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Initial commit of enforced rotation add-on
[gromacs/adressmacs.git] / src / mdlib / mdebin.c
blob67aa2457826ec5d2e0fe02cbc72b5660ec44e63c
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 "typedefs.h"
42 #include "string2.h"
43 #include "mdebin.h"
44 #include "smalloc.h"
45 #include "physics.h"
46 #include "enxio.h"
47 #include "vec.h"
48 #include "disre.h"
49 #include "main.h"
50 #include "network.h"
51 #include "names.h"
52 #include "orires.h"
53 #include "constr.h"
54 #include "mtop_util.h"
55 #include "xvgr.h"
56
57 static bool bEInd[egNR] = { TRUE, TRUE, FALSE, FALSE, FALSE, FALSE, FALSE };
58
59 static bool bEner[F_NRE];
60
61 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
62
63 static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
64
65 static const char *tricl_boxs_nm[] = { "Box-XX", "Box-YX", "Box-YY",
66 "Box-ZX", "Box-ZY", "Box-ZZ" };
67
68 static const char *vol_nm[] = { "Volume" };
69
70 static const char *dens_nm[] = {"Density" };
71
72 static const char *pv_nm[] = {"pV" };
73
74 static const char *boxvel_nm[] = {
75 "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
76 "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
77 };
78
79 #define NBOXS asize(boxs_nm)
80 #define NTRICLBOXS asize(tricl_boxs_nm)
81
82 static bool bConstr,bConstrVir,bTricl,bDynBox;
83 static int f_nre=0,epc,etc,nCrmsd;
84
85 t_mdebin *init_mdebin(int fp_ene,
86 const gmx_mtop_t *mtop,
87 const t_inputrec *ir)
88 {
89 const char *ener_nm[F_NRE];
90 static const char *vir_nm[] = {
91 "Vir-XX", "Vir-XY", "Vir-XZ",
92 "Vir-YX", "Vir-YY", "Vir-YZ",
93 "Vir-ZX", "Vir-ZY", "Vir-ZZ"
94 };
95 static const char *sv_nm[] = {
96 "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
97 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
98 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
99 };
100 static const char *fv_nm[] = {
101 "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
102 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
103 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
104 };
105 static const char *pres_nm[] = {
106 "Pres-XX","Pres-XY","Pres-XZ",
107 "Pres-YX","Pres-YY","Pres-YZ",
108 "Pres-ZX","Pres-ZY","Pres-ZZ"
109 };
110 static const char *surft_nm[] = {
111 "#Surf*SurfTen"
112 };
113 static const char *mu_nm[] = {
114 "Mu-X", "Mu-Y", "Mu-Z"
115 };
116 static const char *vcos_nm[] = {
117 "2CosZ*Vel-X"
118 };
119 static const char *visc_nm[] = {
120 "1/Viscosity"
121 };
122 char **grpnms;
123 const gmx_groups_t *groups;
124 char **gnm;
125 char buf[256];
126 t_mdebin *md;
127 int i,j,ni,nj,n,k,kk,ncon,nset;
128 bool bBHAM,b14;
129
130 groups = &mtop->groups;
131
132 bBHAM = (mtop->ffparams.functype[0] == F_BHAM);
133 b14 = (gmx_mtop_ftype_count(mtop,F_LJ14) > 0 ||
134 gmx_mtop_ftype_count(mtop,F_LJC14_Q) > 0);
135
136 ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
137 nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
138 bConstr = (ncon > 0 || nset > 0);
139 bConstrVir = FALSE;
140 if (bConstr) {
141 if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
142 if (ir->eI == eiSD2)
143 nCrmsd = 2;
144 else
145 nCrmsd = 1;
146 }
147 bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
148 } else {
149 nCrmsd = 0;
150 }
151
152 for(i=0; i<F_NRE; i++) {
153 bEner[i] = FALSE;
154 if (i == F_LJ)
155 bEner[i] = !bBHAM;
156 else if (i == F_BHAM)
157 bEner[i] = bBHAM;
158 else if (i == F_EQM)
159 bEner[i] = ir->bQMMM;
160 else if (i == F_COUL_LR)
161 bEner[i] = (ir->rcoulomb > ir->rlist);
162 else if (i == F_LJ_LR)
163 bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
164 else if (i == F_BHAM_LR)
165 bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
166 else if (i == F_RF_EXCL)
167 bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
168 else if (i == F_COUL_RECIP)
169 bEner[i] = EEL_FULL(ir->coulombtype);
170 else if (i == F_LJ14)
171 bEner[i] = b14;
172 else if (i == F_COUL14)
173 bEner[i] = b14;
174 else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
175 bEner[i] = FALSE;
176 else if ((i == F_DVDL) || (i == F_DKDL))
177 bEner[i] = (ir->efep != efepNO);
178 else if (i == F_DHDL_CON)
179 bEner[i] = (ir->efep != efepNO && bConstr);
180 else if ((interaction_function[i].flags & IF_VSITE) ||
181 (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
182 bEner[i] = FALSE;
183 else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
184 bEner[i] = TRUE;
185 else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
186 bEner[i] = EI_DYNAMICS(ir->eI);
187 else if (i == F_DISPCORR || i == F_PDISPCORR)
188 bEner[i] = (ir->eDispCorr != edispcNO);
189 else if (i == F_DISRESVIOL)
190 bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
191 else if (i == F_ORIRESDEV)
192 bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
193 else if (i == F_CONNBONDS)
194 bEner[i] = FALSE;
195 else if (i == F_COM_PULL)
196 bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
197 else if (i == F_ECONSERVED)
198 bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
199 ir->epc == epcNO);
200 else
201 bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
202 }
203
204 for(i=0; i<F_NRE; i++)
205 {
206 if (bEner[i])
207 {
208 /* FIXME: The constness should not be cast away */
209 ener_nm[f_nre]=(char *)interaction_function[i].longname;
210 f_nre++;
211 }
212 }
213
214 epc = ir->epc;
215 bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
216 bDynBox = DYNAMIC_BOX(*ir);
217 etc = ir->etc;
218
219 /* Energy monitoring */
220 snew(md,1);
221 md->ebin = mk_ebin();
222 /* Pass NULL for unit to let get_ebin_space determine the units
223 * for interaction_function[i].longname
224 */
225 md->ie = get_ebin_space(md->ebin,f_nre,ener_nm,NULL);
226 if (nCrmsd)
227 {
228 /* This should be called directly after the call for md->ie,
229 * such that md->iconrmsd follows directly in the list.
230 */
231 md->iconrmsd = get_ebin_space(md->ebin,nCrmsd,conrmsd_nm,"");
232 }
233 if (bDynBox)
234 {
235 md->ib = get_ebin_space(md->ebin, bTricl ? NTRICLBOXS :
236 NBOXS, bTricl ? tricl_boxs_nm : boxs_nm,
237 unit_length);
238 md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
239 md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
240 md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
241 }
242 if (bConstrVir)
243 {
244 md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
245 md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
246 }
247 md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
248 md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
249 md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
250 unit_surft_bar);
251 if (epc == epcPARRINELLORAHMAN)
252 {
253 md->ipc = get_ebin_space(md->ebin,bTricl ? 6 : 3,boxvel_nm,unit_vel);
254 }
255 md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
256 if (ir->cos_accel != 0)
257 {
258 md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
259 md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
260 unit_invvisc_SI);
261 }
262 if (ir->rcoulomb > ir->rlist)
263 {
264 bEInd[egCOULLR] = TRUE;
265 }
266 if (!bBHAM)
267 {
268 if (ir->rvdw > ir->rlist)
269 {
270 bEInd[egLJLR] = TRUE;
271 }
272 }
273 else
274 {
275 bEInd[egLJSR] = FALSE;
276 bEInd[egBHAMSR] = TRUE;
277 if (ir->rvdw > ir->rlist)
278 {
279 bEInd[egBHAMLR] = TRUE;
280 }
281 }
282 if (b14)
283 {
284 bEInd[egLJ14] = TRUE;
285 bEInd[egCOUL14] = TRUE;
286 }
287 md->nEc=0;
288 for(i=0; (i<egNR); i++)
289 {
290 if (bEInd[i])
291 {
292 md->nEc++;
293 }
294 }
295
296 n=groups->grps[egcENER].nr;
297 md->nEg=n;
298 md->nE=(n*(n+1))/2;
299 snew(md->igrp,md->nE);
300 if (md->nE > 1)
301 {
302 n=0;
303 snew(gnm,md->nEc);
304 for(k=0; (k<md->nEc); k++)
305 {
306 snew(gnm[k],STRLEN);
307 }
308 for(i=0; (i<groups->grps[egcENER].nr); i++)
309 {
310 ni=groups->grps[egcENER].nm_ind[i];
311 for(j=i; (j<groups->grps[egcENER].nr); j++)
312 {
313 nj=groups->grps[egcENER].nm_ind[j];
314 for(k=kk=0; (k<egNR); k++)
315 {
316 if (bEInd[k])
317 {
318 sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
319 *(groups->grpname[ni]),*(groups->grpname[nj]));
320 kk++;
321 }
322 }
323 md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
324 (const char **)gnm,unit_energy);
325 n++;
326 }
327 }
328 for(k=0; (k<md->nEc); k++)
329 {
330 sfree(gnm[k]);
331 }
332 sfree(gnm);
333
334 if (n != md->nE)
335 {
336 gmx_incons("Number of energy terms wrong");
337 }
338 }
339
340 md->nTC=groups->grps[egcTC].nr;
341 snew(md->grpnms,md->nTC);
342 snew(md->tmp_r,md->nTC);
343 snew(md->tmp_v,md->nTC);
344 grpnms = md->grpnms;
345 for(i=0; (i<md->nTC); i++)
346 {
347 ni=groups->grps[egcTC].nm_ind[i];
348 sprintf(buf,"T-%s",*(groups->grpname[ni]));
349 grpnms[i]=strdup(buf);
350 }
351 md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
352 unit_temp_K);
353 if (etc == etcNOSEHOOVER)
354 {
355 for(i=0; (i<md->nTC); i++)
356 {
357 ni=groups->grps[egcTC].nm_ind[i];
358 sprintf(buf,"Xi-%s",*(groups->grpname[ni]));
359 grpnms[i]=strdup(buf);
360 }
361 md->itc=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
362 unit_invtime);
363 }
364 else if (etc == etcBERENDSEN || etc == etcYES || etc == etcVRESCALE)
365 {
366 for(i=0; (i<md->nTC); i++)
367 {
368 ni=groups->grps[egcTC].nm_ind[i];
369 sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
370 grpnms[i]=strdup(buf);
371 }
372 md->itc=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,"");
373 }
374 sfree(grpnms);
375
376 md->nU=groups->grps[egcACC].nr;
377 if (md->nU > 1)
378 {
379 snew(grpnms,3*md->nU);
380 for(i=0; (i<md->nU); i++)
381 {
382 ni=groups->grps[egcACC].nm_ind[i];
383 sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
384 grpnms[3*i+XX]=strdup(buf);
385 sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
386 grpnms[3*i+YY]=strdup(buf);
387 sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
388 grpnms[3*i+ZZ]=strdup(buf);
389 }
390 md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
391 sfree(grpnms);
392 }
393
394 if (fp_ene != -1)
395 {
396 do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
397 }
398
399 return md;
400 }
401
402 FILE *open_dhdl(const char *filename,t_inputrec *ir)
403 {
404 FILE *fp;
405 const char *dhdl="dH/d\\8l\\4",*deltag="\\8D\\4H",*lambda="\\8l\\4";
406 char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
407 int nsets,s;
408 char **setname,buf[STRLEN];
409
410 sprintf(label_x,"%s (%s)","Time",unit_time);
411 if (ir->n_flambda == 0)
412 {
413 sprintf(title,"%s",dhdl);
414 sprintf(label_y,"%s (%s %s)",
415 dhdl,unit_energy,"[\\8l\\4]\\S-1\\N");
416 }
417 else
418 {
419 sprintf(title,"%s, %s",dhdl,deltag);
420 sprintf(label_y,"(%s)",unit_energy);
421 }
422 fp = xvgropen(filename,title,label_x,label_y);
423
424 if (ir->n_flambda > 0)
425 {
426 /* g_bar has to determine the lambda values used in this simulation
427 * from this xvg legend.
428 */
429 nsets = 1 + ir->n_flambda;
430 snew(setname,nsets);
431 sprintf(buf,"%s %s %g",dhdl,lambda,ir->init_lambda);
432 setname[0] = strdup(buf);
433 for(s=1; s<nsets; s++)
434 {
435 sprintf(buf,"%s %s %g",deltag,lambda,ir->flambda[s-1]);
436 setname[s] = strdup(buf);
437 }
438 xvgr_legend(fp,nsets,setname);
439
440 for(s=0; s<nsets; s++)
441 {
442 sfree(setname[s]);
443 }
444 sfree(setname);
445 }
446
447 return fp;
448 }
449
450 static void copy_energy(real e[],real ecpy[])
451 {
452 int i,j;
453
454 for(i=j=0; (i<F_NRE); i++)
455 if (bEner[i])
456 ecpy[j++] = e[i];
457 if (j != f_nre)
458 gmx_incons("Number of energy terms wrong");
459 }
460
461 void upd_mdebin(t_mdebin *md,FILE *fp_dhdl,
462 bool bSum,
463 double time,
464 real tmass,
465 gmx_enerdata_t *enerd,
466 t_state *state,
467 matrix box,
468 tensor svir,
469 tensor fvir,
470 tensor vir,
471 tensor pres,
472 gmx_ekindata_t *ekind,
473 rvec mu_tot,
474 gmx_constr_t constr)
475 {
476 int i,j,k,kk,m,n,gid;
477 real crmsd[2],tmp6[6];
478 real bs[NTRICLBOXS],vol,dens,pv;
479 real eee[egNR];
480 real ecopy[F_NRE];
481 real tmp;
482
483 /* Do NOT use the box in the state variable, but the separate box provided
484 * as an argument. This is because we sometimes need to write the box from
485 * the last timestep to match the trajectory frames.
486 */
487 copy_energy(enerd->term,ecopy);
488 add_ebin(md->ebin,md->ie,f_nre,ecopy,bSum);
489 if (nCrmsd)
490 {
491 crmsd[0] = constr_rmsd(constr,FALSE);
492 if (nCrmsd > 1)
493 {
494 crmsd[1] = constr_rmsd(constr,TRUE);
495 }
496 add_ebin(md->ebin,md->iconrmsd,nCrmsd,crmsd,FALSE);
497 }
498 if (bDynBox)
499 {
500 if(bTricl)
501 {
502 bs[0] = box[XX][XX];
503 bs[1] = box[YY][XX];
504 bs[2] = box[YY][YY];
505 bs[3] = box[ZZ][XX];
506 bs[4] = box[ZZ][YY];
507 bs[5] = box[ZZ][ZZ];
508 }
509 else
510 {
511 bs[0] = box[XX][XX];
512 bs[1] = box[YY][YY];
513 bs[2] = box[ZZ][ZZ];
514 }
515 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
516 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
517
518 /* This is pV (in kJ/mol) */
519 pv = vol*enerd->term[F_PRES]/PRESFAC;
520
521 add_ebin(md->ebin,md->ib ,NBOXS,bs ,bSum);
522 add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
523 add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
524 add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
525 }
526 if (bConstrVir)
527 {
528 add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
529 add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
530 }
531 add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
532 add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
533 tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
534 add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
535 if (epc == epcPARRINELLORAHMAN)
536 {
537 tmp6[0] = state->boxv[XX][XX];
538 tmp6[1] = state->boxv[YY][YY];
539 tmp6[2] = state->boxv[ZZ][ZZ];
540 tmp6[3] = state->boxv[YY][XX];
541 tmp6[4] = state->boxv[ZZ][XX];
542 tmp6[5] = state->boxv[ZZ][YY];
543 add_ebin(md->ebin,md->ipc,bTricl ? 6 : 3,tmp6,bSum);
544 }
545 add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
546 if (ekind && ekind->cosacc.cos_accel != 0)
547 {
548 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
549 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
550 add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
551 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
552 tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
553 *vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
554 add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
555 }
556 if (md->nE > 1)
557 {
558 n=0;
559 for(i=0; (i<md->nEg); i++)
560 {
561 for(j=i; (j<md->nEg); j++)
562 {
563 gid=GID(i,j,md->nEg);
564 for(k=kk=0; (k<egNR); k++)
565 {
566 if (bEInd[k])
567 {
568 eee[kk++] = enerd->grpp.ener[k][gid];
569 }
570 }
571 add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
572 n++;
573 }
574 }
575 }
576
577 if (ekind)
578 {
579 for(i=0; (i<md->nTC); i++)
580 {
581 md->tmp_r[i] = ekind->tcstat[i].T;
582 }
583 add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
584 if (etc == etcNOSEHOOVER)
585 {
586 for(i=0; (i<md->nTC); i++)
587 {
588 md->tmp_r[i] = state->nosehoover_xi[i];
589 }
590 add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
591 }
592 else if (etc == etcBERENDSEN || etc == etcYES || etc == etcVRESCALE)
593 {
594 for(i=0; (i<md->nTC); i++)
595 {
596 md->tmp_r[i] = ekind->tcstat[i].lambda;
597 }
598 add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
599 }
600 }
601
602 if (ekind && md->nU > 1)
603 {
604 for(i=0; (i<md->nU); i++)
605 {
606 copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
607 }
608 add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
609 }
610
611 ebin_increase_count(md->ebin,bSum);
612
613 if (fp_dhdl)
614 {
615 fprintf(fp_dhdl,"%.4f %g",
616 time,
617 enerd->term[F_DVDL]+enerd->term[F_DKDL]+enerd->term[F_DHDL_CON]);
618 for(i=1; i<enerd->n_lambda; i++)
619 {
620 fprintf(fp_dhdl," %g",
621 enerd->enerpart_lambda[i]-enerd->enerpart_lambda[0]);
622 }
623 fprintf(fp_dhdl,"\n");
624 }
625 }
626
627 void upd_mdebin_step(t_mdebin *md)
628 {
629 ebin_increase_count(md->ebin,FALSE);
630 }
631
632 static void npr(FILE *log,int n,char c)
633 {
634 for(; (n>0); n--) fprintf(log,"%c",c);
635 }
636
637 static void pprint(FILE *log,const char *s,t_mdebin *md)
638 {
639 char CHAR='#';
640 int slen;
641 char buf1[22],buf2[22];
642
643 slen = strlen(s);
644 fprintf(log,"\t<====== ");
645 npr(log,slen,CHAR);
646 fprintf(log," ==>\n");
647 fprintf(log,"\t<==== %s ====>\n",s);
648 fprintf(log,"\t<== ");
649 npr(log,slen,CHAR);
650 fprintf(log," ======>\n\n");
651
652 fprintf(log,"\tStatistics over %s steps using %s frames\n",
653 gmx_step_str(md->ebin->nsteps_sim,buf1),
654 gmx_step_str(md->ebin->nsum_sim,buf2));
655 fprintf(log,"\n");
656 }
657
658 void print_ebin_header(FILE *log,gmx_step_t steps,double time,real lamb)
659 {
660 char buf[22];
661
662 fprintf(log," %12s %12s %12s\n"
663 " %12s %12.5f %12.5f\n\n",
664 "Step","Time","Lambda",gmx_step_str(steps,buf),time,lamb);
665 }
666
667 void print_ebin(int fp_ene,bool bEne,bool bDR,bool bOR,
668 FILE *log,
669 gmx_step_t step,double time,
670 int mode,bool bCompact,
671 t_mdebin *md,t_fcdata *fcd,
672 gmx_groups_t *groups,t_grpopts *opts)
673 {
674 static char **grpnms=NULL;
675 char buf[246];
676 int i,j,n,ni,nj,ndr,nor;
677 int nr[enxNR];
678 real *block[enxNR];
679 t_enxframe fr;
680
681 switch (mode)
682 {
683 case eprNORMAL:
684 fr.t = time;
685 fr.step = step;
686 fr.nsteps = md->ebin->nsteps;
687 fr.nsum = md->ebin->nsum;
688 fr.nre = (bEne) ? md->ebin->nener : 0;
689 fr.ener = md->ebin->e;
690 fr.ndisre = bDR ? fcd->disres.npair : 0;
691 fr.disre_rm3tav = fcd->disres.rm3tav;
692 fr.disre_rt = fcd->disres.rt;
693 /* Optional additional blocks */
694 for(i=0; i<enxNR; i++)
695 {
696 nr[i] = 0;
697 }
698 if (fcd->orires.nr > 0 && bOR)
699 {
700 diagonalize_orires_tensors(&(fcd->orires));
701 nr[enxOR] = fcd->orires.nr;
702 block[enxOR] = fcd->orires.otav;
703 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
704 fcd->orires.nr : 0;
705 block[enxORI] = fcd->orires.oinsl;
706 nr[enxORT] = fcd->orires.nex*12;
707 block[enxORT] = fcd->orires.eig;
708 }
709 fr.nblock = 0;
710 for(i=0; i<enxNR; i++)
711 {
712 if (nr[i] > 0)
713 {
714 fr.nblock = i + 1;
715 }
716 }
717 fr.nr = nr;
718 fr.block = block;
719 if (fr.nre || fr.ndisre || fr.nr[enxOR] || fr.nr[enxORI])
720 {
721 do_enx(fp_ene,&fr);
722 if (fr.nre)
723 {
724 /* We have stored the sums, so reset the sum history */
725 reset_ebin_sums(md->ebin);
726 }
727 }
728 break;
729 case eprAVER:
730 if (log)
731 {
732 pprint(log,"A V E R A G E S",md);
733 }
734 break;
735 case eprRMS:
736 if (log)
737 {
738 pprint(log,"R M S - F L U C T U A T I O N S",md);
739 }
740 break;
741 default:
742 gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
743 }
744
745 if (log)
746 {
747 for(i=0;i<opts->ngtc;i++)
748 {
749 if(opts->annealing[i]!=eannNO)
750 {
751 fprintf(log,"Current ref_t for group %s: %8.1f\n",
752 *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),opts->ref_t[i]);
753 }
754 }
755 if (mode==eprNORMAL && fcd->orires.nr>0)
756 {
757 print_orires_log(log,&(fcd->orires));
758 }
759 fprintf(log," Energies (%s)\n",unit_energy);
760 pr_ebin(log,md->ebin,md->ie,f_nre+nCrmsd,5,mode,TRUE);
761 fprintf(log,"\n");
762
763 if (!bCompact)
764 {
765 if (bDynBox)
766 {
767 pr_ebin(log,md->ebin,md->ib, bTricl ? NTRICLBOXS : NBOXS,5,mode,TRUE);
768 fprintf(log,"\n");
769 }
770 if (bConstrVir)
771 {
772 fprintf(log," Constraint Virial (%s)\n",unit_energy);
773 pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
774 fprintf(log,"\n");
775 fprintf(log," Force Virial (%s)\n",unit_energy);
776 pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
777 fprintf(log,"\n");
778 }
779 fprintf(log," Total Virial (%s)\n",unit_energy);
780 pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
781 fprintf(log,"\n");
782 fprintf(log," Pressure (%s)\n",unit_pres_bar);
783 pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
784 fprintf(log,"\n");
785 fprintf(log," Total Dipole (%s)\n",unit_dipole_D);
786 pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
787 fprintf(log,"\n");
788
789 if (md->nE > 1)
790 {
791 if (grpnms==NULL)
792 {
793 snew(grpnms,md->nE);
794 n=0;
795 for(i=0; (i<md->nEg); i++)
796 {
797 ni=groups->grps[egcENER].nm_ind[i];
798 for(j=i; (j<md->nEg); j++)
799 {
800 nj=groups->grps[egcENER].nm_ind[j];
801 sprintf(buf,"%s-%s",*(groups->grpname[ni]),*(groups->grpname[nj]));
802 grpnms[n++]=strdup(buf);
803 }
804 }
805 }
806 sprintf(buf,"Epot (%s)",unit_energy);
807 fprintf(log,"%15s ",buf);
808 for(i=0; (i<egNR); i++)
809 {
810 if (bEInd[i])
811 {
812 fprintf(log,"%12s ",egrp_nm[i]);
813 }
814 }
815 fprintf(log,"\n");
816 for(i=0; (i<md->nE); i++)
817 {
818 fprintf(log,"%15s",grpnms[i]);
819 pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,FALSE);
820 }
821 fprintf(log,"\n");
822 }
823 if (md->nTC > 1)
824 {
825 pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
826 fprintf(log,"\n");
827 }
828 if (md->nU > 1)
829 {
830 fprintf(log,"%15s %12s %12s %12s\n",
831 "Group","Ux","Uy","Uz");
832 for(i=0; (i<md->nU); i++)
833 {
834 ni=groups->grps[egcACC].nm_ind[i];
835 fprintf(log,"%15s",*groups->grpname[ni]);
836 pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
837 }
838 fprintf(log,"\n");
839 }
840 }
841 }
842 }
843
844 void
845 init_energyhistory(energyhistory_t * enerhist)
846 {
847 enerhist->nener = 0;
848
849 enerhist->ener_ave = NULL;
850 enerhist->ener_sum = NULL;
851 enerhist->ener_sum_sim = NULL;
852
853 enerhist->nsteps = 0;
854 enerhist->nsum = 0;
855 enerhist->nsteps_sim = 0;
856 enerhist->nsum_sim = 0;
857 }
858
859 void
860 update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
861 {
862 int i;
863
864 enerhist->nsteps = mdebin->ebin->nsteps;
865 enerhist->nsum = mdebin->ebin->nsum;
866 enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
867 enerhist->nsum_sim = mdebin->ebin->nsum_sim;
868 enerhist->nener = mdebin->ebin->nener;
869
870 if (mdebin->ebin->nsum > 0)
871 {
872 /* Check if we need to allocate first */
873 if(enerhist->ener_ave == NULL)
874 {
875 snew(enerhist->ener_ave,enerhist->nener);
876 snew(enerhist->ener_sum,enerhist->nener);
877 }
878
879 for(i=0;i<enerhist->nener;i++)
880 {
881 enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
882 enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
883 }
884 }
885
886 if (mdebin->ebin->nsum_sim > 0)
887 {
888 /* Check if we need to allocate first */
889 if(enerhist->ener_sum_sim == NULL)
890 {
891 snew(enerhist->ener_sum_sim,enerhist->nener);
892 }
893
894 for(i=0;i<enerhist->nener;i++)
895 {
896 enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
897 }
898 }
899 }
900
901 void
902 restore_energyhistory_from_state(t_mdebin * mdebin,energyhistory_t * enerhist)
903 {
904 int i;
905
906 if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
907 mdebin->ebin->nener != enerhist->nener)
908 {
909 gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
910 mdebin->ebin->nener,enerhist->nener);
911 }
912
913 mdebin->ebin->nsteps = enerhist->nsteps;
914 mdebin->ebin->nsum = enerhist->nsum;
915 mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
916 mdebin->ebin->nsum_sim = enerhist->nsum_sim;
917
918 for(i=0; i<mdebin->ebin->nener; i++)
919 {
920 mdebin->ebin->e[i].eav =
921 (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
922 mdebin->ebin->e[i].esum =
923 (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
924 mdebin->ebin->e_sim[i].esum =
925 (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
926 }
927 }
got merge a long time ago