src/mdlib/mdebin.c

   1 /*
   2  * This file is part of the GROMACS molecular simulation package.
   3  *
   4  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
   5  * Copyright (c) 2001-2004, The GROMACS development team,
   6  * check out http://www.gromacs.org for more information.
   7  * Copyright (c) 2012, by the GROMACS development team, led by
   8  * David van der Spoel, Berk Hess, Erik Lindahl, and including many
   9  * others, as listed in the AUTHORS file in the top-level source
  10  * directory and at http://www.gromacs.org.
  11  *
  12  * GROMACS is free software; you can redistribute it and/or
  13  * modify it under the terms of the GNU Lesser General Public License
  14  * as published by the Free Software Foundation; either version 2.1
  15  * of the License, or (at your option) any later version.
  16  *
  17  * GROMACS is distributed in the hope that it will be useful,
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  19  * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
  20  * Lesser General Public License for more details.
  21  *
  22  * You should have received a copy of the GNU Lesser General Public
  23  * License along with GROMACS; if not, see
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  25  * Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301  USA.
  26  *
  27  * If you want to redistribute modifications to GROMACS, please
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  29  * control is crucial - bugs must be traceable. We will be happy to
  30  * consider code for inclusion in the official distribution, but
  31  * derived work must not be called official GROMACS. Details are found
  32  * in the README & COPYING files - if they are missing, get the
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  34  *
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  36  * the research papers on the package. Check out http://www.gromacs.org.
  37  */
  38 #ifdef HAVE_CONFIG_H
  39 #include <config.h>
  40 #endif
  41
  42 #include <string.h>
  43 #include <float.h>
  44 #include "typedefs.h"
  45 #include "string2.h"
  46 #include "mdebin.h"
  47 #include "smalloc.h"
  48 #include "physics.h"
  49 #include "enxio.h"
  50 #include "vec.h"
  51 #include "disre.h"
  52 #include "main.h"
  53 #include "network.h"
  54 #include "names.h"
  55 #include "orires.h"
  56 #include "constr.h"
  57 #include "mtop_util.h"
  58 #include "xvgr.h"
  59 #include "gmxfio.h"
  60 #include "mdrun.h"
  61 #include "mdebin_bar.h"
  62
  63
  64 static const char *conrmsd_nm[] = { "Constr. rmsd", "Constr.2 rmsd" };
  65
  66 static const char *boxs_nm[] = { "Box-X", "Box-Y", "Box-Z" };
  67
  68 static const char *tricl_boxs_nm[] = {
  69     "Box-XX", "Box-YY", "Box-ZZ",
  70     "Box-YX", "Box-ZX", "Box-ZY"
  71 };
  72
  73 static const char *vol_nm[] = { "Volume" };
  74
  75 static const char *dens_nm[] = {"Density" };
  76
  77 static const char *pv_nm[] = {"pV" };
  78
  79 static const char *enthalpy_nm[] = {"Enthalpy" };
  80
  81 static const char *boxvel_nm[] = {
  82     "Box-Vel-XX", "Box-Vel-YY", "Box-Vel-ZZ",
  83     "Box-Vel-YX", "Box-Vel-ZX", "Box-Vel-ZY"
  84 };
  85
  86 #define NBOXS asize(boxs_nm)
  87 #define NTRICLBOXS asize(tricl_boxs_nm)
  88
  89 t_mdebin *init_mdebin(ener_file_t fp_ene,
  90                       const gmx_mtop_t *mtop,
  91                       const t_inputrec *ir,
  92                       FILE *fp_dhdl)
  93 {
  94     const char *ener_nm[F_NRE];
  95     static const char *vir_nm[] = {
  96         "Vir-XX", "Vir-XY", "Vir-XZ",
  97         "Vir-YX", "Vir-YY", "Vir-YZ",
  98         "Vir-ZX", "Vir-ZY", "Vir-ZZ"
  99     };
 100     static const char *sv_nm[] = {
 101         "ShakeVir-XX", "ShakeVir-XY", "ShakeVir-XZ",
 102         "ShakeVir-YX", "ShakeVir-YY", "ShakeVir-YZ",
 103         "ShakeVir-ZX", "ShakeVir-ZY", "ShakeVir-ZZ"
 104     };
 105     static const char *fv_nm[] = {
 106         "ForceVir-XX", "ForceVir-XY", "ForceVir-XZ",
 107         "ForceVir-YX", "ForceVir-YY", "ForceVir-YZ",
 108         "ForceVir-ZX", "ForceVir-ZY", "ForceVir-ZZ"
 109     };
 110     static const char *pres_nm[] = {
 111         "Pres-XX","Pres-XY","Pres-XZ",
 112         "Pres-YX","Pres-YY","Pres-YZ",
 113         "Pres-ZX","Pres-ZY","Pres-ZZ"
 114     };
 115     static const char *surft_nm[] = {
 116         "#Surf*SurfTen"
 117     };
 118     static const char *mu_nm[] = {
 119         "Mu-X", "Mu-Y", "Mu-Z"
 120     };
 121     static const char *vcos_nm[] = {
 122         "2CosZ*Vel-X"
 123     };
 124     static const char *visc_nm[] = {
 125         "1/Viscosity"
 126     };
 127     static const char *baro_nm[] = {
 128         "Barostat"
 129     };
 130
 131     char     **grpnms;
 132     const gmx_groups_t *groups;
 133     char     **gnm;
 134     char     buf[256];
 135     const char     *bufi;
 136     t_mdebin *md;
 137     int      i,j,ni,nj,n,nh,k,kk,ncon,nset;
 138     gmx_bool     bBHAM,bNoseHoover,b14;
 139
 140     snew(md,1);
 141
 142     md->bVir=TRUE;
 143     md->bPress=TRUE;
 144     md->bSurft=TRUE;
 145     md->bMu=TRUE;
 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 && ir->cutoff_scheme == ecutsGROUP);
 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_COUL && ir->fepvals->separate_dvdl[efptCOUL]) ||
 211                  (i == F_DVDL_VDW  && ir->fepvals->separate_dvdl[efptVDW]) ||
 212                  (i == F_DVDL_BONDED && ir->fepvals->separate_dvdl[efptBONDED]) ||
 213                  (i == F_DVDL_RESTRAINT && ir->fepvals->separate_dvdl[efptRESTRAINT]) ||
 214                  (i == F_DKDL && ir->fepvals->separate_dvdl[efptMASS]) ||
 215                  (i == F_DVDL && ir->fepvals->separate_dvdl[efptFEP]))
 216             md->bEner[i] = (ir->efep != efepNO);
 217         else if ((interaction_function[i].flags & IF_VSITE) ||
 218                  (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
 219             md->bEner[i] = FALSE;
 220         else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES)  || (i==F_EQM))
 221             md->bEner[i] = TRUE;
 222         else if ((i == F_GBPOL) && ir->implicit_solvent==eisGBSA)
 223             md->bEner[i] = TRUE;
 224         else if ((i == F_NPSOLVATION) && ir->implicit_solvent==eisGBSA && (ir->sa_algorithm != esaNO))
 225             md->bEner[i] = TRUE;
 226         else if ((i == F_GB12) || (i == F_GB13) || (i == F_GB14))
 227             md->bEner[i] = FALSE;
 228         else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
 229             md->bEner[i] = EI_DYNAMICS(ir->eI);
 230         else if (i==F_VTEMP)
 231             md->bEner[i] =  (EI_DYNAMICS(ir->eI) && getenv("GMX_VIRIAL_TEMPERATURE"));
 232         else if (i == F_DISPCORR || i == F_PDISPCORR)
 233             md->bEner[i] = (ir->eDispCorr != edispcNO);
 234         else if (i == F_DISRESVIOL)
 235             md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
 236         else if (i == F_ORIRESDEV)
 237             md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
 238         else if (i == F_CONNBONDS)
 239             md->bEner[i] = FALSE;
 240         else if (i == F_COM_PULL)
 241             md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
 242         else if (i == F_ECONSERVED)
 243             md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
 244                             (ir->epc == epcNO || ir->epc==epcMTTK));
 245         else
 246             md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
 247     }
 248 #else
 249     /* OpenMM always produces only the following 4 energy terms */
 250     md->bEner[F_EPOT] = TRUE;
 251     md->bEner[F_EKIN] = TRUE;
 252     md->bEner[F_ETOT] = TRUE;
 253     md->bEner[F_TEMP] = TRUE;
 254 #endif
 255
 256     /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
 257     if (ir->bAdress && !debug) {
 258         for (i = 0; i < F_NRE; i++) {
 259             md->bEner[i] = FALSE;
 260             if(i == F_EKIN){ md->bEner[i] = TRUE;}
 261             if(i == F_TEMP){ md->bEner[i] = TRUE;}
 262         }
 263         md->bVir=FALSE;
 264         md->bPress=FALSE;
 265         md->bSurft=FALSE;
 266         md->bMu=FALSE;
 267     }
 268
 269     md->f_nre=0;
 270     for(i=0; i<F_NRE; i++)
 271     {
 272         if (md->bEner[i])
 273         {
 274             ener_nm[md->f_nre]=interaction_function[i].longname;
 275             md->f_nre++;
 276         }
 277     }
 278
 279     md->epc = ir->epc;
 280     md->bDiagPres = !TRICLINIC(ir->ref_p);
 281     md->ref_p = (ir->ref_p[XX][XX]+ir->ref_p[YY][YY]+ir->ref_p[ZZ][ZZ])/DIM;
 282     md->bTricl = TRICLINIC(ir->compress) || TRICLINIC(ir->deform);
 283     md->bDynBox = DYNAMIC_BOX(*ir);
 284     md->etc = ir->etc;
 285     md->bNHC_trotter = IR_NVT_TROTTER(ir);
 286     md->bPrintNHChains = ir-> bPrintNHChains;
 287     md->bMTTK = (IR_NPT_TROTTER(ir) || IR_NPH_TROTTER(ir));
 288     md->bMu = NEED_MUTOT(*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     {
 335         md->imu    = get_ebin_space(md->ebin,asize(mu_nm),mu_nm,unit_dipole_D);
 336     }
 337     if (ir->cos_accel != 0)
 338     {
 339         md->ivcos = get_ebin_space(md->ebin,asize(vcos_nm),vcos_nm,unit_vel);
 340         md->ivisc = get_ebin_space(md->ebin,asize(visc_nm),visc_nm,
 341                                    unit_invvisc_SI);
 342     }
 343
 344     /* Energy monitoring */
 345     for(i=0;i<egNR;i++)
 346     {
 347         md->bEInd[i] = FALSE;
 348     }
 349     md->bEInd[egCOULSR] = TRUE;
 350     md->bEInd[egLJSR  ] = TRUE;
 351
 352     if (ir->rcoulomb > ir->rlist)
 353     {
 354         md->bEInd[egCOULLR] = TRUE;
 355     }
 356     if (!bBHAM)
 357     {
 358         if (ir->rvdw > ir->rlist)
 359         {
 360             md->bEInd[egLJLR]   = TRUE;
 361         }
 362     }
 363     else
 364     {
 365         md->bEInd[egLJSR]   = FALSE;
 366         md->bEInd[egBHAMSR] = TRUE;
 367         if (ir->rvdw > ir->rlist)
 368         {
 369             md->bEInd[egBHAMLR]   = TRUE;
 370         }
 371     }
 372     if (b14)
 373     {
 374         md->bEInd[egLJ14] = TRUE;
 375         md->bEInd[egCOUL14] = TRUE;
 376     }
 377     md->nEc=0;
 378     for(i=0; (i<egNR); i++)
 379     {
 380         if (md->bEInd[i])
 381         {
 382             md->nEc++;
 383         }
 384     }
 385
 386     n=groups->grps[egcENER].nr;
 387     /* for adress simulations, most energy terms are not meaningfull, and thus disabled*/
 388     if (!ir->bAdress){
 389         /*standard simulation*/
 390         md->nEg=n;
 391         md->nE=(n*(n+1))/2;
 392     }
 393     else if (!debug) {
 394         /*AdResS simulation*/
 395        md->nU=0;
 396        md->nEg=0;
 397        md->nE=0;
 398        md->nEc=0;
 399        md->isvir=FALSE;
 400     }
 401     snew(md->igrp,md->nE);
 402     if (md->nE > 1)
 403     {
 404         n=0;
 405         snew(gnm,md->nEc);
 406         for(k=0; (k<md->nEc); k++)
 407         {
 408             snew(gnm[k],STRLEN);
 409         }
 410         for(i=0; (i<groups->grps[egcENER].nr); i++)
 411         {
 412             ni=groups->grps[egcENER].nm_ind[i];
 413             for(j=i; (j<groups->grps[egcENER].nr); j++)
 414             {
 415                 nj=groups->grps[egcENER].nm_ind[j];
 416                 for(k=kk=0; (k<egNR); k++)
 417                 {
 418                     if (md->bEInd[k])
 419                     {
 420                         sprintf(gnm[kk],"%s:%s-%s",egrp_nm[k],
 421                                 *(groups->grpname[ni]),*(groups->grpname[nj]));
 422                         kk++;
 423                     }
 424                 }
 425                 md->igrp[n]=get_ebin_space(md->ebin,md->nEc,
 426                                            (const char **)gnm,unit_energy);
 427                 n++;
 428             }
 429         }
 430         for(k=0; (k<md->nEc); k++)
 431         {
 432             sfree(gnm[k]);
 433         }
 434         sfree(gnm);
 435
 436         if (n != md->nE)
 437         {
 438             gmx_incons("Number of energy terms wrong");
 439         }
 440     }
 441
 442     md->nTC=groups->grps[egcTC].nr;
 443     md->nNHC = ir->opts.nhchainlength; /* shorthand for number of NH chains */
 444     if (md->bMTTK)
 445     {
 446         md->nTCP = 1;  /* assume only one possible coupling system for barostat
 447                           for now */
 448     }
 449     else
 450     {
 451         md->nTCP = 0;
 452     }
 453     if (md->etc == etcNOSEHOOVER)
 454     {
 455         if (md->bNHC_trotter)
 456         {
 457             md->mde_n = 2*md->nNHC*md->nTC;
 458         }
 459         else
 460         {
 461             md->mde_n = 2*md->nTC;
 462         }
 463         if (md->epc == epcMTTK)
 464         {
 465             md->mdeb_n = 2*md->nNHC*md->nTCP;
 466         }
 467     } else {
 468         md->mde_n = md->nTC;
 469         md->mdeb_n = 0;
 470     }
 471
 472     snew(md->tmp_r,md->mde_n);
 473     snew(md->tmp_v,md->mde_n);
 474     snew(md->grpnms,md->mde_n);
 475     grpnms = md->grpnms;
 476
 477     for(i=0; (i<md->nTC); i++)
 478     {
 479         ni=groups->grps[egcTC].nm_ind[i];
 480         sprintf(buf,"T-%s",*(groups->grpname[ni]));
 481         grpnms[i]=strdup(buf);
 482     }
 483     md->itemp=get_ebin_space(md->ebin,md->nTC,(const char **)grpnms,
 484                              unit_temp_K);
 485
 486     if (md->etc == etcNOSEHOOVER)
 487     {
 488         if (md->bPrintNHChains)
 489         {
 490             if (md->bNHC_trotter)
 491             {
 492                 for(i=0; (i<md->nTC); i++)
 493                 {
 494                     ni=groups->grps[egcTC].nm_ind[i];
 495                     bufi = *(groups->grpname[ni]);
 496                     for(j=0; (j<md->nNHC); j++)
 497                     {
 498                         sprintf(buf,"Xi-%d-%s",j,bufi);
 499                         grpnms[2*(i*md->nNHC+j)]=strdup(buf);
 500                         sprintf(buf,"vXi-%d-%s",j,bufi);
 501                         grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
 502                     }
 503                 }
 504                 md->itc=get_ebin_space(md->ebin,md->mde_n,
 505                                        (const char **)grpnms,unit_invtime);
 506                 if (md->bMTTK)
 507                 {
 508                     for(i=0; (i<md->nTCP); i++)
 509                     {
 510                         bufi = baro_nm[0];  /* All barostat DOF's together for now. */
 511                         for(j=0; (j<md->nNHC); j++)
 512                         {
 513                             sprintf(buf,"Xi-%d-%s",j,bufi);
 514                             grpnms[2*(i*md->nNHC+j)]=strdup(buf);
 515                             sprintf(buf,"vXi-%d-%s",j,bufi);
 516                             grpnms[2*(i*md->nNHC+j)+1]=strdup(buf);
 517                         }
 518                     }
 519                     md->itcb=get_ebin_space(md->ebin,md->mdeb_n,
 520                                             (const char **)grpnms,unit_invtime);
 521                 }
 522             }
 523             else
 524             {
 525                 for(i=0; (i<md->nTC); i++)
 526                 {
 527                     ni=groups->grps[egcTC].nm_ind[i];
 528                     bufi = *(groups->grpname[ni]);
 529                     sprintf(buf,"Xi-%s",bufi);
 530                     grpnms[2*i]=strdup(buf);
 531                     sprintf(buf,"vXi-%s",bufi);
 532                     grpnms[2*i+1]=strdup(buf);
 533                 }
 534                 md->itc=get_ebin_space(md->ebin,md->mde_n,
 535                                        (const char **)grpnms,unit_invtime);
 536             }
 537         }
 538     }
 539     else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
 540              md->etc == etcVRESCALE)
 541     {
 542         for(i=0; (i<md->nTC); i++)
 543         {
 544             ni=groups->grps[egcTC].nm_ind[i];
 545             sprintf(buf,"Lamb-%s",*(groups->grpname[ni]));
 546             grpnms[i]=strdup(buf);
 547         }
 548         md->itc=get_ebin_space(md->ebin,md->mde_n,(const char **)grpnms,"");
 549     }
 550
 551     sfree(grpnms);
 552
 553
 554     md->nU=groups->grps[egcACC].nr;
 555     if (md->nU > 1)
 556     {
 557         snew(grpnms,3*md->nU);
 558         for(i=0; (i<md->nU); i++)
 559         {
 560             ni=groups->grps[egcACC].nm_ind[i];
 561             sprintf(buf,"Ux-%s",*(groups->grpname[ni]));
 562             grpnms[3*i+XX]=strdup(buf);
 563             sprintf(buf,"Uy-%s",*(groups->grpname[ni]));
 564             grpnms[3*i+YY]=strdup(buf);
 565             sprintf(buf,"Uz-%s",*(groups->grpname[ni]));
 566             grpnms[3*i+ZZ]=strdup(buf);
 567         }
 568         md->iu=get_ebin_space(md->ebin,3*md->nU,(const char **)grpnms,unit_vel);
 569         sfree(grpnms);
 570     }
 571
 572     if ( fp_ene )
 573     {
 574         do_enxnms(fp_ene,&md->ebin->nener,&md->ebin->enm);
 575     }
 576
 577     md->print_grpnms=NULL;
 578
 579     /* check whether we're going to write dh histograms */
 580     md->dhc=NULL;
 581     if (ir->fepvals->separate_dhdl_file == esepdhdlfileNO )
 582     {
 583         /* Currently dh histograms are only written with dynamics */
 584         if (EI_DYNAMICS(ir->eI))
 585         {
 586             snew(md->dhc, 1);
 587
 588             mde_delta_h_coll_init(md->dhc, ir);
 589         }
 590         md->fp_dhdl = NULL;
 591     }
 592     else
 593     {
 594         md->fp_dhdl = fp_dhdl;
 595     }
 596     if (ir->bSimTemp) {
 597         int i;
 598         snew(md->temperatures,ir->fepvals->n_lambda);
 599         for (i=0;i<ir->fepvals->n_lambda;i++)
 600         {
 601             md->temperatures[i] = ir->simtempvals->temperatures[i];
 602         }
 603     }
 604     return md;
 605 }
 606
 607 extern FILE *open_dhdl(const char *filename,const t_inputrec *ir,
 608                        const output_env_t oenv)
 609 {
 610     FILE *fp;
 611     const char *dhdl="dH/d\\lambda",*deltag="\\DeltaH",*lambda="\\lambda",
 612         *lambdastate="\\lambda state",*remain="remaining";
 613     char title[STRLEN],label_x[STRLEN],label_y[STRLEN];
 614     int  i,np,nps,nsets,nsets_de,nsetsbegin;
 615     t_lambda *fep;
 616     char **setname;
 617     char buf[STRLEN];
 618     int bufplace=0;
 619
 620     int nsets_dhdl = 0;
 621     int s = 0;
 622     int nsetsextend;
 623
 624     /* for simplicity */
 625     fep = ir->fepvals;
 626
 627     if (fep->n_lambda == 0)
 628     {
 629         sprintf(title,"%s",dhdl);
 630         sprintf(label_x,"Time (ps)");
 631         sprintf(label_y,"%s (%s %s)",
 632                 dhdl,unit_energy,"[\\lambda]\\S-1\\N");
 633     }
 634     else
 635     {
 636         sprintf(title,"%s and %s",dhdl,deltag);
 637         sprintf(label_x,"Time (ps)");
 638         sprintf(label_y,"%s and %s (%s %s)",
 639                 dhdl,deltag,unit_energy,"[\\8l\\4]\\S-1\\N");
 640     }
 641     fp = gmx_fio_fopen(filename,"w+");
 642     xvgr_header(fp,title,label_x,label_y,exvggtXNY,oenv);
 643
 644     if (!(ir->bSimTemp))
 645     {
 646         bufplace = sprintf(buf,"T = %g (K) ",
 647                 ir->opts.ref_t[0]);
 648     }
 649     if (ir->efep != efepSLOWGROWTH)
 650     {
 651         if (fep->n_lambda == 0)
 652         {
 653             sprintf(&(buf[bufplace]),"%s = %g",
 654                     lambda,fep->init_lambda);
 655         }
 656         else
 657         {
 658             sprintf(&(buf[bufplace]),"%s = %d",
 659                     lambdastate,fep->init_fep_state);
 660         }
 661     }
 662     xvgr_subtitle(fp,buf,oenv);
 663
 664     for (i=0;i<efptNR;i++)
 665     {
 666         if (fep->separate_dvdl[i]) {nsets_dhdl++;}
 667     }
 668
 669     /* count the number of delta_g states */
 670     nsets_de = fep->n_lambda;
 671
 672     nsets = nsets_dhdl + nsets_de; /* dhdl + fep differences */
 673
 674     if (fep->n_lambda>0 && ir->bExpanded)
 675     {
 676         nsets += 1;   /*add fep state for expanded ensemble */
 677     }
 678
 679     if (fep->bPrintEnergy)
 680     {
 681         nsets += 1;  /* add energy to the dhdl as well */
 682     }
 683
 684     nsetsextend = nsets;
 685     if ((ir->epc!=epcNO) && (fep->n_lambda>0))
 686     {
 687         nsetsextend += 1; /* for PV term, other terms possible if required for the reduced potential (only needed with foreign lambda) */
 688     }
 689     snew(setname,nsetsextend);
 690
 691     if (ir->bExpanded)
 692     {
 693         /* state for the fep_vals, if we have alchemical sampling */
 694         sprintf(buf,"%s","Thermodynamic state");
 695         setname[s] = strdup(buf);
 696         s+=1;
 697     }
 698
 699     if (fep->bPrintEnergy)
 700     {
 701         sprintf(buf,"%s (%s)","Energy",unit_energy);
 702         setname[s] = strdup(buf);
 703         s+=1;
 704     }
 705
 706     for (i=0;i<efptNR;i++)
 707     {
 708         if (fep->separate_dvdl[i]) {
 709             sprintf(buf,"%s (%s)",dhdl,efpt_names[i]);
 710             setname[s] = strdup(buf);
 711             s+=1;
 712         }
 713     }
 714
 715     if (fep->n_lambda > 0)
 716     {
 717         /* g_bar has to determine the lambda values used in this simulation
 718          * from this xvg legend.
 719          */
 720
 721         if (ir->bExpanded) {
 722             nsetsbegin = 1;  /* for including the expanded ensemble */
 723         } else {
 724             nsetsbegin = 0;
 725         }
 726
 727         if (fep->bPrintEnergy)
 728         {
 729             nsetsbegin += 1;
 730         }
 731         nsetsbegin += nsets_dhdl;
 732
 733         for(s=nsetsbegin; s<nsets; s++)
 734         {
 735             nps = sprintf(buf,"%s %s (",deltag,lambda);
 736             for (i=0;i<efptNR;i++)
 737             {
 738                 if (fep->separate_dvdl[i])
 739                 {
 740                     np = sprintf(&buf[nps],"%g,",fep->all_lambda[i][s-(nsetsbegin)]);
 741                     nps += np;
 742                 }
 743             }
 744             if (ir->bSimTemp)
 745             {
 746                 /* print the temperature for this state if doing simulated annealing */
 747                 sprintf(&buf[nps],"T = %g (%s))",ir->simtempvals->temperatures[s-(nsetsbegin)],unit_temp_K);
 748             }
 749             else
 750             {
 751                 sprintf(&buf[nps-1],")");  /* -1 to overwrite the last comma */
 752             }
 753             setname[s] = strdup(buf);
 754         }
 755         if (ir->epc!=epcNO) {
 756             np = sprintf(buf,"pV (%s)",unit_energy);
 757             setname[nsetsextend-1] = strdup(buf);  /* the first entry after nsets */
 758         }
 759
 760         xvgr_legend(fp,nsetsextend,(const char **)setname,oenv);
 761
 762         for(s=0; s<nsetsextend; s++)
 763         {
 764             sfree(setname[s]);
 765         }
 766         sfree(setname);
 767     }
 768
 769     return fp;
 770 }
 771
 772 static void copy_energy(t_mdebin *md, real e[],real ecpy[])
 773 {
 774     int i,j;
 775
 776     for(i=j=0; (i<F_NRE); i++)
 777         if (md->bEner[i])
 778             ecpy[j++] = e[i];
 779     if (j != md->f_nre)
 780         gmx_incons("Number of energy terms wrong");
 781 }
 782
 783 void upd_mdebin(t_mdebin *md,
 784                 gmx_bool bDoDHDL,
 785                 gmx_bool bSum,
 786                 double time,
 787                 real tmass,
 788                 gmx_enerdata_t *enerd,
 789                 t_state *state,
 790                 t_lambda *fep,
 791                 t_expanded *expand,
 792                 matrix  box,
 793                 tensor svir,
 794                 tensor fvir,
 795                 tensor vir,
 796                 tensor pres,
 797                 gmx_ekindata_t *ekind,
 798                 rvec mu_tot,
 799                 gmx_constr_t constr)
 800 {
 801     int    i,j,k,kk,m,n,gid;
 802     real   crmsd[2],tmp6[6];
 803     real   bs[NTRICLBOXS],vol,dens,pv,enthalpy;
 804     real   eee[egNR];
 805     real   ecopy[F_NRE];
 806     double store_dhdl[efptNR];
 807     double *dE=NULL;
 808     real   store_energy=0;
 809     real   tmp;
 810
 811     /* Do NOT use the box in the state variable, but the separate box provided
 812      * as an argument. This is because we sometimes need to write the box from
 813      * the last timestep to match the trajectory frames.
 814      */
 815     copy_energy(md, enerd->term,ecopy);
 816     add_ebin(md->ebin,md->ie,md->f_nre,ecopy,bSum);
 817     if (md->nCrmsd)
 818     {
 819         crmsd[0] = constr_rmsd(constr,FALSE);
 820         if (md->nCrmsd > 1)
 821         {
 822             crmsd[1] = constr_rmsd(constr,TRUE);
 823         }
 824         add_ebin(md->ebin,md->iconrmsd,md->nCrmsd,crmsd,FALSE);
 825     }
 826     if (md->bDynBox)
 827     {
 828         int nboxs;
 829         if(md->bTricl)
 830         {
 831             bs[0] = box[XX][XX];
 832             bs[1] = box[YY][YY];
 833             bs[2] = box[ZZ][ZZ];
 834             bs[3] = box[YY][XX];
 835             bs[4] = box[ZZ][XX];
 836             bs[5] = box[ZZ][YY];
 837             nboxs=NTRICLBOXS;
 838         }
 839         else
 840         {
 841             bs[0] = box[XX][XX];
 842             bs[1] = box[YY][YY];
 843             bs[2] = box[ZZ][ZZ];
 844             nboxs=NBOXS;
 845         }
 846         vol  = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
 847         dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
 848         add_ebin(md->ebin,md->ib   ,nboxs,bs   ,bSum);
 849         add_ebin(md->ebin,md->ivol ,1    ,&vol ,bSum);
 850         add_ebin(md->ebin,md->idens,1    ,&dens,bSum);
 851
 852         if (md->bDiagPres)
 853         {
 854             /* This is pV (in kJ/mol).  The pressure is the reference pressure,
 855                not the instantaneous pressure */
 856             pv = vol*md->ref_p/PRESFAC;
 857
 858             add_ebin(md->ebin,md->ipv  ,1    ,&pv  ,bSum);
 859             enthalpy = pv + enerd->term[F_ETOT];
 860             add_ebin(md->ebin,md->ienthalpy  ,1    ,&enthalpy  ,bSum);
 861         }
 862     }
 863     if (md->bConstrVir)
 864     {
 865         add_ebin(md->ebin,md->isvir,9,svir[0],bSum);
 866         add_ebin(md->ebin,md->ifvir,9,fvir[0],bSum);
 867     }
 868     if (md->bVir)
 869         add_ebin(md->ebin,md->ivir,9,vir[0],bSum);
 870     if (md->bPress)
 871         add_ebin(md->ebin,md->ipres,9,pres[0],bSum);
 872     if (md->bSurft){
 873         tmp = (pres[ZZ][ZZ]-(pres[XX][XX]+pres[YY][YY])*0.5)*box[ZZ][ZZ];
 874         add_ebin(md->ebin,md->isurft,1,&tmp,bSum);
 875     }
 876     if (md->epc == epcPARRINELLORAHMAN || md->epc == epcMTTK)
 877     {
 878         tmp6[0] = state->boxv[XX][XX];
 879         tmp6[1] = state->boxv[YY][YY];
 880         tmp6[2] = state->boxv[ZZ][ZZ];
 881         tmp6[3] = state->boxv[YY][XX];
 882         tmp6[4] = state->boxv[ZZ][XX];
 883         tmp6[5] = state->boxv[ZZ][YY];
 884         add_ebin(md->ebin,md->ipc,md->bTricl ? 6 : 3,tmp6,bSum);
 885     }
 886     if (md->bMu)
 887     {
 888         add_ebin(md->ebin,md->imu,3,mu_tot,bSum);
 889     }
 890     if (ekind && ekind->cosacc.cos_accel != 0)
 891     {
 892         vol  = box[XX][XX]*box[YY][YY]*box[ZZ][ZZ];
 893         dens = (tmass*AMU)/(vol*NANO*NANO*NANO);
 894         add_ebin(md->ebin,md->ivcos,1,&(ekind->cosacc.vcos),bSum);
 895         /* 1/viscosity, unit 1/(kg m^-1 s^-1) */
 896         tmp = 1/(ekind->cosacc.cos_accel/(ekind->cosacc.vcos*PICO)
 897                  *dens*vol*sqr(box[ZZ][ZZ]*NANO/(2*M_PI)));
 898         add_ebin(md->ebin,md->ivisc,1,&tmp,bSum);
 899     }
 900     if (md->nE > 1)
 901     {
 902         n=0;
 903         for(i=0; (i<md->nEg); i++)
 904         {
 905             for(j=i; (j<md->nEg); j++)
 906             {
 907                 gid=GID(i,j,md->nEg);
 908                 for(k=kk=0; (k<egNR); k++)
 909                 {
 910                     if (md->bEInd[k])
 911                     {
 912                         eee[kk++] = enerd->grpp.ener[k][gid];
 913                     }
 914                 }
 915                 add_ebin(md->ebin,md->igrp[n],md->nEc,eee,bSum);
 916                 n++;
 917             }
 918         }
 919     }
 920
 921     if (ekind)
 922     {
 923         for(i=0; (i<md->nTC); i++)
 924         {
 925             md->tmp_r[i] = ekind->tcstat[i].T;
 926         }
 927         add_ebin(md->ebin,md->itemp,md->nTC,md->tmp_r,bSum);
 928
 929         if (md->etc == etcNOSEHOOVER)
 930         {
 931             /* whether to print Nose-Hoover chains: */
 932             if (md->bPrintNHChains)
 933             {
 934                 if (md->bNHC_trotter)
 935                 {
 936                     for(i=0; (i<md->nTC); i++)
 937                     {
 938                         for (j=0;j<md->nNHC;j++)
 939                         {
 940                             k = i*md->nNHC+j;
 941                             md->tmp_r[2*k] = state->nosehoover_xi[k];
 942                             md->tmp_r[2*k+1] = state->nosehoover_vxi[k];
 943                         }
 944                     }
 945                     add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
 946
 947                     if (md->bMTTK) {
 948                         for(i=0; (i<md->nTCP); i++)
 949                         {
 950                             for (j=0;j<md->nNHC;j++)
 951                             {
 952                                 k = i*md->nNHC+j;
 953                                 md->tmp_r[2*k] = state->nhpres_xi[k];
 954                                 md->tmp_r[2*k+1] = state->nhpres_vxi[k];
 955                             }
 956                         }
 957                         add_ebin(md->ebin,md->itcb,md->mdeb_n,md->tmp_r,bSum);
 958                     }
 959                 }
 960                 else
 961                 {
 962                     for(i=0; (i<md->nTC); i++)
 963                     {
 964                         md->tmp_r[2*i] = state->nosehoover_xi[i];
 965                         md->tmp_r[2*i+1] = state->nosehoover_vxi[i];
 966                     }
 967                     add_ebin(md->ebin,md->itc,md->mde_n,md->tmp_r,bSum);
 968                 }
 969             }
 970         }
 971         else if (md->etc == etcBERENDSEN || md->etc == etcYES ||
 972                  md->etc == etcVRESCALE)
 973         {
 974             for(i=0; (i<md->nTC); i++)
 975             {
 976                 md->tmp_r[i] = ekind->tcstat[i].lambda;
 977             }
 978             add_ebin(md->ebin,md->itc,md->nTC,md->tmp_r,bSum);
 979         }
 980     }
 981
 982     if (ekind && md->nU > 1)
 983     {
 984         for(i=0; (i<md->nU); i++)
 985         {
 986             copy_rvec(ekind->grpstat[i].u,md->tmp_v[i]);
 987         }
 988         add_ebin(md->ebin,md->iu,3*md->nU,md->tmp_v[0],bSum);
 989     }
 990
 991     ebin_increase_count(md->ebin,bSum);
 992
 993     /* BAR + thermodynamic integration values */
 994     if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda > 0))
 995     {
 996         snew(dE,enerd->n_lambda-1);
 997         for(i=0; i<enerd->n_lambda-1; i++) {
 998             dE[i] = enerd->enerpart_lambda[i+1]-enerd->enerpart_lambda[0];  /* zero for simulated tempering */
 999             if (md->temperatures!=NULL)
1000             {
1001                 /* MRS: is this right, given the way we have defined the exchange probabilities? */
1002                 /* is this even useful to have at all? */
1003                 dE[i] += (md->temperatures[i]/md->temperatures[state->fep_state]-1.0)*enerd->term[F_EKIN];
1004             }
1005         }
1006     }
1007
1008     if (md->fp_dhdl && bDoDHDL)
1009     {
1010         fprintf(md->fp_dhdl,"%.4f",time);
1011         /* the current free energy state */
1012
1013         /* print the current state if we are doing expanded ensemble */
1014         if (expand->elmcmove > elmcmoveNO) {
1015             fprintf(md->fp_dhdl," %4d",state->fep_state);
1016         }
1017         /* total energy (for if the temperature changes */
1018         if (fep->bPrintEnergy)
1019         {
1020             store_energy = enerd->term[F_ETOT];
1021             fprintf(md->fp_dhdl," %#.8g",store_energy);
1022         }
1023
1024         for (i=0;i<efptNR;i++)
1025         {
1026             if (fep->separate_dvdl[i])
1027             {
1028                 fprintf(md->fp_dhdl," %#.8g",enerd->term[F_DVDL+i]); /* assumes F_DVDL is first */
1029             }
1030         }
1031         for(i=1; i<enerd->n_lambda; i++)
1032         {
1033             fprintf(md->fp_dhdl," %#.8g",dE[i-1]);
1034
1035         }
1036         if ((md->epc!=epcNO)  && (enerd->n_lambda > 0))
1037         {
1038             fprintf(md->fp_dhdl," %#.8g",pv);   /* PV term only needed when there are alternate state lambda */
1039         }
1040         fprintf(md->fp_dhdl,"\n");
1041         /* and the binary free energy output */
1042     }
1043     if (md->dhc && bDoDHDL)
1044     {
1045         int idhdl = 0;
1046         for (i=0;i<efptNR;i++)
1047         {
1048             if (fep->separate_dvdl[i])
1049             {
1050                 store_dhdl[idhdl] = enerd->term[F_DVDL+i]; /* assumes F_DVDL is first */
1051                 idhdl+=1;
1052             }
1053         }
1054         /* store_dh is dE */
1055         mde_delta_h_coll_add_dh(md->dhc,
1056                                 (double)state->fep_state,
1057                                 store_energy,
1058                                 pv,
1059                                 (expand->elamstats>elamstatsNO),
1060                                 (fep->bPrintEnergy),
1061                                 (md->epc!=epcNO),
1062                                 idhdl,
1063                                 fep->n_lambda,
1064                                 store_dhdl,
1065                                 dE,
1066                                 time);
1067     }
1068     if ((md->fp_dhdl || md->dhc) && bDoDHDL && (enerd->n_lambda >0))
1069     {
1070         sfree(dE);
1071     }
1072 }
1073
1074
1075 void upd_mdebin_step(t_mdebin *md)
1076 {
1077     ebin_increase_count(md->ebin,FALSE);
1078 }
1079
1080 static void npr(FILE *log,int n,char c)
1081 {
1082     for(; (n>0); n--) fprintf(log,"%c",c);
1083 }
1084
1085 static void pprint(FILE *log,const char *s,t_mdebin *md)
1086 {
1087     char CHAR='#';
1088     int  slen;
1089     char buf1[22],buf2[22];
1090
1091     slen = strlen(s);
1092     fprintf(log,"\t<======  ");
1093     npr(log,slen,CHAR);
1094     fprintf(log,"  ==>\n");
1095     fprintf(log,"\t<====  %s  ====>\n",s);
1096     fprintf(log,"\t<==  ");
1097     npr(log,slen,CHAR);
1098     fprintf(log,"  ======>\n\n");
1099
1100     fprintf(log,"\tStatistics over %s steps using %s frames\n",
1101             gmx_step_str(md->ebin->nsteps_sim,buf1),
1102             gmx_step_str(md->ebin->nsum_sim,buf2));
1103     fprintf(log,"\n");
1104 }
1105
1106 void print_ebin_header(FILE *log,gmx_large_int_t steps,double time,real lambda)
1107 {
1108     char buf[22];
1109
1110     fprintf(log,"   %12s   %12s   %12s\n"
1111             "   %12s   %12.5f   %12.5f\n\n",
1112             "Step","Time","Lambda",gmx_step_str(steps,buf),time,lambda);
1113 }
1114
1115 void print_ebin(ener_file_t fp_ene,gmx_bool bEne,gmx_bool bDR,gmx_bool bOR,
1116                 FILE *log,
1117                 gmx_large_int_t step,double time,
1118                 int mode,gmx_bool bCompact,
1119                 t_mdebin *md,t_fcdata *fcd,
1120                 gmx_groups_t *groups,t_grpopts *opts)
1121 {
1122     /*static char **grpnms=NULL;*/
1123     char        buf[246];
1124     int         i,j,n,ni,nj,ndr,nor,b;
1125     int         ndisre=0;
1126     real        *disre_rm3tav, *disre_rt;
1127
1128     /* these are for the old-style blocks (1 subblock, only reals), because
1129        there can be only one per ID for these */
1130     int         nr[enxNR];
1131     int         id[enxNR];
1132     real        *block[enxNR];
1133
1134     /* temporary arrays for the lambda values to write out */
1135     double      enxlambda_data[2];
1136
1137     t_enxframe  fr;
1138
1139     switch (mode)
1140     {
1141         case eprNORMAL:
1142             init_enxframe(&fr);
1143             fr.t            = time;
1144             fr.step         = step;
1145             fr.nsteps       = md->ebin->nsteps;
1146             fr.dt           = md->delta_t;
1147             fr.nsum         = md->ebin->nsum;
1148             fr.nre          = (bEne) ? md->ebin->nener : 0;
1149             fr.ener         = md->ebin->e;
1150             ndisre          = bDR ? fcd->disres.npair : 0;
1151             disre_rm3tav    = fcd->disres.rm3tav;
1152             disre_rt        = fcd->disres.rt;
1153             /* Optional additional old-style (real-only) blocks. */
1154             for(i=0; i<enxNR; i++)
1155             {
1156                 nr[i] = 0;
1157             }
1158             if (fcd->orires.nr > 0 && bOR)
1159             {
1160                 diagonalize_orires_tensors(&(fcd->orires));
1161                 nr[enxOR]     = fcd->orires.nr;
1162                 block[enxOR]  = fcd->orires.otav;
1163                 id[enxOR]     = enxOR;
1164                 nr[enxORI]    = (fcd->orires.oinsl != fcd->orires.otav) ?
1165                           fcd->orires.nr : 0;
1166                 block[enxORI] = fcd->orires.oinsl;
1167                 id[enxORI]    = enxORI;
1168                 nr[enxORT]    = fcd->orires.nex*12;
1169                 block[enxORT] = fcd->orires.eig;
1170                 id[enxORT]    = enxORT;
1171             }
1172
1173             /* whether we are going to wrte anything out: */
1174             if (fr.nre || ndisre || nr[enxOR] || nr[enxORI])
1175             {
1176
1177                 /* the old-style blocks go first */
1178                 fr.nblock = 0;
1179                 for(i=0; i<enxNR; i++)
1180                 {
1181                     if (nr[i] > 0)
1182                     {
1183                         fr.nblock = i + 1;
1184                     }
1185                 }
1186                 add_blocks_enxframe(&fr, fr.nblock);
1187                 for(b=0;b<fr.nblock;b++)
1188                 {
1189                     add_subblocks_enxblock(&(fr.block[b]), 1);
1190                     fr.block[b].id=id[b];
1191                     fr.block[b].sub[0].nr = nr[b];
1192 #ifndef GMX_DOUBLE
1193                     fr.block[b].sub[0].type = xdr_datatype_float;
1194                     fr.block[b].sub[0].fval = block[b];
1195 #else
1196                     fr.block[b].sub[0].type = xdr_datatype_double;
1197                     fr.block[b].sub[0].dval = block[b];
1198 #endif
1199                 }
1200
1201                 /* check for disre block & fill it. */
1202                 if (ndisre>0)
1203                 {
1204                     int db = fr.nblock;
1205                     fr.nblock+=1;
1206                     add_blocks_enxframe(&fr, fr.nblock);
1207
1208                     add_subblocks_enxblock(&(fr.block[db]), 2);
1209                     fr.block[db].id=enxDISRE;
1210                     fr.block[db].sub[0].nr=ndisre;
1211                     fr.block[db].sub[1].nr=ndisre;
1212 #ifndef GMX_DOUBLE
1213                     fr.block[db].sub[0].type=xdr_datatype_float;
1214                     fr.block[db].sub[1].type=xdr_datatype_float;
1215                     fr.block[db].sub[0].fval=disre_rt;
1216                     fr.block[db].sub[1].fval=disre_rm3tav;
1217 #else
1218                     fr.block[db].sub[0].type=xdr_datatype_double;
1219                     fr.block[db].sub[1].type=xdr_datatype_double;
1220                     fr.block[db].sub[0].dval=disre_rt;
1221                     fr.block[db].sub[1].dval=disre_rm3tav;
1222 #endif
1223                 }
1224                 /* here we can put new-style blocks */
1225
1226                 /* Free energy perturbation blocks */
1227                 if (md->dhc)
1228                 {
1229                     mde_delta_h_coll_handle_block(md->dhc, &fr, fr.nblock);
1230                 }
1231
1232                 /* we can now free & reset the data in the blocks */
1233                 if (md->dhc)
1234                 {
1235                     mde_delta_h_coll_reset(md->dhc);
1236                 }
1237
1238                 /* do the actual I/O */
1239                 do_enx(fp_ene,&fr);
1240                 gmx_fio_check_file_position(enx_file_pointer(fp_ene));
1241                 if (fr.nre)
1242                 {
1243                     /* We have stored the sums, so reset the sum history */
1244                     reset_ebin_sums(md->ebin);
1245                 }
1246             }
1247             free_enxframe(&fr);
1248             break;
1249         case eprAVER:
1250             if (log)
1251             {
1252                 pprint(log,"A V E R A G E S",md);
1253             }
1254             break;
1255         case eprRMS:
1256             if (log)
1257             {
1258                 pprint(log,"R M S - F L U C T U A T I O N S",md);
1259             }
1260             break;
1261         default:
1262             gmx_fatal(FARGS,"Invalid print mode (%d)",mode);
1263     }
1264
1265     if (log)
1266     {
1267         for(i=0;i<opts->ngtc;i++)
1268         {
1269             if(opts->annealing[i]!=eannNO)
1270             {
1271                 fprintf(log,"Current ref_t for group %s: %8.1f\n",
1272                         *(groups->grpname[groups->grps[egcTC].nm_ind[i]]),
1273                         opts->ref_t[i]);
1274             }
1275         }
1276         if (mode==eprNORMAL && fcd->orires.nr>0)
1277         {
1278             print_orires_log(log,&(fcd->orires));
1279         }
1280         fprintf(log,"   Energies (%s)\n",unit_energy);
1281         pr_ebin(log,md->ebin,md->ie,md->f_nre+md->nCrmsd,5,mode,TRUE);
1282         fprintf(log,"\n");
1283
1284         if (!bCompact)
1285         {
1286             if (md->bDynBox)
1287             {
1288                 pr_ebin(log,md->ebin,md->ib, md->bTricl ? NTRICLBOXS : NBOXS,5,
1289                         mode,TRUE);
1290                 fprintf(log,"\n");
1291             }
1292             if (md->bConstrVir)
1293             {
1294                 fprintf(log,"   Constraint Virial (%s)\n",unit_energy);
1295                 pr_ebin(log,md->ebin,md->isvir,9,3,mode,FALSE);
1296                 fprintf(log,"\n");
1297                 fprintf(log,"   Force Virial (%s)\n",unit_energy);
1298                 pr_ebin(log,md->ebin,md->ifvir,9,3,mode,FALSE);
1299                 fprintf(log,"\n");
1300             }
1301             if (md->bVir)
1302             {
1303                 fprintf(log,"   Total Virial (%s)\n",unit_energy);
1304                 pr_ebin(log,md->ebin,md->ivir,9,3,mode,FALSE);
1305                 fprintf(log,"\n");
1306             }
1307             if (md->bPress)
1308             {
1309                 fprintf(log,"   Pressure (%s)\n",unit_pres_bar);
1310                 pr_ebin(log,md->ebin,md->ipres,9,3,mode,FALSE);
1311                 fprintf(log,"\n");
1312             }
1313             if (md->bMu)
1314             {
1315                 fprintf(log,"   Total Dipole (%s)\n",unit_dipole_D);
1316                 pr_ebin(log,md->ebin,md->imu,3,3,mode,FALSE);
1317                 fprintf(log,"\n");
1318             }
1319
1320             if (md->nE > 1)
1321             {
1322                 if (md->print_grpnms==NULL)
1323                 {
1324                     snew(md->print_grpnms,md->nE);
1325                     n=0;
1326                     for(i=0; (i<md->nEg); i++)
1327                     {
1328                         ni=groups->grps[egcENER].nm_ind[i];
1329                         for(j=i; (j<md->nEg); j++)
1330                         {
1331                             nj=groups->grps[egcENER].nm_ind[j];
1332                             sprintf(buf,"%s-%s",*(groups->grpname[ni]),
1333                                     *(groups->grpname[nj]));
1334                             md->print_grpnms[n++]=strdup(buf);
1335                         }
1336                     }
1337                 }
1338                 sprintf(buf,"Epot (%s)",unit_energy);
1339                 fprintf(log,"%15s   ",buf);
1340                 for(i=0; (i<egNR); i++)
1341                 {
1342                     if (md->bEInd[i])
1343                     {
1344                         fprintf(log,"%12s   ",egrp_nm[i]);
1345                     }
1346                 }
1347                 fprintf(log,"\n");
1348                 for(i=0; (i<md->nE); i++)
1349                 {
1350                     fprintf(log,"%15s",md->print_grpnms[i]);
1351                     pr_ebin(log,md->ebin,md->igrp[i],md->nEc,md->nEc,mode,
1352                             FALSE);
1353                 }
1354                 fprintf(log,"\n");
1355             }
1356             if (md->nTC > 1)
1357             {
1358                 pr_ebin(log,md->ebin,md->itemp,md->nTC,4,mode,TRUE);
1359                 fprintf(log,"\n");
1360             }
1361             if (md->nU > 1)
1362             {
1363                 fprintf(log,"%15s   %12s   %12s   %12s\n",
1364                         "Group","Ux","Uy","Uz");
1365                 for(i=0; (i<md->nU); i++)
1366                 {
1367                     ni=groups->grps[egcACC].nm_ind[i];
1368                     fprintf(log,"%15s",*groups->grpname[ni]);
1369                     pr_ebin(log,md->ebin,md->iu+3*i,3,3,mode,FALSE);
1370                 }
1371                 fprintf(log,"\n");
1372             }
1373         }
1374     }
1375
1376 }
1377
1378 void update_energyhistory(energyhistory_t * enerhist,t_mdebin * mdebin)
1379 {
1380     int i;
1381
1382     enerhist->nsteps     = mdebin->ebin->nsteps;
1383     enerhist->nsum       = mdebin->ebin->nsum;
1384     enerhist->nsteps_sim = mdebin->ebin->nsteps_sim;
1385     enerhist->nsum_sim   = mdebin->ebin->nsum_sim;
1386     enerhist->nener      = mdebin->ebin->nener;
1387
1388     if (mdebin->ebin->nsum > 0)
1389     {
1390         /* Check if we need to allocate first */
1391         if(enerhist->ener_ave == NULL)
1392         {
1393             snew(enerhist->ener_ave,enerhist->nener);
1394             snew(enerhist->ener_sum,enerhist->nener);
1395         }
1396
1397         for(i=0;i<enerhist->nener;i++)
1398         {
1399             enerhist->ener_ave[i] = mdebin->ebin->e[i].eav;
1400             enerhist->ener_sum[i] = mdebin->ebin->e[i].esum;
1401         }
1402     }
1403
1404     if (mdebin->ebin->nsum_sim > 0)
1405     {
1406         /* Check if we need to allocate first */
1407         if(enerhist->ener_sum_sim == NULL)
1408         {
1409             snew(enerhist->ener_sum_sim,enerhist->nener);
1410         }
1411
1412         for(i=0;i<enerhist->nener;i++)
1413         {
1414             enerhist->ener_sum_sim[i] = mdebin->ebin->e_sim[i].esum;
1415         }
1416     }
1417     if (mdebin->dhc)
1418     {
1419         mde_delta_h_coll_update_energyhistory(mdebin->dhc, enerhist);
1420     }
1421 }
1422
1423 void restore_energyhistory_from_state(t_mdebin * mdebin,
1424                                       energyhistory_t * enerhist)
1425 {
1426     int i;
1427
1428     if ((enerhist->nsum > 0 || enerhist->nsum_sim > 0) &&
1429         mdebin->ebin->nener != enerhist->nener)
1430     {
1431         gmx_fatal(FARGS,"Mismatch between number of energies in run input (%d) and checkpoint file (%d).",
1432                   mdebin->ebin->nener,enerhist->nener);
1433     }
1434
1435     mdebin->ebin->nsteps     = enerhist->nsteps;
1436     mdebin->ebin->nsum       = enerhist->nsum;
1437     mdebin->ebin->nsteps_sim = enerhist->nsteps_sim;
1438     mdebin->ebin->nsum_sim   = enerhist->nsum_sim;
1439
1440     for(i=0; i<mdebin->ebin->nener; i++)
1441     {
1442         mdebin->ebin->e[i].eav  =
1443                   (enerhist->nsum > 0 ? enerhist->ener_ave[i] : 0);
1444         mdebin->ebin->e[i].esum =
1445                   (enerhist->nsum > 0 ? enerhist->ener_sum[i] : 0);
1446         mdebin->ebin->e_sim[i].esum =
1447                   (enerhist->nsum_sim > 0 ? enerhist->ener_sum_sim[i] : 0);
1448     }
1449     if (mdebin->dhc)
1450     {
1451         mde_delta_h_coll_restore_energyhistory(mdebin->dhc, enerhist);
1452     }
1453 }