Fixed DD state collection issue

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

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index c995192a36de1f98b87e0e7e9163d701d1c8c294..2d2ffb0fd5f374367f2c0b18117d552d9406f658 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -1320,7 +1320,6 @@ 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)
     {
@@ -1330,12 +1329,18 @@ 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;
@@ -1351,8 +1356,8 @@ 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;
@@ -1394,7 +1399,7 @@ 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);
@@ -9750,7 +9755,8 @@ 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)
@@ -9769,7 +9775,9 @@ void dd_partition_system(FILE                *fplog,
     if (!(cr->duty & DUTY_PME))
     {
         /* Send the charges and/or c6/sigmas to our PME only node */
-        gmx_pme_send_parameters(cr, mdatoms->nChargePerturbed, mdatoms->nTypePerturbed,
+        gmx_pme_send_parameters(cr,
+                                fr->ic,
+                                mdatoms->nChargePerturbed, mdatoms->nTypePerturbed,
                                 mdatoms->chargeA, mdatoms->chargeB,
                                 mdatoms->sqrt_c6A, mdatoms->sqrt_c6B,
                                 mdatoms->sigmaA, mdatoms->sigmaB,