Clean up cshake() and resolve old issues

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

diff --git a/src/gromacs/mdlib/constr.c b/src/gromacs/mdlib/constr.c
index d3df9392e44b29be77958f98efe7a6ba0afcd2e3..07866e190109f82f8fe21d9a59c6379ad53f93d0 100644 (file)
--- a/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@ -34,35 +34,33 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
+
+#include "gromacs/legacyheaders/constr.h"
 
 #include <assert.h>
 #include <stdlib.h>
 
+#include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/confio.h"
-#include "types/commrec.h"
-#include "constr.h"
-#include "copyrite.h"
-#include "mdrun.h"
-#include "nrnb.h"
-#include "gromacs/math/vec.h"
-#include "names.h"
-#include "txtdump.h"
-#include "domdec.h"
-#include "gromacs/fileio/pdbio.h"
-#include "splitter.h"
-#include "gromacs/topology/mtop_util.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "macros.h"
-#include "gmx_omp_nthreads.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/pulling/pull.h"
-
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/splitter.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
 #include "gromacs/topology/block.h"
 #include "gromacs/topology/invblock.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
@@ -80,7 +78,7 @@ typedef struct gmx_constr {
     int                nblocks;        /* The number of SHAKE blocks         */
     int               *sblock;         /* The SHAKE blocks                   */
     int                sblock_nalloc;  /* The allocation size of sblock      */
-    real              *lagr;           /* Lagrange multipliers for SHAKE     */
+    real              *lagr;           /* -2 times the Lagrange multipliers for SHAKE */
     int                lagr_nalloc;    /* The allocation size of lagr        */
     int                maxwarn;        /* The maximum number of warnings     */
     int                warncount_lincs;
@@ -204,6 +202,18 @@ int n_flexible_constraints(struct gmx_constr *constr)
     return nflexcon;
 }
 
+static void clear_constraint_quantity_nonlocal(gmx_domdec_t *dd, rvec *q)
+{
+    int nonlocal_at_start, nonlocal_at_end, at;
+
+    dd_get_constraint_range(dd, &nonlocal_at_start, &nonlocal_at_end);
+
+    for (at = nonlocal_at_start; at < nonlocal_at_end; at++)
+    {
+        clear_rvec(q[at]);
+    }
+}
+
 void too_many_constraint_warnings(int eConstrAlg, int warncount)
 {
     const char *abort = "- aborting to avoid logfile runaway.\n"
@@ -432,6 +442,15 @@ gmx_bool constrain(FILE *fplog, gmx_bool bLog, gmx_bool bEner,
     if (cr->dd)
     {
         dd_move_x_constraints(cr->dd, box, x, xprime, econq == econqCoord);
+
+        if (v != NULL)
+        {
+            /* We need to initialize the non-local components of v.
+             * We never actually use these values, but we do increment them,
+             * so we should avoid uninitialized variables and overflows.
+             */
+            clear_constraint_quantity_nonlocal(cr->dd, v);
+        }
     }
 
     if (constr->lincsd != NULL)