Bug Summary

File:gromacs/gmxana/gmx_sham.c
Location:line 1159, column 5
Description:Function call argument is an uninitialized value

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#include <math.h>
42#include <stdlib.h>
43#include <string.h>
44
45#include "gromacs/commandline/pargs.h"
46#include "typedefs.h"
47#include "gromacs/utility/smalloc.h"
48#include "macros.h"
49#include "gromacs/utility/fatalerror.h"
50#include "gromacs/math/vec.h"
51#include "gromacs/utility/futil.h"
52#include "readinp.h"
53#include "txtdump.h"
54#include "gstat.h"
55#include "gromacs/fileio/xvgr.h"
56#include "physics.h"
57#include "gromacs/fileio/pdbio.h"
58#include "gromacs/fileio/matio.h"
59#include "gmx_ana.h"
60
61
62static int index2(int *ibox, int x, int y)
63{
64 return (ibox[1]*x+y);
65}
66
67static int index3(int *ibox, int x, int y, int z)
68{
69 return (ibox[2]*(ibox[1]*x+y)+z);
70}
71
72static gmx_int64_t indexn(int ndim, const int *ibox, const int *nxyz)
73{
74 gmx_int64_t d, dd;
75 int k, kk;
76
77 /* Compute index in 1-D array */
78 d = 0;
79 for (k = 0; (k < ndim); k++)
80 {
81 dd = nxyz[k];
82 for (kk = k+1; (kk < ndim); kk++)
83 {
84 dd = dd*ibox[kk];
85 }
86 d += dd;
87 }
88 return d;
89}
90
91typedef struct {
92 int Nx; /* x grid points in unit cell */
93 int Ny; /* y grid points in unit cell */
94 int Nz; /* z grid points in unit cell */
95 int dmin[3]; /* starting point x,y,z*/
96 int dmax[3]; /* ending point x,y,z */
97 real cell[6]; /* usual cell parameters */
98 real * ed; /* data */
99} XplorMap;
100
101static void lo_write_xplor(XplorMap * map, const char * file)
102{
103 FILE * fp;
104 int z, i, j, n;
105
106 fp = gmx_ffopen(file, "w");
107 /* The REMARKS part is the worst part of the XPLOR format
108 * and may cause problems with some programs
109 */
110 fprintf(fp, "\n 2 !NTITLE\n");
111 fprintf(fp, " REMARKS Energy Landscape from GROMACS\n");
112 fprintf(fp, " REMARKS DATE: 2004-12-21 \n");
113 fprintf(fp, " %7d %7d %7d %7d %7d %7d %7d %7d %7d\n",
114 map->Nx, map->dmin[0], map->dmax[0],
115 map->Ny, map->dmin[1], map->dmax[1],
116 map->Nz, map->dmin[2], map->dmax[2]);
117 fprintf(fp, "%12.5E%12.5E%12.5E%12.5E%12.5E%12.5E\n",
118 map->cell[0], map->cell[1], map->cell[2],
119 map->cell[3], map->cell[4], map->cell[5]);
120 fprintf(fp, "ZYX\n");
121
122 z = map->dmin[2];
123 for (n = 0; n < map->Nz; n++, z++)
124 {
125 fprintf(fp, "%8d\n", z);
126 for (i = 0; i < map->Nx*map->Ny; i += 6)
127 {
128 for (j = 0; j < 6; j++)
129 {
130 if (i+j < map->Nx*map->Ny)
131 {
132 fprintf(fp, "%12.5E", map->ed[n*map->Nx*map->Ny+i+j]);
133 }
134 }
135 fprintf(fp, "\n");
136 }
137 }
138 fprintf(fp, " -9999\n");
139 gmx_ffclose(fp);
140}
141
142static void write_xplor(const char *file, real *data, int *ibox, real dmin[], real dmax[])
143{
144 XplorMap *xm;
145 int i, j, k, n;
146
147 snew(xm, 1)(xm) = save_calloc("xm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 147, (1), sizeof(*(xm)));
148 xm->Nx = ibox[XX0];
149 xm->Ny = ibox[YY1];
150 xm->Nz = ibox[ZZ2];
151 snew(xm->ed, xm->Nx*xm->Ny*xm->Nz)(xm->ed) = save_calloc("xm->ed", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 151, (xm->Nx*xm->Ny*xm->Nz), sizeof(*(xm->ed)));
152 n = 0;
153 for (k = 0; (k < xm->Nz); k++)
154 {
155 for (j = 0; (j < xm->Ny); j++)
156 {
157 for (i = 0; (i < xm->Nx); i++)
158 {
159 xm->ed[n++] = data[index3(ibox, i, j, k)];
160 }
161 }
162 }
163 xm->cell[0] = dmax[XX0]-dmin[XX0];
164 xm->cell[1] = dmax[YY1]-dmin[YY1];
165 xm->cell[2] = dmax[ZZ2]-dmin[ZZ2];
166 xm->cell[3] = xm->cell[4] = xm->cell[5] = 90;
167
168 clear_ivec(xm->dmin);
169 xm->dmax[XX0] = ibox[XX0]-1;
170 xm->dmax[YY1] = ibox[YY1]-1;
171 xm->dmax[ZZ2] = ibox[ZZ2]-1;
172
173 lo_write_xplor(xm, file);
174
175 sfree(xm->ed)save_free("xm->ed", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 175, (xm->ed));
176 sfree(xm)save_free("xm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 176, (xm));
177}
178
179static void normalize_p_e(int len, double *P, int *nbin, real *E, real pmin)
180{
181 int i;
182 double Ptot = 0;
183
184 for (i = 0; (i < len); i++)
185 {
186 Ptot += P[i];
187 if (nbin[i] > 0)
188 {
189 E[i] = E[i]/nbin[i];
190 }
191 }
192 printf("Ptot = %g\n", Ptot);
193 for (i = 0; (i < len); i++)
194 {
195 P[i] = P[i]/Ptot;
196 /* Have to check for pmin after normalizing to prevent "stretching"
197 * the energies.
198 */
199 if (P[i] < pmin)
200 {
201 P[i] = 0;
202 }
203 }
204}
205
206typedef struct {
207 gmx_int64_t index;
208 real ener;
209} t_minimum;
210
211static int comp_minima(const void *a, const void *b)
212{
213 t_minimum *ma = (t_minimum *) a;
214 t_minimum *mb = (t_minimum *) b;
215
216 if (ma->ener < mb->ener)
217 {
218 return -1;
219 }
220 else if (ma->ener > mb->ener)
221 {
222 return 1;
223 }
224 else
225 {
226 return 0;
227 }
228}
229
230static gmx_inlineinline
231void print_minimum(FILE *fp, int num, const t_minimum *min)
232{
233 fprintf(fp,
234 "Minimum %d at index " "%"GMX_PRId64"l" "d" " energy %10.3f\n",
235 num, min->index, min->ener);
236}
237
238static gmx_inlineinline
239void add_minimum(FILE *fp, int num, const t_minimum *min, t_minimum *mm)
240{
241 print_minimum(fp, num, min);
242 mm[num].index = min->index;
243 mm[num].ener = min->ener;
244}
245
246static gmx_inlineinline
247gmx_bool is_local_minimum_from_below(const t_minimum *this_min,
248 int dimension_index,
249 int dimension_min,
250 int neighbour_index,
251 real *W)
252{
253 return ((dimension_index == dimension_min) ||
254 ((dimension_index > dimension_min) &&
255 (this_min->ener < W[neighbour_index])));
256 /* Note over/underflow within W cannot occur. */
257}
258
259static gmx_inlineinline
260gmx_bool is_local_minimum_from_above(const t_minimum *this_min,
261 int dimension_index,
262 int dimension_max,
263 int neighbour_index,
264 real *W)
265{
266 return ((dimension_index == dimension_max) ||
267 ((dimension_index < dimension_max) &&
268 (this_min->ener < W[neighbour_index])));
269 /* Note over/underflow within W cannot occur. */
270}
271
272static void pick_minima(const char *logfile, int *ibox, int ndim, int len, real W[])
273{
274 FILE *fp;
275 int i, j, k, nmin;
276 t_minimum *mm, this_min;
277 int *this_point;
278 int loopmax, loopcounter;
279
280 snew(mm, len)(mm) = save_calloc("mm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 280, (len), sizeof(*(mm)));
281 nmin = 0;
282 fp = gmx_ffopen(logfile, "w");
283 /* Loop over each element in the array of dimenion ndim seeking
284 * minima with respect to every dimension. Specialized loops for
285 * speed with ndim == 2 and ndim == 3. */
286 switch (ndim)
287 {
288 case 0:
289 /* This is probably impossible to reach anyway. */
290 break;
291 case 2:
292 for (i = 0; (i < ibox[0]); i++)
293 {
294 for (j = 0; (j < ibox[1]); j++)
295 {
296 /* Get the index of this point in the flat array */
297 this_min.index = index2(ibox, i, j);
298 this_min.ener = W[this_min.index];
299 if (is_local_minimum_from_below(&this_min, i, 0, index2(ibox, i-1, j ), W) &&
300 is_local_minimum_from_above(&this_min, i, ibox[0]-1, index2(ibox, i+1, j ), W) &&
301 is_local_minimum_from_below(&this_min, j, 0, index2(ibox, i, j-1), W) &&
302 is_local_minimum_from_above(&this_min, j, ibox[1]-1, index2(ibox, i, j+1), W))
303 {
304 add_minimum(fp, nmin, &this_min, mm);
305 nmin++;
306 }
307 }
308 }
309 break;
310 case 3:
311 for (i = 0; (i < ibox[0]); i++)
312 {
313 for (j = 0; (j < ibox[1]); j++)
314 {
315 for (k = 0; (k < ibox[2]); k++)
316 {
317 /* Get the index of this point in the flat array */
318 this_min.index = index3(ibox, i, j, k);
319 this_min.ener = W[this_min.index];
320 if (is_local_minimum_from_below(&this_min, i, 0, index3(ibox, i-1, j, k ), W) &&
321 is_local_minimum_from_above(&this_min, i, ibox[0]-1, index3(ibox, i+1, j, k ), W) &&
322 is_local_minimum_from_below(&this_min, j, 0, index3(ibox, i, j-1, k ), W) &&
323 is_local_minimum_from_above(&this_min, j, ibox[1]-1, index3(ibox, i, j+1, k ), W) &&
324 is_local_minimum_from_below(&this_min, k, 0, index3(ibox, i, j, k-1), W) &&
325 is_local_minimum_from_above(&this_min, k, ibox[2]-1, index3(ibox, i, j, k+1), W))
326 {
327 add_minimum(fp, nmin, &this_min, mm);
328 nmin++;
329 }
330 }
331 }
332 }
333 break;
334 default:
335 /* Note this treats ndim == 1 and ndim > 3 */
336
337 /* Set up an ndim-dimensional vector to loop over the points
338 * on the grid. (0,0,0, ... 0) is an acceptable place to
339 * start. */
340 snew(this_point, ndim)(this_point) = save_calloc("this_point", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 340, (ndim), sizeof(*(this_point)));
341
342 /* Determine the number of points of the ndim-dimensional
343 * grid. */
344 loopmax = ibox[0];
345 for (i = 1; i < ndim; i++)
346 {
347 loopmax *= ibox[i];
348 }
349
350 loopcounter = 0;
351 while (loopmax > loopcounter)
352 {
353 gmx_bool bMin = TRUE1;
354
355 /* Get the index of this_point in the flat array */
356 this_min.index = indexn(ndim, ibox, this_point);
357 this_min.ener = W[this_min.index];
358
359 /* Is this_point a minimum from above and below in each
360 * dimension? */
361 for (i = 0; bMin && (i < ndim); i++)
362 {
363 /* Save the index of this_point within the curent
364 * dimension so we can change that index in the
365 * this_point array for use with indexn(). */
366 int index = this_point[i];
367 this_point[i]--;
368 bMin = bMin &&
369 is_local_minimum_from_below(&this_min, index, 0, indexn(ndim, ibox, this_point), W);
370 this_point[i] += 2;
371 bMin = bMin &&
372 is_local_minimum_from_above(&this_min, index, ibox[i]-1, indexn(ndim, ibox, this_point), W);
373 this_point[i]--;
374 }
375 if (bMin)
376 {
377 add_minimum(fp, nmin, &this_min, mm);
378 nmin++;
379 }
380
381 /* update global loop counter */
382 loopcounter++;
383
384 /* Avoid underflow of this_point[i] */
385 if (loopmax > loopcounter)
386 {
387 /* update this_point non-recursively */
388 i = ndim-1;
389 this_point[i]++;
390 while (ibox[i] == this_point[i])
391 {
392 this_point[i] = 0;
393 i--;
394 /* this_point[i] cannot underflow because
395 * loopmax > loopcounter. */
396 this_point[i]++;
397 }
398 }
399 }
400
401 sfree(this_point)save_free("this_point", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 401, (this_point));
402 break;
403 }
404 qsort(mm, nmin, sizeof(mm[0]), comp_minima);
405 fprintf(fp, "Minima sorted after energy\n");
406 for (i = 0; (i < nmin); i++)
407 {
408 print_minimum(fp, i, &mm[i]);
409 }
410 gmx_ffclose(fp);
411 sfree(mm)save_free("mm", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 411, (mm));
412}
413
414static void do_sham(const char *fn, const char *ndx,
415 const char *xpmP, const char *xpm, const char *xpm2,
416 const char *xpm3, const char *xpm4, const char *pdb,
417 const char *logf,
418 int n, int neig, real **eig,
419 gmx_bool bGE, int nenerT, real **enerT,
420 int nmap, real *mapindex, real **map,
421 real Tref,
422 real pmax, real gmax,
423 real *emin, real *emax, int nlevels, real pmin,
424 const char *mname, int *idim, int *ibox,
425 gmx_bool bXmin, real *xmin, gmx_bool bXmax, real *xmax)
426{
427 FILE *fp;
428 real *min_eig, *max_eig;
429 real *axis_x, *axis_y, *axis_z, *axis = NULL((void*)0);
430 double *P;
431 real **PP, *W, *E, **WW, **EE, *S, **SS, *M, **MM, *bE;
432 rvec xxx;
433 char *buf;
434 double *bfac, efac, bref, Pmax, Wmin, Wmax, Winf, Emin, Emax, Einf, Smin, Smax, Sinf, Mmin, Mmax, Minf;
435 real *delta;
436 int i, j, k, imin, len, index, d, *nbin, *bindex, bi;
437 int *nxyz, maxbox;
438 t_blocka *b;
439 gmx_bool bOutside;
440 unsigned int flags;
441 t_rgb rlo = { 0, 0, 0 };
442 t_rgb rhi = { 1, 1, 1 };
443
444 /* Determine extremes for the eigenvectors */
445 snew(min_eig, neig)(min_eig) = save_calloc("min_eig", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 445, (neig), sizeof(*(min_eig)));
446 snew(max_eig, neig)(max_eig) = save_calloc("max_eig", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 446, (neig), sizeof(*(max_eig)));
447 snew(nxyz, neig)(nxyz) = save_calloc("nxyz", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 447, (neig), sizeof(*(nxyz)));
448 snew(bfac, neig)(bfac) = save_calloc("bfac", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 448, (neig), sizeof(*(bfac)));
449 snew(delta, neig)(delta) = save_calloc("delta", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 449, (neig), sizeof(*(delta)));
450
451 for (i = 0; (i < neig); i++)
452 {
453 /* Check for input constraints */
454 min_eig[i] = max_eig[i] = eig[i][0];
455 for (j = 0; (j < n); j++)
456 {
457 min_eig[i] = min(min_eig[i], eig[i][j])(((min_eig[i]) < (eig[i][j])) ? (min_eig[i]) : (eig[i][j])
);
458 max_eig[i] = max(max_eig[i], eig[i][j])(((max_eig[i]) > (eig[i][j])) ? (max_eig[i]) : (eig[i][j])
);
459 delta[i] = (max_eig[i]-min_eig[i])/(2.0*ibox[i]);
460 }
461 /* Add some extra space, half a bin on each side, unless the
462 * user has set the limits.
463 */
464 if (bXmax)
465 {
466 if (max_eig[i] > xmax[i])
467 {
468 gmx_warning("Your xmax[%d] value %f is smaller than the largest data point %f", i, xmax[i], max_eig[i]);
469 }
470 max_eig[i] = xmax[i];
471 }
472 else
473 {
474 max_eig[i] += delta[i];
475 }
476
477 if (bXmin)
478 {
479 if (min_eig[i] < xmin[i])
480 {
481 gmx_warning("Your xmin[%d] value %f is larger than the smallest data point %f", i, xmin[i], min_eig[i]);
482 }
483 min_eig[i] = xmin[i];
484 }
485 else
486 {
487 min_eig[i] -= delta[i];
488 }
489 bfac[i] = ibox[i]/(max_eig[i]-min_eig[i]);
490 }
491 /* Do the binning */
492 bref = 1/(BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*Tref);
493 snew(bE, n)(bE) = save_calloc("bE", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 493, (n), sizeof(*(bE)));
494 if (bGE || nenerT == 2)
495 {
496 Emin = 1e8;
497 for (j = 0; (j < n); j++)
498 {
499 if (bGE)
500 {
501 bE[j] = bref*enerT[0][j];
502 }
503 else
504 {
505 bE[j] = (bref - 1/(BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*enerT[1][j]))*enerT[0][j];
506 }
507 Emin = min(Emin, bE[j])(((Emin) < (bE[j])) ? (Emin) : (bE[j]) );
508 }
509 }
510 else
511 {
512 Emin = 0;
513 }
514 len = 1;
515 for (i = 0; (i < neig); i++)
516 {
517 len = len*ibox[i];
518 }
519 printf("There are %d bins in the %d-dimensional histogram. Beta-Emin = %g\n",
520 len, neig, Emin);
521 snew(P, len)(P) = save_calloc("P", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 521, (len), sizeof(*(P)));
522 snew(W, len)(W) = save_calloc("W", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 522, (len), sizeof(*(W)));
523 snew(E, len)(E) = save_calloc("E", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 523, (len), sizeof(*(E)));
524 snew(S, len)(S) = save_calloc("S", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 524, (len), sizeof(*(S)));
525 snew(M, len)(M) = save_calloc("M", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 525, (len), sizeof(*(M)));
526 snew(nbin, len)(nbin) = save_calloc("nbin", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 526, (len), sizeof(*(nbin)));
527 snew(bindex, n)(bindex) = save_calloc("bindex", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 527, (n), sizeof(*(bindex)));
528
529
530 /* Loop over projections */
531 for (j = 0; (j < n); j++)
532 {
533 /* Loop over dimensions */
534 bOutside = FALSE0;
535 for (i = 0; (i < neig); i++)
536 {
537 nxyz[i] = bfac[i]*(eig[i][j]-min_eig[i]);
538 if (nxyz[i] < 0 || nxyz[i] >= ibox[i])
539 {
540 bOutside = TRUE1;
541 }
542 }
543 if (!bOutside)
544 {
545 index = indexn(neig, ibox, nxyz);
546 range_check(index, 0, len)_range_check(index, 0, len, ((void*)0),"index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 546);
547 /* Compute the exponential factor */
548 if (enerT)
549 {
550 efac = exp(-bE[j]+Emin);
551 }
552 else
553 {
554 efac = 1;
555 }
556 /* Apply the bin volume correction for a multi-dimensional distance */
557 for (i = 0; i < neig; i++)
558 {
559 if (idim[i] == 2)
560 {
561 efac /= eig[i][j];
562 }
563 else if (idim[i] == 3)
564 {
565 efac /= sqr(eig[i][j]);
566 }
567 else if (idim[i] == -1)
568 {
569 efac /= sin(DEG2RAD(3.14159265358979323846/180.0)*eig[i][j]);
570 }
571 }
572 /* Update the probability */
573 P[index] += efac;
574 /* Update the energy */
575 if (enerT)
576 {
577 E[index] += enerT[0][j];
578 }
579 /* Statistics: which "structure" in which bin */
580 nbin[index]++;
581 bindex[j] = index;
582 }
583 }
584 /* Normalize probability */
585 normalize_p_e(len, P, nbin, E, pmin);
586 Pmax = 0;
587 /* Compute boundaries for the Free energy */
588 Wmin = 1e8;
589 imin = -1;
590 Wmax = -1e8;
591 /* Recompute Emin: it may have changed due to averaging */
592 Emin = 1e8;
593 Emax = -1e8;
594 for (i = 0; (i < len); i++)
595 {
596 if (P[i] != 0)
597 {
598 Pmax = max(P[i], Pmax)(((P[i]) > (Pmax)) ? (P[i]) : (Pmax) );
599 W[i] = -BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*Tref*log(P[i]);
600 if (W[i] < Wmin)
601 {
602 Wmin = W[i];
603 imin = i;
604 }
605 Emin = min(E[i], Emin)(((E[i]) < (Emin)) ? (E[i]) : (Emin) );
606 Emax = max(E[i], Emax)(((E[i]) > (Emax)) ? (E[i]) : (Emax) );
607 Wmax = max(W[i], Wmax)(((W[i]) > (Wmax)) ? (W[i]) : (Wmax) );
608 }
609 }
610 if (pmax > 0)
611 {
612 Pmax = pmax;
613 }
614 if (gmax > 0)
615 {
616 Wmax = gmax;
617 }
618 else
619 {
620 Wmax -= Wmin;
621 }
622 Winf = Wmax+1;
623 Einf = Emax+1;
624 Smin = Emin-Wmax;
625 Smax = Emax-Smin;
626 Sinf = Smax+1;
627 /* Write out the free energy as a function of bin index */
628 fp = gmx_ffopen(fn, "w");
629 for (i = 0; (i < len); i++)
630 {
631 if (P[i] != 0)
632 {
633 W[i] -= Wmin;
634 S[i] = E[i]-W[i]-Smin;
635 fprintf(fp, "%5d %10.5e %10.5e %10.5e\n", i, W[i], E[i], S[i]);
636 }
637 else
638 {
639 W[i] = Winf;
640 E[i] = Einf;
641 S[i] = Sinf;
642 }
643 }
644 gmx_ffclose(fp);
645 /* Organize the structures in the bins */
646 snew(b, 1)(b) = save_calloc("b", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 646, (1), sizeof(*(b)));
647 snew(b->index, len+1)(b->index) = save_calloc("b->index", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 647, (len+1), sizeof(*(b->index)));
648 snew(b->a, n)(b->a) = save_calloc("b->a", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 648, (n), sizeof(*(b->a)));
649 b->index[0] = 0;
650 for (i = 0; (i < len); i++)
651 {
652 b->index[i+1] = b->index[i]+nbin[i];
653 nbin[i] = 0;
654 }
655 for (i = 0; (i < n); i++)
656 {
657 bi = bindex[i];
658 b->a[b->index[bi]+nbin[bi]] = i;
659 nbin[bi]++;
660 }
661 /* Consistency check */
662 /* This no longer applies when we allow the plot to be smaller
663 than the sampled space.
664 for(i=0; (i<len); i++) {
665 if (nbin[i] != (b->index[i+1] - b->index[i]))
666 gmx_fatal(FARGS,"nbin[%d] = %d, should be %d",i,nbin[i],
667 b->index[i+1] - b->index[i]);
668 }
669 */
670 /* Write the index file */
671 fp = gmx_ffopen(ndx, "w");
672 for (i = 0; (i < len); i++)
673 {
674 if (nbin[i] > 0)
675 {
676 fprintf(fp, "[ %d ]\n", i);
677 for (j = b->index[i]; (j < b->index[i+1]); j++)
678 {
679 fprintf(fp, "%d\n", b->a[j]+1);
680 }
681 }
682 }
683 gmx_ffclose(fp);
684 snew(axis_x, ibox[0]+1)(axis_x) = save_calloc("axis_x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 684, (ibox[0]+1), sizeof(*(axis_x)));
685 snew(axis_y, ibox[1]+1)(axis_y) = save_calloc("axis_y", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 685, (ibox[1]+1), sizeof(*(axis_y)));
686 snew(axis_z, ibox[2]+1)(axis_z) = save_calloc("axis_z", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 686, (ibox[2]+1), sizeof(*(axis_z)));
687 maxbox = max(ibox[0], max(ibox[1], ibox[2]))(((ibox[0]) > ((((ibox[1]) > (ibox[2])) ? (ibox[1]) : (
ibox[2]) ))) ? (ibox[0]) : ((((ibox[1]) > (ibox[2])) ? (ibox
[1]) : (ibox[2]) )) );
688 snew(PP, maxbox*maxbox)(PP) = save_calloc("PP", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 688, (maxbox*maxbox), sizeof(*(PP)));
689 snew(WW, maxbox*maxbox)(WW) = save_calloc("WW", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 689, (maxbox*maxbox), sizeof(*(WW)));
690 snew(EE, maxbox*maxbox)(EE) = save_calloc("EE", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 690, (maxbox*maxbox), sizeof(*(EE)));
691 snew(SS, maxbox*maxbox)(SS) = save_calloc("SS", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 691, (maxbox*maxbox), sizeof(*(SS)));
692 for (i = 0; (i < min(neig, 3)(((neig) < (3)) ? (neig) : (3) )); i++)
693 {
694 switch (i)
695 {
696 case 0: axis = axis_x; break;
697 case 1: axis = axis_y; break;
698 case 2: axis = axis_z; break;
699 default: break;
700 }
701 for (j = 0; j <= ibox[i]; j++)
702 {
703 axis[j] = min_eig[i] + j/bfac[i];
704 }
705 }
706 if (map)
707 {
708 snew(M, len)(M) = save_calloc("M", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 708, (len), sizeof(*(M)));
709 snew(MM, maxbox*maxbox)(MM) = save_calloc("MM", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 709, (maxbox*maxbox), sizeof(*(MM)));
710 for (i = 0; (i < ibox[0]); i++)
711 {
712 MM[i] = &(M[i*ibox[1]]);
713 }
714 Mmin = 1e8;
715 Mmax = -1e8;
716 for (i = 0; (i < nmap); i++)
717 {
718 Mmin = min(Mmin, map[0][i])(((Mmin) < (map[0][i])) ? (Mmin) : (map[0][i]) );
719 Mmax = max(Mmax, map[0][i])(((Mmax) > (map[0][i])) ? (Mmax) : (map[0][i]) );
720 }
721 Minf = Mmax*1.05;
722 for (i = 0; (i < len); i++)
723 {
724 M[i] = Minf;
725 }
726 for (i = 0; (i < nmap); i++)
727 {
728 index = gmx_nint(mapindex[i]);
729 if (index >= len)
730 {
731 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 731, "Number of bins in file from -mdata option does not correspond to current analysis");
732 }
733
734 if (P[index] != 0)
735 {
736 M[index] = map[0][i];
737 }
738 }
739 }
740 else
741 {
742 MM = NULL((void*)0);
743 Minf = NOTSET-12345;
744 }
745 pick_minima(logf, ibox, neig, len, W);
746 if (gmax <= 0)
747 {
748 gmax = Winf;
749 }
750 flags = MAT_SPATIAL_X(1<<0) | MAT_SPATIAL_Y(1<<1);
751 if (neig == 2)
752 {
753 /* Dump to XPM file */
754 snew(PP, ibox[0])(PP) = save_calloc("PP", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 754, (ibox[0]), sizeof(*(PP)));
755 for (i = 0; (i < ibox[0]); i++)
756 {
757 snew(PP[i], ibox[1])(PP[i]) = save_calloc("PP[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 757, (ibox[1]), sizeof(*(PP[i])));
758 for (j = 0; j < ibox[1]; j++)
759 {
760 PP[i][j] = P[i*ibox[1]+j];
761 }
762 WW[i] = &(W[i*ibox[1]]);
763 EE[i] = &(E[i*ibox[1]]);
764 SS[i] = &(S[i*ibox[1]]);
765 }
766 fp = gmx_ffopen(xpmP, "w");
767 write_xpm(fp, flags, "Probability Distribution", "", "PC1", "PC2",
768 ibox[0], ibox[1], axis_x, axis_y, PP, 0, Pmax, rlo, rhi, &nlevels);
769 gmx_ffclose(fp);
770 fp = gmx_ffopen(xpm, "w");
771 write_xpm(fp, flags, "Gibbs Energy Landscape", "G (kJ/mol)", "PC1", "PC2",
772 ibox[0], ibox[1], axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
773 gmx_ffclose(fp);
774 fp = gmx_ffopen(xpm2, "w");
775 write_xpm(fp, flags, "Enthalpy Landscape", "H (kJ/mol)", "PC1", "PC2",
776 ibox[0], ibox[1], axis_x, axis_y, EE,
777 emin ? *emin : Emin, emax ? *emax : Einf, rlo, rhi, &nlevels);
778 gmx_ffclose(fp);
779 fp = gmx_ffopen(xpm3, "w");
780 write_xpm(fp, flags, "Entropy Landscape", "TDS (kJ/mol)", "PC1", "PC2",
781 ibox[0], ibox[1], axis_x, axis_y, SS, 0, Sinf, rlo, rhi, &nlevels);
782 gmx_ffclose(fp);
783 if (map)
784 {
785 fp = gmx_ffopen(xpm4, "w");
786 write_xpm(fp, flags, "Custom Landscape", mname, "PC1", "PC2",
787 ibox[0], ibox[1], axis_x, axis_y, MM, 0, Minf, rlo, rhi, &nlevels);
788 gmx_ffclose(fp);
789 }
790 }
791 else if (neig == 3)
792 {
793 /* Dump to PDB file */
794 fp = gmx_ffopen(pdb, "w");
795 for (i = 0; (i < ibox[0]); i++)
796 {
797 xxx[XX0] = 3*(i+0.5-ibox[0]/2);
798 for (j = 0; (j < ibox[1]); j++)
799 {
800 xxx[YY1] = 3*(j+0.5-ibox[1]/2);
801 for (k = 0; (k < ibox[2]); k++)
802 {
803 xxx[ZZ2] = 3*(k+0.5-ibox[2]/2);
804 index = index3(ibox, i, j, k);
805 if (P[index] > 0)
806 {
807 fprintf(fp, "%-6s%5u %-4.4s%3.3s %4d %8.3f%8.3f%8.3f%6.2f%6.2f\n",
808 "ATOM", (index+1) %10000, "H", "H", (index+1)%10000,
809 xxx[XX0], xxx[YY1], xxx[ZZ2], 1.0, W[index]);
810 }
811 }
812 }
813 }
814 gmx_ffclose(fp);
815 write_xplor("out.xplor", W, ibox, min_eig, max_eig);
816 if (map)
817 {
818 write_xplor("user.xplor", M, ibox, min_eig, max_eig);
819 }
820 nxyz[XX0] = imin/(ibox[1]*ibox[2]);
821 nxyz[YY1] = (imin-nxyz[XX0]*ibox[1]*ibox[2])/ibox[2];
822 nxyz[ZZ2] = imin % ibox[2];
823 for (i = 0; (i < ibox[0]); i++)
824 {
825 snew(WW[i], maxbox)(WW[i]) = save_calloc("WW[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 825, (maxbox), sizeof(*(WW[i])));
826 for (j = 0; (j < ibox[1]); j++)
827 {
828 WW[i][j] = W[index3(ibox, i, j, nxyz[ZZ2])];
829 }
830 }
831 snew(buf, strlen(xpm)+4)(buf) = save_calloc("buf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 831, (strlen(xpm)+4), sizeof(*(buf)));
832 sprintf(buf, "%s", xpm);
833 sprintf(&buf[strlen(xpm)-4], "12.xpm");
834 fp = gmx_ffopen(buf, "w");
835 write_xpm(fp, flags, "Gibbs Energy Landscape", "W (kJ/mol)", "PC1", "PC2",
836 ibox[0], ibox[1], axis_x, axis_y, WW, 0, gmax, rlo, rhi, &nlevels);
837 gmx_ffclose(fp);
838 for (i = 0; (i < ibox[0]); i++)
839 {
840 for (j = 0; (j < ibox[2]); j++)
841 {
842 WW[i][j] = W[index3(ibox, i, nxyz[YY1], j)];
843 }
844 }
845 sprintf(&buf[strlen(xpm)-4], "13.xpm");
846 fp = gmx_ffopen(buf, "w");
847 write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC1", "PC3",
848 ibox[0], ibox[2], axis_x, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
849 gmx_ffclose(fp);
850 for (i = 0; (i < ibox[1]); i++)
851 {
852 for (j = 0; (j < ibox[2]); j++)
853 {
854 WW[i][j] = W[index3(ibox, nxyz[XX0], i, j)];
855 }
856 }
857 sprintf(&buf[strlen(xpm)-4], "23.xpm");
858 fp = gmx_ffopen(buf, "w");
859 write_xpm(fp, flags, "SHAM Energy Landscape", "kJ/mol", "PC2", "PC3",
860 ibox[1], ibox[2], axis_y, axis_z, WW, 0, gmax, rlo, rhi, &nlevels);
861 gmx_ffclose(fp);
862 sfree(buf)save_free("buf", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 862, (buf));
863 }
864 if (map)
865 {
866 sfree(MM)save_free("MM", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 866, (MM));
867 sfree(M)save_free("M", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 867, (M));
868 }
869}
870
871static void ehisto(const char *fh, int n, real **enerT, const output_env_t oenv)
872{
873 FILE *fp;
874 int i, j, k, nbin, blength;
875 int *bindex;
876 real *T, bmin, bmax, bwidth;
877 int **histo;
878
879 bmin = 1e8;
880 bmax = -1e8;
881 snew(bindex, n)(bindex) = save_calloc("bindex", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 881, (n), sizeof(*(bindex)));
882 snew(T, n)(T) = save_calloc("T", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 882, (n), sizeof(*(T)));
883 nbin = 0;
884 for (j = 1; (j < n); j++)
885 {
886 for (k = 0; (k < nbin); k++)
887 {
888 if (T[k] == enerT[1][j])
889 {
890 bindex[j] = k;
891 break;
892 }
893 }
894 if (k == nbin)
895 {
896 bindex[j] = nbin;
897 T[nbin] = enerT[1][j];
898 nbin++;
899 }
900 bmin = min(enerT[0][j], bmin)(((enerT[0][j]) < (bmin)) ? (enerT[0][j]) : (bmin) );
901 bmax = max(enerT[0][j], bmax)(((enerT[0][j]) > (bmax)) ? (enerT[0][j]) : (bmax) );
902 }
903 bwidth = 1.0;
904 blength = (bmax - bmin)/bwidth + 2;
905 snew(histo, nbin)(histo) = save_calloc("histo", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 905, (nbin), sizeof(*(histo)));
906 for (i = 0; (i < nbin); i++)
907 {
908 snew(histo[i], blength)(histo[i]) = save_calloc("histo[i]", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 908, (blength), sizeof(*(histo[i])));
909 }
910 for (j = 0; (j < n); j++)
911 {
912 k = (enerT[0][j]-bmin)/bwidth;
913 histo[bindex[j]][k]++;
914 }
915 fp = xvgropen(fh, "Energy distribution", "E (kJ/mol)", "", oenv);
916 for (j = 0; (j < blength); j++)
917 {
918 fprintf(fp, "%8.3f", bmin+j*bwidth);
919 for (k = 0; (k < nbin); k++)
920 {
921 fprintf(fp, " %6d", histo[k][j]);
922 }
923 fprintf(fp, "\n");
924 }
925 gmx_ffclose(fp);
926}
927
928int gmx_sham(int argc, char *argv[])
929{
930 const char *desc[] = {
931 "[THISMODULE] makes multi-dimensional free-energy, enthalpy and entropy plots.",
932 "[THISMODULE] reads one or more [TT].xvg[tt] files and analyzes data sets.",
933 "The basic purpose of [THISMODULE] is to plot Gibbs free energy landscapes",
934 "(option [TT]-ls[tt])",
935 "by Bolzmann inverting multi-dimensional histograms (option [TT]-lp[tt]),",
936 "but it can also",
937 "make enthalpy (option [TT]-lsh[tt]) and entropy (option [TT]-lss[tt])",
938 "plots. The histograms can be made for any quantities the user supplies.",
939 "A line in the input file may start with a time",
940 "(see option [TT]-time[tt]) and any number of [IT]y[it]-values may follow.",
941 "Multiple sets can also be",
942 "read when they are separated by & (option [TT]-n[tt]),",
943 "in this case only one [IT]y[it]-value is read from each line.",
944 "All lines starting with # and @ are skipped.",
945 "[PAR]",
946 "Option [TT]-ge[tt] can be used to supply a file with free energies",
947 "when the ensemble is not a Boltzmann ensemble, but needs to be biased",
948 "by this free energy. One free energy value is required for each",
949 "(multi-dimensional) data point in the [TT]-f[tt] input.",
950 "[PAR]",
951 "Option [TT]-ene[tt] can be used to supply a file with energies.",
952 "These energies are used as a weighting function in the single",
953 "histogram analysis method by Kumar et al. When temperatures",
954 "are supplied (as a second column in the file), an experimental",
955 "weighting scheme is applied. In addition the vales",
956 "are used for making enthalpy and entropy plots.",
957 "[PAR]",
958 "With option [TT]-dim[tt], dimensions can be gives for distances.",
959 "When a distance is 2- or 3-dimensional, the circumference or surface",
960 "sampled by two particles increases with increasing distance.",
961 "Depending on what one would like to show, one can choose to correct",
962 "the histogram and free-energy for this volume effect.",
963 "The probability is normalized by r and r^2 for dimensions of 2 and 3, ",
964 "respectively.",
965 "A value of -1 is used to indicate an angle in degrees between two",
966 "vectors: a sin(angle) normalization will be applied.",
967 "[BB]Note[bb] that for angles between vectors the inner-product or cosine",
968 "is the natural quantity to use, as it will produce bins of the same",
969 "volume."
970 };
971 static real tb = -1, te = -1, frac = 0.5, filtlen = 0;
972 static gmx_bool bHaveT = TRUE1, bDer = FALSE0, bSubAv = TRUE1, bAverCorr = FALSE0, bXYdy = FALSE0;
973 static gmx_bool bEESEF = FALSE0, bEENLC = FALSE0, bEeFitAc = FALSE0, bPower = FALSE0;
974 static gmx_bool bShamEner = TRUE1, bSham = TRUE1;
975 static real Tref = 298.15, pmin = 0, ttol = 0, pmax = 0, gmax = 0, emin = 0, emax = 0;
976 static rvec nrdim = {1, 1, 1};
977 static rvec nrbox = {32, 32, 32};
978 static rvec xmin = {0, 0, 0}, xmax = {1, 1, 1};
979 static int nsets_in = 1, nb_min = 4, resol = 10, nlevels = 25;
980 static const char *mname = "";
981 t_pargs pa[] = {
982 { "-time", FALSE0, etBOOL, {&bHaveT},
983 "Expect a time in the input" },
984 { "-b", FALSE0, etREAL, {&tb},
985 "First time to read from set" },
986 { "-e", FALSE0, etREAL, {&te},
987 "Last time to read from set" },
988 { "-ttol", FALSE0, etREAL, {&ttol},
989 "Tolerance on time in appropriate units (usually ps)" },
990 { "-n", FALSE0, etINT, {&nsets_in},
991 "Read this number of sets separated by lines containing only an ampersand" },
992 { "-d", FALSE0, etBOOL, {&bDer},
993 "Use the derivative" },
994 { "-sham", FALSE0, etBOOL, {&bSham},
995 "Turn off energy weighting even if energies are given" },
996 { "-tsham", FALSE0, etREAL, {&Tref},
997 "Temperature for single histogram analysis" },
998 { "-pmin", FALSE0, etREAL, {&pmin},
999 "Minimum probability. Anything lower than this will be set to zero" },
1000 { "-dim", FALSE0, etRVEC, {nrdim},
1001 "Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last)" },
1002 { "-ngrid", FALSE0, etRVEC, {nrbox},
1003 "Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last)" },
1004 { "-xmin", FALSE0, etRVEC, {xmin},
1005 "Minimum for the axes in energy landscape (see above for > 3 dimensions)" },
1006 { "-xmax", FALSE0, etRVEC, {xmax},
1007 "Maximum for the axes in energy landscape (see above for > 3 dimensions)" },
1008 { "-pmax", FALSE0, etREAL, {&pmax},
1009 "Maximum probability in output, default is calculate" },
1010 { "-gmax", FALSE0, etREAL, {&gmax},
1011 "Maximum free energy in output, default is calculate" },
1012 { "-emin", FALSE0, etREAL, {&emin},
1013 "Minimum enthalpy in output, default is calculate" },
1014 { "-emax", FALSE0, etREAL, {&emax},
1015 "Maximum enthalpy in output, default is calculate" },
1016 { "-nlevels", FALSE0, etINT, {&nlevels},
1017 "Number of levels for energy landscape" },
1018 { "-mname", FALSE0, etSTR, {&mname},
1019 "Legend label for the custom landscape" },
1020 };
1021#define NPA((int)(sizeof(pa)/sizeof((pa)[0]))) asize(pa)((int)(sizeof(pa)/sizeof((pa)[0])))
1022
1023 FILE *out;
1024 int n, e_n, d_n, nlast, s, nset, e_nset, d_nset, i, j = 0, *idim, *ibox;
1
'e_nset' declared without an initial value
→
1025 real **val, **et_val, **dt_val, *t, *e_t, e_dt, d_dt, *d_t, dt, tot, error;
1026 real *rmin, *rmax;
1027 double *av, *sig, cum1, cum2, cum3, cum4, db;
1028 const char *fn_ge, *fn_ene;
1029 output_env_t oenv;
1030 gmx_int64_t num_grid_points;
1031
1032 t_filenm fnm[] = {
1033 { efXVG, "-f", "graph", ffREAD1<<1 },
1034 { efXVG, "-ge", "gibbs", ffOPTRD(1<<1 | 1<<3) },
1035 { efXVG, "-ene", "esham", ffOPTRD(1<<1 | 1<<3) },
1036 { efXVG, "-dist", "ener", ffOPTWR(1<<2| 1<<3) },
1037 { efXVG, "-histo", "edist", ffOPTWR(1<<2| 1<<3) },
1038 { efNDX, "-bin", "bindex", ffOPTWR(1<<2| 1<<3) },
1039 { efXPM, "-lp", "prob", ffOPTWR(1<<2| 1<<3) },
1040 { efXPM, "-ls", "gibbs", ffOPTWR(1<<2| 1<<3) },
1041 { efXPM, "-lsh", "enthalpy", ffOPTWR(1<<2| 1<<3) },
1042 { efXPM, "-lss", "entropy", ffOPTWR(1<<2| 1<<3) },
1043 { efXPM, "-map", "map", ffOPTWR(1<<2| 1<<3) },
1044 { efPDB, "-ls3", "gibbs3", ffOPTWR(1<<2| 1<<3) },
1045 { efXVG, "-mdata", "mapdata", ffOPTRD(1<<1 | 1<<3) },
1046 { efLOG, "-g", "shamlog", ffOPTWR(1<<2| 1<<3) }
1047 };
1048#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
1049
1050 int npargs;
1051
1052 npargs = asize(pa)((int)(sizeof(pa)/sizeof((pa)[0])));
1053 if (!parse_common_args(&argc, argv, PCA_CAN_VIEW(1<<5) | PCA_BE_NICE(1<<13),
2
←
Taking false branch
→
1054 NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, npargs, pa, asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, 0, NULL((void*)0), &oenv))
1055 {
1056 return 0;
1057 }
1058
1059 val = read_xvg_time(opt2fn("-f", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), bHaveT,
1060 opt2parg_bSet("-b", npargs, pa), tb-ttol,
1061 opt2parg_bSet("-e", npargs, pa), te+ttol,
1062 nsets_in, &nset, &n, &dt, &t);
1063 printf("Read %d sets of %d points, dt = %g\n\n", nset, n, dt);
1064
1065 fn_ge = opt2fn_null("-ge", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
1066 fn_ene = opt2fn_null("-ene", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
1067
1068 if (fn_ge && fn_ene)
1069 {
1070 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1070, "Can not do free energy and energy corrections at the same time");
1071 }
1072
1073 if (fn_ge || fn_ene)
3
←
Taking false branch
→
1074 {
1075 et_val = read_xvg_time(fn_ge ? fn_ge : fn_ene, bHaveT,
1076 opt2parg_bSet("-b", npargs, pa), tb-ttol,
1077 opt2parg_bSet("-e", npargs, pa), te+ttol,
1078 1, &e_nset, &e_n, &e_dt, &e_t);
1079 if (fn_ge)
1080 {
1081 if (e_nset != 1)
1082 {
1083 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1083, "Can only handle one free energy component in %s",
1084 fn_ge);
1085 }
1086 }
1087 else
1088 {
1089 if (e_nset != 1 && e_nset != 2)
1090 {
1091 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1091, "Can only handle one energy component or one energy and one T in %s",
1092 fn_ene);
1093 }
1094 }
1095 if (e_n != n)
1096 {
1097 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1097, "Number of energies (%d) does not match number of entries (%d) in %s", e_n, n, opt2fn("-f", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1098 }
1099 }
1100 else
1101 {
1102 et_val = NULL((void*)0);
1103 }
1104
1105 if (opt2fn_null("-mdata", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm) != NULL((void*)0))
4
←
Taking false branch
→
1106 {
1107 dt_val = read_xvg_time(opt2fn("-mdata", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), bHaveT,
1108 FALSE0, tb, FALSE0, te,
1109 nsets_in, &d_nset, &d_n, &d_dt, &d_t);
1110 if (d_nset != 1)
1111 {
1112 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1112, "Can only handle one mapping data column in %s",
1113 opt2fn("-mdata", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1114 }
1115 }
1116 else
1117 {
1118 dt_val = NULL((void*)0);
1119 }
1120
1121 if (fn_ene && et_val)
1122 {
1123 ehisto(opt2fn("-histo", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), e_n, et_val, oenv);
1124 }
1125
1126 snew(idim, max(3, nset))(idim) = save_calloc("idim", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1126, ((((3) > (nset)) ? (3) : (nset) )), sizeof(*(idim)
));
1127 snew(ibox, max(3, nset))(ibox) = save_calloc("ibox", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1127, ((((3) > (nset)) ? (3) : (nset) )), sizeof(*(ibox)
));
1128 snew(rmin, max(3, nset))(rmin) = save_calloc("rmin", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1128, ((((3) > (nset)) ? (3) : (nset) )), sizeof(*(rmin)
));
1129 snew(rmax, max(3, nset))(rmax) = save_calloc("rmax", "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1129, ((((3) > (nset)) ? (3) : (nset) )), sizeof(*(rmax)
));
1130 for (i = 0; (i < min(3, nset)(((3) < (nset)) ? (3) : (nset) )); i++)
5
←
Loop condition is false. Execution continues on line 1137
→
1131 {
1132 idim[i] = nrdim[i];
1133 ibox[i] = nrbox[i];
1134 rmin[i] = xmin[i];
1135 rmax[i] = xmax[i];
1136 }
1137 for (; (i < nset); i++)
6
←
Loop condition is false. Execution continues on line 1146
→
1138 {
1139 idim[i] = nrdim[2];
1140 ibox[i] = nrbox[2];
1141 rmin[i] = xmin[2];
1142 rmax[i] = xmax[2];
1143 }
1144
1145 /* Check that the grid size is manageable. */
1146 num_grid_points = ibox[0];
1147 for (i = 1; i < nset; i++)
7
←
Loop condition is false. Execution continues on line 1159
→
1148 {
1149 gmx_int64_t result;
1150 if (!check_int_multiply_for_overflow(num_grid_points, ibox[i], &result))
1151 {
1152 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxana/gmx_sham.c"
, 1152,
1153 "The number of dimensions and grid points is too large for this tool.\n");
1154 }
1155 num_grid_points = result;
1156 }
1157 /* The number of grid points fits in a gmx_int64_t. */
1158
1159 do_sham(opt2fn("-dist", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), opt2fn("-bin", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
10
←
Function call argument is an uninitialized value
1160 opt2fn("-lp", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1161 opt2fn("-ls", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), opt2fn("-lsh", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1162 opt2fn("-lss", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), opt2fn("-map", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1163 opt2fn("-ls3", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), opt2fn("-g", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1164 n, nset, val, fn_ge != NULL((void*)0), e_nset, et_val, d_n, d_t, dt_val, Tref,
1165 pmax, gmax,
1166 opt2parg_bSet("-emin", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa) ? &emin : NULL((void*)0),
8
←
'?' condition is false
→
1167 opt2parg_bSet("-emax", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa) ? &emax : NULL((void*)0),
9
←
'?' condition is false
→
1168 nlevels, pmin,
1169 mname, idim, ibox,
1170 opt2parg_bSet("-xmin", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa), rmin,
1171 opt2parg_bSet("-xmax", NPA((int)(sizeof(pa)/sizeof((pa)[0]))), pa), rmax);
1172
1173 return 0;
1174}