Move ns.h and nsgrid.h to mdlib/

Two more headers out of legacyheaders/.  Remove unnecessary include from
nonbonded.cpp to avoid a circular dependency.

Change-Id: I8936e770407eef9f92abb0477b8e24c2b3d0ec7a

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index d2160435acb700f6e35360bf60afe03db5d80d85..9ce1f617429ef2b046146d493270e113481f9430 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -62,7 +62,6 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
@@ -85,6 +84,7 @@
 #include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_grid.h"
+#include "gromacs/mdlib/nsgrid.h"
 #include "gromacs/mdlib/shellfc.h"
 #include "gromacs/mdlib/vsite.h"
 #include "gromacs/pbcutil/ishift.h"

diff --git a/src/gromacs/domdec/domdec_box.cpp b/src/gromacs/domdec/domdec_box.cpp
index 170e36b97621577895ef910d82cb3c966474102d..d99280f5c0e16f65e6e796f9bcfd232fbe26f926 100644 (file)
--- a/src/gromacs/domdec/domdec_box.cpp
+++ b/src/gromacs/domdec/domdec_box.cpp
@@ -47,10 +47,10 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_network.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/nsgrid.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/fatalerror.h"
 

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
index d99e71b7fb6c39c91742654c1a0bc7f112bfc66d..7f1ed638b0718d1bf132d3f2ec7bc2e6e84b01ef 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.cpp
@@ -53,7 +53,6 @@
 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index aba274c66c0c21af38ee10d025b76c66b397251b..a1f9a9236d818c972c2fb1b099c0db1f28204286 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -54,7 +54,6 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -62,6 +61,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/forcerec-threading.h"
 #include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index 647be0f8fc9255248b50fe7323a72043c3875c8e..afe159b44d70e47cba047ee716d8907464230b80 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -60,7 +60,6 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -80,6 +79,7 @@
 #include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 #include "gromacs/mdlib/nbnxn_util.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index 165272d39cd4a896a059023e728b1c0f6c3c48eb..da9487e1c27950c734150aba2af1ca2804217c5b 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -64,7 +64,6 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -79,6 +78,7 @@
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdebin.h"
 #include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdlib/trajectory_writing.h"

diff --git a/src/gromacs/mdlib/nbnxn_search.cpp b/src/gromacs/mdlib/nbnxn_search.cpp
index 9fa72185b8af3771e26d2d9b4386da96493a7660..8ac340a40c4c0d18d7d6d28c6881174d8f88cabe 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.cpp
+++ b/src/gromacs/mdlib/nbnxn_search.cpp
@@ -48,7 +48,6 @@
 
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/math/utilities.h"
@@ -60,6 +59,7 @@
 #include "gromacs/mdlib/nbnxn_internal.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 #include "gromacs/mdlib/nbnxn_util.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/simd/simd.h"

diff --git a/src/gromacs/mdlib/ns.cpp b/src/gromacs/mdlib/ns.cpp
index 5409fa3892e32e5f02dc265de38c457154cfc0b7..931d48e079684fcf6a3f600721547ed38568fa2d 100644 (file)
--- a/src/gromacs/mdlib/ns.cpp
+++ b/src/gromacs/mdlib/ns.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/ns.h"
+#include "ns.h"
 
 #include <math.h>
 #include <stdlib.h>
@@ -51,7 +51,6 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/nsgrid.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
@@ -59,6 +58,7 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/nsgrid.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/legacyheaders/ns.h b/src/gromacs/mdlib/ns.h
similarity index 92%
rename from src/gromacs/legacyheaders/ns.h
rename to src/gromacs/mdlib/ns.h
index be53735751856e27e5d0c128c0df1f5fabca79f6..66407dd2b794728ec79cc0ab5b8ad39f9a1bf90b 100644 (file)
--- a/src/gromacs/legacyheaders/ns.h
+++ b/src/gromacs/mdlib/ns.h
@@ -34,9 +34,8 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-#ifndef _ns_h
-#define _ns_h
+#ifndef GMX_MDLIB_NS_H
+#define GMX_MDLIB_NS_H
 
 #include <stdio.h>
 
@@ -49,10 +48,6 @@ struct t_mdatoms;
 struct t_nblist;
 struct t_nrnb;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 /****************************************************
  *
  *    U T I L I T I E S May be found in ns.c
@@ -80,21 +75,21 @@ int calc_naaj(int icg, int cgtot);
  *    Return total number of pairs searched
  *
  ****************************************************/
-void init_ns(FILE *fplog, const struct t_commrec *cr,
+void init_ns(FILE *fplog, const t_commrec *cr,
              gmx_ns_t *ns, t_forcerec *fr,
              const gmx_mtop_t *mtop);
 
 int search_neighbours(FILE *log, t_forcerec *fr, matrix box,
                       gmx_localtop_t *top,
                       gmx_groups_t *groups,
-                      struct t_commrec *cr,
+                      t_commrec *cr,
                       t_nrnb *nrnb, t_mdatoms *md,
                       gmx_bool bFillGrid,
                       gmx_bool bDoLongRangeNS);
 
 
 /* Debugging routines from wnblist.c */
-void dump_nblist(FILE *out, struct t_commrec *cr, t_forcerec *fr, int nDNL);
+void dump_nblist(FILE *out, t_commrec *cr, t_forcerec *fr, int nDNL);
 
 int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
 /* Returns total number of neighbors. If bSymm the matrix is symmetrized. */
@@ -102,9 +97,4 @@ int read_nblist(FILE *in, FILE *out, int **mat, int natoms, gmx_bool bSymm);
 void reallocate_nblist(t_nblist *nl);
 /* List reallocation, only exported for Verlet scheme use with FEP */
 
-#ifdef __cplusplus
-}
 #endif
-
-
-#endif  /* _ns_h */

diff --git a/src/gromacs/mdlib/nsgrid.cpp b/src/gromacs/mdlib/nsgrid.cpp
index b20f041bc56c4737e9fb6bd1c737cf5c211222a6..c7660af48e1fe20561bbe0b0a76c9607d47dbe80 100644 (file)
--- a/src/gromacs/mdlib/nsgrid.cpp
+++ b/src/gromacs/mdlib/nsgrid.cpp
@@ -37,7 +37,7 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/nsgrid.h"
+#include "nsgrid.h"
 
 #include <stdio.h>
 #include <stdlib.h>

diff --git a/src/gromacs/legacyheaders/nsgrid.h b/src/gromacs/mdlib/nsgrid.h
similarity index 98%
rename from src/gromacs/legacyheaders/nsgrid.h
rename to src/gromacs/mdlib/nsgrid.h
index 10ca6ef9b5d99ada1e055b218fe7b63766857341..a4795be292d07431c3ee8cd5760250249691a649 100644 (file)
--- a/src/gromacs/legacyheaders/nsgrid.h
+++ b/src/gromacs/mdlib/nsgrid.h
@@ -34,6 +34,8 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
+#ifndef GMX_MDLIB_NSGRID_H
+#define GMX_MDLIB_NSGRID_H
 
 #include "gromacs/legacyheaders/typedefs.h"
 
@@ -43,10 +45,6 @@ struct gmx_ddbox_t;
 struct t_forcerec;
 struct t_grid;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 /*! \brief Used when estimating the interaction density.
  *
  * GRID_STDDEV_FAC * stddev estimates the interaction density. The
@@ -118,6 +116,4 @@ void check_grid(t_grid *grid);
 
 void print_grid(FILE *log, t_grid *grid);
 
-#ifdef __cplusplus
-}
 #endif

diff --git a/src/gromacs/mdlib/qm_gamess.cpp b/src/gromacs/mdlib/qm_gamess.cpp
index e3f9b6d26550d5d703eaf642c8c09b6626701f6f..7b1f280f038f65d64d1e7b0f4484edcd687e0087 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.cpp
+++ b/src/gromacs/mdlib/qm_gamess.cpp
@@ -49,13 +49,13 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/qm_gaussian.cpp b/src/gromacs/mdlib/qm_gaussian.cpp
index 069bb3d6c88f2383e4b735c25d3161552c6f2618..3d09f9291a5c03e6a1245c26d8de9fdf569be953 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.cpp
+++ b/src/gromacs/mdlib/qm_gaussian.cpp
@@ -49,12 +49,12 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/qm_mopac.cpp b/src/gromacs/mdlib/qm_mopac.cpp
index 0277d4b2ab3e7e708d1b28781a37ad5ac509f5c3..178cfc7e1090a83b2ec49579968b8811eb98fefe 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.cpp
+++ b/src/gromacs/mdlib/qm_mopac.cpp
@@ -49,12 +49,12 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/qm_orca.cpp b/src/gromacs/mdlib/qm_orca.cpp
index 4347120bf2ab4b4108ecfc9a101775b0664e072c..a9e9f179dc13c353f31b738576961bd1789a1f4b 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.cpp
+++ b/src/gromacs/mdlib/qm_orca.cpp
@@ -45,12 +45,12 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/qmmm.cpp b/src/gromacs/mdlib/qmmm.cpp
index af1311145d4b7cd0926877513bc4db3117234c0d..357ac6a935dc21917b659b35ccf8e02cc5110b65 100644 (file)
--- a/src/gromacs/mdlib/qmmm.cpp
+++ b/src/gromacs/mdlib/qmmm.cpp
@@ -53,7 +53,6 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -61,6 +60,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/mdlib/tpi.cpp b/src/gromacs/mdlib/tpi.cpp
index 0cce08ad7762f963db241da8eb83eb7688127508..936f4b5541692726fdb2c1610221dbdc8203b2f0 100644 (file)
--- a/src/gromacs/mdlib/tpi.cpp
+++ b/src/gromacs/mdlib/tpi.cpp
@@ -63,7 +63,6 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -75,6 +74,7 @@
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdebin.h"
 #include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdlib/update.h"

diff --git a/src/gromacs/mdlib/wnblist.cpp b/src/gromacs/mdlib/wnblist.cpp
index 76b4bd9a40a8d53215e51d5cb0f274fb9e31bc46..e32339056f90fc998aa47ad3660596733ab94964 100644 (file)
--- a/src/gromacs/mdlib/wnblist.cpp
+++ b/src/gromacs/mdlib/wnblist.cpp
@@ -46,9 +46,9 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/mdlib/force.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index ee0ce8775b623091ab7a2d5f18197767096f3d5f..b9ed43a0a3d045dfa02cf522165290f5bc4e8fc3 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -60,7 +60,6 @@
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
@@ -90,6 +89,7 @@
 #include "gromacs/mdlib/mdrun_signalling.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
+#include "gromacs/mdlib/ns.h"
 #include "gromacs/mdlib/shellfc.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/mdlib/tgroup.h"