Move some headers from legacyheaders to mdlib/gmxlib

These still need to be reorganized from gmxlib/mdlib to proper modules,
but at least there they reveal dependencies better.

Change-Id: If6e7bfd8b76d8953ab26f766fe023ce9db277f1c

diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt
index 35b8a0abbb0f6f2a0f24b953062f7bf716743baa..e3d2126d8c7f4d123fc73cdbac76b185d62cddcc 100644 (file)
--- a/docs/doxygen/cycle-suppressions.txt
+++ b/docs/doxygen/cycle-suppressions.txt
@@ -7,6 +7,7 @@ domdec -> ewald
 domdec -> mdlib
 domdec -> pulling
 domdec -> swap
+gmxlib -> listed-forces
 mdlib -> essentialdynamics
 mdlib -> imd
 mdlib -> ewald

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index f3d8f1cf3bbc7fae011291fc23c7cfed46d795fb..1da9af6caa2b694a3290ea425c5365ac3038cf0a 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -65,7 +65,6 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/nsgrid.h"
-#include "gromacs/legacyheaders/shellfc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
 #include "gromacs/legacyheaders/types/commrec.h"
@@ -87,6 +86,7 @@
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_grid.h"
+#include "gromacs/mdlib/shellfc.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"

diff --git a/src/gromacs/ewald/pme-load-balancing.cpp b/src/gromacs/ewald/pme-load-balancing.cpp
index 159b8411a1e974196916d100eb51343acfb0d596..6bf9934e1fbd2888b6b0de3ed59e2a75455b9ded 100644 (file)
--- a/src/gromacs/ewald/pme-load-balancing.cpp
+++ b/src/gromacs/ewald/pme-load-balancing.cpp
@@ -55,7 +55,7 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_network.h"
-#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/network.h"

diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index baaccfba9a3a0fd7cff73cf96fb0a2e934893875..6ae8f3863ec5933d1d3f309eb6228ae029d4b50f 100644 (file)
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -49,7 +49,6 @@
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/legacyheaders/calcmu.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/txtdump.h"

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index 9e9b776850a5ad124c649074d6d24305d644077c..9cb25a50caf30c1a2ea5bfea3a479ebd6a369e8b 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -51,7 +51,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/gmxlib/disre.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/mdatoms.h"

diff --git a/src/gromacs/gmxana/gmx_eneconv.cpp b/src/gromacs/gmxana/gmx_eneconv.cpp
index bde1be03310cd195297b122269c7047fa49c396e..acbe04cf9136b2393cdba028f503ee8cde3f80bb 100644 (file)
--- a/src/gromacs/gmxana/gmx_eneconv.cpp
+++ b/src/gromacs/gmxana/gmx_eneconv.cpp
@@ -46,7 +46,7 @@
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/gmxlib/disre.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index cf52926b941f081273b30202b6b764b54ed0a4b9..b19fae572c129ea0a159cf75ec5f06035f5731f1 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -43,7 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/main.h"

diff --git a/src/gromacs/gmxana/gmx_tune_pme.cpp b/src/gromacs/gmxana/gmx_tune_pme.cpp
index 44a3f448ec8be2bb7f9c715510d1a58a0c34861c..53f486e236eb6e7e0d8554a1b4138a19b7d44dd0 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.cpp
+++ b/src/gromacs/gmxana/gmx_tune_pme.cpp
@@ -50,7 +50,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/legacyheaders/calcgrid.h"
+#include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/names.h"

diff --git a/src/gromacs/gmxlib/calcgrid.cpp b/src/gromacs/gmxlib/calcgrid.cpp
index b1e7aa8e073d9e9d34f08db0806c5b4f9a4e062e..384594e2396c1d6f5d3974a7a2b7c908b9d09732 100644 (file)
--- a/src/gromacs/gmxlib/calcgrid.cpp
+++ b/src/gromacs/gmxlib/calcgrid.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/calcgrid.h"
+#include "calcgrid.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/legacyheaders/calcgrid.h b/src/gromacs/gmxlib/calcgrid.h
similarity index 93%
rename from src/gromacs/legacyheaders/calcgrid.h
rename to src/gromacs/gmxlib/calcgrid.h
index 251b9e3d57bfdc6f3491a1b9314aca51b1479b90..214baa42f98de3d512937734471974e32b134c17 100644 (file)
--- a/src/gromacs/legacyheaders/calcgrid.h
+++ b/src/gromacs/gmxlib/calcgrid.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015, 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.
@@ -34,8 +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_LEGACYHEADERS_CALCGRID_H
-#define GMX_LEGACYHEADERS_CALCGRID_H
+#ifndef GMX_GMXLIB_CALCGRID_H
+#define GMX_GMXLIB_CALCGRID_H
 
 #include <stdio.h>
 

diff --git a/src/gromacs/gmxlib/disre.cpp b/src/gromacs/gmxlib/disre.cpp
index b28658ad5c10d8bf1aeec84b555819531e558862..4964b8b3136aaac0bca59096a66287e507b47ee0 100644 (file)
--- a/src/gromacs/gmxlib/disre.cpp
+++ b/src/gromacs/gmxlib/disre.cpp
@@ -37,7 +37,7 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/disre.h"
+#include "disre.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/legacyheaders/disre.h b/src/gromacs/gmxlib/disre.h
similarity index 98%
rename from src/gromacs/legacyheaders/disre.h
rename to src/gromacs/gmxlib/disre.h
index 549aaf422d11d96c3f7e48a9da76b97411f09d68..d030413f99fda6423d2639fb0b24267aff89fd86 100644 (file)
--- a/src/gromacs/legacyheaders/disre.h
+++ b/src/gromacs/gmxlib/disre.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 _disre_h
-#define _disre_h
+#ifndef GMX_GMXLIB_DISRE_H
+#define GMX_GMXLIB_DISRE_H
 
 #include <stdio.h>
 

diff --git a/src/gromacs/gmxlib/ifunc.cpp b/src/gromacs/gmxlib/ifunc.cpp
index 09a91e2d346cf3d44d9eca19b546ff70818b5d58..a0a312a3794e57a30d6485008a05b3ce2dccf578 100644 (file)
--- a/src/gromacs/gmxlib/ifunc.cpp
+++ b/src/gromacs/gmxlib/ifunc.cpp
@@ -37,9 +37,9 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/genborn.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/listed-forces/bonded.h"
 

diff --git a/src/gromacs/gmxlib/orires.cpp b/src/gromacs/gmxlib/orires.cpp
index 7e8f5bdf5d8cd14a9dc7620a83996c883d39825d..4be17d711574600b467b03ca80b9f89bb9565901 100644 (file)
--- a/src/gromacs/gmxlib/orires.cpp
+++ b/src/gromacs/gmxlib/orires.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/orires.h"
+#include "orires.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/legacyheaders/orires.h b/src/gromacs/gmxlib/orires.h
similarity index 98%
rename from src/gromacs/legacyheaders/orires.h
rename to src/gromacs/gmxlib/orires.h
index a36d5ca095e314c6547e1a314295a7040447e521..f76b252002f61d912444c6b9fbace59a5d6f3385 100644 (file)
--- a/src/gromacs/legacyheaders/orires.h
+++ b/src/gromacs/gmxlib/orires.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 _orires_h
-#define _orires_h
+#ifndef GMX_GMXLIB_ORIRES_H
+#define GMX_GMXLIB_ORIRES_H
 
 #include <stdio.h>
 

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 04cba38e479c06ad6addf97d4d002f6798f0f6c5..f92330f39e82ea72ea7729a607ae2cd7f24a48b2 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -54,6 +54,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/convparm.h"
 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
@@ -66,7 +67,6 @@
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/gmxpreprocess/vsite_parm.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/calcgrid.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/perf_est.h"

diff --git a/src/gromacs/listed-forces/listed-forces.cpp b/src/gromacs/listed-forces/listed-forces.cpp
index ba841d264da931604517d86558a132ffb49dfb33..72b8f0781d5cd5f20566ddf36e61603260467b5a 100644 (file)
--- a/src/gromacs/listed-forces/listed-forces.cpp
+++ b/src/gromacs/listed-forces/listed-forces.cpp
@@ -51,11 +51,11 @@
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/force_flags.h"
 #include "gromacs/listed-forces/bonded.h"

diff --git a/src/gromacs/mdlib/calcmu.cpp b/src/gromacs/mdlib/calcmu.cpp
index 7f2d383ca15b3fd250fd40777e008b5bab9a2ede..63cb5c54eee2e4509da66ddcfe404d480cc06f94 100644 (file)
--- a/src/gromacs/mdlib/calcmu.cpp
+++ b/src/gromacs/mdlib/calcmu.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2014, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014,2015, 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.
@@ -37,7 +37,7 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/calcmu.h"
+#include "calcmu.h"
 
 #include <stdio.h>
 #include <stdlib.h>

diff --git a/src/gromacs/legacyheaders/calcmu.h b/src/gromacs/mdlib/calcmu.h
similarity index 94%
rename from src/gromacs/legacyheaders/calcmu.h
rename to src/gromacs/mdlib/calcmu.h
index c9ed792d7bfa2cdec0185245eecf02b717d583df..7a74d13797c42999e368b490d9bdefd7989beab8 100644 (file)
--- a/src/gromacs/legacyheaders/calcmu.h
+++ b/src/gromacs/mdlib/calcmu.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010,2014, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014,2015, 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.
@@ -34,8 +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 _calcmu_h
-#define _calcmu_h
+#ifndef GMX_MDLIB_CALCMU_H
+#define GMX_MDLIB_CALCMU_H
 
 #include <stdio.h>
 

diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp
index 6a3d24221f9e18f492c9d095de369c2248091565..44ee25f26130c2fe4f81ba1e9ca4df2526018c4a 100644 (file)
--- a/src/gromacs/mdlib/expanded.cpp
+++ b/src/gromacs/mdlib/expanded.cpp
@@ -44,21 +44,21 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xtcio.h"
-#include "gromacs/legacyheaders/calcmu.h"
+#include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/orires.h"
 #include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/force.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/orires.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/random/random.h"
 #include "gromacs/timing/wallcycle.h"

diff --git a/src/gromacs/mdlib/mdebin.cpp b/src/gromacs/mdlib/mdebin.cpp
index 4a11853d47bc40e756fdfeeb51ac6b27726763e7..8ee2e1bc6a6b48fa8635356fb870a1f87be6045a 100644 (file)
--- a/src/gromacs/mdlib/mdebin.cpp
+++ b/src/gromacs/mdlib/mdebin.cpp
@@ -45,11 +45,11 @@
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/disre.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/orires.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/legacyheaders/types/group.h"

diff --git a/src/gromacs/mdlib/shellfc.cpp b/src/gromacs/mdlib/shellfc.cpp
index 02fe92db8cab7c1ce3411b0fb6b70f195ca0c7a5..23cca75124954a65485415cdf87d6f8f23345a5b 100644 (file)
--- a/src/gromacs/mdlib/shellfc.cpp
+++ b/src/gromacs/mdlib/shellfc.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/shellfc.h"
+#include "shellfc.h"
 
 #include <stdlib.h>
 #include <string.h>

diff --git a/src/gromacs/legacyheaders/shellfc.h b/src/gromacs/mdlib/shellfc.h
similarity index 98%
rename from src/gromacs/legacyheaders/shellfc.h
rename to src/gromacs/mdlib/shellfc.h
index 472c37681e14266fe32f698f0d1d771e97fc7da3..0fb85c20c814f2d6ec781e3dc9476be02dfa63d2 100644 (file)
--- a/src/gromacs/legacyheaders/shellfc.h
+++ b/src/gromacs/mdlib/shellfc.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_SHELLFC_H
+#define GMX_MDLIB_SHELLFC_H
 
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vsite.h"
@@ -75,3 +77,5 @@ int relax_shell_flexcon(FILE *log, t_commrec *cr, gmx_bool bVerbose,
                         gmx_bool *bConverged,
                         gmx_vsite_t *vsite,
                         FILE *fp_field);
+
+#endif

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index c1dfcf9f31331a421a90b492be50cef48c7d36ea..d587a4c1c75f99759448ba3e9cf5ae9cf4694ef5 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -48,13 +48,13 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/ewald/pme.h"
+#include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/orires.h"
 #include "gromacs/gmxlib/nonbonded/nb_free_energy.h"
 #include "gromacs/gmxlib/nonbonded/nb_kernel.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/calcmu.h"
 #include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
@@ -64,7 +64,6 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
@@ -73,6 +72,7 @@
 #include "gromacs/listed-forces/bonded.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/calcmu.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/nb_verlet.h"

diff --git a/src/gromacs/mdlib/update.cpp b/src/gromacs/mdlib/update.cpp
index e5a7517f1c658e3020bfe1f9542211f19cb44535..debd1a3b6fdd8bd5ca915cb8d9571b27ebbacf7d 100644 (file)
--- a/src/gromacs/mdlib/update.cpp
+++ b/src/gromacs/mdlib/update.cpp
@@ -44,13 +44,13 @@
 #include <algorithm>
 
 #include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/disre.h"
+#include "gromacs/gmxlib/disre.h"
+#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/orires.h"
 #include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index b860b7099758d457e19d4e088efd5c734ca36f7f..e09abc63500ef5479433b8afaa2c667f088ca783 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -66,7 +66,6 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/shellfc.h"
 #include "gromacs/legacyheaders/sighandler.h"
 #include "gromacs/legacyheaders/sim_util.h"
 #include "gromacs/legacyheaders/tgroup.h"
@@ -97,6 +96,7 @@
 #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/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index c3cff38bff54f954f71f17f9ff9c77035f264687..04ea7562c448a2840bcefc610341fbad6e897a34 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -60,10 +60,11 @@
 #include "gromacs/fileio/oenv.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/gmxlib/disre.h"
+#include "gromacs/gmxlib/orires.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
@@ -76,7 +77,6 @@
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/orires.h"
 #include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/sighandler.h"
 #include "gromacs/legacyheaders/txtdump.h"