Removed topology pointers from DD struct

The reverse topology struct in the domain decomposition data used
pointers to the global and local topologies for printing errors.
Since the call now the error function can now pass those pointers,
these pointers no longer need to be copied.
Also added const qualifiers to some data structures.

Change-Id: I5d2236982748214591aa5d19f77f0ab8d27553ab

diff --git a/src/gromacs/domdec/domdec.h b/src/gromacs/domdec/domdec.h
index a4fa742ead50add9629be57caa95933d22f56481..520aae1d1330da2dd99aaf22574925b75eef87d5 100644 (file)
--- a/src/gromacs/domdec/domdec.h
+++ b/src/gromacs/domdec/domdec.h
@@ -314,7 +314,10 @@ int *dd_constraints_nlocalatoms(struct gmx_domdec_t *dd);
 
 /*! \brief Print error output when interactions are missing */
 void dd_print_missing_interactions(FILE *fplog, struct t_commrec *cr,
-                                   int local_count,  gmx_mtop_t *top_global, t_state *state_local);
+                                   int local_count,
+                                   gmx_mtop_t *top_global,
+                                   const gmx_localtop_t *top_local,
+                                   t_state *state_local);
 
 /*! \brief Generate and store the reverse topology */
 void dd_make_reverse_top(FILE *fplog,

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index 73df362986c43341cf6492da2ec993eef04fa2c4..ee8b7d736aede7159bf3b5a2eca3dd6ed3403eb8 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -128,10 +128,6 @@ struct gmx_reverse_top_t
     /* Work data structures for multi-threading */
     int            nthread;           /**< The number of threads to be used */
     thread_work_t *th_work;           /**< Thread work array for local topology generation */
-
-    /* Pointers only used for an error message */
-    gmx_mtop_t     *err_top_global; /**< Pointer to the global top, only used for error reporting */
-    gmx_localtop_t *err_top_local;  /**< Pointer to the local top, only used for error reporting */
     //! @endcond
 };
 
@@ -178,47 +174,42 @@ static void print_error_header(FILE *fplog, char *moltypename, int nprint)
 
 /*! \brief Help print error output when interactions are missing */
 static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
-                                          gmx_reverse_top_t *rt,
+                                          const gmx_reverse_top_t *rt,
                                           char *moltypename,
-                                          reverse_ilist_t *ril,
+                                          const reverse_ilist_t *ril,
                                           int a_start, int a_end,
                                           int nat_mol, int nmol,
-                                          t_idef *idef)
+                                          const t_idef *idef)
 {
-    int      nril_mol, *assigned, *gatindex;
-    int      ftype, ftype_j, nral, i, j_mol, j, a0, a0_mol, mol, a;
-    int      nprint;
-    t_ilist *il;
-    t_iatom *ia;
-    gmx_bool bFound;
+    int *assigned;
 
-    nril_mol = ril->index[nat_mol];
+    int  nril_mol = ril->index[nat_mol];
     snew(assigned, nmol*nril_mol);
 
-    gatindex = cr->dd->gatindex;
-    for (ftype = 0; ftype < F_NRE; ftype++)
+    int *gatindex = cr->dd->gatindex;
+    for (int ftype = 0; ftype < F_NRE; ftype++)
     {
         if (dd_check_ftype(ftype, rt->bBCheck, rt->bConstr, rt->bSettle))
         {
-            nral = NRAL(ftype);
-            il   = &idef->il[ftype];
-            ia   = il->iatoms;
-            for (i = 0; i < il->nr; i += 1+nral)
+            int            nral = NRAL(ftype);
+            const t_ilist *il   = &idef->il[ftype];
+            const t_iatom *ia   = il->iatoms;
+            for (int i = 0; i < il->nr; i += 1+nral)
             {
-                a0     = gatindex[ia[1]];
+                int a0 = gatindex[ia[1]];
                 /* Check if this interaction is in
                  * the currently checked molblock.
                  */
                 if (a0 >= a_start && a0 < a_end)
                 {
-                    mol    = (a0 - a_start)/nat_mol;
-                    a0_mol = (a0 - a_start) - mol*nat_mol;
-                    j_mol  = ril->index[a0_mol];
-                    bFound = FALSE;
-                    while (j_mol < ril->index[a0_mol+1] && !bFound)
+                    int  mol    = (a0 - a_start)/nat_mol;
+                    int  a0_mol = (a0 - a_start) - mol*nat_mol;
+                    int  j_mol  = ril->index[a0_mol];
+                    bool found  = false;
+                    while (j_mol < ril->index[a0_mol+1] && !found)
                     {
-                        j       = mol*nril_mol + j_mol;
-                        ftype_j = ril->il[j_mol];
+                        int j       = mol*nril_mol + j_mol;
+                        int ftype_j = ril->il[j_mol];
                         /* Here we need to check if this interaction has
                          * not already been assigned, since we could have
                          * multiply defined interactions.
@@ -227,23 +218,23 @@ static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
                             assigned[j] == 0)
                         {
                             /* Check the atoms */
-                            bFound = TRUE;
-                            for (a = 0; a < nral; a++)
+                            found = true;
+                            for (int a = 0; a < nral; a++)
                             {
                                 if (gatindex[ia[1+a]] !=
                                     a_start + mol*nat_mol + ril->il[j_mol+2+a])
                                 {
-                                    bFound = FALSE;
+                                    found = false;
                                 }
                             }
-                            if (bFound)
+                            if (found)
                             {
                                 assigned[j] = 1;
                             }
                         }
                         j_mol += 2 + nral_rt(ftype_j);
                     }
-                    if (!bFound)
+                    if (!found)
                     {
                         gmx_incons("Some interactions seem to be assigned multiple times");
                     }
@@ -255,16 +246,16 @@ static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
 
     gmx_sumi(nmol*nril_mol, assigned, cr);
 
-    nprint = 10;
-    i      = 0;
-    for (mol = 0; mol < nmol; mol++)
+    int nprint = 10;
+    int i      = 0;
+    for (int mol = 0; mol < nmol; mol++)
     {
-        j_mol = 0;
+        int j_mol = 0;
         while (j_mol < nril_mol)
         {
-            ftype = ril->il[j_mol];
-            nral  = NRAL(ftype);
-            j     = mol*nril_mol + j_mol;
+            int ftype = ril->il[j_mol];
+            int nral  = NRAL(ftype);
+            int j     = mol*nril_mol + j_mol;
             if (assigned[j] == 0 &&
                 !(interaction_function[ftype].flags & IF_VSITE))
             {
@@ -278,6 +269,7 @@ static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
                             interaction_function[ftype].longname);
                     fprintf(stderr, "%20s atoms",
                             interaction_function[ftype].longname);
+                    int a;
                     for (a = 0; a < nral; a++)
                     {
                         fprintf(fplog, "%5d", ril->il[j_mol+2+a]+1);
@@ -316,7 +308,8 @@ static void print_missing_interactions_mb(FILE *fplog, t_commrec *cr,
 
 /*! \brief Help print error output when interactions are missing */
 static void print_missing_interactions_atoms(FILE *fplog, t_commrec *cr,
-                                             gmx_mtop_t *mtop, t_idef *idef)
+                                             const gmx_mtop_t *mtop,
+                                             const t_idef *idef)
 {
     int                mb, a_start, a_end;
     gmx_molblock_t    *molb;
@@ -341,20 +334,19 @@ static void print_missing_interactions_atoms(FILE *fplog, t_commrec *cr,
     }
 }
 
-void dd_print_missing_interactions(FILE *fplog, t_commrec *cr, int local_count,  gmx_mtop_t *top_global, t_state *state_local)
+void dd_print_missing_interactions(FILE *fplog, t_commrec *cr,
+                                   int local_count,
+                                   gmx_mtop_t *top_global,
+                                   const gmx_localtop_t *top_local,
+                                   t_state *state_local)
 {
     int             ndiff_tot, cl[F_NRE], n, ndiff, rest_global, rest_local;
     int             ftype, nral;
     char            buf[STRLEN];
     gmx_domdec_t   *dd;
-    gmx_mtop_t     *err_top_global;
-    gmx_localtop_t *err_top_local;
 
     dd = cr->dd;
 
-    err_top_global = dd->reverse_top->err_top_global;
-    err_top_local  = dd->reverse_top->err_top_local;
-
     if (fplog)
     {
         fprintf(fplog, "\nNot all bonded interactions have been properly assigned to the domain decomposition cells\n");
@@ -366,7 +358,7 @@ void dd_print_missing_interactions(FILE *fplog, t_commrec *cr, int local_count,
     for (ftype = 0; ftype < F_NRE; ftype++)
     {
         nral      = NRAL(ftype);
-        cl[ftype] = err_top_local->idef.il[ftype].nr/(1+nral);
+        cl[ftype] = top_local->idef.il[ftype].nr/(1+nral);
     }
 
     gmx_sumi(F_NRE, cl, cr);
@@ -392,10 +384,10 @@ void dd_print_missing_interactions(FILE *fplog, t_commrec *cr, int local_count,
                 || (dd->reverse_top->bConstr && ftype == F_CONSTR)
                 || (dd->reverse_top->bSettle && ftype == F_SETTLE))
             {
-                n    = gmx_mtop_ftype_count(err_top_global, ftype);
+                n    = gmx_mtop_ftype_count(top_global, ftype);
                 if (ftype == F_CONSTR)
                 {
-                    n += gmx_mtop_ftype_count(err_top_global, F_CONSTRNC);
+                    n += gmx_mtop_ftype_count(top_global, F_CONSTRNC);
                 }
                 ndiff = cl[ftype] - n;
                 if (ndiff != 0)
@@ -426,8 +418,7 @@ void dd_print_missing_interactions(FILE *fplog, t_commrec *cr, int local_count,
         }
     }
 
-    print_missing_interactions_atoms(fplog, cr, err_top_global,
-                                     &err_top_local->idef);
+    print_missing_interactions_atoms(fplog, cr, top_global, &top_local->idef);
     write_dd_pdb("dd_dump_err", 0, "dump", top_global, cr,
                  -1, state_local->x, state_local->box);
 
@@ -2223,10 +2214,6 @@ void dd_make_local_top(gmx_domdec_t *dd, gmx_domdec_zones_t *zones,
     }
 
     ltop->atomtypes  = mtop->atomtypes;
-
-    /* For an error message only */
-    dd->reverse_top->err_top_global = mtop;
-    dd->reverse_top->err_top_local  = ltop;
 }
 
 void dd_sort_local_top(gmx_domdec_t *dd, t_mdatoms *mdatoms,

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index 5f15f3e9397b8eb0d7c9b4663d164e9d70e388f3..74fd5d37947fa95bc54bbb7c38a308e11dcdc9e5 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -127,6 +127,7 @@
  * \param[in]    cr                                     Communication object
  * \param[in]    totalNumberOfBondedInteractions        Result of the global reduction over the number of bonds treated in each domain
  * \param[in]    top_global                             Global topology for the error message
+ * \param[in]    top_local                              Local topology for the error message
  * \param[in]    state                                  Global state for the error message
  * \param[inout] shouldCheckNumberOfBondedInteractions  Whether we should do the check.
  *
@@ -134,14 +135,14 @@
  * is always set to false after exit.
  */
 static void checkNumberOfBondedInteractions(FILE *fplog, t_commrec *cr, int totalNumberOfBondedInteractions,
-                                            gmx_mtop_t *top_global, t_state *state,
+                                            gmx_mtop_t *top_global, gmx_localtop_t *top_local, t_state *state,
                                             bool *shouldCheckNumberOfBondedInteractions)
 {
     if (*shouldCheckNumberOfBondedInteractions)
     {
         if (totalNumberOfBondedInteractions != cr->dd->nbonded_global)
         {
-            dd_print_missing_interactions(fplog, cr, totalNumberOfBondedInteractions, top_global, state); // Does not return
+            dd_print_missing_interactions(fplog, cr, totalNumberOfBondedInteractions, top_global, top_local, state); // Does not return
         }
         *shouldCheckNumberOfBondedInteractions = false;
     }
@@ -1175,7 +1176,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                    b) If we are using EkinAveEkin for the kinetic energy for the temperature control, we still feed in
                    EkinAveVel because it's needed for the pressure */
                 checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
-                                                top_global, state,
+                                                top_global, top, state,
                                                 &shouldCheckNumberOfBondedInteractions);
                 wallcycle_start(wcycle, ewcUPDATE);
             }
@@ -1526,7 +1527,7 @@ double gmx::do_md(FILE *fplog, t_commrec *cr, int nfile, const t_filenm fnm[],
                             | (shouldCheckNumberOfBondedInteractions ? CGLO_CHECK_NUMBER_OF_BONDED_INTERACTIONS : 0)
                             );
             checkNumberOfBondedInteractions(fplog, cr, totalNumberOfBondedInteractions,
-                                            top_global, state,
+                                            top_global, top, state,
                                             &shouldCheckNumberOfBondedInteractions);
         }