Merge branch release-2016

Minor clashes mostly from nullptr and logger introduction in master
branch. Resolved all in favour of release-2016 logic implemented with
in master-branch functionality.

Change-Id: Ic30ce3b3aadaab6e74f6d9606ca00fb275a6ccb3

diff --cc cmake/gmxVersionInfo.cmake
Simple merge

diff --cc docs/CMakeLists.txt
Simple merge

diff --cc src/gromacs/gmxana/gmx_order.cpp
Simple merge

diff --cc src/gromacs/gmxana/gmx_rmsf.cpp
index 9c3989a279ecb0018b11368faa684bb3e9a8234d,8b5118003ef44f5e39f94c28a23a6537b2a144bc..6c78ce216500c5b78ca063bbe0e77bbef84ee738
--- 1/src/gromacs/gmxana/gmx_rmsf.cpp
--- 2/src/gromacs/gmxana/gmx_rmsf.cpp
+++ b/src/gromacs/gmxana/gmx_rmsf.cpp
@@@ -321,10 -316,12 +321,12 @@@ int gmx_rmsf(int argc, char *argv[]
          t_topology *top_pdb;
          snew(top_pdb, 1);
          /* Read coordinates twice */
 -        read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, NULL, NULL, NULL, pdbbox, FALSE);
 +        read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, nullptr, nullptr, nullptr, pdbbox, FALSE);
          snew(pdbatoms, 1);
          *pdbatoms = top_pdb->atoms;
 -        read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, NULL, &pdbx, NULL, pdbbox, FALSE);
 +        read_tps_conf(opt2fn("-q", NFILE, fnm), top_pdb, nullptr, &pdbx, nullptr, pdbbox, FALSE);
+         /* TODO Should this assert that top_pdb->atoms.nr == top.atoms.nr?
+          * See discussion at https://gerrit.gromacs.org/#/c/6430/1 */
          title = *top_pdb->name;
          snew(refatoms, 1);
          *refatoms = top_pdb->atoms;
@@@ -554,10 -550,10 +556,10 @@@
          /* Write a .pdb file with B-factors and optionally anisou records */
          for (i = 0; i < isize; i++)
          {
-             rvec_inc(xref[index[i]], xcm);
+             rvec_inc(pdbx[index[i]], xcm);
          }
          write_sto_conf_indexed(opt2fn("-oq", NFILE, fnm), title, pdbatoms, pdbx,
 -                               NULL, ePBC, pdbbox, isize, index);
 +                               nullptr, ePBC, pdbbox, isize, index);
      }
      if (opt2bSet("-ox", NFILE, fnm))
      {
@@@ -570,8 -567,9 +573,9 @@@
              }
          }
          /* Write a .pdb file with B-factors and optionally anisou records */
-         write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, xref, nullptr,
 -        write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, NULL,
++        write_sto_conf_indexed(opt2fn("-ox", NFILE, fnm), title, pdbatoms, bFactorX, nullptr,
                                 ePBC, pdbbox, isize, index);
+         sfree(bFactorX);
      }
      if (bAniso)
      {

diff --cc src/gromacs/gmxpreprocess/grompp.cpp
index 250a1597171eec796b6f3b27a874c10665bb5d68,be33e421c5067827141f017865d26577ec79a0bd..3f0ca7d84de24d890f48a38c033c6d2991f067e8
--- 1/src/gromacs/gmxpreprocess/grompp.cpp
--- 2/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@@ -74,9 -73,9 +74,10 @@@
  #include "gromacs/math/vec.h"
  #include "gromacs/mdlib/calc_verletbuf.h"
  #include "gromacs/mdlib/compute_io.h"
+ #include "gromacs/mdlib/constr.h"
  #include "gromacs/mdlib/genborn.h"
  #include "gromacs/mdlib/perf_est.h"
 +#include "gromacs/mdrunutility/mdmodules.h"
  #include "gromacs/mdtypes/inputrec.h"
  #include "gromacs/mdtypes/md_enums.h"
  #include "gromacs/mdtypes/nblist.h"

diff --cc src/gromacs/gmxpreprocess/insert-molecules.cpp
Simple merge

diff --cc src/gromacs/gmxpreprocess/solvate.cpp
Simple merge

diff --cc src/gromacs/gmxpreprocess/toppush.cpp
Simple merge

diff --cc src/gromacs/mdlib/md_support.cpp
Simple merge

diff --cc src/gromacs/mdlib/md_support.h
index f2f904b2bd5af1f87279a29f7a40d2336ccbc334,b2b8b25b8ce5b6e39f3f0ba71c09f4282c1a9429..0ad1879c35c65c7f4294dc69a34c70347ae834e8
--- 1/src/gromacs/mdlib/md_support.h
--- 2/src/gromacs/mdlib/md_support.h
+++ b/src/gromacs/mdlib/md_support.h
@@@ -102,8 -110,12 +102,8 @@@ bool multisim_int_all_are_equal(const g
                                  gmx_int64_t           value);
  
  void rerun_parallel_comm(t_commrec *cr, t_trxframe *fr,
-                          gmx_bool *bNotLastFrame);
+                          gmx_bool *bLastStep);
  
 -/* get the conserved energy associated with the ensemble type*/
 -real compute_conserved_from_auxiliary(t_inputrec *ir, t_state *state,
 -                                      t_extmass *MassQ);
 -
  /* set the lambda values at each step of mdrun when they change */
  void set_current_lambdas(gmx_int64_t step, t_lambda *fepvals, gmx_bool bRerunMD,
                           t_trxframe *rerun_fr, t_state *state_global, t_state *state, double lam0[]);

diff --cc src/gromacs/mdlib/sim_util.cpp
index 555678cd89f43510a467629d3bc4b596b869f734,11a2f4faca27b4d98738f9e080265ddcf56d05d3..d58b58a8947ba94b1453614fe281a8beb5bed947
--- 1/src/gromacs/mdlib/sim_util.cpp
--- 2/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@@ -106,6 -103,6 +106,7 @@@
  #include "gromacs/utility/fatalerror.h"
  #include "gromacs/utility/gmxassert.h"
  #include "gromacs/utility/gmxmpi.h"
++#include "gromacs/utility/logger.h"
  #include "gromacs/utility/pleasecite.h"
  #include "gromacs/utility/smalloc.h"
  #include "gromacs/utility/sysinfo.h"
@@@ -2481,6 -2575,13 +2482,12 @@@ void finish_run(FILE *fplog, const gmx:
              elapsed_time_over_all_threads,
              elapsed_time_over_all_threads_over_all_ranks;
  
 -        md_print_warn(cr, fplog,
 -                      "Simulation ended prematurely, no performance report will be written.");
+     if (!walltime_accounting_get_valid_finish(walltime_accounting))
+     {
++        GMX_LOG(mdlog.warning).asParagraph().appendText("Simulation ended prematurely, no performance report will be written.");
+         return;
+     }
+ 
      if (cr->nnodes > 1)
      {
          snew(nrnb_tot, 1);

diff --cc src/gromacs/timing/walltime_accounting.cpp
Simple merge

diff --cc src/gromacs/utility/arrayref.h
Simple merge

diff --cc src/programs/mdrun/md.cpp
Simple merge