Sort all includes in src/gromacs

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

diff --git a/src/gromacs/mdlib/clincs.c b/src/gromacs/mdlib/clincs.c
index e07ff313b1b629d5e50e5675a13b5984b33f3a01..3423b0811aa733c4d664c7a781237e268337848c 100644 (file)
--- a/src/gromacs/mdlib/clincs.c
+++ b/src/gromacs/mdlib/clincs.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -35,27 +35,27 @@
  * the research papers on the package. Check out http://www.gromacs.org.
  */
 /* This file is completely threadsafe - keep it that way! */
-#ifdef HAVE_CONFIG_H
-#include <config.h>
-#endif
+#include "gmxpre.h"
 
 #include <math.h>
-#include "main.h"
-#include "constr.h"
-#include "copyrite.h"
-#include "physics.h"
-#include "vec.h"
-#include "pbc.h"
-#include "smalloc.h"
-#include "mdrun.h"
-#include "nrnb.h"
-#include "domdec.h"
-#include "partdec.h"
-#include "mtop_util.h"
-#include "gmx_omp_nthreads.h"
+#include <stdlib.h>
 
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/legacyheaders/constr.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
+#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/mtop_util.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     int    b0;         /* first constraint for this thread */
@@ -532,10 +532,6 @@ static void do_lincs(rvec *x, rvec *xp, matrix box, t_pbc *pbc,
     {
         nlocat = dd_constraints_nlocalatoms(cr->dd);
     }
-    else if (PARTDECOMP(cr))
-    {
-        nlocat = pd_constraints_nlocalatoms(cr->pd);
-    }
     else
     {
         nlocat = NULL;
@@ -622,8 +618,7 @@ static void do_lincs(rvec *x, rvec *xp, matrix box, t_pbc *pbc,
 
     for (iter = 0; iter < lincsd->nIter; iter++)
     {
-        if ((lincsd->bCommIter && DOMAINDECOMP(cr) && cr->dd->constraints) ||
-            PARTDECOMP(cr))
+        if ((lincsd->bCommIter && DOMAINDECOMP(cr) && cr->dd->constraints))
         {
 #pragma omp barrier
 #pragma omp master
@@ -631,11 +626,7 @@ static void do_lincs(rvec *x, rvec *xp, matrix box, t_pbc *pbc,
                 /* Communicate the corrected non-local coordinates */
                 if (DOMAINDECOMP(cr))
                 {
-                    dd_move_x_constraints(cr->dd, box, xp, NULL);
-                }
-                else
-                {
-                    pd_move_x_constraints(cr, xp, NULL);
+                    dd_move_x_constraints(cr->dd, box, xp, NULL, FALSE);
                 }
             }
         }
@@ -656,6 +647,7 @@ static void do_lincs(rvec *x, rvec *xp, matrix box, t_pbc *pbc,
             dlen2 = 2*len2 - norm2(dx);
             if (dlen2 < wfac*len2 && (nlocat == NULL || nlocat[b]))
             {
+                /* not race free - see detailed comment in caller */
                 *warn = b;
             }
             if (dlen2 > 0)
@@ -1205,13 +1197,9 @@ void set_lincs(t_idef *idef, t_mdatoms *md,
         }
         start = 0;
     }
-    else if (PARTDECOMP(cr))
-    {
-        pd_get_constraint_range(cr->pd, &start, &natoms);
-    }
     else
     {
-        start  = md->start;
+        start  = 0;
         natoms = md->homenr;
     }
     at2con = make_at2con(start, natoms, idef->il, idef->iparams, bDynamics,