,
1817 gmx_moltype_t *molt)
1818{
1819 indent = pr_title_n(fp, indent, title, n);
1820 (void) pr_indent(fp, indent);
1821 (void) fprintf(fp, "%-20s = %d \"%s\"\n",
1822 "moltype", molb->type, *(molt[molb->type].name));
1823 pr_int(fp, indent, "#molecules", molb->nmol);
1824 pr_int(fp, indent, "#atoms_mol", molb->natoms_mol);
1825 pr_int(fp, indent, "#posres_xA", molb->nposres_xA);
1826 if (molb->nposres_xA > 0)
1827 {
1828 pr_rvecs(fp, indent, "posres_xA", molb->posres_xA, molb->nposres_xA);
1829 }
1830 pr_int(fp, indent, "#posres_xB", molb->nposres_xB);
1831 if (molb->nposres_xB > 0)
1832 {
1833 pr_rvecs(fp, indent, "posres_xB", molb->posres_xB, molb->nposres_xB);
1834 }
1835}
1836
1837void pr_mtop(FILE *fp, int indent, const char *title, gmx_mtop_t *mtop,
1838 gmx_bool bShowNumbers)
1839{
1840 int mt, mb;
1841
1842 if (available(fp, mtop, indent, title))
1843 {
1844 indent = pr_title(fp, indent, title);
1845 (void) pr_indent(fp, indent);
1846 (void) fprintf(fp, "name=\"%s\"\n", *(mtop->name));
1847 pr_int(fp, indent, "#atoms", mtop->natoms);
1848 pr_int(fp, indent, "#molblock", mtop->nmolblock);
1849 for (mb = 0; mb < mtop->nmolblock; mb++)
1850 {
1851 pr_molblock(fp, indent, "molblock", &mtop->molblock[mb], mb, mtop->moltype);
1852 }
1853 pr_ffparams(fp, indent, "ffparams", &(mtop->ffparams), bShowNumbers);
1854 pr_atomtypes(fp, indent, "atomtypes", &(mtop->atomtypes), bShowNumbers);
1855 for (mt = 0; mt < mtop->nmoltype; mt++)
1856 {
1857 pr_moltype(fp, indent, "moltype", &mtop->moltype[mt], mt,
1858 &mtop->ffparams, bShowNumbers);
1859 }
1860 pr_groups(fp, indent, &mtop->groups, bShowNumbers);
1861 }
1862}
1863
1864void pr_top(FILE *fp, int indent, const char *title, t_topology *top, gmx_bool bShowNumbers)
1865{
1866 if (available(fp, top, indent, title))
1867 {
1868 indent = pr_title(fp, indent, title);
1869 (void) pr_indent(fp, indent);
1870 (void) fprintf(fp, "name=\"%s\"\n", *(top->name));
1871 pr_atoms(fp, indent, "atoms", &(top->atoms), bShowNumbers);
1872 pr_atomtypes(fp, indent, "atomtypes", &(top->atomtypes), bShowNumbers);
1873 pr_block(fp, indent, "cgs", &top->cgs, bShowNumbers);
1874 pr_block(fp, indent, "mols", &top->mols, bShowNumbers);
1875 pr_blocka(fp, indent, "excls", &top->excls, bShowNumbers);
1876 pr_idef(fp, indent, "idef", &top->idef, bShowNumbers);
1877 }
1878}
1879
1880void pr_header(FILE *fp, int indent, const char *title, t_tpxheader *sh)
1881{
1882 char buf[22];
1883
1884 if (available(fp, sh, indent, title))
1885 {
1886 indent = pr_title(fp, indent, title);
1887 pr_indent(fp, indent);
1888 fprintf(fp, "bIr = %spresent\n", sh->bIr ? "" : "not ");
1889 pr_indent(fp, indent);
1890 fprintf(fp, "bBox = %spresent\n", sh->bBox ? "" : "not ");
1891 pr_indent(fp, indent);
1892 fprintf(fp, "bTop = %spresent\n", sh->bTop ? "" : "not ");
1893 pr_indent(fp, indent);
1894 fprintf(fp, "bX = %spresent\n", sh->bX ? "" : "not ");
1895 pr_indent(fp, indent);
1896 fprintf(fp, "bV = %spresent\n", sh->bV ? "" : "not ");
1897 pr_indent(fp, indent);
1898 fprintf(fp, "bF = %spresent\n", sh->bF ? "" : "not ");
1899
1900 pr_indent(fp, indent);
1901 fprintf(fp, "natoms = %d\n", sh->natoms);
1902 pr_indent(fp, indent);
1903 fprintf(fp, "lambda = %e\n", sh->lambda);
1904 }
1905}
1906
1907void pr_commrec(FILE *fp, int indent, t_commrec *cr)
1908{
1909 pr_indent(fp, indent);
1910 fprintf(fp, "commrec:\n");
1911 indent += 2;
1912 pr_indent(fp, indent);
1913 fprintf(fp, "nodeid = %d\n", cr->nodeid);
1914 pr_indent(fp, indent);
1915 fprintf(fp, "nnodes = %d\n", cr->nnodes);
1916 pr_indent(fp, indent);
1917 fprintf(fp, "npmenodes = %d\n", cr->npmenodes);
1918 /*
1919 pr_indent(fp,indent);
1920 fprintf(fp,"threadid = %d\n",cr->threadid);
1921 pr_indent(fp,indent);
1922 fprintf(fp,"nthreads = %d\n",cr->nthreads);
1923 */
1924}