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Merge branch 'master' of git://git.gromacs.org/gromacs
[gromacs/adressmacs.git] / src / mdlib / mdebin.c
blob394ca899232c84da7056ea7b194111faabeed95c
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
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20 *
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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.
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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
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 static gmx_bool bTricl,bDynBox;
88 static int f_nre=0,epc,etc,nCrmsd;
89
90
91
92
93
94 t_mdebin *init_mdebin(ener_file_t fp_ene,
95 const gmx_mtop_t *mtop,
96 const t_inputrec *ir,
97 FILE *fp_dhdl)
98 {
99 const char *ener_nm[F_NRE];
100 static const char *vir_nm[] = {
101 "Vir-XX", "Vir-XY", "Vir-XZ",
102 "Vir-YX", "Vir-YY", "Vir-YZ",
103 "Vir-ZX", "Vir-ZY", "Vir-ZZ"
104 };
105 static const char *sv_nm[] = {
106 "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
107 "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
108 "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
109 };
110 static const char *fv_nm[] = {
111 "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
112 "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
113 "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
114 };
115 static const char *pres_nm[] = {
116 "Pres-XX","Pres-XY","Pres-XZ",
117 "Pres-YX","Pres-YY","Pres-YZ",
118 "Pres-ZX","Pres-ZY","Pres-ZZ"
119 };
120 static const char *surft_nm[] = {
121 "#Surf*SurfTen"
122 };
123 static const char *mu_nm[] = {
124 "Mu-X", "Mu-Y", "Mu-Z"
125 };
126 static const char *vcos_nm[] = {
127 "2CosZ*Vel-X"
128 };
129 static const char *visc_nm[] = {
130 "1/Viscosity"
131 };
132 static const char *baro_nm[] = {
133 "Barostat"
134 };
135
136 char **grpnms;
137 const gmx_groups_t *groups;
138 char **gnm;
139 char buf[256];
140 const char *bufi;
141 t_mdebin *md;
142 int i,j,ni,nj,n,nh,k,kk,ncon,nset;
143 gmx_bool bBHAM,bNoseHoover,b14;
144
145 snew(md,1);
146
147 if (EI_DYNAMICS(ir->eI))
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 = FALSE;
166 if (md->bConstr) {
167 if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
168 if (ir->eI == eiSD2)
169 md->nCrmsd = 2;
170 else
171 md->nCrmsd = 1;
172 }
173 md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
174 } else {
175 md->nCrmsd = 0;
176 }
177
178 /* Energy monitoring */
179 for(i=0;i<egNR;i++)
180 {
181 md->bEInd[i]=FALSE;
182 }
183
184 #ifndef GMX_OPENMM
185 for(i=0; i<F_NRE; i++)
186 {
187 md->bEner[i] = FALSE;
188 if (i == F_LJ)
189 md->bEner[i] = !bBHAM;
190 else if (i == F_BHAM)
191 md->bEner[i] = bBHAM;
192 else if (i == F_EQM)
193 md->bEner[i] = ir->bQMMM;
194 else if (i == F_COUL_LR)
195 md->bEner[i] = (ir->rcoulomb > ir->rlist);
196 else if (i == F_LJ_LR)
197 md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
198 else if (i == F_BHAM_LR)
199 md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
200 else if (i == F_RF_EXCL)
201 md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
202 else if (i == F_COUL_RECIP)
203 md->bEner[i] = EEL_FULL(ir->coulombtype);
204 else if (i == F_LJ14)
205 md->bEner[i] = b14;
206 else if (i == F_COUL14)
207 md->bEner[i] = b14;
208 else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
209 md->bEner[i] = FALSE;
210 else if ((i == F_DVDL) || (i == F_DKDL))
211 md->bEner[i] = (ir->efep != efepNO);
212 else if (i == F_DHDL_CON)
213 md->bEner[i] = (ir->efep != efepNO && md->bConstr);
214 else if ((interaction_function[i].flags & IF_VSITE) ||
215 (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
216 md->bEner[i] = FALSE;
217 else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES) || (i==F_EQM))
218 md->bEner[i] = TRUE;
219 else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
220 md->bEner[i] = TRUE;
221 else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
222 md->bEner[i] = TRUE;
223 else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
224 md->bEner[i] = FALSE;
225 else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
226 md->bEner[i] = EI_DYNAMICS(ir->eI);
227 else if (i==F_VTEMP)
228 md->bEner[i] = (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
229 else if (i == F_DISPCORR || i == F_PDISPCORR)
230 md->bEner[i] = (ir->eDispCorr != edispcNO);
231 else if (i == F_DISRESVIOL)
232 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
233 else if (i == F_ORIRESDEV)
234 md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
235 else if (i == F_CONNBONDS)
236 md->bEner[i] = FALSE;
237 else if (i == F_COM_PULL)
238 md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
239 else if (i == F_ECONSERVED)
240 md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
241 (ir->epc == epcNO || ir->epc==epcMTTK));
242 else
243 md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
244 }
245 #else
246 /* OpenMM always produces only the following 4 energy terms */
247 md->bEner[F_EPOT] = TRUE;
248 md->bEner[F_EKIN] = TRUE;
249 md->bEner[F_ETOT] = TRUE;
250 md->bEner[F_TEMP] = TRUE;
251 #endif
252
253 md->f_nre=0;
254 for(i=0; i<F_NRE; i++)
255 {
256 if (md->bEner[i])
257 {
258 /* FIXME: The constness should not be cast away */
259 /*ener_nm[f_nre]=(char *)interaction_function[i].longname;*/
260 ener_nm[md->f_nre]=interaction_function[i].longname;
261 md->f_nre++;
262 }
263 }
264
265 md->epc = ir->epc;
266 for (i=0;i<DIM;i++)
267 {
268 for (j=0;j<DIM;j++)
269 {
270 md->ref_p[i][j] = ir->ref_p[i][j];
271 }
272 }
273 md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
274 md->bDynBox = DYNAMIC_BOX(*ir);
275 md->etc = ir->etc;
276 md->bNHC_trotter = IR_NVT_TROTTER(ir);
277 md->bMTTK = IR_NPT_TROTTER(ir);
278
279 md->ebin = mk_ebin();
280 /* Pass NULL for unit to let get_ebin_space determine the units
281 * for interaction_function[i].longname
282 */
283 md->ie = get_ebin_space(md->ebin,md->f_nre,ener_nm,NULL);
284 if (md->nCrmsd)
285 {
286 /* This should be called directly after the call for md->ie,
287 * such that md->iconrmsd follows directly in the list.
288 */
289 md->iconrmsd = get_ebin_space(md->ebin,md->nCrmsd,conrmsd_nm,"");
290 }
291 if (md->bDynBox)
292 {
293 md->ib = get_ebin_space(md->ebin,
294 md->bTricl ? NTRICLBOXS : NBOXS,
295 md->bTricl ? tricl_boxs_nm : boxs_nm,
296 unit_length);
297 md->ivol = get_ebin_space(md->ebin, 1, vol_nm, unit_volume);
298 md->idens = get_ebin_space(md->ebin, 1, dens_nm, unit_density_SI);
299 md->ipv = get_ebin_space(md->ebin, 1, pv_nm, unit_energy);
300 md->ienthalpy = get_ebin_space(md->ebin, 1, enthalpy_nm, unit_energy);
301 }
302 if (md->bConstrVir)
303 {
304 md->isvir = get_ebin_space(md->ebin,asize(sv_nm),sv_nm,unit_energy);
305 md->ifvir = get_ebin_space(md->ebin,asize(fv_nm),fv_nm,unit_energy);
306 }
307 md->ivir = get_ebin_space(md->ebin,asize(vir_nm),vir_nm,unit_energy);
308 md->ipres = get_ebin_space(md->ebin,asize(pres_nm),pres_nm,unit_pres_bar);
309 md->isurft = get_ebin_space(md->ebin,asize(surft_nm),surft_nm,
310 unit_surft_bar);
311 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
312 {
313 md->ipc = get_ebin_space(md->ebin,md->bTricl ? 6 : 3,
314 boxvel_nm,unit_vel);
315 }
316 md->imu = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
317 if (ir->cos_accel != 0)
318 {
319 md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
320 md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
321 unit_invvisc_SI);
322 }
323
324 /* Energy monitoring */
325 for(i=0;i<egNR;i++)
326 {
327 md->bEInd[i] = FALSE;
328 }
329 md->bEInd[egCOULSR] = TRUE;
330 md->bEInd[egLJSR ] = TRUE;
331
332 if (ir->rcoulomb > ir->rlist)
333 {
334 md->bEInd[egCOULLR] = TRUE;
335 }
336 if (!bBHAM)
337 {
338 if (ir->rvdw > ir->rlist)
339 {
340 md->bEInd[egLJLR] = TRUE;
341 }
342 }
343 else
344 {
345 md->bEInd[egLJSR] = FALSE;
346 md->bEInd[egBHAMSR] = TRUE;
347 if (ir->rvdw > ir->rlist)
348 {
349 md->bEInd[egBHAMLR] = TRUE;
350 }
351 }
352 if (b14)
353 {
354 md->bEInd[egLJ14] = TRUE;
355 md->bEInd[egCOUL14] = TRUE;
356 }
357 md->nEc=0;
358 for(i=0; (i<egNR); i++)
359 {
360 if (md->bEInd[i])
361 {
362 md->nEc++;
363 }
364 }
365
366 n=groups->grps[egcENER].nr;
367 md->nEg=n;
368 md->nE=(n*(n+1))/2;
369 snew(md->igrp,md->nE);
370 if (md->nE > 1)
371 {
372 n=0;
373 snew(gnm,md->nEc);
374 for(k=0; (k<md->nEc); k++)
375 {
376 snew(gnm[k],STRLEN);
377 }
378 for(i=0; (i<groups->grps[egcENER].nr); i++)
379 {
380 ni=groups->grps[egcENER].nm_ind[i];
381 for(j=i; (j<groups->grps[egcENER].nr); j++)
382 {
383 nj=groups->grps[egcENER].nm_ind[j];
384 for(k=kk=0; (k<egNR); k++)
385 {
386 if (md->bEInd[k])
387 {
388 sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
389 *(groups->grpname[ni]),*(groups->grpname[nj]));
390 kk++;
391 }
392 }
393 md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
394 (const char **)gnm,unit_energy);
395 n++;
396 }
397 }
398 for(k=0; (k<md->nEc); k++)
399 {
400 sfree(gnm[k]);
401 }
402 sfree(gnm);
403
404 if (n != md->nE)
405 {
406 gmx_incons("Number of energy terms wrong");
407 }
408 }
409
410 md->nTC=groups->grps[egcTC].nr;
411 md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
412 if (md->bMTTK)
413 {
414 md->nTCP = 1; /* assume only one possible coupling system for barostat
415 for now */
416 }
417 else
418 {
419 md->nTCP = 0;
420 }
421
422 if (md->etc == etcNOSEHOOVER) {
423 if (md->bNHC_trotter) {
424 md->mde_n = 2*md->nNHC*md->nTC;
425 }
426 else
427 {
428 md->mde_n = 2*md->nTC;
429 }
430 if (md->epc == epcMTTK)
431 {
432 md->mdeb_n = 2*md->nNHC*md->nTCP;
433 }
434 } else {
435 md->mde_n = md->nTC;
436 md->mdeb_n = 0;
437 }
438
439 snew(md->tmp_r,md->mde_n);
440 snew(md->tmp_v,md->mde_n);
441 snew(md->grpnms,md->mde_n);
442 grpnms = md->grpnms;
443
444 for(i=0; (i<md->nTC); i++)
445 {
446 ni=groups->grps[egcTC].nm_ind[i];
447 sprintf(buf,"T-%s",*(groups->grpname[ni]));
448 grpnms[i]=strdup(buf);
449 }
450 md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
451 unit_temp_K);
452
453 bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL); /* whether to print Nose-Hoover chains */
454
455 if (md->etc == etcNOSEHOOVER)
456 {
457 if (bNoseHoover)
458 {
459 if (md->bNHC_trotter)
460 {
461 for(i=0; (i<md->nTC); i++)
462 {
463 ni=groups->grps[egcTC].nm_ind[i];
464 bufi = *(groups->grpname[ni]);
465 for(j=0; (j<md->nNHC); j++)
466 {
467 sprintf(buf,"Xi-%d-%s",j,bufi);
468 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
469 sprintf(buf,"vXi-%d-%s",j,bufi);
470 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
471 }
472 }
473 md->itc=get_ebin_space(md->ebin,md->mde_n,
474 (const char **)grpnms,unit_invtime);
475 if (md->bMTTK)
476 {
477 for(i=0; (i<md->nTCP); i++)
478 {
479 bufi = baro_nm[0]; /* All barostat DOF's together for now. */
480 for(j=0; (j<md->nNHC); j++)
481 {
482 sprintf(buf,"Xi-%d-%s",j,bufi);
483 grpnms[2*(i*md->nNHC+j)]=strdup(buf);
484 sprintf(buf,"vXi-%d-%s",j,bufi);
485 grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
486 }
487 }
488 md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
489 (const char **)grpnms,unit_invtime);
490 }
491 }
492 else
493 {
494 for(i=0; (i<md->nTC); i++)
495 {
496 ni=groups->grps[egcTC].nm_ind[i];
497 bufi = *(groups->grpname[ni]);
498 sprintf(buf,"Xi-%s",bufi);
499 grpnms[2*i]=strdup(buf);
500 sprintf(buf,"vXi-%s",bufi);
501 grpnms[2*i+1]=strdup(buf);
502 }
503 md->itc=get_ebin_space(md->ebin,md->mde_n,
504 (const char **)grpnms,unit_invtime);
505 }
506 }
507 }
508 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
509 md->etc == etcVRESCALE)
510 {
511 for(i=0; (i<md->nTC); i++)
512 {
513 ni=groups->grps[egcTC].nm_ind[i];
514 sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
515 grpnms[i]=strdup(buf);
516 }
517 md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
518 }
519
520 sfree(grpnms);
521
522
523 md->nU=groups->grps[egcACC].nr;
524 if (md->nU > 1)
525 {
526 snew(grpnms,3*md->nU);
527 for(i=0; (i<md->nU); i++)
528 {
529 ni=groups->grps[egcACC].nm_ind[i];
530 sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
531 grpnms[3*i+XX]=strdup(buf);
532 sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
533 grpnms[3*i+YY]=strdup(buf);
534 sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
535 grpnms[3*i+ZZ]=strdup(buf);
536 }
537 md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
538 sfree(grpnms);
539 }
540
541 if ( fp_ene )
542 {
543 do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
544 }
545
546 md->print_grpnms=NULL;
547
548 /* check whether we're going to write dh histograms */
549 md->dhc=NULL;
550 if (ir->separate_dhdl_file == sepdhdlfileNO )
551 {
552 int i;
553 snew(md->dhc, 1);
554
555 mde_delta_h_coll_init(md->dhc, ir);
556 md->fp_dhdl = NULL;
557 }
558 else
559 {
560 md->fp_dhdl = fp_dhdl;
561 }
562 md->dhdl_derivatives = (ir->dhdl_derivatives==dhdlderivativesYES);
563 return md;
564 }
565
566 FILE *open_dhdl(const char *filename,const t_inputrec *ir,
567 const output_env_t oenv)
568 {
569 FILE *fp;
570 const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda";
571 char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
572 char **setname;
573 char buf[STRLEN];
574
575 sprintf(label_x,"%s (%s)","Time",unit_time);
576 if (ir->n_flambda == 0)
577 {
578 sprintf(title,"%s",dhdl);
579 sprintf(label_y,"%s (%s %s)",
580 dhdl,unit_energy,"[\\lambda]\\S-1\\N");
581 }
582 else
583 {
584 sprintf(title,"%s, %s",dhdl,deltag);
585 sprintf(label_y,"(%s)",unit_energy);
586 }
587 fp = gmx_fio_fopen(filename,"w+");
588 xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
589
590 if (ir->delta_lambda == 0)
591 {
592 sprintf(buf,"T = %g (K), %s = %g",
593 ir->opts.ref_t[0],lambda,ir->init_lambda);
594 }
595 else
596 {
597 sprintf(buf,"T = %g (K)",
598 ir->opts.ref_t[0]);
599 }
600 xvgr_subtitle(fp,buf,oenv);
601
602 if (ir->n_flambda > 0)
603 {
604 int nsets,s,nsi=0;
605 /* g_bar has to determine the lambda values used in this simulation
606 * from this xvg legend. */
607 nsets = ( (ir->dhdl_derivatives==dhdlderivativesYES) ? 1 : 0) +
608 ir->n_flambda;
609 snew(setname,nsets);
610 if (ir->dhdl_derivatives == dhdlderivativesYES)
611 {
612 sprintf(buf,"%s %s %g",dhdl,lambda,ir->init_lambda);
613 setname[nsi++] = strdup(buf);
614 }
615 for(s=0; s<ir->n_flambda; s++)
616 {
617 sprintf(buf,"%s %s %g",deltag,lambda,ir->flambda[s]);
618 setname[nsi++] = strdup(buf);
619 }
620 xvgr_legend(fp,nsets,(const char**)setname,oenv);
621
622 for(s=0; s<nsets; s++)
623 {
624 sfree(setname[s]);
625 }
626 sfree(setname);
627 }
628
629 return fp;
630 }
631
632 static void copy_energy(t_mdebin *md, real e[],real ecpy[])
633 {
634 int i,j;
635
636 for(i=j=0; (i<F_NRE); i++)
637 if (md->bEner[i])
638 ecpy[j++] = e[i];
639 if (j != md->f_nre)
640 gmx_incons("Number of energy terms wrong");
641 }
642
643 void upd_mdebin(t_mdebin *md, gmx_bool write_dhdl,
644 gmx_bool bSum,
645 double time,
646 real tmass,
647 gmx_enerdata_t *enerd,
648 t_state *state,
649 matrix box,
650 tensor svir,
651 tensor fvir,
652 tensor vir,
653 tensor pres,
654 gmx_ekindata_t *ekind,
655 rvec mu_tot,
656 gmx_constr_t constr)
657 {
658 int i,j,k,kk,m,n,gid;
659 real crmsd[2],tmp6[6];
660 real bs[NTRICLBOXS],vol,dens,pv,enthalpy;
661 real eee[egNR];
662 real ecopy[F_NRE];
663 real tmp;
664 gmx_bool bNoseHoover;
665
666 /* Do NOT use the box in the state variable, but the separate box provided
667 * as an argument. This is because we sometimes need to write the box from
668 * the last timestep to match the trajectory frames.
669 */
670 copy_energy(md, enerd->term,ecopy);
671 add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
672 if (md->nCrmsd)
673 {
674 crmsd[0] = constr_rmsd(constr,FALSE);
675 if (md->nCrmsd > 1)
676 {
677 crmsd[1] = constr_rmsd(constr,TRUE);
678 }
679 add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
680 }
681 if (md->bDynBox)
682 {
683 int nboxs;
684 if(md->bTricl)
685 {
686 bs[0] = box[XX][XX];
687 bs[1] = box[YY][YY];
688 bs[2] = box[ZZ][ZZ];
689 bs[3] = box[YY][XX];
690 bs[4] = box[ZZ][XX];
691 bs[5] = box[ZZ][YY];
692 nboxs=NTRICLBOXS;
693 }
694 else
695 {
696 bs[0] = box[XX][XX];
697 bs[1] = box[YY][YY];
698 bs[2] = box[ZZ][ZZ];
699 nboxs=NBOXS;
700 }
701 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
702 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
703
704 /* This is pV (in kJ/mol). The pressure is the reference pressure,
705 not the instantaneous pressure */
706 pv = 0;
707 for (i=0;i<DIM;i++)
708 {
709 for (j=0;j<DIM;j++)
710 {
711 if (i>j)
712 {
713 pv += box[i][j]*md->ref_p[i][j]/PRESFAC;
714 }
715 else
716 {
717 pv += box[j][i]*md->ref_p[j][i]/PRESFAC;
718 }
719 }
720 }
721
722 add_ebin(md->ebin,md->ib ,nboxs,bs ,bSum);
723 add_ebin(md->ebin,md->ivol ,1 ,&vol ,bSum);
724 add_ebin(md->ebin,md->idens,1 ,&dens,bSum);
725 add_ebin(md->ebin,md->ipv ,1 ,&pv ,bSum);
726 enthalpy = pv + enerd->term[F_ETOT];
727 add_ebin(md->ebin,md->ienthalpy ,1 ,&enthalpy ,bSum);
728 }
729 if (md->bConstrVir)
730 {
731 add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
732 add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
733 }
734 add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
735 add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
736 tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
737 add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
738 if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
739 {
740 tmp6[0] = state->boxv[XX][XX];
741 tmp6[1] = state->boxv[YY][YY];
742 tmp6[2] = state->boxv[ZZ][ZZ];
743 tmp6[3] = state->boxv[YY][XX];
744 tmp6[4] = state->boxv[ZZ][XX];
745 tmp6[5] = state->boxv[ZZ][YY];
746 add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
747 }
748 add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
749 if (ekind && ekind->cosacc.cos_accel != 0)
750 {
751 vol = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
752 dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
753 add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
754 /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
755 tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
756 *vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
757 add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
758 }
759 if (md->nE > 1)
760 {
761 n=0;
762 for(i=0; (i<md->nEg); i++)
763 {
764 for(j=i; (j<md->nEg); j++)
765 {
766 gid=GID(i,j,md->nEg);
767 for(k=kk=0; (k<egNR); k++)
768 {
769 if (md->bEInd[k])
770 {
771 eee[kk++] = enerd->grpp.ener[k][gid];
772 }
773 }
774 add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
775 n++;
776 }
777 }
778 }
779
780 if (ekind)
781 {
782 for(i=0; (i<md->nTC); i++)
783 {
784 md->tmp_r[i] = ekind->tcstat[i].T;
785 }
786 add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
787
788 /* whether to print Nose-Hoover chains: */
789 bNoseHoover = (getenv("GMX_NOSEHOOVER_CHAINS") != NULL);
790
791 if (md->etc == etcNOSEHOOVER)
792 {
793 if (bNoseHoover)
794 {
795 if (md->bNHC_trotter)
796 {
797 for(i=0; (i<md->nTC); i++)
798 {
799 for (j=0;j<md->nNHC;j++)
800 {
801 k = i*md->nNHC+j;
802 md->tmp_r[2*k] = state->nosehoover_xi[k];
803 md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
804 }
805 }
806 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
807
808 if (md->bMTTK) {
809 for(i=0; (i<md->nTCP); i++)
810 {
811 for (j=0;j<md->nNHC;j++)
812 {
813 k = i*md->nNHC+j;
814 md->tmp_r[2*k] = state->nhpres_xi[k];
815 md->tmp_r[2*k+1] = state->nhpres_vxi[k];
816 }
817 }
818 add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
819 }
820
821 }
822 else
823 {
824 for(i=0; (i<md->nTC); i++)
825 {
826 md->tmp_r[2*i] = state->nosehoover_xi[i];
827 md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
828 }
829 add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
830 }
831 }
832 }
833 else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
834 md->etc == etcVRESCALE)
835 {
836 for(i=0; (i<md->nTC); i++)
837 {
838 md->tmp_r[i] = ekind->tcstat[i].lambda;
839 }
840 add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
841 }
842 }
843
844 if (ekind && md->nU > 1)
845 {
846 for(i=0; (i<md->nU); i++)
847 {
848 copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
849 }
850 add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
851 }
852
853 ebin_increase_count(md->ebin,bSum);
854
855 /* BAR + thermodynamic integration values */
856 if (write_dhdl)
857 {
858 if (md->fp_dhdl)
859 {
860 fprintf(md->fp_dhdl,"%.4f", time);
861
862 if (md->dhdl_derivatives)
863 {
864 fprintf(md->fp_dhdl," %g", enerd->term[F_DVDL]+
865 enerd->term[F_DKDL]+
866 enerd->term[F_DHDL_CON]);
867 }
868 for(i=1; i<enerd->n_lambda; i++)
869 {
870 fprintf(md->fp_dhdl," %g",
871 enerd->enerpart_lambda[i]-enerd->enerpart_lambda[0]);
872 }
873 fprintf(md->fp_dhdl,"\n");
874 }
875 /* and the binary BAR output */
876 if (md->dhc)
877 {
878 mde_delta_h_coll_add_dh(md->dhc,
879 enerd->term[F_DVDL]+ enerd->term[F_DKDL]+
880 enerd->term[F_DHDL_CON],
881 enerd->enerpart_lambda, time,
882 state->lambda);
883 }
884 }
885 }
886
887 void upd_mdebin_step(t_mdebin *md)
888 {
889 ebin_increase_count(md->ebin,FALSE);
890 }
891
892 static void npr(FILE *log,int n,char c)
893 {
894 for(; (n>0); n--) fprintf(log,"%c",c);
895 }
896
897 static void pprint(FILE *log,const char *s,t_mdebin *md)
898 {
899 char CHAR='#';
900 int slen;
901 char buf1[22],buf2[22];
902
903 slen = strlen(s);
904 fprintf(log,"\t<====== ");
905 npr(log,slen,CHAR);
906 fprintf(log," ==>\n");
907 fprintf(log,"\t<==== %s ====>\n",s);
908 fprintf(log,"\t<== ");
909 npr(log,slen,CHAR);
910 fprintf(log," ======>\n\n");
911
912 fprintf(log,"\tStatistics over %s steps using %s frames\n",
913 gmx_step_str(md->ebin->nsteps_sim,buf1),
914 gmx_step_str(md->ebin->nsum_sim,buf2));
915 fprintf(log,"\n");
916 }
917
918 void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lamb)
919 {
920 char buf[22];
921
922 fprintf(log," %12s %12s %12s\n"
923 " %12s %12.5f %12.5f\n\n",
924 "Step","Time","Lambda",gmx_step_str(steps,buf),time,lamb);
925 }
926
927 void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
928 FILE *log,
929 gmx_large_int_t step,double time,
930 int mode,gmx_bool bCompact,
931 t_mdebin *md,t_fcdata *fcd,
932 gmx_groups_t *groups,t_grpopts *opts)
933 {
934 /*static char **grpnms=NULL;*/
935 char buf[246];
936 int i,j,n,ni,nj,ndr,nor,b;
937 int ndisre=0;
938 real *disre_rm3tav, *disre_rt;
939
940 /* these are for the old-style blocks (1 subblock, only reals), because
941 there can be only one per ID for these */
942 int nr[enxNR];
943 int id[enxNR];
944 real *block[enxNR];
945
946 /* temporary arrays for the lambda values to write out */
947 double enxlambda_data[2];
948
949 t_enxframe fr;
950
951 switch (mode)
952 {
953 case eprNORMAL:
954 init_enxframe(&fr);
955 fr.t = time;
956 fr.step = step;
957 fr.nsteps = md->ebin->nsteps;
958 fr.dt = md->delta_t;
959 fr.nsum = md->ebin->nsum;
960 fr.nre = (bEne) ? md->ebin->nener : 0;
961 fr.ener = md->ebin->e;
962 ndisre = bDR ? fcd->disres.npair : 0;
963 disre_rm3tav = fcd->disres.rm3tav;
964 disre_rt = fcd->disres.rt;
965 /* Optional additional old-style (real-only) blocks. */
966 for(i=0; i<enxNR; i++)
967 {
968 nr[i] = 0;
969 }
970 if (fcd->orires.nr > 0 && bOR)
971 {
972 diagonalize_orires_tensors(&(fcd->orires));
973 nr[enxOR] = fcd->orires.nr;
974 block[enxOR] = fcd->orires.otav;
975 id[enxOR] = enxOR;
976 nr[enxORI] = (fcd->orires.oinsl != fcd->orires.otav) ?
977 fcd->orires.nr : 0;
978 block[enxORI] = fcd->orires.oinsl;
979 id[enxORI] = enxORI;
980 nr[enxORT] = fcd->orires.nex*12;
981 block[enxORT] = fcd->orires.eig;
982 id[enxORT] = enxORT;
983 }
984
985 /* whether we are going to wrte anything out: */
986 if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
987 {
988
989 /* the old-style blocks go first */
990 fr.nblock = 0;
991 for(i=0; i<enxNR; i++)
992 {
993 if (nr[i] > 0)
994 {
995 fr.nblock = i + 1;
996 }
997 }
998 add_blocks_enxframe(&fr, fr.nblock);
999 for(b=0;b<fr.nblock;b++)
1000 {
1001 add_subblocks_enxblock(&(fr.block[b]), 1);
1002 fr.block[b].id=id[b];
1003 fr.block[b].sub[0].nr = nr[b];
1004 #ifndef GMX_DOUBLE
1005 fr.block[b].sub[0].type = xdr_datatype_float;
1006 fr.block[b].sub[0].fval = block[b];
1007 #else
1008 fr.block[b].sub[0].type = xdr_datatype_double;
1009 fr.block[b].sub[0].dval = block[b];
1010 #endif
1011 }
1012
1013 /* check for disre block & fill it. */
1014 if (ndisre>0)
1015 {
1016 int db = fr.nblock;
1017 fr.nblock+=1;
1018 add_blocks_enxframe(&fr, fr.nblock);
1019
1020 add_subblocks_enxblock(&(fr.block[db]), 2);
1021 fr.block[db].id=enxDISRE;
1022 fr.block[db].sub[0].nr=ndisre;
1023 fr.block[db].sub[1].nr=ndisre;
1024 #ifndef GMX_DOUBLE
1025 fr.block[db].sub[0].type=xdr_datatype_float;
1026 fr.block[db].sub[1].type=xdr_datatype_float;
1027 fr.block[db].sub[0].fval=disre_rt;
1028 fr.block[db].sub[1].fval=disre_rm3tav;
1029 #else
1030 fr.block[db].sub[0].type=xdr_datatype_double;
1031 fr.block[db].sub[1].type=xdr_datatype_double;
1032 fr.block[db].sub[0].dval=disre_rt;
1033 fr.block[db].sub[1].dval=disre_rm3tav;
1034 #endif
1035 }
1036 /* here we can put new-style blocks */
1037
1038 /* Free energy perturbation blocks */
1039 if (md->dhc)
1040 {
1041 mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
1042 }
1043
1044 /* do the actual I/O */
1045 do_enx(fp_ene,&fr);
1046 gmx_fio_check_file_position(enx_file_pointer(fp_ene));
1047 if (fr.nre)
1048 {
1049 /* We have stored the sums, so reset the sum history */
1050 reset_ebin_sums(md->ebin);
1051 }
1052
1053 /* we can now free & reset the data in the blocks */
1054 if (md->dhc)
1055 mde_delta_h_coll_reset(md->dhc);
1056 }
1057 free_enxframe(&fr);
1058 break;
1059 case eprAVER:
1060 if (log)
1061 {
1062 pprint(log,"A V E R A G E S",md);
1063 }
1064 break;
1065 case eprRMS:
1066 if (log)
1067 {
1068 pprint(log,"R M S - F L U C T U A T I O N S",md);
1069 }
1070 break;
1071 default:
1072 gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
1073 }
1074
1075 if (log)
1076 {
1077 for(i=0;i<opts->ngtc;i++)
1078 {
1079 if(opts->annealing[i]!=eannNO)
1080 {
1081 fprintf(log,"Current ref_t for group %s: %8.1f\n",
1082 *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
1083 opts->ref_t[i]);
1084 }
1085 }
1086 if (mode==eprNORMAL && fcd->orires.nr>0)
1087 {
1088 print_orires_log(log,&(fcd->orires));
1089 }
1090 fprintf(log," Energies (%s)\n",unit_energy);
1091 pr_ebin(log,md->ebin,md->ie,md->f_nre+md->nCrmsd,5,mode,TRUE);
1092 fprintf(log,"\n");
1093
1094 if (!bCompact)
1095 {
1096 if (md->bDynBox)
1097 {
1098 pr_ebin(log,md->ebin,md->ib, md->bTricl ? NTRICLBOXS : NBOXS,5,
1099 mode,TRUE);
1100 fprintf(log,"\n");
1101 }
1102 if (md->bConstrVir)
1103 {
1104 fprintf(log," Constraint Virial (%s)\n",unit_energy);
1105 pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
1106 fprintf(log,"\n");
1107 fprintf(log," Force Virial (%s)\n",unit_energy);
1108 pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
1109 fprintf(log,"\n");
1110 }
1111 fprintf(log," Total Virial (%s)\n",unit_energy);
1112 pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
1113 fprintf(log,"\n");
1114 fprintf(log," Pressure (%s)\n",unit_pres_bar);
1115 pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
1116 fprintf(log,"\n");
1117 fprintf(log," Total Dipole (%s)\n",unit_dipole_D);
1118 pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
1119 fprintf(log,"\n");
1120
1121 if (md->nE > 1)
1122 {
1123 if (md->print_grpnms==NULL)
1124 {
1125 snew(md->print_grpnms,md->nE);
1126 n=0;
1127 for(i=0; (i<md->nEg); i++)
1128 {
1129 ni=groups->grps[egcENER].nm_ind[i];
1130 for(j=i; (j<md->nEg); j++)
1131 {
1132 nj=groups->grps[egcENER].nm_ind[j];
1133 sprintf(buf,"%s-%s",*(groups->grpname[ni]),
1134 *(groups->grpname[nj]));
1135 md->print_grpnms[n++]=strdup(buf);
1136 }
1137 }
1138 }
1139 sprintf(buf,"Epot (%s)",unit_energy);
1140 fprintf(log,"%15s ",buf);
1141 for(i=0; (i<egNR); i++)
1142 {
1143 if (md->bEInd[i])
1144 {
1145 fprintf(log,"%12s ",egrp_nm[i]);
1146 }
1147 }
1148 fprintf(log,"\n");
1149 for(i=0; (i<md->nE); i++)
1150 {
1151 fprintf(log,"%15s",md->print_grpnms[i]);
1152 pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,
1153 FALSE);
1154 }
1155 fprintf(log,"\n");
1156 }
1157 if (md->nTC > 1)
1158 {
1159 pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
1160 fprintf(log,"\n");
1161 }
1162 if (md->nU > 1)
1163 {
1164 fprintf(log,"%15s %12s %12s %12s\n",
1165 "Group","Ux","Uy","Uz");
1166 for(i=0; (i<md->nU); i++)
1167 {
1168 ni=groups->grps[egcACC].nm_ind[i];
1169 fprintf(log,"%15s",*groups->grpname[ni]);
1170 pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
1171 }
1172 fprintf(log,"\n");
1173 }
1174 }
1175 }
1176
1177 }
1178
1179 void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
1180 {
1181 int i;
1182
1183 enerhist->nsteps = mdebin->ebin->nsteps;
1184 enerhist->nsum = mdebin->ebin->nsum;
1185 enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
1186 enerhist->nsum_sim = mdebin->ebin->nsum_sim;
1187 enerhist->nener = mdebin->ebin->nener;
1188
1189 if (mdebin->ebin->nsum > 0)
1190 {
1191 /* Check if we need to allocate first */
1192 if(enerhist->ener_ave == NULL)
1193 {
1194 snew(enerhist->ener_ave,enerhist->nener);
1195 snew(enerhist->ener_sum,enerhist->nener);
1196 }
1197
1198 for(i=0;i<enerhist->nener;i++)
1199 {
1200 enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
1201 enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
1202 }
1203 }
1204
1205 if (mdebin->ebin->nsum_sim > 0)
1206 {
1207 /* Check if we need to allocate first */
1208 if(enerhist->ener_sum_sim == NULL)
1209 {
1210 snew(enerhist->ener_sum_sim,enerhist->nener);
1211 }
1212
1213 for(i=0;i<enerhist->nener;i++)
1214 {
1215 enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
1216 }
1217 }
1218 if (mdebin->dhc)
1219 {
1220 mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
1221 }
1222 }
1223
1224 void restore_energyhistory_from_state(t_mdebin * mdebin,
1225 energyhistory_t * enerhist)
1226 {
1227 int i;
1228
1229 if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
1230 mdebin->ebin->nener != enerhist->nener)
1231 {
1232 gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
1233 mdebin->ebin->nener,enerhist->nener);
1234 }
1235
1236 mdebin->ebin->nsteps = enerhist->nsteps;
1237 mdebin->ebin->nsum = enerhist->nsum;
1238 mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
1239 mdebin->ebin->nsum_sim = enerhist->nsum_sim;
1240
1241 for(i=0; i<mdebin->ebin->nener; i++)
1242 {
1243 mdebin->ebin->e[i].eav =
1244 (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
1245 mdebin->ebin->e[i].esum =
1246 (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
1247 mdebin->ebin->e_sim[i].esum =
1248 (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
1249 }
1250 if (mdebin->dhc)
1251 {
1252 mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);
1253 }
1254 }
got merge a long time ago