Merged in changes from master branch

diff --cc include/edsam.h
Simple merge

diff --cc include/types/inputrec.h
Simple merge

diff --cc src/gmxlib/network.c
Simple merge

diff --cc src/gmxlib/tpxio.c
Simple merge

diff --cc src/gmxlib/txtdump.c
Simple merge

diff --cc src/kernel/md.c
index 0d24e026c2976860691eb4a138dfb36f7e86e1be,12ff94917f7645bd63798770218fd3d4678bc2a8..498caa673e114abf8af0764aadfd7f33d69710b8
--- 1/src/kernel/md.c
--- 2/src/kernel/md.c
+++ b/src/kernel/md.c
@@@ -511,18 -662,12 +663,18 @@@ int mdrunner(FILE *fplog,t_commrec *cr,
          if (inputrec->ePull != epullNO)
          {
              /* Initialize pull code */
-             init_pull(fplog,inputrec,nfile,fnm,mtop,cr,
+             init_pull(fplog,inputrec,nfile,fnm,mtop,cr,oenv,
                        EI_DYNAMICS(inputrec->eI) && MASTER(cr),Flags);
          }
 +        
 +        if (inputrec->bRot)
 +        {
 +           /* Initialize enforced rotation code */
 +           init_rot(fplog,inputrec,cr,box,state->x,Flags);
 +        }
  
          constr = init_constraints(fplog,mtop,inputrec,ed,state,cr);
-         
+ 
          if (DOMAINDECOMP(cr))
          {
              dd_init_bondeds(fplog,cr->dd,mtop,vsite,constr,inputrec,

diff --cc src/kernel/readir.c
Simple merge

diff --cc src/kernel/readir.h
Simple merge

diff --cc src/mdlib/domdec.c
Simple merge

diff --cc src/mdlib/edsam.c
index e74ead1d7dec73dfa7638bf1153d95637f088259,a608e73344c63931387ffb13efb7f0ed57ced3e4..65ac93dbf3998f920e7a936608ccd139dd19ec22
--- 1/src/mdlib/edsam.c
--- 2/src/mdlib/edsam.c
+++ b/src/mdlib/edsam.c
@@@ -422,9 -428,10 +428,9 @@@ static void dump_edi(t_edpar *edpars, t
      dump_edi_eigenvecs(out, &edpars->flood.vecs, "FLOODING"  , edpars->sav.nr);
  
      /* Dump ed local buffer */
-     fprintf(out, "buf->do_edfit         =%p\n", edpars->buf->do_edfit         );
-     fprintf(out, "buf->do_edsam         =%p\n", edpars->buf->do_edsam         );
-     fprintf(out, "buf->do_radcon        =%p\n", edpars->buf->do_radcon        );
 -    /*fprintf(out, "buf->fitit            =%p\n", (void*)edpars->buf->fitit );*/
+     fprintf(out, "buf->do_edfit         =%p\n", (void*)edpars->buf->do_edfit  );
+     fprintf(out, "buf->do_edsam         =%p\n", (void*)edpars->buf->do_edsam  );
+     fprintf(out, "buf->do_radcon        =%p\n", (void*)edpars->buf->do_radcon );
  
      ffclose(out);
  }

diff --cc src/mdlib/gmx_wallcycle.c
Simple merge

diff --cc src/mdlib/mdebin.c
index 67aa2457826ec5d2e0fe02cbc72b5660ec44e63c,66981340d48e1518ea31334597e4f25f3ad6797b..ea3e20f9a917b2a9dcab9ef853b41bc8422c5206
--- 1/src/mdlib/mdebin.c
--- 2/src/mdlib/mdebin.c
+++ b/src/mdlib/mdebin.c
@@@ -135,79 -130,88 +130,88 @@@ t_mdebin *init_mdebin(ener_file_t fp_en
  
    ncon = gmx_mtop_ftype_count(mtop,F_CONSTR);
    nset = gmx_mtop_ftype_count(mtop,F_SETTLE);
-   bConstr    = (ncon > 0 || nset > 0);
-   bConstrVir = FALSE;
-   if (bConstr) {
+   md->bConstr    = (ncon > 0 || nset > 0);
+   md->bConstrVir = FALSE;
+   if (md->bConstr) {
      if (ncon > 0 && ir->eConstrAlg == econtLINCS) {
        if (ir->eI == eiSD2)
-       nCrmsd = 2;
+       md->nCrmsd = 2;
        else
-       nCrmsd = 1;
+       md->nCrmsd = 1;
      }
-     bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
+     md->bConstrVir = (getenv("GMX_CONSTRAINTVIR") != NULL);
    } else {
-     nCrmsd = 0;
+     md->nCrmsd = 0;
    }
  
+   /* Energy monitoring */
+   for(i=0;i<egNR;i++)
+   {
+     md->bEInd[i]=FALSE;
+   }
+ 
+ 
    for(i=0; i<F_NRE; i++) {
-     bEner[i] = FALSE;
+     md->bEner[i] = FALSE;
      if (i == F_LJ)
-       bEner[i] = !bBHAM;
+       md->bEner[i] = !bBHAM;
      else if (i == F_BHAM)
-       bEner[i] = bBHAM;
+       md->bEner[i] = bBHAM;
      else if (i == F_EQM)
-       bEner[i] = ir->bQMMM;
+       md->bEner[i] = ir->bQMMM;
      else if (i == F_COUL_LR)
-       bEner[i] = (ir->rcoulomb > ir->rlist);
+       md->bEner[i] = (ir->rcoulomb > ir->rlist);
      else if (i == F_LJ_LR)
-       bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
+       md->bEner[i] = (!bBHAM && ir->rvdw > ir->rlist);
      else if (i == F_BHAM_LR)
-       bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
+       md->bEner[i] = (bBHAM && ir->rvdw > ir->rlist);
      else if (i == F_RF_EXCL)
-       bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
+       md->bEner[i] = (EEL_RF(ir->coulombtype) && ir->coulombtype != eelRF_NEC);
      else if (i == F_COUL_RECIP)
-       bEner[i] = EEL_FULL(ir->coulombtype);
+       md->bEner[i] = EEL_FULL(ir->coulombtype);
      else if (i == F_LJ14)
-       bEner[i] = b14;
+       md->bEner[i] = b14;
      else if (i == F_COUL14)
-       bEner[i] = b14;
+       md->bEner[i] = b14;
      else if (i == F_LJC14_Q || i == F_LJC_PAIRS_NB)
-       bEner[i] = FALSE;
+       md->bEner[i] = FALSE;
      else if ((i == F_DVDL) || (i == F_DKDL))
-       bEner[i] = (ir->efep != efepNO);
+       md->bEner[i] = (ir->efep != efepNO);
      else if (i == F_DHDL_CON)
-       bEner[i] = (ir->efep != efepNO && bConstr);
+       md->bEner[i] = (ir->efep != efepNO && md->bConstr);
      else if ((interaction_function[i].flags & IF_VSITE) ||
             (i == F_CONSTR) || (i == F_CONSTRNC) || (i == F_SETTLE))
-       bEner[i] = FALSE;
+       md->bEner[i] = FALSE;
      else if ((i == F_COUL_SR) || (i == F_EPOT) || (i == F_PRES)  || (i==F_EQM))
-       bEner[i] = TRUE;
+       md->bEner[i] = TRUE;
      else if ((i == F_ETOT) || (i == F_EKIN) || (i == F_TEMP))
-       bEner[i] = EI_DYNAMICS(ir->eI);
+       md->bEner[i] = EI_DYNAMICS(ir->eI);
      else if (i == F_DISPCORR || i == F_PDISPCORR)
-       bEner[i] = (ir->eDispCorr != edispcNO);
+       md->bEner[i] = (ir->eDispCorr != edispcNO);
      else if (i == F_DISRESVIOL)
-       bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
+       md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_DISRES) > 0);
      else if (i == F_ORIRESDEV)
-       bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
+       md->bEner[i] = (gmx_mtop_ftype_count(mtop,F_ORIRES) > 0);
      else if (i == F_CONNBONDS)
-       bEner[i] = FALSE;
+       md->bEner[i] = FALSE;
      else if (i == F_COM_PULL)
-       bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
 -      md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F);
++      md->bEner[i] = (ir->ePull == epullUMBRELLA || ir->ePull == epullCONST_F || ir->bRot);
      else if (i == F_ECONSERVED)
-       bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
+       md->bEner[i] = ((ir->etc == etcNOSEHOOVER || ir->etc == etcVRESCALE) &&
                  ir->epc == epcNO);
      else
-       bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
+       md->bEner[i] = (gmx_mtop_ftype_count(mtop,i) > 0);
    }
  
+     md->f_nre=0;
      for(i=0; i<F_NRE; i++)
      {
-         if (bEner[i])
+         if (md->bEner[i])
          {
              /* FIXME: The constness should not be cast away */
-             ener_nm[f_nre]=(char *)interaction_function[i].longname;
-             f_nre++;
+             /*ener_nm[f_nre]=(char *)interaction_function[i].longname;*/
+             ener_nm[md->f_nre]=interaction_function[i].longname;
+             md->f_nre++;
          }
      }
  

diff --cc src/mdlib/sim_util.c
Simple merge