Merge branch release-2016

Resolutions straightforward apart from the question about the
correctness of the gmx_wham fix in release-2016 branch.

Change-Id: I908a9a6d8f5767da49c3f00495beeec2a4f95ca7

diff --cc src/gromacs/commandline/cmdlinemodulemanager.cpp
Simple merge

diff --cc src/gromacs/domdec/domdec.cpp
Simple merge

diff --cc src/gromacs/gmxana/gmx_wham.cpp
index 9c34afabe15b8759b03568549616b0dea2c30155,b9beb58660fc564ac00671a024760a911c6780cd..e6205f23d4977f25c87ab136c8117c5d31382dba
--- 1/src/gromacs/gmxana/gmx_wham.cpp
--- 2/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@@ -2067,25 -2067,22 +2068,22 @@@ void read_tpr_header(const char *fn, t_
      }
  
      /* Read overall pull info */
-     header->npullcrds     = ir->pull->ncoord;
-     header->nCOMGrpsPullx = 0;
-     if (ir->pull->bPrintCOM)
-     {
-         header->nCOMGrpsPullx += ir->pull->ngroup;
-     }
 -    header->npullcrds      = ir.pull->ncoord;
 -    header->bPrintCOM      = ir.pull->bPrintCOM;
 -    header->bPrintRefValue = ir.pull->bPrintRefValue;
 -    header->bPrintComp     = ir.pull->bPrintComp;
++    header->npullcrds      = ir->pull->ncoord;
++    header->bPrintCOM      = ir->pull->bPrintCOM;
 +    header->bPrintRefValue = ir->pull->bPrintRefValue;
 +    header->bPrintComp     = ir->pull->bPrintComp;
  
      /* Read pull coordinates */
      snew(header->pcrd, header->npullcrds);
 -    for (i = 0; i < ir.pull->ncoord; i++)
 +    for (int i = 0; i < ir->pull->ncoord; i++)
      {
 -        header->pcrd[i].pull_type     = ir.pull->coord[i].eType;
 -        header->pcrd[i].geometry      = ir.pull->coord[i].eGeom;
 -        header->pcrd[i].ngroup        = ir.pull->coord[i].ngroup;
 -        header->pcrd[i].k             = ir.pull->coord[i].k;
 -        header->pcrd[i].init_dist     = ir.pull->coord[i].init;
 +        header->pcrd[i].pull_type     = ir->pull->coord[i].eType;
 +        header->pcrd[i].geometry      = ir->pull->coord[i].eGeom;
++        header->pcrd[i].ngroup        = ir->pull->coord[i].ngroup;
 +        header->pcrd[i].k             = ir->pull->coord[i].k;
 +        header->pcrd[i].init_dist     = ir->pull->coord[i].init;
  
 -        copy_ivec(ir.pull->coord[i].dim, header->pcrd[i].dim);
 +        copy_ivec(ir->pull->coord[i].dim, header->pcrd[i].dim);
          header->pcrd[i].ndim         = header->pcrd[i].dim[XX] + header->pcrd[i].dim[YY] + header->pcrd[i].dim[ZZ];
  
          std::strcpy(header->pcrd[i].coord_unit,
@@@ -2174,19 -2171,8 +2172,8 @@@
                     epullg_names[header->pcrd[i].geometry], header->pcrd[i].k, header->pcrd[i].init_dist,
                     int2YN(header->pcrd[i].dim[XX]), int2YN(header->pcrd[i].dim[YY]), int2YN(header->pcrd[i].dim[ZZ]),
                     header->pcrd[i].ndim, use ? "Yes" : "No");
-         }
-         switch (header->nCOMGrpsPullx)
-         {
-             case 0:
-                 printf("\tNo pull group coordinates expected in pullx files.\n");
-                 break;
-             case 1:
-                 printf("\tPull group coordinates of one group expected in pullx files.\n");
-                 break;
-             case 2:
-                 printf("\tPull group coordinates of two groups expected in pullx files.\n");
-                 break;
++            printf("\tPull group coordinates of %d groups expected in pullx files.\n", ir->pull->bPrintCOM ? header->pcrd[i].ngroup : 0);
          }
 -        printf("\tPull group coordinates of %d groups expected in pullx files.\n", ir.pull->bPrintCOM ? header->pcrd[i].ngroup : 0);
          printf("\tReference value of the coordinate%s expected in pullx files.\n",
                 header->bPrintRefValue ? "" : " not");
      }

diff --cc src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
Simple merge