Merge release-5-0 into master

Conflicts:
	src/contrib/pmetest.c
	src/gromacs/gmxpreprocess/pdb2top.cpp
	src/programs/mdrun/repl_ex.cpp

Fixed minor issues in:
	src/gromacs/gmxana/gmx_principal.c
	src/gromacs/gmxlib/checkpoint.cpp
	src/gromacs/gmxlib/nonbonded/nb_free_energy.c
	src/gromacs/mdlib/shellfc.c

Change-Id: Idbd2ef28223f8a868ca313f9702c8e6890e6ddc1

diff --cc CMakeLists.txt
Simple merge

diff --cc cmake/gmxCFlags.cmake
Simple merge

diff --cc manual/monster.bib
Simple merge

diff --cc src/gromacs/CMakeLists.txt
Simple merge

diff --cc src/gromacs/fileio/libxdrf.c
Simple merge

diff --cc src/gromacs/fileio/pdbio.c
Simple merge

diff --cc src/gromacs/fileio/pdbio.h
index a8f41a62b384d3a9fb7275fa5fcf05ba25ce974a,ab53be32925cc2863acbc36776a5e02db3e4213f..241239a8a6aa27039b43b75b254f9682d9a45a9e
--- 1/src/gromacs/fileio/pdbio.h
--- 2/src/gromacs/fileio/pdbio.h
+++ b/src/gromacs/fileio/pdbio.h
@@@ -46,16 -47,8 +46,12 @@@
  extern "C" {
  #endif
  
 +struct gmx_atomprop;
 +struct t_atoms;
 +struct t_topology;
 +
  typedef struct gmx_conect_t *gmx_conect;
  
- /* THE pdb format (for ATOM/HETATOM lines) */
- const char* get_pdbformat(void);
- const char* get_pdbformat4(void);
- 
  /* Enumerated type for pdb records. The other entries are ignored
   * when reading a pdb file
   */

diff --cc src/gromacs/fileio/tngio.cpp
Simple merge

diff --cc src/gromacs/fileio/tpxio.c
Simple merge

diff --cc src/gromacs/fileio/trx.h
Simple merge

diff --cc src/gromacs/fileio/trxio.c
Simple merge

diff --cc src/gromacs/gmxana/anadih.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_anaeig.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_analyze.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_angle.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_chi.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_cluster.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_density.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_dos.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_editconf.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_enemat.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_energy.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_genpr.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_mdmat.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_mindist.c
index c13e907598c98bf30bd0796a7bf1a2b901ae70fd,8fbb7d3712a6b426e4743d5e5b8adebadf2677dd..6897befaa0437f0852e6772de446896d645f0e96
--- 1/src/gromacs/gmxana/gmx_mindist.c
--- 2/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@@ -45,31 -46,47 +45,48 @@@
  #include "typedefs.h"
  #include "gromacs/utility/smalloc.h"
  #include "macros.h"
 -#include "vec.h"
 -#include "xvgr.h"
 -#include "pbc.h"
 -#include "gromacs/fileio/futil.h"
 +#include "gromacs/math/vec.h"
 +#include "gromacs/fileio/xvgr.h"
 +#include "viewit.h"
 +#include "gromacs/pbcutil/pbc.h"
 +#include "gromacs/utility/futil.h"
  #include "gromacs/commandline/pargs.h"
 -#include "index.h"
 +#include "gromacs/topology/index.h"
  #include "gromacs/fileio/tpxio.h"
  #include "gromacs/fileio/trxio.h"
 -#include "rmpbc.h"
 +#include "gromacs/pbcutil/rmpbc.h"
  #include "gmx_ana.h"
+ #include "names.h"
  
  
- static void periodic_dist(matrix box, rvec x[], int n, atom_id index[],
+ static void periodic_dist(int ePBC,
+                           matrix box, rvec x[], int n, atom_id index[],
                            real *rmin, real *rmax, int *min_ind)
  {
- #define NSHIFT 26
-     int  sx, sy, sz, i, j, s;
+ #define NSHIFT_MAX 26
+     int  nsz, nshift, sx, sy, sz, i, j, s;
      real sqr_box, r2min, r2max, r2;
-     rvec shift[NSHIFT], d0, d;
+     rvec shift[NSHIFT_MAX], d0, d;
  
-     sqr_box = sqr(min(norm(box[XX]), min(norm(box[YY]), norm(box[ZZ]))));
+     sqr_box = min(norm2(box[XX]), norm2(box[YY]));
+     if (ePBC == epbcXYZ)
+     {
+         sqr_box = min(sqr_box, norm2(box[ZZ]));
+         nsz     = 1;
+     }
+     else if (ePBC == epbcXY)
+     {
+         nsz = 0;
+     }
+     else
+     {
+         gmx_fatal(FARGS, "pbc = %s is not supported by g_mindist",
+                   epbc_names[ePBC]);
+         nsz = 0; /* Keep compilers quiet */
+     }
  
-     s = 0;
-     for (sz = -1; sz <= 1; sz++)
+     nshift = 0;
+     for (sz = -nsz; sz <= nsz; sz++)
      {
          for (sy = -1; sy <= 1; sy++)
          {

diff --cc src/gromacs/gmxana/gmx_polystat.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_principal.c
index 8e9a2d46299b51c0cb7271d092e2121fc17422ec,2e668f05f11f2cb0f6a112c228515c037b624817..b0ee02ca013400f53eb043bf160b85f59102d8b9
--- 1/src/gromacs/gmxana/gmx_principal.c
--- 2/src/gromacs/gmxana/gmx_principal.c
+++ b/src/gromacs/gmxana/gmx_principal.c
@@@ -53,6 -57,6 +53,7 @@@
  #include "txtdump.h"
  #include "gromacs/fileio/tpxio.h"
  #include "gromacs/fileio/trxio.h"
++#include "gromacs/fileio/xvgr.h"
  #include "gstat.h"
  #include "gmx_ana.h"
  

diff --cc src/gromacs/gmxana/gmx_rama.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_rms.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_tcaf.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_traj.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_trjconv.c
Simple merge

diff --cc src/gromacs/gmxana/gmx_vanhove.c
Simple merge

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

diff --cc src/gromacs/gmxlib/bondfree.c
Simple merge

diff --cc src/gromacs/gmxlib/checkpoint.cpp
index 5cb9a23cdc827fc8abe7417e04b0969fb62f47ce,825a8968dad1cbb59ef6e5b94ce8b750b8019395..05edae309621284e92bdac2e981c4e7284c056b0
--- 1/src/gromacs/gmxlib/checkpoint.cpp
--- 2/src/gromacs/gmxlib/checkpoint.c
+++ b/src/gromacs/gmxlib/checkpoint.cpp
@@@ -1780,11 -1789,26 +1780,26 @@@ static void check_match(FILE *fplog
                          ivec dd_nc, ivec dd_nc_f)
  {
      int      npp;
-     gmx_bool mm;
- 
-     mm = FALSE;
+     gmx_bool mm                 = FALSE;
+     gmx_bool patchlevel_differs = FALSE;
+     gmx_bool version_differs    = FALSE;
  
      check_string(fplog, "Version", gmx_version(), version, &mm);
 -        sscanf(gmx_version(), "VERSION %d.%d", &gmx_major, &gmx_minor);
 -        sscanf(version, "VERSION %d.%d", &cpt_major, &cpt_minor);
+     patchlevel_differs = mm;
+ 
+     if (patchlevel_differs)
+     {
+         /* Gromacs should be able to continue from checkpoints between
+          * different patch level versions, but we do not guarantee
+          * compatibility between different major/minor versions - check this.
+          */
+         int   gmx_major, gmx_minor;
+         int   cpt_major, cpt_minor;
++        sscanf(gmx_version(), "VERSION %5d.%5d", &gmx_major, &gmx_minor);
++        sscanf(version, "VERSION %5d.%5d", &cpt_major, &cpt_minor);
+         version_differs = (gmx_major != cpt_major || gmx_minor != cpt_minor);
+     }
+ 
      check_string(fplog, "Build time", BUILD_TIME, btime, &mm);
      check_string(fplog, "Build user", BUILD_USER, buser, &mm);
      check_string(fplog, "Build host", BUILD_HOST, bhost, &mm);

diff --cc src/gromacs/gmxlib/nonbonded/nb_free_energy.c
index 5414c668c6936a22a2238e2a079fba88c91e34ae,058b2a87eb2df4fae11ecc0e39fbded877bb2803..bba7805fb74a88edb74174ec5c280092130a7797
--- 1/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
--- 2/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
@@@ -164,7 -175,7 +175,6 @@@ gmx_nb_free_energy_kernel(const t_nblis
      bDoPotential        = kernel_data->flags & GMX_NONBONDED_DO_POTENTIAL;
  
      rcoulomb            = fr->rcoulomb;
--    sh_ewald            = fr->ic->sh_ewald;
      rvdw                = fr->rvdw;
      sh_invrc6           = fr->ic->sh_invrc6;
  

diff --cc src/gromacs/gmxlib/nonbonded/nb_generic.c
Simple merge

diff --cc src/gromacs/gmxlib/nonbonded/nonbonded.c
Simple merge

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

diff --cc src/gromacs/gmxpreprocess/addconf.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/grompp.c
index 2eef5b7b63baf691e67e63330d927c7fda4ff653,04ee47de4053d37c9ffca49f81165448a4312224..1aab6bf4eafd20121076baa7e910c71554bf55db
--- 1/src/gromacs/gmxpreprocess/grompp.c
--- 2/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@@ -79,14 -86,8 +79,15 @@@
  #include "calc_verletbuf.h"
  #include "tomorse.h"
  #include "gromacs/imd/imd.h"
+ #include "gromacs/utility/cstringutil.h"
  
 +#include "gromacs/commandline/pargs.h"
 +#include "gromacs/pbcutil/pbc.h"
 +#include "gromacs/random/random.h"
 +#include "gromacs/topology/symtab.h"
 +#include "gromacs/topology/topology.h"
 +#include "gromacs/utility/fatalerror.h"
 +#include "gromacs/utility/smalloc.h"
  
  static int rm_interactions(int ifunc, int nrmols, t_molinfo mols[])
  {

diff --cc src/gromacs/gmxpreprocess/hackblock.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/pdb2gmx.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/pdb2top.cpp
index 9a688ce2dbe8ea6b08a96e181a8f7f5701bcb2fd,befb6a6a7ff01f3a912d874a5893680b7dbbf242..7b08b863c42bc69caf7e78d21223ceba7401bb0b
--- 1/src/gromacs/gmxpreprocess/pdb2top.cpp
--- 2/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@@ -441,8 -442,8 +441,8 @@@ void choose_watermodel(const char *wmse
      sfree(model);
  }
  
- static int name2type(t_atoms *at, int **cgnr, gpp_atomtype_t atype,
+ static int name2type(t_atoms *at, int **cgnr,
 -                     t_restp restp[], gmx_residuetype_t rt)
 +                     t_restp restp[], gmx_residuetype_t *rt)
  {
      int         i, j, prevresind, resind, i0, prevcg, cg, curcg;
      char       *name;

diff --cc src/gromacs/gmxpreprocess/readir.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/readpull.c
Simple merge

diff --cc src/gromacs/gmxpreprocess/topio.c
Simple merge

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

diff --cc src/gromacs/gmxpreprocess/xlate.c
Simple merge

diff --cc src/gromacs/legacyheaders/nonbonded.h
Simple merge

diff --cc src/gromacs/legacyheaders/shellfc.h
Simple merge

diff --cc src/gromacs/legacyheaders/types/inputrec.h
Simple merge

diff --cc src/gromacs/mdlib/constr.c
Simple merge

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

diff --cc src/gromacs/mdlib/forcerec.c
Simple merge

diff --cc src/gromacs/mdlib/ns.c
Simple merge

diff --cc src/gromacs/mdlib/pme.c
Simple merge

diff --cc src/gromacs/mdlib/shellfc.c
index 8ddbc94859f6c3b1150e41d49a5398d89a422c78,7c1f8679f44741ccb1d2d16ad8c5842106623e89..ffe4469567ba13ef7bc539a0567b45be8fc3e539
--- 1/src/gromacs/mdlib/shellfc.c
--- 2/src/gromacs/mdlib/shellfc.c
+++ b/src/gromacs/mdlib/shellfc.c
@@@ -58,10 -59,6 +58,11 @@@
  #include "chargegroup.h"
  #include "macros.h"
  
 +#include "gromacs/math/vec.h"
 +#include "gromacs/pbcutil/mshift.h"
++#include "gromacs/pbcutil/pbc.h"
 +#include "gromacs/utility/fatalerror.h"
 +#include "gromacs/utility/smalloc.h"
  
  typedef struct {
      int     nnucl;

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

diff --cc src/gromacs/mdlib/tables.c
Simple merge

diff --cc src/gromacs/mdlib/update.c
Simple merge

diff --cc src/gromacs/mdlib/wall.c
Simple merge

diff --cc src/gromacs/pulling/pull.c
Simple merge

diff --cc src/gromacs/tools/compare.c
Simple merge

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

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

diff --cc src/programs/mdrun/repl_ex.cpp
index 47a3d94e262f6ac0390d4af0369963edf2149672,46a9bc0113cd1cd6755cca7903cc71128c2386f4..2fa1ff6d51fb26f66350a373da916f6ec6576907
--- 1/src/programs/mdrun/repl_ex.cpp
--- 2/src/programs/mdrun/repl_ex.c
+++ b/src/programs/mdrun/repl_ex.cpp
@@@ -898,9 -905,10 +908,9 @@@ test_for_replica_exchange(FIL
      gmx_bool  bEpot    = FALSE;
      gmx_bool  bDLambda = FALSE;
      gmx_bool  bVol     = FALSE;
 -    gmx_rng_t rng;
  
      bMultiEx = (re->nex > 1);  /* multiple exchanges at each state */
-     fprintf(fplog, "Replica exchange at step " "%" GMX_PRId64 " time %g\n", step, time);
 -    fprintf(fplog, "Replica exchange at step " "%"GMX_PRId64 " time %.5f\n", step, time);
++    fprintf(fplog, "Replica exchange at step %" GMX_PRId64 " time %.5f\n", step, time);
  
      if (re->bNPT)
      {

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