Bug Summary

File:gromacs/gmxpreprocess/grompp.c
Location:line 1954, column 9
Description:Value stored to 'max_spacing' 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#include "grompp.h"
38
39#ifdef HAVE_CONFIG_H1
40#include <config.h>
41#endif
42
43#include <sys/types.h>
44#include <math.h>
45#include <string.h>
46#include <errno(*__errno_location ()).h>
47#include <limits.h>
48#include <assert.h>
49
50#include "gromacs/utility/smalloc.h"
51#include "macros.h"
52#include "readir.h"
53#include "toputil.h"
54#include "topio.h"
55#include "gromacs/fileio/confio.h"
56#include "readir.h"
57#include "symtab.h"
58#include "names.h"
59#include "grompp-impl.h"
60#include "gromacs/random/random.h"
61#include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
62#include "gromacs/math/vec.h"
63#include "gromacs/utility/futil.h"
64#include "gromacs/commandline/pargs.h"
65#include "splitter.h"
66#include "gromacs/gmxpreprocess/sortwater.h"
67#include "convparm.h"
68#include "gromacs/utility/fatalerror.h"
69#include "warninp.h"
70#include "index.h"
71#include "gromacs/fileio/gmxfio.h"
72#include "gromacs/fileio/trnio.h"
73#include "gromacs/fileio/tpxio.h"
74#include "gromacs/fileio/trxio.h"
75#include "vsite_parm.h"
76#include "txtdump.h"
77#include "calcgrid.h"
78#include "add_par.h"
79#include "gromacs/fileio/enxio.h"
80#include "perf_est.h"
81#include "compute_io.h"
82#include "gpp_atomtype.h"
83#include "mtop_util.h"
84#include "genborn.h"
85#include "calc_verletbuf.h"
86#include "tomorse.h"
87#include "gromacs/imd/imd.h"
88
89
90static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
91{
92 int i, n;
93
94 n = 0;
95 /* For all the molecule types */
96 for (i = 0; i < nrmols; i++)
97 {
98 n += mols[i].plist[ifunc].nr;
99 mols[i].plist[ifunc].nr = 0;
100 }
101 return n;
102}
103
104static int check_atom_names(const char *fn1, const char *fn2,
105 gmx_mtop_t *mtop, t_atoms *at)
106{
107 int mb, m, i, j, nmismatch;
108 t_atoms *tat;
109#define MAXMISMATCH20 20
110
111 if (mtop->natoms != at->nr)
112 {
113 gmx_incons("comparing atom names")_gmx_error("incons", "comparing atom names", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 113);
114 }
115
116 nmismatch = 0;
117 i = 0;
118 for (mb = 0; mb < mtop->nmolblock; mb++)
119 {
120 tat = &mtop->moltype[mtop->molblock[mb].type].atoms;
121 for (m = 0; m < mtop->molblock[mb].nmol; m++)
122 {
123 for (j = 0; j < tat->nr; j++)
124 {
125 if (strcmp( *(tat->atomname[j]), *(at->atomname[i]) )__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(*(tat->atomname[j])) && __builtin_constant_p (*(
at->atomname[i])) && (__s1_len = strlen (*(tat->
atomname[j])), __s2_len = strlen (*(at->atomname[i])), (!(
(size_t)(const void *)((*(tat->atomname[j])) + 1) - (size_t
)(const void *)(*(tat->atomname[j])) == 1) || __s1_len >=
4) && (!((size_t)(const void *)((*(at->atomname[i
])) + 1) - (size_t)(const void *)(*(at->atomname[i])) == 1
) || __s2_len >= 4)) ? __builtin_strcmp (*(tat->atomname
[j]), *(at->atomname[i])) : (__builtin_constant_p (*(tat->
atomname[j])) && ((size_t)(const void *)((*(tat->atomname
[j])) + 1) - (size_t)(const void *)(*(tat->atomname[j])) ==
1) && (__s1_len = strlen (*(tat->atomname[j])), __s1_len
< 4) ? (__builtin_constant_p (*(at->atomname[i])) &&
((size_t)(const void *)((*(at->atomname[i])) + 1) - (size_t
)(const void *)(*(at->atomname[i])) == 1) ? __builtin_strcmp
(*(tat->atomname[j]), *(at->atomname[i])) : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (*(at->atomname[i])); int __result = (((const unsigned
char *) (const char *) (*(tat->atomname[j])))[0] - __s2[0
]); if (__s1_len > 0 && __result == 0) { __result =
(((const unsigned char *) (const char *) (*(tat->atomname
[j])))[1] - __s2[1]); if (__s1_len > 1 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
*(tat->atomname[j])))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (*(tat->atomname[j])))[3] - __s2[3]); } } __result; })
)) : (__builtin_constant_p (*(at->atomname[i])) &&
((size_t)(const void *)((*(at->atomname[i])) + 1) - (size_t
)(const void *)(*(at->atomname[i])) == 1) && (__s2_len
= strlen (*(at->atomname[i])), __s2_len < 4) ? (__builtin_constant_p
(*(tat->atomname[j])) && ((size_t)(const void *)(
(*(tat->atomname[j])) + 1) - (size_t)(const void *)(*(tat->
atomname[j])) == 1) ? __builtin_strcmp (*(tat->atomname[j]
), *(at->atomname[i])) : (- (__extension__ ({ const unsigned
char *__s2 = (const unsigned char *) (const char *) (*(tat->
atomname[j])); int __result = (((const unsigned char *) (const
char *) (*(at->atomname[i])))[0] - __s2[0]); if (__s2_len
> 0 && __result == 0) { __result = (((const unsigned
char *) (const char *) (*(at->atomname[i])))[1] - __s2[1]
); if (__s2_len > 1 && __result == 0) { __result =
(((const unsigned char *) (const char *) (*(at->atomname[
i])))[2] - __s2[2]); if (__s2_len > 2 && __result ==
0) __result = (((const unsigned char *) (const char *) (*(at
->atomname[i])))[3] - __s2[3]); } } __result; })))) : __builtin_strcmp
(*(tat->atomname[j]), *(at->atomname[i]))))); }) != 0)
126 {
127 if (nmismatch < MAXMISMATCH20)
128 {
129 fprintf(stderrstderr,
130 "Warning: atom name %d in %s and %s does not match (%s - %s)\n",
131 i+1, fn1, fn2, *(tat->atomname[j]), *(at->atomname[i]));
132 }
133 else if (nmismatch == MAXMISMATCH20)
134 {
135 fprintf(stderrstderr, "(more than %d non-matching atom names)\n", MAXMISMATCH20);
136 }
137 nmismatch++;
138 }
139 i++;
140 }
141 }
142 }
143
144 return nmismatch;
145}
146
147static void check_eg_vs_cg(gmx_mtop_t *mtop)
148{
149 int astart, mb, m, cg, j, firstj;
150 unsigned char firsteg, eg;
151 gmx_moltype_t *molt;
152
153 /* Go through all the charge groups and make sure all their
154 * atoms are in the same energy group.
155 */
156
157 astart = 0;
158 for (mb = 0; mb < mtop->nmolblock; mb++)
159 {
160 molt = &mtop->moltype[mtop->molblock[mb].type];
161 for (m = 0; m < mtop->molblock[mb].nmol; m++)
162 {
163 for (cg = 0; cg < molt->cgs.nr; cg++)
164 {
165 /* Get the energy group of the first atom in this charge group */
166 firstj = astart + molt->cgs.index[cg];
167 firsteg = ggrpnr(&mtop->groups, egcENER, firstj)((&mtop->groups)->grpnr[egcENER] ? (&mtop->groups
)->grpnr[egcENER][firstj] : 0);
168 for (j = molt->cgs.index[cg]+1; j < molt->cgs.index[cg+1]; j++)
169 {
170 eg = ggrpnr(&mtop->groups, egcENER, astart+j)((&mtop->groups)->grpnr[egcENER] ? (&mtop->groups
)->grpnr[egcENER][astart+j] : 0);
171 if (eg != firsteg)
172 {
173 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 173, "atoms %d and %d in charge group %d of molecule type '%s' are in different energy groups",
174 firstj+1, astart+j+1, cg+1, *molt->name);
175 }
176 }
177 }
178 astart += molt->atoms.nr;
179 }
180 }
181}
182
183static void check_cg_sizes(const char *topfn, t_block *cgs, warninp_t wi)
184{
185 int maxsize, cg;
186 char warn_buf[STRLEN4096];
187
188 maxsize = 0;
189 for (cg = 0; cg < cgs->nr; cg++)
190 {
191 maxsize = max(maxsize, cgs->index[cg+1]-cgs->index[cg])(((maxsize) > (cgs->index[cg+1]-cgs->index[cg])) ? (
maxsize) : (cgs->index[cg+1]-cgs->index[cg]) );
192 }
193
194 if (maxsize > MAX_CHARGEGROUP_SIZE32)
195 {
196 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 196, "The largest charge group contains %d atoms. The maximum is %d.", maxsize, MAX_CHARGEGROUP_SIZE32);
197 }
198 else if (maxsize > 10)
199 {
200 set_warning_line(wi, topfn, -1);
201 sprintf(warn_buf,
202 "The largest charge group contains %d atoms.\n"
203 "Since atoms only see each other when the centers of geometry of the charge groups they belong to are within the cut-off distance, too large charge groups can lead to serious cut-off artifacts.\n"
204 "For efficiency and accuracy, charge group should consist of a few atoms.\n"
205 "For all-atom force fields use: CH3, CH2, CH, NH2, NH, OH, CO2, CO, etc.",
206 maxsize);
207 warning_note(wi, warn_buf);
208 }
209}
210
211static void check_bonds_timestep(gmx_mtop_t *mtop, double dt, warninp_t wi)
212{
213 /* This check is not intended to ensure accurate integration,
214 * rather it is to signal mistakes in the mdp settings.
215 * A common mistake is to forget to turn on constraints
216 * for MD after energy minimization with flexible bonds.
217 * This check can also detect too large time steps for flexible water
218 * models, but such errors will often be masked by the constraints
219 * mdp options, which turns flexible water into water with bond constraints,
220 * but without an angle constraint. Unfortunately such incorrect use
221 * of water models can not easily be detected without checking
222 * for specific model names.
223 *
224 * The stability limit of leap-frog or velocity verlet is 4.44 steps
225 * per oscillational period.
226 * But accurate bonds distributions are lost far before that limit.
227 * To allow relatively common schemes (although not common with Gromacs)
228 * of dt=1 fs without constraints and dt=2 fs with only H-bond constraints
229 * we set the note limit to 10.
230 */
231 int min_steps_warn = 5;
232 int min_steps_note = 10;
233 t_iparams *ip;
234 int molt;
235 gmx_moltype_t *moltype, *w_moltype;
236 t_atom *atom;
237 t_ilist *ilist, *ilb, *ilc, *ils;
238 int ftype;
239 int i, a1, a2, w_a1, w_a2, j;
240 real twopi2, limit2, fc, re, m1, m2, period2, w_period2;
241 gmx_bool bFound, bWater, bWarn;
242 char warn_buf[STRLEN4096];
243
244 ip = mtop->ffparams.iparams;
245
246 twopi2 = sqr(2*M_PI3.14159265358979323846);
247
248 limit2 = sqr(min_steps_note*dt);
249
250 w_a1 = w_a2 = -1;
251 w_period2 = -1.0;
252
253 w_moltype = NULL((void*)0);
254 for (molt = 0; molt < mtop->nmoltype; molt++)
255 {
256 moltype = &mtop->moltype[molt];
257 atom = moltype->atoms.atom;
258 ilist = moltype->ilist;
259 ilc = &ilist[F_CONSTR];
260 ils = &ilist[F_SETTLE];
261 for (ftype = 0; ftype < F_NRE; ftype++)
262 {
263 if (!(ftype == F_BONDS || ftype == F_G96BONDS || ftype == F_HARMONIC))
264 {
265 continue;
266 }
267
268 ilb = &ilist[ftype];
269 for (i = 0; i < ilb->nr; i += 3)
270 {
271 fc = ip[ilb->iatoms[i]].harmonic.krA;
272 re = ip[ilb->iatoms[i]].harmonic.rA;
273 if (ftype == F_G96BONDS)
274 {
275 /* Convert squared sqaure fc to harmonic fc */
276 fc = 2*fc*re;
277 }
278 a1 = ilb->iatoms[i+1];
279 a2 = ilb->iatoms[i+2];
280 m1 = atom[a1].m;
281 m2 = atom[a2].m;
282 if (fc > 0 && m1 > 0 && m2 > 0)
283 {
284 period2 = twopi2*m1*m2/((m1 + m2)*fc);
285 }
286 else
287 {
288 period2 = GMX_FLOAT_MAX3.40282346E+38;
289 }
290 if (debug)
291 {
292 fprintf(debug, "fc %g m1 %g m2 %g period %g\n",
293 fc, m1, m2, sqrt(period2));
294 }
295 if (period2 < limit2)
296 {
297 bFound = FALSE0;
298 for (j = 0; j < ilc->nr; j += 3)
299 {
300 if ((ilc->iatoms[j+1] == a1 && ilc->iatoms[j+2] == a2) ||
301 (ilc->iatoms[j+1] == a2 && ilc->iatoms[j+2] == a1))
302 {
303 bFound = TRUE1;
304 }
305 }
306 for (j = 0; j < ils->nr; j += 4)
307 {
308 if ((a1 == ils->iatoms[j+1] || a1 == ils->iatoms[j+2] || a1 == ils->iatoms[j+3]) &&
309 (a2 == ils->iatoms[j+1] || a2 == ils->iatoms[j+2] || a2 == ils->iatoms[j+3]))
310 {
311 bFound = TRUE1;
312 }
313 }
314 if (!bFound &&
315 (w_moltype == NULL((void*)0) || period2 < w_period2))
316 {
317 w_moltype = moltype;
318 w_a1 = a1;
319 w_a2 = a2;
320 w_period2 = period2;
321 }
322 }
323 }
324 }
325 }
326
327 if (w_moltype != NULL((void*)0))
328 {
329 bWarn = (w_period2 < sqr(min_steps_warn*dt));
330 /* A check that would recognize most water models */
331 bWater = ((*w_moltype->atoms.atomname[0])[0] == 'O' &&
332 w_moltype->atoms.nr <= 5);
333 sprintf(warn_buf, "The bond in molecule-type %s between atoms %d %s and %d %s has an estimated oscillational period of %.1e ps, which is less than %d times the time step of %.1e ps.\n"
334 "%s",
335 *w_moltype->name,
336 w_a1+1, *w_moltype->atoms.atomname[w_a1],
337 w_a2+1, *w_moltype->atoms.atomname[w_a2],
338 sqrt(w_period2), bWarn ? min_steps_warn : min_steps_note, dt,
339 bWater ?
340 "Maybe you asked for fexible water." :
341 "Maybe you forgot to change the constraints mdp option.");
342 if (bWarn)
343 {
344 warning(wi, warn_buf);
345 }
346 else
347 {
348 warning_note(wi, warn_buf);
349 }
350 }
351}
352
353static void check_vel(gmx_mtop_t *mtop, rvec v[])
354{
355 gmx_mtop_atomloop_all_t aloop;
356 t_atom *atom;
357 int a;
358
359 aloop = gmx_mtop_atomloop_all_init(mtop);
360 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
361 {
362 if (atom->ptype == eptShell ||
363 atom->ptype == eptBond ||
364 atom->ptype == eptVSite)
365 {
366 clear_rvec(v[a]);
367 }
368 }
369}
370
371static gmx_bool nint_ftype(gmx_mtop_t *mtop, t_molinfo *mi, int ftype)
372{
373 int nint, mb;
374
375 nint = 0;
376 for (mb = 0; mb < mtop->nmolblock; mb++)
377 {
378 nint += mtop->molblock[mb].nmol*mi[mtop->molblock[mb].type].plist[ftype].nr;
379 }
380
381 return nint;
382}
383
384/* This routine reorders the molecule type array
385 * in the order of use in the molblocks,
386 * unused molecule types are deleted.
387 */
388static void renumber_moltypes(gmx_mtop_t *sys,
389 int *nmolinfo, t_molinfo **molinfo)
390{
391 int *order, norder, i;
392 int mb, mi;
393 t_molinfo *minew;
394
395 snew(order, *nmolinfo)(order) = save_calloc("order", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 395, (*nmolinfo), sizeof(*(order)));
396 norder = 0;
397 for (mb = 0; mb < sys->nmolblock; mb++)
398 {
399 for (i = 0; i < norder; i++)
400 {
401 if (order[i] == sys->molblock[mb].type)
402 {
403 break;
404 }
405 }
406 if (i == norder)
407 {
408 /* This type did not occur yet, add it */
409 order[norder] = sys->molblock[mb].type;
410 /* Renumber the moltype in the topology */
411 norder++;
412 }
413 sys->molblock[mb].type = i;
414 }
415
416 /* We still need to reorder the molinfo structs */
417 snew(minew, norder)(minew) = save_calloc("minew", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 417, (norder), sizeof(*(minew)));
418 for (mi = 0; mi < *nmolinfo; mi++)
419 {
420 for (i = 0; i < norder; i++)
421 {
422 if (order[i] == mi)
423 {
424 break;
425 }
426 }
427 if (i == norder)
428 {
429 done_mi(&(*molinfo)[mi]);
430 }
431 else
432 {
433 minew[i] = (*molinfo)[mi];
434 }
435 }
436 sfree(*molinfo)save_free("*molinfo", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 436, (*molinfo));
437
438 *nmolinfo = norder;
439 *molinfo = minew;
440}
441
442static void molinfo2mtop(int nmi, t_molinfo *mi, gmx_mtop_t *mtop)
443{
444 int m;
445 gmx_moltype_t *molt;
446
447 mtop->nmoltype = nmi;
448 snew(mtop->moltype, nmi)(mtop->moltype) = save_calloc("mtop->moltype", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 448, (nmi), sizeof(*(mtop->moltype)));
449 for (m = 0; m < nmi; m++)
450 {
451 molt = &mtop->moltype[m];
452 molt->name = mi[m].name;
453 molt->atoms = mi[m].atoms;
454 /* ilists are copied later */
455 molt->cgs = mi[m].cgs;
456 molt->excls = mi[m].excls;
457 }
458}
459
460static void
461new_status(const char *topfile, const char *topppfile, const char *confin,
462 t_gromppopts *opts, t_inputrec *ir, gmx_bool bZero,
463 gmx_bool bGenVel, gmx_bool bVerbose, t_state *state,
464 gpp_atomtype_t atype, gmx_mtop_t *sys,
465 int *nmi, t_molinfo **mi, t_params plist[],
466 int *comb, double *reppow, real *fudgeQQ,
467 gmx_bool bMorse,
468 warninp_t wi)
469{
470 t_molinfo *molinfo = NULL((void*)0);
471 int nmolblock;
472 gmx_molblock_t *molblock, *molbs;
473 t_atoms *confat;
474 int mb, i, nrmols, nmismatch;
475 char buf[STRLEN4096];
476 gmx_bool bGB = FALSE0;
477 char warn_buf[STRLEN4096];
478
479 init_mtop(sys);
480
481 /* Set gmx_boolean for GB */
482 if (ir->implicit_solvent)
483 {
484 bGB = TRUE1;
485 }
486
487 /* TOPOLOGY processing */
488 sys->name = do_top(bVerbose, topfile, topppfile, opts, bZero, &(sys->symtab),
489 plist, comb, reppow, fudgeQQ,
490 atype, &nrmols, &molinfo, ir,
491 &nmolblock, &molblock, bGB,
492 wi);
493
494 sys->nmolblock = 0;
495 snew(sys->molblock, nmolblock)(sys->molblock) = save_calloc("sys->molblock", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 495, (nmolblock), sizeof(*(sys->molblock)));
496
497 sys->natoms = 0;
498 for (mb = 0; mb < nmolblock; mb++)
499 {
500 if (sys->nmolblock > 0 &&
501 molblock[mb].type == sys->molblock[sys->nmolblock-1].type)
502 {
503 /* Merge consecutive blocks with the same molecule type */
504 sys->molblock[sys->nmolblock-1].nmol += molblock[mb].nmol;
505 sys->natoms += molblock[mb].nmol*sys->molblock[sys->nmolblock-1].natoms_mol;
506 }
507 else if (molblock[mb].nmol > 0)
508 {
509 /* Add a new molblock to the topology */
510 molbs = &sys->molblock[sys->nmolblock];
511 *molbs = molblock[mb];
512 molbs->natoms_mol = molinfo[molbs->type].atoms.nr;
513 molbs->nposres_xA = 0;
514 molbs->nposres_xB = 0;
515 sys->natoms += molbs->nmol*molbs->natoms_mol;
516 sys->nmolblock++;
517 }
518 }
519 if (sys->nmolblock == 0)
520 {
521 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 521, "No molecules were defined in the system");
522 }
523
524 renumber_moltypes(sys, &nrmols, &molinfo);
525
526 if (bMorse)
527 {
528 convert_harmonics(nrmols, molinfo, atype);
529 }
530
531 if (ir->eDisre == edrNone)
532 {
533 i = rm_interactions(F_DISRES, nrmols, molinfo);
534 if (i > 0)
535 {
536 set_warning_line(wi, "unknown", -1);
537 sprintf(warn_buf, "disre = no, removed %d distance restraints", i);
538 warning_note(wi, warn_buf);
539 }
540 }
541 if (opts->bOrire == FALSE0)
542 {
543 i = rm_interactions(F_ORIRES, nrmols, molinfo);
544 if (i > 0)
545 {
546 set_warning_line(wi, "unknown", -1);
547 sprintf(warn_buf, "orire = no, removed %d orientation restraints", i);
548 warning_note(wi, warn_buf);
549 }
550 }
551
552 /* Copy structures from msys to sys */
553 molinfo2mtop(nrmols, molinfo, sys);
554
555 gmx_mtop_finalize(sys);
556
557 /* COORDINATE file processing */
558 if (bVerbose)
559 {
560 fprintf(stderrstderr, "processing coordinates...\n");
561 }
562
563 get_stx_coordnum(confin, &state->natoms);
564 if (state->natoms != sys->natoms)
565 {
566 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 566, "number of coordinates in coordinate file (%s, %d)\n"
567 " does not match topology (%s, %d)",
568 confin, state->natoms, topfile, sys->natoms);
569 }
570 else
571 {
572 /* make space for coordinates and velocities */
573 char title[STRLEN4096];
574 snew(confat, 1)(confat) = save_calloc("confat", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 574, (1), sizeof(*(confat)));
575 init_t_atoms(confat, state->natoms, FALSE0);
576 init_state(state, state->natoms, 0, 0, 0, 0);
577 read_stx_conf(confin, title, confat, state->x, state->v, NULL((void*)0), state->box);
578 /* This call fixes the box shape for runs with pressure scaling */
579 set_box_rel(ir, state);
580
581 nmismatch = check_atom_names(topfile, confin, sys, confat);
582 free_t_atoms(confat, TRUE1);
583 sfree(confat)save_free("confat", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 583, (confat));
584
585 if (nmismatch)
586 {
587 sprintf(buf, "%d non-matching atom name%s\n"
588 "atom names from %s will be used\n"
589 "atom names from %s will be ignored\n",
590 nmismatch, (nmismatch == 1) ? "" : "s", topfile, confin);
591 warning(wi, buf);
592 }
593 if (bVerbose)
594 {
595 fprintf(stderrstderr, "double-checking input for internal consistency...\n");
596 }
597 double_check(ir, state->box, nint_ftype(sys, molinfo, F_CONSTR), wi);
598 }
599
600 if (bGenVel)
601 {
602 real *mass;
603 gmx_mtop_atomloop_all_t aloop;
604 t_atom *atom;
605 unsigned int useed;
606
607 snew(mass, state->natoms)(mass) = save_calloc("mass", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 607, (state->natoms), sizeof(*(mass)));
608 aloop = gmx_mtop_atomloop_all_init(sys);
609 while (gmx_mtop_atomloop_all_next(aloop, &i, &atom))
610 {
611 mass[i] = atom->m;
612 }
613
614 useed = opts->seed;
615 if (opts->seed == -1)
616 {
617 useed = (int)gmx_rng_make_seed();
618 fprintf(stderrstderr, "Setting gen_seed to %u\n", useed);
619 }
620 maxwell_speed(opts->tempi, useed, sys, state->v);
621
622 stop_cm(stdoutstdout, state->natoms, mass, state->x, state->v);
623 sfree(mass)save_free("mass", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 623, (mass));
624 }
625
626 *nmi = nrmols;
627 *mi = molinfo;
628}
629
630static void copy_state(const char *slog, t_trxframe *fr,
631 gmx_bool bReadVel, t_state *state,
632 double *use_time)
633{
634 int i;
635
636 if (fr->not_ok & FRAME_NOT_OK((1<<0) | (1<<1)))
637 {
638 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 638, "Can not start from an incomplete frame");
639 }
640 if (!fr->bX)
641 {
642 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 642, "Did not find a frame with coordinates in file %s",
643 slog);
644 }
645
646 for (i = 0; i < state->natoms; i++)
647 {
648 copy_rvec(fr->x[i], state->x[i]);
649 }
650 if (bReadVel)
651 {
652 if (!fr->bV)
653 {
654 gmx_incons("Trajecory frame unexpectedly does not contain velocities")_gmx_error("incons", "Trajecory frame unexpectedly does not contain velocities"
, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 654);
655 }
656 for (i = 0; i < state->natoms; i++)
657 {
658 copy_rvec(fr->v[i], state->v[i]);
659 }
660 }
661 if (fr->bBox)
662 {
663 copy_mat(fr->box, state->box);
664 }
665
666 *use_time = fr->time;
667}
668
669static void cont_status(const char *slog, const char *ener,
670 gmx_bool bNeedVel, gmx_bool bGenVel, real fr_time,
671 t_inputrec *ir, t_state *state,
672 gmx_mtop_t *sys,
673 const output_env_t oenv)
674/* If fr_time == -1 read the last frame available which is complete */
675{
676 gmx_bool bReadVel;
677 t_trxframe fr;
678 t_trxstatus *fp;
679 int i;
680 double use_time;
681
682 bReadVel = (bNeedVel && !bGenVel);
683
684 fprintf(stderrstderr,
685 "Reading Coordinates%s and Box size from old trajectory\n",
686 bReadVel ? ", Velocities" : "");
687 if (fr_time == -1)
688 {
689 fprintf(stderrstderr, "Will read whole trajectory\n");
690 }
691 else
692 {
693 fprintf(stderrstderr, "Will read till time %g\n", fr_time);
694 }
695 if (!bReadVel)
696 {
697 if (bGenVel)
698 {
699 fprintf(stderrstderr, "Velocities generated: "
700 "ignoring velocities in input trajectory\n");
701 }
702 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X(1<<1));
703 }
704 else
705 {
706 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X(1<<1) | TRX_NEED_V(1<<3));
707
708 if (!fr.bV)
709 {
710 fprintf(stderrstderr,
711 "\n"
712 "WARNING: Did not find a frame with velocities in file %s,\n"
713 " all velocities will be set to zero!\n\n", slog);
714 for (i = 0; i < sys->natoms; i++)
715 {
716 clear_rvec(state->v[i]);
717 }
718 close_trj(fp);
719 /* Search for a frame without velocities */
720 bReadVel = FALSE0;
721 read_first_frame(oenv, &fp, slog, &fr, TRX_NEED_X(1<<1));
722 }
723 }
724
725 state->natoms = fr.natoms;
726
727 if (sys->natoms != state->natoms)
728 {
729 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 729, "Number of atoms in Topology "
730 "is not the same as in Trajectory");
731 }
732 copy_state(slog, &fr, bReadVel, state, &use_time);
733
734 /* Find the appropriate frame */
735 while ((fr_time == -1 || fr.time < fr_time) &&
736 read_next_frame(oenv, fp, &fr))
737 {
738 copy_state(slog, &fr, bReadVel, state, &use_time);
739 }
740
741 close_trj(fp);
742
743 /* Set the relative box lengths for preserving the box shape.
744 * Note that this call can lead to differences in the last bit
745 * with respect to using gmx convert-tpr to create a [TT].tpx[tt] file.
746 */
747 set_box_rel(ir, state);
748
749 fprintf(stderrstderr, "Using frame at t = %g ps\n", use_time);
750 fprintf(stderrstderr, "Starting time for run is %g ps\n", ir->init_t);
751
752 if ((ir->epc != epcNO || ir->etc == etcNOSEHOOVER) && ener)
753 {
754 get_enx_state(ener, use_time, &sys->groups, ir, state);
755 preserve_box_shape(ir, state->box_rel, state->boxv);
756 }
757}
758
759static void read_posres(gmx_mtop_t *mtop, t_molinfo *molinfo, gmx_bool bTopB,
760 char *fn,
761 int rc_scaling, int ePBC,
762 rvec com,
763 warninp_t wi)
764{
765 gmx_bool bFirst = TRUE1, *hadAtom;
766 rvec *x, *v, *xp;
767 dvec sum;
768 double totmass;
769 t_atoms dumat;
770 matrix box, invbox;
771 int natoms, npbcdim = 0;
772 char warn_buf[STRLEN4096], title[STRLEN4096];
773 int a, i, ai, j, k, mb, nat_molb;
774 gmx_molblock_t *molb;
775 t_params *pr, *prfb;
776 t_atom *atom;
777
778 get_stx_coordnum(fn, &natoms);
779 if (natoms != mtop->natoms)
780 {
781 sprintf(warn_buf, "The number of atoms in %s (%d) does not match the number of atoms in the topology (%d). Will assume that the first %d atoms in the topology and %s match.", fn, natoms, mtop->natoms, min(mtop->natoms, natoms)(((mtop->natoms) < (natoms)) ? (mtop->natoms) : (natoms
) ), fn);
782 warning(wi, warn_buf);
783 }
784 snew(x, natoms)(x) = save_calloc("x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 784, (natoms), sizeof(*(x)));
785 snew(v, natoms)(v) = save_calloc("v", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 785, (natoms), sizeof(*(v)));
786 init_t_atoms(&dumat, natoms, FALSE0);
787 read_stx_conf(fn, title, &dumat, x, v, NULL((void*)0), box);
788
789 npbcdim = ePBC2npbcdim(ePBC);
790 clear_rvec(com);
791 if (rc_scaling != erscNO)
792 {
793 copy_mat(box, invbox);
794 for (j = npbcdim; j < DIM3; j++)
795 {
796 clear_rvec(invbox[j]);
797 invbox[j][j] = 1;
798 }
799 m_inv_ur0(invbox, invbox);
800 }
801
802 /* Copy the reference coordinates to mtop */
803 clear_dvec(sum);
804 totmass = 0;
805 a = 0;
806 snew(hadAtom, natoms)(hadAtom) = save_calloc("hadAtom", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 806, (natoms), sizeof(*(hadAtom)));
807 for (mb = 0; mb < mtop->nmolblock; mb++)
808 {
809 molb = &mtop->molblock[mb];
810 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
811 pr = &(molinfo[molb->type].plist[F_POSRES]);
812 prfb = &(molinfo[molb->type].plist[F_FBPOSRES]);
813 if (pr->nr > 0 || prfb->nr > 0)
814 {
815 atom = mtop->moltype[molb->type].atoms.atom;
816 for (i = 0; (i < pr->nr); i++)
817 {
818 ai = pr->param[i].AIa[0];
819 if (ai >= natoms)
820 {
821 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 821, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
822 ai+1, *molinfo[molb->type].name, fn, natoms);
823 }
824 hadAtom[ai] = TRUE1;
825 if (rc_scaling == erscCOM)
826 {
827 /* Determine the center of mass of the posres reference coordinates */
828 for (j = 0; j < npbcdim; j++)
829 {
830 sum[j] += atom[ai].m*x[a+ai][j];
831 }
832 totmass += atom[ai].m;
833 }
834 }
835 /* Same for flat-bottomed posres, but do not count an atom twice for COM */
836 for (i = 0; (i < prfb->nr); i++)
837 {
838 ai = prfb->param[i].AIa[0];
839 if (ai >= natoms)
840 {
841 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 841, "Position restraint atom index (%d) in moltype '%s' is larger than number of atoms in %s (%d).\n",
842 ai+1, *molinfo[molb->type].name, fn, natoms);
843 }
844 if (rc_scaling == erscCOM && hadAtom[ai] == FALSE0)
845 {
846 /* Determine the center of mass of the posres reference coordinates */
847 for (j = 0; j < npbcdim; j++)
848 {
849 sum[j] += atom[ai].m*x[a+ai][j];
850 }
851 totmass += atom[ai].m;
852 }
853 }
854 if (!bTopB)
855 {
856 molb->nposres_xA = nat_molb;
857 snew(molb->posres_xA, molb->nposres_xA)(molb->posres_xA) = save_calloc("molb->posres_xA", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 857, (molb->nposres_xA), sizeof(*(molb->posres_xA)));
858 for (i = 0; i < nat_molb; i++)
859 {
860 copy_rvec(x[a+i], molb->posres_xA[i]);
861 }
862 }
863 else
864 {
865 molb->nposres_xB = nat_molb;
866 snew(molb->posres_xB, molb->nposres_xB)(molb->posres_xB) = save_calloc("molb->posres_xB", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 866, (molb->nposres_xB), sizeof(*(molb->posres_xB)));
867 for (i = 0; i < nat_molb; i++)
868 {
869 copy_rvec(x[a+i], molb->posres_xB[i]);
870 }
871 }
872 }
873 a += nat_molb;
874 }
875 if (rc_scaling == erscCOM)
876 {
877 if (totmass == 0)
878 {
879 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 879, "The total mass of the position restraint atoms is 0");
880 }
881 for (j = 0; j < npbcdim; j++)
882 {
883 com[j] = sum[j]/totmass;
884 }
885 fprintf(stderrstderr, "The center of mass of the position restraint coord's is %6.3f %6.3f %6.3f\n", com[XX0], com[YY1], com[ZZ2]);
886 }
887
888 if (rc_scaling != erscNO)
889 {
890 assert(npbcdim <= DIM)((void) (0));
891
892 for (mb = 0; mb < mtop->nmolblock; mb++)
893 {
894 molb = &mtop->molblock[mb];
895 nat_molb = molb->nmol*mtop->moltype[molb->type].atoms.nr;
896 if (molb->nposres_xA > 0 || molb->nposres_xB > 0)
897 {
898 xp = (!bTopB ? molb->posres_xA : molb->posres_xB);
899 for (i = 0; i < nat_molb; i++)
900 {
901 for (j = 0; j < npbcdim; j++)
902 {
903 if (rc_scaling == erscALL)
904 {
905 /* Convert from Cartesian to crystal coordinates */
906 xp[i][j] *= invbox[j][j];
907 for (k = j+1; k < npbcdim; k++)
908 {
909 xp[i][j] += invbox[k][j]*xp[i][k];
910 }
911 }
912 else if (rc_scaling == erscCOM)
913 {
914 /* Subtract the center of mass */
915 xp[i][j] -= com[j];
916 }
917 }
918 }
919 }
920 }
921
922 if (rc_scaling == erscCOM)
923 {
924 /* Convert the COM from Cartesian to crystal coordinates */
925 for (j = 0; j < npbcdim; j++)
926 {
927 com[j] *= invbox[j][j];
928 for (k = j+1; k < npbcdim; k++)
929 {
930 com[j] += invbox[k][j]*com[k];
931 }
932 }
933 }
934 }
935
936 free_t_atoms(&dumat, TRUE1);
937 sfree(x)save_free("x", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 937, (x));
938 sfree(v)save_free("v", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 938, (v));
939 sfree(hadAtom)save_free("hadAtom", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 939, (hadAtom));
940}
941
942static void gen_posres(gmx_mtop_t *mtop, t_molinfo *mi,
943 char *fnA, char *fnB,
944 int rc_scaling, int ePBC,
945 rvec com, rvec comB,
946 warninp_t wi)
947{
948 int i, j;
949
950 read_posres (mtop, mi, FALSE0, fnA, rc_scaling, ePBC, com, wi);
951 if (strcmp(fnA, fnB)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(fnA) && __builtin_constant_p (fnB) && (__s1_len
= strlen (fnA), __s2_len = strlen (fnB), (!((size_t)(const void
*)((fnA) + 1) - (size_t)(const void *)(fnA) == 1) || __s1_len
>= 4) && (!((size_t)(const void *)((fnB) + 1) - (
size_t)(const void *)(fnB) == 1) || __s2_len >= 4)) ? __builtin_strcmp
(fnA, fnB) : (__builtin_constant_p (fnA) && ((size_t
)(const void *)((fnA) + 1) - (size_t)(const void *)(fnA) == 1
) && (__s1_len = strlen (fnA), __s1_len < 4) ? (__builtin_constant_p
(fnB) && ((size_t)(const void *)((fnB) + 1) - (size_t
)(const void *)(fnB) == 1) ? __builtin_strcmp (fnA, fnB) : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (fnB); int __result = (((const unsigned char *) (const
char *) (fnA))[0] - __s2[0]); if (__s1_len > 0 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (fnA))[1] - __s2[1]); if (__s1_len > 1 &&
__result == 0) { __result = (((const unsigned char *) (const
char *) (fnA))[2] - __s2[2]); if (__s1_len > 2 &&
__result == 0) __result = (((const unsigned char *) (const char
*) (fnA))[3] - __s2[3]); } } __result; }))) : (__builtin_constant_p
(fnB) && ((size_t)(const void *)((fnB) + 1) - (size_t
)(const void *)(fnB) == 1) && (__s2_len = strlen (fnB
), __s2_len < 4) ? (__builtin_constant_p (fnA) && (
(size_t)(const void *)((fnA) + 1) - (size_t)(const void *)(fnA
) == 1) ? __builtin_strcmp (fnA, fnB) : (- (__extension__ ({ const
unsigned char *__s2 = (const unsigned char *) (const char *)
(fnA); int __result = (((const unsigned char *) (const char *
) (fnB))[0] - __s2[0]); if (__s2_len > 0 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
fnB))[1] - __s2[1]); if (__s2_len > 1 && __result ==
0) { __result = (((const unsigned char *) (const char *) (fnB
))[2] - __s2[2]); if (__s2_len > 2 && __result == 0
) __result = (((const unsigned char *) (const char *) (fnB))[
3] - __s2[3]); } } __result; })))) : __builtin_strcmp (fnA, fnB
)))); }) != 0)
952 {
953 read_posres(mtop, mi, TRUE1, fnB, rc_scaling, ePBC, comB, wi);
954 }
955}
956
957static void set_wall_atomtype(gpp_atomtype_t at, t_gromppopts *opts,
958 t_inputrec *ir, warninp_t wi)
959{
960 int i;
961 char warn_buf[STRLEN4096];
962
963 if (ir->nwall > 0)
964 {
965 fprintf(stderrstderr, "Searching the wall atom type(s)\n");
966 }
967 for (i = 0; i < ir->nwall; i++)
968 {
969 ir->wall_atomtype[i] = get_atomtype_type(opts->wall_atomtype[i], at);
970 if (ir->wall_atomtype[i] == NOTSET-12345)
971 {
972 sprintf(warn_buf, "Specified wall atom type %s is not defined", opts->wall_atomtype[i]);
973 warning_error(wi, warn_buf);
974 }
975 }
976}
977
978static int nrdf_internal(t_atoms *atoms)
979{
980 int i, nmass, nrdf;
981
982 nmass = 0;
983 for (i = 0; i < atoms->nr; i++)
984 {
985 /* Vsite ptype might not be set here yet, so also check the mass */
986 if ((atoms->atom[i].ptype == eptAtom ||
987 atoms->atom[i].ptype == eptNucleus)
988 && atoms->atom[i].m > 0)
989 {
990 nmass++;
991 }
992 }
993 switch (nmass)
994 {
995 case 0: nrdf = 0; break;
996 case 1: nrdf = 0; break;
997 case 2: nrdf = 1; break;
998 default: nrdf = nmass*3 - 6; break;
999 }
1000
1001 return nrdf;
1002}
1003
1004void
1005spline1d( double dx,
1006 double * y,
1007 int n,
1008 double * u,
1009 double * y2 )
1010{
1011 int i;
1012 double p, q;
1013
1014 y2[0] = 0.0;
1015 u[0] = 0.0;
1016
1017 for (i = 1; i < n-1; i++)
1018 {
1019 p = 0.5*y2[i-1]+2.0;
1020 y2[i] = -0.5/p;
1021 q = (y[i+1]-2.0*y[i]+y[i-1])/dx;
1022 u[i] = (3.0*q/dx-0.5*u[i-1])/p;
1023 }
1024
1025 y2[n-1] = 0.0;
1026
1027 for (i = n-2; i >= 0; i--)
1028 {
1029 y2[i] = y2[i]*y2[i+1]+u[i];
1030 }
1031}
1032
1033
1034void
1035interpolate1d( double xmin,
1036 double dx,
1037 double * ya,
1038 double * y2a,
1039 double x,
1040 double * y,
1041 double * y1)
1042{
1043 int ix;
1044 double a, b;
1045
1046 ix = (x-xmin)/dx;
1047
1048 a = (xmin+(ix+1)*dx-x)/dx;
1049 b = (x-xmin-ix*dx)/dx;
1050
1051 *y = a*ya[ix]+b*ya[ix+1]+((a*a*a-a)*y2a[ix]+(b*b*b-b)*y2a[ix+1])*(dx*dx)/6.0;
1052 *y1 = (ya[ix+1]-ya[ix])/dx-(3.0*a*a-1.0)/6.0*dx*y2a[ix]+(3.0*b*b-1.0)/6.0*dx*y2a[ix+1];
1053}
1054
1055
1056void
1057setup_cmap (int grid_spacing,
1058 int nc,
1059 real * grid,
1060 gmx_cmap_t * cmap_grid)
1061{
1062 double *tmp_u, *tmp_u2, *tmp_yy, *tmp_y1, *tmp_t2, *tmp_grid;
1063
1064 int i, j, k, ii, jj, kk, idx;
1065 int offset;
1066 double dx, xmin, v, v1, v2, v12;
1067 double phi, psi;
1068
1069 snew(tmp_u, 2*grid_spacing)(tmp_u) = save_calloc("tmp_u", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1069, (2*grid_spacing), sizeof(*(tmp_u)));
1070 snew(tmp_u2, 2*grid_spacing)(tmp_u2) = save_calloc("tmp_u2", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1070, (2*grid_spacing), sizeof(*(tmp_u2)));
1071 snew(tmp_yy, 2*grid_spacing)(tmp_yy) = save_calloc("tmp_yy", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1071, (2*grid_spacing), sizeof(*(tmp_yy)));
1072 snew(tmp_y1, 2*grid_spacing)(tmp_y1) = save_calloc("tmp_y1", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1072, (2*grid_spacing), sizeof(*(tmp_y1)));
1073 snew(tmp_t2, 2*grid_spacing*2*grid_spacing)(tmp_t2) = save_calloc("tmp_t2", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1073, (2*grid_spacing*2*grid_spacing), sizeof(*(tmp_t2)));
1074 snew(tmp_grid, 2*grid_spacing*2*grid_spacing)(tmp_grid) = save_calloc("tmp_grid", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1074, (2*grid_spacing*2*grid_spacing), sizeof(*(tmp_grid)));
1075
1076 dx = 360.0/grid_spacing;
1077 xmin = -180.0-dx*grid_spacing/2;
1078
1079 for (kk = 0; kk < nc; kk++)
1080 {
1081 /* Compute an offset depending on which cmap we are using
1082 * Offset will be the map number multiplied with the
1083 * grid_spacing * grid_spacing * 2
1084 */
1085 offset = kk * grid_spacing * grid_spacing * 2;
1086
1087 for (i = 0; i < 2*grid_spacing; i++)
1088 {
1089 ii = (i+grid_spacing-grid_spacing/2)%grid_spacing;
1090
1091 for (j = 0; j < 2*grid_spacing; j++)
1092 {
1093 jj = (j+grid_spacing-grid_spacing/2)%grid_spacing;
1094 tmp_grid[i*grid_spacing*2+j] = grid[offset+ii*grid_spacing+jj];
1095 }
1096 }
1097
1098 for (i = 0; i < 2*grid_spacing; i++)
1099 {
1100 spline1d(dx, &(tmp_grid[2*grid_spacing*i]), 2*grid_spacing, tmp_u, &(tmp_t2[2*grid_spacing*i]));
1101 }
1102
1103 for (i = grid_spacing/2; i < grid_spacing+grid_spacing/2; i++)
1104 {
1105 ii = i-grid_spacing/2;
1106 phi = ii*dx-180.0;
1107
1108 for (j = grid_spacing/2; j < grid_spacing+grid_spacing/2; j++)
1109 {
1110 jj = j-grid_spacing/2;
1111 psi = jj*dx-180.0;
1112
1113 for (k = 0; k < 2*grid_spacing; k++)
1114 {
1115 interpolate1d(xmin, dx, &(tmp_grid[2*grid_spacing*k]),
1116 &(tmp_t2[2*grid_spacing*k]), psi, &tmp_yy[k], &tmp_y1[k]);
1117 }
1118
1119 spline1d(dx, tmp_yy, 2*grid_spacing, tmp_u, tmp_u2);
1120 interpolate1d(xmin, dx, tmp_yy, tmp_u2, phi, &v, &v1);
1121 spline1d(dx, tmp_y1, 2*grid_spacing, tmp_u, tmp_u2);
1122 interpolate1d(xmin, dx, tmp_y1, tmp_u2, phi, &v2, &v12);
1123
1124 idx = ii*grid_spacing+jj;
1125 cmap_grid->cmapdata[kk].cmap[idx*4] = grid[offset+ii*grid_spacing+jj];
1126 cmap_grid->cmapdata[kk].cmap[idx*4+1] = v1;
1127 cmap_grid->cmapdata[kk].cmap[idx*4+2] = v2;
1128 cmap_grid->cmapdata[kk].cmap[idx*4+3] = v12;
1129 }
1130 }
1131 }
1132}
1133
1134void init_cmap_grid(gmx_cmap_t *cmap_grid, int ngrid, int grid_spacing)
1135{
1136 int i, k, nelem;
1137
1138 cmap_grid->ngrid = ngrid;
1139 cmap_grid->grid_spacing = grid_spacing;
1140 nelem = cmap_grid->grid_spacing*cmap_grid->grid_spacing;
1141
1142 snew(cmap_grid->cmapdata, ngrid)(cmap_grid->cmapdata) = save_calloc("cmap_grid->cmapdata"
, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1142, (ngrid), sizeof(*(cmap_grid->cmapdata)));
1143
1144 for (i = 0; i < cmap_grid->ngrid; i++)
1145 {
1146 snew(cmap_grid->cmapdata[i].cmap, 4*nelem)(cmap_grid->cmapdata[i].cmap) = save_calloc("cmap_grid->cmapdata[i].cmap"
, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1146, (4*nelem), sizeof(*(cmap_grid->cmapdata[i].cmap)));
1147 }
1148}
1149
1150
1151static int count_constraints(gmx_mtop_t *mtop, t_molinfo *mi, warninp_t wi)
1152{
1153 int count, count_mol, i, mb;
1154 gmx_molblock_t *molb;
1155 t_params *plist;
1156 char buf[STRLEN4096];
1157
1158 count = 0;
1159 for (mb = 0; mb < mtop->nmolblock; mb++)
1160 {
1161 count_mol = 0;
1162 molb = &mtop->molblock[mb];
1163 plist = mi[molb->type].plist;
1164
1165 for (i = 0; i < F_NRE; i++)
1166 {
1167 if (i == F_SETTLE)
1168 {
1169 count_mol += 3*plist[i].nr;
1170 }
1171 else if (interaction_function[i].flags & IF_CONSTRAINT1<<2)
1172 {
1173 count_mol += plist[i].nr;
1174 }
1175 }
1176
1177 if (count_mol > nrdf_internal(&mi[molb->type].atoms))
1178 {
1179 sprintf(buf,
1180 "Molecule type '%s' has %d constraints.\n"
1181 "For stability and efficiency there should not be more constraints than internal number of degrees of freedom: %d.\n",
1182 *mi[molb->type].name, count_mol,
1183 nrdf_internal(&mi[molb->type].atoms));
1184 warning(wi, buf);
1185 }
1186 count += molb->nmol*count_mol;
1187 }
1188
1189 return count;
1190}
1191
1192static void check_gbsa_params_charged(gmx_mtop_t *sys, gpp_atomtype_t atype)
1193{
1194 int i, nmiss, natoms, mt;
1195 real q;
1196 const t_atoms *atoms;
1197
1198 nmiss = 0;
1199 for (mt = 0; mt < sys->nmoltype; mt++)
1200 {
1201 atoms = &sys->moltype[mt].atoms;
1202 natoms = atoms->nr;
1203
1204 for (i = 0; i < natoms; i++)
1205 {
1206 q = atoms->atom[i].q;
1207 if ((get_atomtype_radius(atoms->atom[i].type, atype) == 0 ||
1208 get_atomtype_vol(atoms->atom[i].type, atype) == 0 ||
1209 get_atomtype_surftens(atoms->atom[i].type, atype) == 0 ||
1210 get_atomtype_gb_radius(atoms->atom[i].type, atype) == 0 ||
1211 get_atomtype_S_hct(atoms->atom[i].type, atype) == 0) &&
1212 q != 0)
1213 {
1214 fprintf(stderrstderr, "\nGB parameter(s) zero for atom type '%s' while charge is %g\n",
1215 get_atomtype_name(atoms->atom[i].type, atype), q);
1216 nmiss++;
1217 }
1218 }
1219 }
1220
1221 if (nmiss > 0)
1222 {
1223 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1223, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield has parameters with value zero for %d atomtypes that occur as charged atoms.", nmiss);
1224 }
1225}
1226
1227
1228static void check_gbsa_params(gpp_atomtype_t atype)
1229{
1230 int nmiss, i;
1231
1232 /* If we are doing GBSA, check that we got the parameters we need
1233 * This checking is to see if there are GBSA paratmeters for all
1234 * atoms in the force field. To go around this for testing purposes
1235 * comment out the nerror++ counter temporarily
1236 */
1237 nmiss = 0;
1238 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1239 {
1240 if (get_atomtype_radius(i, atype) < 0 ||
1241 get_atomtype_vol(i, atype) < 0 ||
1242 get_atomtype_surftens(i, atype) < 0 ||
1243 get_atomtype_gb_radius(i, atype) < 0 ||
1244 get_atomtype_S_hct(i, atype) < 0)
1245 {
1246 fprintf(stderrstderr, "\nGB parameter(s) missing or negative for atom type '%s'\n",
1247 get_atomtype_name(i, atype));
1248 nmiss++;
1249 }
1250 }
1251
1252 if (nmiss > 0)
1253 {
1254 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1254, "Can't do GB electrostatics; the implicit_genborn_params section of the forcefield is missing parameters for %d atomtypes or they might be negative.", nmiss);
1255 }
1256
1257}
1258
1259static real calc_temp(const gmx_mtop_t *mtop,
1260 const t_inputrec *ir,
1261 rvec *v)
1262{
1263 double sum_mv2;
1264 gmx_mtop_atomloop_all_t aloop;
1265 t_atom *atom;
1266 int a;
1267 int nrdf, g;
1268
1269 sum_mv2 = 0;
1270
1271 aloop = gmx_mtop_atomloop_all_init(mtop);
1272 while (gmx_mtop_atomloop_all_next(aloop, &a, &atom))
1273 {
1274 sum_mv2 += atom->m*norm2(v[a]);
1275 }
1276
1277 nrdf = 0;
1278 for (g = 0; g < ir->opts.ngtc; g++)
1279 {
1280 nrdf += ir->opts.nrdf[g];
1281 }
1282
1283 return sum_mv2/(nrdf*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3)));
1284}
1285
1286static real get_max_reference_temp(const t_inputrec *ir,
1287 warninp_t wi)
1288{
1289 real ref_t;
1290 int i;
1291 gmx_bool bNoCoupl;
1292
1293 ref_t = 0;
1294 bNoCoupl = FALSE0;
1295 for (i = 0; i < ir->opts.ngtc; i++)
1296 {
1297 if (ir->opts.tau_t[i] < 0)
1298 {
1299 bNoCoupl = TRUE1;
1300 }
1301 else
1302 {
1303 ref_t = max(ref_t, ir->opts.ref_t[i])(((ref_t) > (ir->opts.ref_t[i])) ? (ref_t) : (ir->opts
.ref_t[i]) );
1304 }
1305 }
1306
1307 if (bNoCoupl)
1308 {
1309 char buf[STRLEN4096];
1310
1311 sprintf(buf, "Some temperature coupling groups do not use temperature coupling. We will assume their temperature is not more than %.3f K. If their temperature is higher, the energy error and the Verlet buffer might be underestimated.",
1312 ref_t);
1313 warning(wi, buf);
1314 }
1315
1316 return ref_t;
1317}
1318
1319static void set_verlet_buffer(const gmx_mtop_t *mtop,
1320 t_inputrec *ir,
1321 real buffer_temp,
1322 matrix box,
1323 warninp_t wi)
1324{
1325 int i;
1326 verletbuf_list_setup_t ls;
1327 real rlist_1x1;
1328 int n_nonlin_vsite;
1329 char warn_buf[STRLEN4096];
1330
1331 printf("Determining Verlet buffer for a tolerance of %g kJ/mol/ps at %g K\n", ir->verletbuf_tol, buffer_temp);
1332
1333 /* Calculate the buffer size for simple atom vs atoms list */
1334 ls.cluster_size_i = 1;
1335 ls.cluster_size_j = 1;
1336 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1337 &ls, &n_nonlin_vsite, &rlist_1x1);
1338
1339 /* Set the pair-list buffer size in ir */
1340 verletbuf_get_list_setup(FALSE0, &ls);
1341 calc_verlet_buffer_size(mtop, det(box), ir, buffer_temp,
1342 &ls, &n_nonlin_vsite, &ir->rlist);
1343
1344 if (n_nonlin_vsite > 0)
1345 {
1346 sprintf(warn_buf, "There are %d non-linear virtual site constructions. Their contribution to the energy error is approximated. In most cases this does not affect the error significantly.", n_nonlin_vsite);
1347 warning_note(wi, warn_buf);
1348 }
1349
1350 printf("Calculated rlist for %dx%d atom pair-list as %.3f nm, buffer size %.3f nm\n",
1351 1, 1, rlist_1x1, rlist_1x1-max(ir->rvdw, ir->rcoulomb)(((ir->rvdw) > (ir->rcoulomb)) ? (ir->rvdw) : (ir
->rcoulomb) ));
1352
1353 ir->rlistlong = ir->rlist;
1354 printf("Set rlist, assuming %dx%d atom pair-list, to %.3f nm, buffer size %.3f nm\n",
1355 ls.cluster_size_i, ls.cluster_size_j,
1356 ir->rlist, ir->rlist-max(ir->rvdw, ir->rcoulomb)(((ir->rvdw) > (ir->rcoulomb)) ? (ir->rvdw) : (ir
->rcoulomb) ));
1357
1358 if (sqr(ir->rlistlong) >= max_cutoff2(ir->ePBC, box))
1359 {
1360 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1360, "The pair-list cut-off (%g nm) is longer than half the shortest box vector or longer than the smallest box diagonal element (%g nm). Increase the box size or decrease nstlist or increase verlet-buffer-tolerance.", ir->rlistlong, sqrt(max_cutoff2(ir->ePBC, box)));
1361 }
1362}
1363
1364int gmx_grompp(int argc, char *argv[])
1365{
1366 static const char *desc[] = {
1367 "[THISMODULE] (the gromacs preprocessor)",
1368 "reads a molecular topology file, checks the validity of the",
1369 "file, expands the topology from a molecular description to an atomic",
1370 "description. The topology file contains information about",
1371 "molecule types and the number of molecules, the preprocessor",
1372 "copies each molecule as needed. ",
1373 "There is no limitation on the number of molecule types. ",
1374 "Bonds and bond-angles can be converted into constraints, separately",
1375 "for hydrogens and heavy atoms.",
1376 "Then a coordinate file is read and velocities can be generated",
1377 "from a Maxwellian distribution if requested.",
1378 "[THISMODULE] also reads parameters for [gmx-mdrun] ",
1379 "(eg. number of MD steps, time step, cut-off), and others such as",
1380 "NEMD parameters, which are corrected so that the net acceleration",
1381 "is zero.",
1382 "Eventually a binary file is produced that can serve as the sole input",
1383 "file for the MD program.[PAR]",
1384
1385 "[THISMODULE] uses the atom names from the topology file. The atom names",
1386 "in the coordinate file (option [TT]-c[tt]) are only read to generate",
1387 "warnings when they do not match the atom names in the topology.",
1388 "Note that the atom names are irrelevant for the simulation as",
1389 "only the atom types are used for generating interaction parameters.[PAR]",
1390
1391 "[THISMODULE] uses a built-in preprocessor to resolve includes, macros, ",
1392 "etc. The preprocessor supports the following keywords:[PAR]",
1393 "#ifdef VARIABLE[BR]",
1394 "#ifndef VARIABLE[BR]",
1395 "#else[BR]",
1396 "#endif[BR]",
1397 "#define VARIABLE[BR]",
1398 "#undef VARIABLE[BR]"
1399 "#include \"filename\"[BR]",
1400 "#include <filename>[PAR]",
1401 "The functioning of these statements in your topology may be modulated by",
1402 "using the following two flags in your [TT].mdp[tt] file:[PAR]",
1403 "[TT]define = -DVARIABLE1 -DVARIABLE2[BR]",
1404 "include = -I/home/john/doe[tt][BR]",
1405 "For further information a C-programming textbook may help you out.",
1406 "Specifying the [TT]-pp[tt] flag will get the pre-processed",
1407 "topology file written out so that you can verify its contents.[PAR]",
1408
1409 /* cpp has been unnecessary for some time, hasn't it?
1410 "If your system does not have a C-preprocessor, you can still",
1411 "use [TT]grompp[tt], but you do not have access to the features ",
1412 "from the cpp. Command line options to the C-preprocessor can be given",
1413 "in the [TT].mdp[tt] file. See your local manual (man cpp).[PAR]",
1414 */
1415
1416 "When using position restraints a file with restraint coordinates",
1417 "can be supplied with [TT]-r[tt], otherwise restraining will be done",
1418 "with respect to the conformation from the [TT]-c[tt] option.",
1419 "For free energy calculation the the coordinates for the B topology",
1420 "can be supplied with [TT]-rb[tt], otherwise they will be equal to",
1421 "those of the A topology.[PAR]",
1422
1423 "Starting coordinates can be read from trajectory with [TT]-t[tt].",
1424 "The last frame with coordinates and velocities will be read,",
1425 "unless the [TT]-time[tt] option is used. Only if this information",
1426 "is absent will the coordinates in the [TT]-c[tt] file be used.",
1427 "Note that these velocities will not be used when [TT]gen_vel = yes[tt]",
1428 "in your [TT].mdp[tt] file. An energy file can be supplied with",
1429 "[TT]-e[tt] to read Nose-Hoover and/or Parrinello-Rahman coupling",
1430 "variables.[PAR]",
1431
1432 "[THISMODULE] can be used to restart simulations (preserving",
1433 "continuity) by supplying just a checkpoint file with [TT]-t[tt].",
1434 "However, for simply changing the number of run steps to extend",
1435 "a run, using [gmx-convert-tpr] is more convenient than [THISMODULE].",
1436 "You then supply the old checkpoint file directly to [gmx-mdrun]",
1437 "with [TT]-cpi[tt]. If you wish to change the ensemble or things",
1438 "like output frequency, then supplying the checkpoint file to",
1439 "[THISMODULE] with [TT]-t[tt] along with a new [TT].mdp[tt] file",
1440 "with [TT]-f[tt] is the recommended procedure.[PAR]",
1441
1442 "By default, all bonded interactions which have constant energy due to",
1443 "virtual site constructions will be removed. If this constant energy is",
1444 "not zero, this will result in a shift in the total energy. All bonded",
1445 "interactions can be kept by turning off [TT]-rmvsbds[tt]. Additionally,",
1446 "all constraints for distances which will be constant anyway because",
1447 "of virtual site constructions will be removed. If any constraints remain",
1448 "which involve virtual sites, a fatal error will result.[PAR]"
1449
1450 "To verify your run input file, please take note of all warnings",
1451 "on the screen, and correct where necessary. Do also look at the contents",
1452 "of the [TT]mdout.mdp[tt] file; this contains comment lines, as well as",
1453 "the input that [THISMODULE] has read. If in doubt, you can start [THISMODULE]",
1454 "with the [TT]-debug[tt] option which will give you more information",
1455 "in a file called [TT]grompp.log[tt] (along with real debug info). You",
1456 "can see the contents of the run input file with the [gmx-dump]",
1457 "program. [gmx-check] can be used to compare the contents of two",
1458 "run input files.[PAR]"
1459
1460 "The [TT]-maxwarn[tt] option can be used to override warnings printed",
1461 "by [THISMODULE] that otherwise halt output. In some cases, warnings are",
1462 "harmless, but usually they are not. The user is advised to carefully",
1463 "interpret the output messages before attempting to bypass them with",
1464 "this option."
1465 };
1466 t_gromppopts *opts;
1467 gmx_mtop_t *sys;
1468 int nmi;
1469 t_molinfo *mi;
1470 gpp_atomtype_t atype;
1471 t_inputrec *ir;
1472 int natoms, nvsite, comb, mt;
1473 t_params *plist;
1474 t_state state;
1475 matrix box;
1476 real max_spacing, fudgeQQ;
1477 double reppow;
1478 char fn[STRLEN4096], fnB[STRLEN4096];
1479 const char *mdparin;
1480 int ntype;
1481 gmx_bool bNeedVel, bGenVel;
1482 gmx_bool have_atomnumber;
1483 int n12, n13, n14;
1484 t_params *gb_plist = NULL((void*)0);
1485 gmx_genborn_t *born = NULL((void*)0);
1486 output_env_t oenv;
1487 gmx_bool bVerbose = FALSE0;
1488 warninp_t wi;
1489 char warn_buf[STRLEN4096];
1490 unsigned int useed;
1491 t_atoms IMDatoms; /* Atoms to be operated on interactively (IMD) */
1492
1493 t_filenm fnm[] = {
1494 { efMDP, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
1495 { efMDP, "-po", "mdout", ffWRITE1<<2 },
1496 { efSTX, "-c", NULL((void*)0), ffREAD1<<1 },
1497 { efSTX, "-r", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
1498 { efSTX, "-rb", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
1499 { efNDX, NULL((void*)0), NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
1500 { efTOP, NULL((void*)0), NULL((void*)0), ffREAD1<<1 },
1501 { efTOP, "-pp", "processed", ffOPTWR(1<<2| 1<<3) },
1502 { efTPX, "-o", NULL((void*)0), ffWRITE1<<2 },
1503 { efTRN, "-t", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
1504 { efEDR, "-e", NULL((void*)0), ffOPTRD(1<<1 | 1<<3) },
1505 /* This group is needed by the VMD viewer as the start configuration for IMD sessions: */
1506 { efGRO, "-imd", "imdgroup", ffOPTWR(1<<2| 1<<3) },
1507 { efTRN, "-ref", "rotref", ffOPTRW((1<<1 | 1<<2) | 1<<3) }
1508 };
1509#define NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))) asize(fnm)((int)(sizeof(fnm)/sizeof((fnm)[0])))
1510
1511 /* Command line options */
1512 static gmx_bool bRenum = TRUE1;
1513 static gmx_bool bRmVSBds = TRUE1, bZero = FALSE0;
1514 static int i, maxwarn = 0;
1515 static real fr_time = -1;
1516 t_pargs pa[] = {
1517 { "-v", FALSE0, etBOOL, {&bVerbose},
1518 "Be loud and noisy" },
1519 { "-time", FALSE0, etREAL, {&fr_time},
1520 "Take frame at or first after this time." },
1521 { "-rmvsbds", FALSE0, etBOOL, {&bRmVSBds},
1522 "Remove constant bonded interactions with virtual sites" },
1523 { "-maxwarn", FALSE0, etINT, {&maxwarn},
1524 "Number of allowed warnings during input processing. Not for normal use and may generate unstable systems" },
1525 { "-zero", FALSE0, etBOOL, {&bZero},
1526 "Set parameters for bonded interactions without defaults to zero instead of generating an error" },
1527 { "-renum", FALSE0, etBOOL, {&bRenum},
1528 "Renumber atomtypes and minimize number of atomtypes" }
1529 };
1530
1531 /* Initiate some variables */
1532 snew(ir, 1)(ir) = save_calloc("ir", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1532, (1), sizeof(*(ir)));
1533 snew(opts, 1)(opts) = save_calloc("opts", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1533, (1), sizeof(*(opts)));
1534 init_ir(ir, opts);
1535
1536 /* Parse the command line */
1537 if (!parse_common_args(&argc, argv, 0, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm, asize(pa)((int)(sizeof(pa)/sizeof((pa)[0]))), pa,
1538 asize(desc)((int)(sizeof(desc)/sizeof((desc)[0]))), desc, 0, NULL((void*)0), &oenv))
1539 {
1540 return 0;
1541 }
1542
1543 wi = init_warning(TRUE1, maxwarn);
1544
1545 /* PARAMETER file processing */
1546 mdparin = opt2fn("-f", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
1547 set_warning_line(wi, mdparin, -1);
1548 get_ir(mdparin, opt2fn("-po", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), ir, opts, wi);
1549
1550 if (bVerbose)
1551 {
1552 fprintf(stderrstderr, "checking input for internal consistency...\n");
1553 }
1554 check_ir(mdparin, ir, opts, wi);
1555
1556 if (ir->ld_seed == -1)
1557 {
1558 ir->ld_seed = (gmx_int64_t)gmx_rng_make_seed();
1559 fprintf(stderrstderr, "Setting the LD random seed to %"GMX_PRId64"l" "d" "\n", ir->ld_seed);
1560 }
1561
1562 if (ir->expandedvals->lmc_seed == -1)
1563 {
1564 ir->expandedvals->lmc_seed = (int)gmx_rng_make_seed();
1565 fprintf(stderrstderr, "Setting the lambda MC random seed to %d\n", ir->expandedvals->lmc_seed);
1566 }
1567
1568 bNeedVel = EI_STATE_VELOCITY(ir->eI)(((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) || ((ir->eI) == eiSD1 || (ir->eI) == eiSD2));
1569 bGenVel = (bNeedVel && opts->bGenVel);
1570 if (bGenVel && ir->bContinuation)
1571 {
1572 sprintf(warn_buf,
1573 "Generating velocities is inconsistent with attempting "
1574 "to continue a previous run. Choose only one of "
1575 "gen-vel = yes and continuation = yes.");
1576 warning_error(wi, warn_buf);
1577 }
1578
1579 snew(plist, F_NRE)(plist) = save_calloc("plist", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1579, (F_NRE), sizeof(*(plist)));
1580 init_plist(plist);
1581 snew(sys, 1)(sys) = save_calloc("sys", "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1581, (1), sizeof(*(sys)));
1582 atype = init_atomtype();
1583 if (debug)
1584 {
1585 pr_symtab(debug, 0, "Just opened", &sys->symtab);
1586 }
1587
1588 strcpy(fn, ftp2fn(efTOP, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1589 if (!gmx_fexist(fn))
1590 {
1591 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1591, "%s does not exist", fn);
1592 }
1593 new_status(fn, opt2fn_null("-pp", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), opt2fn("-c", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1594 opts, ir, bZero, bGenVel, bVerbose, &state,
1595 atype, sys, &nmi, &mi, plist, &comb, &reppow, &fudgeQQ,
1596 opts->bMorse,
1597 wi);
1598
1599 if (debug)
1600 {
1601 pr_symtab(debug, 0, "After new_status", &sys->symtab);
1602 }
1603
1604 nvsite = 0;
1605 /* set parameters for virtual site construction (not for vsiten) */
1606 for (mt = 0; mt < sys->nmoltype; mt++)
1607 {
1608 nvsite +=
1609 set_vsites(bVerbose, &sys->moltype[mt].atoms, atype, mi[mt].plist);
1610 }
1611 /* now throw away all obsolete bonds, angles and dihedrals: */
1612 /* note: constraints are ALWAYS removed */
1613 if (nvsite)
1614 {
1615 for (mt = 0; mt < sys->nmoltype; mt++)
1616 {
1617 clean_vsite_bondeds(mi[mt].plist, sys->moltype[mt].atoms.nr, bRmVSBds);
1618 }
1619 }
1620
1621 if (ir->cutoff_scheme == ecutsVERLET)
1622 {
1623 fprintf(stderrstderr, "Removing all charge groups because cutoff-scheme=%s\n",
1624 ecutscheme_names[ir->cutoff_scheme]);
1625
1626 /* Remove all charge groups */
1627 gmx_mtop_remove_chargegroups(sys);
1628 }
1629
1630 if (count_constraints(sys, mi, wi) && (ir->eConstrAlg == econtSHAKE))
1631 {
1632 if (ir->eI == eiCG || ir->eI == eiLBFGS)
1633 {
1634 sprintf(warn_buf, "Can not do %s with %s, use %s",
1635 EI(ir->eI)((((ir->eI) < 0) || ((ir->eI) >= (eiNR))) ? "UNDEFINED"
: (ei_names)[ir->eI]), econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1636 warning_error(wi, warn_buf);
1637 }
1638 if (ir->bPeriodicMols)
1639 {
1640 sprintf(warn_buf, "Can not do periodic molecules with %s, use %s",
1641 econstr_names[econtSHAKE], econstr_names[econtLINCS]);
1642 warning_error(wi, warn_buf);
1643 }
1644 }
1645
1646 if (EI_SD (ir->eI)((ir->eI) == eiSD1 || (ir->eI) == eiSD2) && ir->etc != etcNO)
1647 {
1648 warning_note(wi, "Temperature coupling is ignored with SD integrators.");
1649 }
1650
1651 /* If we are doing QM/MM, check that we got the atom numbers */
1652 have_atomnumber = TRUE1;
1653 for (i = 0; i < get_atomtype_ntypes(atype); i++)
1654 {
1655 have_atomnumber = have_atomnumber && (get_atomtype_atomnumber(i, atype) >= 0);
1656 }
1657 if (!have_atomnumber && ir->bQMMM)
1658 {
1659 warning_error(wi,
1660 "\n"
1661 "It appears as if you are trying to run a QM/MM calculation, but the force\n"
1662 "field you are using does not contain atom numbers fields. This is an\n"
1663 "optional field (introduced in Gromacs 3.3) for general runs, but mandatory\n"
1664 "for QM/MM. The good news is that it is easy to add - put the atom number as\n"
1665 "an integer just before the mass column in ffXXXnb.itp.\n"
1666 "NB: United atoms have the same atom numbers as normal ones.\n\n");
1667 }
1668
1669 if (ir->bAdress)
1670 {
1671 if ((ir->adress->const_wf > 1) || (ir->adress->const_wf < 0))
1672 {
1673 warning_error(wi, "AdResS contant weighting function should be between 0 and 1\n\n");
1674 }
1675 /** TODO check size of ex+hy width against box size */
1676 }
1677
1678 /* Check for errors in the input now, since they might cause problems
1679 * during processing further down.
1680 */
1681 check_warning_error(wi, FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1681);
1682
1683 if (opt2bSet("-r", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm))
1684 {
1685 sprintf(fn, "%s", opt2fn("-r", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1686 }
1687 else
1688 {
1689 sprintf(fn, "%s", opt2fn("-c", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1690 }
1691 if (opt2bSet("-rb", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm))
1692 {
1693 sprintf(fnB, "%s", opt2fn("-rb", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm));
1694 }
1695 else
1696 {
1697 strcpy(fnB, fn);
1698 }
1699
1700 if (nint_ftype(sys, mi, F_POSRES) > 0 || nint_ftype(sys, mi, F_FBPOSRES) > 0)
1701 {
1702 if (bVerbose)
1703 {
1704 fprintf(stderrstderr, "Reading position restraint coords from %s", fn);
1705 if (strcmp(fn, fnB)__extension__ ({ size_t __s1_len, __s2_len; (__builtin_constant_p
(fn) && __builtin_constant_p (fnB) && (__s1_len
= strlen (fn), __s2_len = strlen (fnB), (!((size_t)(const void
*)((fn) + 1) - (size_t)(const void *)(fn) == 1) || __s1_len >=
4) && (!((size_t)(const void *)((fnB) + 1) - (size_t
)(const void *)(fnB) == 1) || __s2_len >= 4)) ? __builtin_strcmp
(fn, fnB) : (__builtin_constant_p (fn) && ((size_t)(
const void *)((fn) + 1) - (size_t)(const void *)(fn) == 1) &&
(__s1_len = strlen (fn), __s1_len < 4) ? (__builtin_constant_p
(fnB) && ((size_t)(const void *)((fnB) + 1) - (size_t
)(const void *)(fnB) == 1) ? __builtin_strcmp (fn, fnB) : (__extension__
({ const unsigned char *__s2 = (const unsigned char *) (const
char *) (fnB); int __result = (((const unsigned char *) (const
char *) (fn))[0] - __s2[0]); if (__s1_len > 0 && __result
== 0) { __result = (((const unsigned char *) (const char *) (
fn))[1] - __s2[1]); if (__s1_len > 1 && __result ==
0) { __result = (((const unsigned char *) (const char *) (fn
))[2] - __s2[2]); if (__s1_len > 2 && __result == 0
) __result = (((const unsigned char *) (const char *) (fn))[3
] - __s2[3]); } } __result; }))) : (__builtin_constant_p (fnB
) && ((size_t)(const void *)((fnB) + 1) - (size_t)(const
void *)(fnB) == 1) && (__s2_len = strlen (fnB), __s2_len
< 4) ? (__builtin_constant_p (fn) && ((size_t)(const
void *)((fn) + 1) - (size_t)(const void *)(fn) == 1) ? __builtin_strcmp
(fn, fnB) : (- (__extension__ ({ const unsigned char *__s2 =
(const unsigned char *) (const char *) (fn); int __result = (
((const unsigned char *) (const char *) (fnB))[0] - __s2[0]);
if (__s2_len > 0 && __result == 0) { __result = (
((const unsigned char *) (const char *) (fnB))[1] - __s2[1]);
if (__s2_len > 1 && __result == 0) { __result = (
((const unsigned char *) (const char *) (fnB))[2] - __s2[2]);
if (__s2_len > 2 && __result == 0) __result = (((
const unsigned char *) (const char *) (fnB))[3] - __s2[3]); }
} __result; })))) : __builtin_strcmp (fn, fnB)))); }) == 0)
1706 {
1707 fprintf(stderrstderr, "\n");
1708 }
1709 else
1710 {
1711 fprintf(stderrstderr, " and %s\n", fnB);
1712 }
1713 }
1714 gen_posres(sys, mi, fn, fnB,
1715 ir->refcoord_scaling, ir->ePBC,
1716 ir->posres_com, ir->posres_comB,
1717 wi);
1718 }
1719
1720 /* If we are using CMAP, setup the pre-interpolation grid */
1721 if (plist->ncmap > 0)
1722 {
1723 init_cmap_grid(&sys->ffparams.cmap_grid, plist->nc, plist->grid_spacing);
1724 setup_cmap(plist->grid_spacing, plist->nc, plist->cmap, &sys->ffparams.cmap_grid);
1725 }
1726
1727 set_wall_atomtype(atype, opts, ir, wi);
1728 if (bRenum)
1729 {
1730 renum_atype(plist, sys, ir->wall_atomtype, atype, bVerbose);
1731 ntype = get_atomtype_ntypes(atype);
1732 }
1733
1734 if (ir->implicit_solvent != eisNO)
1735 {
1736 /* Now we have renumbered the atom types, we can check the GBSA params */
1737 check_gbsa_params(atype);
1738
1739 /* Check that all atoms that have charge and/or LJ-parameters also have
1740 * sensible GB-parameters
1741 */
1742 check_gbsa_params_charged(sys, atype);
1743 }
1744
1745 /* PELA: Copy the atomtype data to the topology atomtype list */
1746 copy_atomtype_atomtypes(atype, &(sys->atomtypes));
1747
1748 if (debug)
1749 {
1750 pr_symtab(debug, 0, "After renum_atype", &sys->symtab);
1751 }
1752
1753 if (bVerbose)
1754 {
1755 fprintf(stderrstderr, "converting bonded parameters...\n");
1756 }
1757
1758 ntype = get_atomtype_ntypes(atype);
1759 convert_params(ntype, plist, mi, comb, reppow, fudgeQQ, sys);
1760
1761 if (debug)
1762 {
1763 pr_symtab(debug, 0, "After convert_params", &sys->symtab);
1764 }
1765
1766 /* set ptype to VSite for virtual sites */
1767 for (mt = 0; mt < sys->nmoltype; mt++)
1768 {
1769 set_vsites_ptype(FALSE0, &sys->moltype[mt]);
1770 }
1771 if (debug)
1772 {
1773 pr_symtab(debug, 0, "After virtual sites", &sys->symtab);
1774 }
1775 /* Check velocity for virtual sites and shells */
1776 if (bGenVel)
1777 {
1778 check_vel(sys, state.v);
1779 }
1780
1781 /* check masses */
1782 check_mol(sys, wi);
1783
1784 for (i = 0; i < sys->nmoltype; i++)
1785 {
1786 check_cg_sizes(ftp2fn(efTOP, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), &sys->moltype[i].cgs, wi);
1787 }
1788
1789 if (EI_DYNAMICS(ir->eI)(((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) || ((ir->eI) == eiSD1 || (ir->eI) == eiSD2) ||
(ir->eI) == eiBD) && ir->eI != eiBD)
1790 {
1791 check_bonds_timestep(sys, ir->delta_t, wi);
1792 }
1793
1794 if (EI_ENERGY_MINIMIZATION(ir->eI)((ir->eI) == eiSteep || (ir->eI) == eiCG || (ir->eI)
== eiLBFGS) && 0 == ir->nsteps)
1795 {
1796 warning_note(wi, "Zero-step energy minimization will alter the coordinates before calculating the energy. If you just want the energy of a single point, try zero-step MD (with unconstrained_start = yes). To do multiple single-point energy evaluations of different configurations of the same topology, use mdrun -rerun.");
1797 }
1798
1799 check_warning_error(wi, FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1799);
1800
1801 if (bVerbose)
1802 {
1803 fprintf(stderrstderr, "initialising group options...\n");
1804 }
1805 do_index(mdparin, ftp2fn_null(efNDX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1806 sys, bVerbose, ir,
1807 bGenVel ? state.v : NULL((void*)0),
1808 wi);
1809
1810 if (ir->cutoff_scheme == ecutsVERLET && ir->verletbuf_tol > 0 &&
1811 ir->nstlist > 1)
1812 {
1813 if (EI_DYNAMICS(ir->eI)(((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) || ((ir->eI) == eiSD1 || (ir->eI) == eiSD2) ||
(ir->eI) == eiBD) && inputrec2nboundeddim(ir) == 3)
1814 {
1815 real buffer_temp;
1816
1817 if (EI_MD(ir->eI)((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) && ir->etc == etcNO)
1818 {
1819 if (bGenVel)
1820 {
1821 buffer_temp = opts->tempi;
1822 }
1823 else
1824 {
1825 buffer_temp = calc_temp(sys, ir, state.v);
1826 }
1827 if (buffer_temp > 0)
1828 {
1829 sprintf(warn_buf, "NVE simulation: will use the initial temperature of %.3f K for determining the Verlet buffer size", buffer_temp);
1830 warning_note(wi, warn_buf);
1831 }
1832 else
1833 {
1834 sprintf(warn_buf, "NVE simulation with an initial temperature of zero: will use a Verlet buffer of %d%%. Check your energy drift!",
1835 (int)(verlet_buffer_ratio_NVE_T0*100 + 0.5));
1836 warning_note(wi, warn_buf);
1837 }
1838 }
1839 else
1840 {
1841 buffer_temp = get_max_reference_temp(ir, wi);
1842 }
1843
1844 if (EI_MD(ir->eI)((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) && ir->etc == etcNO && buffer_temp == 0)
1845 {
1846 /* NVE with initial T=0: we add a fixed ratio to rlist.
1847 * Since we don't actually use verletbuf_tol, we set it to -1
1848 * so it can't be misused later.
1849 */
1850 ir->rlist *= 1.0 + verlet_buffer_ratio_NVE_T0;
1851 ir->verletbuf_tol = -1;
1852 }
1853 else
1854 {
1855 /* We warn for NVE simulations with >1(.1)% drift tolerance */
1856 const real drift_tol = 0.01;
1857 real ener_runtime;
1858
1859 /* We use 2 DOF per atom = 2kT pot+kin energy, to be on
1860 * the safe side with constraints (without constraints: 3 DOF).
1861 */
1862 ener_runtime = 2*BOLTZ(((1.380658e-23)*(6.0221367e23))/(1e3))*buffer_temp/(ir->nsteps*ir->delta_t);
1863
1864 if (EI_MD(ir->eI)((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) && ir->etc == etcNO && ir->nstlist > 1 &&
1865 ir->nsteps > 0 &&
1866 ir->verletbuf_tol > 1.1*drift_tol*ener_runtime)
1867 {
1868 sprintf(warn_buf, "You are using a Verlet buffer tolerance of %g kJ/mol/ps for an NVE simulation of length %g ps, which can give a final drift of %d%%. For conserving energy to %d%%, you might need to set verlet-buffer-tolerance to %.1e.",
1869 ir->verletbuf_tol, ir->nsteps*ir->delta_t,
1870 (int)(ir->verletbuf_tol/ener_runtime*100 + 0.5),
1871 (int)(100*drift_tol + 0.5),
1872 drift_tol*ener_runtime);
1873 warning_note(wi, warn_buf);
1874 }
1875
1876 set_verlet_buffer(sys, ir, buffer_temp, state.box, wi);
1877 }
1878 }
1879 }
1880
1881 /* Init the temperature coupling state */
1882 init_gtc_state(&state, ir->opts.ngtc, 0, ir->opts.nhchainlength); /* need to add nnhpres here? */
1883
1884 if (bVerbose)
1885 {
1886 fprintf(stderrstderr, "Checking consistency between energy and charge groups...\n");
1887 }
1888 check_eg_vs_cg(sys);
1889
1890 if (debug)
1891 {
1892 pr_symtab(debug, 0, "After index", &sys->symtab);
1893 }
1894
1895 triple_check(mdparin, ir, sys, wi);
1896 close_symtab(&sys->symtab);
1897 if (debug)
1898 {
1899 pr_symtab(debug, 0, "After close", &sys->symtab);
1900 }
1901
1902 /* make exclusions between QM atoms */
1903 if (ir->bQMMM)
1904 {
1905 if (ir->QMMMscheme == eQMMMschemenormal && ir->ns_type == ensSIMPLE)
1906 {
1907 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1907, "electrostatic embedding only works with grid neighboursearching, use ns-type=grid instead\n");
1908 }
1909 else
1910 {
1911 generate_qmexcl(sys, ir, wi);
1912 }
1913 }
1914
1915 if (ftp2bSet(efTRN, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm))
1916 {
1917 if (bVerbose)
1918 {
1919 fprintf(stderrstderr, "getting data from old trajectory ...\n");
1920 }
1921 cont_status(ftp2fn(efTRN, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), ftp2fn_null(efEDR, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1922 bNeedVel, bGenVel, fr_time, ir, &state, sys, oenv);
1923 }
1924
1925 if (ir->ePBC == epbcXY && ir->nwall != 2)
1926 {
1927 clear_rvec(state.box[ZZ2]);
1928 }
1929
1930 if (ir->cutoff_scheme != ecutsVERLET && ir->rlist > 0)
1931 {
1932 set_warning_line(wi, mdparin, -1);
1933 check_chargegroup_radii(sys, ir, state.x, wi);
1934 }
1935
1936 if (EEL_FULL(ir->coulombtype)((((ir->coulombtype) == eelPME || (ir->coulombtype) == eelPMESWITCH
|| (ir->coulombtype) == eelPMEUSER || (ir->coulombtype
) == eelPMEUSERSWITCH || (ir->coulombtype) == eelP3M_AD) ||
(ir->coulombtype) == eelEWALD) || (ir->coulombtype) ==
eelPOISSON) || EVDW_PME(ir->vdwtype)((ir->vdwtype) == evdwPME))
1937 {
1938 /* Calculate the optimal grid dimensions */
1939 copy_mat(state.box, box);
1940 if (ir->ePBC == epbcXY && ir->nwall == 2)
1941 {
1942 svmul(ir->wall_ewald_zfac, box[ZZ2], box[ZZ2]);
1943 }
1944 if (ir->nkx > 0 && ir->nky > 0 && ir->nkz > 0)
1945 {
1946 /* Mark fourier_spacing as not used */
1947 ir->fourier_spacing = 0;
1948 }
1949 else if (ir->nkx != 0 && ir->nky != 0 && ir->nkz != 0)
1950 {
1951 set_warning_line(wi, mdparin, -1);
1952 warning_error(wi, "Some of the Fourier grid sizes are set, but all of them need to be set.");
1953 }
1954 max_spacing = calc_grid(stdoutstdout, box, ir->fourier_spacing,
Value stored to 'max_spacing' is never read
1955 &(ir->nkx), &(ir->nky), &(ir->nkz));
1956 }
1957
1958 /* MRS: eventually figure out better logic for initializing the fep
1959 values that makes declaring the lambda and declaring the state not
1960 potentially conflict if not handled correctly. */
1961 if (ir->efep != efepNO)
1962 {
1963 state.fep_state = ir->fepvals->init_fep_state;
1964 for (i = 0; i < efptNR; i++)
1965 {
1966 /* init_lambda trumps state definitions*/
1967 if (ir->fepvals->init_lambda >= 0)
1968 {
1969 state.lambda[i] = ir->fepvals->init_lambda;
1970 }
1971 else
1972 {
1973 if (ir->fepvals->all_lambda[i] == NULL((void*)0))
1974 {
1975 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 1975, "Values of lambda not set for a free energy calculation!");
1976 }
1977 else
1978 {
1979 state.lambda[i] = ir->fepvals->all_lambda[i][state.fep_state];
1980 }
1981 }
1982 }
1983 }
1984
1985 if (ir->ePull != epullNO)
1986 {
1987 set_pull_init(ir, sys, state.x, state.box, state.lambda[efptMASS], oenv, opts->pull_start);
1988 }
1989
1990 if (ir->bRot)
1991 {
1992 set_reference_positions(ir->rot, state.x, state.box,
1993 opt2fn("-ref", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), opt2bSet("-ref", NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm),
1994 wi);
1995 }
1996
1997 /* reset_multinr(sys); */
1998
1999 if (EEL_PME(ir->coulombtype)((ir->coulombtype) == eelPME || (ir->coulombtype) == eelPMESWITCH
|| (ir->coulombtype) == eelPMEUSER || (ir->coulombtype
) == eelPMEUSERSWITCH || (ir->coulombtype) == eelP3M_AD))
2000 {
2001 float ratio = pme_load_estimate(sys, ir, state.box);
2002 fprintf(stderrstderr, "Estimate for the relative computational load of the PME mesh part: %.2f\n", ratio);
2003 /* With free energy we might need to do PME both for the A and B state
2004 * charges. This will double the cost, but the optimal performance will
2005 * then probably be at a slightly larger cut-off and grid spacing.
2006 */
2007 if ((ir->efep == efepNO && ratio > 1.0/2.0) ||
2008 (ir->efep != efepNO && ratio > 2.0/3.0))
2009 {
2010 warning_note(wi,
2011 "The optimal PME mesh load for parallel simulations is below 0.5\n"
2012 "and for highly parallel simulations between 0.25 and 0.33,\n"
2013 "for higher performance, increase the cut-off and the PME grid spacing.\n");
2014 if (ir->efep != efepNO)
2015 {
2016 warning_note(wi,
2017 "For free energy simulations, the optimal load limit increases from 0.5 to 0.667\n");
2018 }
2019 }
2020 }
2021
2022 {
2023 char warn_buf[STRLEN4096];
2024 double cio = compute_io(ir, sys->natoms, &sys->groups, F_NRE, 1);
2025 sprintf(warn_buf, "This run will generate roughly %.0f Mb of data", cio);
2026 if (cio > 2000)
2027 {
2028 set_warning_line(wi, mdparin, -1);
2029 warning_note(wi, warn_buf);
2030 }
2031 else
2032 {
2033 printf("%s\n", warn_buf);
2034 }
2035 }
2036
2037 if (bVerbose)
2038 {
2039 fprintf(stderrstderr, "writing run input file...\n");
2040 }
2041
2042 done_warning(wi, FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/gmxpreprocess/grompp.c"
, 2042);
2043 write_tpx_state(ftp2fn(efTPX, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm), ir, &state, sys);
2044
2045 /* Output IMD group, if bIMD is TRUE */
2046 write_IMDgroup_to_file(ir->bIMD, ir, &state, sys, NFILE((int)(sizeof(fnm)/sizeof((fnm)[0]))), fnm);
2047
2048 done_atomtype(atype);
2049 done_mtop(sys, TRUE1);
2050 done_inputrec_strings();
2051
2052 return 0;
2053}