Bug Summary

File:gromacs/mdlib/mdebin.c
Location:line 935, column 13
Description:Value stored to 'np' 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 *
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17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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20 *
21 * You should have received a copy of the GNU Lesser General Public
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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
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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 <float.h>
42#include <stdlib.h>
43#include <string.h>
44
45#include "typedefs.h"
46#include "mdebin.h"
47#include "gromacs/utility/smalloc.h"
48#include "physics.h"
49#include "gromacs/fileio/enxio.h"
50#include "gromacs/math/vec.h"
51#include "disre.h"
52#include "network.h"
53#include "names.h"
54#include "orires.h"
55#include "constr.h"
56#include "mtop_util.h"
57#include "gromacs/fileio/xvgr.h"
58#include "gromacs/fileio/gmxfio.h"
59#include "macros.h"
60#include "mdrun.h"
61#include "mdebin_bar.h"
62
63
64static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
65
66static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
67
68static const char *tricl_boxs_nm[] = {
69 "Box-XX", "Box-YY", "Box-ZZ",
70 "Box-YX", "Box-ZX", "Box-ZY"
71};
72
73static const char *vol_nm[] = { "Volume" };
74
75static const char *dens_nm[] = {"Density" };
76
77static const char *pv_nm[] = {"pV" };
78
79static const char *enthalpy_nm[] = {"Enthalpy" };
80
81static const char *boxvel_nm[] = {
82 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
83 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
84};
85
86#define NBOXS((int)(sizeof(boxs_nm)/sizeof((boxs_nm)[0]))) asize(boxs_nm)((int)(sizeof(boxs_nm)/sizeof((boxs_nm)[0])))
87#define NTRICLBOXS((int)(sizeof(tricl_boxs_nm)/sizeof((tricl_boxs_nm)[0]))) asize(tricl_boxs_nm)((int)(sizeof(tricl_boxs_nm)/sizeof((tricl_boxs_nm)[0])))
88
89t_mdebin *init_mdebin(ener_file_t fp_ene,
90 const gmx_mtop_t *mtop,
91 const t_inputrec *ir,
92 FILE *fp_dhdl)
93{
94 const char *ener_nm[F_NRE];
95 static const char *vir_nm[] = {
96 "Vir-XX", "Vir-XY", "Vir-XZ",
97 "Vir-YX", "Vir-YY", "Vir-YZ",
98 "Vir-ZX", "Vir-ZY", "Vir-ZZ"
99 };
100 static const char *sv_nm[] = {
101 "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
102 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
103 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
104 };
105 static const char *fv_nm[] = {
106 "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
107 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
108 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
109 };
110 static const char *pres_nm[] = {
111 "Pres-XX", "Pres-XY", "Pres-XZ",
112 "Pres-YX", "Pres-YY", "Pres-YZ",
113 "Pres-ZX", "Pres-ZY", "Pres-ZZ"
114 };
115 static const char *surft_nm[] = {
116 "#Surf*SurfTen"
117 };
118 static const char *mu_nm[] = {
119 "Mu-X", "Mu-Y", "Mu-Z"
120 };
121 static const char *vcos_nm[] = {
122 "2CosZ*Vel-X"
123 };
124 static const char *visc_nm[] = {
125 "1/Viscosity"
126 };
127 static const char *baro_nm[] = {
128 "Barostat"
129 };
130
131 char **grpnms;
132 const gmx_groups_t *groups;
133 char **gnm;
134 char buf[256];
135 const char *bufi;
136 t_mdebin *md;
137 int i, j, ni, nj, n, nh, k, kk, ncon, nset;
138 gmx_bool bBHAM, bNoseHoover, b14;
139
140 snew(md, 1)(md) = save_calloc("md", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 140, (1), sizeof(*(md)));
141
142 md->bVir = TRUE1;
143 md->bPress = TRUE1;
144 md->bSurft = TRUE1;
145 md->bMu = TRUE1;
146
147 if (EI_DYNAMICS(ir->eI)(((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) || ((ir->eI) == eiSD1 || (ir->eI) == eiSD2) ||
(ir->eI) == eiBD))
148 {
149 md->delta_t = ir->delta_t;
150 }
151 else
152 {
153 md->delta_t = 0;
154 }
155
156 groups = &mtop->groups;
157
158 bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
159 b14 = (gmx_mtop_ftype_count(mtop, F_LJ14) > 0 ||
160 gmx_mtop_ftype_count(mtop, F_LJC14_Q) > 0);
161
162 ncon = gmx_mtop_ftype_count(mtop, F_CONSTR);
163 nset = gmx_mtop_ftype_count(mtop, F_SETTLE);
164 md->bConstr = (ncon > 0 || nset > 0);
165 md->bConstrVir = FALSE0;
166 if (md->bConstr)
167 {
168 if (ncon > 0 && ir->eConstrAlg == econtLINCS)
169 {
170 if (ir->eI == eiSD2)
171 {
172 md->nCrmsd = 2;
173 }
174 else
175 {
176 md->nCrmsd = 1;
177 }
178 }
179 md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL((void*)0));
180 }
181 else
182 {
183 md->nCrmsd = 0;
184 }
185
186 /* Energy monitoring */
187 for (i = 0; i < egNR; i++)
188 {
189 md->bEInd[i] = FALSE0;
190 }
191
192 for (i = 0; i < F_NRE; i++)
193 {
194 md->bEner[i] = FALSE0;
195 if (i == F_LJ)
196 {
197 md->bEner[i] = !bBHAM;
198 }
199 else if (i == F_BHAM)
200 {
201 md->bEner[i] = bBHAM;
202 }
203 else if (i == F_EQM)
204 {
205 md->bEner[i] = ir->bQMMM;
206 }
207 else if (i == F_COUL_LR)
208 {
209 md->bEner[i] = (ir->rcoulomb > ir->rlist);
210 }
211 else if (i == F_LJ_LR)
212 {
213 md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
214 }
215 else if (i == F_BHAM_LR)
216 {
217 md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
218 }
219 else if (i == F_RF_EXCL)
220 {
221 md->bEner[i] = (EEL_RF(ir->coulombtype)((ir->coulombtype) == eelRF || (ir->coulombtype) == eelGRF
|| (ir->coulombtype) == eelRF_NEC || (ir->coulombtype)
== eelRF_ZERO ) && ir->coulombtype != eelRF_NEC && ir->cutoff_scheme == ecutsGROUP);
222 }
223 else if (i == F_COUL_RECIP)
224 {
225 md->bEner[i] = 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);
226 }
227 else if (i == F_LJ_RECIP)
228 {
229 md->bEner[i] = EVDW_PME(ir->vdwtype)((ir->vdwtype) == evdwPME);
230 }
231 else if (i == F_LJ14)
232 {
233 md->bEner[i] = b14;
234 }
235 else if (i == F_COUL14)
236 {
237 md->bEner[i] = b14;
238 }
239 else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
240 {
241 md->bEner[i] = FALSE0;
242 }
243 else if ((i == F_DVDL_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
244 (i == F_DVDL_VDW && ir->fepvals->separate_dvdl[efptVDW]) ||
245 (i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
246 (i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
247 (i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
248 (i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
249 {
250 md->bEner[i] = (ir->efep != efepNO);
251 }
252 else if ((interaction_function[i].flags & IF_VSITE1<<1) ||
253 (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
254 {
255 md->bEner[i] = FALSE0;
256 }
257 else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i == F_EQM))
258 {
259 md->bEner[i] = TRUE1;
260 }
261 else if ((i == F_GBPOL) && ir->implicit_solvent == eisGBSA)
262 {
263 md->bEner[i] = TRUE1;
264 }
265 else if ((i == F_NPSOLVATION) && ir->implicit_solvent == eisGBSA && (ir->sa_algorithm != esaNO))
266 {
267 md->bEner[i] = TRUE1;
268 }
269 else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
270 {
271 md->bEner[i] = FALSE0;
272 }
273 else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
274 {
275 md->bEner[i] = EI_DYNAMICS(ir->eI)(((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) || ((ir->eI) == eiSD1 || (ir->eI) == eiSD2) ||
(ir->eI) == eiBD);
276 }
277 else if (i == F_DISPCORR || i == F_PDISPCORR)
278 {
279 md->bEner[i] = (ir->eDispCorr != edispcNO);
280 }
281 else if (i == F_DISRESVIOL)
282 {
283 md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_DISRES) > 0);
284 }
285 else if (i == F_ORIRESDEV)
286 {
287 md->bEner[i] = (gmx_mtop_ftype_count(mtop, F_ORIRES) > 0);
288 }
289 else if (i == F_CONNBONDS)
290 {
291 md->bEner[i] = FALSE0;
292 }
293 else if (i == F_COM_PULL)
294 {
295 md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
296 }
297 else if (i == F_ECONSERVED)
298 {
299 md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
300 (ir->epc == epcNO || ir->epc == epcMTTK));
301 }
302 else
303 {
304 md->bEner[i] = (gmx_mtop_ftype_count(mtop, i) > 0);
305 }
306 }
307
308 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
309 if (ir->bAdress && !debug)
310 {
311 for (i = 0; i < F_NRE; i++)
312 {
313 md->bEner[i] = FALSE0;
314 if (i == F_EKIN)
315 {
316 md->bEner[i] = TRUE1;
317 }
318 if (i == F_TEMP)
319 {
320 md->bEner[i] = TRUE1;
321 }
322 }
323 md->bVir = FALSE0;
324 md->bPress = FALSE0;
325 md->bSurft = FALSE0;
326 md->bMu = FALSE0;
327 }
328
329 md->f_nre = 0;
330 for (i = 0; i < F_NRE; i++)
331 {
332 if (md->bEner[i])
333 {
334 ener_nm[md->f_nre] = interaction_function[i].longname;
335 md->f_nre++;
336 }
337 }
338
339 md->epc = ir->epc;
340 md->bDiagPres = !TRICLINIC(ir->ref_p)(ir->ref_p[1][0] != 0 || ir->ref_p[2][0] != 0 || ir->
ref_p[2][1] != 0);
341 md->ref_p = (ir->ref_p[XX0][XX0]+ir->ref_p[YY1][YY1]+ir->ref_p[ZZ2][ZZ2])/DIM3;
342 md->bTricl = TRICLINIC(ir->compress)(ir->compress[1][0] != 0 || ir->compress[2][0] != 0 || ir
->compress[2][1] != 0) || TRICLINIC(ir->deform)(ir->deform[1][0] != 0 || ir->deform[2][0] != 0 || ir->
deform[2][1] != 0);
343 md->bDynBox = DYNAMIC_BOX(*ir)((*ir).epc != epcNO || (*ir).eI == eiTPI || ((*ir).deform[0][
0] != 0 || (*ir).deform[1][1] != 0 || (*ir).deform[2][2] != 0
|| (*ir).deform[1][0] != 0 || (*ir).deform[2][0] != 0 || (*ir
).deform[2][1] != 0));
344 md->etc = ir->etc;
345 md->bNHC_trotter = IR_NVT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
((!((ir)->epc == epcMTTK)) && ((ir)->etc == etcNOSEHOOVER
)));
346 md->bPrintNHChains = ir->bPrintNHChains;
347 md->bMTTK = (IR_NPT_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && ((ir)->etc == etcNOSEHOOVER
))) || IR_NPH_TROTTER(ir)((((ir)->eI == eiVV) || ((ir)->eI == eiVVAK)) &&
(((ir)->epc == epcMTTK) && (!(((ir)->etc == etcNOSEHOOVER
))))));
348 md->bMu = NEED_MUTOT(*ir)(((*ir).coulombtype == eelEWALD || (((*ir).coulombtype) == eelPME
|| ((*ir).coulombtype) == eelPMESWITCH || ((*ir).coulombtype
) == eelPMEUSER || ((*ir).coulombtype) == eelPMEUSERSWITCH ||
((*ir).coulombtype) == eelP3M_AD)) && ((*ir).ewald_geometry
== eewg3DC || (*ir).epsilon_surface != 0));
349
350 md->ebin = mk_ebin();
351 /* Pass NULL for unit to let get_ebin_space determine the units
352 * for interaction_function[i].longname
353 */
354 md->ie = get_ebin_space(md->ebin, md->f_nre, ener_nm, NULL((void*)0));
355 if (md->nCrmsd)
356 {
357 /* This should be called directly after the call for md->ie,
358 * such that md->iconrmsd follows directly in the list.
359 */
360 md->iconrmsd = get_ebin_space(md->ebin, md->nCrmsd, conrmsd_nm, "");
361 }
362 if (md->bDynBox)
363 {
364 md->ib = get_ebin_space(md->ebin,
365 md->bTricl ? NTRICLBOXS((int)(sizeof(tricl_boxs_nm)/sizeof((tricl_boxs_nm)[0]))) : NBOXS((int)(sizeof(boxs_nm)/sizeof((boxs_nm)[0]))),
366 md->bTricl ? tricl_boxs_nm : boxs_nm,
367 unit_length"nm");
368 md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume"nm" "^3");
369 md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI"kg" "/" "m" "^3");
370 if (md->bDiagPres)
371 {
372 md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy"kJ/mol");
373 md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy"kJ/mol");
374 }
375 }
376 if (md->bConstrVir)
377 {
378 md->isvir = get_ebin_space(md->ebin, asize(sv_nm)((int)(sizeof(sv_nm)/sizeof((sv_nm)[0]))), sv_nm, unit_energy"kJ/mol");
379 md->ifvir = get_ebin_space(md->ebin, asize(fv_nm)((int)(sizeof(fv_nm)/sizeof((fv_nm)[0]))), fv_nm, unit_energy"kJ/mol");
380 }
381 if (md->bVir)
382 {
383 md->ivir = get_ebin_space(md->ebin, asize(vir_nm)((int)(sizeof(vir_nm)/sizeof((vir_nm)[0]))), vir_nm, unit_energy"kJ/mol");
384 }
385 if (md->bPress)
386 {
387 md->ipres = get_ebin_space(md->ebin, asize(pres_nm)((int)(sizeof(pres_nm)/sizeof((pres_nm)[0]))), pres_nm, unit_pres_bar"bar");
388 }
389 if (md->bSurft)
390 {
391 md->isurft = get_ebin_space(md->ebin, asize(surft_nm)((int)(sizeof(surft_nm)/sizeof((surft_nm)[0]))), surft_nm,
392 unit_surft_bar"bar" " " "nm");
393 }
394 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
395 {
396 md->ipc = get_ebin_space(md->ebin, md->bTricl ? 6 : 3,
397 boxvel_nm, unit_vel"nm" "/" "ps");
398 }
399 if (md->bMu)
400 {
401 md->imu = get_ebin_space(md->ebin, asize(mu_nm)((int)(sizeof(mu_nm)/sizeof((mu_nm)[0]))), mu_nm, unit_dipole_D"D");
402 }
403 if (ir->cos_accel != 0)
404 {
405 md->ivcos = get_ebin_space(md->ebin, asize(vcos_nm)((int)(sizeof(vcos_nm)/sizeof((vcos_nm)[0]))), vcos_nm, unit_vel"nm" "/" "ps");
406 md->ivisc = get_ebin_space(md->ebin, asize(visc_nm)((int)(sizeof(visc_nm)/sizeof((visc_nm)[0]))), visc_nm,
407 unit_invvisc_SI"m" " " "s" "/" "kg");
408 }
409
410 /* Energy monitoring */
411 for (i = 0; i < egNR; i++)
412 {
413 md->bEInd[i] = FALSE0;
414 }
415 md->bEInd[egCOULSR] = TRUE1;
416 md->bEInd[egLJSR ] = TRUE1;
417
418 if (ir->rcoulomb > ir->rlist)
419 {
420 md->bEInd[egCOULLR] = TRUE1;
421 }
422 if (!bBHAM)
423 {
424 if (ir->rvdw > ir->rlist)
425 {
426 md->bEInd[egLJLR] = TRUE1;
427 }
428 }
429 else
430 {
431 md->bEInd[egLJSR] = FALSE0;
432 md->bEInd[egBHAMSR] = TRUE1;
433 if (ir->rvdw > ir->rlist)
434 {
435 md->bEInd[egBHAMLR] = TRUE1;
436 }
437 }
438 if (b14)
439 {
440 md->bEInd[egLJ14] = TRUE1;
441 md->bEInd[egCOUL14] = TRUE1;
442 }
443 md->nEc = 0;
444 for (i = 0; (i < egNR); i++)
445 {
446 if (md->bEInd[i])
447 {
448 md->nEc++;
449 }
450 }
451
452 n = groups->grps[egcENER].nr;
453 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
454 if (!ir->bAdress)
455 {
456 /*standard simulation*/
457 md->nEg = n;
458 md->nE = (n*(n+1))/2;
459 }
460 else if (!debug)
461 {
462 /*AdResS simulation*/
463 md->nU = 0;
464 md->nEg = 0;
465 md->nE = 0;
466 md->nEc = 0;
467 md->isvir = FALSE0;
468 }
469 snew(md->igrp, md->nE)(md->igrp) = save_calloc("md->igrp", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 469, (md->nE), sizeof(*(md->igrp)));
470 if (md->nE > 1)
471 {
472 n = 0;
473 snew(gnm, md->nEc)(gnm) = save_calloc("gnm", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 473, (md->nEc), sizeof(*(gnm)));
474 for (k = 0; (k < md->nEc); k++)
475 {
476 snew(gnm[k], STRLEN)(gnm[k]) = save_calloc("gnm[k]", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 476, (4096), sizeof(*(gnm[k])));
477 }
478 for (i = 0; (i < groups->grps[egcENER].nr); i++)
479 {
480 ni = groups->grps[egcENER].nm_ind[i];
481 for (j = i; (j < groups->grps[egcENER].nr); j++)
482 {
483 nj = groups->grps[egcENER].nm_ind[j];
484 for (k = kk = 0; (k < egNR); k++)
485 {
486 if (md->bEInd[k])
487 {
488 sprintf(gnm[kk], "%s:%s-%s", egrp_nm[k],
489 *(groups->grpname[ni]), *(groups->grpname[nj]));
490 kk++;
491 }
492 }
493 md->igrp[n] = get_ebin_space(md->ebin, md->nEc,
494 (const char **)gnm, unit_energy"kJ/mol");
495 n++;
496 }
497 }
498 for (k = 0; (k < md->nEc); k++)
499 {
500 sfree(gnm[k])save_free("gnm[k]", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 500, (gnm[k]));
501 }
502 sfree(gnm)save_free("gnm", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 502, (gnm));
503
504 if (n != md->nE)
505 {
506 gmx_incons("Number of energy terms wrong")_gmx_error("incons", "Number of energy terms wrong", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 506);
507 }
508 }
509
510 md->nTC = groups->grps[egcTC].nr;
511 md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
512 if (md->bMTTK)
513 {
514 md->nTCP = 1; /* assume only one possible coupling system for barostat
515 for now */
516 }
517 else
518 {
519 md->nTCP = 0;
520 }
521 if (md->etc == etcNOSEHOOVER)
522 {
523 if (md->bNHC_trotter)
524 {
525 md->mde_n = 2*md->nNHC*md->nTC;
526 }
527 else
528 {
529 md->mde_n = 2*md->nTC;
530 }
531 if (md->epc == epcMTTK)
532 {
533 md->mdeb_n = 2*md->nNHC*md->nTCP;
534 }
535 }
536 else
537 {
538 md->mde_n = md->nTC;
539 md->mdeb_n = 0;
540 }
541
542 snew(md->tmp_r, md->mde_n)(md->tmp_r) = save_calloc("md->tmp_r", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 542, (md->mde_n), sizeof(*(md->tmp_r)));
543 snew(md->tmp_v, md->mde_n)(md->tmp_v) = save_calloc("md->tmp_v", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 543, (md->mde_n), sizeof(*(md->tmp_v)));
544 snew(md->grpnms, md->mde_n)(md->grpnms) = save_calloc("md->grpnms", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 544, (md->mde_n), sizeof(*(md->grpnms)));
545 grpnms = md->grpnms;
546
547 for (i = 0; (i < md->nTC); i++)
548 {
549 ni = groups->grps[egcTC].nm_ind[i];
550 sprintf(buf, "T-%s", *(groups->grpname[ni]));
551 grpnms[i] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
552 }
553 md->itemp = get_ebin_space(md->ebin, md->nTC, (const char **)grpnms,
554 unit_temp_K"K");
555
556 if (md->etc == etcNOSEHOOVER)
557 {
558 if (md->bPrintNHChains)
559 {
560 if (md->bNHC_trotter)
561 {
562 for (i = 0; (i < md->nTC); i++)
563 {
564 ni = groups->grps[egcTC].nm_ind[i];
565 bufi = *(groups->grpname[ni]);
566 for (j = 0; (j < md->nNHC); j++)
567 {
568 sprintf(buf, "Xi-%d-%s", j, bufi);
569 grpnms[2*(i*md->nNHC+j)] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
570 sprintf(buf, "vXi-%d-%s", j, bufi);
571 grpnms[2*(i*md->nNHC+j)+1] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
572 }
573 }
574 md->itc = get_ebin_space(md->ebin, md->mde_n,
575 (const char **)grpnms, unit_invtime"1/" "ps");
576 if (md->bMTTK)
577 {
578 for (i = 0; (i < md->nTCP); i++)
579 {
580 bufi = baro_nm[0]; /* All barostat DOF's together for now. */
581 for (j = 0; (j < md->nNHC); j++)
582 {
583 sprintf(buf, "Xi-%d-%s", j, bufi);
584 grpnms[2*(i*md->nNHC+j)] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
585 sprintf(buf, "vXi-%d-%s", j, bufi);
586 grpnms[2*(i*md->nNHC+j)+1] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
587 }
588 }
589 md->itcb = get_ebin_space(md->ebin, md->mdeb_n,
590 (const char **)grpnms, unit_invtime"1/" "ps");
591 }
592 }
593 else
594 {
595 for (i = 0; (i < md->nTC); i++)
596 {
597 ni = groups->grps[egcTC].nm_ind[i];
598 bufi = *(groups->grpname[ni]);
599 sprintf(buf, "Xi-%s", bufi);
600 grpnms[2*i] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
601 sprintf(buf, "vXi-%s", bufi);
602 grpnms[2*i+1] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
603 }
604 md->itc = get_ebin_space(md->ebin, md->mde_n,
605 (const char **)grpnms, unit_invtime"1/" "ps");
606 }
607 }
608 }
609 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
610 md->etc == etcVRESCALE)
611 {
612 for (i = 0; (i < md->nTC); i++)
613 {
614 ni = groups->grps[egcTC].nm_ind[i];
615 sprintf(buf, "Lamb-%s", *(groups->grpname[ni]));
616 grpnms[i] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
617 }
618 md->itc = get_ebin_space(md->ebin, md->mde_n, (const char **)grpnms, "");
619 }
620
621 sfree(grpnms)save_free("grpnms", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 621, (grpnms));
622
623
624 md->nU = groups->grps[egcACC].nr;
625 if (md->nU > 1)
626 {
627 snew(grpnms, 3*md->nU)(grpnms) = save_calloc("grpnms", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 627, (3*md->nU), sizeof(*(grpnms)));
628 for (i = 0; (i < md->nU); i++)
629 {
630 ni = groups->grps[egcACC].nm_ind[i];
631 sprintf(buf, "Ux-%s", *(groups->grpname[ni]));
632 grpnms[3*i+XX0] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
633 sprintf(buf, "Uy-%s", *(groups->grpname[ni]));
634 grpnms[3*i+YY1] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
635 sprintf(buf, "Uz-%s", *(groups->grpname[ni]));
636 grpnms[3*i+ZZ2] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
637 }
638 md->iu = get_ebin_space(md->ebin, 3*md->nU, (const char **)grpnms, unit_vel"nm" "/" "ps");
639 sfree(grpnms)save_free("grpnms", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 639, (grpnms));
640 }
641
642 if (fp_ene)
643 {
644 do_enxnms(fp_ene, &md->ebin->nener, &md->ebin->enm);
645 }
646
647 md->print_grpnms = NULL((void*)0);
648
649 /* check whether we're going to write dh histograms */
650 md->dhc = NULL((void*)0);
651 if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO)
652 {
653 /* Currently dh histograms are only written with dynamics */
654 if (EI_DYNAMICS(ir->eI)(((ir->eI) == eiMD || ((ir->eI) == eiVV || (ir->eI) ==
eiVVAK)) || ((ir->eI) == eiSD1 || (ir->eI) == eiSD2) ||
(ir->eI) == eiBD))
655 {
656 snew(md->dhc, 1)(md->dhc) = save_calloc("md->dhc", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 656, (1), sizeof(*(md->dhc)));
657
658 mde_delta_h_coll_init(md->dhc, ir);
659 }
660 md->fp_dhdl = NULL((void*)0);
661 snew(md->dE, ir->fepvals->n_lambda)(md->dE) = save_calloc("md->dE", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 661, (ir->fepvals->n_lambda), sizeof(*(md->dE)));
662 }
663 else
664 {
665 md->fp_dhdl = fp_dhdl;
666 snew(md->dE, ir->fepvals->n_lambda)(md->dE) = save_calloc("md->dE", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 666, (ir->fepvals->n_lambda), sizeof(*(md->dE)));
667 }
668 if (ir->bSimTemp)
669 {
670 int i;
671 snew(md->temperatures, ir->fepvals->n_lambda)(md->temperatures) = save_calloc("md->temperatures", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 671, (ir->fepvals->n_lambda), sizeof(*(md->temperatures
)));
672 for (i = 0; i < ir->fepvals->n_lambda; i++)
673 {
674 md->temperatures[i] = ir->simtempvals->temperatures[i];
675 }
676 }
677 return md;
678}
679
680/* print a lambda vector to a string
681 fep = the inputrec's FEP input data
682 i = the index of the lambda vector
683 get_native_lambda = whether to print the native lambda
684 get_names = whether to print the names rather than the values
685 str = the pre-allocated string buffer to print to. */
686static void print_lambda_vector(t_lambda *fep, int i,
687 gmx_bool get_native_lambda, gmx_bool get_names,
688 char *str)
689{
690 size_t nps = 0, np;
691 int j, k = 0;
692 int Nsep = 0;
693
694 for (j = 0; j < efptNR; j++)
695 {
696 if (fep->separate_dvdl[j])
697 {
698 Nsep++;
699 }
700 }
701 str[0] = 0; /* reset the string */
702 if (Nsep > 1)
703 {
704 str += sprintf(str, "("); /* set the opening parenthesis*/
705 }
706 for (j = 0; j < efptNR; j++)
707 {
708 if (fep->separate_dvdl[j])
709 {
710 double lam;
711 if (!get_names)
712 {
713 if (get_native_lambda && fep->init_lambda >= 0)
714 {
715 str += sprintf(str, "%.4f", fep->init_lambda);
716 }
717 else
718 {
719 str += sprintf(str, "%.4f", fep->all_lambda[j][i]);
720 }
721 }
722 else
723 {
724 str += sprintf(str, "%s", efpt_singular_names[j]);
725 }
726 /* print comma for the next item */
727 if (k < Nsep-1)
728 {
729 str += sprintf(str, ", ");
730 }
731 k++;
732 }
733 }
734 if (Nsep > 1)
735 {
736 /* and add the closing parenthesis */
737 str += sprintf(str, ")");
738 }
739}
740
741
742extern FILE *open_dhdl(const char *filename, const t_inputrec *ir,
743 const output_env_t oenv)
744{
745 FILE *fp;
746 const char *dhdl = "dH/d\\lambda", *deltag = "\\DeltaH", *lambda = "\\lambda",
747 *lambdastate = "\\lambda state", *remain = "remaining";
748 char title[STRLEN4096], label_x[STRLEN4096], label_y[STRLEN4096];
749 int i, np, nps, nsets, nsets_de, nsetsbegin;
750 int n_lambda_terms = 0;
751 t_lambda *fep = ir->fepvals; /* for simplicity */
752 t_expanded *expand = ir->expandedvals;
753 char **setname;
754 char buf[STRLEN4096], lambda_vec_str[STRLEN4096], lambda_name_str[STRLEN4096];
755 int bufplace = 0;
756
757 int nsets_dhdl = 0;
758 int s = 0;
759 int nsetsextend;
760 gmx_bool write_pV = FALSE0;
761
762 /* count the number of different lambda terms */
763 for (i = 0; i < efptNR; i++)
764 {
765 if (fep->separate_dvdl[i])
766 {
767 n_lambda_terms++;
768 }
769 }
770
771 if (fep->n_lambda == 0)
772 {
773 sprintf(title, "%s", dhdl);
774 sprintf(label_x, "Time (ps)");
775 sprintf(label_y, "%s (%s %s)",
776 dhdl, unit_energy"kJ/mol", "[\\lambda]\\S-1\\N");
777 }
778 else
779 {
780 sprintf(title, "%s and %s", dhdl, deltag);
781 sprintf(label_x, "Time (ps)");
782 sprintf(label_y, "%s and %s (%s %s)",
783 dhdl, deltag, unit_energy"kJ/mol", "[\\8l\\4]\\S-1\\N");
784 }
785 fp = gmx_fio_fopen(filename, "w+");
786 xvgr_header(fp, title, label_x, label_y, exvggtXNY, oenv);
787
788 if (!(ir->bSimTemp))
789 {
790 bufplace = sprintf(buf, "T = %g (K) ",
791 ir->opts.ref_t[0]);
792 }
793 if ((ir->efep != efepSLOWGROWTH) && (ir->efep != efepEXPANDED))
794 {
795 if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
796 {
797 /* compatibility output */
798 sprintf(&(buf[bufplace]), "%s = %.4f", lambda, fep->init_lambda);
799 }
800 else
801 {
802 print_lambda_vector(fep, fep->init_fep_state, TRUE1, FALSE0,
803 lambda_vec_str);
804 print_lambda_vector(fep, fep->init_fep_state, TRUE1, TRUE1,
805 lambda_name_str);
806 sprintf(&(buf[bufplace]), "%s %d: %s = %s",
807 lambdastate, fep->init_fep_state,
808 lambda_name_str, lambda_vec_str);
809 }
810 }
811 xvgr_subtitle(fp, buf, oenv);
812
813
814 nsets_dhdl = 0;
815 if (fep->dhdl_derivatives == edhdlderivativesYES)
816 {
817 nsets_dhdl = n_lambda_terms;
818 }
819 /* count the number of delta_g states */
820 nsets_de = fep->lambda_stop_n - fep->lambda_start_n;
821
822 nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
823
824 if (fep->n_lambda > 0 && (expand->elmcmove > elmcmoveNO))
825 {
826 nsets += 1; /*add fep state for expanded ensemble */
827 }
828
829 if (fep->bPrintEnergy)
830 {
831 nsets += 1; /* add energy to the dhdl as well */
832 }
833
834 nsetsextend = nsets;
835 if ((ir->epc != epcNO) && (fep->n_lambda > 0) && (fep->init_lambda < 0))
836 {
837 nsetsextend += 1; /* for PV term, other terms possible if required for
838 the reduced potential (only needed with foreign
839 lambda, and only output when init_lambda is not
840 set in order to maintain compatibility of the
841 dhdl.xvg file) */
842 write_pV = TRUE1;
843 }
844 snew(setname, nsetsextend)(setname) = save_calloc("setname", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 844, (nsetsextend), sizeof(*(setname)));
845
846 if (expand->elmcmove > elmcmoveNO)
847 {
848 /* state for the fep_vals, if we have alchemical sampling */
849 sprintf(buf, "%s", "Thermodynamic state");
850 setname[s] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
851 s += 1;
852 }
853
854 if (fep->bPrintEnergy)
855 {
856 sprintf(buf, "%s (%s)", "Energy", unit_energy"kJ/mol");
857 setname[s] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
858 s += 1;
859 }
860
861 if (fep->dhdl_derivatives == edhdlderivativesYES)
862 {
863 for (i = 0; i < efptNR; i++)
864 {
865 if (fep->separate_dvdl[i])
866 {
867
868 if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
869 {
870 /* compatibility output */
871 sprintf(buf, "%s %s %.4f", dhdl, lambda, fep->init_lambda);
872 }
873 else
874 {
875 double lam = fep->init_lambda;
876 if (fep->init_lambda < 0)
877 {
878 lam = fep->all_lambda[i][fep->init_fep_state];
879 }
880 sprintf(buf, "%s %s = %.4f", dhdl, efpt_singular_names[i],
881 lam);
882 }
883 setname[s] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
884 s += 1;
885 }
886 }
887 }
888
889 if (fep->n_lambda > 0)
890 {
891 /* g_bar has to determine the lambda values used in this simulation
892 * from this xvg legend.
893 */
894
895 if (expand->elmcmove > elmcmoveNO)
896 {
897 nsetsbegin = 1; /* for including the expanded ensemble */
898 }
899 else
900 {
901 nsetsbegin = 0;
902 }
903
904 if (fep->bPrintEnergy)
905 {
906 nsetsbegin += 1;
907 }
908 nsetsbegin += nsets_dhdl;
909
910 for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
911 {
912 print_lambda_vector(fep, i, FALSE0, FALSE0, lambda_vec_str);
913 if ( (fep->init_lambda >= 0) && (n_lambda_terms == 1 ))
914 {
915 /* for compatible dhdl.xvg files */
916 nps = sprintf(buf, "%s %s %s", deltag, lambda, lambda_vec_str);
917 }
918 else
919 {
920 nps = sprintf(buf, "%s %s to %s", deltag, lambda, lambda_vec_str);
921 }
922
923 if (ir->bSimTemp)
924 {
925 /* print the temperature for this state if doing simulated annealing */
926 sprintf(&buf[nps], "T = %g (%s)",
927 ir->simtempvals->temperatures[s-(nsetsbegin)],
928 unit_temp_K"K");
929 }
930 setname[s] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
931 s++;
932 }
933 if (write_pV)
934 {
935 np = sprintf(buf, "pV (%s)", unit_energy"kJ/mol");
Value stored to 'np' is never read
936 setname[nsetsextend-1] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf))); /* the first entry after
937 nsets */
938 }
939
940 xvgr_legend(fp, nsetsextend, (const char **)setname, oenv);
941
942 for (s = 0; s < nsetsextend; s++)
943 {
944 sfree(setname[s])save_free("setname[s]", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 944, (setname[s]));
945 }
946 sfree(setname)save_free("setname", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 946, (setname));
947 }
948
949 return fp;
950}
951
952static void copy_energy(t_mdebin *md, real e[], real ecpy[])
953{
954 int i, j;
955
956 for (i = j = 0; (i < F_NRE); i++)
957 {
958 if (md->bEner[i])
959 {
960 ecpy[j++] = e[i];
961 }
962 }
963 if (j != md->f_nre)
964 {
965 gmx_incons("Number of energy terms wrong")_gmx_error("incons", "Number of energy terms wrong", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 965);
966 }
967}
968
969void upd_mdebin(t_mdebin *md,
970 gmx_bool bDoDHDL,
971 gmx_bool bSum,
972 double time,
973 real tmass,
974 gmx_enerdata_t *enerd,
975 t_state *state,
976 t_lambda *fep,
977 t_expanded *expand,
978 matrix box,
979 tensor svir,
980 tensor fvir,
981 tensor vir,
982 tensor pres,
983 gmx_ekindata_t *ekind,
984 rvec mu_tot,
985 gmx_constr_t constr)
986{
987 int i, j, k, kk, m, n, gid;
988 real crmsd[2], tmp6[6];
989 real bs[NTRICLBOXS((int)(sizeof(tricl_boxs_nm)/sizeof((tricl_boxs_nm)[0])))], vol, dens, pv, enthalpy;
990 real eee[egNR];
991 real ecopy[F_NRE];
992 double store_dhdl[efptNR];
993 real store_energy = 0;
994 real tmp;
995
996 /* Do NOT use the box in the state variable, but the separate box provided
997 * as an argument. This is because we sometimes need to write the box from
998 * the last timestep to match the trajectory frames.
999 */
1000 copy_energy(md, enerd->term, ecopy);
1001 add_ebin(md->ebin, md->ie, md->f_nre, ecopy, bSum);
1002 if (md->nCrmsd)
1003 {
1004 crmsd[0] = constr_rmsd(constr, FALSE0);
1005 if (md->nCrmsd > 1)
1006 {
1007 crmsd[1] = constr_rmsd(constr, TRUE1);
1008 }
1009 add_ebin(md->ebin, md->iconrmsd, md->nCrmsd, crmsd, FALSE0);
1010 }
1011 if (md->bDynBox)
1012 {
1013 int nboxs;
1014 if (md->bTricl)
1015 {
1016 bs[0] = box[XX0][XX0];
1017 bs[1] = box[YY1][YY1];
1018 bs[2] = box[ZZ2][ZZ2];
1019 bs[3] = box[YY1][XX0];
1020 bs[4] = box[ZZ2][XX0];
1021 bs[5] = box[ZZ2][YY1];
1022 nboxs = NTRICLBOXS((int)(sizeof(tricl_boxs_nm)/sizeof((tricl_boxs_nm)[0])));
1023 }
1024 else
1025 {
1026 bs[0] = box[XX0][XX0];
1027 bs[1] = box[YY1][YY1];
1028 bs[2] = box[ZZ2][ZZ2];
1029 nboxs = NBOXS((int)(sizeof(boxs_nm)/sizeof((boxs_nm)[0])));
1030 }
1031 vol = box[XX0][XX0]*box[YY1][YY1]*box[ZZ2][ZZ2];
1032 dens = (tmass*AMU(1.6605402e-27))/(vol*NANO(1e-9)*NANO(1e-9)*NANO(1e-9));
1033 add_ebin(md->ebin, md->ib, nboxs, bs, bSum);
1034 add_ebin(md->ebin, md->ivol, 1, &vol, bSum);
1035 add_ebin(md->ebin, md->idens, 1, &dens, bSum);
1036
1037 if (md->bDiagPres)
1038 {
1039 /* This is pV (in kJ/mol). The pressure is the reference pressure,
1040 not the instantaneous pressure */
1041 pv = vol*md->ref_p/PRESFAC(16.6054);
1042
1043 add_ebin(md->ebin, md->ipv, 1, &pv, bSum);
1044 enthalpy = pv + enerd->term[F_ETOT];
1045 add_ebin(md->ebin, md->ienthalpy, 1, &enthalpy, bSum);
1046 }
1047 }
1048 if (md->bConstrVir)
1049 {
1050 add_ebin(md->ebin, md->isvir, 9, svir[0], bSum);
1051 add_ebin(md->ebin, md->ifvir, 9, fvir[0], bSum);
1052 }
1053 if (md->bVir)
1054 {
1055 add_ebin(md->ebin, md->ivir, 9, vir[0], bSum);
1056 }
1057 if (md->bPress)
1058 {
1059 add_ebin(md->ebin, md->ipres, 9, pres[0], bSum);
1060 }
1061 if (md->bSurft)
1062 {
1063 tmp = (pres[ZZ2][ZZ2]-(pres[XX0][XX0]+pres[YY1][YY1])*0.5)*box[ZZ2][ZZ2];
1064 add_ebin(md->ebin, md->isurft, 1, &tmp, bSum);
1065 }
1066 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
1067 {
1068 tmp6[0] = state->boxv[XX0][XX0];
1069 tmp6[1] = state->boxv[YY1][YY1];
1070 tmp6[2] = state->boxv[ZZ2][ZZ2];
1071 tmp6[3] = state->boxv[YY1][XX0];
1072 tmp6[4] = state->boxv[ZZ2][XX0];
1073 tmp6[5] = state->boxv[ZZ2][YY1];
1074 add_ebin(md->ebin, md->ipc, md->bTricl ? 6 : 3, tmp6, bSum);
1075 }
1076 if (md->bMu)
1077 {
1078 add_ebin(md->ebin, md->imu, 3, mu_tot, bSum);
1079 }
1080 if (ekind && ekind->cosacc.cos_accel != 0)
1081 {
1082 vol = box[XX0][XX0]*box[YY1][YY1]*box[ZZ2][ZZ2];
1083 dens = (tmass*AMU(1.6605402e-27))/(vol*NANO(1e-9)*NANO(1e-9)*NANO(1e-9));
1084 add_ebin(md->ebin, md->ivcos, 1, &(ekind->cosacc.vcos), bSum);
1085 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
1086 tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO(1e-12))
1087 *dens*sqr(box[ZZ2][ZZ2]*NANO(1e-9)/(2*M_PI3.14159265358979323846)));
1088 add_ebin(md->ebin, md->ivisc, 1, &tmp, bSum);
1089 }
1090 if (md->nE > 1)
1091 {
1092 n = 0;
1093 for (i = 0; (i < md->nEg); i++)
1094 {
1095 for (j = i; (j < md->nEg); j++)
1096 {
1097 gid = GID(i, j, md->nEg)((i < j) ? (i*md->nEg+j) : (j*md->nEg+i));
1098 for (k = kk = 0; (k < egNR); k++)
1099 {
1100 if (md->bEInd[k])
1101 {
1102 eee[kk++] = enerd->grpp.ener[k][gid];
1103 }
1104 }
1105 add_ebin(md->ebin, md->igrp[n], md->nEc, eee, bSum);
1106 n++;
1107 }
1108 }
1109 }
1110
1111 if (ekind)
1112 {
1113 for (i = 0; (i < md->nTC); i++)
1114 {
1115 md->tmp_r[i] = ekind->tcstat[i].T;
1116 }
1117 add_ebin(md->ebin, md->itemp, md->nTC, md->tmp_r, bSum);
1118
1119 if (md->etc == etcNOSEHOOVER)
1120 {
1121 /* whether to print Nose-Hoover chains: */
1122 if (md->bPrintNHChains)
1123 {
1124 if (md->bNHC_trotter)
1125 {
1126 for (i = 0; (i < md->nTC); i++)
1127 {
1128 for (j = 0; j < md->nNHC; j++)
1129 {
1130 k = i*md->nNHC+j;
1131 md->tmp_r[2*k] = state->nosehoover_xi[k];
1132 md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
1133 }
1134 }
1135 add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
1136
1137 if (md->bMTTK)
1138 {
1139 for (i = 0; (i < md->nTCP); i++)
1140 {
1141 for (j = 0; j < md->nNHC; j++)
1142 {
1143 k = i*md->nNHC+j;
1144 md->tmp_r[2*k] = state->nhpres_xi[k];
1145 md->tmp_r[2*k+1] = state->nhpres_vxi[k];
1146 }
1147 }
1148 add_ebin(md->ebin, md->itcb, md->mdeb_n, md->tmp_r, bSum);
1149 }
1150 }
1151 else
1152 {
1153 for (i = 0; (i < md->nTC); i++)
1154 {
1155 md->tmp_r[2*i] = state->nosehoover_xi[i];
1156 md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
1157 }
1158 add_ebin(md->ebin, md->itc, md->mde_n, md->tmp_r, bSum);
1159 }
1160 }
1161 }
1162 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
1163 md->etc == etcVRESCALE)
1164 {
1165 for (i = 0; (i < md->nTC); i++)
1166 {
1167 md->tmp_r[i] = ekind->tcstat[i].lambda;
1168 }
1169 add_ebin(md->ebin, md->itc, md->nTC, md->tmp_r, bSum);
1170 }
1171 }
1172
1173 if (ekind && md->nU > 1)
1174 {
1175 for (i = 0; (i < md->nU); i++)
1176 {
1177 copy_rvec(ekind->grpstat[i].u, md->tmp_v[i]);
1178 }
1179 add_ebin(md->ebin, md->iu, 3*md->nU, md->tmp_v[0], bSum);
1180 }
1181
1182 ebin_increase_count(md->ebin, bSum);
1183
1184 /* BAR + thermodynamic integration values */
1185 if ((md->fp_dhdl || md->dhc) && bDoDHDL)
1186 {
1187 for (i = 0; i < enerd->n_lambda-1; i++)
1188 {
1189 /* zero for simulated tempering */
1190 md->dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];
1191 if (md->temperatures != NULL((void*)0))
1192 {
1193 /* MRS: is this right, given the way we have defined the exchange probabilities? */
1194 /* is this even useful to have at all? */
1195 md->dE[i] += (md->temperatures[i]/
1196 md->temperatures[state->fep_state]-1.0)*
1197 enerd->term[F_EKIN];
1198 }
1199 }
1200
1201 if (md->fp_dhdl)
1202 {
1203 fprintf(md->fp_dhdl, "%.4f", time);
1204 /* the current free energy state */
1205
1206 /* print the current state if we are doing expanded ensemble */
1207 if (expand->elmcmove > elmcmoveNO)
1208 {
1209 fprintf(md->fp_dhdl, " %4d", state->fep_state);
1210 }
1211 /* total energy (for if the temperature changes */
1212 if (fep->bPrintEnergy)
1213 {
1214 store_energy = enerd->term[F_ETOT];
1215 fprintf(md->fp_dhdl, " %#.8g", store_energy);
1216 }
1217
1218 if (fep->dhdl_derivatives == edhdlderivativesYES)
1219 {
1220 for (i = 0; i < efptNR; i++)
1221 {
1222 if (fep->separate_dvdl[i])
1223 {
1224 /* assumes F_DVDL is first */
1225 fprintf(md->fp_dhdl, " %#.8g", enerd->term[F_DVDL+i]);
1226 }
1227 }
1228 }
1229 for (i = fep->lambda_start_n; i < fep->lambda_stop_n; i++)
1230 {
1231 fprintf(md->fp_dhdl, " %#.8g", md->dE[i]);
1232 }
1233 if ((md->epc != epcNO) &&
1234 (enerd->n_lambda > 0) &&
1235 (fep->init_lambda < 0))
1236 {
1237 fprintf(md->fp_dhdl, " %#.8g", pv); /* PV term only needed when
1238 there are alternate state
1239 lambda and we're not in
1240 compatibility mode */
1241 }
1242 fprintf(md->fp_dhdl, "\n");
1243 /* and the binary free energy output */
1244 }
1245 if (md->dhc && bDoDHDL)
1246 {
1247 int idhdl = 0;
1248 for (i = 0; i < efptNR; i++)
1249 {
1250 if (fep->separate_dvdl[i])
1251 {
1252 /* assumes F_DVDL is first */
1253 store_dhdl[idhdl] = enerd->term[F_DVDL+i];
1254 idhdl += 1;
1255 }
1256 }
1257 store_energy = enerd->term[F_ETOT];
1258 /* store_dh is dE */
1259 mde_delta_h_coll_add_dh(md->dhc,
1260 (double)state->fep_state,
1261 store_energy,
1262 pv,
1263 store_dhdl,
1264 md->dE + fep->lambda_start_n,
1265 time);
1266 }
1267 }
1268}
1269
1270
1271void upd_mdebin_step(t_mdebin *md)
1272{
1273 ebin_increase_count(md->ebin, FALSE0);
1274}
1275
1276static void npr(FILE *log, int n, char c)
1277{
1278 for (; (n > 0); n--)
1279 {
1280 fprintf(log, "%c", c);
1281 }
1282}
1283
1284static void pprint(FILE *log, const char *s, t_mdebin *md)
1285{
1286 char CHAR = '#';
1287 int slen;
1288 char buf1[22], buf2[22];
1289
1290 slen = strlen(s);
1291 fprintf(log, "\t<====== ");
1292 npr(log, slen, CHAR);
1293 fprintf(log, " ==>\n");
1294 fprintf(log, "\t<==== %s ====>\n", s);
1295 fprintf(log, "\t<== ");
1296 npr(log, slen, CHAR);
1297 fprintf(log, " ======>\n\n");
1298
1299 fprintf(log, "\tStatistics over %s steps using %s frames\n",
1300 gmx_step_str(md->ebin->nsteps_sim, buf1),
1301 gmx_step_str(md->ebin->nsum_sim, buf2));
1302 fprintf(log, "\n");
1303}
1304
1305void print_ebin_header(FILE *log, gmx_int64_t steps, double time, real lambda)
1306{
1307 char buf[22];
1308
1309 fprintf(log, " %12s %12s %12s\n"
1310 " %12s %12.5f %12.5f\n\n",
1311 "Step", "Time", "Lambda", gmx_step_str(steps, buf), time, lambda);
1312}
1313
1314void print_ebin(ener_file_t fp_ene, gmx_bool bEne, gmx_bool bDR, gmx_bool bOR,
1315 FILE *log,
1316 gmx_int64_t step, double time,
1317 int mode, gmx_bool bCompact,
1318 t_mdebin *md, t_fcdata *fcd,
1319 gmx_groups_t *groups, t_grpopts *opts)
1320{
1321 /*static char **grpnms=NULL;*/
1322 char buf[246];
1323 int i, j, n, ni, nj, ndr, nor, b;
1324 int ndisre = 0;
1325 real *disre_rm3tav, *disre_rt;
1326
1327 /* these are for the old-style blocks (1 subblock, only reals), because
1328 there can be only one per ID for these */
1329 int nr[enxNR];
1330 int id[enxNR];
1331 real *block[enxNR];
1332
1333 /* temporary arrays for the lambda values to write out */
1334 double enxlambda_data[2];
1335
1336 t_enxframe fr;
1337
1338 switch (mode)
1339 {
1340 case eprNORMAL:
1341 init_enxframe(&fr);
1342 fr.t = time;
1343 fr.step = step;
1344 fr.nsteps = md->ebin->nsteps;
1345 fr.dt = md->delta_t;
1346 fr.nsum = md->ebin->nsum;
1347 fr.nre = (bEne) ? md->ebin->nener : 0;
1348 fr.ener = md->ebin->e;
1349 ndisre = bDR ? fcd->disres.npair : 0;
1350 disre_rm3tav = fcd->disres.rm3tav;
1351 disre_rt = fcd->disres.rt;
1352 /* Optional additional old-style (real-only) blocks. */
1353 for (i = 0; i < enxNR; i++)
1354 {
1355 nr[i] = 0;
1356 }
1357 if (fcd->orires.nr > 0 && bOR)
1358 {
1359 diagonalize_orires_tensors(&(fcd->orires));
1360 nr[enxOR] = fcd->orires.nr;
1361 block[enxOR] = fcd->orires.otav;
1362 id[enxOR] = enxOR;
1363 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
1364 fcd->orires.nr : 0;
1365 block[enxORI] = fcd->orires.oinsl;
1366 id[enxORI] = enxORI;
1367 nr[enxORT] = fcd->orires.nex*12;
1368 block[enxORT] = fcd->orires.eig;
1369 id[enxORT] = enxORT;
1370 }
1371
1372 /* whether we are going to wrte anything out: */
1373 if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
1374 {
1375
1376 /* the old-style blocks go first */
1377 fr.nblock = 0;
1378 for (i = 0; i < enxNR; i++)
1379 {
1380 if (nr[i] > 0)
1381 {
1382 fr.nblock = i + 1;
1383 }
1384 }
1385 add_blocks_enxframe(&fr, fr.nblock);
1386 for (b = 0; b < fr.nblock; b++)
1387 {
1388 add_subblocks_enxblock(&(fr.block[b]), 1);
1389 fr.block[b].id = id[b];
1390 fr.block[b].sub[0].nr = nr[b];
1391#ifndef GMX_DOUBLE
1392 fr.block[b].sub[0].type = xdr_datatype_float;
1393 fr.block[b].sub[0].fval = block[b];
1394#else
1395 fr.block[b].sub[0].type = xdr_datatype_double;
1396 fr.block[b].sub[0].dval = block[b];
1397#endif
1398 }
1399
1400 /* check for disre block & fill it. */
1401 if (ndisre > 0)
1402 {
1403 int db = fr.nblock;
1404 fr.nblock += 1;
1405 add_blocks_enxframe(&fr, fr.nblock);
1406
1407 add_subblocks_enxblock(&(fr.block[db]), 2);
1408 fr.block[db].id = enxDISRE;
1409 fr.block[db].sub[0].nr = ndisre;
1410 fr.block[db].sub[1].nr = ndisre;
1411#ifndef GMX_DOUBLE
1412 fr.block[db].sub[0].type = xdr_datatype_float;
1413 fr.block[db].sub[1].type = xdr_datatype_float;
1414 fr.block[db].sub[0].fval = disre_rt;
1415 fr.block[db].sub[1].fval = disre_rm3tav;
1416#else
1417 fr.block[db].sub[0].type = xdr_datatype_double;
1418 fr.block[db].sub[1].type = xdr_datatype_double;
1419 fr.block[db].sub[0].dval = disre_rt;
1420 fr.block[db].sub[1].dval = disre_rm3tav;
1421#endif
1422 }
1423 /* here we can put new-style blocks */
1424
1425 /* Free energy perturbation blocks */
1426 if (md->dhc)
1427 {
1428 mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
1429 }
1430
1431 /* we can now free & reset the data in the blocks */
1432 if (md->dhc)
1433 {
1434 mde_delta_h_coll_reset(md->dhc);
1435 }
1436
1437 /* do the actual I/O */
1438 do_enx(fp_ene, &fr);
1439 if (fr.nre)
1440 {
1441 /* We have stored the sums, so reset the sum history */
1442 reset_ebin_sums(md->ebin);
1443 }
1444 }
1445 free_enxframe(&fr);
1446 break;
1447 case eprAVER:
1448 if (log)
1449 {
1450 pprint(log, "A V E R A G E S", md);
1451 }
1452 break;
1453 case eprRMS:
1454 if (log)
1455 {
1456 pprint(log, "R M S - F L U C T U A T I O N S", md);
1457 }
1458 break;
1459 default:
1460 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c",
1460, "Invalid print mode (%d)", mode);
1461 }
1462
1463 if (log)
1464 {
1465 for (i = 0; i < opts->ngtc; i++)
1466 {
1467 if (opts->annealing[i] != eannNO)
1468 {
1469 fprintf(log, "Current ref_t for group %s: %8.1f\n",
1470 *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
1471 opts->ref_t[i]);
1472 }
1473 }
1474 if (mode == eprNORMAL && fcd->orires.nr > 0)
1475 {
1476 print_orires_log(log, &(fcd->orires));
1477 }
1478 fprintf(log, " Energies (%s)\n", unit_energy"kJ/mol");
1479 pr_ebin(log, md->ebin, md->ie, md->f_nre+md->nCrmsd, 5, mode, TRUE1);
1480 fprintf(log, "\n");
1481
1482 if (!bCompact)
1483 {
1484 if (md->bDynBox)
1485 {
1486 pr_ebin(log, md->ebin, md->ib, md->bTricl ? NTRICLBOXS((int)(sizeof(tricl_boxs_nm)/sizeof((tricl_boxs_nm)[0]))) : NBOXS((int)(sizeof(boxs_nm)/sizeof((boxs_nm)[0]))), 5,
1487 mode, TRUE1);
1488 fprintf(log, "\n");
1489 }
1490 if (md->bConstrVir)
1491 {
1492 fprintf(log, " Constraint Virial (%s)\n", unit_energy"kJ/mol");
1493 pr_ebin(log, md->ebin, md->isvir, 9, 3, mode, FALSE0);
1494 fprintf(log, "\n");
1495 fprintf(log, " Force Virial (%s)\n", unit_energy"kJ/mol");
1496 pr_ebin(log, md->ebin, md->ifvir, 9, 3, mode, FALSE0);
1497 fprintf(log, "\n");
1498 }
1499 if (md->bVir)
1500 {
1501 fprintf(log, " Total Virial (%s)\n", unit_energy"kJ/mol");
1502 pr_ebin(log, md->ebin, md->ivir, 9, 3, mode, FALSE0);
1503 fprintf(log, "\n");
1504 }
1505 if (md->bPress)
1506 {
1507 fprintf(log, " Pressure (%s)\n", unit_pres_bar"bar");
1508 pr_ebin(log, md->ebin, md->ipres, 9, 3, mode, FALSE0);
1509 fprintf(log, "\n");
1510 }
1511 if (md->bMu)
1512 {
1513 fprintf(log, " Total Dipole (%s)\n", unit_dipole_D"D");
1514 pr_ebin(log, md->ebin, md->imu, 3, 3, mode, FALSE0);
1515 fprintf(log, "\n");
1516 }
1517
1518 if (md->nE > 1)
1519 {
1520 if (md->print_grpnms == NULL((void*)0))
1521 {
1522 snew(md->print_grpnms, md->nE)(md->print_grpnms) = save_calloc("md->print_grpnms", "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c"
, 1522, (md->nE), sizeof(*(md->print_grpnms)));
1523 n = 0;
1524 for (i = 0; (i < md->nEg); i++)
1525 {
1526 ni = groups->grps[egcENER].nm_ind[i];
1527 for (j = i; (j < md->nEg); j++)
1528 {
1529 nj = groups->grps[egcENER].nm_ind[j];
1530 sprintf(buf, "%s-%s", *(groups->grpname[ni]),
1531 *(groups->grpname[nj]));
1532 md->print_grpnms[n++] = strdup(buf)(__extension__ (__builtin_constant_p (buf) && ((size_t
)(const void *)((buf) + 1) - (size_t)(const void *)(buf) == 1
) ? (((const char *) (buf))[0] == '\0' ? (char *) calloc ((size_t
) 1, (size_t) 1) : ({ size_t __len = strlen (buf) + 1; char *
__retval = (char *) malloc (__len); if (__retval != ((void*)0
)) __retval = (char *) memcpy (__retval, buf, __len); __retval
; })) : __strdup (buf)));
1533 }
1534 }
1535 }
1536 sprintf(buf, "Epot (%s)", unit_energy"kJ/mol");
1537 fprintf(log, "%15s ", buf);
1538 for (i = 0; (i < egNR); i++)
1539 {
1540 if (md->bEInd[i])
1541 {
1542 fprintf(log, "%12s ", egrp_nm[i]);
1543 }
1544 }
1545 fprintf(log, "\n");
1546 for (i = 0; (i < md->nE); i++)
1547 {
1548 fprintf(log, "%15s", md->print_grpnms[i]);
1549 pr_ebin(log, md->ebin, md->igrp[i], md->nEc, md->nEc, mode,
1550 FALSE0);
1551 }
1552 fprintf(log, "\n");
1553 }
1554 if (md->nTC > 1)
1555 {
1556 pr_ebin(log, md->ebin, md->itemp, md->nTC, 4, mode, TRUE1);
1557 fprintf(log, "\n");
1558 }
1559 if (md->nU > 1)
1560 {
1561 fprintf(log, "%15s %12s %12s %12s\n",
1562 "Group", "Ux", "Uy", "Uz");
1563 for (i = 0; (i < md->nU); i++)
1564 {
1565 ni = groups->grps[egcACC].nm_ind[i];
1566 fprintf(log, "%15s", *groups->grpname[ni]);
1567 pr_ebin(log, md->ebin, md->iu+3*i, 3, 3, mode, FALSE0);
1568 }
1569 fprintf(log, "\n");
1570 }
1571 }
1572 }
1573
1574}
1575
1576void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin)
1577{
1578 int i;
1579
1580 enerhist->nsteps = mdebin->ebin->nsteps;
1581 enerhist->nsum = mdebin->ebin->nsum;
1582 enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
1583 enerhist->nsum_sim = mdebin->ebin->nsum_sim;
1584 enerhist->nener = mdebin->ebin->nener;
1585
1586 if (mdebin->ebin->nsum > 0)
1587 {
1588 /* Check if we need to allocate first */
1589 if (enerhist->ener_ave == NULL((void*)0))
1590 {
1591 snew(enerhist->ener_ave, enerhist->nener)(enerhist->ener_ave) = save_calloc("enerhist->ener_ave"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c", 1591
, (enerhist->nener), sizeof(*(enerhist->ener_ave)));
1592 snew(enerhist->ener_sum, enerhist->nener)(enerhist->ener_sum) = save_calloc("enerhist->ener_sum"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c", 1592
, (enerhist->nener), sizeof(*(enerhist->ener_sum)));
1593 }
1594
1595 for (i = 0; i < enerhist->nener; i++)
1596 {
1597 enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
1598 enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
1599 }
1600 }
1601
1602 if (mdebin->ebin->nsum_sim > 0)
1603 {
1604 /* Check if we need to allocate first */
1605 if (enerhist->ener_sum_sim == NULL((void*)0))
1606 {
1607 snew(enerhist->ener_sum_sim, enerhist->nener)(enerhist->ener_sum_sim) = save_calloc("enerhist->ener_sum_sim"
, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c", 1607
, (enerhist->nener), sizeof(*(enerhist->ener_sum_sim)));
1608 }
1609
1610 for (i = 0; i < enerhist->nener; i++)
1611 {
1612 enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
1613 }
1614 }
1615 if (mdebin->dhc)
1616 {
1617 mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
1618 }
1619}
1620
1621void restore_energyhistory_from_state(t_mdebin * mdebin,
1622 energyhistory_t * enerhist)
1623{
1624 int i;
1625
1626 if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
1627 mdebin->ebin->nener != enerhist->nener)
1628 {
1629 gmx_fatal(FARGS0, "/home/alexxy/Develop/gromacs/src/gromacs/mdlib/mdebin.c",
1629, "Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
1630 mdebin->ebin->nener, enerhist->nener);
1631 }
1632
1633 mdebin->ebin->nsteps = enerhist->nsteps;
1634 mdebin->ebin->nsum = enerhist->nsum;
1635 mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
1636 mdebin->ebin->nsum_sim = enerhist->nsum_sim;
1637
1638 for (i = 0; i < mdebin->ebin->nener; i++)
1639 {
1640 mdebin->ebin->e[i].eav =
1641 (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
1642 mdebin->ebin->e[i].esum =
1643 (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
1644 mdebin->ebin->e_sim[i].esum =
1645 (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
1646 }
1647 if (mdebin->dhc)
1648 {
1649 mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);
1650 }
1651}