Sort all includes in src/gromacs

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

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index c871588c016642038331d61808e18bb9185c4e3a..bad4092e3ebe4060c7721a4a54984436a5f8098a 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -35,51 +35,52 @@
 
 #include "gmxpre.h"
 
+#include "gromacs/legacyheaders/domdec.h"
+
 #include "config.h"
 
-#include <stdio.h>
-#include <time.h>
+#include <assert.h>
 #include <math.h>
-#include <string.h>
+#include <stdio.h>
 #include <stdlib.h>
-#include <assert.h>
+#include <string.h>
+#include <time.h>
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/domdec.h"
-#include "gromacs/legacyheaders/domdec_network.h"
-#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/bonded-threading.h"
 #include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/constr.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/domdec_network.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 "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "nbnxn_search.h"
-#include "gromacs/legacyheaders/bondf.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/gpu_utils.h"
-
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/imd/imd.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdatoms.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/nsgrid.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/shellfc.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/pulling/pull_rotation.h"
 #include "gromacs/swap/swapcoords.h"
 #include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/qsort_threadsafe.h"
 #include "gromacs/utility/smalloc.h"
@@ -1323,7 +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)
     {
@@ -1333,12 +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;
@@ -1354,8 +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;
@@ -1397,7 +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);
@@ -9753,7 +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)