Merge "grompp now retains the order of bonds converted to constraints" into release-4-6

diff --git a/src/kernel/topshake.c b/src/kernel/topshake.c
index 4094559d9c363ba6af837a7cd3584ea96d3b010b..78961c5ea8cb5e98b5a1ea9350be032504e8c7dd 100644 (file)
--- a/src/kernel/topshake.c
+++ b/src/kernel/topshake.c
@@ -193,7 +193,8 @@ void make_shake (t_params plist[],t_atoms *atoms,gpp_atomtype_t at,int nshake)
     for (ftype=0; (ftype < F_NRE); ftype++) {
       if (interaction_function[ftype].flags & IF_BTYPE) {
        pr = &(plist[ftype]);
-       for (i=0; (i < pr->nr); ) {
+        j = 0;
+       for(i=0; i<pr->nr; i++) {
          if ( (nshake != eshHBONDS) || 
               (count_hydrogens (info,2,pr->param[i].a) > 0) ) {
            /* append this bond to the shake list */
@@ -202,16 +203,11 @@ void make_shake (t_params plist[],t_atoms *atoms,gpp_atomtype_t at,int nshake)
            p.C0 = pr->param[i].C0;
            p.C1 = pr->param[i].C2;
            add_param_to_list (&(plist[F_CONSTR]),&p);
-           
-           /* move the last bond to this position */
-           copy_bond (pr,i,pr->nr-1);
-           
-           /* should free memory here!! */
-           pr->nr--;
+         } else {
+             copy_bond(pr,j++,i); 
          }
-         else
-           i++;
        }
+       pr->nr = j;
       }
     }
   }