More headers out of legacyheaders

Change-Id: I38ce8fd62a1c969814c85d112c30eeaa80f7980a

diff --git a/docs/doxygen/cycle-suppressions.txt b/docs/doxygen/cycle-suppressions.txt
index e3d2126d8c7f4d123fc73cdbac76b185d62cddcc..9c796a8cd076cc8512aa9f6e6a6a41a1499bf51d 100644 (file)
--- a/docs/doxygen/cycle-suppressions.txt
+++ b/docs/doxygen/cycle-suppressions.txt
@@ -15,6 +15,7 @@ mdlib -> pulling
 legacyheaders -> swap
 legacyheaders -> fileio
 timing -> legacyheaders
+timing -> gmxlib
 topology -> fileio
 topology -> legacyheaders
 pbcutil -> fileio

diff --git a/src/gromacs/ewald/pme-load-balancing.cpp b/src/gromacs/ewald/pme-load-balancing.cpp
index 6bf9934e1fbd2888b6b0de3ed59e2a75455b9ded..88cccde7644a1270b0b9bccc2decacc9cf6ff968 100644 (file)
--- a/src/gromacs/ewald/pme-load-balancing.cpp
+++ b/src/gromacs/ewald/pme-load-balancing.cpp
@@ -56,8 +56,8 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/domdec/domdec_network.h"
 #include "gromacs/gmxlib/calcgrid.h"
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/sim_util.h"
 #include "gromacs/legacyheaders/types/commrec.h"

diff --git a/src/gromacs/fileio/trxio.cpp b/src/gromacs/fileio/trxio.cpp
index 8a517624a4e2e0d3d0b7a36ee32cf0b3c3005b21..d7dfbb324d6dc0eb7d8d301dd1d8f7f06549b647 100644 (file)
--- a/src/gromacs/fileio/trxio.cpp
+++ b/src/gromacs/fileio/trxio.cpp
@@ -42,6 +42,7 @@
 
 #include <cassert>
 #include <cmath>
+#include <cstring>
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/g96io.h"
@@ -734,7 +735,7 @@ static gmx_bool pdb_next_x(t_trxstatus *status, FILE *fp, t_trxframe *fr)
         fr->bStep = TRUE;
         fr->step  = model_nr;
     }
-    time = strstr(title, " t= ");
+    time = std::strstr(title, " t= ");
     if (time)
     {
         fr->bTime = TRUE;

diff --git a/src/gromacs/fileio/trxio.h b/src/gromacs/fileio/trxio.h
index da84a138a1808f08a52634d05436dcf994348a73..ef891d986cc3fc090502ecd04d85ebfc56741498 100644 (file)
--- a/src/gromacs/fileio/trxio.h
+++ b/src/gromacs/fileio/trxio.h
@@ -40,7 +40,6 @@
 
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gromacs/legacyheaders/readinp.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/gmxana/gmx_analyze.cpp b/src/gromacs/gmxana/gmx_analyze.cpp
index 52833489e8b81d669bb5af0781cdb436480f23a2..b3ed3917a253649d82403d6c83a23f0a3c501766 100644 (file)
--- a/src/gromacs/gmxana/gmx_analyze.cpp
+++ b/src/gromacs/gmxana/gmx_analyze.cpp
@@ -47,8 +47,8 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"

diff --git a/src/gromacs/gmxana/gmx_make_edi.cpp b/src/gromacs/gmxana/gmx_make_edi.cpp
index 1fa500a69f29b7c3b7489640db267d7c6066ad00..b5f94a1eecb044def5a291131415e12e6e391ce0 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_edi.cpp
+++ b/src/gromacs/gmxana/gmx_make_edi.cpp
@@ -49,7 +49,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/eigio.h"
 #include "gromacs/gmxana/gmx_ana.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/txtdump.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 8ec4783be59ab73a4610406edb1a7729a0d6a1e2..c3270d0079471b8d3a3f878f3724efe75cfb422e 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -44,11 +44,11 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxlib/calcgrid.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/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"

diff --git a/src/gromacs/gmxana/gmx_sham.cpp b/src/gromacs/gmxana/gmx_sham.cpp
index 2506afe55485ce2d0c2f5987811b66586379a5c1..38621c7449247d28a7205f571b7e60b06749275a 100644 (file)
--- a/src/gromacs/gmxana/gmx_sham.cpp
+++ b/src/gromacs/gmxana/gmx_sham.cpp
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/xvgr.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxana/gstat.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/gmxana/gmx_tune_pme.cpp b/src/gromacs/gmxana/gmx_tune_pme.cpp
index 066c45e1864bddcc07282eca3b5fce652a4a5b17..06c712ca72c2c5eb5547d31454c4972c8de174a9 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.cpp
+++ b/src/gromacs/gmxana/gmx_tune_pme.cpp
@@ -51,10 +51,10 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/gmxlib/calcgrid.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/gmxana/gmx_xpm2ps.cpp b/src/gromacs/gmxana/gmx_xpm2ps.cpp
index c1ba061d7a0949028f09d8cbaf08984670042f0c..2478cf0e47344976c890dcd7385698e5652f1f47 100644 (file)
--- a/src/gromacs/gmxana/gmx_xpm2ps.cpp
+++ b/src/gromacs/gmxana/gmx_xpm2ps.cpp
@@ -48,6 +48,8 @@
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/writeps.h"
 #include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxlib/readinp.h"
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/utility/arraysize.h"

diff --git a/src/gromacs/gmxlib/gmx_detect_hardware.cpp b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
index 819225ed498725b61d89c478772df112c0f8ad87..13aa2b85ebac26bf202e0268be93a13f615a7753 100644 (file)
--- a/src/gromacs/gmxlib/gmx_detect_hardware.cpp
+++ b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
@@ -56,10 +56,10 @@
 
 #include "thread_mpi/threads.h"
 
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_cpuid.h"
-#include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/enums.h"

diff --git a/src/gromacs/gmxlib/gmx_omp_nthreads.cpp b/src/gromacs/gmxlib/gmx_omp_nthreads.cpp
index 5333933ac7f7c8873d798278bd2d43ad6d50bca8..c397426af62110df1630978ed9cc083b473fa97b 100644 (file)
--- a/src/gromacs/gmxlib/gmx_omp_nthreads.cpp
+++ b/src/gromacs/gmxlib/gmx_omp_nthreads.cpp
@@ -43,8 +43,8 @@
 #include <cstdlib>
 #include <cstring>
 
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"

diff --git a/src/gromacs/gmxlib/gmx_thread_affinity.cpp b/src/gromacs/gmxlib/gmx_thread_affinity.cpp
index 945211b68edafc3e2fba19fdc39e84f4e60f918f..ae1ba4bf5cb3138b1da3f9b6ea4714c0c11a0ed2 100644 (file)
--- a/src/gromacs/gmxlib/gmx_thread_affinity.cpp
+++ b/src/gromacs/gmxlib/gmx_thread_affinity.cpp
@@ -49,10 +49,10 @@
 
 #include "thread_mpi/threads.h"
 
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_cpuid.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/hw_info.h"

diff --git a/src/gromacs/gmxlib/md_logging.cpp b/src/gromacs/gmxlib/md_logging.cpp
index 6636117d98adbc05c9beeb9c2839310d63d72e4c..f1ac5981dba70ce6bb6a2f8cd5c0d43a66b3b88f 100644 (file)
--- a/src/gromacs/gmxlib/md_logging.cpp
+++ b/src/gromacs/gmxlib/md_logging.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/md_logging.h"
+#include "md_logging.h"
 
 #include <cstdarg>
 #include <cstdio>

diff --git a/src/gromacs/legacyheaders/md_logging.h b/src/gromacs/gmxlib/md_logging.h
similarity index 87%
rename from src/gromacs/legacyheaders/md_logging.h
rename to src/gromacs/gmxlib/md_logging.h
index d610c3d573b919b56de2aa9039dd8776b9a7b1f3..8da09734f09707d10d5748e3bad2e042a4b5b5f3 100644 (file)
--- a/src/gromacs/legacyheaders/md_logging.h
+++ b/src/gromacs/gmxlib/md_logging.h
@@ -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.
@@ -34,19 +34,14 @@
  * 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_MD_LOGGING_H
+#define GMX_GMXLIB_MD_LOGGING_H
 
-#ifndef _md_logging_h
-#define _md_logging_h
-
-#include <stdio.h>
-
-#ifdef __cplusplus
-extern "C" {
-#endif
+#include <cstdio>
 
 struct t_commrec;
 
-void md_print_info(const struct t_commrec *cr, FILE *fplog,
+void md_print_info(const t_commrec *cr, FILE *fplog,
                    const char *fmt, ...);
 /* Print an general information message to stderr on the master node
  * and to fplog if fplog!=NULL.
@@ -54,15 +49,11 @@ void md_print_info(const struct t_commrec *cr, FILE *fplog,
  * the arguments after that contain the values to be printed, as in printf.
  */
 
-void md_print_warn(const struct t_commrec *cr, FILE *fplog,
+void md_print_warn(const t_commrec *cr, FILE *fplog,
                    const char *fmt, ...);
 /* As md_print_info above, but for important notices or warnings.
  * The only difference with md_print_info is that a newline is printed
  * before and after the message such that it stands out.
  */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _md_logging_h */

diff --git a/src/gromacs/gmxlib/readinp.cpp b/src/gromacs/gmxlib/readinp.cpp
index cb8129941c34a1d483ba1b3299924d9f92cc70bc..770b0b70e68bbd9503af26bc6a4d33e2e53fb5d4 100644 (file)
--- a/src/gromacs/gmxlib/readinp.cpp
+++ b/src/gromacs/gmxlib/readinp.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/readinp.h"
+#include "readinp.h"
 
 #include <cstdio>
 #include <cstdlib>
@@ -45,9 +45,9 @@
 #include <algorithm>
 
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/warninp.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/legacyheaders/readinp.h b/src/gromacs/gmxlib/readinp.h
similarity index 94%
rename from src/gromacs/legacyheaders/readinp.h
rename to src/gromacs/gmxlib/readinp.h
index 29b7a65baede5abd32f87c38f36ba5c9539f34d5..dba47c5d8b3303cb3543db08bf693d24dbad33c7 100644 (file)
--- a/src/gromacs/legacyheaders/readinp.h
+++ b/src/gromacs/gmxlib/readinp.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.
@@ -34,19 +34,14 @@
  * 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_READINP_H
+#define GMX_GMXLIB_READINP_H
 
-#ifndef _readinp_h
-#define _readinp_h
+#include <cstring>
 
-#include <string.h>
-
-#include "gromacs/legacyheaders/warninp.h"
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 typedef struct {
     int      count;     /* sort order for output  */
     gmx_bool bObsolete; /* whether it is an obsolete param value */
@@ -103,7 +98,7 @@ int get_eenum(int *ninp, t_inpfile **inp, const char *name, const char **defs);
  */
 #define REM_TYPE(name)       replace_inp_entry(ninp, inp, name, NULL)
 #define REPL_TYPE(old, new)   replace_inp_entry(ninp, inp, old, new)
-#define STYPE(name, var, def)  if ((tmp = get_estr(&ninp, &inp, name, def)) != NULL) strcpy(var, tmp)
+#define STYPE(name, var, def)  if ((tmp = get_estr(&ninp, &inp, name, def)) != NULL) std::strcpy(var, tmp)
 #define STYPENC(name, def) get_estr(&ninp, &inp, name, def)
 #define ITYPE(name, var, def)  var    = get_eint(&ninp, &inp, name, def, wi)
 #define STEPTYPE(name, var, def)  var = get_eint64(&ninp, &inp, name, def, wi)
@@ -114,8 +109,4 @@ int get_eenum(int *ninp, t_inpfile **inp, const char *name, const char **defs);
 #define CTYPE(s)  STYPENC("; " s, NULL)
 /* This last one prints a comment line where you can add some explanation */
 
-#ifdef __cplusplus
-}
-#endif
-
 #endif

diff --git a/src/gromacs/gmxlib/warninp.cpp b/src/gromacs/gmxlib/warninp.cpp
index 3d1eb9cadf9bfd691a47c90b2bbe2ce67d32e934..a5609701a1f080d93e543658c349cd13540d732d 100644 (file)
--- a/src/gromacs/gmxlib/warninp.cpp
+++ b/src/gromacs/gmxlib/warninp.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/warninp.h"
+#include "warninp.h"
 
 #include <cstring>
 

diff --git a/src/gromacs/legacyheaders/warninp.h b/src/gromacs/gmxlib/warninp.h
similarity index 95%
rename from src/gromacs/legacyheaders/warninp.h
rename to src/gromacs/gmxlib/warninp.h
index cd3f32c84aa2ed2ec4a11d01cdb04dde8556b288..cedf6c542a37e45ae4bd046af879757f9c3d7f5a 100644 (file)
--- a/src/gromacs/legacyheaders/warninp.h
+++ b/src/gromacs/gmxlib/warninp.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.
@@ -34,17 +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 _warninp_h
-#define _warninp_h
+#ifndef GMX_GMXLIB_WARNINP_H
+#define GMX_GMXLIB_WARNINP_H
 
 #include "gromacs/utility/basedefinitions.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
-
 /* Abstract type for warning bookkeeping */
 typedef struct warninp *warninp_t;
 
@@ -126,8 +120,4 @@ _incorrect_n_param(warninp_t wi, const char *fn, int line);
 #define incorrect_n_param(wi) _incorrect_n_param(wi, __FILE__, __LINE__)
 /* Issue a warning stating 'Incorrect number of parameters' */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _warninp_h */

diff --git a/src/gromacs/gmxpreprocess/genconf.cpp b/src/gromacs/gmxpreprocess/genconf.cpp
index fa35d36b0a07fa9db9fdf84c44d9cb2e4bb19c27..36443056a293c45e9d98dec484cf28f56d9ce015 100644 (file)
--- a/src/gromacs/gmxpreprocess/genconf.cpp
+++ b/src/gromacs/gmxpreprocess/genconf.cpp
@@ -41,9 +41,9 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxpreprocess/sortwater.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/math/3dtransforms.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/gmxpreprocess/grompp.cpp b/src/gromacs/gmxpreprocess/grompp.cpp
index 41f5b3a12ba3332fe0228f183daa0976dc3d8d20..324ed189fc2fd75efd5678a425d9c168ae51297b 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.cpp
+++ b/src/gromacs/gmxpreprocess/grompp.cpp
@@ -56,6 +56,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/gmxlib/calcgrid.h"
 #include "gromacs/gmxlib/splitter.h"
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/add_par.h"
 #include "gromacs/gmxpreprocess/convparm.h"
 #include "gromacs/gmxpreprocess/gen_maxwell_velocities.h"
@@ -71,7 +72,6 @@
 #include "gromacs/legacyheaders/genborn.h"
 #include "gromacs/legacyheaders/names.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"

diff --git a/src/gromacs/gmxpreprocess/nm2type.cpp b/src/gromacs/gmxpreprocess/nm2type.cpp
index 51ce92c44b0322ab4a1d269a8c74378a65175fa3..6e9344cca49d1b01cbe38bd7725de02f3cd86c24 100644 (file)
--- a/src/gromacs/gmxpreprocess/nm2type.cpp
+++ b/src/gromacs/gmxpreprocess/nm2type.cpp
@@ -44,13 +44,13 @@
 #include <algorithm>
 
 #include "gromacs/fileio/confio.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
 #include "gromacs/gmxpreprocess/pdb2top.h"
 #include "gromacs/gmxpreprocess/toppush.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.cpp b/src/gromacs/gmxpreprocess/pdb2gmx.cpp
index cdd3daf13e668eee7032a115f322c252ad2940c2..14cedc5d2ae4d1b04e22448bcbe1195484f3fc75 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.cpp
@@ -49,6 +49,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxpreprocess/fflibutil.h"
 #include "gromacs/gmxpreprocess/genhydro.h"
 #include "gromacs/gmxpreprocess/h_db.h"
@@ -61,7 +62,6 @@
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/gmxpreprocess/xlate.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/topology/atomprop.h"

diff --git a/src/gromacs/gmxpreprocess/readir.cpp b/src/gromacs/gmxpreprocess/readir.cpp
index 1b5fbd8c78c0a35210add8b8b0f7e20508801224..1e3341d232bdd9c1fe2678f66f8cdcdde7623e3e 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.cpp
+++ b/src/gromacs/gmxpreprocess/readir.cpp
@@ -47,13 +47,13 @@
 #include <algorithm>
 
 #include "gromacs/gmxlib/chargegroup.h"
+#include "gromacs/gmxlib/readinp.h"
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/warninp.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"

diff --git a/src/gromacs/gmxpreprocess/readir.h b/src/gromacs/gmxpreprocess/readir.h
index 924681e895f8c3a94959ba6bbeb857577862a430..fc491c33828bf3af89d5e151756674fb5eddffe0 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.h
+++ b/src/gromacs/gmxpreprocess/readir.h
@@ -38,8 +38,8 @@
 #ifndef GMX_GMXPREPROCESS_READIR_H
 #define GMX_GMXPREPROCESS_READIR_H
 
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxpreprocess/grompp-impl.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 
 enum {

diff --git a/src/gromacs/gmxpreprocess/readpull.cpp b/src/gromacs/gmxpreprocess/readpull.cpp
index e9769e5e91f7035bcec195da248e6040eb17d451..413063cd34084e3085a2449cf42478e60f53c202 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.cpp
+++ b/src/gromacs/gmxpreprocess/readpull.cpp
@@ -39,9 +39,9 @@
 #include <stdlib.h>
 #include <string.h>
 
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxpreprocess/readir.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"

diff --git a/src/gromacs/gmxpreprocess/topio.cpp b/src/gromacs/gmxpreprocess/topio.cpp
index b92fe2087a4f740b02ebb62a1955c96aeb5b0ac9..5979bb6299f032ad93aad3a0e726e9023be8fda7 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.cpp
+++ b/src/gromacs/gmxpreprocess/topio.cpp
@@ -49,6 +49,7 @@
 #include <sys/types.h>
 
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/gmxcpp.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
@@ -62,7 +63,6 @@
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/warninp.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.cpp b/src/gromacs/gmxpreprocess/toppush.cpp
index 5c2e8c21e8d6fc29f1a7e4a339d1818195c88d50..24401bab6ac93099a838239d4cc249aaf3c0f3f6 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.cpp
+++ b/src/gromacs/gmxpreprocess/toppush.cpp
@@ -45,13 +45,13 @@
 
 #include <algorithm>
 
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
 #include "gromacs/gmxpreprocess/readir.h"
 #include "gromacs/gmxpreprocess/topdirs.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/warninp.h"
 #include "gromacs/legacyheaders/types/ifunc.h"
 #include "gromacs/topology/symtab.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.h b/src/gromacs/gmxpreprocess/toppush.h
index 8ee48618dfd8a7b7e2df47c59ad92ff35c179ff5..f6c7398a1cfe5fdb8a479b2a0288958d6c8eec3a 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.h
+++ b/src/gromacs/gmxpreprocess/toppush.h
@@ -38,11 +38,11 @@
 #ifndef GMX_GMXPREPROCESS_TOPPUSH_H
 #define GMX_GMXPREPROCESS_TOPPUSH_H
 
+#include "gromacs/gmxlib/warninp.h"
 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
 #include "gromacs/gmxpreprocess/gpp_bond_atomtype.h"
 #include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/warninp.h"
 
 typedef struct {
     int       nr;   /* The number of entries in the list            */

diff --git a/src/gromacs/gmxpreprocess/x2top.cpp b/src/gromacs/gmxpreprocess/x2top.cpp
index 65cea88ddc83570f664b8da55f9b5422ca1cf23b..02648d5e779869c18efb53acdc4ed53efd9cb867 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.cpp
+++ b/src/gromacs/gmxpreprocess/x2top.cpp
@@ -43,6 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/gmxpreprocess/gen_ad.h"
 #include "gromacs/gmxpreprocess/gpp_nextnb.h"
 #include "gromacs/gmxpreprocess/hackblock.h"
@@ -51,7 +52,6 @@
 #include "gromacs/gmxpreprocess/toppush.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/listed-forces/bonded.h"
 #include "gromacs/math/units.h"

diff --git a/src/gromacs/mdlib/force.cpp b/src/gromacs/mdlib/force.cpp
index 3f1607743bd22d971a60e437ef69256c926ca71f..c2d56fb0345fa28fe554a325ea7c3dee3aee0809 100644 (file)
--- a/src/gromacs/mdlib/force.cpp
+++ b/src/gromacs/mdlib/force.cpp
@@ -55,13 +55,13 @@
 #include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/listed-forces/listed-forces.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/forcerec.cpp b/src/gromacs/mdlib/forcerec.cpp
index 66f7512f2a87484c96d3b10126cdaf370ff0be5b..a088b6aa86f753f6435d725e3445d4ee7018f2f2 100644 (file)
--- a/src/gromacs/mdlib/forcerec.cpp
+++ b/src/gromacs/mdlib/forcerec.cpp
@@ -50,19 +50,17 @@
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/ewald/ewald.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/tables.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
@@ -75,12 +73,14 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/forcerec-threading.h"
+#include "gromacs/mdlib/md_support.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_search.h"
 #include "gromacs/mdlib/nbnxn_simd.h"
 #include "gromacs/mdlib/nbnxn_util.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/simd/simd.h"

diff --git a/src/gromacs/mdlib/md_support.cpp b/src/gromacs/mdlib/md_support.cpp
index 5aceded430409e8abee9b32da411bc10af21f384..083d17c2190ea38563ffafe791f9a4ebd175692c 100644 (file)
--- a/src/gromacs/mdlib/md_support.cpp
+++ b/src/gromacs/mdlib/md_support.cpp
@@ -37,13 +37,13 @@
 
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/md_support.h"
+#include "md_support.h"
 
 #include <algorithm>
 
 #include "gromacs/domdec/domdec.h"
 #include "gromacs/fileio/trx.h"
-#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/nrnb.h"

diff --git a/src/gromacs/legacyheaders/md_support.h b/src/gromacs/mdlib/md_support.h
similarity index 94%
rename from src/gromacs/legacyheaders/md_support.h
rename to src/gromacs/mdlib/md_support.h
index 7cdfb9d8272bcc6dece42c40a45f0bd538212580..aca3ad7e1b2024a3e05aff7278d9328c7c209ad0 100644 (file)
--- a/src/gromacs/legacyheaders/md_support.h
+++ b/src/gromacs/mdlib/md_support.h
@@ -34,19 +34,14 @@
  * 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 _md_support_h
-#define _md_support_h
+#ifndef GMX_MDLIB_MD_SUPPORT_H
+#define GMX_MDLIB_MD_SUPPORT_H
 
 #include "gromacs/legacyheaders/sim_util.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vcm.h"
 #include "gromacs/timing/wallcycle.h"
 
-#ifdef __cplusplus
-extern "C" {
-#endif
-
 struct gmx_constr;
 struct gmx_signalling_t;
 struct t_trxframe;
@@ -119,13 +114,9 @@ void compute_globals(FILE *fplog, gmx_global_stat_t gstat, t_commrec *cr, t_inpu
                      t_state *state, t_state *state_global, t_mdatoms *mdatoms,
                      t_nrnb *nrnb, t_vcm *vcm, gmx_wallcycle_t wcycle,
                      gmx_enerdata_t *enerd, tensor force_vir, tensor shake_vir, tensor total_vir,
-                     tensor pres, rvec mu_tot, struct gmx_constr *constr,
-                     struct gmx_signalling_t *gs, gmx_bool bInterSimGS,
+                     tensor pres, rvec mu_tot, gmx_constr *constr,
+                     gmx_signalling_t *gs, gmx_bool bInterSimGS,
                      matrix box, gmx_mtop_t *top_global, gmx_bool *bSumEkinhOld, int flags);
 /* Compute global variables during integration */
 
-#ifdef __cplusplus
-}
 #endif
-
-#endif  /* _md_support_h */

diff --git a/src/gromacs/mdlib/mdatoms.cpp b/src/gromacs/mdlib/mdatoms.cpp
index 212a4fee43186ec9c3a95f9b2e2be4370ad60185..e972cca6a76cc44058668b42ee71f7a541562e6d 100644 (file)
--- a/src/gromacs/mdlib/mdatoms.cpp
+++ b/src/gromacs/mdlib/mdatoms.cpp
@@ -41,8 +41,8 @@
 #include <math.h>
 
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/mdrun_signalling.cpp b/src/gromacs/mdlib/mdrun_signalling.cpp
index cc3b3a5129a13fd16711897287b03630a1bedc35..f69840beabf8b0b3d2c38deec2c1c8c41db72f82 100644 (file)
--- a/src/gromacs/mdlib/mdrun_signalling.cpp
+++ b/src/gromacs/mdlib/mdrun_signalling.cpp
@@ -52,9 +52,9 @@
 
 #include <algorithm>
 
-#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/types/inputrec.h"
+#include "gromacs/mdlib/md_support.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/real.h"

diff --git a/src/gromacs/mdlib/minimize.cpp b/src/gromacs/mdlib/minimize.cpp
index 88be46a063fb7b23db238e3c3aa379c649443459..f2056b15d59f034745bc3b55a02cd000c9be5efa 100644 (file)
--- a/src/gromacs/mdlib/minimize.cpp
+++ b/src/gromacs/mdlib/minimize.cpp
@@ -59,11 +59,10 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/mtxio.h"
 #include "gromacs/fileio/trajectory_writing.h"
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/imd/imd.h"
 #include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
@@ -82,6 +81,7 @@
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/pbcutil/mshift.h"
 #include "gromacs/pbcutil/pbc.h"

diff --git a/src/gromacs/mdlib/qm_gamess.cpp b/src/gromacs/mdlib/qm_gamess.cpp
index 7161b8f5079d76ec6dc45df8bfe4440075695d41..d185161d9fca01006d779fef98516cb40da8c403 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.cpp
+++ b/src/gromacs/mdlib/qm_gamess.cpp
@@ -51,12 +51,12 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/qm_gaussian.cpp b/src/gromacs/mdlib/qm_gaussian.cpp
index 2776ff4299eb553232f1734aadc4b4016988e4a8..e7b7b26092ccc492475e5d88bfac82501aa23533 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.cpp
+++ b/src/gromacs/mdlib/qm_gaussian.cpp
@@ -51,11 +51,11 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/mdlib/qm_mopac.cpp b/src/gromacs/mdlib/qm_mopac.cpp
index 209313c4d80d84ade80b2f8f5633434f0e2b4ca9..28d9a6bd55c35657321d95926eb0918b66cc7225 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.cpp
+++ b/src/gromacs/mdlib/qm_mopac.cpp
@@ -51,11 +51,11 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/qm_orca.cpp b/src/gromacs/mdlib/qm_orca.cpp
index ac4b609b9609443fc8c8c559dc8eaf3b57697f62..47a892bf2ff14e80c8146ea9f7b594466c1b08a6 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.cpp
+++ b/src/gromacs/mdlib/qm_orca.cpp
@@ -47,11 +47,11 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nrnb.h"
 #include "gromacs/legacyheaders/ns.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/units.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/mdlib/qmmm.cpp b/src/gromacs/mdlib/qmmm.cpp
index 234fe68b72bb77f6e1d0bf7a934d8b7ffa94bf36..e0e1cd388a7113945c4698b0db25895ecb34ccff 100644 (file)
--- a/src/gromacs/mdlib/qmmm.cpp
+++ b/src/gromacs/mdlib/qmmm.cpp
@@ -36,7 +36,7 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/legacyheaders/qmmm.h"
+#include "qmmm.h"
 
 #include "config.h"
 

diff --git a/src/gromacs/legacyheaders/qmmm.h b/src/gromacs/mdlib/qmmm.h
similarity index 97%
rename from src/gromacs/legacyheaders/qmmm.h
rename to src/gromacs/mdlib/qmmm.h
index d3b5839f86c3b81335118a570f94db75137843cd..231c0020b7cfc93f3db8d5f21065feb15aefa05a 100644 (file)
--- a/src/gromacs/legacyheaders/qmmm.h
+++ b/src/gromacs/mdlib/qmmm.h
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, 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.

diff --git a/src/gromacs/mdlib/sim_util.cpp b/src/gromacs/mdlib/sim_util.cpp
index 7049961e269886320f916aa839a1130acd86a094..dd386957f735464baacb5d8975effad77c39f2b7 100644 (file)
--- a/src/gromacs/mdlib/sim_util.cpp
+++ b/src/gromacs/mdlib/sim_util.cpp
@@ -63,7 +63,6 @@
 #include "gromacs/legacyheaders/network.h"
 #include "gromacs/legacyheaders/nonbonded.h"
 #include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/update.h"
@@ -79,6 +78,7 @@
 #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/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/stat.cpp b/src/gromacs/mdlib/stat.cpp
index d25385084824bbf9c27f63bf4d32f1953708d3f6..5940926e156c1c7e0a6b00c4f158ece86570a463 100644 (file)
--- a/src/gromacs/mdlib/stat.cpp
+++ b/src/gromacs/mdlib/stat.cpp
@@ -43,7 +43,6 @@
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
@@ -57,6 +56,7 @@
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/rbin.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"

diff --git a/src/gromacs/timing/wallcycle.cpp b/src/gromacs/timing/wallcycle.cpp
index e954db2a8d66490e7fd9538e588b0233598a0b51..2c20d56ed5169eee25d94f4d8f0248b0d024de3f 100644 (file)
--- a/src/gromacs/timing/wallcycle.cpp
+++ b/src/gromacs/timing/wallcycle.cpp
@@ -42,7 +42,7 @@
 
 #include <cstdlib>
 
-#include "gromacs/legacyheaders/md_logging.h"
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/timing/cyclecounter.h"
 #include "gromacs/timing/gpu_timing.h"

diff --git a/src/programs/mdrun/md.cpp b/src/programs/mdrun/md.cpp
index b08e2277c113a80cf4fb781005cdf198cdcac1c2..d8eef45009c72e02289c6621faf64353321e6eb1 100644 (file)
--- a/src/programs/mdrun/md.cpp
+++ b/src/programs/mdrun/md.cpp
@@ -55,12 +55,11 @@
 #include "gromacs/fileio/trajectory_writing.h"
 #include "gromacs/fileio/trx.h"
 #include "gromacs/fileio/trxio.h"
+#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/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/mdebin.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/network.h"
@@ -91,6 +90,7 @@
 #include "gromacs/mdlib/compute_io.h"
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
+#include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/mdrun_signalling.h"
 #include "gromacs/mdlib/nb_verlet.h"

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index 65098f81610e0eb2ecf2ba89f6020e93da61882a..cd531f4f27e45d197400f4f8c811c73a419f3246 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -59,10 +59,10 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/filenm.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/mdrunutility/handlerestart.h"

diff --git a/src/programs/mdrun/membed.cpp b/src/programs/mdrun/membed.cpp
index fb194498ca1a7dc1f4ef7b0db88ee8d0abece148..947581a57bc582a1365d56ceec7b05abc2d00b2a 100644 (file)
--- a/src/programs/mdrun/membed.cpp
+++ b/src/programs/mdrun/membed.cpp
@@ -41,9 +41,9 @@
 
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/fileio/tpxio.h"
+#include "gromacs/gmxlib/readinp.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/readinp.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/vec.h"

diff --git a/src/programs/mdrun/resource-division.cpp b/src/programs/mdrun/resource-division.cpp
index 0ef7b583f4903c68bb4a67c83ff20048a99b804c..d82ee3b739db5d8f51610a2064e53c3cd556c36e 100644 (file)
--- a/src/programs/mdrun/resource-division.cpp
+++ b/src/programs/mdrun/resource-division.cpp
@@ -44,9 +44,9 @@
 
 #include <algorithm>
 
+#include "gromacs/gmxlib/md_logging.h"
 #include "gromacs/legacyheaders/gmx_detect_hardware.h"
 #include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/md_logging.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/programs/mdrun/runner.cpp b/src/programs/mdrun/runner.cpp
index 98b5c1d02ef6c9d570316667db448b3f900797aa..93fd059e13d6d3f62fb48a7c1dd5023e596cee79 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/md_logging.h"
 #include "gromacs/gmxlib/orires.h"
 #include "gromacs/gmxlib/sighandler.h"
 #include "gromacs/gmxlib/gpu_utils/gpu_utils.h"
@@ -72,12 +73,9 @@
 #include "gromacs/legacyheaders/gmx_thread_affinity.h"
 #include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/md_logging.h"
-#include "gromacs/legacyheaders/md_support.h"
 #include "gromacs/legacyheaders/mdrun.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/qmmm.h"
 #include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/math/calculate-ewald-splitting-coefficient.h"
@@ -86,9 +84,11 @@
 #include "gromacs/mdlib/constr.h"
 #include "gromacs/mdlib/forcerec.h"
 #include "gromacs/mdlib/integrator.h"
+#include "gromacs/mdlib/md_support.h"
 #include "gromacs/mdlib/mdatoms.h"
 #include "gromacs/mdlib/minimize.h"
 #include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/qmmm.h"
 #include "gromacs/mdlib/tpi.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pulling/pull.h"