added Verlet scheme and NxN non-bonded functionality

[alexxy/gromacs.git] / include / mtop_util.h

diff --git a/include/mtop_util.h b/include/mtop_util.h
index a9a43b25ee6abbc35b0266e7edd6cc2d74d5a3c5..c43e33512909d1a8f0bfae683665b64775084d63 100644 (file)
--- a/include/mtop_util.h
+++ b/include/mtop_util.h
@@ -50,13 +50,33 @@ gmx_mtop_finalize(gmx_mtop_t *mtop);
 int
 ncg_mtop(const gmx_mtop_t *mtop);
 
+/* Removes the charge groups, i.e. makes single atom charge groups, in mtop */
+void gmx_mtop_remove_chargegroups(gmx_mtop_t *mtop);
+
+
+/* Abstract data type for looking up atoms by global atom number */
+typedef struct gmx_mtop_atomlookup *gmx_mtop_atomlookup_t;
+
+/* Initialize atom lookup by global atom number */
+gmx_mtop_atomlookup_t
+gmx_mtop_atomlookup_init(const gmx_mtop_t *mtop);
+
+/* As gmx_mtop_atomlookup_init, but optimized for atoms involved in settle */
+gmx_mtop_atomlookup_t
+gmx_mtop_atomlookup_settle_init(const gmx_mtop_t *mtop);
+
+/* Destroy a gmx_mtop_atomlookup_t data structure */
+void
+gmx_mtop_atomlookup_destroy(gmx_mtop_atomlookup_t alook);
+
 
 /* Returns a pointer to the t_atom struct belonging to atnr_global.
  * This can be an expensive operation, so if possible use
  * one of the atom loop constructs below.
  */
 void
-gmx_mtop_atomnr_to_atom(const gmx_mtop_t *mtop,int atnr_global,
+gmx_mtop_atomnr_to_atom(const gmx_mtop_atomlookup_t alook,
+                       int atnr_global,
                        t_atom **atom);
 
 
@@ -64,7 +84,8 @@ gmx_mtop_atomnr_to_atom(const gmx_mtop_t *mtop,int atnr_global,
  * and the local atom number in the molecule belonging to atnr_global.
  */
 void
-gmx_mtop_atomnr_to_ilist(const gmx_mtop_t *mtop,int atnr_global,
+gmx_mtop_atomnr_to_ilist(const gmx_mtop_atomlookup_t alook,
+                        int atnr_global,
                         t_ilist **ilist_mol,int *atnr_offset);
 
 
@@ -74,7 +95,8 @@ gmx_mtop_atomnr_to_ilist(const gmx_mtop_t *mtop,int atnr_global,
  * belonging to atnr_global.
  */
 void
-gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_t *mtop,int atnr_global,
+gmx_mtop_atomnr_to_molblock_ind(const gmx_mtop_atomlookup_t alook,
+                               int atnr_global,
                                int *molb,int *molnr,int *atnr_mol);