Merge branch 'release-4-5-patches'

diff --combined include/string2.h
index 61ba9ee615602c1c659cfca156f917bb56953c9a,6d949384c437659478161dcea0e0e054b44b7c7a..95cd558880b6eb05d9d298c92c125e9b80a714da
--- 1/include/string2.h
--- 2/include/string2.h
+++ b/include/string2.h
@@@ -109,7 -109,7 +109,7 @@@ char *gmx_strsep(char **stringp, const 
  
  
  char *wrap_lines(const char *buf,int line_width, int indent,
-                       bool bIndentFirst);
+                       gmx_bool bIndentFirst);
  /* wraps lines at 'linewidth', indenting all following
   * lines by 'indent' spaces. A temp buffer is allocated and returned,
   * which can be disposed of if no longer needed.
@@@ -118,7 -118,7 +118,7 @@@
   */
  
  
 -char **split(char sep,char *str);
 +char **split(char sep,const char *str);
  /* Implementation of the well-known Perl function split */
  
  gmx_large_int_t str_to_large_int_t(const char *str, char **endptr);

diff --combined src/gmxlib/string2.c
index 3784c384e36b1f60f26086ecc12b827949fd0f71,8f5f20b3d4c9a87b0140084ac2ccee479072e6c0..1e91cb89a4735dfdeb8fbbe417b488a62f6896f7
--- 1/src/gmxlib/string2.c
--- 2/src/gmxlib/string2.c
+++ b/src/gmxlib/string2.c
@@@ -397,11 -397,11 +397,11 @@@ gmx_wcmatch(const char *pattern, const 
      return (*str == 0) ? 0 : GMX_NO_WCMATCH;
  }
  
- char *wrap_lines(const char *buf,int line_width, int indent,bool bIndentFirst)
+ char *wrap_lines(const char *buf,int line_width, int indent,gmx_bool bIndentFirst)
  {
    char *b2;
    int i,i0,i2,j,b2len,lspace=0,l2space=0;
-   bool bFirst,bFitsOnLine;
+   gmx_bool bFirst,bFitsOnLine;
  
    /* characters are copied from buf to b2 with possible spaces changed
     * into newlines and extra space added for indentation.
@@@ -480,7 -480,7 +480,7 @@@
    return b2;
  }
  
 -char **split(char sep,char *str)
 +char **split(char sep,const char *str)
  {
    char **ptr = NULL;
    int  n,nn,nptr = 0;

diff --combined src/mdlib/ns.c
index 9cd7bcc883a16b4cd0576289177a25bd1079ef8d,81e35ac181c4de21b8c3cde6daea3bb4a21a7d36..0f455c40f6d4abd8476ee5c2cd64fa409aa9aeb5
--- 1/src/mdlib/ns.c
--- 2/src/mdlib/ns.c
+++ b/src/mdlib/ns.c
@@@ -72,14 -72,14 +72,14 @@@ static void SETEXCL_(t_excl e[],atom_i
  {   e[j] = e[j] | (1<<i); }
  static void RMEXCL_(t_excl e[],atom_id i,atom_id j) 
  { e[j]=e[j] & ~(1<<i); }
- static bool ISEXCL_(t_excl e[],atom_id i,atom_id j) 
- { return (bool)(e[j] & (1<<i)); }
- static bool NOTEXCL_(t_excl e[],atom_id i,atom_id j)
+ static gmx_bool ISEXCL_(t_excl e[],atom_id i,atom_id j) 
+ { return (gmx_bool)(e[j] & (1<<i)); }
+ static gmx_bool NOTEXCL_(t_excl e[],atom_id i,atom_id j)
  {  return !(ISEXCL(e,i,j)); }
  #else
  #define SETEXCL(e,i,j) (e)[((atom_id) (j))] |= (1<<((atom_id) (i)))
  #define RMEXCL(e,i,j)  (e)[((atom_id) (j))] &= (~(1<<((atom_id) (i))))
- #define ISEXCL(e,i,j)  (bool) ((e)[((atom_id) (j))] & (1<<((atom_id) (i))))
+ #define ISEXCL(e,i,j)  (gmx_bool) ((e)[((atom_id) (j))] & (1<<((atom_id) (i))))
  #define NOTEXCL(e,i,j) !(ISEXCL(e,i,j))
  #endif
  
@@@ -110,7 -110,7 +110,7 @@@ static void reallocate_nblist(t_nblist 
   * can set an innerloop index here. The obvious choice for this would have
   * been the vdwtype/coultype values in the forcerecord, but unfortunately 
   * those types are braindead - for instance both Buckingham and normal 
-  * Lennard-Jones use the same value (evdwCUT), and a separate boolean variable
+  * Lennard-Jones use the same value (evdwCUT), and a separate gmx_boolean variable
   * to determine which interaction is used. There is further no special value
   * for 'no interaction'. For backward compatibility with old TPR files we won't
   * change this in the 3.x series, so when calling this routine you should use:
@@@ -130,7 -130,7 +130,7 @@@
  static void init_nblist(t_nblist *nl_sr,t_nblist *nl_lr,
                          int maxsr,int maxlr,
                          int ivdw, int icoul, 
-                         bool bfree, int enlist)
+                         gmx_bool bfree, int enlist)
  {
      t_nblist *nl;
      int      homenr;
@@@ -389,7 -389,7 +389,7 @@@ static void reset_nblist(t_nblist *nl
       }
  }
  
- static void reset_neighbor_list(t_forcerec *fr,bool bLR,int nls,int eNL)
+ static void reset_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL)
  {
      int n,i;
    
@@@ -418,7 -418,7 +418,7 @@@
  
  
  static inline void new_i_nblist(t_nblist *nlist,
-                                 bool bLR,atom_id i_atom,int shift,int gid)
+                                 gmx_bool bLR,atom_id i_atom,int shift,int gid)
  {
      int    i,k,nri,nshift;
      
@@@ -484,8 -484,8 +484,8 @@@ static inline void close_nblist(t_nblis
      }
  }
  
- static inline void close_neighbor_list(t_forcerec *fr,bool bLR,int nls,int eNL, 
-                                        bool bMakeQMMMnblist)
+ static inline void close_neighbor_list(t_forcerec *fr,gmx_bool bLR,int nls,int eNL, 
+                                        gmx_bool bMakeQMMMnblist)
  {
      int n,i;
      
@@@ -514,7 -514,7 +514,7 @@@
      }
  }
  
- static inline void add_j_to_nblist(t_nblist *nlist,atom_id j_atom,bool bLR)
+ static inline void add_j_to_nblist(t_nblist *nlist,atom_id j_atom,gmx_bool bLR)
  {
      int nrj=nlist->nrj;
      
@@@ -534,7 -534,7 +534,7 @@@
  
  static inline void add_j_to_nblist_cg(t_nblist *nlist,
                                        atom_id j_start,int j_end,
-                                       t_excl *bexcl,bool bLR)
+                                       t_excl *bexcl,gmx_bool bLR)
  {
      int nrj=nlist->nrj;
      int j;
@@@ -569,7 -569,7 +569,7 @@@
  }
  
  typedef void
- put_in_list_t(bool              bHaveVdW[],
+ put_in_list_t(gmx_bool              bHaveVdW[],
                int               ngid,
                t_mdatoms *       md,
                int               icg,
@@@ -580,12 -580,12 +580,12 @@@
                t_excl            bExcl[],
                int               shift,
                t_forcerec *      fr,
-               bool              bLR,
-               bool              bDoVdW,
-               bool              bDoCoul);
+               gmx_bool              bLR,
+               gmx_bool              bDoVdW,
+               gmx_bool              bDoCoul);
  
  static void 
- put_in_list_at(bool              bHaveVdW[],
+ put_in_list_at(gmx_bool              bHaveVdW[],
                 int               ngid,
                 t_mdatoms *       md,
                 int               icg,
@@@ -596,9 -596,9 +596,9 @@@
                 t_excl            bExcl[],
                 int               shift,
                 t_forcerec *      fr,
-                bool              bLR,
-                bool              bDoVdW,
-                bool              bDoCoul)
+                gmx_bool              bLR,
+                gmx_bool              bDoVdW,
+                gmx_bool              bDoCoul)
  {
      /* The a[] index has been removed,
       * to put it back in i_atom should be a[i0] and jj should be a[jj].
@@@ -620,8 -620,8 +620,8 @@@
      int       *type,*typeB;
      real      *charge,*chargeB;
      real      qi,qiB,qq,rlj;
-     bool      bFreeEnergy,bFree,bFreeJ,bNotEx,*bPert;
-     bool      bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;
+     gmx_bool      bFreeEnergy,bFree,bFreeJ,bNotEx,*bPert;
+     gmx_bool      bDoVdW_i,bDoCoul_i,bDoCoul_i_sol;
      int       iwater,jwater;
      t_nblist  *nlist;
      
@@@ -1122,7 -1122,7 +1122,7 @@@
  }
  
  static void 
- put_in_list_qmmm(bool              bHaveVdW[],
+ put_in_list_qmmm(gmx_bool              bHaveVdW[],
                   int               ngid,
                   t_mdatoms *       md,
                   int               icg,
@@@ -1133,15 -1133,15 +1133,15 @@@
                   t_excl            bExcl[],
                   int               shift,
                   t_forcerec *      fr,
-                  bool              bLR,
-                  bool              bDoVdW,
-                  bool              bDoCoul)
+                  gmx_bool              bLR,
+                  gmx_bool              bDoVdW,
+                  gmx_bool              bDoCoul)
  {
      t_nblist *   coul;
      int         i,j,jcg,igid,gid;
      atom_id   jj,jj0,jj1,i_atom;
      int       i0,nicg;
-     bool      bNotEx;
+     gmx_bool      bNotEx;
      
      /* Get atom range */
      i0     = index[icg];
@@@ -1184,7 -1184,7 +1184,7 @@@
  }
  
  static void 
- put_in_list_cg(bool              bHaveVdW[],
+ put_in_list_cg(gmx_bool              bHaveVdW[],
                 int               ngid,
                 t_mdatoms *       md,
                 int               icg,
@@@ -1195,9 -1195,9 +1195,9 @@@
                 t_excl            bExcl[],
                 int               shift,
                 t_forcerec *      fr,
-                bool              bLR,
-                bool              bDoVdW,
-                bool              bDoCoul)
+                gmx_bool              bLR,
+                gmx_bool              bDoVdW,
+                gmx_bool              bDoCoul)
  {
      int          cginfo;
      int          igid,gid,nbl_ind;
@@@ -1251,7 -1251,7 +1251,7 @@@
      close_i_nblist(vdwc);  
  }
  
- static void setexcl(atom_id start,atom_id end,t_blocka *excl,bool b,
+ static void setexcl(atom_id start,atom_id end,t_blocka *excl,gmx_bool b,
                      t_excl bexcl[])
  {
      atom_id i,k;
@@@ -1418,7 -1418,7 +1418,7 @@@ static real calc_image_rect(rvec xi,rve
  }
  
  static void add_simple(t_ns_buf *nsbuf,int nrj,atom_id cg_j,
-                        bool bHaveVdW[],int ngid,t_mdatoms *md,
+                        gmx_bool bHaveVdW[],int ngid,t_mdatoms *md,
                         int icg,int jgid,t_block *cgs,t_excl bexcl[],
                         int shift,t_forcerec *fr,put_in_list_t *put_in_list)
  {
@@@ -1437,7 -1437,7 +1437,7 @@@ static void ns_inner_tric(rvec x[],int 
                            int njcg,atom_id jcg[],
                            matrix box,rvec b_inv,real rcut2,
                            t_block *cgs,t_ns_buf **ns_buf,
-                           bool bHaveVdW[],int ngid,t_mdatoms *md,
+                           gmx_bool bHaveVdW[],int ngid,t_mdatoms *md,
                            t_excl bexcl[],t_forcerec *fr,
                            put_in_list_t *put_in_list)
  {
@@@ -1468,9 -1468,9 +1468,9 @@@
  
  static void ns_inner_rect(rvec x[],int icg,int *i_egp_flags,
                            int njcg,atom_id jcg[],
-                           bool bBox,rvec box_size,rvec b_inv,real rcut2,
+                           gmx_bool bBox,rvec box_size,rvec b_inv,real rcut2,
                            t_block *cgs,t_ns_buf **ns_buf,
-                           bool bHaveVdW[],int ngid,t_mdatoms *md,
+                           gmx_bool bHaveVdW[],int ngid,t_mdatoms *md,
                            t_excl bexcl[],t_forcerec *fr,
                            put_in_list_t *put_in_list)
  {
@@@ -1527,7 -1527,7 +1527,7 @@@ static int ns_simple_core(t_forcerec *f
                            matrix box,rvec box_size,
                            t_excl bexcl[],atom_id *aaj,
                            int ngid,t_ns_buf **ns_buf,
-                           put_in_list_t *put_in_list,bool bHaveVdW[])
+                           put_in_list_t *put_in_list,gmx_bool bHaveVdW[])
  {
      int      naaj,k;
      real     rlist2;
@@@ -1539,7 -1539,7 +1539,7 @@@
      t_blocka *excl=&(top->excls);
      rvec     b_inv;
      int      m;
-     bool     bBox,bTriclinic;
+     gmx_bool     bBox,bTriclinic;
      int      *i_egp_flags;
      
      rlist2 = sqr(fr->rlist);
@@@ -1549,7 -1549,7 +1549,7 @@@
      {
          for(m=0; (m<DIM); m++)
          {
 -            b_inv[m] = divide(1.0,box_size[m]);
 +            b_inv[m] = divide_err(1.0,box_size[m]);
          }
          bTriclinic = TRICLINIC(box);
      }
@@@ -1773,10 -1773,10 +1773,10 @@@ static void do_longrange(t_commrec *cr,
                           rvec x[],rvec box_size,t_nrnb *nrnb,
                           real lambda,real *dvdlambda,
                           gmx_grppairener_t *grppener,
-                          bool bDoVdW,bool bDoCoul,
-                          bool bEvaluateNow,put_in_list_t *put_in_list,
-                          bool bHaveVdW[],
-                          bool bDoForces,rvec *f)
+                          gmx_bool bDoVdW,gmx_bool bDoCoul,
+                          gmx_bool bEvaluateNow,put_in_list_t *put_in_list,
+                          gmx_bool bHaveVdW[],
+                          gmx_bool bDoForces,rvec *f)
  {
      int n,i;
      t_nblist *nl;
@@@ -1811,7 -1811,7 +1811,7 @@@
      }
  }
  
- static void get_cutoff2(t_forcerec *fr,bool bDoLongRange,
+ static void get_cutoff2(t_forcerec *fr,gmx_bool bDoLongRange,
                          real *rvdw2,real *rcoul2,
                          real *rs2,real *rm2,real *rl2)
  {
@@@ -1897,14 -1897,14 +1897,14 @@@ static int nsgrid_core(FILE *log,t_comm
                         matrix box,rvec box_size,int ngid,
                         gmx_localtop_t *top,
                         t_grid *grid,rvec x[],
-                        t_excl bexcl[],bool *bExcludeAlleg,
+                        t_excl bexcl[],gmx_bool *bExcludeAlleg,
                         t_nrnb *nrnb,t_mdatoms *md,
                         real lambda,real *dvdlambda,
                         gmx_grppairener_t *grppener,
                         put_in_list_t *put_in_list,
-                        bool bHaveVdW[],
-                        bool bDoLongRange,bool bDoForces,rvec *f,
-                        bool bMakeQMMMnblist)
+                        gmx_bool bHaveVdW[],
+                        gmx_bool bDoLongRange,gmx_bool bDoForces,rvec *f,
+                        gmx_bool bMakeQMMMnblist)
  {
      gmx_ns_t *ns;
      atom_id **nl_lr_ljc,**nl_lr_one,**nl_sr;
@@@ -1927,11 -1927,11 +1927,11 @@@
      int     cg0,cg1,icg=-1,cgsnr,i0,igid,nri,naaj,max_jcg;
      int     jcg0,jcg1,jjcg,cgj0,jgid;
      int     *grida,*gridnra,*gridind;
-     bool    rvdw_lt_rcoul,rcoul_lt_rvdw;
+     gmx_bool    rvdw_lt_rcoul,rcoul_lt_rvdw;
      rvec    xi,*cgcm,grid_offset;
      real    r2,rs2,rvdw2,rcoul2,rm2,rl2,XI,YI,ZI,dcx,dcy,dcz,tmp1,tmp2;
      int     *i_egp_flags;
-     bool    bDomDec,bTriclinicX,bTriclinicY;
+     gmx_bool    bDomDec,bTriclinicX,bTriclinicY;
      ivec    ncpddc;
      
      ns = &fr->ns;
@@@ -2495,18 -2495,18 +2495,18 @@@ int search_neighbours(FILE *log,t_force
                        t_nrnb *nrnb,t_mdatoms *md,
                        real lambda,real *dvdlambda,
                        gmx_grppairener_t *grppener,
-                       bool bFillGrid,
-                       bool bDoLongRange,
-                       bool bDoForces,rvec *f)
+                       gmx_bool bFillGrid,
+                       gmx_bool bDoLongRange,
+                       gmx_bool bDoForces,rvec *f)
  {
      t_block  *cgs=&(top->cgs);
      rvec     box_size,grid_x0,grid_x1;
      int      i,j,m,ngid;
      real     min_size,grid_dens;
      int      nsearch;
-     bool     bGrid;
+     gmx_bool     bGrid;
      char     *ptr;
-     bool     *i_egp_flags;
+     gmx_bool     *i_egp_flags;
      int      cg_start,cg_end,start,end;
      gmx_ns_t *ns;
      t_grid   *grid;
@@@ -2677,7 -2677,7 +2677,7 @@@ int natoms_beyond_ns_buffer(t_inputrec 
      int  cg0,cg1,cg,a0,a1,a,i,j;
      real rint,hbuf2,scale;
      rvec *cg_cm,cgsc;
-     bool bIsotropic;
+     gmx_bool bIsotropic;
      int  nBeyond;
      
      nBeyond = 0;