src/gromacs/mdlib/mdebin.c

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