Merge release-5-0 into master

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

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index 09480a4be4b1b5017706b7c70cef6a6257c572a1..27d2bcb14a76e8191b4341857b80396afae1c51e 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -33,6 +33,8 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 
+#include "gmxpre.h"
+
 #include "config.h"
 
 #include <stdio.h>
@@ -42,28 +44,29 @@
 #include <stdlib.h>
 #include <assert.h>
 
-#include "typedefs.h"
-#include "network.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/network.h"
 #include "gromacs/math/vec.h"
-#include "domdec.h"
-#include "domdec_network.h"
-#include "nrnb.h"
-#include "chargegroup.h"
-#include "constr.h"
-#include "mdatoms.h"
-#include "names.h"
-#include "force.h"
-#include "pme.h"
-#include "mdrun.h"
-#include "nsgrid.h"
-#include "shellfc.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/domdec_network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/force.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/shellfc.h"
 #include "gromacs/topology/mtop_util.h"
-#include "gmx_ga2la.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/gmx_ga2la.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "nbnxn_search.h"
-#include "bondf.h"
-#include "gmx_omp_nthreads.h"
-#include "gpu_utils.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/gpu_utils.h"
 
 #include "gromacs/utility/futil.h"
 #include "gromacs/fileio/gmxfio.h"
@@ -1321,7 +1324,6 @@ static void dd_collect_cg(gmx_domdec_t *dd,
 {
     gmx_domdec_master_t *ma = NULL;
     int                  buf2[2], *ibuf, i, ncg_home = 0, *cg = NULL, nat_home = 0;
-    t_block             *cgs_gl;
 
     if (state_local->ddp_count == dd->comm->master_cg_ddp_count)
     {
@@ -1331,12 +1333,18 @@ static void dd_collect_cg(gmx_domdec_t *dd,
 
     if (state_local->ddp_count == dd->ddp_count)
     {
+        /* The local state and DD are in sync, use the DD indices */
         ncg_home = dd->ncg_home;
         cg       = dd->index_gl;
         nat_home = dd->nat_home;
     }
     else if (state_local->ddp_count_cg_gl == state_local->ddp_count)
     {
+        /* The DD is out of sync with the local state, but we have stored
+         * the cg indices with the local state, so we can use those.
+         */
+        t_block *cgs_gl;
+
         cgs_gl = &dd->comm->cgs_gl;
 
         ncg_home = state_local->ncg_gl;
@@ -1352,8 +1360,8 @@ static void dd_collect_cg(gmx_domdec_t *dd,
         gmx_incons("Attempted to collect a vector for a state for which the charge group distribution is unknown");
     }
 
-    buf2[0] = dd->ncg_home;
-    buf2[1] = dd->nat_home;
+    buf2[0] = ncg_home;
+    buf2[1] = nat_home;
     if (DDMASTER(dd))
     {
         ma   = dd->ma;
@@ -1395,7 +1403,7 @@ static void dd_collect_cg(gmx_domdec_t *dd,
 
     /* Collect the charge group indices on the master */
     dd_gatherv(dd,
-               dd->ncg_home*sizeof(int), dd->index_gl,
+               ncg_home*sizeof(int), cg,
                DDMASTER(dd) ? ma->ibuf : NULL,
                DDMASTER(dd) ? ma->ibuf+dd->nnodes : NULL,
                DDMASTER(dd) ? ma->cg : NULL);
@@ -9751,7 +9759,8 @@ void dd_partition_system(FILE                *fplog,
     if (vsite != NULL)
     {
         /* Now we have updated mdatoms, we can do the last vsite bookkeeping */
-        split_vsites_over_threads(top_local->idef.il, mdatoms, FALSE, vsite);
+        split_vsites_over_threads(top_local->idef.il, top_local->idef.iparams,
+                                  mdatoms, FALSE, vsite);
     }
 
     if (shellfc)