added Verlet scheme and NxN non-bonded functionality

[alexxy/gromacs.git] / src / mdlib / edsam.c

diff --git a/src/mdlib/edsam.c b/src/mdlib/edsam.c
index 15fdd6873b416f23058f858bd719c56cc4e94f4d..3101f68eb9c1c466c73763f2c3e146c58dd8f9df 100644 (file)
--- a/src/mdlib/edsam.c
+++ b/src/mdlib/edsam.c
@@ -1189,6 +1189,7 @@ static void init_edi(gmx_mtop_t *mtop,t_inputrec *ir,
     int  i;
     real totalmass = 0.0;
     rvec com;
+    gmx_mtop_atomlookup_t alook=NULL;
     t_atom *atom;
 
     /* NOTE Init_edi is executed on the master process only
@@ -1202,13 +1203,15 @@ static void init_edi(gmx_mtop_t *mtop,t_inputrec *ir,
                      || edi->vecs.radacc.neig
                      || edi->vecs.radcon.neig;
 
+    alook = gmx_mtop_atomlookup_init(mtop);
+
     /* evaluate masses (reference structure) */
     snew(edi->sref.m, edi->sref.nr);
     for (i = 0; i < edi->sref.nr; i++)
     {
         if (edi->fitmas)
         {
-            gmx_mtop_atomnr_to_atom(mtop,edi->sref.anrs[i],&atom);
+            gmx_mtop_atomnr_to_atom(alook,edi->sref.anrs[i],&atom);
             edi->sref.m[i] = atom->m;
         }
         else
@@ -1236,7 +1239,7 @@ static void init_edi(gmx_mtop_t *mtop,t_inputrec *ir,
     snew(edi->sav.m    , edi->sav.nr );
     for (i = 0; i < edi->sav.nr; i++)
     {
-        gmx_mtop_atomnr_to_atom(mtop,edi->sav.anrs[i],&atom);
+        gmx_mtop_atomnr_to_atom(alook,edi->sav.anrs[i],&atom);
         edi->sav.m[i] = atom->m;
         if (edi->pcamas)
         {
@@ -1258,6 +1261,8 @@ static void init_edi(gmx_mtop_t *mtop,t_inputrec *ir,
         }
     }
 
+    gmx_mtop_atomlookup_destroy(alook);
+
     /* put reference structure in origin */
     get_center(edi->sref.x, edi->sref.m, edi->sref.nr, com);
     com[XX] = -com[XX];