More legacyheaders to gmxlib/mdlib

The movement here is trivial in the sense that they do not
introduce/identify any additional dependencies.

Change-Id: Ie7a23b03409c5c0fe9a44d6943f7b1325a7f080f

diff --git a/src/gromacs/domdec/domdec.cpp b/src/gromacs/domdec/domdec.cpp
index 1da9af6caa2b694a3290ea425c5365ac3038cf0a..122ad56c4be80cde6a0f9975e07a07653cbddc27 100644 (file)
--- a/src/gromacs/domdec/domdec.cpp
+++ b/src/gromacs/domdec/domdec.cpp
@@ -52,14 +52,13 @@
 #include "gromacs/ewald/pme.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
+#include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/imd/imd.h"
-#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
@@ -84,6 +83,7 @@
 #include "gromacs/math/vectypes.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_grid.h"
 #include "gromacs/mdlib/shellfc.h"

diff --git a/src/gromacs/domdec/domdec_setup.cpp b/src/gromacs/domdec/domdec_setup.cpp
index fd93cd42971c2ccc89f3e043c4cc75b102a72059..23a23b9dc8911c6fefab7df8a23dc9d3ac609fb4 100644 (file)
--- a/src/gromacs/domdec/domdec_setup.cpp
+++ b/src/gromacs/domdec/domdec_setup.cpp
@@ -52,10 +52,10 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/perf_est.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/perf_est.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/domdec/domdec_topology.cpp b/src/gromacs/domdec/domdec_topology.cpp
index fb97e35c50133a0941bc3a14ef4b7e3a91415d14..b43abd9d410665dcea6ff5aa8a103289c8380138 100644 (file)
--- a/src/gromacs/domdec/domdec_topology.cpp
+++ b/src/gromacs/domdec/domdec_topology.cpp
@@ -53,7 +53,7 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_network.h"
-#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_ga2la.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"

diff --git a/src/gromacs/ewald/pme-pp.cpp b/src/gromacs/ewald/pme-pp.cpp
index d2fddb3bfae570ff3e0d01adbf6f4f044b4fa629..5b7ea59c68747a2855e6f8ba97d28d44346a37b5 100644 (file)
--- a/src/gromacs/ewald/pme-pp.cpp
+++ b/src/gromacs/ewald/pme-pp.cpp
@@ -54,8 +54,8 @@
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/ewald/pme.h"
+#include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/sighandler.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxana/gmx_disre.cpp b/src/gromacs/gmxana/gmx_disre.cpp
index 9cb25a50caf30c1a2ea5bfea3a479ebd6a369e8b..53cdc2bdfdadb6d4a2de7cbad7faeb8cba3825a8 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.cpp
+++ b/src/gromacs/gmxana/gmx_disre.cpp
@@ -54,7 +54,6 @@
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"
@@ -63,6 +62,7 @@
 #include "gromacs/legacyheaders/types/fcdata.h"
 #include "gromacs/math/do_fit.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index b19fae572c129ea0a159cf75ec5f06035f5731f1..8ec4783be59ab73a4610406edb1a7729a0d6a1e2 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -47,7 +47,6 @@
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"

diff --git a/src/gromacs/gmxana/gmx_tune_pme.cpp b/src/gromacs/gmxana/gmx_tune_pme.cpp
index 53f486e236eb6e7e0d8554a1b4138a19b7d44dd0..066c45e1864bddcc07282eca3b5fce652a4a5b17 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.cpp
+++ b/src/gromacs/gmxana/gmx_tune_pme.cpp
@@ -54,12 +54,12 @@
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/perf_est.h"
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/perf_est.h"
 #include "gromacs/timing/walltime_accounting.h"
 #include "gromacs/utility/arraysize.h"
 #include "gromacs/utility/baseversion.h"

diff --git a/src/gromacs/gmxlib/chargegroup.cpp b/src/gromacs/gmxlib/chargegroup.cpp
index 30553d8e0be7e5a05de4480d71ea73f8a877f1f6..2625f86b56f16617b17738ce7a158d5fed0f99c6 100644 (file)
--- a/src/gromacs/gmxlib/chargegroup.cpp
+++ b/src/gromacs/gmxlib/chargegroup.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/chargegroup.h"
+#include "chargegroup.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/legacyheaders/chargegroup.h b/src/gromacs/gmxlib/chargegroup.h
similarity index 87%
rename from src/gromacs/legacyheaders/chargegroup.h
rename to src/gromacs/gmxlib/chargegroup.h
index 1429e85d3fd864a1a188edcce3a0b33823581353..f22c772bea36fcac61309a9b003f3fc4ff821636 100644 (file)
--- a/src/gromacs/legacyheaders/chargegroup.h
+++ b/src/gromacs/gmxlib/chargegroup.h
@@ -34,45 +34,36 @@
  * 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_GMXLIB_CHARGEGROUP_H
+#define GMX_GMXLIB_CHARGEGROUP_H
 
-#ifndef _chargegroup_h
-#define _chargegroup_h
-
-#include <stdio.h>
+#include <cstdio>
 
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/real.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct gmx_mtop_t;
 struct t_block;
 
-void calc_chargegroup_radii(const struct gmx_mtop_t *mtop, rvec *x,
+void calc_chargegroup_radii(const gmx_mtop_t *mtop, rvec *x,
                             real *rvdw1, real *rvdw2,
                             real *rcoul1, real *rcoul2);
 /* This routine calculates the two largest charge group radii in x,
  * separately for VdW and Coulomb interactions.
  */
 
-void calc_cgcm(FILE *log, int cg0, int cg1, const struct t_block *cgs,
+void calc_cgcm(FILE *log, int cg0, int cg1, const t_block *cgs,
                rvec pos[], rvec cg_cm[]);
 /* Routine to compute centers of geometry of charge groups. No periodicity
  * is used.
  */
 
 void put_charge_groups_in_box (FILE *log, int cg0, int cg1,
-                               int ePBC, matrix box, struct t_block *cgs,
+                               int ePBC, matrix box, t_block *cgs,
                                rvec pos[],
                                rvec cg_cm[]);
 /* This routine puts charge groups in the periodic box, keeping them
  * together.
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _chargegroup_h */

diff --git a/src/gromacs/gmxlib/sighandler.cpp b/src/gromacs/gmxlib/sighandler.cpp
index 58943ee1328ddee04a50e93599ee36d50a9ae24c..0ca4e57b7b72aad649f207eefeb39f1d82791b3a 100644 (file)
--- a/src/gromacs/gmxlib/sighandler.cpp
+++ b/src/gromacs/gmxlib/sighandler.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/sighandler.h"
+#include "sighandler.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/legacyheaders/sighandler.h b/src/gromacs/gmxlib/sighandler.h
similarity index 94%
rename from src/gromacs/legacyheaders/sighandler.h
rename to src/gromacs/gmxlib/sighandler.h
index b2531a67e97960e46bed9624b21b2b0006de4e7f..20d501a33c6d4b710f032e0e0017502e8956cf20 100644 (file)
--- a/src/gromacs/legacyheaders/sighandler.h
+++ b/src/gromacs/gmxlib/sighandler.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.
@@ -34,18 +34,13 @@
  * 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 _sighandler_h
-#define _sighandler_h
+#ifndef GMX_GMXLIB_SIGHANDLER_H
+#define GMX_GMXLIB_SIGHANDLER_H
 
 #include <signal.h>
 
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 /* NOTE: the terminology is:
    incoming signals (provided by the operating system, or transmitted from
    other nodes) lead to stop conditions. These stop conditions should be
@@ -84,10 +79,4 @@ const char *gmx_get_signal_name(void);
    only returns TRUE once for a single signal. */
 gmx_bool gmx_got_usr_signal(void);
 
-
-#ifdef __cplusplus
-}
 #endif
-
-
-#endif  /* _sighandler_h */

diff --git a/src/gromacs/gmxlib/splitter.cpp b/src/gromacs/gmxlib/splitter.cpp
index fc4ce9170f7a7465732082f8e4dc0d2cca55c5f2..1bbbd9ed097093364b27d4a5f93f03dad2dea898 100644 (file)
--- a/src/gromacs/gmxlib/splitter.cpp
+++ b/src/gromacs/gmxlib/splitter.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/splitter.h"
+#include "splitter.h"
 
 #include <cstdlib>
 #include <cstring>

diff --git a/src/gromacs/legacyheaders/splitter.h b/src/gromacs/gmxlib/splitter.h
similarity index 88%
rename from src/gromacs/legacyheaders/splitter.h
rename to src/gromacs/gmxlib/splitter.h
index 7db0fcf5ac7980f3fef758b988dd57e844193bd5..5377cbe50ed9d8cde7ec4597347dc52e7ade446d 100644 (file)
--- a/src/gromacs/legacyheaders/splitter.h
+++ b/src/gromacs/gmxlib/splitter.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.
@@ -34,30 +34,21 @@
  * 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_GMXLIB_SPLITTER_H
+#define GMX_GMXLIB_SPLITTER_H
 
-#ifndef _splitter_h
-#define _splitter_h
-
-#include <stdio.h>
+#include <cstdio>
 
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct t_blocka;
 struct t_idef;
 
 void gen_sblocks(FILE *fp, int at_start, int at_end,
-                 struct t_idef *idef, struct t_blocka *sblock,
+                 t_idef *idef, t_blocka *sblock,
                  gmx_bool bSettle);
 /* Generate shake blocks from the constraint list. Set bSettle to yes for shake
  * blocks including settles. You normally do not want this.
  */
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index f92330f39e82ea72ea7729a607ae2cd7f24a48b2..41f5b3a12ba3332fe0228f183daa0976dc3d8d20 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -55,6 +55,7 @@
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxlib/calcgrid.h"
+#include "gromacs/gmxlib/splitter.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/convparm.h"
 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
@@ -69,14 +70,13 @@
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/legacyheaders/splitter.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/warninp.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/calc_verletbuf.h"
 #include "gromacs/mdlib/compute_io.h"
+#include "gromacs/mdlib/perf_est.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/random/random.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index f2af500673934ad4dd2424c64034af10cda45df6..1b5fbd8c78c0a35210add8b8b0f7e20508801224 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -46,8 +46,8 @@
 
 #include <algorithm>
 
+#include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxpreprocess/toputil.h"
-#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"

diff --git a/src/gromacs/gmxpreprocess/readpull.cpp b/src/gromacs/gmxpreprocess/readpull.cpp
index 7a59b8c5c9eb079b6d514885619ebcfcf957bb13..e9769e5e91f7035bcec195da248e6040eb17d451 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.cpp
+++ b/src/gromacs/gmxpreprocess/readpull.cpp
@@ -40,11 +40,11 @@
 #include <string.h>
 
 #include "gromacs/gmxpreprocess/readir.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/imd/imd.cpp b/src/gromacs/imd/imd.cpp
index 873e0e85caa94a5dfefff0ee32e1aa4ed84eddce..e808790c1d37d82c6fc5854dd48666206df14af1 100644 (file)
--- a/src/gromacs/imd/imd.cpp
+++ b/src/gromacs/imd/imd.cpp
@@ -63,12 +63,12 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xvgr.h"
+#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/sighandler.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/constr.cpp b/src/gromacs/mdlib/constr.cpp
index ac5bdb99960effe1c99928a4bdd72c2731a5f580..35178cf0c427f3ecd6b6b835f483a8345fdc6975 100644 (file)
--- a/src/gromacs/mdlib/constr.cpp
+++ b/src/gromacs/mdlib/constr.cpp
@@ -50,12 +50,12 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/pdbio.h"
+#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/splitter.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/mdlib/expanded.cpp b/src/gromacs/mdlib/expanded.cpp
index 44ee25f26130c2fe4f81ba1e9ca4df2526018c4a..6dc33b3810b0ba39394f09fc4ea1919df5475b52 100644 (file)
--- a/src/gromacs/mdlib/expanded.cpp
+++ b/src/gromacs/mdlib/expanded.cpp
@@ -44,11 +44,10 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xtcio.h"
+#include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/orires.h"
-#include "gromacs/legacyheaders/chargegroup.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"

diff --git a/src/gromacs/mdlib/mdatom.cpp b/src/gromacs/mdlib/mdatoms.cpp
similarity index 99%
rename from src/gromacs/mdlib/mdatom.cpp
rename to src/gromacs/mdlib/mdatoms.cpp
index 7903d09a5901dcb79b7141b81638be9520831b7a..212a4fee43186ec9c3a95f9b2e2be4370ad60185 100644 (file)
--- a/src/gromacs/mdlib/mdatom.cpp
+++ b/src/gromacs/mdlib/mdatoms.cpp
@@ -36,10 +36,11 @@
  */
 #include "gmxpre.h"
 
+#include "mdatoms.h"
+
 #include <math.h>
 
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/topology/mtop_util.h"

diff --git a/src/gromacs/legacyheaders/mdatoms.h b/src/gromacs/mdlib/mdatoms.h
similarity index 89%
rename from src/gromacs/legacyheaders/mdatoms.h
rename to src/gromacs/mdlib/mdatoms.h
index c6961a1c9755df0b221a2c7000b287547fd6f3e8..4d6b63c8f2986b2f9f493d26bfea651ecc05d7bb 100644 (file)
--- a/src/gromacs/legacyheaders/mdatoms.h
+++ b/src/gromacs/mdlib/mdatoms.h
@@ -34,26 +34,21 @@
  * 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_MDATOMS_H
+#define GMX_MDLIB_MDATOMS_H
 
-#ifndef _mdatoms_h
-#define _mdatoms_h
-
-#include <stdio.h>
+#include <cstdio>
 
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/legacyheaders/types/mdatom.h"
 #include "gromacs/utility/basedefinitions.h"
 #include "gromacs/utility/real.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct gmx_mtop_t;
 
-t_mdatoms *init_mdatoms(FILE *fp, const struct gmx_mtop_t *mtop, gmx_bool bFreeEnergy);
+t_mdatoms *init_mdatoms(FILE *fp, const gmx_mtop_t *mtop, gmx_bool bFreeEnergy);
 
-void atoms2md(const struct gmx_mtop_t *mtop, const t_inputrec *ir,
+void atoms2md(const gmx_mtop_t *mtop, const t_inputrec *ir,
               int nindex, const int *index,
               int homenr,
               t_mdatoms *md);
@@ -64,8 +59,4 @@ void atoms2md(const struct gmx_mtop_t *mtop, const t_inputrec *ir,
 void update_mdatoms(t_mdatoms *md, real lambda);
 /* (Re)set all the mass parameters */
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index bb36dbb0d07aab959c32eb1d8ba2978e92ee12cf..7922224cac1a930547e277af5dc654fa1aea9d2f 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -64,7 +64,6 @@
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
@@ -83,6 +82,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/timing/wallcycle.h"

diff --git a/src/gromacs/mdlib/perf_est.cpp b/src/gromacs/mdlib/perf_est.cpp
index 5dd73f215bdbe888eff79be35706824a0c94bbf8..8e5ba771cfb98255425fd38db20a41a1a3ee808d 100644 (file)
--- a/src/gromacs/mdlib/perf_est.cpp
+++ b/src/gromacs/mdlib/perf_est.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/perf_est.h"
+#include "perf_est.h"
 
 #include <cmath>
 

diff --git a/src/gromacs/legacyheaders/perf_est.h b/src/gromacs/mdlib/perf_est.h
similarity index 89%
rename from src/gromacs/legacyheaders/perf_est.h
rename to src/gromacs/mdlib/perf_est.h
index b462cc2b48c9741c96da2b941dd8ffc1b716520b..ede4d8000cbfca5e545f16b13a0cd37ba950aff6 100644 (file)
--- a/src/gromacs/legacyheaders/perf_est.h
+++ b/src/gromacs/mdlib/perf_est.h
@@ -34,33 +34,25 @@
  * 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 _perf_est_h
-#define _perf_est_h
+#ifndef GMX_MDLIB_PERF_EST_H
+#define GMX_MDLIB_PERF_EST_H
 
 #include "gromacs/legacyheaders/types/inputrec.h"
 #include "gromacs/math/vectypes.h"
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct gmx_mtop_t;
 
-int n_bonded_dx(const struct gmx_mtop_t *mtop, gmx_bool bExcl);
+int n_bonded_dx(const gmx_mtop_t *mtop, gmx_bool bExcl);
 /* Returns the number of pbc_rvec_sub calls required for bonded interactions.
  * This number is also roughly proportional to the computational cost.
  */
 
-float pme_load_estimate(const struct gmx_mtop_t *mtop, const t_inputrec *ir,
+float pme_load_estimate(const gmx_mtop_t *mtop, const t_inputrec *ir,
                         matrix box);
 /* Returns an estimate for the relative load of the PME mesh calculation
  * in the total force calculation.
  * This estimate is reasonable for recent Intel and AMD x86_64 CPUs.
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _perf_est_h */

diff --git a/src/gromacs/gmxlib/rbin.cpp b/src/gromacs/mdlib/rbin.cpp
similarity index 99%
rename from src/gromacs/gmxlib/rbin.cpp
rename to src/gromacs/mdlib/rbin.cpp
index c650d40e9e6d9afa4e0a2913266cb7efffa96d0d..c5720e6a7fa1dc985024c18c6467c00a62527821 100644 (file)
--- a/src/gromacs/gmxlib/rbin.cpp
+++ b/src/gromacs/mdlib/rbin.cpp
@@ -37,7 +37,7 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/rbin.h"
+#include "rbin.h"
 
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"

diff --git a/src/gromacs/legacyheaders/rbin.h b/src/gromacs/mdlib/rbin.h
similarity index 93%
rename from src/gromacs/legacyheaders/rbin.h
rename to src/gromacs/mdlib/rbin.h
index fb0f7d6433847295410f87dcec78351f99b82d02..c868b1edf535bcb367faf1d51fc938b36a61cfa6 100644 (file)
--- a/src/gromacs/legacyheaders/rbin.h
+++ b/src/gromacs/mdlib/rbin.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.
@@ -34,16 +34,11 @@
  * 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 _rbin_h
-#define _rbin_h
+#ifndef GMX_MDLIB_RBIN_H
+#define GMX_MDLIB_RBIN_H
 
 #include "gromacs/utility/real.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct t_commrec;
 
 typedef struct {
@@ -72,8 +67,4 @@ void extract_binr(t_bin *b, int index, int nr, real r[]);
 void extract_bind(t_bin *b, int index, int nr, double r[]);
 /* Extract values from the bin, starting from index (see add_bin) */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _rbin_h */

diff --git a/src/gromacs/mdlib/shellfc.cpp b/src/gromacs/mdlib/shellfc.cpp
index 23cca75124954a65485415cdf87d6f8f23345a5b..9198fdcc99161974e194fc4dfae4b83764b0c7bb 100644 (file)
--- a/src/gromacs/mdlib/shellfc.cpp
+++ b/src/gromacs/mdlib/shellfc.cpp
@@ -44,9 +44,8 @@
 #include <algorithm>
 
 #include "gromacs/domdec/domdec.h"
-#include "gromacs/legacyheaders/chargegroup.h"
+#include "gromacs/gmxlib/chargegroup.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"

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index d587a4c1c75f99759448ba3e9cf5ae9cf4694ef5..7049961e269886320f916aa839a1130acd86a094 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -48,17 +48,16 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/ewald/pme.h"
+#include "gromacs/gmxlib/chargegroup.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/chargegroup.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"

diff --git a/src/gromacs/mdlib/stat.cpp b/src/gromacs/mdlib/stat.cpp
index d60ceb6f763f0ae396f5bb25fa5a92f920f497c0..d25385084824bbf9c27f63bf4d32f1953708d3f6 100644 (file)
--- a/src/gromacs/mdlib/stat.cpp
+++ b/src/gromacs/mdlib/stat.cpp
@@ -47,7 +47,6 @@
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/rbin.h"
 #include "gromacs/legacyheaders/sim_util.h"
 #include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/txtdump.h"
@@ -58,6 +57,7 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/rbin.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 7b3a45a294f6af8decdc6444cd22916a3e695e88..473a6b5b39a66910e1e0dc6d3d42e49f77d0f028 100644 (file)
--- a/src/gromacs/mdlib/tgroup.cpp
+++ b/src/gromacs/mdlib/tgroup.cpp
@@ -43,10 +43,10 @@
 
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/rbin.h"
 #include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/group.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/rbin.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/mdlib/tpi.cpp b/src/gromacs/mdlib/tpi.cpp
index 7902941f9af04ea8d09d9a2719f0c91ea452da57..9055b7124f8234f38b64d1b2146975354fed513b 100644 (file)
--- a/src/gromacs/mdlib/tpi.cpp
+++ b/src/gromacs/mdlib/tpi.cpp
@@ -58,10 +58,9 @@
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxlib/chargegroup.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
-#include "gromacs/legacyheaders/chargegroup.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
@@ -78,6 +77,7 @@
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/random/random.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index e09abc63500ef5479433b8afaa2c667f088ca783..a4dbe1c99630b19addd523f301f5cfbc677cfd84 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -55,18 +55,17 @@
 #include "gromacs/fileio/trajectory_writing.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/ebin.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.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/sighandler.h"
 #include "gromacs/legacyheaders/sim_util.h"
 #include "gromacs/legacyheaders/tgroup.h"
 #include "gromacs/legacyheaders/typedefs.h"
@@ -93,6 +92,7 @@
 #include "gromacs/mdlib/compute_io.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdrun_signalling.h"
 #include "gromacs/mdlib/nb_verlet.h"
 #include "gromacs/mdlib/nbnxn_gpu_data_mgmt.h"

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index 04ea7562c448a2840bcefc610341fbad6e897a34..42836368e3dcc70ed17da1efbe939d6514a7dbe4 100644 (file)
--- a/src/programs/mdrun/runner.cpp
+++ b/src/programs/mdrun/runner.cpp
@@ -62,6 +62,7 @@
 #include "gromacs/fileio/trx.h"
 #include "gromacs/gmxlib/disre.h"
 #include "gromacs/gmxlib/orires.h"
+#include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
@@ -73,12 +74,10 @@
 #include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/md_support.h"
-#include "gromacs/legacyheaders/mdatoms.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/qmmm.h"
-#include "gromacs/legacyheaders/sighandler.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
@@ -87,6 +86,7 @@
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/integrator.h"
+#include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/minimize.h"
 #include "gromacs/mdlib/nbnxn_search.h"
 #include "gromacs/mdlib/tpi.h"