Manually sort some includes in src/gromacs

Sort manually includes in files where there are #ifdefs within the
include statements and the automatic sorter does not do a good job
because of this.

This commit does this for files found in src/gromacs/.  Files from other
locations will be done in a separate change if there are any.

Fix nbnxn_cuda.h to work without requiring code to include
nbnxn_pairlist.h first.

Change-Id: I26fa1a28ea9094a62c826d8ee65ddabac345da68

diff --git a/src/gromacs/fft/fft5d.cpp b/src/gromacs/fft/fft5d.cpp
index 69a689aaa8fe469f03c8814fe902fb63c5e6928a..1e9e11bd70a7757568d5115bf35726db5f5072f2 100644 (file)
--- a/src/gromacs/fft/fft5d.cpp
+++ b/src/gromacs/fft/fft5d.cpp
@@ -34,14 +34,23 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
-#include <algorithm>
+#include "fft5d.h"
 
+#include <assert.h>
+#include <float.h>
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include <algorithm>
+
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/gmxmpi.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "config.h"
+
 #ifdef NOGMX
 #define GMX_PARALLEL_ENV_INITIALIZED 1
 #else
@@ -52,8 +61,6 @@
 #endif
 #endif
 
-#include "gromacs/utility/gmxmpi.h"
-
 #ifdef GMX_OPENMP
 /* TODO: Do we still need this? Are we still planning ot use fftw + OpenMP? */
 #define FFT5D_THREADS
@@ -61,12 +68,6 @@
 /* #define FFT5D_FFTW_THREADS (now set by cmake) */
 #endif
 
-#include "fft5d.h"
-#include <float.h>
-#include <math.h>
-#include <assert.h>
-#include "gromacs/utility/smalloc.h"
-
 #ifndef __FLT_EPSILON__
 #define __FLT_EPSILON__ FLT_EPSILON
 #define __DBL_EPSILON__ DBL_EPSILON
@@ -76,11 +77,9 @@
 FILE* debug = 0;
 #endif
 
-#include "gromacs/utility/fatalerror.h"
-
-
 #ifdef GMX_FFT_FFTW3
 #include "thread_mpi/mutex.h"
+
 #include "gromacs/utility/exceptions.h"
 /* none of the fftw3 calls, except execute(), are thread-safe, so
    we need to serialize them with this mutex. */

diff --git a/src/gromacs/fft/fft_fftw3.cpp b/src/gromacs/fft/fft_fftw3.cpp
index e9de7eb0d1fa0a59d7aaf031c53924bdf3cec9cd..d83d0f591b0604f7a8cdec3dc5a988eec0d9fce2 100644 (file)
--- a/src/gromacs/fft/fft_fftw3.cpp
+++ b/src/gromacs/fft/fft_fftw3.cpp
@@ -35,25 +35,25 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <errno.h>
 #include <stdlib.h>
 
 #include <fftw3.h>
 
+#include "thread_mpi/mutex.h"
+
 #include "gromacs/fft/fft.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
 
+#include "config.h"
+
 #ifdef GMX_DOUBLE
 #define FFTWPREFIX(name) fftw_ ## name
 #else
 #define FFTWPREFIX(name) fftwf_ ## name
 #endif
 
-#include "thread_mpi/mutex.h"
-#include "gromacs/utility/exceptions.h"
-
 /* none of the fftw3 calls, except execute(), are thread-safe, so
    we need to serialize them with this mutex. */
 static tMPI::mutex big_fftw_mutex;

diff --git a/src/gromacs/fileio/gmxfio.c b/src/gromacs/fileio/gmxfio.c
index 24dbc9f54a26b3b2ef46c767432d48d5e749c27a..e191b217e96d614f1ac6eb276dc5d1fe817a456b 100644 (file)
--- a/src/gromacs/fileio/gmxfio.c
+++ b/src/gromacs/fileio/gmxfio.c
@@ -36,11 +36,14 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
+#include "gmxfio.h"
 
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
+
+#include "config.h"
+
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
@@ -50,16 +53,14 @@
 
 #include "thread_mpi/threads.h"
 
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "filenm.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 /* This is the new improved and thread safe version of gmxfio. */
 

diff --git a/src/gromacs/fileio/gmxfio_asc.c b/src/gromacs/fileio/gmxfio_asc.c
index 28ea2377eee013d1025ba3186abaf6b00134aaed..b2f04b7ff8464de349ee1e459a4fa9e9b3e29e4e 100644 (file)
--- a/src/gromacs/fileio/gmxfio_asc.c
+++ b/src/gromacs/fileio/gmxfio_asc.c
@@ -34,30 +34,28 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-
-
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <ctype.h>
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
+
+#include "config.h"
+
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
 
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
-#include "gromacs/utility/futil.h"
-#include "filenm.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /* This is the part that reads dummy and ascii files.  */

diff --git a/src/gromacs/fileio/gmxfio_bin.c b/src/gromacs/fileio/gmxfio_bin.c
index e8db04822e356ff8f09e993c60127f30363a81b7..498a795eb4da99a8bf5544e08da2f17a8b793ac9 100644 (file)
--- a/src/gromacs/fileio/gmxfio_bin.c
+++ b/src/gromacs/fileio/gmxfio_bin.c
@@ -36,23 +36,23 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
+
+#include "config.h"
+
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
 
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/smalloc.h"
 
 /* This is the part that reads dummy and ascii files.  */
 

diff --git a/src/gromacs/fileio/gmxfio_rw.c b/src/gromacs/fileio/gmxfio_rw.c
index 1b74123e3be9c9da24600d3ce2c6693eba664a75..d41d19176a953be2c43d9a4b14625ad23ca79612 100644 (file)
--- a/src/gromacs/fileio/gmxfio_rw.c
+++ b/src/gromacs/fileio/gmxfio_rw.c
@@ -36,22 +36,22 @@
  */
 #include "gmxpre.h"
 
+#include <errno.h>
+#include <stdio.h>
+
 #include "config.h"
 
-#include <stdio.h>
-#include <errno.h>
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
 
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/smalloc.h"
 
 
 /*******************************************************************

diff --git a/src/gromacs/fileio/gmxfio_xdr.c b/src/gromacs/fileio/gmxfio_xdr.c
index 77ca2f9f1653573ae8d08dc64a07b4245b70d952..6054be42f9db211b2e9f7bad508407feadbb1d0e 100644 (file)
--- a/src/gromacs/fileio/gmxfio_xdr.c
+++ b/src/gromacs/fileio/gmxfio_xdr.c
@@ -36,24 +36,24 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <errno.h>
 #include <stdio.h>
 #include <string.h>
+
+#include "config.h"
+
 #ifdef HAVE_IO_H
 #include <io.h>
 #endif
 
-#include "gromacs/utility/fatalerror.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/gmxfio_int.h"
+#include "gromacs/fileio/md5.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "filenm.h"
-#include "gmxfio.h"
-#include "md5.h"
-
-#include "gmxfio_int.h"
+#include "gromacs/utility/smalloc.h"
 
 /* This is the part that reads xdr files.  */
 

diff --git a/src/gromacs/fileio/tngio_for_tools.cpp b/src/gromacs/fileio/tngio_for_tools.cpp
index f15d15dafc6cf36050015bd53c392cfdc93e66ac..cdc1263badc34a153dd42962508eb19d2150c77f 100644 (file)
--- a/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@ -36,17 +36,16 @@
 
 #include "tngio_for_tools.h"
 
-#include "config.h"
-
 #include <math.h>
 
-#include "tngio.h"
-#include "trx.h"
+#include "config.h"
 
 #ifdef GMX_USE_TNG
 #include "tng/tng_io.h"
 #endif
 
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/trx.h"
 #include "gromacs/math/units.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/fileio/trxio.c b/src/gromacs/fileio/trxio.c
index 0f39b6c46bff835fdae21542bea79b9e068c6095..b6098ce5b39e829833f13fa8fbf002650fed27ee 100644 (file)
--- a/src/gromacs/fileio/trxio.c
+++ b/src/gromacs/fileio/trxio.c
@@ -38,35 +38,34 @@
 
 #include "trxio.h"
 
-#include "config.h"
-
 #include <assert.h>
 #include <math.h>
 
-#ifdef GMX_USE_PLUGINS
-#include "vmdio.h"
-#endif
-#include "gmxfio.h"
-#include "trxio.h"
-#include "tpxio.h"
-#include "trnio.h"
-#include "tngio.h"
-#include "tngio_for_tools.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/utility/futil.h"
-#include "xtcio.h"
-#include "pdbio.h"
-#include "confio.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "xdrf.h"
-
+#include "gromacs/fileio/confio.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/timecontrol.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/trx.h"
+#include "gromacs/fileio/xdrf.h"
+#include "gromacs/fileio/xtcio.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/topology/atoms.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
+#include "config.h"
+
+#ifdef GMX_USE_PLUGINS
+#include "gromacs/fileio/vmdio.h"
+#endif
+
 /* defines for frame counter output */
 #define SKIP1   10
 #define SKIP2  100

diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index c226bed5bf4a732f59c03255958526c1742167e4..46a4da6497421dd91dff67852d91e383d69a6ab3 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -36,34 +36,34 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
 #include <math.h>
 
-/*#define HAVE_NN_LOOPS*/
-
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/matio.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trxio.h"
+#include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/correl.h"
+#include "gromacs/gmxana/geminate.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/gmxana/gstat.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/fatalerror.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/fileio/xvgr.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gstat.h"
-#include "gromacs/utility/cstringutil.h"
 #include "gromacs/pbcutil/pbc.h"
-#include "correl.h"
-#include "gmx_ana.h"
-#include "geminate.h"
-
+#include "gromacs/topology/index.h"
+#include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/fileio/matio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
 #include "gromacs/utility/gmxomp.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "config.h"
+
+/*#define HAVE_NN_LOOPS*/
 
 typedef short int t_E;
 typedef int t_EEst;

diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index 29e064f74b87f73dcf7c6e8e8c45eb88446a0cbe..f0aa6b5d808eac396d8d787f63fc9cb64717fcf8 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -36,43 +36,42 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <math.h>
 #include <stdlib.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/typedefs.h"
+#include "config.h"
+
+#ifdef HAVE_UNISTD_H
+#include <unistd.h>
+#endif
+
+#include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/pdbio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/trnio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/pdbio.h"
-#include "gromacs/fileio/confio.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/topology/index.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/fileio/trxio.h"
 #include "gromacs/fileio/xtcio.h"
-#include "gromacs/legacyheaders/viewit.h"
-#include "gmx_ana.h"
-
-#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/xvgr.h"
+#include "gromacs/gmxana/gmx_ana.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/viewit.h"
 #include "gromacs/math/do_fit.h"
+#include "gromacs/math/vec.h"
 #include "gromacs/pbcutil/pbc.h"
 #include "gromacs/pbcutil/rmpbc.h"
+#include "gromacs/topology/index.h"
 #include "gromacs/topology/topology.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
-#ifdef HAVE_UNISTD_H
-#include <unistd.h>
-#endif
-
 enum {
     euSel, euRect, euTric, euCompact, euNR
 };

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index 80a86c4df411b605bf21f91d321df07054973dd2..990ec4738dfcaaafd09ddffba4034c3add6a19e6 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -34,32 +34,32 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <stdlib.h>
 #include <time.h>
+
+#include "config.h"
+
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/math/vec.h"
+#include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/gmxana/gmx_ana.h"
 #include "gromacs/legacyheaders/calcgrid.h"
 #include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/inputrec.h"
 #include "gromacs/legacyheaders/macros.h"
-#include "gmx_ana.h"
 #include "gromacs/legacyheaders/names.h"
 #include "gromacs/legacyheaders/perf_est.h"
-#include "gromacs/legacyheaders/inputrec.h"
-#include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/legacyheaders/readinp.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/utilities.h"
-
-#include "gromacs/commandline/pargs.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/timing/walltime_accounting.h"
 #include "gromacs/utility/baseversion.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/gmxlib/checkpoint.cpp b/src/gromacs/gmxlib/checkpoint.cpp
index b2c9c37e9704f25be89963b3a9893a7e9605d61a..bec5b71652101e227368ff40e1adaf74889d425f 100644 (file)
--- a/src/gromacs/gmxlib/checkpoint.cpp
+++ b/src/gromacs/gmxlib/checkpoint.cpp
@@ -39,49 +39,46 @@
 
 #include "gromacs/legacyheaders/checkpoint.h"
 
-#include "config.h"
-
 #include <errno.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
 #include <fcntl.h>
+
+#include "config.h"
+
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
-
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
-
 #ifdef GMX_NATIVE_WINDOWS
 /* _chsize_s */
 #include <io.h>
 #include <sys/locking.h>
 #endif
 
+#include "buildinfo.h"
+#include "gromacs/fileio/filenm.h"
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/fileio/xdr_datatype.h"
+#include "gromacs/fileio/xdrf.h"
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/network.h"
-
-#include "gromacs/fileio/filenm.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/xdrf.h"
-#include "gromacs/fileio/xdr_datatype.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/baseversion.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "buildinfo.h"
-
 #ifdef GMX_FAHCORE
 #include "corewrap.h"
 #endif

diff --git a/src/gromacs/gmxlib/copyrite.cpp b/src/gromacs/gmxlib/copyrite.cpp
index e2a2da88cbc7e755adc9facf74e8541a3045896d..c1b94f0ebec12e6d5f45cfeb5e70c3e60babffcb 100644 (file)
--- a/src/gromacs/gmxlib/copyrite.cpp
+++ b/src/gromacs/gmxlib/copyrite.cpp
@@ -38,29 +38,27 @@
 
 #include "gromacs/legacyheaders/copyrite.h"
 
-#include "config.h"
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 #include <time.h>
 
+#include "config.h"
+
 #ifdef HAVE_LIBMKL
 #include <mkl.h>
 #endif
-
 #ifdef HAVE_EXTRAE
- #include "extrae_user_events.h"
+#include <extrae_user_events.h>
 #endif
-
 #include <boost/version.hpp>
 
 /* This file is completely threadsafe - keep it that way! */
 
-#include "gromacs/legacyheaders/macros.h"
-
+#include "buildinfo.h"
 #include "gromacs/fft/fft.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
 #include "gromacs/random/random.h"
 #include "gromacs/utility/baseversion.h"
@@ -71,8 +69,6 @@
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"
 
-#include "buildinfo.h"
-
 static gmx_bool be_cool(void)
 {
     /* Yes, it is bad to check the environment variable every call,

diff --git a/src/gromacs/gmxlib/gmx_detect_hardware.cpp b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
index 3158d79f0d67ad8b1d660104646474e122eb747e..e05629a5122d20532c97e034ed17a15914f5b5c3 100644 (file)
--- a/src/gromacs/gmxlib/gmx_detect_hardware.cpp
+++ b/src/gromacs/gmxlib/gmx_detect_hardware.cpp
@@ -34,32 +34,36 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
-#include <string>
-#include <vector>
+#include "gromacs/legacyheaders/gmx_detect_hardware.h"
 
 #include <assert.h>
 #include <errno.h>
 #include <stdlib.h>
 #include <string.h>
 
+#include <string>
+#include <vector>
+
+#include "config.h"
+
 #ifdef HAVE_UNISTD_H
 /* For sysconf */
 #include <unistd.h>
 #endif
+#ifdef GMX_NATIVE_WINDOWS
+#include <windows.h>
+#endif
 
-#include "gromacs/legacyheaders/types/enums.h"
-#include "gromacs/legacyheaders/types/hw_info.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/md_logging.h"
+#include "thread_mpi/threads.h"
+
+#include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_cpuid.h"
 #include "gromacs/legacyheaders/gpu_utils.h"
-#include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_detect_hardware.h"
 #include "gromacs/legacyheaders/md_logging.h"
-
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/enums.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
@@ -68,12 +72,6 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
-#include "thread_mpi/threads.h"
-
-#ifdef GMX_NATIVE_WINDOWS
-#include <windows.h>
-#endif
-
 #ifdef GMX_GPU
 const gmx_bool bGPUBinary = TRUE;
 #else

diff --git a/src/gromacs/gmxlib/gmx_thread_affinity.c b/src/gromacs/gmxlib/gmx_thread_affinity.c
index 703ec4cf713c4196ed8053800fc497f707ddda66..69e256fbca94283f969d57c9f7473f63103b940d 100644 (file)
--- a/src/gromacs/gmxlib/gmx_thread_affinity.c
+++ b/src/gromacs/gmxlib/gmx_thread_affinity.c
@@ -35,6 +35,7 @@
 #include "gmxpre.h"
 
 #include "config.h"
+
 #ifdef HAVE_SCHED_AFFINITY
 #  ifndef _GNU_SOURCE
 #    define _GNU_SOURCE 1
@@ -42,22 +43,23 @@
 #  include <sched.h>
 #  include <sys/syscall.h>
 #endif
-#include <string.h>
-#include <errno.h>
+
+#include "gromacs/legacyheaders/gmx_thread_affinity.h"
+
 #include <assert.h>
+#include <errno.h>
 #include <stdio.h>
+#include <string.h>
 
 #include "thread_mpi/threads.h"
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/types/hw_info.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/gmx_thread_affinity.h"
-
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/types/hw_info.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/fatalerror.h"

diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index dffa2ad7d88ee45b08ad5eff0fcde02732cbf111..a91b41e2e4e54f0147e9397c53aaac320071aaa7 100644 (file)
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -36,37 +36,37 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
+#include "gromacs/legacyheaders/main.h"
 
+#include <limits.h>
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include <limits.h>
 #include <time.h>
 
+#include "config.h"
+
+#ifdef GMX_NATIVE_WINDOWS
+#include <process.h>
+#endif
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
-#ifdef GMX_NATIVE_WINDOWS
-#include <process.h>
-#endif
 
-#include "gromacs/legacyheaders/types/commrec.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/main.h"
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/utility/futil.h"
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/legacyheaders/copyrite.h"
-
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/utility/basenetwork.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/fflibutil.cpp b/src/gromacs/gmxpreprocess/fflibutil.cpp
index c08255fa8c41aad2386b38065b66f11d3adc02a3..b47aa18b7c86c5acc632c6561c94a64c1186b4f5 100644 (file)
--- a/src/gromacs/gmxpreprocess/fflibutil.cpp
+++ b/src/gromacs/gmxpreprocess/fflibutil.cpp
@@ -34,26 +34,27 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
+#include "fflibutil.h"
 
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
 #include <fcntl.h>
-#include <sys/types.h>
 #include <sys/stat.h>
+#include <sys/types.h>
+
+#include "config.h"
+
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
 
 #include "gromacs/legacyheaders/network.h"
-#include "fflibutil.h"
-
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/futil.h"
-#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/path.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.c b/src/gromacs/gmxpreprocess/gpp_nextnb.c
index ff7bbaff4e0dfca3ee41b657e798926c923aba4c..ac779b14bdb2489eb34c261b3a3bc26a23597475 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.c
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.c
@@ -37,15 +37,16 @@
 /* This file is completely threadsafe - keep it that way! */
 #include "gmxpre.h"
 
-#include <stdlib.h>
-
-/* #define DEBUG_NNB */
 #include "gpp_nextnb.h"
-#include "toputil.h"
 
+#include <stdlib.h>
+
+#include "gromacs/gmxpreprocess/toputil.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
+/* #define DEBUG_NNB */
+
 typedef struct {
     int ai, aj;
 } sortable;

diff --git a/src/gromacs/imd/imd.c b/src/gromacs/imd/imd.c
index 3392fe138860d1f7a8ac1e9d5d76f0919776aee8..7c6585260e25f5c75927454e674357403846071a 100644 (file)
--- a/src/gromacs/imd/imd.c
+++ b/src/gromacs/imd/imd.c
@@ -45,35 +45,34 @@
  *
  * \ingroup module_imd
  */
-
 #include "gmxpre.h"
 
-#include "config.h"
+#include "imd.h"
 
 #include <errno.h>
 #include <string.h>
 
+#include "config.h"
+
 #ifdef GMX_NATIVE_WINDOWS
 #include <windows.h>
 #else
 #include <unistd.h>
 #endif
 
-#include "imd.h"
-#include "imdsocket.h"
-#include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/sighandler.h"
-#include "gromacs/legacyheaders/gmx_ga2la.h"
-#include "gromacs/mdlib/groupcoord.h"
 #include "gromacs/fileio/confio.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/timing/wallcycle.h"
-
 #include "gromacs/fileio/xvgr.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"
+#include "gromacs/timing/wallcycle.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 

diff --git a/src/gromacs/math/utilities.c b/src/gromacs/math/utilities.c
index 4e40b88d1ddbb4cc41c049bdd9fe8cc9d0bdf054..c2df23ec2ee333d4cadb77154b0205d4c0e56439 100644 (file)
--- a/src/gromacs/math/utilities.c
+++ b/src/gromacs/math/utilities.c
@@ -36,13 +36,14 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/math/utilities.h"
-
-#include "config.h"
+#include "utilities.h"
 
 #include <assert.h>
-#include <math.h>
 #include <limits.h>
+#include <math.h>
+
+#include "config.h"
+
 #ifdef HAVE__FINITE
 #include <float.h>
 #endif

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
index 2d48a302ba72fbfbfb734c827010255d7f23dab5..301627d872629cbe009bccfe6a6df9146113574e 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.cu
@@ -34,10 +34,12 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
+#include "nbnxn_cuda.h"
 
-#include <stdlib.h>
 #include <assert.h>
+#include <stdlib.h>
+
+#include "config.h"
 
 #if defined(_MSVC)
 #include <limits>
@@ -45,21 +47,18 @@
 
 #include <cuda.h>
 
-#include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/mdlib/nbnxn_pairlist.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/legacyheaders/types/force_flags.h"
-#include "../nbnxn_consts.h"
-
 #ifdef TMPI_ATOMICS
 #include "thread_mpi/atomic.h"
 #endif
 
-#include "nbnxn_cuda_types.h"
-#include "../../gmxlib/cuda_tools/cudautils.cuh"
-#include "nbnxn_cuda.h"
+#include "gromacs/gmxlib/cuda_tools/cudautils.cuh"
+#include "gromacs/legacyheaders/types/force_flags.h"
+#include "gromacs/legacyheaders/types/simple.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/mdlib/nbnxn_pairlist.h"
 #include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.h"
-
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_types.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/utility/cstringutil.h"
 
@@ -81,7 +80,7 @@ texture<float, 1, cudaReadModeElementType> coulomb_tab_texref;
 #define CL_SIZE                 (NBNXN_GPU_CLUSTER_SIZE)
 
 /***** The kernels come here *****/
-#include "nbnxn_cuda_kernel_utils.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernel_utils.cuh"
 
 /* Top-level kernel generation: will generate through multiple inclusion the
  * following flavors for all kernels:
@@ -91,19 +90,19 @@ texture<float, 1, cudaReadModeElementType> coulomb_tab_texref;
  * - force and energy output with pair list pruning.
  */
 /** Force only **/
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
 /** Force & energy **/
 #define CALC_ENERGIES
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
 #undef CALC_ENERGIES
 
 /*** Pair-list pruning kernels ***/
 /** Force only **/
 #define PRUNE_NBL
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
 /** Force & energy **/
 #define CALC_ENERGIES
-#include "nbnxn_cuda_kernels.cuh"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_kernels.cuh"
 #undef CALC_ENERGIES
 #undef PRUNE_NBL
 

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
index 17995e901eb2a3f1f80c644ba19a113a41e86b9c..6ccce27efdc3dcb939baae70da00f22e1151c629 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h
@@ -32,15 +32,14 @@
  * 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 NBNXN_CUDA_H
 #define NBNXN_CUDA_H
 
-#include "config.h"
-
 #include "gromacs/legacyheaders/types/nbnxn_cuda_types_ext.h"
 #include "gromacs/legacyheaders/types/simple.h"
 
+#include "config.h"
+
 #ifdef GMX_GPU
 #define FUNC_TERM ;
 #else
@@ -51,6 +50,8 @@
 extern "C" {
 #endif
 
+struct nbnxn_atomdata_t;
+
 /*! \brief
  * Launch asynchronously the nonbonded force calculations.
  *
@@ -61,31 +62,31 @@ extern "C" {
  *  The local and non-local interaction calculations are launched in two
  *  separate streams.
  */
-void nbnxn_cuda_launch_kernel(nbnxn_cuda_ptr_t       gmx_unused  cu_nb,
-                              const nbnxn_atomdata_t gmx_unused *nbdata,
-                              int                    gmx_unused  flags,
-                              int                    gmx_unused  iloc) FUNC_TERM
+void nbnxn_cuda_launch_kernel(nbnxn_cuda_ptr_t              gmx_unused  cu_nb,
+                              const struct nbnxn_atomdata_t gmx_unused *nbdata,
+                              int                           gmx_unused  flags,
+                              int                           gmx_unused  iloc) FUNC_TERM
 
 /*! \brief
  * Launch asynchronously the download of nonbonded forces from the GPU
  * (and energies/shift forces if required).
  */
-void nbnxn_cuda_launch_cpyback(nbnxn_cuda_ptr_t       gmx_unused  cu_nb,
-                               const nbnxn_atomdata_t gmx_unused *nbatom,
-                               int                    gmx_unused  flags,
-                               int                    gmx_unused  aloc) FUNC_TERM
+void nbnxn_cuda_launch_cpyback(nbnxn_cuda_ptr_t              gmx_unused  cu_nb,
+                               const struct nbnxn_atomdata_t gmx_unused *nbatom,
+                               int                           gmx_unused  flags,
+                               int                           gmx_unused  aloc) FUNC_TERM
 
 /*! \brief
  * Wait for the asynchronously launched nonbonded calculations and data
  * transfers to finish.
  */
-void nbnxn_cuda_wait_gpu(nbnxn_cuda_ptr_t       gmx_unused  cu_nb,
-                         const nbnxn_atomdata_t gmx_unused *nbatom,
-                         int                    gmx_unused  flags,
-                         int                    gmx_unused  aloc,
-                         real                   gmx_unused *e_lj,
-                         real                   gmx_unused *e_el,
-                         rvec                   gmx_unused *fshift) FUNC_TERM
+void nbnxn_cuda_wait_gpu(nbnxn_cuda_ptr_t              gmx_unused  cu_nb,
+                         const struct nbnxn_atomdata_t gmx_unused *nbatom,
+                         int                           gmx_unused  flags,
+                         int                           gmx_unused  aloc,
+                         real                          gmx_unused *e_lj,
+                         real                          gmx_unused *e_el,
+                         rvec                          gmx_unused *fshift) FUNC_TERM
 
 #ifdef __cplusplus
 }

diff --git a/src/gromacs/mdlib/nbnxn_search.c b/src/gromacs/mdlib/nbnxn_search.c
index 5e2882122d6af224fafecbd29173a88851fd13e3..6c1e301a0719ba0ada67042d4639c4e22487d7aa 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.c
+++ b/src/gromacs/mdlib/nbnxn_search.c
@@ -35,32 +35,33 @@
 
 #include "gmxpre.h"
 
-#include "config.h"
+#include "nbnxn_search.h"
 
+#include <assert.h>
 #include <math.h>
 #include <string.h>
-#include <assert.h>
 
-#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
 #include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/ns.h"
+#include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/math/vec.h"
-#include "nbnxn_consts.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_consts.h"
+#include "gromacs/pbcutil/ishift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/smalloc.h"
+
+#include "config.h"
+
 /* nbnxn_internal.h included gromacs/simd/macros.h */
-#include "nbnxn_internal.h"
+#include "gromacs/mdlib/nbnxn_internal.h"
 #ifdef GMX_SIMD
 #include "gromacs/simd/vector_operations.h"
 #endif
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/ns.h"
-
-#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/mdlib/nb_verlet.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/utility/smalloc.h"
 
 #ifdef NBNXN_SEARCH_BB_SIMD4
 /* Always use 4-wide SIMD for bounding box calculations */
@@ -2941,10 +2942,10 @@ static void make_cluster_list_simple(const nbnxn_grid_t *gridj,
 }
 
 #ifdef GMX_NBNXN_SIMD_4XN
-#include "nbnxn_search_simd_4xn.h"
+#include "gromacs/mdlib/nbnxn_search_simd_4xn.h"
 #endif
 #ifdef GMX_NBNXN_SIMD_2XNN
-#include "nbnxn_search_simd_2xnn.h"
+#include "gromacs/mdlib/nbnxn_search_simd_2xnn.h"
 #endif
 
 /* Plain C or SIMD4 code for making a pair list of super-cell sci vs scj.

diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index 30de5e9b37bce73f8682210399bd5c5978d24572..4090760008135c7cce14eacd163c55c11f2108a5 100644 (file)
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -36,70 +36,68 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
+#include "gromacs/legacyheaders/sim_util.h"
 
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
+
+#include "config.h"
+
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
 
-#include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/utility/cstringutil.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/legacyheaders/chargegroup.h"
-#include "gromacs/math/vec.h"
-#include "gromacs/legacyheaders/nrnb.h"
-#include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/sim_util.h"
-#include "gromacs/legacyheaders/update.h"
-#include "gromacs/math/units.h"
-#include "gromacs/legacyheaders/mdatoms.h"
-#include "gromacs/legacyheaders/force.h"
-#include "gromacs/legacyheaders/pme.h"
-#include "gromacs/legacyheaders/disre.h"
-#include "gromacs/legacyheaders/orires.h"
-#include "gromacs/legacyheaders/network.h"
+#include "gromacs/bonded/bonded.h"
+#include "gromacs/essentialdynamics/edsam.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/constr.h"
 #include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/disre.h"
 #include "gromacs/legacyheaders/domdec.h"
+#include "gromacs/legacyheaders/force.h"
 #include "gromacs/legacyheaders/genborn.h"
-#include "nbnxn_atomdata.h"
-#include "nbnxn_search.h"
-#include "nbnxn_kernels/nbnxn_kernel_ref.h"
-#include "nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
-#include "nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.h"
-#include "nbnxn_kernels/nbnxn_kernel_gpu_ref.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"
 #include "gromacs/legacyheaders/nonbonded.h"
-#include "../gmxlib/nonbonded/nb_kernel.h"
-#include "../gmxlib/nonbonded/nb_free_energy.h"
-
-#include "gromacs/bonded/bonded.h"
+#include "gromacs/legacyheaders/nrnb.h"
+#include "gromacs/legacyheaders/orires.h"
+#include "gromacs/legacyheaders/pme.h"
+#include "gromacs/legacyheaders/qmmm.h"
+#include "gromacs/legacyheaders/txtdump.h"
+#include "gromacs/legacyheaders/typedefs.h"
+#include "gromacs/legacyheaders/update.h"
 #include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/math/units.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/adress.h"
+#include "gromacs/mdlib/nb_verlet.h"
+#include "gromacs/mdlib/nbnxn_atomdata.h"
+#include "gromacs/mdlib/nbnxn_search.h"
+#include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda.h"
 #include "gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.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"
+#include "gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.h"
 #include "gromacs/pbcutil/ishift.h"
 #include "gromacs/pbcutil/mshift.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/pulling/pull.h"
+#include "gromacs/pulling/pull_rotation.h"
 #include "gromacs/timing/wallcycle.h"
 #include "gromacs/timing/walltime_accounting.h"
+#include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/gmxmpi.h"
 #include "gromacs/utility/smalloc.h"
-#include "gromacs/essentialdynamics/edsam.h"
-#include "gromacs/pulling/pull.h"
-#include "gromacs/pulling/pull_rotation.h"
-#include "gromacs/imd/imd.h"
-#include "adress.h"
-#include "gromacs/legacyheaders/qmmm.h"
-
-#include "gromacs/legacyheaders/gmx_omp_nthreads.h"
-
-#include "nbnxn_cuda/nbnxn_cuda.h"
-
-#include "nb_verlet.h"
 
 void print_time(FILE                     *out,
                 gmx_walltime_accounting_t walltime_accounting,

diff --git a/src/gromacs/random/random.c b/src/gromacs/random/random.c
index 4004db7ad51f15c48726f303173f9fdb4d062e05..9150e64f3eb12f7425d02e5f09c05e7cf6f58838 100644 (file)
--- a/src/gromacs/random/random.c
+++ b/src/gromacs/random/random.c
@@ -36,25 +36,26 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include "random.h"
 
+#include <math.h>
 #include <stdio.h>
 #include <stdlib.h>
+#include <time.h>
+
+#include "config.h"
+
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
-#include <time.h>
-#include <math.h>
 #ifdef GMX_NATIVE_WINDOWS
 #include <process.h>
 #endif
 
-#include "external/Random123-1.08/include/Random123/threefry.h"
-
 #include "gromacs/math/utilities.h"
-#include "random_gausstable.h"
+#include "gromacs/random/random_gausstable.h"
+
+#include "external/Random123-1.08/include/Random123/threefry.h"
 
 #define RNG_N 624
 #define RNG_M 397

diff --git a/src/gromacs/timing/cyclecounter.c b/src/gromacs/timing/cyclecounter.c
index 037d3952c144fb9fa9e6f7bbce9e5cd9e90348ac..a48bf35aa1c42d69ca54fa6154cf1ac83bc7b036 100644 (file)
--- a/src/gromacs/timing/cyclecounter.c
+++ b/src/gromacs/timing/cyclecounter.c
@@ -35,15 +35,15 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/timing/cyclecounter.h"
+#include "cyclecounter.h"
+
+#include <time.h>
 
 #include "config.h"
 
-#include <time.h>
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif
-
 #ifdef _MSC_VER
 #include <windows.h>
 #endif

diff --git a/src/gromacs/timing/walltime_accounting.c b/src/gromacs/timing/walltime_accounting.c
index 8dc9ac17be581e06ce8cdfd7d45613bc0d83eb74..d7c711127f606dddf1751301799992fe50c16d34 100644 (file)
--- a/src/gromacs/timing/walltime_accounting.c
+++ b/src/gromacs/timing/walltime_accounting.c
@@ -35,11 +35,12 @@
  */
 #include "gmxpre.h"
 
-#include "gromacs/timing/walltime_accounting.h"
+#include "walltime_accounting.h"
+
+#include <time.h>
 
 #include "config.h"
 
-#include <time.h>
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.c
index c87fe831ce544f51ffb63b6af7bcde9c94218d27..9c57a293d435a1c97bc95b4e9dd3b814e311bb25 100644 (file)
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.c
@@ -36,37 +36,35 @@
  */
 #include "gmxpre.h"
 
-#include "config.h"
-
 #include <assert.h>
 #include <math.h>
 #include <stdio.h>
 #include <string.h>
 
-#include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/names.h"
-#include "gromacs/legacyheaders/txtdump.h"
-#include "gromacs/legacyheaders/checkpoint.h"
-#include "gromacs/topology/mtop_util.h"
-#include "gromacs/fileio/xtcio.h"
-#include "gromacs/fileio/enxio.h"
-#include "gromacs/fileio/gmxfio.h"
-#include "gromacs/fileio/tpxio.h"
-#include "gromacs/fileio/trnio.h"
-#include "gromacs/utility/futil.h"
-#include "gromacs/fileio/tngio.h"
-#include "gromacs/fileio/tngio_for_tools.h"
+#include "config.h"
 
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif
 
 #include "gromacs/commandline/pargs.h"
+#include "gromacs/fileio/enxio.h"
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/mtxio.h"
+#include "gromacs/fileio/tngio.h"
+#include "gromacs/fileio/tngio_for_tools.h"
+#include "gromacs/fileio/tpxio.h"
+#include "gromacs/fileio/trnio.h"
+#include "gromacs/fileio/xtcio.h"
 #include "gromacs/gmxpreprocess/gmxcpp.h"
+#include "gromacs/legacyheaders/checkpoint.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/names.h"
+#include "gromacs/legacyheaders/txtdump.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/topology/mtop_util.h"
 #include "gromacs/utility/fatalerror.h"
+#include "gromacs/utility/futil.h"
 #include "gromacs/utility/smalloc.h"
 
 static void list_tpx(const char *fn, gmx_bool bShowNumbers, const char *mdpfn,

diff --git a/src/gromacs/trajectoryanalysis/modules/nsc.c b/src/gromacs/trajectoryanalysis/modules/nsc.c
index ffc58420e39ac3d414131e91c29ff920165eabd2..29f9875b6e10e28c4d213dfb7f176ea40c13e0ff 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/nsc.c
+++ b/src/gromacs/trajectoryanalysis/modules/nsc.c
@@ -36,18 +36,18 @@
  */
 #include "gmxpre.h"
 
-#include <stdio.h>
-#include <string.h>
-#include <stdlib.h>
+#include "nsc.h"
+
 #include <math.h>
 #include <stdarg.h>
+#include <stdio.h>
+#include <stdlib.h>
+#include <string.h>
 
-/* Modified DvdS */
-#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/math/vec.h"
+#include "gromacs/pbcutil/pbc.h"
 #include "gromacs/utility/smalloc.h"
-#include "nsc.h"
 
 #define TEST_NSC 0
 

diff --git a/src/gromacs/utility/cstringutil.c b/src/gromacs/utility/cstringutil.c
index 0768c5086410cfe35b4caf93f71c319210519316..85cbd41c0af55b776340fcaa385f24f2992ce70a 100644 (file)
--- a/src/gromacs/utility/cstringutil.c
+++ b/src/gromacs/utility/cstringutil.c
@@ -39,8 +39,6 @@
 
 #include "cstringutil.h"
 
-#include "config.h"
-
 #include <assert.h>
 #include <ctype.h>
 #include <stdio.h>
@@ -49,6 +47,9 @@
 #include <time.h>
 
 #include <sys/types.h>
+
+#include "config.h"
+
 #ifdef HAVE_SYS_TIME_H
 #include <sys/time.h>
 #endif

diff --git a/src/gromacs/utility/file.cpp b/src/gromacs/utility/file.cpp
index 30c900e7a0bf7ca96f1303003528fc2cf59d05a1..31055f28b8637ee408f8dbb038a15b512f5c46fc 100644 (file)
--- a/src/gromacs/utility/file.cpp
+++ b/src/gromacs/utility/file.cpp
@@ -51,9 +51,10 @@
 #include <string>
 #include <vector>
 
+#include <sys/stat.h>
+
 #include "config.h"
 
-#include <sys/stat.h>
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
 #endif

diff --git a/src/gromacs/utility/gmxregex.cpp b/src/gromacs/utility/gmxregex.cpp
index cf0fc9746b2c7c90525a66e8fb83971bc6be30a1..81efa86870b212326be4bf1c1623354bf26efa3d 100644 (file)
--- a/src/gromacs/utility/gmxregex.cpp
+++ b/src/gromacs/utility/gmxregex.cpp
@@ -46,8 +46,8 @@
 #include "config.h"
 
 #if defined(HAVE_POSIX_REGEX)
-// old Mac needs sys/types.h before regex.h
 #include <sys/types.h>
+// old Mac needs sys/types.h before regex.h
 #include <regex.h>
 #define USE_POSIX_REGEX
 #elif defined(HAVE_CXX11_REGEX)
@@ -55,8 +55,8 @@
 #define USE_CXX11_REGEX
 #endif
 
-#include "exceptions.h"
-#include "stringutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/stringutil.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/utility/path.cpp b/src/gromacs/utility/path.cpp
index 6257d2875ae4e77174cac17b70dae398d13f0f76..0a0e54bc7618069440356f37bd90fe3b29efbf9d 100644 (file)
--- a/src/gromacs/utility/path.cpp
+++ b/src/gromacs/utility/path.cpp
@@ -50,9 +50,10 @@
 
 #include <algorithm>
 
+#include <sys/stat.h>
+
 #include "config.h"
 
-#include <sys/stat.h>
 #ifdef GMX_NATIVE_WINDOWS
 #include <direct.h>
 #else