More headers out of legacyheaders

Another bunch of headers moved to gmxlib and mdlib, keeping existing
module-level dependencies intact.

Change-Id: I04639785ae1385e3bef41e524894a68370d9b40b

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 85be976e7ce055fc07087344817d28c1b957f739..f99b4181e61c8e359a87683395911ceeaf64a23b 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -59,7 +59,6 @@
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -84,6 +83,7 @@
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_grid.h"
 #include "gromacs/mdlib/shellfc.h"

diff --git a/src/gromacs/essentialdynamics/edsam.cpp b/src/gromacs/essentialdynamics/edsam.cpp
index 11ea84074759eb52be348fbd3e870035120148ac..49a644b0529aaf4f0a33104cd6907249651d81ed 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.cpp
+++ b/src/gromacs/essentialdynamics/edsam.cpp
@@ -45,18 +45,18 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/update.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxana/gmx_bar.cpp b/src/gromacs/gmxana/gmx_bar.cpp
index fdd11c4a1a488cc8f1a1e5db35a7d352d1849c65..b9ddc9512740a36d1c17167181cc0915cac23736 100644 (file)
--- a/src/gromacs/gmxana/gmx_bar.cpp
+++ b/src/gromacs/gmxana/gmx_bar.cpp
@@ -47,11 +47,11 @@
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"
+#include "gromacs/mdlib/mdebin.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/dir_separator.h"

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index 0875cbe5db459b141b6a093db450d9b6f0c65fb9..c75b806564c35cedf0ecdfa10a1b37c8b5fc28de 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -53,9 +53,8 @@
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
 #include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/typedefs.h"
@@ -64,6 +63,7 @@
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/gmxana/gmx_energy.cpp b/src/gromacs/gmxana/gmx_energy.cpp
index 009b42947f173d8eb1f7b55293e2c2ae45865e96..236b13ff1fe89b654ce2ccdd2d59971f12c19f9b 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.cpp
+++ b/src/gromacs/gmxana/gmx_energy.cpp
@@ -53,12 +53,12 @@
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdebin.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxana/gmx_genion.cpp b/src/gromacs/gmxana/gmx_genion.cpp
index b5ae29c1e963d4f94bede6989f36a457f1cf4973..98888397d55a7dba591e9b8bb7393e99b986d4c7 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.cpp
+++ b/src/gromacs/gmxana/gmx_genion.cpp
@@ -44,9 +44,9 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
 #include "gromacs/topology/index.h"

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 87a65fdb991b403f6245650703e3f572e8112ece..ef2303d1de02e635853c9244e0ad07e505c5e4bd 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -44,10 +44,10 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxlib/calcgrid.h"
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"

diff --git a/src/gromacs/gmxlib/disre.cpp b/src/gromacs/gmxlib/disre.cpp
index c9681eae997b856f680407dddd639b3412a35b75..256b9bef1658ca8334399223efee315d3f6781d9 100644 (file)
--- a/src/gromacs/gmxlib/disre.cpp
+++ b/src/gromacs/gmxlib/disre.cpp
@@ -47,8 +47,8 @@
 
 #include <algorithm>
 
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"

diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index 4d216be86413f39e303055d6c11c030d6f0fe74b..41bea0bbd95b104c7b5b000415eef771e4354233 100644 (file)
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/main.h"
+#include "main.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/legacyheaders/main.h b/src/gromacs/gmxlib/main.h
similarity index 96%
rename from src/gromacs/legacyheaders/main.h
rename to src/gromacs/gmxlib/main.h
index 0447b4e934a965f8833eb2af64ea5092f4990ec8..daeee099b5d208919967dd2122b417673745f38f 100644 (file)
--- a/src/gromacs/legacyheaders/main.h
+++ b/src/gromacs/gmxlib/main.h
@@ -34,10 +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 _main_h
-#define _main_h
-
+#ifndef GMX_GMXLIB_MAIN_H
+#define GMX_GMXLIB_MAIN_H
 
 #include <stdio.h>
 
@@ -46,10 +44,6 @@
 
 struct gmx_multisim_t;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 void gmx_log_open(const char *fn, const t_commrec *cr,
                   gmx_bool bAppendFiles, FILE**);
 /* Open the log file, if necessary (nprocs > 1) the logfile name is
@@ -79,8 +73,4 @@ void init_multisystem(t_commrec *cr, int nsim, char **multidirs,
  * If bParFn is set, the nodeid is appended to the tpx and each output file.
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _main_h */

diff --git a/src/gromacs/gmxlib/orires.cpp b/src/gromacs/gmxlib/orires.cpp
index df1fb6594214be36099ca41f2a6f8f28e35e5343..c41cd1b118104b1d5c3600b78a375a50e8200d62 100644 (file)
--- a/src/gromacs/gmxlib/orires.cpp
+++ b/src/gromacs/gmxlib/orires.cpp
@@ -40,8 +40,8 @@
 
 #include <cmath>
 
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"

diff --git a/src/gromacs/imd/imd.cpp b/src/gromacs/imd/imd.cpp
index 1bffd8fe1c1c8d6d55ffe2d06d2f7be1d5f41de9..0e73e335eec894eeb7a54adc0bba1986848c9f25 100644 (file)
--- a/src/gromacs/imd/imd.cpp
+++ b/src/gromacs/imd/imd.cpp
@@ -66,12 +66,12 @@
 #include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/imd/imdsocket.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"

diff --git a/src/gromacs/mdlib/broadcaststructs.cpp b/src/gromacs/mdlib/broadcaststructs.cpp
index 582def639aab141f15c384673eb74be3a2c3cf95..bda4dc5d3642fd5a7cf8b91b4f2b727237dab5ab 100644 (file)
--- a/src/gromacs/mdlib/broadcaststructs.cpp
+++ b/src/gromacs/mdlib/broadcaststructs.cpp
@@ -39,15 +39,15 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdrun.h"
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/tgroup.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/clincs.cpp b/src/gromacs/mdlib/clincs.cpp
index 007c371d4f809396b0b79aa8fe925033cffa87ab..b0215739ff5b807e91fc4afeefd64e16e1dfb01f 100644 (file)
--- a/src/gromacs/mdlib/clincs.cpp
+++ b/src/gromacs/mdlib/clincs.cpp
@@ -48,12 +48,12 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/legacyheaders/copyrite.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/mdlib/constr.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/pbc-simd.h"
 #include "gromacs/simd/simd.h"

diff --git a/src/gromacs/mdlib/constr.cpp b/src/gromacs/mdlib/constr.cpp
index 35178cf0c427f3ecd6b6b835f483a8345fdc6975..dc29cbd80ef706def325dbe79b4900c2c984a75c 100644 (file)
--- a/src/gromacs/mdlib/constr.cpp
+++ b/src/gromacs/mdlib/constr.cpp
@@ -53,12 +53,12 @@
 #include "gromacs/gmxlib/splitter.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/topology/block.h"

diff --git a/src/gromacs/mdlib/coupling.cpp b/src/gromacs/mdlib/coupling.cpp
index 25fcf9fbca3d0b63a0544ed11b095de8b4368201..797265ed2e0a68e4e9f067a94121e6b439ee359b 100644 (file)
--- a/src/gromacs/mdlib/coupling.cpp
+++ b/src/gromacs/mdlib/coupling.cpp
@@ -41,19 +41,19 @@
 #include <algorithm>
 
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/energy.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/legacyheaders/types/nrnb.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/update.h"
 #include "gromacs/random/random.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/ebin.cpp b/src/gromacs/mdlib/ebin.cpp
index 22b21d42510b64f0ccaffe44074b68e146a88c42..57f4f3087b0e2472db59ee9400ee26f13a2c3661 100644 (file)
--- a/src/gromacs/mdlib/ebin.cpp
+++ b/src/gromacs/mdlib/ebin.cpp
@@ -37,7 +37,7 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/ebin.h"
+#include "ebin.h"
 
 #include <math.h>
 #include <string.h>

diff --git a/src/gromacs/legacyheaders/ebin.h b/src/gromacs/mdlib/ebin.h
similarity index 95%
rename from src/gromacs/legacyheaders/ebin.h
rename to src/gromacs/mdlib/ebin.h
index f0bd0e79140d77a73e9a6a13572879725a332ee7..ee9b0918b82fea57fe747d227f174ad8109d600b 100644 (file)
--- a/src/gromacs/legacyheaders/ebin.h
+++ b/src/gromacs/mdlib/ebin.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -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 _ebin_h
-#define _ebin_h
+#ifndef GMX_MDLIB_EBIN_H
+#define GMX_MDLIB_EBIN_H
 
 #include <stdio.h>
 
@@ -44,11 +43,6 @@
 #include "gromacs/legacyheaders/types/energy.h"
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
 /* This is a running averaging structure ('energy bin') for use during mdrun. */
 typedef struct {
     int             nener;
@@ -101,8 +95,4 @@ void pr_ebin(FILE *fp, t_ebin *eb, int index, int nener, int nperline,
  * If bPrHead than the header is printed.
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _ebin_h */

diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp
index 6dc33b3810b0ba39394f09fc4ea1919df5475b52..2b840ec4e2993a4740544d4e51bbd46991322af5 100644 (file)
--- a/src/gromacs/mdlib/expanded.cpp
+++ b/src/gromacs/mdlib/expanded.cpp
@@ -48,17 +48,17 @@
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/calcmu.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/mdrun.h"
+#include "gromacs/mdlib/update.h"
 #include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index 84abe41bc86d6f501ab3cecdecb3aaa8fee4729c..6481ebebe1f9213068fef342a3099f057b6d180f 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -50,7 +50,6 @@
 #include "gromacs/ewald/pme.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
@@ -62,6 +61,7 @@
 #include "gromacs/listed-forces/listed-forces.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/qmmm.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"

diff --git a/src/gromacs/mdlib/forcerec.h b/src/gromacs/mdlib/forcerec.h
index 30ecf5961c45a873f9bacab8faba4dedc2714924..2bea6b346753f5f835eeb3c712a97b7ac023dd5f 100644 (file)
--- a/src/gromacs/mdlib/forcerec.h
+++ b/src/gromacs/mdlib/forcerec.h
@@ -39,11 +39,11 @@
 
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
+#include "gromacs/mdlib/tgroup.h"
 #include "gromacs/timing/wallcycle.h"
 
 struct t_fcdata;

diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp
index cc42975c22d288373bef398c676ae3a57cacddc7..c5717c959ab699068cafec4837c6bcebce593b93 100644 (file)
--- a/src/gromacs/mdlib/md_support.cpp
+++ b/src/gromacs/mdlib/md_support.cpp
@@ -44,16 +44,16 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/gmxlib/md_logging.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/mdrun_signalling.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/vcm.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/arrayref.h"

diff --git a/src/gromacs/mdlib/md_support.h b/src/gromacs/mdlib/md_support.h
index a572b1c00cc80c3f840d205e575df7cb6e7f4810..4aaf28c768a0c315fbd87631982a7c89903f1460 100644 (file)
--- a/src/gromacs/mdlib/md_support.h
+++ b/src/gromacs/mdlib/md_support.h
@@ -38,8 +38,8 @@
 #define GMX_MDLIB_MD_SUPPORT_H
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/vcm.h"
 #include "gromacs/timing/wallcycle.h"
 
 struct gmx_constr;

diff --git a/src/gromacs/mdlib/mdebin.cpp b/src/gromacs/mdlib/mdebin.cpp
index 8ee2e1bc6a6b48fa8635356fb870a1f87be6045a..9879aa273f4b83075c024c7d1d1ede401ef26e64 100644 (file)
--- a/src/gromacs/mdlib/mdebin.cpp
+++ b/src/gromacs/mdlib/mdebin.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/mdebin.h"
+#include "mdebin.h"
 
 #include <float.h>
 #include <stdlib.h>
@@ -47,7 +47,6 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/orires.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
@@ -57,6 +56,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/mdebin_bar.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/legacyheaders/mdebin.h b/src/gromacs/mdlib/mdebin.h
similarity index 96%
rename from src/gromacs/legacyheaders/mdebin.h
rename to src/gromacs/mdlib/mdebin.h
index 4258c974c99c048f09d8d57d6b6f66ec5865c850..81f7ce4bbe362cfacdd4fbaac60a5b413ab37b9f 100644 (file)
--- a/src/gromacs/legacyheaders/mdebin.h
+++ b/src/gromacs/mdlib/mdebin.h
@@ -34,16 +34,15 @@
  * 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 _mdebin_h
-#define _mdebin_h
+#ifndef GMX_MDLIB_MDEBIN_H
+#define GMX_MDLIB_MDEBIN_H
 
 #include <stdio.h>
 
 #include "gromacs/fileio/enxio.h"
-#include "gromacs/legacyheaders/ebin.h"
 #include "gromacs/legacyheaders/types/forcerec.h"
 #include "gromacs/legacyheaders/types/state.h"
+#include "gromacs/mdlib/ebin.h"
 
 struct gmx_constr;
 struct gmx_ekindata_t;
@@ -51,10 +50,6 @@ struct gmx_mtop_t;
 struct gmx_output_env_t;
 struct t_fcdata;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 /* The functions & data structures here determine the content for outputting
    the .edr file; the file format and actual writing is done with functions
    defined in enxio.h */
@@ -144,9 +139,9 @@ void upd_mdebin(t_mdebin                 *md,
                 tensor                    fvir,
                 tensor                    vir,
                 tensor                    pres,
-                struct gmx_ekindata_t    *ekind,
+                gmx_ekindata_t           *ekind,
                 rvec                      mu_tot,
-                struct gmx_constr        *constr);
+                gmx_constr               *constr);
 
 void upd_mdebin_step(t_mdebin *md);
 /* Updates only the step count in md */
@@ -174,8 +169,4 @@ void update_energyhistory(energyhistory_t * enerhist, t_mdebin * mdebin);
 void restore_energyhistory_from_state(t_mdebin        * mdebin,
                                       energyhistory_t * enerhist);
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _mdebin_h */

diff --git a/src/gromacs/mdlib/mdebin_bar.cpp b/src/gromacs/mdlib/mdebin_bar.cpp
index a6d7c2ce8c1fe8709afaebbe5f4af7f771b91949..05da3ea5a37e7394f653656013174cef3caad8b4 100644 (file)
--- a/src/gromacs/mdlib/mdebin_bar.cpp
+++ b/src/gromacs/mdlib/mdebin_bar.cpp
@@ -43,8 +43,8 @@
 #include <string.h>
 
 #include "gromacs/fileio/enxio.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/mdebin.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/mdebin_bar.h b/src/gromacs/mdlib/mdebin_bar.h
index c31a068edf96544f35a31252af2e9219ee7bc881..b0af7caec5dd0b0631ff5ceb5d4f0bb507f24a05 100644 (file)
--- a/src/gromacs/mdlib/mdebin_bar.h
+++ b/src/gromacs/mdlib/mdebin_bar.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -38,7 +38,7 @@
 #ifndef _mdebin_bar_h
 #define _mdebin_bar_h
 
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/mdlib/mdebin.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/mdlib/mdoutf.cpp b/src/gromacs/mdlib/mdoutf.cpp
index 5bac2f7a3676b9a866212911e048ff4dec9085d4..d262f3a00a562ac85b19b8d9d6d8a7c991ddea3f 100644 (file)
--- a/src/gromacs/mdlib/mdoutf.cpp
+++ b/src/gromacs/mdlib/mdoutf.cpp
@@ -44,9 +44,9 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/trajectory_writing.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/legacyheaders/mdrun.h b/src/gromacs/mdlib/mdrun.h
similarity index 95%
rename from src/gromacs/legacyheaders/mdrun.h
rename to src/gromacs/mdlib/mdrun.h
index 1d00e9827cbdaa02f6f05e85aac868b6ca1ef772..571db820f4bed0b44497c812c74afc7afefec52c 100644 (file)
--- a/src/gromacs/legacyheaders/mdrun.h
+++ b/src/gromacs/mdlib/mdrun.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 _mdrun_h
-#define _mdrun_h
+#ifndef GMX_MDLIB_MDRUN_H
+#define GMX_MDLIB_MDRUN_H
 
 #include <stdio.h>
 #include <time.h>
@@ -48,15 +47,12 @@
 struct gmx_constr;
 struct gmx_edsam;
 struct gmx_enerdata_t;
+struct t_commrec;
 struct t_expanded;
 struct t_lambda;
 struct t_mdatoms;
 struct t_simtemp;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 #define MD_POLARISE       (1<<2)
 #define MD_RERUN          (1<<4)
 #define MD_RERUN_VSITE    (1<<5)
@@ -104,12 +100,8 @@ void set_state_entries(t_state *state, const t_inputrec *ir);
 void init_parallel(t_commrec *cr, t_inputrec *inputrec,
                    gmx_mtop_t *mtop);
 
-void bcast_state(const struct t_commrec *cr, t_state *state);
+void bcast_state(const t_commrec *cr, t_state *state);
 /* Broadcasts state from the master to all nodes in cr->mpi_comm_mygroup.
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _mdrun_h */

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index 165cd3fa2ac183d9d8edcce3f0af230b78d188e9..d8676b1ed8821d0109b12333c9f6f63a3ef84130 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -62,16 +62,12 @@
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
@@ -82,8 +78,12 @@
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/update.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"

diff --git a/src/gromacs/mdlib/qmmm.h b/src/gromacs/mdlib/qmmm.h
index d9e23b9650324284fe9a8f2a5127c0693cbf6b3a..57a6d81fbcbeca770627b86230bd1575bcbfdb93 100644 (file)
--- a/src/gromacs/mdlib/qmmm.h
+++ b/src/gromacs/mdlib/qmmm.h
@@ -39,8 +39,8 @@
 #define _QMMM_h
 
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/tgroup.h"
 
 struct t_forcerec;
 struct t_QMMMrec;

diff --git a/src/gromacs/mdlib/shellfc.cpp b/src/gromacs/mdlib/shellfc.cpp
index 9198fdcc99161974e194fc4dfae4b83764b0c7bb..05822bfa8fcd673e83b836bf5c02283667c71fe8 100644 (file)
--- a/src/gromacs/mdlib/shellfc.cpp
+++ b/src/gromacs/mdlib/shellfc.cpp
@@ -46,7 +46,6 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/txtdump.h"
@@ -56,6 +55,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 18cdb35be808aaa1bcb605a8c313ea8179731bab..8e9f363d0fbd82eb3f2201c8f29013f393d71063 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -58,14 +58,12 @@
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/listed-forces/bonded.h"
 #include "gromacs/math/units.h"
@@ -73,12 +71,14 @@
 #include "gromacs/mdlib/calcmu.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_atomdata.h"
 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
 #include "gromacs/mdlib/nbnxn_grid.h"
 #include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/mdlib/qmmm.h"
+#include "gromacs/mdlib/update.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_gpu_ref.h"
 #include "gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.h"
 #include "gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"

diff --git a/src/gromacs/mdlib/sim_util.h b/src/gromacs/mdlib/sim_util.h
index 113356c5dca36b6ca90f2fe38c0a5819bfc98020..db375b1b83f06e2bd7d7c973d70bd894dcda00c4 100644 (file)
--- a/src/gromacs/mdlib/sim_util.h
+++ b/src/gromacs/mdlib/sim_util.h
@@ -38,11 +38,11 @@
 #define GMX_MDLIB_SIM_UTIL_H
 
 #include "gromacs/fileio/enxio.h"
-#include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/vcm.h"
+#include "gromacs/mdlib/mdebin.h"
 #include "gromacs/mdlib/mdoutf.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vcm.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
 

diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp
index 922c2475a2b43c7de22e8daed48460835c3473b6..806e744b00b247fed390830bdf315af24d528245 100644 (file)
--- a/src/gromacs/mdlib/stat.cpp
+++ b/src/gromacs/mdlib/stat.cpp
@@ -43,21 +43,21 @@
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/md_support.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/rbin.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/vcm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/tgroup.cpp b/src/gromacs/mdlib/tgroup.cpp
index 659db9a13c17c7bfa9df58ed2bcc3eba2f501324..af62dfca1fb489b0ea5ea5cf1d3b3b0b3783bff8 100644 (file)
--- a/src/gromacs/mdlib/tgroup.cpp
+++ b/src/gromacs/mdlib/tgroup.cpp
@@ -37,17 +37,17 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/tgroup.h"
+#include "tgroup.h"
 
 #include <math.h>
 
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/rbin.h"
+#include "gromacs/mdlib/update.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/legacyheaders/tgroup.h b/src/gromacs/mdlib/tgroup.h
similarity index 79%
rename from src/gromacs/legacyheaders/tgroup.h
rename to src/gromacs/mdlib/tgroup.h
index 7194bde173976b339a4846eebcefc54e53c3f127..9661f69c8ac89750bcfcb6094ef1b2e9f2664a41 100644 (file)
--- a/src/gromacs/legacyheaders/tgroup.h
+++ b/src/gromacs/mdlib/tgroup.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 _tgroup_h
-#define _tgroup_h
+#ifndef GMX_MDLIB_TGROUP_H
+#define GMX_MDLIB_TGROUP_H
 
 #include "gromacs/legacyheaders/typedefs.h"
 
@@ -45,39 +44,31 @@ struct t_commrec;
 struct t_grpopts;
 struct t_mdatoms;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 void init_ekindata(FILE *log, gmx_mtop_t *mtop,
-                   struct t_grpopts *opts,
-                   struct gmx_ekindata_t *ekind);
+                   t_grpopts *opts,
+                   gmx_ekindata_t *ekind);
 /* Allocate memory and set the grpnr array. */
 
-void done_ekindata(struct gmx_ekindata_t *ekind);
+void done_ekindata(gmx_ekindata_t *ekind);
 /* Free the memory */
 
-void accumulate_u(struct t_commrec *cr, struct t_grpopts *opts,
-                  struct gmx_ekindata_t *ekind);
+void accumulate_u(t_commrec *cr, t_grpopts *opts,
+                  gmx_ekindata_t *ekind);
 
 /* Communicate subsystem - group velocities and subsystem ekin respectively
  * and sum them up. Return them in grps.
  */
 
-real sum_ekin(struct t_grpopts *opts, struct gmx_ekindata_t *ekind, real *dekindlambda,
+real sum_ekin(t_grpopts *opts, gmx_ekindata_t *ekind, real *dekindlambda,
               gmx_bool bEkinFullStep, gmx_bool bScaleEkin);
 /* Sum the group ekins into total ekin and calc temp per group,
  * return total temperature.
  */
 
-void update_ekindata(int start, int homenr, struct gmx_ekindata_t *ekind,
-                     struct t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda);
+void update_ekindata(int start, int homenr, gmx_ekindata_t *ekind,
+                     t_grpopts *opts, rvec v[], t_mdatoms *md, real lambda);
 /* Do the update of group velocities (if bNEMD) and
  * (partial) group ekin.
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _tgroup_h */

diff --git a/src/gromacs/mdlib/tpi.cpp b/src/gromacs/mdlib/tpi.cpp
index a8d665cc54ba720a4eb03473619ce7abff0925d1..c317c321d3ffd00412a117bddc558bb2c28d7c15 100644 (file)
--- a/src/gromacs/mdlib/tpi.cpp
+++ b/src/gromacs/mdlib/tpi.cpp
@@ -61,16 +61,12 @@
 #include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/group.h"
@@ -78,7 +74,11 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdebin.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/tgroup.h"
+#include "gromacs/mdlib/update.h"
 #include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"

diff --git a/src/gromacs/mdlib/trajectory_writing.cpp b/src/gromacs/mdlib/trajectory_writing.cpp
index 88407ba8390e0b3cb53b72fc99e5b14edd0cc444..ec7f0d83426292913b0e411a0e34764971ba4578 100644 (file)
--- a/src/gromacs/mdlib/trajectory_writing.cpp
+++ b/src/gromacs/mdlib/trajectory_writing.cpp
@@ -37,11 +37,11 @@
 #include "trajectory_writing.h"
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/mdoutf.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/trajectory_writing.h b/src/gromacs/mdlib/trajectory_writing.h
index 081d08b35628c867ff2d087bf8204113ddcfc3d5..e1dc92835aac087d30ddb767d3e227ab2f4fe793 100644 (file)
--- a/src/gromacs/mdlib/trajectory_writing.h
+++ b/src/gromacs/mdlib/trajectory_writing.h
@@ -40,7 +40,7 @@
 #include <stdio.h>
 
 #include "gromacs/fileio/filenm.h"
-#include "gromacs/legacyheaders/mdebin.h"
+#include "gromacs/mdlib/mdebin.h"
 #include "gromacs/mdlib/mdoutf.h"
 #include "gromacs/timing/wallcycle.h"
 

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index 8da42bfe13af1389d584822adbb643f3ced8428e..13dc2e8a964874aa38cfdb0a9130bf6cc7d99ac1 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/update.h"
+#include "update.h"
 
 #include <math.h>
 #include <stdio.h>
@@ -48,10 +48,8 @@
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -59,7 +57,9 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/tgroup.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"

diff --git a/src/gromacs/legacyheaders/update.h b/src/gromacs/mdlib/update.h
similarity index 96%
rename from src/gromacs/legacyheaders/update.h
rename to src/gromacs/mdlib/update.h
index fbba4b0ca2d90a7109fed2472bc482baa8d3f4cc..3b1cb45f899e83656d1645690625b49622bf1701 100644 (file)
--- a/src/gromacs/legacyheaders/update.h
+++ b/src/gromacs/mdlib/update.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 _update_h
-#define _update_h
+#ifndef GMX_MDLIB_UPDATE_H
+#define GMX_MDLIB_UPDATE_H
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/timing/wallcycle.h"
@@ -50,10 +49,6 @@ struct t_grpopts;
 struct t_mdatoms;
 struct t_nrnb;
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 /* Abstract type for stochastic dynamics */
 typedef struct gmx_update *gmx_update_t;
 
@@ -106,12 +101,12 @@ void update_coords(FILE              *fplog,
                    int                bUpdatePart,
                    t_commrec         *cr, /* these shouldn't be here -- need to think about it */
                    t_nrnb            *nrnb,
-                   struct gmx_constr *constr,
+                   gmx_constr        *constr,
                    t_idef            *idef);
 
 /* Return TRUE if OK, FALSE in case of Shake Error */
 
-extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr, t_mdatoms *md, t_state *state, gmx_update_t upd, struct gmx_constr *constr);
+extern gmx_bool update_randomize_velocities(t_inputrec *ir, gmx_int64_t step, const t_commrec *cr, t_mdatoms *md, t_state *state, gmx_update_t upd, gmx_constr *constr);
 
 void update_constraints(FILE              *fplog,
                         gmx_int64_t        step,
@@ -120,7 +115,7 @@ void update_constraints(FILE              *fplog,
                         t_mdatoms         *md,
                         t_state           *state,
                         gmx_bool           bMolPBC,
-                        struct t_graph    *graph,
+                        t_graph           *graph,
                         rvec               force[], /* forces on home particles */
                         t_idef            *idef,
                         tensor             vir_part,
@@ -128,7 +123,7 @@ void update_constraints(FILE              *fplog,
                         t_nrnb            *nrnb,
                         gmx_wallcycle_t    wcycle,
                         gmx_update_t       upd,
-                        struct gmx_constr *constr,
+                        gmx_constr        *constr,
                         gmx_bool           bFirstHalf,
                         gmx_bool           bCalcVir);
 
@@ -243,9 +238,4 @@ void correct_ekin(FILE *log, int start, int end, rvec v[],
                   rvec vcm, real mass[], real tmass, tensor ekin);
 /* Correct ekin for vcm */
 
-
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _update_h */

diff --git a/src/gromacs/mdlib/vcm.cpp b/src/gromacs/mdlib/vcm.cpp
index ee6740fa23b1428a7e9320b23c4196755eadb42f..8d9a2372aca0da27ccf79b7307e2ae15085691e0 100644 (file)
--- a/src/gromacs/mdlib/vcm.cpp
+++ b/src/gromacs/mdlib/vcm.cpp
@@ -37,7 +37,7 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/vcm.h"
+#include "vcm.h"
 
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"

diff --git a/src/gromacs/legacyheaders/vcm.h b/src/gromacs/mdlib/vcm.h
similarity index 92%
rename from src/gromacs/legacyheaders/vcm.h
rename to src/gromacs/mdlib/vcm.h
index aaab02a8064f1da9e803286123fcfbde1c9f5367..071c71fcf8914c5aa2977f349f03d4932362f2be 100644 (file)
--- a/src/gromacs/legacyheaders/vcm.h
+++ b/src/gromacs/mdlib/vcm.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015, 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.
@@ -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 _vcm_h
-#define _vcm_h
+#ifndef GMX_MDLIB_VCM_H
+#define GMX_MDLIB_VCM_H
 
 #include <stdio.h>
 
@@ -46,10 +45,6 @@
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct gmx_groups_t;
 
 typedef struct {
@@ -67,7 +62,7 @@ typedef struct {
     char     **group_name;     /* These two are copies to pointers in */
 } t_vcm;
 
-t_vcm *init_vcm(FILE *fp, struct gmx_groups_t *groups, t_inputrec *ir);
+t_vcm *init_vcm(FILE *fp, gmx_groups_t *groups, t_inputrec *ir);
 
 /* Do a per group center of mass things */
 void calc_vcm_grp(int start, int homenr, t_mdatoms *md,
@@ -79,10 +74,4 @@ void do_stopcm_grp(int start, int homenr,
 
 void check_cm_grp(FILE *fp, t_vcm *vcm, t_inputrec *ir, real Temp_Max);
 
-
-#ifdef __cplusplus
-}
 #endif
-
-
-#endif /* _vcm_h */

diff --git a/src/gromacs/mdrunutility/handlerestart.cpp b/src/gromacs/mdrunutility/handlerestart.cpp
index 6e9b4528e586eb600c2e2fd0511c7f4e21614b52..59a1e8f9b46dc5e39b189ff37d503d2031052861 100644 (file)
--- a/src/gromacs/mdrunutility/handlerestart.cpp
+++ b/src/gromacs/mdrunutility/handlerestart.cpp
@@ -55,8 +55,8 @@
 
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/basedefinitions.h"

diff --git a/src/gromacs/pulling/pull.cpp b/src/gromacs/pulling/pull.cpp
index 3bf7dc6ad5dfa5f7946a63e802dc911965243be0..b73fca9289d28b53e90ca469c4588476c90bfc0c 100644 (file)
--- a/src/gromacs/pulling/pull.cpp
+++ b/src/gromacs/pulling/pull.cpp
@@ -53,13 +53,13 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull_internal.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/pulling/pull_rotation.cpp b/src/gromacs/pulling/pull_rotation.cpp
index 350364c15415bc026a30547d845d9c61b8cf436d..e5b91ed85b1a46581f71ded34be5a896c1cba045 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.cpp
+++ b/src/gromacs/pulling/pull_rotation.cpp
@@ -51,7 +51,6 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/txtdump.h"
@@ -60,6 +59,7 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/cyclecounter.h"

diff --git a/src/gromacs/swap/swapcoords.cpp b/src/gromacs/swap/swapcoords.cpp
index a70aef4d6807726b3d966aa473a9b0e4cae5a16c..c76eeaf4ccee27a6cf6a2f4a96288bff0fc7aff5 100644 (file)
--- a/src/gromacs/swap/swapcoords.cpp
+++ b/src/gromacs/swap/swapcoords.cpp
@@ -52,13 +52,13 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/sim_util.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index 89e57960ab4c377f78bf0f8a33d5ac816d648f4d..66193e96b5f225c56bfdcf62ae2af6bb2cec7cb4 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -56,17 +56,11 @@
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/ebin.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdebin.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"
@@ -85,16 +79,22 @@
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/compute_io.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/ebin.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdebin.h"
 #include "gromacs/mdlib/mdoutf.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/mdrun_signalling.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"
 #include "gromacs/mdlib/shellfc.h"
 #include "gromacs/mdlib/sim_util.h"
+#include "gromacs/mdlib/tgroup.h"
 #include "gromacs/mdlib/trajectory_writing.h"
+#include "gromacs/mdlib/update.h"
+#include "gromacs/mdlib/vcm.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index e6a8b7162fde53882dfcf222340ad8beaa1451fe..d0387236c4d6b2808cc4b2c58db596621d10ce89 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -59,12 +59,12 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/filenm.h"
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/readinp.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdrunutility/handlerestart.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/programs/mdrun/repl_ex.cpp b/src/programs/mdrun/repl_ex.cpp
index c15d39f949596dca72d03b3566f2a2fe8597d508..082e2b965da0f2457ab90bdab9f4b69ef46df332 100644 (file)
--- a/src/programs/mdrun/repl_ex.cpp
+++ b/src/programs/mdrun/repl_ex.cpp
@@ -44,8 +44,8 @@
 #include <math.h>
 
 #include "gromacs/domdec/domdec.h"
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index c88ad73fcd2a1a171981af78b9ed6c9e7aa0f1d3..23d087fb3be33df7c2f64754be10a45efc48521a 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -61,6 +61,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/main.h"
 #include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/gmxlib/sighandler.h"
@@ -72,8 +73,6 @@
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/gmx_thread_affinity.h"
 #include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/txtdump.h"
@@ -86,6 +85,7 @@
 #include "gromacs/mdlib/integrator.h"
 #include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
+#include "gromacs/mdlib/mdrun.h"
 #include "gromacs/mdlib/minimize.h"
 #include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/mdlib/qmmm.h"