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added Verlet scheme and NxN non-bonded functionality
[gromacs.git] / src / mdlib / mdebin.c
blob8255c6ad8ba30765a959d3fd9536ea8a7808e832
1 /* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*-
2 *
3 *
4 * This source code is part of
5 *
6 * G R O M A C S
7 *
8 * GROningen MAchine for Chemical Simulations
9 *
10 * VERSION 3.2.0
11 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
12 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
13 * Copyright (c) 2001-2004, The GROMACS development team,
14 * check out http://www.gromacs.org for more information.
15
16 * This program is free software; you can redistribute it and/or
17 * modify it under the terms of the GNU General Public License
18 * as published by the Free Software Foundation; either version 2
19 * of the License, or (at your option) any later version.
20 *
21 * If you want to redistribute modifications, please consider that
22 * scientific software is very special. Version control is crucial -
23 * bugs must be traceable. We will be happy to consider code for
24 * inclusion in the official distribution, but derived work must not
25 * be called official GROMACS. Details are found in the README & COPYING
26 * files - if they are missing, get the official version at www.gromacs.org.
27 *
28 * To help us fund GROMACS development, we humbly ask that you cite
29 * the papers on the package - you can find them in the top README file.
30 *
31 * For more info, check our website at http://www.gromacs.org
32 *
33 * And Hey:
34 * GROwing Monsters And Cloning Shrimps
35 */
36 #ifdef HAVE_CONFIG_H
37 #include <config.h>
38 #endif
39
40 #include <string.h>
41 #include <float.h>
42 #include "typedefs.h"
43 #include "string2.h"
44 #include "mdebin.h"
45 #include "smalloc.h"
46 #include "physics.h"
47 #include "enxio.h"
48 #include "vec.h"
49 #include "disre.h"
50 #include "main.h"
51 #include "network.h"
52 #include "names.h"
53 #include "orires.h"
54 #include "constr.h"
55 #include "mtop_util.h"
56 #include "xvgr.h"
57 #include "gmxfio.h"
58 #include "mdrun.h"
59 #include "mdebin_bar.h"
60
61
62 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
63
64 static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
65
66 static const char *tricl_boxs_nm[] = {
67 "Box-XX", "Box-YY", "Box-ZZ",
68 "Box-YX", "Box-ZX", "Box-ZY"
69 };
70
71 static const char *vol_nm[] = { "Volume" };
72
73 static const char *dens_nm[] = {"Density" };
74
75 static const char *pv_nm[] = {"pV" };
76
77 static const char *enthalpy_nm[] = {"Enthalpy" };
78
79 static const char *boxvel_nm[] = {
80 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
81 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
82 };
83
84 #define NBOXS asize(boxs_nm)
85 #define NTRICLBOXS asize(tricl_boxs_nm)
86
87 t_mdebin *init_mdebin(ener_file_t fp_ene,
88 const gmx_mtop_t *mtop,
89 const t_inputrec *ir,
90 FILE *fp_dhdl)
91 {
92 const char *ener_nm[F_NRE];
93 static const char *vir_nm[] = {
94 "Vir-XX", "Vir-XY", "Vir-XZ",
95 "Vir-YX", "Vir-YY", "Vir-YZ",
96 "Vir-ZX", "Vir-ZY", "Vir-ZZ"
97 };
98 static const char *sv_nm[] = {
99 "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
100 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
101 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
102 };
103 static const char *fv_nm[] = {
104 "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
105 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
106 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
107 };
108 static const char *pres_nm[] = {
109 "Pres-XX","Pres-XY","Pres-XZ",
110 "Pres-YX","Pres-YY","Pres-YZ",
111 "Pres-ZX","Pres-ZY","Pres-ZZ"
112 };
113 static const char *surft_nm[] = {
114 "#Surf*SurfTen"
115 };
116 static const char *mu_nm[] = {
117 "Mu-X", "Mu-Y", "Mu-Z"
118 };
119 static const char *vcos_nm[] = {
120 "2CosZ*Vel-X"
121 };
122 static const char *visc_nm[] = {
123 "1/Viscosity"
124 };
125 static const char *baro_nm[] = {
126 "Barostat"
127 };
128
129 char **grpnms;
130 const gmx_groups_t *groups;
131 char **gnm;
132 char buf[256];
133 const char *bufi;
134 t_mdebin *md;
135 int i,j,ni,nj,n,nh,k,kk,ncon,nset;
136 gmx_bool bBHAM,bNoseHoover,b14;
137
138 snew(md,1);
139
140 md->bVir=TRUE;
141 md->bPress=TRUE;
142 md->bSurft=TRUE;
143 md->bMu=TRUE;
144
145 if (EI_DYNAMICS(ir->eI))
146 {
147 md->delta_t = ir->delta_t;
148 }
149 else
150 {
151 md->delta_t = 0;
152 }
153
154 groups = &mtop->groups;
155
156 bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
157 b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
158 gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
159
160 ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
161 nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
162 md->bConstr = (ncon > 0 || nset > 0);
163 md->bConstrVir = FALSE;
164 if (md->bConstr) {
165 if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
166 if (ir->eI == eiSD2)
167 md->nCrmsd = 2;
168 else
169 md->nCrmsd = 1;
170 }
171 md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
172 } else {
173 md->nCrmsd = 0;
174 }
175
176 /* Energy monitoring */
177 for(i=0;i<egNR;i++)
178 {
179 md->bEInd[i]=FALSE;
180 }
181
182 #ifndef GMX_OPENMM
183 for(i=0; i<F_NRE; i++)
184 {
185 md->bEner[i] = FALSE;
186 if (i == F_LJ)
187 md->bEner[i] = !bBHAM;
188 else if (i == F_BHAM)
189 md->bEner[i] = bBHAM;
190 else if (i == F_EQM)
191 md->bEner[i] = ir->bQMMM;
192 else if (i == F_COUL_LR)
193 md->bEner[i] = (ir->rcoulomb > ir->rlist);
194 else if (i == F_LJ_LR)
195 md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
196 else if (i == F_BHAM_LR)
197 md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
198 else if (i == F_RF_EXCL)
199 md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC && ir->cutoff_scheme == ecutsGROUP);
200 else if (i == F_COUL_RECIP)
201 md->bEner[i] = EEL_FULL(ir->coulombtype);
202 else if (i == F_LJ14)
203 md->bEner[i] = b14;
204 else if (i == F_COUL14)
205 md->bEner[i] = b14;
206 else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
207 md->bEner[i] = FALSE;
208 else if ((i == F_DVDL_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
209 (i == F_DVDL_VDW && ir->fepvals->separate_dvdl[efptVDW]) ||
210 (i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
211 (i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
212 (i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
213 (i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
214 md->bEner[i] = (ir->efep != efepNO);
215 else if ((interaction_function[i].flags & IF_VSITE) ||
216 (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
217 md->bEner[i] = FALSE;
218 else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
219 md->bEner[i] = TRUE;
220 else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
221 md->bEner[i] = TRUE;
222 else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
223 md->bEner[i] = TRUE;
224 else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
225 md->bEner[i] = FALSE;
226 else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
227 md->bEner[i] = EI_DYNAMICS(ir->eI);
228 else if (i==F_VTEMP)
229 md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
230 else if (i == F_DISPCORR || i == F_PDISPCORR)
231 md->bEner[i] = (ir->eDispCorr != edispcNO);
232 else if (i == F_DISRESVIOL)
233 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
234 else if (i == F_ORIRESDEV)
235 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
236 else if (i == F_CONNBONDS)
237 md->bEner[i] = FALSE;
238 else if (i == F_COM_PULL)
239 md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
240 else if (i == F_ECONSERVED)
241 md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
242 (ir->epc == epcNO || ir->epc==epcMTTK));
243 else
244 md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
245 }
246 #else
247 /* OpenMM always produces only the following 4 energy terms */
248 md->bEner[F_EPOT] = TRUE;
249 md->bEner[F_EKIN] = TRUE;
250 md->bEner[F_ETOT] = TRUE;
251 md->bEner[F_TEMP] = TRUE;
252 #endif
253
254 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
255 if (ir->bAdress && !debug) {
256 for (i = 0; i < F_NRE; i++) {
257 md->bEner[i] = FALSE;
258 if(i == F_EKIN){ md->bEner[i] = TRUE;}
259 if(i == F_TEMP){ md->bEner[i] = TRUE;}
260 }
261 md->bVir=FALSE;
262 md->bPress=FALSE;
263 md->bSurft=FALSE;
264 md->bMu=FALSE;
265 }
266
267 md->f_nre=0;
268 for(i=0; i<F_NRE; i++)
269 {
270 if (md->bEner[i])
271 {
272 ener_nm[md->f_nre]=interaction_function[i].longname;
273 md->f_nre++;
274 }
275 }
276
277 md->epc = ir->epc;
278 md->bDiagPres = !TRICLINIC(ir->ref_p);
279 md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
280 md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
281 md->bDynBox = DYNAMIC_BOX(*ir);
282 md->etc = ir->etc;
283 md->bNHC_trotter = IR_NVT_TROTTER(ir);
284 md->bPrintNHChains = ir-> bPrintNHChains;
285 md->bMTTK = (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir));
286 md->bMu = NEED_MUTOT(*ir);
287
288 md->ebin = mk_ebin();
289 /* Pass NULL for unit to let get_ebin_space determine the units
290 * for interaction_function[i].longname
291 */
292 md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL);
293 if (md->nCrmsd)
294 {
295 /* This should be called directly after the call for md->ie,
296 * such that md->iconrmsd follows directly in the list.
297 */
298 md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,"");
299 }
300 if (md->bDynBox)
301 {
302 md->ib = get_ebin_space(md->ebin,
303 md->bTricl ? NTRICLBOXS : NBOXS,
304 md->bTricl ? tricl_boxs_nm : boxs_nm,
305 unit_length);
306 md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
307 md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
308 if (md->bDiagPres)
309 {
310 md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
311 md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
312 }
313 }
314 if (md->bConstrVir)
315 {
316 md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
317 md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
318 }
319 if (md->bVir)
320 md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
321 if (md->bPress)
322 md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
323 if (md->bSurft)
324 md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
325 unit_surft_bar);
326 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
327 {
328 md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3,
329 boxvel_nm,unit_vel);
330 }
331 if (md->bMu)
332 {
333 md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
334 }
335 if (ir->cos_accel != 0)
336 {
337 md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
338 md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
339 unit_invvisc_SI);
340 }
341
342 /* Energy monitoring */
343 for(i=0;i<egNR;i++)
344 {
345 md->bEInd[i] = FALSE;
346 }
347 md->bEInd[egCOULSR] = TRUE;
348 md->bEInd[egLJSR ] = TRUE;
349
350 if (ir->rcoulomb > ir->rlist)
351 {
352 md->bEInd[egCOULLR] = TRUE;
353 }
354 if (!bBHAM)
355 {
356 if (ir->rvdw > ir->rlist)
357 {
358 md->bEInd[egLJLR] = TRUE;
359 }
360 }
361 else
362 {
363 md->bEInd[egLJSR] = FALSE;
364 md->bEInd[egBHAMSR] = TRUE;
365 if (ir->rvdw > ir->rlist)
366 {
367 md->bEInd[egBHAMLR] = TRUE;
368 }
369 }
370 if (b14)
371 {
372 md->bEInd[egLJ14] = TRUE;
373 md->bEInd[egCOUL14] = TRUE;
374 }
375 md->nEc=0;
376 for(i=0; (i<egNR); i++)
377 {
378 if (md->bEInd[i])
379 {
380 md->nEc++;
381 }
382 }
383
384 n=groups->grps[egcENER].nr;
385 /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
386 if (!ir->bAdress){
387 /*standard simulation*/
388 md->nEg=n;
389 md->nE=(n*(n+1))/2;
390 }
391 else if (!debug) {
392 /*AdResS simulation*/
393 md->nU=0;
394 md->nEg=0;
395 md->nE=0;
396 md->nEc=0;
397 md->isvir=FALSE;
398 }
399 snew(md->igrp,md->nE);
400 if (md->nE > 1)
401 {
402 n=0;
403 snew(gnm,md->nEc);
404 for(k=0; (k<md->nEc); k++)
405 {
406 snew(gnm[k],STRLEN);
407 }
408 for(i=0; (i<groups->grps[egcENER].nr); i++)
409 {
410 ni=groups->grps[egcENER].nm_ind[i];
411 for(j=i; (j<groups->grps[egcENER].nr); j++)
412 {
413 nj=groups->grps[egcENER].nm_ind[j];
414 for(k=kk=0; (k<egNR); k++)
415 {
416 if (md->bEInd[k])
417 {
418 sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
419 *(groups->grpname[ni]),*(groups->grpname[nj]));
420 kk++;
421 }
422 }
423 md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
424 (const char **)gnm,unit_energy);
425 n++;
426 }
427 }
428 for(k=0; (k<md->nEc); k++)
429 {
430 sfree(gnm[k]);
431 }
432 sfree(gnm);
433
434 if (n != md->nE)
435 {
436 gmx_incons("Number of energy terms wrong");
437 }
438 }
439
440 md->nTC=groups->grps[egcTC].nr;
441 md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
442 if (md->bMTTK)
443 {
444 md->nTCP = 1; /* assume only one possible coupling system for barostat
445 for now */
446 }
447 else
448 {
449 md->nTCP = 0;
450 }
451 if (md->etc == etcNOSEHOOVER)
452 {
453 if (md->bNHC_trotter)
454 {
455 md->mde_n = 2*md->nNHC*md->nTC;
456 }
457 else
458 {
459 md->mde_n = 2*md->nTC;
460 }
461 if (md->epc == epcMTTK)
462 {
463 md->mdeb_n = 2*md->nNHC*md->nTCP;
464 }
465 } else {
466 md->mde_n = md->nTC;
467 md->mdeb_n = 0;
468 }
469
470 snew(md->tmp_r,md->mde_n);
471 snew(md->tmp_v,md->mde_n);
472 snew(md->grpnms,md->mde_n);
473 grpnms = md->grpnms;
474
475 for(i=0; (i<md->nTC); i++)
476 {
477 ni=groups->grps[egcTC].nm_ind[i];
478 sprintf(buf,"T-%s",*(groups->grpname[ni]));
479 grpnms[i]=strdup(buf);
480 }
481 md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
482 unit_temp_K);
483
484 if (md->etc == etcNOSEHOOVER)
485 {
486 if (md->bPrintNHChains)
487 {
488 if (md->bNHC_trotter)
489 {
490 for(i=0; (i<md->nTC); i++)
491 {
492 ni=groups->grps[egcTC].nm_ind[i];
493 bufi = *(groups->grpname[ni]);
494 for(j=0; (j<md->nNHC); j++)
495 {
496 sprintf(buf,"Xi-%d-%s",j,bufi);
497 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
498 sprintf(buf,"vXi-%d-%s",j,bufi);
499 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
500 }
501 }
502 md->itc=get_ebin_space(md->ebin,md->mde_n,
503 (const char **)grpnms,unit_invtime);
504 if (md->bMTTK)
505 {
506 for(i=0; (i<md->nTCP); i++)
507 {
508 bufi = baro_nm[0]; /* All barostat DOF's together for now. */
509 for(j=0; (j<md->nNHC); j++)
510 {
511 sprintf(buf,"Xi-%d-%s",j,bufi);
512 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
513 sprintf(buf,"vXi-%d-%s",j,bufi);
514 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
515 }
516 }
517 md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
518 (const char **)grpnms,unit_invtime);
519 }
520 }
521 else
522 {
523 for(i=0; (i<md->nTC); i++)
524 {
525 ni=groups->grps[egcTC].nm_ind[i];
526 bufi = *(groups->grpname[ni]);
527 sprintf(buf,"Xi-%s",bufi);
528 grpnms[2*i]=strdup(buf);
529 sprintf(buf,"vXi-%s",bufi);
530 grpnms[2*i+1]=strdup(buf);
531 }
532 md->itc=get_ebin_space(md->ebin,md->mde_n,
533 (const char **)grpnms,unit_invtime);
534 }
535 }
536 }
537 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
538 md->etc == etcVRESCALE)
539 {
540 for(i=0; (i<md->nTC); i++)
541 {
542 ni=groups->grps[egcTC].nm_ind[i];
543 sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
544 grpnms[i]=strdup(buf);
545 }
546 md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
547 }
548
549 sfree(grpnms);
550
551
552 md->nU=groups->grps[egcACC].nr;
553 if (md->nU > 1)
554 {
555 snew(grpnms,3*md->nU);
556 for(i=0; (i<md->nU); i++)
557 {
558 ni=groups->grps[egcACC].nm_ind[i];
559 sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
560 grpnms[3*i+XX]=strdup(buf);
561 sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
562 grpnms[3*i+YY]=strdup(buf);
563 sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
564 grpnms[3*i+ZZ]=strdup(buf);
565 }
566 md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
567 sfree(grpnms);
568 }
569
570 if ( fp_ene )
571 {
572 do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
573 }
574
575 md->print_grpnms=NULL;
576
577 /* check whether we're going to write dh histograms */
578 md->dhc=NULL;
579 if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO )
580 {
581 /* Currently dh histograms are only written with dynamics */
582 if (EI_DYNAMICS(ir->eI))
583 {
584 snew(md->dhc, 1);
585
586 mde_delta_h_coll_init(md->dhc, ir);
587 }
588 md->fp_dhdl = NULL;
589 }
590 else
591 {
592 md->fp_dhdl = fp_dhdl;
593 }
594 if (ir->bSimTemp) {
595 int i;
596 snew(md->temperatures,ir->fepvals->n_lambda);
597 for (i=0;i<ir->fepvals->n_lambda;i++)
598 {
599 md->temperatures[i] = ir->simtempvals->temperatures[i];
600 }
601 }
602 return md;
603 }
604
605 extern FILE *open_dhdl(const char *filename,const t_inputrec *ir,
606 const output_env_t oenv)
607 {
608 FILE *fp;
609 const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda",
610 *lambdastate="\\lambda state",*remain="remaining";
611 char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
612 int i,np,nps,nsets,nsets_de,nsetsbegin;
613 t_lambda *fep;
614 char **setname;
615 char buf[STRLEN];
616 int bufplace=0;
617
618 int nsets_dhdl = 0;
619 int s = 0;
620 int nsetsextend;
621
622 /* for simplicity */
623 fep = ir->fepvals;
624
625 if (fep->n_lambda == 0)
626 {
627 sprintf(title,"%s",dhdl);
628 sprintf(label_x,"Time (ps)");
629 sprintf(label_y,"%s (%s %s)",
630 dhdl,unit_energy,"[\\lambda]\\S-1\\N");
631 }
632 else
633 {
634 sprintf(title,"%s and %s",dhdl,deltag);
635 sprintf(label_x,"Time (ps)");
636 sprintf(label_y,"%s and %s (%s %s)",
637 dhdl,deltag,unit_energy,"[\\8l\\4]\\S-1\\N");
638 }
639 fp = gmx_fio_fopen(filename,"w+");
640 xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
641
642 if (!(ir->bSimTemp))
643 {
644 bufplace = sprintf(buf,"T = %g (K) ",
645 ir->opts.ref_t[0]);
646 }
647 if (ir->efep != efepSLOWGROWTH)
648 {
649 if (fep->n_lambda == 0)
650 {
651 sprintf(&(buf[bufplace]),"%s = %g",
652 lambda,fep->init_lambda);
653 }
654 else
655 {
656 sprintf(&(buf[bufplace]),"%s = %d",
657 lambdastate,fep->init_fep_state);
658 }
659 }
660 xvgr_subtitle(fp,buf,oenv);
661
662 for (i=0;i<efptNR;i++)
663 {
664 if (fep->separate_dvdl[i]) {nsets_dhdl++;}
665 }
666
667 /* count the number of delta_g states */
668 nsets_de = fep->n_lambda;
669
670 nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
671
672 if (fep->n_lambda>0 && ir->bExpanded)
673 {
674 nsets += 1; /*add fep state for expanded ensemble */
675 }
676
677 if (fep->bPrintEnergy)
678 {
679 nsets += 1; /* add energy to the dhdl as well */
680 }
681
682 nsetsextend = nsets;
683 if ((ir->epc!=epcNO) && (fep->n_lambda>0))
684 {
685 nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda) */
686 }
687 snew(setname,nsetsextend);
688
689 if (ir->bExpanded)
690 {
691 /* state for the fep_vals, if we have alchemical sampling */
692 sprintf(buf,"%s","Thermodynamic state");
693 setname[s] = strdup(buf);
694 s+=1;
695 }
696
697 if (fep->bPrintEnergy)
698 {
699 sprintf(buf,"%s (%s)","Energy",unit_energy);
700 setname[s] = strdup(buf);
701 s+=1;
702 }
703
704 for (i=0;i<efptNR;i++)
705 {
706 if (fep->separate_dvdl[i]) {
707 sprintf(buf,"%s (%s)",dhdl,efpt_names[i]);
708 setname[s] = strdup(buf);
709 s+=1;
710 }
711 }
712
713 if (fep->n_lambda > 0)
714 {
715 /* g_bar has to determine the lambda values used in this simulation
716 * from this xvg legend.
717 */
718
719 if (ir->bExpanded) {
720 nsetsbegin = 1; /* for including the expanded ensemble */
721 } else {
722 nsetsbegin = 0;
723 }
724
725 if (fep->bPrintEnergy)
726 {
727 nsetsbegin += 1;
728 }
729 nsetsbegin += nsets_dhdl;
730
731 for(s=nsetsbegin; s<nsets; s++)
732 {
733 nps = sprintf(buf,"%s %s (",deltag,lambda);
734 for (i=0;i<efptNR;i++)
735 {
736 if (fep->separate_dvdl[i])
737 {
738 np = sprintf(&buf[nps],"%g,",fep->all_lambda[i][s-(nsetsbegin)]);
739 nps += np;
740 }
741 }
742 if (ir->bSimTemp)
743 {
744 /* print the temperature for this state if doing simulated annealing */
745 sprintf(&buf[nps],"T = %g (%s))",ir->simtempvals->temperatures[s-(nsetsbegin)],unit_temp_K);
746 }
747 else
748 {
749 sprintf(&buf[nps-1],")"); /* -1 to overwrite the last comma */
750 }
751 setname[s] = strdup(buf);
752 }
753 if (ir->epc!=epcNO) {
754 np = sprintf(buf,"pV (%s)",unit_energy);
755 setname[nsetsextend-1] = strdup(buf); /* the first entry after nsets */
756 }
757
758 xvgr_legend(fp,nsetsextend,(const char **)setname,oenv);
759
760 for(s=0; s<nsetsextend; s++)
761 {
762 sfree(setname[s]);
763 }
764 sfree(setname);
765 }
766
767 return fp;
768 }
769
770 static void copy_energy(t_mdebin *md, real e[],real ecpy[])
771 {
772 int i,j;
773
774 for(i=j=0; (i<F_NRE); i++)
775 if (md->bEner[i])
776 ecpy[j++] = e[i];
777 if (j != md->f_nre)
778 gmx_incons("Number of energy terms wrong");
779 }
780
781 void upd_mdebin(t_mdebin *md,
782 gmx_bool bDoDHDL,
783 gmx_bool bSum,
784 double time,
785 real tmass,
786 gmx_enerdata_t *enerd,
787 t_state *state,
788 t_lambda *fep,
789 t_expanded *expand,
790 matrix box,
791 tensor svir,
792 tensor fvir,
793 tensor vir,
794 tensor pres,
795 gmx_ekindata_t *ekind,
796 rvec mu_tot,
797 gmx_constr_t constr)
798 {
799 int i,j,k,kk,m,n,gid;
800 real crmsd[2],tmp6[6];
801 real bs[NTRICLBOXS],vol,dens,pv,enthalpy;
802 real eee[egNR];
803 real ecopy[F_NRE];
804 double store_dhdl[efptNR];
805 double *dE=NULL;
806 real store_energy=0;
807 real tmp;
808
809 /* Do NOT use the box in the state variable, but the separate box provided
810 * as an argument. This is because we sometimes need to write the box from
811 * the last timestep to match the trajectory frames.
812 */
813 copy_energy(md, enerd->term,ecopy);
814 add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
815 if (md->nCrmsd)
816 {
817 crmsd[0] = constr_rmsd(constr,FALSE);
818 if (md->nCrmsd > 1)
819 {
820 crmsd[1] = constr_rmsd(constr,TRUE);
821 }
822 add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
823 }
824 if (md->bDynBox)
825 {
826 int nboxs;
827 if(md->bTricl)
828 {
829 bs[0] = box[XX][XX];
830 bs[1] = box[YY][YY];
831 bs[2] = box[ZZ][ZZ];
832 bs[3] = box[YY][XX];
833 bs[4] = box[ZZ][XX];
834 bs[5] = box[ZZ][YY];
835 nboxs=NTRICLBOXS;
836 }
837 else
838 {
839 bs[0] = box[XX][XX];
840 bs[1] = box[YY][YY];
841 bs[2] = box[ZZ][ZZ];
842 nboxs=NBOXS;
843 }
844 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
845 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
846 add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
847 add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
848 add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
849
850 if (md->bDiagPres)
851 {
852 /* This is pV (in kJ/mol). The pressure is the reference pressure,
853 not the instantaneous pressure */
854 pv = vol*md->ref_p/PRESFAC;
855
856 add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
857 enthalpy = pv + enerd->term[F_ETOT];
858 add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
859 }
860 }
861 if (md->bConstrVir)
862 {
863 add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
864 add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
865 }
866 if (md->bVir)
867 add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
868 if (md->bPress)
869 add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
870 if (md->bSurft){
871 tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
872 add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
873 }
874 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
875 {
876 tmp6[0] = state->boxv[XX][XX];
877 tmp6[1] = state->boxv[YY][YY];
878 tmp6[2] = state->boxv[ZZ][ZZ];
879 tmp6[3] = state->boxv[YY][XX];
880 tmp6[4] = state->boxv[ZZ][XX];
881 tmp6[5] = state->boxv[ZZ][YY];
882 add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
883 }
884 if (md->bMu)
885 {
886 add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
887 }
888 if (ekind && ekind->cosacc.cos_accel != 0)
889 {
890 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
891 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
892 add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
893 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
894 tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
895 *dens*vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
896 add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
897 }
898 if (md->nE > 1)
899 {
900 n=0;
901 for(i=0; (i<md->nEg); i++)
902 {
903 for(j=i; (j<md->nEg); j++)
904 {
905 gid=GID(i,j,md->nEg);
906 for(k=kk=0; (k<egNR); k++)
907 {
908 if (md->bEInd[k])
909 {
910 eee[kk++] = enerd->grpp.ener[k][gid];
911 }
912 }
913 add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
914 n++;
915 }
916 }
917 }
918
919 if (ekind)
920 {
921 for(i=0; (i<md->nTC); i++)
922 {
923 md->tmp_r[i] = ekind->tcstat[i].T;
924 }
925 add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
926
927 if (md->etc == etcNOSEHOOVER)
928 {
929 /* whether to print Nose-Hoover chains: */
930 if (md->bPrintNHChains)
931 {
932 if (md->bNHC_trotter)
933 {
934 for(i=0; (i<md->nTC); i++)
935 {
936 for (j=0;j<md->nNHC;j++)
937 {
938 k = i*md->nNHC+j;
939 md->tmp_r[2*k] = state->nosehoover_xi[k];
940 md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
941 }
942 }
943 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
944
945 if (md->bMTTK) {
946 for(i=0; (i<md->nTCP); i++)
947 {
948 for (j=0;j<md->nNHC;j++)
949 {
950 k = i*md->nNHC+j;
951 md->tmp_r[2*k] = state->nhpres_xi[k];
952 md->tmp_r[2*k+1] = state->nhpres_vxi[k];
953 }
954 }
955 add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
956 }
957 }
958 else
959 {
960 for(i=0; (i<md->nTC); i++)
961 {
962 md->tmp_r[2*i] = state->nosehoover_xi[i];
963 md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
964 }
965 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
966 }
967 }
968 }
969 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
970 md->etc == etcVRESCALE)
971 {
972 for(i=0; (i<md->nTC); i++)
973 {
974 md->tmp_r[i] = ekind->tcstat[i].lambda;
975 }
976 add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
977 }
978 }
979
980 if (ekind && md->nU > 1)
981 {
982 for(i=0; (i<md->nU); i++)
983 {
984 copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
985 }
986 add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
987 }
988
989 ebin_increase_count(md->ebin,bSum);
990
991 /* BAR + thermodynamic integration values */
992 if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda > 0))
993 {
994 snew(dE,enerd->n_lambda-1);
995 for(i=0; i<enerd->n_lambda-1; i++) {
996 dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0]; /* zero for simulated tempering */
997 if (md->temperatures!=NULL)
998 {
999 /* MRS: is this right, given the way we have defined the exchange probabilities? */
1000 /* is this even useful to have at all? */
1001 dE[i] += (md->temperatures[i]/md->temperatures[state->fep_state]-1.0)*enerd->term[F_EKIN];
1002 }
1003 }
1004 }
1005
1006 if (md->fp_dhdl && bDoDHDL)
1007 {
1008 fprintf(md->fp_dhdl,"%.4f",time);
1009 /* the current free energy state */
1010
1011 /* print the current state if we are doing expanded ensemble */
1012 if (expand->elmcmove > elmcmoveNO) {
1013 fprintf(md->fp_dhdl," %4d",state->fep_state);
1014 }
1015 /* total energy (for if the temperature changes */
1016 if (fep->bPrintEnergy)
1017 {
1018 store_energy = enerd->term[F_ETOT];
1019 fprintf(md->fp_dhdl," %#.8g",store_energy);
1020 }
1021
1022 for (i=0;i<efptNR;i++)
1023 {
1024 if (fep->separate_dvdl[i])
1025 {
1026 fprintf(md->fp_dhdl," %#.8g",enerd->term[F_DVDL+i]); /* assumes F_DVDL is first */
1027 }
1028 }
1029 for(i=1; i<enerd->n_lambda; i++)
1030 {
1031 fprintf(md->fp_dhdl," %#.8g",dE[i-1]);
1032
1033 }
1034 if ((md->epc!=epcNO) && (enerd->n_lambda > 0))
1035 {
1036 fprintf(md->fp_dhdl," %#.8g",pv); /* PV term only needed when there are alternate state lambda */
1037 }
1038 fprintf(md->fp_dhdl,"\n");
1039 /* and the binary free energy output */
1040 }
1041 if (md->dhc && bDoDHDL)
1042 {
1043 int idhdl = 0;
1044 for (i=0;i<efptNR;i++)
1045 {
1046 if (fep->separate_dvdl[i])
1047 {
1048 store_dhdl[idhdl] = enerd->term[F_DVDL+i]; /* assumes F_DVDL is first */
1049 idhdl+=1;
1050 }
1051 }
1052 /* store_dh is dE */
1053 mde_delta_h_coll_add_dh(md->dhc,
1054 (double)state->fep_state,
1055 store_energy,
1056 pv,
1057 (expand->elamstats>elamstatsNO),
1058 (fep->bPrintEnergy),
1059 (md->epc!=epcNO),
1060 idhdl,
1061 fep->n_lambda,
1062 store_dhdl,
1063 dE,
1064 time);
1065 }
1066 if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda >0))
1067 {
1068 sfree(dE);
1069 }
1070 }
1071
1072
1073 void upd_mdebin_step(t_mdebin *md)
1074 {
1075 ebin_increase_count(md->ebin,FALSE);
1076 }
1077
1078 static void npr(FILE *log,int n,char c)
1079 {
1080 for(; (n>0); n--) fprintf(log,"%c",c);
1081 }
1082
1083 static void pprint(FILE *log,const char *s,t_mdebin *md)
1084 {
1085 char CHAR='#';
1086 int slen;
1087 char buf1[22],buf2[22];
1088
1089 slen = strlen(s);
1090 fprintf(log,"\t<====== ");
1091 npr(log,slen,CHAR);
1092 fprintf(log," ==>\n");
1093 fprintf(log,"\t<==== %s ====>\n",s);
1094 fprintf(log,"\t<== ");
1095 npr(log,slen,CHAR);
1096 fprintf(log," ======>\n\n");
1097
1098 fprintf(log,"\tStatistics over %s steps using %s frames\n",
1099 gmx_step_str(md->ebin->nsteps_sim,buf1),
1100 gmx_step_str(md->ebin->nsum_sim,buf2));
1101 fprintf(log,"\n");
1102 }
1103
1104 void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lambda)
1105 {
1106 char buf[22];
1107
1108 fprintf(log," %12s %12s %12s\n"
1109 " %12s %12.5f %12.5f\n\n",
1110 "Step","Time","Lambda",gmx_step_str(steps,buf),time,lambda);
1111 }
1112
1113 void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
1114 FILE *log,
1115 gmx_large_int_t step,double time,
1116 int mode,gmx_bool bCompact,
1117 t_mdebin *md,t_fcdata *fcd,
1118 gmx_groups_t *groups,t_grpopts *opts)
1119 {
1120 /*static char **grpnms=NULL;*/
1121 char buf[246];
1122 int i,j,n,ni,nj,ndr,nor,b;
1123 int ndisre=0;
1124 real *disre_rm3tav, *disre_rt;
1125
1126 /* these are for the old-style blocks (1 subblock, only reals), because
1127 there can be only one per ID for these */
1128 int nr[enxNR];
1129 int id[enxNR];
1130 real *block[enxNR];
1131
1132 /* temporary arrays for the lambda values to write out */
1133 double enxlambda_data[2];
1134
1135 t_enxframe fr;
1136
1137 switch (mode)
1138 {
1139 case eprNORMAL:
1140 init_enxframe(&fr);
1141 fr.t = time;
1142 fr.step = step;
1143 fr.nsteps = md->ebin->nsteps;
1144 fr.dt = md->delta_t;
1145 fr.nsum = md->ebin->nsum;
1146 fr.nre = (bEne) ? md->ebin->nener : 0;
1147 fr.ener = md->ebin->e;
1148 ndisre = bDR ? fcd->disres.npair : 0;
1149 disre_rm3tav = fcd->disres.rm3tav;
1150 disre_rt = fcd->disres.rt;
1151 /* Optional additional old-style (real-only) blocks. */
1152 for(i=0; i<enxNR; i++)
1153 {
1154 nr[i] = 0;
1155 }
1156 if (fcd->orires.nr > 0 && bOR)
1157 {
1158 diagonalize_orires_tensors(&(fcd->orires));
1159 nr[enxOR] = fcd->orires.nr;
1160 block[enxOR] = fcd->orires.otav;
1161 id[enxOR] = enxOR;
1162 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
1163 fcd->orires.nr : 0;
1164 block[enxORI] = fcd->orires.oinsl;
1165 id[enxORI] = enxORI;
1166 nr[enxORT] = fcd->orires.nex*12;
1167 block[enxORT] = fcd->orires.eig;
1168 id[enxORT] = enxORT;
1169 }
1170
1171 /* whether we are going to wrte anything out: */
1172 if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
1173 {
1174
1175 /* the old-style blocks go first */
1176 fr.nblock = 0;
1177 for(i=0; i<enxNR; i++)
1178 {
1179 if (nr[i] > 0)
1180 {
1181 fr.nblock = i + 1;
1182 }
1183 }
1184 add_blocks_enxframe(&fr, fr.nblock);
1185 for(b=0;b<fr.nblock;b++)
1186 {
1187 add_subblocks_enxblock(&(fr.block[b]), 1);
1188 fr.block[b].id=id[b];
1189 fr.block[b].sub[0].nr = nr[b];
1190 #ifndef GMX_DOUBLE
1191 fr.block[b].sub[0].type = xdr_datatype_float;
1192 fr.block[b].sub[0].fval = block[b];
1193 #else
1194 fr.block[b].sub[0].type = xdr_datatype_double;
1195 fr.block[b].sub[0].dval = block[b];
1196 #endif
1197 }
1198
1199 /* check for disre block & fill it. */
1200 if (ndisre>0)
1201 {
1202 int db = fr.nblock;
1203 fr.nblock+=1;
1204 add_blocks_enxframe(&fr, fr.nblock);
1205
1206 add_subblocks_enxblock(&(fr.block[db]), 2);
1207 fr.block[db].id=enxDISRE;
1208 fr.block[db].sub[0].nr=ndisre;
1209 fr.block[db].sub[1].nr=ndisre;
1210 #ifndef GMX_DOUBLE
1211 fr.block[db].sub[0].type=xdr_datatype_float;
1212 fr.block[db].sub[1].type=xdr_datatype_float;
1213 fr.block[db].sub[0].fval=disre_rt;
1214 fr.block[db].sub[1].fval=disre_rm3tav;
1215 #else
1216 fr.block[db].sub[0].type=xdr_datatype_double;
1217 fr.block[db].sub[1].type=xdr_datatype_double;
1218 fr.block[db].sub[0].dval=disre_rt;
1219 fr.block[db].sub[1].dval=disre_rm3tav;
1220 #endif
1221 }
1222 /* here we can put new-style blocks */
1223
1224 /* Free energy perturbation blocks */
1225 if (md->dhc)
1226 {
1227 mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
1228 }
1229
1230 /* we can now free & reset the data in the blocks */
1231 if (md->dhc)
1232 {
1233 mde_delta_h_coll_reset(md->dhc);
1234 }
1235
1236 /* do the actual I/O */
1237 do_enx(fp_ene,&fr);
1238 gmx_fio_check_file_position(enx_file_pointer(fp_ene));
1239 if (fr.nre)
1240 {
1241 /* We have stored the sums, so reset the sum history */
1242 reset_ebin_sums(md->ebin);
1243 }
1244 }
1245 free_enxframe(&fr);
1246 break;
1247 case eprAVER:
1248 if (log)
1249 {
1250 pprint(log,"A V E R A G E S",md);
1251 }
1252 break;
1253 case eprRMS:
1254 if (log)
1255 {
1256 pprint(log,"R M S - F L U C T U A T I O N S",md);
1257 }
1258 break;
1259 default:
1260 gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
1261 }
1262
1263 if (log)
1264 {
1265 for(i=0;i<opts->ngtc;i++)
1266 {
1267 if(opts->annealing[i]!=eannNO)
1268 {
1269 fprintf(log,"Current ref_t for group %s: %8.1f\n",
1270 *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
1271 opts->ref_t[i]);
1272 }
1273 }
1274 if (mode==eprNORMAL && fcd->orires.nr>0)
1275 {
1276 print_orires_log(log,&(fcd->orires));
1277 }
1278 fprintf(log," Energies (%s)\n",unit_energy);
1279 pr_ebin(log,md->ebin,md->ie,md->f_nre+md->nCrmsd,5,mode,TRUE);
1280 fprintf(log,"\n");
1281
1282 if (!bCompact)
1283 {
1284 if (md->bDynBox)
1285 {
1286 pr_ebin(log,md->ebin,md->ib, md->bTricl ? NTRICLBOXS : NBOXS,5,
1287 mode,TRUE);
1288 fprintf(log,"\n");
1289 }
1290 if (md->bConstrVir)
1291 {
1292 fprintf(log," Constraint Virial (%s)\n",unit_energy);
1293 pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
1294 fprintf(log,"\n");
1295 fprintf(log," Force Virial (%s)\n",unit_energy);
1296 pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
1297 fprintf(log,"\n");
1298 }
1299 if (md->bVir)
1300 {
1301 fprintf(log," Total Virial (%s)\n",unit_energy);
1302 pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
1303 fprintf(log,"\n");
1304 }
1305 if (md->bPress)
1306 {
1307 fprintf(log," Pressure (%s)\n",unit_pres_bar);
1308 pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
1309 fprintf(log,"\n");
1310 }
1311 if (md->bMu)
1312 {
1313 fprintf(log," Total Dipole (%s)\n",unit_dipole_D);
1314 pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
1315 fprintf(log,"\n");
1316 }
1317
1318 if (md->nE > 1)
1319 {
1320 if (md->print_grpnms==NULL)
1321 {
1322 snew(md->print_grpnms,md->nE);
1323 n=0;
1324 for(i=0; (i<md->nEg); i++)
1325 {
1326 ni=groups->grps[egcENER].nm_ind[i];
1327 for(j=i; (j<md->nEg); j++)
1328 {
1329 nj=groups->grps[egcENER].nm_ind[j];
1330 sprintf(buf,"%s-%s",*(groups->grpname[ni]),
1331 *(groups->grpname[nj]));
1332 md->print_grpnms[n++]=strdup(buf);
1333 }
1334 }
1335 }
1336 sprintf(buf,"Epot (%s)",unit_energy);
1337 fprintf(log,"%15s ",buf);
1338 for(i=0; (i<egNR); i++)
1339 {
1340 if (md->bEInd[i])
1341 {
1342 fprintf(log,"%12s ",egrp_nm[i]);
1343 }
1344 }
1345 fprintf(log,"\n");
1346 for(i=0; (i<md->nE); i++)
1347 {
1348 fprintf(log,"%15s",md->print_grpnms[i]);
1349 pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,
1350 FALSE);
1351 }
1352 fprintf(log,"\n");
1353 }
1354 if (md->nTC > 1)
1355 {
1356 pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
1357 fprintf(log,"\n");
1358 }
1359 if (md->nU > 1)
1360 {
1361 fprintf(log,"%15s %12s %12s %12s\n",
1362 "Group","Ux","Uy","Uz");
1363 for(i=0; (i<md->nU); i++)
1364 {
1365 ni=groups->grps[egcACC].nm_ind[i];
1366 fprintf(log,"%15s",*groups->grpname[ni]);
1367 pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
1368 }
1369 fprintf(log,"\n");
1370 }
1371 }
1372 }
1373
1374 }
1375
1376 void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
1377 {
1378 int i;
1379
1380 enerhist->nsteps = mdebin->ebin->nsteps;
1381 enerhist->nsum = mdebin->ebin->nsum;
1382 enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
1383 enerhist->nsum_sim = mdebin->ebin->nsum_sim;
1384 enerhist->nener = mdebin->ebin->nener;
1385
1386 if (mdebin->ebin->nsum > 0)
1387 {
1388 /* Check if we need to allocate first */
1389 if(enerhist->ener_ave == NULL)
1390 {
1391 snew(enerhist->ener_ave,enerhist->nener);
1392 snew(enerhist->ener_sum,enerhist->nener);
1393 }
1394
1395 for(i=0;i<enerhist->nener;i++)
1396 {
1397 enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
1398 enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
1399 }
1400 }
1401
1402 if (mdebin->ebin->nsum_sim > 0)
1403 {
1404 /* Check if we need to allocate first */
1405 if(enerhist->ener_sum_sim == NULL)
1406 {
1407 snew(enerhist->ener_sum_sim,enerhist->nener);
1408 }
1409
1410 for(i=0;i<enerhist->nener;i++)
1411 {
1412 enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
1413 }
1414 }
1415 if (mdebin->dhc)
1416 {
1417 mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
1418 }
1419 }
1420
1421 void restore_energyhistory_from_state(t_mdebin * mdebin,
1422 energyhistory_t * enerhist)
1423 {
1424 int i;
1425
1426 if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
1427 mdebin->ebin->nener != enerhist->nener)
1428 {
1429 gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
1430 mdebin->ebin->nener,enerhist->nener);
1431 }
1432
1433 mdebin->ebin->nsteps = enerhist->nsteps;
1434 mdebin->ebin->nsum = enerhist->nsum;
1435 mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
1436 mdebin->ebin->nsum_sim = enerhist->nsum_sim;
1437
1438 for(i=0; i<mdebin->ebin->nener; i++)
1439 {
1440 mdebin->ebin->e[i].eav =
1441 (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
1442 mdebin->ebin->e[i].esum =
1443 (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
1444 mdebin->ebin->e_sim[i].esum =
1445 (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
1446 }
1447 if (mdebin->dhc)
1448 {
1449 mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);
1450 }
1451 }
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