Merge branch 'master' into rotation

Conflicts:
	src/gmxlib/tpxio.c
	src/kernel/runner.c

diff --cc include/mpelogging.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
index 8d7b94dc194a9e23dd0dc1892f9ff872b3d12a11,19c5194752c6d96c4867ff7f2fefc4d6af16bd72..c6e46cd7c2e191ac32bfcbcb5452c85888964396
--- 1/src/gmxlib/tpxio.c
--- 2/src/gmxlib/tpxio.c
+++ b/src/gmxlib/tpxio.c
@@@ -242,48 -244,11 +244,50 @@@ static void do_pull(t_fileio *fio, t_pu
    if (bRead)
      snew(pull->grp,pull->ngrp+1);
    for(g=0; g<pull->ngrp+1; g++)
-     do_pullgrp(&pull->grp[g],bRead,file_version);
+     do_pullgrp(fio,&pull->grp[g],bRead,file_version);
  }
  
- static void do_rotgrp(t_rotgrp *rotg,bool bRead, int file_version)
++
++static void do_rotgrp(t_fileio *fio, t_rotgrp *rotg,bool bRead, int file_version)
 +{
 +  bool bDum=TRUE;
 +  int  i;
 +
-   do_int(rotg->eType);
-   do_int(rotg->bMassW);
-   do_int(rotg->nat);
++  gmx_fio_do_int(fio,rotg->eType);
++  gmx_fio_do_int(fio,rotg->bMassW);
++  gmx_fio_do_int(fio,rotg->nat);
 +  if (bRead)
 +    snew(rotg->ind,rotg->nat);
-   ndo_int(rotg->ind,rotg->nat,bDum);
++  gmx_fio_ndo_int(fio,rotg->ind,rotg->nat);
 +  if (bRead)
 +      snew(rotg->x_ref,rotg->nat);
-   ndo_rvec(rotg->x_ref,rotg->nat);
-   do_rvec(rotg->vec);
-   do_rvec(rotg->pivot);
-   do_real(rotg->rate);
-   do_real(rotg->k);
-   do_real(rotg->slab_dist);
-   do_real(rotg->min_gaussian);
-   do_real(rotg->eps);
-   do_int(rotg->eFittype);
++  gmx_fio_ndo_rvec(fio,rotg->x_ref,rotg->nat);
++  gmx_fio_do_rvec(fio,rotg->vec);
++  gmx_fio_do_rvec(fio,rotg->pivot);
++  gmx_fio_do_real(fio,rotg->rate);
++  gmx_fio_do_real(fio,rotg->k);
++  gmx_fio_do_real(fio,rotg->slab_dist);
++  gmx_fio_do_real(fio,rotg->min_gaussian);
++  gmx_fio_do_real(fio,rotg->eps);
++  gmx_fio_do_int(fio,rotg->eFittype);
 +}
 +
- static void do_rot(t_rot *rot,bool bRead, int file_version)
++static void do_rot(t_fileio *fio, t_rot *rot,bool bRead, int file_version)
 +{
 +  int g;
 +
-   do_int(rot->ngrp);
-   do_int(rot->nstrout);
-   do_int(rot->nsttout);
++  gmx_fio_do_int(fio,rot->ngrp);
++  gmx_fio_do_int(fio,rot->nstrout);
++  gmx_fio_do_int(fio,rot->nsttout);
 +  if (bRead)
 +    snew(rot->grp,rot->ngrp);
 +  for(g=0; g<rot->ngrp; g++)
-     do_rotgrp(&rot->grp[g],bRead,file_version);
++    do_rotgrp(fio, &rot->grp[g],bRead,file_version);
 +}
 +
- static void do_inputrec(t_inputrec *ir,bool bRead, int file_version,
-                       real *fudgeQQ)
++
+ static void do_inputrec(t_fileio *fio, t_inputrec *ir,bool bRead, 
+                         int file_version, real *fudgeQQ)
  {
    int  i,j,k,*tmp,idum=0; 
    bool bDum=TRUE;
@@@ -710,22 -675,10 +714,22 @@@
        ir->ePull = epullNO;
      }
      
-         do_int(ir->bRot);
 +    /* Enforced rotation */
 +    if (file_version >= 71) {
-             do_rot(ir->rot,bRead,file_version);
++        gmx_fio_do_int(fio,ir->bRot);
 +        if (ir->bRot == TRUE) {
 +            if (bRead)
 +                snew(ir->rot,1);
++            do_rot(fio, ir->rot,bRead,file_version);
 +        }
 +    } else {
 +        ir->bRot = FALSE;
 +    }
 +    
      /* grpopts stuff */
-     do_int(ir->opts.ngtc); 
+     gmx_fio_do_int(fio,ir->opts.ngtc); 
      if (file_version >= 69) {
-       do_int(ir->opts.nhchainlength);
+       gmx_fio_do_int(fio,ir->opts.nhchainlength);
      } else {
        ir->opts.nhchainlength = 1;
      }

diff --cc src/kernel/Makefile.am
Simple merge

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

diff --cc src/kernel/mdrun.c
index 712dca246f0c197fb8b5283edbb31b350b41ea58,b0bc626f5daf6fe2522fb85e8fb1f77e012068f2..fda1b044612f1a1929bde994dac23930872d2b60
--- 1/src/kernel/mdrun.c
--- 2/src/kernel/mdrun.c
+++ b/src/kernel/mdrun.c
@@@ -363,13 -370,8 +370,12 @@@ int main(int argc,char *argv[]
      { efXVG, "-runav",  "runaver",  ffOPTWR },
      { efXVG, "-px",     "pullx",    ffOPTWR },
      { efXVG, "-pf",     "pullf",    ffOPTWR },
 +    { efXVG, "-ro",     "rotation", ffOPTWR },
 +    { efLOG, "-ra",     "rotangles",ffOPTWR },
 +    { efLOG, "-rs",     "rotslabs", ffOPTWR },
 +    { efLOG, "-rt",     "rottorque",ffOPTWR },
      { efMTX, "-mtx",    "nm",       ffOPTWR },
      { efNDX, "-dn",     "dipole",   ffOPTWR }
- #endif
    };
  #define NFILE asize(fnm)
  

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

diff --cc src/kernel/runner.c
index 7292b1d399a76a1f73deef110212828f16158b93,bfa2536fdd2fc15a3b9871b4aa256853204b9a5c..073cc26c8f1ed39e023d4417d477524b7184f102
--- 1/src/kernel/runner.c
--- 2/src/kernel/runner.c
+++ b/src/kernel/runner.c
@@@ -69,8 -69,10 +69,10 @@@
  #include "mvdata.h"
  #include "checkpoint.h"
  #include "mtop_util.h"
- #include "pull_rotation.h"
  #include "sighandler.h"
 -
+ #include "tpxio.h"
+ #include "txtdump.h"
++#include "pull_rotation.h"
  #include "md_openmm.h"
  
  #ifdef GMX_LIB_MPI

diff --cc src/mdlib/Makefile.am
Simple merge

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

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

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

diff --cc src/tools/gmx_tune_pme.c
Simple merge