Move gmx_fatal.* to utility/fatalerror.*

One more included-by-all header to utility/.
Mainly mechanical replacement of include paths, some reordering in C++
files.  Minor clean-up in the moved files.
gmx_fatal_collective.h not moved at this point, as it is unclear whether
it should go here, or somewhere else (utility/ should not depend on
t_commrec...).

Now, it's mainly types/simple.h that prevents removing some module-level
dependencies to legacyheaders/.  Finding a good location for that (or
its contents, if it needs to be split), and reorganizing the code a bit
more should now allow really putting utility/ at the bottom of the
dependency stack where it belongs.

Part of #1415.

Change-Id: I6e487566d5bd7c9ec7a1455a2d31bd6d645bada3

diff --git a/src/contrib/anaf.c b/src/contrib/anaf.c
index c71140f3b97bbb7020ea6489137e090e2eee1b71..1a31057a2ea36bc220784c5843ff99bf2be198cd 100644 (file)
--- a/src/contrib/anaf.c
+++ b/src/contrib/anaf.c
@@ -46,7 +46,7 @@
 #include "copyrite.h"
 #include "sysstuff.h"
 #include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/contrib/do_multiprot.c b/src/contrib/do_multiprot.c
index 23459e1c55ea603e7a8b287fbf7273bd105cbea4..9fd9f012016e28c252ac27e891b3d1bbc7ccca69 100644 (file)
--- a/src/contrib/do_multiprot.c
+++ b/src/contrib/do_multiprot.c
@@ -47,7 +47,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xvgr.h"
 #include "gromacs/fileio/matio.h"
 #include "index.h"

diff --git a/src/contrib/do_shift.c b/src/contrib/do_shift.c
index d99072f1b90102c6afb9d40e54c132b99b0124eb..3f8cd2851bc65a43de727cde9739fb0c89cda7a8 100644 (file)
--- a/src/contrib/do_shift.c
+++ b/src/contrib/do_shift.c
@@ -47,7 +47,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"
 #include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xvgr.h"
 #include "gstat.h"
 #include "index.h"

diff --git a/src/contrib/ehanal.c b/src/contrib/ehanal.c
index bd625ce29b4bd314c387cc1a63c527bce6168293..12d99e5666d76e999775100f360acb20de34f0d7 100644 (file)
--- a/src/contrib/ehanal.c
+++ b/src/contrib/ehanal.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "random.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/contrib/ehdata.c b/src/contrib/ehdata.c
index f0f5d2c85ecb74896b7f3b5a9c31492635ff2342..19a780b9398b7199a672d0fc56bf6e55630ac823 100644 (file)
--- a/src/contrib/ehdata.c
+++ b/src/contrib/ehdata.c
@@ -41,7 +41,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "random.h"
 #include "gromacs/fileio/strdb.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/contrib/ehole.c b/src/contrib/ehole.c
index 39ac52b22e92bec7f82bf2ac4c64f5aaa57c65b1..6faa2a4bf36c3a290f767b8f9b9c537cbbdd5da3 100644 (file)
--- a/src/contrib/ehole.c
+++ b/src/contrib/ehole.c
@@ -44,7 +44,7 @@
 #include "macros.h"
 #include "copyrite.h"
 #include "gromacs/commandline/pargs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "random.h"
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/contrib/gmx_sdf.c b/src/contrib/gmx_sdf.c
index 03bbf17d5c3f198aabf0765717ed3eacddd73ff2..9270a46ee7847bf9314bb64b6e0d63f0a1eda3cc 100644 (file)
--- a/src/contrib/gmx_sdf.c
+++ b/src/contrib/gmx_sdf.c
@@ -35,7 +35,7 @@
 #include "nrnb.h"
 #include "gstat.h"
 #include "gromacs/fileio/matio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 
 #define G_REF1      0

diff --git a/src/contrib/mkice.c b/src/contrib/mkice.c
index 91fb0657ab5e47c6c73632dc3fd39700979405fd..d90fb3f0226cc029afc312cf9545563e02ea3240 100644 (file)
--- a/src/contrib/mkice.c
+++ b/src/contrib/mkice.c
@@ -41,7 +41,7 @@
 #include "typedefs.h"
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/pdbio.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/contrib/pmetest.c b/src/contrib/pmetest.c
index 3f03bb7d067aab63d4fd6462a7546e23c470f901..8a3ccccad6fffb595dc9ef454c8f268d61f97292 100644 (file)
--- a/src/contrib/pmetest.c
+++ b/src/contrib/pmetest.c
@@ -46,7 +46,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "mdatoms.h"
 #include "coulomb.h"

diff --git a/src/contrib/test.c b/src/contrib/test.c
index 3bea84f5d96fe1da230d6d2de07681ea1d8b88b8..449bcaebd91a9f826e65dbd838546042e63b9052 100644 (file)
--- a/src/contrib/test.c
+++ b/src/contrib/test.c
@@ -41,7 +41,7 @@
 #include "typedefs.h"
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xvgr.h"
 #include "gromacs/fileio/pdbio.h"
 #include "macros.h"

diff --git a/src/contrib/test_fatal.c b/src/contrib/test_fatal.c
index b2e52fe23dca5452144fd81e9d10cdc5b5eb1b3a..c7f2849314adaa097ab13e7b4c0ae087812e270f 100644 (file)
--- a/src/contrib/test_fatal.c
+++ b/src/contrib/test_fatal.c
@@ -1,4 +1,4 @@
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 void my_func(char *msg)
 {

diff --git a/src/gromacs/commandline/pargs.cpp b/src/gromacs/commandline/pargs.cpp
index e7236740c4f1d7666f01d81bf4e1719e75d461b9..1a476f020b12a9470ccb305e38fb51b6d1c5fd35 100644 (file)
--- a/src/gromacs/commandline/pargs.cpp
+++ b/src/gromacs/commandline/pargs.cpp
@@ -52,7 +52,6 @@
 
 #include "thread_mpi/threads.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/network.h"
 
@@ -66,6 +65,7 @@
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/essentialdynamics/edsam.c b/src/gromacs/essentialdynamics/edsam.c
index 8c63fdf3514a7649aa0a61b471b0555a4681055c..8c0443dc9d69a3d2334e8d920a704d4b94112bbe 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.c
+++ b/src/gromacs/essentialdynamics/edsam.c
@@ -61,7 +61,7 @@
 #include "gromacs/mdlib/groupcoord.h"
 
 #include "gromacs/linearalgebra/nrjac.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* We use the same defines as in mvdata.c here */
 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))

diff --git a/src/gromacs/fft/fft.c b/src/gromacs/fft/fft.c
index 591ff87e708fd9f4fedbcf4e239f65ef137f6ff7..b55aaef95fe8172df63f31d8f6b77d94b2deafb8 100644 (file)
--- a/src/gromacs/fft/fft.c
+++ b/src/gromacs/fft/fft.c
@@ -43,7 +43,7 @@
 #include <errno.h>
 
 #include "types/simple.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fft/fft.h"
 #include "gromacs/math/gmxcomplex.h"
 

diff --git a/src/gromacs/fft/fft5d.cpp b/src/gromacs/fft/fft5d.cpp
index 06e0826a7dd7de6484fe353a422e72537eb0558a..4c7f40c235e97555bdfbcea6f51a1e35cde54362 100644 (file)
--- a/src/gromacs/fft/fft5d.cpp
+++ b/src/gromacs/fft/fft5d.cpp
@@ -76,7 +76,7 @@
 FILE* debug = 0;
 #endif
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 
 #ifdef GMX_FFT_FFTW3

diff --git a/src/gromacs/fft/fft_fftpack.c b/src/gromacs/fft/fft_fftpack.c
index f56f40d0b0ba9492a68639e7234e57c7d59723c9..954870f3e712e8ee052c0d9675b28bf7cd390018 100644 (file)
--- a/src/gromacs/fft/fft_fftpack.c
+++ b/src/gromacs/fft/fft_fftpack.c
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -44,7 +44,7 @@
 
 #include "gromacs/fft/fft.h"
 #include "gromacs/legacyheaders/types/simple.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #include "external/fftpack/fftpack.h"
 

diff --git a/src/gromacs/fft/fft_fftw3.cpp b/src/gromacs/fft/fft_fftw3.cpp
index 16900074fa1e117f318a96a6ca658195b71f85bd..81af1fe85c2de1df4647b8bb1059f0da1ce052dd 100644 (file)
--- a/src/gromacs/fft/fft_fftw3.cpp
+++ b/src/gromacs/fft/fft_fftw3.cpp
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -43,7 +43,7 @@
 #include <fftw3.h>
 
 #include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #ifdef GMX_DOUBLE
 #define FFTWPREFIX(name) fftw_ ## name

diff --git a/src/gromacs/fft/fft_mkl.c b/src/gromacs/fft/fft_mkl.c
index e142c84d3bfbcd117bd6bf933584c88e7a76927b..1a12c280fef249e1b0961000868b3ce5c4a2da8b 100644 (file)
--- a/src/gromacs/fft/fft_mkl.c
+++ b/src/gromacs/fft/fft_mkl.c
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 1991-2003 David van der Spoel, Erik Lindahl, University of Groningen.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -44,7 +44,7 @@
 #include <mkl_service.h>
 
 #include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 
 /* For MKL version (<10.0), we should define MKL_LONG. */

diff --git a/src/gromacs/fft/parallel_3dfft.c b/src/gromacs/fft/parallel_3dfft.c
index 7312cbedc79309abdb6fb5b3b9fc31ac0ed91766..0e3c4ef19887fba9ef4e8b5db0979156e8c95663 100644 (file)
--- a/src/gromacs/fft/parallel_3dfft.c
+++ b/src/gromacs/fft/parallel_3dfft.c
@@ -47,7 +47,7 @@
 #include "gromacs/utility/gmxmpi.h"
 
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #include "fft5d.h"
 

diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.c
index 9033b326a8a0c51c1c1a662c82a9773078e64815..03a3c59d9530fa1e2ca3dc5fd3a9ce58f0a42f84 100644 (file)
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.c
@@ -55,7 +55,7 @@
 #include "pdbio.h"
 #include "tpxio.h"
 #include "trxio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "copyrite.h"
 #include "pbc.h"
 #include "mtop_util.h"

diff --git a/src/gromacs/fileio/enxio.c b/src/gromacs/fileio/enxio.c
index 1a7585f3fbaf2141c44f9bcf68682ade01a883d8..3486d8a8c2b817755a6c3d8299e3709a8ad789e7 100644 (file)
--- a/src/gromacs/fileio/enxio.c
+++ b/src/gromacs/fileio/enxio.c
@@ -41,7 +41,7 @@
 #include <string.h>
 
 #include "futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "gmxfio.h"
 #include "enxio.h"

diff --git a/src/gromacs/fileio/filenm.c b/src/gromacs/fileio/filenm.c
index 62f4521d86fc3b3e9b664dac290d898e73f0e6f5..bc6511dadf01be74cdbd546516ab1f99cb827762 100644 (file)
--- a/src/gromacs/fileio/filenm.c
+++ b/src/gromacs/fileio/filenm.c
@@ -45,7 +45,7 @@
 #include <string.h>
 
 #include "futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"

diff --git a/src/gromacs/fileio/futil.cpp b/src/gromacs/fileio/futil.cpp
index 6f272aa76aa81e7c3d0a0a54219bf8e3e40f2248..a56dff6f91cab7e81362bda6816f436b8d6d68fa 100644 (file)
--- a/src/gromacs/fileio/futil.cpp
+++ b/src/gromacs/fileio/futil.cpp
@@ -67,7 +67,6 @@
 
 #include "thread_mpi/threads.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/network.h"
 
@@ -75,6 +74,7 @@
 #include "gromacs/fileio/path.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"

diff --git a/src/gromacs/fileio/gmxfio.c b/src/gromacs/fileio/gmxfio.c
index ab627936dc5dea208bea37df04a73c6cadbfb808..18133f032614046429ecf991938a1f9a63b5e313 100644 (file)
--- a/src/gromacs/fileio/gmxfio.c
+++ b/src/gromacs/fileio/gmxfio.c
@@ -50,7 +50,7 @@
 
 #include "thread_mpi/threads.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
 #include "futil.h"

diff --git a/src/gromacs/fileio/gmxfio_asc.c b/src/gromacs/fileio/gmxfio_asc.c
index f27756aa49e06186ec259548a2f23ebb7905e53d..2b3881015b9a1a4d1ddcb9216253885962635888 100644 (file)
--- a/src/gromacs/fileio/gmxfio_asc.c
+++ b/src/gromacs/fileio/gmxfio_asc.c
@@ -48,7 +48,7 @@
 #include <io.h>
 #endif
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
 #include "futil.h"

diff --git a/src/gromacs/fileio/gmxfio_xdr.c b/src/gromacs/fileio/gmxfio_xdr.c
index 47ad3ca59c3c9a37592d6a9293a37720caea027b..47bfddd968d23fb5e5ef4a34dd2240474356d867 100644 (file)
--- a/src/gromacs/fileio/gmxfio_xdr.c
+++ b/src/gromacs/fileio/gmxfio_xdr.c
@@ -45,7 +45,7 @@
 #include <io.h>
 #endif
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
 #include "futil.h"

diff --git a/src/gromacs/fileio/matio.cpp b/src/gromacs/fileio/matio.cpp
index 0adabce0269e1217adf51793c754c5ed7e84eb1f..3d3dceb167454383a58b2df61b53074b6beb134a 100644 (file)
--- a/src/gromacs/fileio/matio.cpp
+++ b/src/gromacs/fileio/matio.cpp
@@ -48,7 +48,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "matio.h"
 #include "gmxfio.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/fileio/mdoutf.c b/src/gromacs/fileio/mdoutf.c
index 4b50c2a6c08302a9646fa1a96852a4769a4704e9..a8c09547f4d999979bc88f34b32ffce86166bbbd 100644 (file)
--- a/src/gromacs/fileio/mdoutf.c
+++ b/src/gromacs/fileio/mdoutf.c
@@ -46,7 +46,7 @@
 #include "checkpoint.h"
 #include "copyrite.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 struct gmx_mdoutf {

diff --git a/src/gromacs/fileio/pdbio.c b/src/gromacs/fileio/pdbio.c
index 16fa4a23dba0b04afd903b9d02e6520116a5ea18..aa97fcf1d360bc0eaa8c1383903207c52383a02b 100644 (file)
--- a/src/gromacs/fileio/pdbio.c
+++ b/src/gromacs/fileio/pdbio.c
@@ -56,7 +56,7 @@
 #include "pbc.h"
 #include "gmxfio.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     int ai, aj;

diff --git a/src/gromacs/fileio/strdb.c b/src/gromacs/fileio/strdb.c
index d46168b576a313c2360c3e51a27244cc1f80b287..8fb8929497d8db01c2cffb7936ac79e40777bcdb 100644 (file)
--- a/src/gromacs/fileio/strdb.c
+++ b/src/gromacs/fileio/strdb.c
@@ -44,7 +44,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
 

diff --git a/src/gromacs/fileio/timecontrol.c b/src/gromacs/fileio/timecontrol.c
index 062a771665a1fb0dce1f2be6150288ee9f910d5c..c4618e69ed40f34f476e69d326f2c75ace6bd8bc 100644 (file)
--- a/src/gromacs/fileio/timecontrol.c
+++ b/src/gromacs/fileio/timecontrol.c
@@ -43,7 +43,7 @@
 #include "thread_mpi/threads.h"
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* The source code in this file should be thread-safe.
          Please keep it that way. */

diff --git a/src/gromacs/fileio/tngio.cpp b/src/gromacs/fileio/tngio.cpp
index c8854a3db762d410deff2c30df26a502fb9e7bff..518426a67423b8e2659371816f3ec9eca2fdf07f 100644 (file)
--- a/src/gromacs/fileio/tngio.cpp
+++ b/src/gromacs/fileio/tngio.cpp
@@ -47,14 +47,15 @@
 #endif
 
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/physics.h"
+
+#include "gromacs/fileio/gmxfio.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/utility/common.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/programcontext.h"
-#include "gmxfio.h"
 
 static const char *modeToVerb(char mode)
 {

diff --git a/src/gromacs/fileio/tngio_for_tools.cpp b/src/gromacs/fileio/tngio_for_tools.cpp
index 3d7954d1365c6806f0eb337751d8eb532d5cf5a1..d8fae47a14d65440bd54dee499f341d2929fce40 100644 (file)
--- a/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@ -49,9 +49,9 @@
 
 #include "gromacs/legacyheaders/types/atoms.h"
 #include "gromacs/legacyheaders/physics.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 
 #include "gromacs/utility/common.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 void gmx_prepare_tng_writing(const char              *filename,

diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c
index 0fdb93aad232ad294dcbff7889c45db0b123dce9..7aa1c0ad37e9b34bce123cfd4dc48c8468d813b5 100644 (file)
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.c
@@ -45,7 +45,7 @@
 #include "sysstuff.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "names.h"
 #include "symtab.h"

diff --git a/src/gromacs/fileio/trnio.c b/src/gromacs/fileio/trnio.c
index 91634ce09acf1d3074dec4a721fab2e2de0c54d4..bae6b1e61d0af4243f11b197d316a37fb8e6e954 100644 (file)
--- a/src/gromacs/fileio/trnio.c
+++ b/src/gromacs/fileio/trnio.c
@@ -41,7 +41,7 @@
 #include <string.h>
 #include "sysstuff.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "txtdump.h"
 #include "names.h"
 #include "futil.h"

diff --git a/src/gromacs/fileio/trxio.c b/src/gromacs/fileio/trxio.c
index 25d3dd1fa4f57088401873eb716e39251bf9f23b..192e21fd5d3d9a16c704069e17f839a32ade8d03 100644 (file)
--- a/src/gromacs/fileio/trxio.c
+++ b/src/gromacs/fileio/trxio.c
@@ -66,7 +66,7 @@
 #include "xdrf.h"
 
 #include "gromacs/fileio/timecontrol.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* defines for frame counter output */
 #define SKIP1   10

diff --git a/src/gromacs/fileio/writeps.c b/src/gromacs/fileio/writeps.c
index dba6c5c15eb6dc57338160bd98eb033dc8bbf7fc..fa6491d7e68f0903047689abb209a2cbc90bdf28 100644 (file)
--- a/src/gromacs/fileio/writeps.c
+++ b/src/gromacs/fileio/writeps.c
@@ -42,7 +42,7 @@
 
 #include <stdio.h>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/fileio/xdrd.c b/src/gromacs/fileio/xdrd.c
index e48afd19bbe2acb1e05c82e3a6203aed8a4b88fe..e05cbdd4fd84a16ed4cd9c7b28b240163074eca5 100644 (file)
--- a/src/gromacs/fileio/xdrd.c
+++ b/src/gromacs/fileio/xdrd.c
@@ -40,7 +40,7 @@
 
 #include "typedefs.h"
 #include "xdrf.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 int xdr_real(XDR *xdrs, real *r)

diff --git a/src/gromacs/fileio/xtcio.c b/src/gromacs/fileio/xtcio.c
index da52ac6bc24cb12c78b909bc1f953158c3ef2ae7..48fdcf475b75d6a91c59a76b5b1723a6413c4730 100644 (file)
--- a/src/gromacs/fileio/xtcio.c
+++ b/src/gromacs/fileio/xtcio.c
@@ -46,7 +46,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define XTC_MAGIC 1995
 

diff --git a/src/gromacs/gmxana/anadih.c b/src/gromacs/gmxana/anadih.c
index a9d28823e8d8af3d6cfd1a4054d8ae3191ef7f65..a6e926d3c2b24375e4e0422405d98ba9ce0c0244 100644 (file)
--- a/src/gromacs/gmxana/anadih.c
+++ b/src/gromacs/gmxana/anadih.c
@@ -53,7 +53,7 @@
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/trxio.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 void print_one(const output_env_t oenv, const char *base, const char *name,
                const char *title, const char *ylabel, int nf, real time[],

diff --git a/src/gromacs/gmxana/autocorr.c b/src/gromacs/gmxana/autocorr.c
index 5aca984fc62c2d03de44757fb8fdc1ddba03964c..d84f8b23b073dfa6a5c4272b6085a0702df56636 100644 (file)
--- a/src/gromacs/gmxana/autocorr.c
+++ b/src/gromacs/gmxana/autocorr.c
@@ -50,7 +50,7 @@
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "correl.h"
 

diff --git a/src/gromacs/gmxana/binsearch.c b/src/gromacs/gmxana/binsearch.c
index 5e273a0bc01f8172f893e405a42fcf776711bcd8..f68522095c656c5ec7b54dd060d7d9d83f83b4b0 100644 (file)
--- a/src/gromacs/gmxana/binsearch.c
+++ b/src/gromacs/gmxana/binsearch.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2013,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -37,7 +37,7 @@
 #endif
 #include <stdio.h>
 #include "types/simple.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /*Make range-array (Permutation identity) for sorting */
 void rangeArray(int *ar, int size)

diff --git a/src/gromacs/gmxana/dlist.c b/src/gromacs/gmxana/dlist.c
index 11ee4eaea02e047789b1a88be26da662a4fa3cbc..3f86100cbe6562910a6498c5568b77d4e6ba0419 100644 (file)
--- a/src/gromacs/gmxana/dlist.c
+++ b/src/gromacs/gmxana/dlist.c
@@ -43,7 +43,7 @@
 
 #include "gromacs/utility/smalloc.h"
 #include "gstat.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "index.h"
 
 t_dlist *mk_dlist(FILE *log,

diff --git a/src/gromacs/gmxana/edittop.c b/src/gromacs/gmxana/edittop.c
index 973660bdc8654ad10f65c819274892ef285f93ec..50dd7731c7308d9f2eb2c4395dbdab8212479811 100644 (file)
--- a/src/gromacs/gmxana/edittop.c
+++ b/src/gromacs/gmxana/edittop.c
@@ -39,7 +39,7 @@
 #endif
 
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "symtab.h"
 
 void replace_atom(t_topology *top, int inr, char *anm, char *resnm,

diff --git a/src/gromacs/gmxana/expfit.c b/src/gromacs/gmxana/expfit.c
index 406f5a36b184476784bb2ce3aba394b7d16d8f18..874f0bae1bedbee3792d2bdab86a2abe813c862e 100644 (file)
--- a/src/gromacs/gmxana/expfit.c
+++ b/src/gromacs/gmxana/expfit.c
@@ -49,7 +49,7 @@
 #include "vec.h"
 #include "index.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 const int   nfp_ffn[effnNR] = { 0, 1, 2, 3, 2, 5, 7, 9, 4, 3};
 

diff --git a/src/gromacs/gmxana/fitahx.c b/src/gromacs/gmxana/fitahx.c
index 7ee4bf867cb51ed0ac2df7b43e14c9dbd5bf01e2..ebf5b50f6b84da3332e54c74374c4b876294de59 100644 (file)
--- a/src/gromacs/gmxana/fitahx.c
+++ b/src/gromacs/gmxana/fitahx.c
@@ -42,7 +42,7 @@
 #include "vec.h"
 
 #include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 static void my_calc_xcm(int nbb, atom_id bbind[], rvec x[], rvec xcm)

diff --git a/src/gromacs/gmxana/geminate.c b/src/gromacs/gmxana/geminate.c
index 79dc949fd34513b316c3684b7de219dde6fb8751..10d965044b1454af62aff9ad646a89d9c650c0a5 100644 (file)
--- a/src/gromacs/gmxana/geminate.c
+++ b/src/gromacs/gmxana/geminate.c
@@ -42,7 +42,7 @@
 #include "vec.h"
 #include "geminate.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 
 static void missing_code_message()

diff --git a/src/gromacs/gmxana/gmx_anadock.c b/src/gromacs/gmxana/gmx_anadock.c
index 67bb1e7c6c339fe5c684fa8d0ec629c658c35bb9..e70293c9baf714c8dc7336d7ce9543714ff0570b 100644 (file)
--- a/src/gromacs/gmxana/gmx_anadock.c
+++ b/src/gromacs/gmxana/gmx_anadock.c
@@ -43,7 +43,7 @@
 #include "gromacs/fileio/confio.h"
 #include "copyrite.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
index f59b1130d807e8be4ecea627030dfd60ed670c1a..f34c0a94d06473b6312c74e7f46608fa50cc0dee 100644 (file)
--- a/src/gromacs/gmxana/gmx_anaeig.c
+++ b/src/gromacs/gmxana/gmx_anaeig.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "pbc.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/gmx_analyze.c b/src/gromacs/gmxana/gmx_analyze.c
index 494e19e3e0dca82b5429ccf6c1e89ebdb47c75f4..f7dec6335227286f69707fa8f3a00a8b0d19ddc5 100644 (file)
--- a/src/gromacs/gmxana/gmx_analyze.c
+++ b/src/gromacs/gmxana/gmx_analyze.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "copyrite.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
index 65bfad1cc58973aa04ece639ec9bfd9ca565ae55..44fbc543325c16b5c4dd5bda8419f07e54fdbb06 100644 (file)
--- a/src/gromacs/gmxana/gmx_angle.c
+++ b/src/gromacs/gmxana/gmx_angle.c
@@ -50,7 +50,7 @@
 #include "vec.h"
 #include "index.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xvgr.h"
 #include "gstat.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/gromacs/gmxana/gmx_bar.c b/src/gromacs/gmxana/gmx_bar.c
index b692574685521ae180bb371b745bac9f53bb77d4..32f0fdb55de7ef31dbfcf5a8d1918c4876782258 100644 (file)
--- a/src/gromacs/gmxana/gmx_bar.c
+++ b/src/gromacs/gmxana/gmx_bar.c
@@ -50,7 +50,7 @@
 #include "macros.h"
 #include "gromacs/fileio/enxio.h"
 #include "physics.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xvgr.h"
 #include "gmx_ana.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/gmxana/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
index 263ed985e4c7f30acafff0542b98f696ec0c68da..bc948021174ee132107d83cdb29b9a07ed3c4fb7 100644 (file)
--- a/src/gromacs/gmxana/gmx_bundle.c
+++ b/src/gromacs/gmxana/gmx_bundle.c
@@ -55,7 +55,7 @@
 #include "physics.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define MAX_ENDS 3
 

diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 9bee8377f24ecbbd44936ff34b3c8bef2c32b264..fca424d0b9358daa1b06438ac7c0908b2d278f44 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -42,7 +42,7 @@
 
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index 1e5a9e6d5a96f092eb579d24b147657a9e2c65be..cd5db1018ddc2917c8988153f2ab8404ac1c7eb1 100644 (file)
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -64,7 +64,7 @@
 
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* print to two file pointers at once (i.e. stderr and log) */
 static gmx_inline

diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index d84c79c2d82050fd6f2605cb30371ed03228d608..544ab6e143b4e954ebe8ffa73e821a045553b757 100644 (file)
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -63,7 +63,7 @@
 #include "mtop_util.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void clust_size(const char *ndx, const char *trx, const char *xpm,
                        const char *xpmw, const char *ncl, const char *acl,

diff --git a/src/gromacs/gmxana/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
index 4b9391fd1f6f8317cf888c12fbb32eeb8403c582..5d087c968386cb441c9339f5c1937b7e2f4681c6 100644 (file)
--- a/src/gromacs/gmxana/gmx_confrms.c
+++ b/src/gromacs/gmxana/gmx_confrms.c
@@ -51,7 +51,7 @@
 #include "vec.h"
 #include "index.h"
 #include "pbc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/pdbio.h"

diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index 501597e9acb7addff70ca18cbb79a2a8eb22395d..d56d37b76c464a6b650aa7913e6591f54fefd30e 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -70,7 +70,7 @@
 
 #include "gromacs/linearalgebra/eigensolver.h"
 #include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 int gmx_covar(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index c706b40be5b1c35159b77c012b2c4ca38f57ba81..14be9bc5a85b2df64dee77bc8fd7e9f83409a99d 100644 (file)
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -51,7 +51,7 @@
 #include "gmx_ana.h"
 #include "macros.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define SQR(x) (pow(x, 2.0))
 #define EPSI0 (EPSILON0*E_CHARGE*E_CHARGE*AVOGADRO/(KILO*NANO)) /* EPSILON0 in SI units */

diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index a6b89c7b05e074c228e6e87e16d2198365bc5b50..6d027dab8f3a327f6abb58e7002b89b6a75964f7 100644 (file)
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -59,7 +59,7 @@
 #include "gmx_ana.h"
 #include "macros.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     char *atomname;

diff --git a/src/gromacs/gmxana/gmx_densmap.c b/src/gromacs/gmxana/gmx_densmap.c
index 8675a164358a603785d9e9a8ea62142a87c59c8e..078691e28b6c9e4d48d70eefaae6843c1061f976 100644 (file)
--- a/src/gromacs/gmxana/gmx_densmap.c
+++ b/src/gromacs/gmxana/gmx_densmap.c
@@ -62,7 +62,7 @@
 #include "pbc.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 int gmx_densmap(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index 16f98c0c035d9847f0415367981008f04c0803d1..7b90e24824c13fe4650cad2affaefe3117398041 100644 (file)
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -63,7 +63,7 @@
 #include "copyrite.h"
 
 #include "gromacs/utility/exceptions.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/programcontext.h"
 
 #ifdef GMX_DOUBLE

diff --git a/src/gromacs/gmxana/gmx_dielectric.c b/src/gromacs/gmxana/gmx_dielectric.c
index 13faf8be965e79c4c2a521c47af13d2ab36635d6..e6b84fbadb405852be45a56a42e27d124c5b15a7 100644 (file)
--- a/src/gromacs/gmxana/gmx_dielectric.c
+++ b/src/gromacs/gmxana/gmx_dielectric.c
@@ -50,7 +50,7 @@
 #include "xvgr.h"
 #include "correl.h"
 #include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #include "gromacs/fileio/futil.h"
 #include "gromacs/math/gmxcomplex.h"

diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 11c2328b6c884522b376f2175cd5b7f3b1f206b3..cb3ea8f396d42b16321a79c67cc148573c778781 100644 (file)
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -67,7 +67,7 @@
 
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/utility/exceptions.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/programcontext.h"
 
 #define e2d(x) ENM2DEBYE*(x)

diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index eb41e318998920a109c8c1f9b59103afc72e481a..84ebace731160fcc9af9dd0d38caab3cec4c1c1d 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -65,7 +65,7 @@
 #include "gmx_ana.h"
 
 #include "gromacs/math/do_fit.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     int  n;

diff --git a/src/gromacs/gmxana/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.c
index 9f9901065376dec55e7dfa39a39e60133f4c643e..7098fbc2b8abcbe164db77dc55983c9ddfce8741 100644 (file)
--- a/src/gromacs/gmxana/gmx_do_dssp.c
+++ b/src/gromacs/gmxana/gmx_do_dssp.c
@@ -47,7 +47,7 @@
 #include "mshift.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/pdbio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xvgr.h"
 #include "gromacs/fileio/matio.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index 8d5438c3fb980ff29c877e8611eccd45b7229467..578beaedc0bddb5829ce5fb13404e4e4489bc6e8 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -40,7 +40,7 @@
 
 #include "gromacs/fileio/confio.h"
 #include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/gmx_dyecoupl.c b/src/gromacs/gmxana/gmx_dyecoupl.c
index 5eebeb12320eae0bac99a2ff48b77554efdd08dc..30d2ba1943c728de2b9c3aa9c4714f554f65e47d 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyecoupl.c
+++ b/src/gromacs/gmxana/gmx_dyecoupl.c
@@ -42,7 +42,7 @@
 #include "xvgr.h"
 #include "gromacs/fileio/trxio.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 int gmx_dyecoupl(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxana/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
index 65de201a1b6284567932f364b18bb7a34d93fc47..7b1b6c7a1ab2fd3f8c15915e8f78bbfd08fb10bd 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyndom.c
+++ b/src/gromacs/gmxana/gmx_dyndom.c
@@ -43,7 +43,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "index.h"
 #include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "physics.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
index 28adc9e5a2f4a6f1c706b6b74f8255f0087f7ef9..b4ca3a376ac07273ffde5dc4850a1f3b25040cea 100644 (file)
--- a/src/gromacs/gmxana/gmx_editconf.c
+++ b/src/gromacs/gmxana/gmx_editconf.c
@@ -63,7 +63,7 @@
 #include "rmpbc.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct
 {

diff --git a/src/gromacs/gmxana/gmx_eneconv.c b/src/gromacs/gmxana/gmx_eneconv.c
index b0ad9f342eadd5d9d0658cb580608afe36ae8f55..b789cad7e5e89999456e45059c0ea74a6c2e4fff 100644 (file)
--- a/src/gromacs/gmxana/gmx_eneconv.c
+++ b/src/gromacs/gmxana/gmx_eneconv.c
@@ -46,7 +46,7 @@
 #include "disre.h"
 #include "names.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/enxio.h"
 #include "vec.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_enemat.c b/src/gromacs/gmxana/gmx_enemat.c
index f0c7730eb74f6f1373f2cdf893977bd6676745c8..f09f1b4897ebd22e1e65be390c3b80ae6bfffefb 100644 (file)
--- a/src/gromacs/gmxana/gmx_enemat.c
+++ b/src/gromacs/gmxana/gmx_enemat.c
@@ -42,7 +42,7 @@
 
 #include "gromacs/utility/cstringutil.h"
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/enxio.h"

diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index 38555952e0896c1953d68a11e801dc4337a9b014..3b510e14119bc1d61d34a999f6bfe354ca44e6c8 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index 7e7fbfa5f923d15d79ed1694de9215b6e1bbc1dd..358cc258ea280fcf3b6a0cb6f5569d68a2285255 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -48,7 +48,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "pbc.h"
 #include "force.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/math/utilities.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/gmx_genpr.c b/src/gromacs/gmxana/gmx_genpr.c
index 6257f6a6742d7f6b081e5dc79d56268455531a77..41861705f637833395bc91caa4050ada72a834ed 100644 (file)
--- a/src/gromacs/gmxana/gmx_genpr.c
+++ b/src/gromacs/gmxana/gmx_genpr.c
@@ -49,7 +49,7 @@
 #include "macros.h"
 #include "vec.h"
 #include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gmx_ana.h"
 
 int gmx_genpr(int argc, char *argv[])

diff --git a/src/gromacs/gmxana/gmx_gyrate.c b/src/gromacs/gmxana/gmx_gyrate.c
index 9ffb8f10512e19797b723fdba28223980fbfcbbd..291ed6d41eaabd016cdecddc160464d48c9a9339 100644 (file)
--- a/src/gromacs/gmxana/gmx_gyrate.c
+++ b/src/gromacs/gmxana/gmx_gyrate.c
@@ -60,7 +60,7 @@
 #include "gstat.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 real calc_gyro(rvec x[], int gnx, atom_id index[], t_atom atom[], real tm,
                rvec gvec, rvec d, gmx_bool bQ, gmx_bool bRot, gmx_bool bMOI, matrix trans)

diff --git a/src/gromacs/gmxana/gmx_h2order.c b/src/gromacs/gmxana/gmx_h2order.c
index 697fb54d7c9041e5e1b94e3825f49c438f1edb69..ffd7c1f1822e8b07a3a9ac96f03c38e388522c8d 100644 (file)
--- a/src/gromacs/gmxana/gmx_h2order.c
+++ b/src/gromacs/gmxana/gmx_h2order.c
@@ -56,7 +56,7 @@
 #include "gmx_ana.h"
 #include "gromacs/fileio/trxio.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /****************************************************************************/
 /* This program calculates the ordering of water molecules across a box, as */

diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index a9b8942786282e4042d0503e49fcd67695cb66c7..2665acb30762e3467ef735fae5dcdbd08db0ec16 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -47,7 +47,7 @@
 #include "txtdump.h"
 #include "physics.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "index.h"
 #include "gromacs/utility/smalloc.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index 78a020004815d4aac163e3af608a195c1f9f4711..7b0bca8ff5b8aa88ed21cf095dc50398dfe97ece 100644 (file)
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -41,7 +41,7 @@
 #include <math.h>
 
 #include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "fitahx.h"
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"

diff --git a/src/gromacs/gmxana/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
index 981047233635dbfe8007f3317d04e3cc8b26a245..523e8f39fd1696c2f27fe899f4be486ea5d920d6 100644 (file)
--- a/src/gromacs/gmxana/gmx_helixorient.c
+++ b/src/gromacs/gmxana/gmx_helixorient.c
@@ -48,7 +48,7 @@
 #include "vec.h"
 #include "index.h"
 #include "pbc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gstat.h"
 #include "pbc.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
index d9bbed9bada1b394ae047064d232bd3b46148ffb..24205fce4e7c802b5fa51adc9a73bcab3254c461 100644 (file)
--- a/src/gromacs/gmxana/gmx_hydorder.c
+++ b/src/gromacs/gmxana/gmx_hydorder.c
@@ -57,7 +57,7 @@
 #include "binsearch.h"
 #include "powerspect.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* Print name of first atom in all groups in index file */
 static void print_types(atom_id index[], atom_id a[], int ngrps,

diff --git a/src/gromacs/gmxana/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
index ace4812aec2ea8696fb905111b29477df92d19ca..4a230dfda2029c699fc8d9795cb090ea3a5ceddf 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_edi.c
+++ b/src/gromacs/gmxana/gmx_make_edi.c
@@ -50,7 +50,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "pbc.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.c
index 7c8f276f9721ecae0c9e9e40e942dfeaf27de03e..e382bf54c211fde951a60aaa30a0a8468b7724c6 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.c
@@ -53,7 +53,7 @@
 #include "vec.h"
 #include "index.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define MAXNAMES 30
 #define NAME_LEN 30

diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
index 09900e1ff4e0dafcc67534f0c320cf13f5593c42..d0c33307f6b536cc78522cde39a2d4b5b96b4238 100644 (file)
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.c
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/filenm.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/matio.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_mk_angndx.c b/src/gromacs/gmxana/gmx_mk_angndx.c
index 9e684f300d7c22f945d9aebbe6c5d2b4b99a1e07..420444fe377b8d8498a692dcdda1e1ef631d16d4 100644 (file)
--- a/src/gromacs/gmxana/gmx_mk_angndx.c
+++ b/src/gromacs/gmxana/gmx_mk_angndx.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "macros.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/trxio.h"
 
 static int calc_ntype(int nft, int *ft, t_idef *idef)

diff --git a/src/gromacs/gmxana/gmx_morph.c b/src/gromacs/gmxana/gmx_morph.c
index 38c4fa11439ee8deb11101120d57e5306eade527..4210b9a2bc083b46bfbeab0f4de2d93e2df8cbec 100644 (file)
--- a/src/gromacs/gmxana/gmx_morph.c
+++ b/src/gromacs/gmxana/gmx_morph.c
@@ -45,7 +45,7 @@
 #include "xvgr.h"
 #include "index.h"
 #include "gmx_ana.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/trxio.h"
 
 #include "gromacs/math/do_fit.h"

diff --git a/src/gromacs/gmxana/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
index d73f262606000225400d80864de904f7c1171ba2..8f39a411d2e8ab20b9e23364b87566cf567a55ef 100644 (file)
--- a/src/gromacs/gmxana/gmx_msd.c
+++ b/src/gromacs/gmxana/gmx_msd.c
@@ -59,7 +59,7 @@
 #include "gromacs/fileio/confio.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define FACTOR  1000.0  /* Convert nm^2/ps to 10e-5 cm^2/s */
 /* NORMAL = total diffusion coefficient (default). X,Y,Z is diffusion

diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
index e41ca0dd41494a0095702e31118ce9e64660c8fa..a8abbc8c3891d455405380a5f711a39edd4ec9e1 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.c
@@ -46,7 +46,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "gromacs/fileio/futil.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
index 10ec827609d8e295166074f68aa8fb1e33bdd460..2086144387e6fe8006919805fce7269c9dd8b1b1 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmtraj.c
+++ b/src/gromacs/gmxana/gmx_nmtraj.c
@@ -46,7 +46,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "gromacs/fileio/futil.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index 98dd1865990695ba0fadb60397112ce05d23e4a4..ca83401731b8094caabd24826e152a5a63119970 100644 (file)
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -58,7 +58,7 @@
 #include "cmat.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /****************************************************************************/
 /* This program calculates the order parameter per atom for an interface or */

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 3d4766ca1a3db311715affc5404faab1699e5c6c..e079ba526d44f8e12e394974ac1e2dc3be1df2fb 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -54,7 +54,7 @@
 #include "main.h"
 #include "macros.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* We use the same defines as in mvdata.c here */
 #define  block_bc(cr,   d) gmx_bcast(     sizeof(d),     &(d), (cr))

diff --git a/src/gromacs/gmxana/gmx_potential.c b/src/gromacs/gmxana/gmx_potential.c
index 29fa31584bbb98ccb8df4ab23f7bb44eb72243b4..806571f2c091c97a98b62d1df189532166f263b0 100644 (file)
--- a/src/gromacs/gmxana/gmx_potential.c
+++ b/src/gromacs/gmxana/gmx_potential.c
@@ -58,7 +58,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/fileio/trxio.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define EPS0 8.85419E-12
 #define ELC 1.60219E-19

diff --git a/src/gromacs/gmxana/gmx_rdf.c b/src/gromacs/gmxana/gmx_rdf.c
index 22234f91cc6485c0009d21c452408c60b2c9d672..8d566b8bf55aed4e158a881268cd0b3ba76bcba6 100644 (file)
--- a/src/gromacs/gmxana/gmx_rdf.c
+++ b/src/gromacs/gmxana/gmx_rdf.c
@@ -62,7 +62,7 @@
 #include "gmx_ana.h"
 #include "names.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void check_box_c(matrix box)
 {

diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index 13aeb6c807a88773a68b382568b3ee7dbaf598c3..49b55c004df95694182fb8f496cf05666bb51c77 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -47,7 +47,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "vec.h"
 #include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "princ.h"
 #include "rmpbc.h"

diff --git a/src/gromacs/gmxana/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
index b540f38d2c3dd96fb9387c4de40b4e5256c5b379..9c5f266794e7e3e48e5dfbb2ed8eafd6ca3de36a 100644 (file)
--- a/src/gromacs/gmxana/gmx_rotacf.c
+++ b/src/gromacs/gmxana/gmx_rotacf.c
@@ -48,7 +48,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "index.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xvgr.h"
 #include "gstat.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_saltbr.c b/src/gromacs/gmxana/gmx_saltbr.c
index 90c69cdf323dd38a2a31a001267792ce41ac2689..e9b8cd3636b4597b869855a17b3cb8fb990c4515 100644 (file)
--- a/src/gromacs/gmxana/gmx_saltbr.c
+++ b/src/gromacs/gmxana/gmx_saltbr.c
@@ -48,13 +48,13 @@
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 #include "xvgr.h"
 #include "gmx_ana.h"
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     char *label;

diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index 68904bcdca163d8e3b1b3f1eda7841fe5cacd7a5..7677d62acf8ae6e8e09658dfc110ba4934b61d73 100644 (file)
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -55,7 +55,7 @@
 #include "gromacs/fileio/matio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 
 int gmx_sans(int argc, char *argv[])

diff --git a/src/gromacs/gmxana/gmx_sham.c b/src/gromacs/gmxana/gmx_sham.c
index 9d670c4897bb8706eb4941b82417df63a7f84a7a..32d4263eda2c817a8eaa144324aad0ef4a4f12f5 100644 (file)
--- a/src/gromacs/gmxana/gmx_sham.c
+++ b/src/gromacs/gmxana/gmx_sham.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "gromacs/fileio/futil.h"
 #include "readinp.h"

diff --git a/src/gromacs/gmxana/gmx_sorient.c b/src/gromacs/gmxana/gmx_sorient.c
index 8ad45f3f3880112267b873f2ba884a7f70e3c874..def8b8f6ecf4a7ca8664946064480291123535d0 100644 (file)
--- a/src/gromacs/gmxana/gmx_sorient.c
+++ b/src/gromacs/gmxana/gmx_sorient.c
@@ -50,7 +50,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "gmx_ana.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
                          atom_id index[], rvec xref, gmx_bool bPBC)

diff --git a/src/gromacs/gmxana/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
index b4734d79d50d597dca24575ee180c1596eb22b40..ff06395b4eb2f95db7fc2d15e87203fce34fe948 100644 (file)
--- a/src/gromacs/gmxana/gmx_spol.c
+++ b/src/gromacs/gmxana/gmx_spol.c
@@ -51,7 +51,7 @@
 #include "physics.h"
 #include "gmx_ana.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void calc_com_pbc(int nrefat, t_topology *top, rvec x[], t_pbc *pbc,
                          atom_id index[], rvec xref, int ePBC)

diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.c
index 15738d8c4fbce2b48742d28e6df2fcd8844ffa42..a8584ed851dbecfc7c10cb54bbabe8cb8ab0c71d 100644 (file)
--- a/src/gromacs/gmxana/gmx_tcaf.c
+++ b/src/gromacs/gmxana/gmx_tcaf.c
@@ -41,7 +41,7 @@
 
 #include <math.h>
 #include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
index 29f1bd49c329cd940e231d8f4181ddc5ae78e680..2beec11833f300a6bc3de27b2c10ef60551c07f1 100644 (file)
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.c
@@ -59,7 +59,7 @@
 #include "gmx_ana.h"
 
 #include "gromacs/linearalgebra/nrjac.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void low_print_data(FILE *fp, real time, rvec x[], int n, atom_id *index,
                            gmx_bool bDim[], const char *sffmt)

diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index 629f221d0b6dc4ad02fb2d560860845d9e0587a6..ec3966c18c7ab50a9f54df08cfc441bd4df36206 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -63,7 +63,7 @@
 #include "xvgr.h"
 #include "gmx_ana.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define TIME_EXPLICIT 0
 #define TIME_CONTINUE 1

diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index 48f4560bd1bf85f463caf40d36e8aa4c55c2e883..3f12536c767fbdfbf2a39e943940e3983d2306a3 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -66,7 +66,7 @@
 #include "gmx_ana.h"
 
 #include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>

diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
index 6b357e1b801515098dcaab03cdb253c60cc5cc86..9b4cfe3ea18264da08c5ba7af3fba501802ce095 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.c
@@ -58,7 +58,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "gmx_ana.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     atom_id i;

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index b0a7fb80cbcdc24df146d71240dae02d579c831b..c2a3e40d518fd194eb551e0359bb8cfc277a6340 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -60,7 +60,7 @@
 #include "gromacs/timing/walltime_accounting.h"
 #include "gromacs/math/utilities.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* Enum for situations that can occur during log file parsing, the
  * corresponding string entries can be found in do_the_tests() in

diff --git a/src/gromacs/gmxana/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
index 77fe30fc3a0dad877bacc0708b4d3c7067f21b5b..fa8eb0966a28115d84c75b89ed53bb7f7ea84e6b 100644 (file)
--- a/src/gromacs/gmxana/gmx_velacc.c
+++ b/src/gromacs/gmxana/gmx_velacc.c
@@ -41,7 +41,7 @@
 #include <math.h>
 
 #include "gromacs/fileio/confio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index 6e63e7a5c0372dfb6035c40f218e61c87dbf5538..2950d89fdf991c1db9401ec52a4f4b2bd9ea7c28 100644 (file)
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -65,7 +65,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "xvgr.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 //! longest file names allowed in input files
 #define WHAM_MAXFILELEN 2048

diff --git a/src/gromacs/gmxana/gmx_wheel.c b/src/gromacs/gmxana/gmx_wheel.c
index d33ebf1abb97f20850c8e1fe4ab65deb113729f3..93229b009068fdc2d3bcb5aeb02877c92d6f3f3d 100644 (file)
--- a/src/gromacs/gmxana/gmx_wheel.c
+++ b/src/gromacs/gmxana/gmx_wheel.c
@@ -54,7 +54,7 @@
 #include "pbc.h"
 #include "index.h"
 #include "gstat.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gmx_ana.h"
 
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_xpm2ps.c b/src/gromacs/gmxana/gmx_xpm2ps.c
index 064e667c3c4806806378c1011f6440aae18874f3..7a415a716d1ae28eec3e089088ddccdc7906f6bc 100644 (file)
--- a/src/gromacs/gmxana/gmx_xpm2ps.c
+++ b/src/gromacs/gmxana/gmx_xpm2ps.c
@@ -43,7 +43,7 @@
 #include <math.h>
 #include "typedefs.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "viewit.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/hxprops.c b/src/gromacs/gmxana/hxprops.c
index ee949e9c4db9ae5c2e7461181976ae7250e06882..531aa92c3fc4f6dad9db1c610887242247bc20fd 100644 (file)
--- a/src/gromacs/gmxana/hxprops.c
+++ b/src/gromacs/gmxana/hxprops.c
@@ -50,7 +50,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "bondf.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 real ellipticity(int nres, t_bb bb[])
 {

diff --git a/src/gromacs/gmxana/nrama.c b/src/gromacs/gmxana/nrama.c
index e20501f7df862fff4bd2ab67b033f9be9cadede3..f7a295b19abde124ae458ed0b21d29e67cffe761 100644 (file)
--- a/src/gromacs/gmxana/nrama.c
+++ b/src/gromacs/gmxana/nrama.c
@@ -45,7 +45,7 @@
 #include "typedefs.h"
 #include "bondf.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "rmpbc.h"
 
 static const char *pp_pat[] = { "C", "N", "CA", "C", "N" };

diff --git a/src/gromacs/gmxana/nsfactor.c b/src/gromacs/gmxana/nsfactor.c
index 4b15a573c91f7ef6cec75ec8e0b59e7b66294e90..2997d54edb29b2afa9f6e1ac764267e268354be0 100644 (file)
--- a/src/gromacs/gmxana/nsfactor.c
+++ b/src/gromacs/gmxana/nsfactor.c
@@ -46,7 +46,7 @@
 
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/strdb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 
 void check_binwidth(real binwidth)

diff --git a/src/gromacs/gmxana/polynomials.c b/src/gromacs/gmxana/polynomials.c
index de47f1aa7ad2880dd5c159d7fcb97bc06892ffba..4b739cc29f7c24235f61dad374a95076554ad390 100644 (file)
--- a/src/gromacs/gmxana/polynomials.c
+++ b/src/gromacs/gmxana/polynomials.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -41,7 +41,7 @@
 #include <stdio.h>
 #include <math.h>
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gstat.h"
 
 real LegendreP(real x, unsigned long m)

diff --git a/src/gromacs/gmxana/powerspect.c b/src/gromacs/gmxana/powerspect.c
index 06e7d94caec5060d51609446ea6d4de20e574489..1c2be272cc37c0b22e2dbf3fc64678c4f9afc3e7 100644 (file)
--- a/src/gromacs/gmxana/powerspect.c
+++ b/src/gromacs/gmxana/powerspect.c
@@ -39,7 +39,7 @@
 
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fft/fft.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "interf.h"
 #include "powerspect.h"

diff --git a/src/gromacs/gmxana/pp2shift.c b/src/gromacs/gmxana/pp2shift.c
index 85e29ac4eb8f10c3d4c00e5f63ba1b0d9e6afc7c..f97719f908a87abe0ff10f7056531c3cfcdbaf04 100644 (file)
--- a/src/gromacs/gmxana/pp2shift.c
+++ b/src/gromacs/gmxana/pp2shift.c
@@ -48,7 +48,7 @@
 #include "gstat.h"
 #include "gromacs/fileio/matio.h"
 #include "copyrite.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     int    nx, ny;

diff --git a/src/gromacs/gmxlib/atomprop.c b/src/gromacs/gmxlib/atomprop.c
index c899adceaaa26a54b51da4eb97a5233d432c7ee2..aa89148b868632586472cbff13def0e83e2f1225 100644 (file)
--- a/src/gromacs/gmxlib/atomprop.c
+++ b/src/gromacs/gmxlib/atomprop.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "atomprop.h"
 #include "macros.h"
 #include "index.h"

diff --git a/src/gromacs/gmxlib/bondfree.c b/src/gromacs/gmxlib/bondfree.c
index 6d696e93f7ade05a3c9d51543dcef58109ea999e..d291fb59d02039b028ff4fd6e4dd0fe90d6682dc 100644 (file)
--- a/src/gromacs/gmxlib/bondfree.c
+++ b/src/gromacs/gmxlib/bondfree.c
@@ -50,7 +50,7 @@
 #include "ns.h"
 #include "macros.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "mshift.h"
 #include "main.h"
 #include "disre.h"

diff --git a/src/gromacs/gmxlib/calcgrid.c b/src/gromacs/gmxlib/calcgrid.c
index 3d1e70d909ef0bb0932bbd80df9cd12976c46120..f9f16ccff19f7f74893a3f64aaecf1d3e15fb70c 100644 (file)
--- a/src/gromacs/gmxlib/calcgrid.c
+++ b/src/gromacs/gmxlib/calcgrid.c
@@ -42,7 +42,7 @@
 
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "calcgrid.h"
 
 /* The grid sizes below are based on timing of a 3D cubic grid in fftw

diff --git a/src/gromacs/gmxlib/calch.c b/src/gromacs/gmxlib/calch.c
index 397ab2dba87f198807e7fb6b4141b67e3ff8deb6..b28411a5dce96514e6efcb4edd442738d523fe77 100644 (file)
--- a/src/gromacs/gmxlib/calch.c
+++ b/src/gromacs/gmxlib/calch.c
@@ -44,7 +44,7 @@
 #include "vec.h"
 #include "physics.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define xAI xa[0]
 #define xAJ xa[1]

diff --git a/src/gromacs/gmxlib/chargegroup.c b/src/gromacs/gmxlib/chargegroup.c
index 93df8e1a1d9587037fa45c8f4ed4f10f8f3ac9df..a21357d8fda1ccb088c3c5147da3e020515a1d3b 100644 (file)
--- a/src/gromacs/gmxlib/chargegroup.c
+++ b/src/gromacs/gmxlib/chargegroup.c
@@ -44,7 +44,7 @@
 #include "vec.h"
 #include "pbc.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "chargegroup.h"
 
 

diff --git a/src/gromacs/gmxlib/checkpoint.c b/src/gromacs/gmxlib/checkpoint.c
index 1dd000c09eb9573876d7cffe64693afd91e9864f..4719f55e2e065be783b080d96496c2d3fc0c1562 100644 (file)
--- a/src/gromacs/gmxlib/checkpoint.c
+++ b/src/gromacs/gmxlib/checkpoint.c
@@ -77,7 +77,7 @@
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/fileio/xdr_datatype.h"
 #include "gromacs/utility/baseversion.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #include "buildinfo.h"
 

diff --git a/src/gromacs/gmxlib/cuda_tools/cudautils.cuh b/src/gromacs/gmxlib/cuda_tools/cudautils.cuh
index 2cccc16c6714da4ead8366567f5d4089529decc3..b48dc29d701bc30f1142aee0be3d90ad6e3c730a 100644 (file)
--- a/src/gromacs/gmxlib/cuda_tools/cudautils.cuh
+++ b/src/gromacs/gmxlib/cuda_tools/cudautils.cuh
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, by the GROMACS development team, led by
  * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
  * and including many others, as listed in the AUTHORS file in the
  * top-level source directory and at http://www.gromacs.org.
@@ -38,7 +38,7 @@
 
 #include <stdio.h>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* CUDA library and hardware related defines */
 /* TODO list some constants instead that can be used for consistency checks to

diff --git a/src/gromacs/gmxlib/disre.c b/src/gromacs/gmxlib/disre.c
index 061521d9f218c6ed4c6766fcf01866ec7001ec42..41eb948295c8b8a203a0e26a9277778cc076f09d 100644 (file)
--- a/src/gromacs/gmxlib/disre.c
+++ b/src/gromacs/gmxlib/disre.c
@@ -48,7 +48,7 @@
 #include "vec.h"
 #include "gromacs/fileio/futil.h"
 #include "xvgr.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "bondf.h"
 #include "copyrite.h"
 #include "disre.h"

diff --git a/src/gromacs/gmxlib/gmx_detect_hardware.c b/src/gromacs/gmxlib/gmx_detect_hardware.c
index 9aa1105bb3193e79912e57e8aa9b45e714356b6f..1bcf866eead3f015b85ea3cf8bf34034566f7238 100644 (file)
--- a/src/gromacs/gmxlib/gmx_detect_hardware.c
+++ b/src/gromacs/gmxlib/gmx_detect_hardware.c
@@ -48,7 +48,7 @@
 #include "types/enums.h"
 #include "types/hw_info.h"
 #include "types/commrec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gmx_fatal_collective.h"
 #include "md_logging.h"
 #include "gmx_cpuid.h"

diff --git a/src/gromacs/gmxlib/gmx_omp_nthreads.c b/src/gromacs/gmxlib/gmx_omp_nthreads.c
index 4ba916002121835a6d233733a882f79c080c5121..9407bd7f8c838ae1ab1c21d3614e51afdc8cabfe 100644 (file)
--- a/src/gromacs/gmxlib/gmx_omp_nthreads.c
+++ b/src/gromacs/gmxlib/gmx_omp_nthreads.c
@@ -42,7 +42,7 @@
 #include <config.h>
 #endif
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
 #include "macros.h"
 #include "network.h"

diff --git a/src/gromacs/gmxlib/gmx_thread_affinity.c b/src/gromacs/gmxlib/gmx_thread_affinity.c
index 9752fb0295c6c4066b9b8cb8c6ee6111c98fba28..64a68d1fa483de20a9bd7b7ffbad1f19a37c308a 100644 (file)
--- a/src/gromacs/gmxlib/gmx_thread_affinity.c
+++ b/src/gromacs/gmxlib/gmx_thread_affinity.c
@@ -56,7 +56,7 @@
 #include "md_logging.h"
 #include "gmx_thread_affinity.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 
 static int

diff --git a/src/gromacs/gmxlib/index.c b/src/gromacs/gmxlib/index.c
index 1ac6062a0b12652b029106200c1a2d3b8e91dd7f..89ebc2f58b34156bcc68664e106c8e3ffae3363c 100644 (file)
--- a/src/gromacs/gmxlib/index.c
+++ b/src/gromacs/gmxlib/index.c
@@ -56,7 +56,7 @@
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/strdb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 const char gmx_residuetype_undefined[] = "Other";
 

diff --git a/src/gromacs/gmxlib/inputrec.c b/src/gromacs/gmxlib/inputrec.c
index 1ba89ef3aa71f9a140f550dacd0c49bf60f05e67..c600bd189d5304803ee0aab15c80fec302ca2989 100644 (file)
--- a/src/gromacs/gmxlib/inputrec.c
+++ b/src/gromacs/gmxlib/inputrec.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "inputrec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 
 /* The minimum number of integration steps required for reasonably accurate

diff --git a/src/gromacs/gmxlib/invblock.c b/src/gromacs/gmxlib/invblock.c
index 235a1f6c2a4768c9b35fefb5ead9e16bf908e1ea..0d9326e3ee41894d6802fa1207ac8a105b83847a 100644 (file)
--- a/src/gromacs/gmxlib/invblock.c
+++ b/src/gromacs/gmxlib/invblock.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
 #include "invblock.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 atom_id *make_invblock(const t_block *block, int nr)
 {

diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index 170c606ac69f89bc35705254ca6919b886e4f0e9..c18996504daefa496c818e474905aad89e964d32 100644 (file)
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -50,7 +50,7 @@
 
 #include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "network.h"
 #include "main.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxlib/mshift.c b/src/gromacs/gmxlib/mshift.c
index 6b6ad831a216389af6ef77e2d2aa5557b398382f..5f6bb1942721c5bba69256429edf9ba9e3230184 100644 (file)
--- a/src/gromacs/gmxlib/mshift.c
+++ b/src/gromacs/gmxlib/mshift.c
@@ -40,7 +40,7 @@
 
 #include <string.h>
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "vec.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxlib/mtop_util.c b/src/gromacs/gmxlib/mtop_util.c
index 83c615634ea71e672df443ae5ac7fb5d144d4c93..39ffce6d61492541a3931728df10a6dfe802563d 100644 (file)
--- a/src/gromacs/gmxlib/mtop_util.c
+++ b/src/gromacs/gmxlib/mtop_util.c
@@ -43,7 +43,7 @@
 #include "mtop_util.h"
 #include "topsort.h"
 #include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static int gmx_mtop_maxresnr(const gmx_mtop_t *mtop, int maxres_renum)
 {

diff --git a/src/gromacs/gmxlib/mvdata.c b/src/gromacs/gmxlib/mvdata.c
index 62b88991556b53c4ed3f7f836941cec56736f78b..329631ae26e76bc411c26cbfe9dc103bab826802 100644 (file)
--- a/src/gromacs/gmxlib/mvdata.c
+++ b/src/gromacs/gmxlib/mvdata.c
@@ -47,7 +47,7 @@
 #include "types/commrec.h"
 #include "network.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "symtab.h"
 #include "vec.h"
 #include "tgroup.h"

diff --git a/src/gromacs/gmxlib/network.c b/src/gromacs/gmxlib/network.c
index 346f8cff30f38f83e0a30b72a7770684b74dda6f..e01523bdd00fb8c4e8a6f7ebd74a3575937cae2d 100644 (file)
--- a/src/gromacs/gmxlib/network.c
+++ b/src/gromacs/gmxlib/network.c
@@ -39,7 +39,7 @@
 #endif
 
 #include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "main.h"
 #include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nb_free_energy.c b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
index 4ed5663833054212993d9d897eb59ac7bb0614d9..fe4bd270fc851f0d23a033d572b5915bea3c95d0 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_free_energy.c
@@ -48,7 +48,7 @@
 #include "macros.h"
 #include "nb_free_energy.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 void
 gmx_nb_free_energy_kernel(const t_nblist * gmx_restrict    nlist,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic.c b/src/gromacs/gmxlib/nonbonded/nb_generic.c
index 4f29311deaa61d044f465093dd9dd9c998e0639a..db837244eae392545f61160b56f6a97feb175c34 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic.c
@@ -46,7 +46,7 @@
 #include "nb_generic.h"
 #include "nrnb.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #include "nonbonded.h"
 #include "nb_kernel.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
index 10b687b020b39713f5c25c59537ab4471dc798f5..97873b8498bcdde739763c607c905e4e4f0b5976 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_adress.c
@@ -46,7 +46,7 @@
 #include "nb_generic_adress.h"
 #include "nrnb.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #include "nonbonded.h"
 #include "nb_kernel.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
index 61198647eab34d78b89c3f6d1fee08a31bfa197a..6d1cfae43548242f0a0ca2927c2b86e6953ab01b 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_generic_cg.c
@@ -48,7 +48,7 @@
 #include "nb_kernel.h"
 #include "nrnb.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 void
 gmx_nb_generic_cg_kernel(t_nblist *                nlist,

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel.c b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
index b983e314c30eb508cefb1a5130e88bc02f822398..d69c4c09e0d688879ed32141939b8da09f1cffd3 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
@@ -43,7 +43,7 @@
 #include "nb_kernel.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 
 /* Static data structures to find kernels */

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index 6a93fff21614f4fd6697213b86561b6a0184886b..f7390de2ebd8f0dbe51dc88144687def95f6ef19 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -55,7 +55,7 @@
 #include "names.h"
 #include "main.h"
 #include "xvgr.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "physics.h"
 #include "force.h"
 #include "bondf.h"

diff --git a/src/gromacs/gmxlib/orires.c b/src/gromacs/gmxlib/orires.c
index da920db11dc0952780397f8a216dd9e60e9faf8d..2741240abc38e02a243f5f4c869c48d5f85d2766 100644 (file)
--- a/src/gromacs/gmxlib/orires.c
+++ b/src/gromacs/gmxlib/orires.c
@@ -51,7 +51,7 @@
 
 #include "gromacs/linearalgebra/nrjac.h"
 #include "gromacs/math/do_fit.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 void init_orires(FILE *fplog, const gmx_mtop_t *mtop,
                  rvec xref[],

diff --git a/src/gromacs/gmxlib/pbc.c b/src/gromacs/gmxlib/pbc.c
index c96eba4f063ba40dcfd3ca446584b0442838406b..cac2dd9cbcb05b5d5ef427c4b8b464227b5b91c0 100644 (file)
--- a/src/gromacs/gmxlib/pbc.c
+++ b/src/gromacs/gmxlib/pbc.c
@@ -50,7 +50,7 @@
 #include "pbc.h"
 #include "gromacs/utility/smalloc.h"
 #include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "names.h"
 #include "macros.h"
 #include "gmx_omp_nthreads.h"

diff --git a/src/gromacs/gmxlib/readinp.c b/src/gromacs/gmxlib/readinp.c
index e7cef773eda608b88d20cc2f5bea7280eabd9613..0d3ddb0d190a94f6734e94ce9a560eb250bc6936 100644 (file)
--- a/src/gromacs/gmxlib/readinp.c
+++ b/src/gromacs/gmxlib/readinp.c
@@ -49,7 +49,7 @@
 #include "gromacs/fileio/gmxfio.h"
 #include "names.h"
 #include "warninp.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 t_inpfile *read_inpfile(const char *fn, int *ninp,
                         warninp_t wi)

diff --git a/src/gromacs/gmxlib/rmpbc.c b/src/gromacs/gmxlib/rmpbc.c
index 1c0e0c9acff32da4ce714f96ded71ea260274325..622358b96083c8f0a4bf7c39d1200935a813361d 100644 (file)
--- a/src/gromacs/gmxlib/rmpbc.c
+++ b/src/gromacs/gmxlib/rmpbc.c
@@ -46,7 +46,7 @@
 #include "vec.h"
 
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 typedef struct {

diff --git a/src/gromacs/gmxlib/sfactor.c b/src/gromacs/gmxlib/sfactor.c
index 1684a5490b16f91b920c60cba5c0e5fa688bee5b..0f4948ec28a667c9fc129ff12902a3c783dc59e0 100644 (file)
--- a/src/gromacs/gmxlib/sfactor.c
+++ b/src/gromacs/gmxlib/sfactor.c
@@ -42,7 +42,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/math/utilities.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "macros.h"
 #include "index.h"

diff --git a/src/gromacs/gmxlib/sighandler.c b/src/gromacs/gmxlib/sighandler.c
index 841b43e35e89754a9e4c8223fab8ca3d9f46f26b..d42be8a220353039bc5e2425b4fbbbcd4d0692c5 100644 (file)
--- a/src/gromacs/gmxlib/sighandler.c
+++ b/src/gromacs/gmxlib/sighandler.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012, by the GROMACS development team, led by
+ * Copyright (c) 2012,2014, 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.
@@ -39,7 +39,7 @@
 #endif
 
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "sighandler.h"
 
 

diff --git a/src/gromacs/gmxlib/splitter.c b/src/gromacs/gmxlib/splitter.c
index 1d98dc2c8d2319c5a8b8a570b4c77305bfd3df06..78e9e479a6b266c71dd44a9c29dfd022ad5324f6 100644 (file)
--- a/src/gromacs/gmxlib/splitter.c
+++ b/src/gromacs/gmxlib/splitter.c
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
 #include "mshift.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     int atom, sid;

diff --git a/src/gromacs/gmxlib/symtab.c b/src/gromacs/gmxlib/symtab.c
index 7e9d65a450b934208623da5b242bad61e4cb1756..66e49cc4a68d117fb046b19deeab2f45ddade837 100644 (file)
--- a/src/gromacs/gmxlib/symtab.c
+++ b/src/gromacs/gmxlib/symtab.c
@@ -42,7 +42,7 @@
 #include <string.h>
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "txtdump.h"
 #include "symtab.h"

diff --git a/src/gromacs/gmxlib/topsort.c b/src/gromacs/gmxlib/topsort.c
index 7d1f5e5fb33530cbe0878876bb62aede35cac87f..0fe9719a7cc6238c0bd189f522c1e6d120d0c06c 100644 (file)
--- a/src/gromacs/gmxlib/topsort.c
+++ b/src/gromacs/gmxlib/topsort.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "topsort.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static gmx_bool ip_pert(int ftype, const t_iparams *ip)
 {

diff --git a/src/gromacs/gmxlib/txtdump.c b/src/gromacs/gmxlib/txtdump.c
index e1705d20d0d96d83882d5b2bfce16bff745940bb..a84e2e4b49ea67f428bead18af781f5c784a825c 100644 (file)
--- a/src/gromacs/gmxlib/txtdump.c
+++ b/src/gromacs/gmxlib/txtdump.c
@@ -48,7 +48,7 @@
 #include "vec.h"
 #include "macros.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 int pr_indent(FILE *fp, int n)

diff --git a/src/gromacs/gmxlib/viewit.c b/src/gromacs/gmxlib/viewit.c
index feb6898642ea2889218f119ef73a0519b399b84e..fe685e43d1d7fcfd3a6fae71d8cf5f50d67f231d 100644 (file)
--- a/src/gromacs/gmxlib/viewit.c
+++ b/src/gromacs/gmxlib/viewit.c
@@ -46,7 +46,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/fileio/filenm.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static const int   can_view_ftp[] = {
     0,

diff --git a/src/gromacs/gmxlib/warninp.c b/src/gromacs/gmxlib/warninp.c
index 0e18160c6b2012948365e17614596d3c44897f2a..d7a8b10ca351308a216f6fed3c035e9f58834430 100644 (file)
--- a/src/gromacs/gmxlib/warninp.c
+++ b/src/gromacs/gmxlib/warninp.c
@@ -43,7 +43,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "copyrite.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "warninp.h"
 
 typedef struct warninp {

diff --git a/src/gromacs/gmxlib/xvgr.cpp b/src/gromacs/gmxlib/xvgr.cpp
index 11e362ebeb5a7a3db4876dde9a4a0577d569c9c0..708816f334894477647a1f0cbee690d69b3ec122 100644 (file)
--- a/src/gromacs/gmxlib/xvgr.cpp
+++ b/src/gromacs/gmxlib/xvgr.cpp
@@ -58,7 +58,7 @@
 #include "gromacs/fileio/gmxfio.h"
 
 #include "gromacs/utility/exceptions.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/programcontext.h"
 
 gmx_bool output_env_get_print_xvgr_codes(const output_env_t oenv)

diff --git a/src/gromacs/gmxpreprocess/add_par.c b/src/gromacs/gmxpreprocess/add_par.c
index 429e78849cc14f1cdc0d1980cfeeab08abb5906c..85bbd465c20320852cd70bfe88b67a682bd80534 100644 (file)
--- a/src/gromacs/gmxpreprocess/add_par.c
+++ b/src/gromacs/gmxpreprocess/add_par.c
@@ -47,7 +47,7 @@
 #include "toputil.h"
 #include "hackblock.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void clear_atom_list(int i0, atom_id a[])
 {

diff --git a/src/gromacs/gmxpreprocess/calc_verletbuf.c b/src/gromacs/gmxpreprocess/calc_verletbuf.c
index a96bd0679e12189f7deb961679b78280de87c349..a506e9b1ceada1184a304ce16726dac33711bfac 100644 (file)
--- a/src/gromacs/gmxpreprocess/calc_verletbuf.c
+++ b/src/gromacs/gmxpreprocess/calc_verletbuf.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "physics.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "vec.h"
 #include "coulomb.h"

diff --git a/src/gromacs/gmxpreprocess/convparm.c b/src/gromacs/gmxpreprocess/convparm.c
index fb97126e251b77bac8d21c24c8a1aa72bd01df57..08f3b98fff601dc541924a550b4110c4b9a6b3eb 100644 (file)
--- a/src/gromacs/gmxpreprocess/convparm.c
+++ b/src/gromacs/gmxpreprocess/convparm.c
@@ -47,7 +47,7 @@
 #include "vec.h"
 #include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "topio.h"
 #include "toputil.h"
 #include "convparm.h"

diff --git a/src/gromacs/gmxpreprocess/fflibutil.cpp b/src/gromacs/gmxpreprocess/fflibutil.cpp
index f1cdf02aa3c7e75105f37a756caaa48e76d2b68c..f41bf90e37ded031c9641a285592e8ff3e68888d 100644 (file)
--- a/src/gromacs/gmxpreprocess/fflibutil.cpp
+++ b/src/gromacs/gmxpreprocess/fflibutil.cpp
@@ -44,7 +44,7 @@
 #include <fcntl.h>
 #include "sysstuff.h"
 #include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 #ifdef HAVE_UNISTD_H

diff --git a/src/gromacs/gmxpreprocess/gen_ad.c b/src/gromacs/gmxpreprocess/gen_ad.c
index 7e8bfad88c19e864e1ccfc00113f24c68a6b34fe..f4c7fb32b03eedbb4bfb4cf700583026d939b000 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_ad.c
+++ b/src/gromacs/gmxpreprocess/gen_ad.c
@@ -55,7 +55,7 @@
 #include "gpp_nextnb.h"
 #include "symtab.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "pgutil.h"
 #include "resall.h"
 #include "gen_ad.h"

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index 4afe493cb3c097e6fa19e3108d41bf06944702aa..c797392be358bd091759ab64a76197bb67443569 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -57,7 +57,7 @@
 #include "fflibutil.h"
 #include "macros.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define MAXNAME 32
 #define OPENDIR     '[' /* starting sign for directive         */

diff --git a/src/gromacs/gmxpreprocess/genconf.c b/src/gromacs/gmxpreprocess/genconf.c
index 52b7b048b38769c14b51ec8ac8fc23c327918f4b..b459283c5e815acacc30269aa4de79a2a284d1ee 100644 (file)
--- a/src/gromacs/gmxpreprocess/genconf.c
+++ b/src/gromacs/gmxpreprocess/genconf.c
@@ -51,7 +51,7 @@
 #include "sortwater.h"
 #include "gromacs/fileio/trxio.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void rand_rot(int natoms, rvec x[], rvec v[], vec4 xrot[], vec4 vrot[],
                      gmx_rng_t rng, rvec max_rot)

diff --git a/src/gromacs/gmxpreprocess/genhydro.c b/src/gromacs/gmxpreprocess/genhydro.c
index afcadb43b4b09b5f96df7d4f074426171ccc133f..55940aed9af5defe6649e6cbbb08e895c54dc835 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.c
+++ b/src/gromacs/gmxpreprocess/genhydro.c
@@ -48,7 +48,7 @@
 #include "symtab.h"
 #include "vec.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "physics.h"
 #include "calch.h"
 #include "genhydro.h"

diff --git a/src/gromacs/gmxpreprocess/gmxcpp.c b/src/gromacs/gmxpreprocess/gmxcpp.c
index d9265d483192da1f736873455a97df2281008037..733ee51da4473db88b0b7eac7a04ac8d8c543b40 100644 (file)
--- a/src/gromacs/gmxpreprocess/gmxcpp.c
+++ b/src/gromacs/gmxpreprocess/gmxcpp.c
@@ -51,7 +51,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gmxcpp.h"
 
 typedef struct {

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.c b/src/gromacs/gmxpreprocess/gpp_atomtype.c
index 31a39aec157e9438ef17b08ee9464b8bdc2fb43b..481ee8a15c0bf7e3b73e0d9bfc476d5ceefde8c4 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.c
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.c
@@ -49,7 +49,7 @@
 #include "topdirs.h"
 #include "toputil.h"
 #include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "txtdump.h"
 #include "gpp_atomtype.h"
 

diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.c b/src/gromacs/gmxpreprocess/gpp_nextnb.c
index b90c82274286efc4b578f09df67a01f91fa47809..d50ef4c6e6a03c71bca9847208dc1bafe655a1f5 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.c
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.c
@@ -44,7 +44,7 @@
 #include "macros.h"
 /* #define DEBUG_NNB */
 #include "gpp_nextnb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "toputil.h"
 
 typedef struct {

diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index 872c670990c99807997386445ec424ecab86cc7e..808898cfbd49f1352f8ed2ec07e28a4d55b47716 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -66,7 +66,7 @@
 #include "splitter.h"
 #include "gromacs/gmxpreprocess/sortwater.h"
 #include "convparm.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "warninp.h"
 #include "index.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/gmxpreprocess/h_db.c b/src/gromacs/gmxpreprocess/h_db.c
index 25ec285e06fe24d57ae029989b7aaddaf0910e4b..aa2e0fa221b820d07f8b85265b889dd1ab918707 100644 (file)
--- a/src/gromacs/gmxpreprocess/h_db.c
+++ b/src/gromacs/gmxpreprocess/h_db.c
@@ -48,7 +48,7 @@
 #include "h_db.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "fflibutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 
 /* Number of control atoms for each 'add' type.

diff --git a/src/gromacs/gmxpreprocess/hizzie.c b/src/gromacs/gmxpreprocess/hizzie.c
index 4274d779880b47adfd6d1958006918bd3010ec08..0bb9e1873c289c848a1a9d7f237a4380f06e8b70 100644 (file)
--- a/src/gromacs/gmxpreprocess/hizzie.c
+++ b/src/gromacs/gmxpreprocess/hizzie.c
@@ -51,7 +51,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "macros.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static int in_strings(char *key, int nstr, const char **str)
 {

diff --git a/src/gromacs/gmxpreprocess/insert-molecules.cpp b/src/gromacs/gmxpreprocess/insert-molecules.cpp
index c60b4d0d03c2678e25e7db81d38669ecabc3905d..b240cda303ae59860072499b21de35a1597d2a9b 100644 (file)
--- a/src/gromacs/gmxpreprocess/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/insert-molecules.cpp
@@ -52,7 +52,7 @@
 #include "atomprop.h"
 #include "names.h"
 #include "vec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 #include "addconf.h"

diff --git a/src/gromacs/gmxpreprocess/nm2type.c b/src/gromacs/gmxpreprocess/nm2type.c
index e9dd3961f18f3935f578f4c48f472923257bc2d2..8edd20ed5e05d044e4c2c15fd28db3d8312b2aff 100644 (file)
--- a/src/gromacs/gmxpreprocess/nm2type.c
+++ b/src/gromacs/gmxpreprocess/nm2type.c
@@ -62,7 +62,7 @@
 
 #include "nm2type.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void rd_nm2type_file(const char *fn, int *nnm, t_nm2type **nmp)
 {

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.c b/src/gromacs/gmxpreprocess/pdb2gmx.c
index b8686eefefcd92c62760f21da3956f1ab28fa1ca..827340c5e8753c6b7dad885fb244edcb02e213dc 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.c
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.c
@@ -55,7 +55,7 @@
 #include "vec.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/pdbio.h"
 #include "toputil.h"
 #include "h_db.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index 2110a4b32e5d7747649855e736db2a58223ebff3..804527e556f9b0d60148fcf99babbeb2ea9a0483 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -47,7 +47,7 @@
 #include "macros.h"
 #include "symtab.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "pdb2top.h"
 #include "gpp_nextnb.h"
 #include "topdirs.h"

diff --git a/src/gromacs/gmxpreprocess/pgutil.c b/src/gromacs/gmxpreprocess/pgutil.c
index 80088875f820b240cfd02beeeeb03f4e497f8959..c9ad5fd2767bb68023facb161c9a126dd6ecd62b 100644 (file)
--- a/src/gromacs/gmxpreprocess/pgutil.c
+++ b/src/gromacs/gmxpreprocess/pgutil.c
@@ -42,7 +42,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "pgutil.h"
 #include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define BUFSIZE 1024
 static void atom_not_found(int fatal_errno, const char *file, int line,

diff --git a/src/gromacs/gmxpreprocess/protonate.c b/src/gromacs/gmxpreprocess/protonate.c
index 38bf7cdc97bf5adcffe1c84f491ec2557da7aefe..ebd539a7f8dc0cdcd6836c83d610a4fe9eac0916 100644 (file)
--- a/src/gromacs/gmxpreprocess/protonate.c
+++ b/src/gromacs/gmxpreprocess/protonate.c
@@ -54,7 +54,7 @@
 #include "vec.h"
 #include "hackblock.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 int gmx_protonate(int argc, char *argv[])
 {

diff --git a/src/gromacs/gmxpreprocess/readadress.c b/src/gromacs/gmxpreprocess/readadress.c
index 7f3668484463f424648eb30a965b4821ef847336..f8aa8b6971413ca52a9e7a90eecfa8bf20955e42 100644 (file)
--- a/src/gromacs/gmxpreprocess/readadress.c
+++ b/src/gromacs/gmxpreprocess/readadress.c
@@ -39,7 +39,7 @@
 #include "readir.h"
 #include "names.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define MAXPTR 254
 

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index 19f9411761ec217d33e849c7b3a0eb0e2fbae597..e170db8756fcfe1d55bb0078b63ce880f83507fc 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -46,7 +46,7 @@
 #include "typedefs.h"
 #include "physics.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "index.h"
 #include "symtab.h"

diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c
index c23aa35668d2f74ac0f729b33b4f4765301895bd..b208d7fe59002d37488cc7f7fc6674ce151d3df6 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.c
+++ b/src/gromacs/gmxpreprocess/readpull.c
@@ -49,7 +49,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "index.h"
 #include "symtab.h"

diff --git a/src/gromacs/gmxpreprocess/readrot.c b/src/gromacs/gmxpreprocess/readrot.c
index cc25957b1adcde7ceebac92a68449460e2b782e9..43ca16add88ba9be100b56606cab0d43d0171726 100644 (file)
--- a/src/gromacs/gmxpreprocess/readrot.c
+++ b/src/gromacs/gmxpreprocess/readrot.c
@@ -46,7 +46,7 @@
 #include "gromacs/fileio/trnio.h"
 #include "txtdump.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static char *RotStr = {"Enforced rotation:"};
 

diff --git a/src/gromacs/gmxpreprocess/resall.c b/src/gromacs/gmxpreprocess/resall.c
index 91aa32613a2600320b8fac3efdd68e9812e7e56e..5ccece8744806f9b2b6ccf11a793bdc905b2fcfe 100644 (file)
--- a/src/gromacs/gmxpreprocess/resall.c
+++ b/src/gromacs/gmxpreprocess/resall.c
@@ -45,7 +45,7 @@
 #include "gromacs/utility/cstringutil.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "symtab.h"
 #include "macros.h"
 #include "resall.h"

diff --git a/src/gromacs/gmxpreprocess/solvate.cpp b/src/gromacs/gmxpreprocess/solvate.cpp
index 27623f165ebfa059dab3cd68761a0c8177b1dd9a..eaa59b60876180bdf25646d025baca115b917d21 100644 (file)
--- a/src/gromacs/gmxpreprocess/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/solvate.cpp
@@ -52,7 +52,7 @@
 #include "atomprop.h"
 #include "names.h"
 #include "vec.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/gmxlib/conformation-utilities.h"
 #include "addconf.h"

diff --git a/src/gromacs/gmxpreprocess/ter_db.c b/src/gromacs/gmxpreprocess/ter_db.c
index 09758f8e3b497a586881d1245098e1b254b2c10c..43a1b49c30c0fc3536ff0903b8134fe447d13acb 100644 (file)
--- a/src/gromacs/gmxpreprocess/ter_db.c
+++ b/src/gromacs/gmxpreprocess/ter_db.c
@@ -49,7 +49,7 @@
 #include "resall.h"
 #include "h_db.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "ter_db.h"
 #include "toputil.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/gmxpreprocess/tomorse.c b/src/gromacs/gmxpreprocess/tomorse.c
index 5bcf84f73756f10bca574acdd659e9ed26a719bb..7472af93267b4e67320caa9122d2e59dea818c8e 100644 (file)
--- a/src/gromacs/gmxpreprocess/tomorse.c
+++ b/src/gromacs/gmxpreprocess/tomorse.c
@@ -50,7 +50,7 @@
 #include "gromacs/fileio/futil.h"
 #include "gromacs/utility/smalloc.h"
 #include "toputil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gpp_atomtype.h"
 #include "macros.h"
 

diff --git a/src/gromacs/gmxpreprocess/topdirs.c b/src/gromacs/gmxpreprocess/topdirs.c
index 212bf1ea6fbeed464803ac01731ee1b945bcf31e..14132f2e5f6a5c351776b0656a1a36ccbcb8969e 100644 (file)
--- a/src/gromacs/gmxpreprocess/topdirs.c
+++ b/src/gromacs/gmxpreprocess/topdirs.c
@@ -45,7 +45,7 @@
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/utility/cstringutil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "topdirs.h"
 
 /* Must correspond to the directive enum in grompp-impl.h */

diff --git a/src/gromacs/gmxpreprocess/topio.c b/src/gromacs/gmxpreprocess/topio.c
index 52dcdd51cc6edc258b7fd8436fae6ef994592359..a2008fd8425931a34109ad08e42282d59547e53d 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.c
+++ b/src/gromacs/gmxpreprocess/topio.c
@@ -58,7 +58,7 @@
 #include "names.h"
 #include "gromacs/utility/cstringutil.h"
 #include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "warninp.h"
 #include "vsite_parm.h"
 

diff --git a/src/gromacs/gmxpreprocess/toppush.c b/src/gromacs/gmxpreprocess/toppush.c
index 8f25139fd2cb8cb44a320eefad4886d1c69b254c..52dba0ee0c1a1756ef045c0e87572b5a489cf124 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.c
+++ b/src/gromacs/gmxpreprocess/toppush.c
@@ -52,7 +52,7 @@
 #include "topdirs.h"
 #include "readir.h"
 #include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "warninp.h"
 #include "gpp_atomtype.h"
 #include "gpp_bond_atomtype.h"

diff --git a/src/gromacs/gmxpreprocess/topshake.c b/src/gromacs/gmxpreprocess/topshake.c
index fa00694a6e534e1e702638c33f48149e94a06d4a..cf6b3ce01c3bd80f3ed5071a08baca10f3a4b1d7 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.c
+++ b/src/gromacs/gmxpreprocess/topshake.c
@@ -52,7 +52,7 @@
 #include "toputil.h"
 #include "topdirs.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void copy_bond (t_params *pr, int to, int from)
 /* copies an entry in a bond list to another position.

diff --git a/src/gromacs/gmxpreprocess/toputil.c b/src/gromacs/gmxpreprocess/toputil.c
index 33db83ee49aa90a11fe2897cea52118e38fdcfef..892ee0b86610a4a7a6d4b993410e446c44ee91ad 100644 (file)
--- a/src/gromacs/gmxpreprocess/toputil.c
+++ b/src/gromacs/gmxpreprocess/toputil.c
@@ -47,7 +47,7 @@
 #include "topdirs.h"
 #include "toputil.h"
 #include "symtab.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gpp_atomtype.h"
 
 /* UTILITIES */

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
index 87b7763c3860c828f864bc6e33f69292fa5c4e26..d7b4a5fef1a733f58ed8072775ad14b2fd8d5b92 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.c
+++ b/src/gromacs/gmxpreprocess/vsite_parm.c
@@ -51,7 +51,7 @@
 #include "physics.h"
 #include "index.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/cstringutil.h"
 #include "physics.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxpreprocess/x2top.c b/src/gromacs/gmxpreprocess/x2top.c
index 5a0c27af1bdc6eb6d0497fca0af31fa134a230d3..05aef5d093b320516d812b99a0de022cf7eb7a76 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.c
+++ b/src/gromacs/gmxpreprocess/x2top.c
@@ -67,7 +67,7 @@
 #include "hackblock.h"
 #include "nm2type.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 char atp[7] = "HCNOSX";
 #define NATP (asize(atp)-1)

diff --git a/src/gromacs/gmxpreprocess/xlate.c b/src/gromacs/gmxpreprocess/xlate.c
index dac0b3cd652d78b2783ba6e8ebbaabe369c3f491..0e7bdb7cb3af431c2414f4ff67b1c864b8f51f8c 100644 (file)
--- a/src/gromacs/gmxpreprocess/xlate.c
+++ b/src/gromacs/gmxpreprocess/xlate.c
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/futil.h"
 #include "fflibutil.h"
 #include "hackblock.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "xlate.h"
 
 #include "gromacs/fileio/strdb.h"

diff --git a/src/gromacs/imd/imd.c b/src/gromacs/imd/imd.c
index 2e8cbcece8b67194f923e556f0954eb8c5aecd0c..2f919d6326224f5132e855b04cafce12ee5fa565 100644 (file)
--- a/src/gromacs/imd/imd.c
+++ b/src/gromacs/imd/imd.c
@@ -73,7 +73,7 @@
 #include "names.h"
 #include "gromacs/timing/wallcycle.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /*! \brief How long shall we wait in seconds until we check for a connection again? */
 #define IMDLOOPWAIT 1

diff --git a/src/gromacs/imd/imdsocket.c b/src/gromacs/imd/imdsocket.c
index 6febf83e55b57d45d739bb681b2bf49d3275e7dc..3c0d08a0ca23a8b184ae00e28ca26950b1787ef0 100644 (file)
--- a/src/gromacs/imd/imdsocket.c
+++ b/src/gromacs/imd/imdsocket.c
@@ -53,7 +53,7 @@
 
 #include <string.h>
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "imdsocket.h"
 #include "imd.h"
 

diff --git a/src/gromacs/legacyheaders/gmx_hash.h b/src/gromacs/legacyheaders/gmx_hash.h
index a241ee0def4f5f4695784237dd20dc978fc3dfe6..da399214daf57da218e4dc2c0f501bc54e160d31 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_hash.h
+++ b/src/gromacs/legacyheaders/gmx_hash.h
@@ -37,7 +37,7 @@
 
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/network.h b/src/gromacs/legacyheaders/network.h
index 8d4d4f17a3c8cc2a8a7388f0d83326cf70542da3..3bfc9a7f3901368e1d27aba81ca2c3e96df4a8b1 100644 (file)
--- a/src/gromacs/legacyheaders/network.h
+++ b/src/gromacs/legacyheaders/network.h
@@ -48,7 +48,7 @@
 #include "types/simple.h"
 #include "typedefs.h"
 #include "main.h"
-#include "gmx_fatal.h"
+#include "../utility/fatalerror.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/vec.h b/src/gromacs/legacyheaders/vec.h
index a14dc49dc90f77eb7e1d36c1cbba72adde3f3ea2..a8300ea00b5d278e5f8de6aae35f34c6ec69c1cd 100644 (file)
--- a/src/gromacs/legacyheaders/vec.h
+++ b/src/gromacs/legacyheaders/vec.h
@@ -113,14 +113,16 @@
 #include <config.h>
 #endif
 
+#include <math.h>
+
 #include "types/simple.h"
-#include "../math/utilities.h"
 #include "typedefs.h"
 #include "sysstuff.h"
-#include "gmx_fatal.h"
-#include <math.h>
 #include "physics.h"
 
+#include "../math/utilities.h"
+#include "../utility/fatalerror.h"
+
 #ifdef __cplusplus
 extern "C" {
 #elif 0

diff --git a/src/gromacs/linearalgebra/eigensolver.c b/src/gromacs/linearalgebra/eigensolver.c
index a0221be3c7a95407a2eb791659687c6223aaa21f..06af5423c2c239fc452a5740976e6be32b341499 100644 (file)
--- a/src/gromacs/linearalgebra/eigensolver.c
+++ b/src/gromacs/linearalgebra/eigensolver.c
@@ -37,9 +37,9 @@
 #include "eigensolver.h"
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 
 #include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "gmx_lapack.h"

diff --git a/src/gromacs/linearalgebra/matrix.c b/src/gromacs/linearalgebra/matrix.c
index ccbd22ec19a4e4b248ee3ad7ac60a8498040cf28..eda4e452cbef8987e9d4e0f665342c99a2d68bd0 100644 (file)
--- a/src/gromacs/linearalgebra/matrix.c
+++ b/src/gromacs/linearalgebra/matrix.c
@@ -42,9 +42,9 @@
 
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/vec.h"
 
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 #include "gmx_lapack.h"

diff --git a/src/gromacs/linearalgebra/mtxio.c b/src/gromacs/linearalgebra/mtxio.c
index 0a82d271c600941c7e831ddf2e527162977fc9d0..a446feed9b9fae5f63c9b061d227bc2134b41659 100644 (file)
--- a/src/gromacs/linearalgebra/mtxio.c
+++ b/src/gromacs/linearalgebra/mtxio.c
@@ -46,11 +46,10 @@
  */
 
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
-
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 /* Just a number to identify our file type */

diff --git a/src/gromacs/linearalgebra/nrjac.c b/src/gromacs/linearalgebra/nrjac.c
index b5cf7066b4612f26ce79b0962fa8621b6c8a9329..485f1ad973fe7fb1ce21c4fdd58e3bd1ce913f1a 100644 (file)
--- a/src/gromacs/linearalgebra/nrjac.c
+++ b/src/gromacs/linearalgebra/nrjac.c
@@ -39,7 +39,7 @@
 
 #include <math.h>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 static gmx_inline

diff --git a/src/gromacs/math/3dview.c b/src/gromacs/math/3dview.c
index 5e8a06c41e7f1ad8d8926caef273ae9f596fdb13..bc3262344d2af4d8b6620eeadb7ec69b2979d2eb 100644 (file)
--- a/src/gromacs/math/3dview.c
+++ b/src/gromacs/math/3dview.c
@@ -48,7 +48,7 @@
 #include "pbc.h"
 #include "vec.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define N 4
 

diff --git a/src/gromacs/math/do_fit.c b/src/gromacs/math/do_fit.c
index 9701f769ab30982c3063c8c84012b2cc89ace86a..96dabfa22db60cbe579c95b6599e81070b5c2f82 100644 (file)
--- a/src/gromacs/math/do_fit.c
+++ b/src/gromacs/math/do_fit.c
@@ -43,7 +43,7 @@
 #include "txtdump.h"
 
 #include "gromacs/linearalgebra/nrjac.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 real calc_similar_ind(gmx_bool bRho, int nind, atom_id *index, real mass[],

diff --git a/src/gromacs/mdlib/adress.c b/src/gromacs/mdlib/adress.c
index d2ac44d54c0c68a89ee35cdb7a2d92850cbfb5e8..ba290c1431ea76786bccf45b25eb0fd198219ece 100644 (file)
--- a/src/gromacs/mdlib/adress.c
+++ b/src/gromacs/mdlib/adress.c
@@ -41,7 +41,7 @@
 #include "typedefs.h"
 #include "vec.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 real
 adress_weight(rvec                 x,

diff --git a/src/gromacs/mdlib/clincs.c b/src/gromacs/mdlib/clincs.c
index d215cbdac63273fe065b56b4cde398c0de98866a..298eea4a59ed63e2238d9483c50342f4f61f123c 100644 (file)
--- a/src/gromacs/mdlib/clincs.c
+++ b/src/gromacs/mdlib/clincs.c
@@ -54,7 +54,7 @@
 #include "gmx_omp_nthreads.h"
 
 #include "gromacs/fileio/gmxfio.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxomp.h"
 
 typedef struct {

diff --git a/src/gromacs/mdlib/constr.c b/src/gromacs/mdlib/constr.c
index 1f5addc99b990da065e764d3c2095f16f9f982eb..3c972df072ef578abb7661fb585e04a745dfc14f 100644 (file)
--- a/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@ -61,7 +61,7 @@
 #include "gromacs/essentialdynamics/edsam.h"
 #include "gromacs/pulling/pull.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct gmx_constr {
     int                ncon_tot;       /* The total number of constraints    */

diff --git a/src/gromacs/mdlib/coupling.c b/src/gromacs/mdlib/coupling.c
index c0ca0111489f07271b62b622fcd873924eca4c7a..3a3b71a9a6a6a9c6cb24aa663ad102703747500d 100644 (file)
--- a/src/gromacs/mdlib/coupling.c
+++ b/src/gromacs/mdlib/coupling.c
@@ -47,7 +47,7 @@
 #include "macros.h"
 #include "physics.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "txtdump.h"
 #include "nrnb.h"
 #include "gromacs/random/random.h"

diff --git a/src/gromacs/mdlib/csettle.c b/src/gromacs/mdlib/csettle.c
index 281f3973c2aa9721df5bf717be24d554b3d9a474..68f9b3268f10502b49b7fabfbb6929bd4b2be8fe 100644 (file)
--- a/src/gromacs/mdlib/csettle.c
+++ b/src/gromacs/mdlib/csettle.c
@@ -42,7 +42,7 @@
 #include <stdio.h>
 #include "vec.h"
 #include "constr.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index fc82a2d455ba1a7e9ec7e49cf7e08f658a221404..5caeaaa5309505a56f85585afa3d54b67f7f0fbe 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -46,7 +46,7 @@
 
 #include "typedefs.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gmx_fatal_collective.h"
 #include "vec.h"
 #include "domdec.h"

diff --git a/src/gromacs/mdlib/domdec_box.c b/src/gromacs/mdlib/domdec_box.c
index 6b20dd987c3a58d475fecb4c4b49a6899a605579..1302ffec3b0dd0cc301578faaf1567a12ee2cd3b 100644 (file)
--- a/src/gromacs/mdlib/domdec_box.c
+++ b/src/gromacs/mdlib/domdec_box.c
@@ -46,7 +46,7 @@
 #include "nsgrid.h"
 #include "network.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 static void calc_cgcm_av_stddev(t_block *cgs, int n, rvec *x, rvec av, rvec stddev,
                                 t_commrec *cr_sum)

diff --git a/src/gromacs/mdlib/domdec_con.c b/src/gromacs/mdlib/domdec_con.c
index d79ffb5065988f0cd9dd9fb8af448a275da60401..c09ec52fdd5e76f9b7ed015dfdf9dc7fe09fb927 100644 (file)
--- a/src/gromacs/mdlib/domdec_con.c
+++ b/src/gromacs/mdlib/domdec_con.c
@@ -50,7 +50,7 @@
 #include "gmx_omp_nthreads.h"
 #include "macros.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 typedef struct {
     int  nsend;

diff --git a/src/gromacs/mdlib/domdec_top.c b/src/gromacs/mdlib/domdec_top.c
index 8aa77bfb6aa21c3c14d196339775c7979a486509..3b65f8997994b1e6f836fc2aa728271124021456 100644 (file)
--- a/src/gromacs/mdlib/domdec_top.c
+++ b/src/gromacs/mdlib/domdec_top.c
@@ -56,7 +56,7 @@
 #include "force.h"
 #include "gmx_omp_nthreads.h"
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /* for dd_init_local_state */
 #define NITEM_DD_INIT_LOCAL_STATE 5

diff --git a/src/gromacs/mdlib/ebin.c b/src/gromacs/mdlib/ebin.c
index 4760fcf32e1ea8d2397a16551d0b29c3200d42b9..feaec2ccc7139202bf1e296e7483c549e8ba38bd 100644 (file)
--- a/src/gromacs/mdlib/ebin.c
+++ b/src/gromacs/mdlib/ebin.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "ebin.h"
 #include "main.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/mdlib/ewald.c b/src/gromacs/mdlib/ewald.c
index 9a12d41e884c51b9c52b1573aba8762d46010cb4..059b0ea31b38d53bc3e80241d57b092f0492f691 100644 (file)
--- a/src/gromacs/mdlib/ewald.c
+++ b/src/gromacs/mdlib/ewald.c
@@ -44,7 +44,7 @@
 #include "types/commrec.h"
 #include "vec.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "physics.h"
 #include "coulomb.h"
 #include "macros.h"

diff --git a/src/gromacs/mdlib/expanded.c b/src/gromacs/mdlib/expanded.c
index 14d0e7ea3d3a23ef7227d323928affa55e8e17e5..c0fe8d8cd277fef2192422b7b57e790b67b076ec 100644 (file)
--- a/src/gromacs/mdlib/expanded.c
+++ b/src/gromacs/mdlib/expanded.c
@@ -71,7 +71,7 @@
 #include "gromacs/fileio/trnio.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/timing/wallcycle.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/gmxmpi.h"
 
 static void init_df_history_weights(df_history_t *dfhist, t_expanded *expand, int nlim)

diff --git a/src/gromacs/mdlib/force.c b/src/gromacs/mdlib/force.c
index 0726402913b01bb5d6f79fc79317132f73680163..af92598bb77b310339c073086c2e15c368b929fd 100644 (file)
--- a/src/gromacs/mdlib/force.c
+++ b/src/gromacs/mdlib/force.c
@@ -65,7 +65,7 @@
 #include "gmx_omp_nthreads.h"
 
 #include "gromacs/timing/wallcycle.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 void ns(FILE              *fp,
         t_forcerec        *fr,

diff --git a/src/gromacs/mdlib/forcerec.c b/src/gromacs/mdlib/forcerec.c
index 67cd36f34184ba820b4ab4a6196dd56fc135078a..9703bfaabd401f6c31847b0264a86ef2c6b544d4 100644 (file)
--- a/src/gromacs/mdlib/forcerec.c
+++ b/src/gromacs/mdlib/forcerec.c
@@ -49,7 +49,7 @@
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "physics.h"
 #include "force.h"
 #include "tables.h"

diff --git a/src/gromacs/mdlib/genborn.c b/src/gromacs/mdlib/genborn.c
index 6c20080c5f8a5ee44823975b91a53f776c416eb8..559169659298c40f504d71f5c0955f8a93ca2837 100644 (file)
--- a/src/gromacs/mdlib/genborn.c
+++ b/src/gromacs/mdlib/genborn.c
@@ -52,7 +52,7 @@
 #include "physics.h"
 #include "domdec.h"
 #include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "mtop_util.h"
 #include "pbc.h"
 #include "nrnb.h"

diff --git a/src/gromacs/mdlib/genborn_sse2_double.c b/src/gromacs/mdlib/genborn_sse2_double.c
index 7e71bf8ba437977065a6fd0ada88a1917f1c0bec..345933f3e4b2b64dfac228e95eaa6dc9e113479c 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_sse2_double.c
@@ -50,7 +50,7 @@
 #include "physics.h"
 #include "domdec.h"
 #include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "mtop_util.h"
 #include "genborn.h"
 

diff --git a/src/gromacs/mdlib/genborn_sse2_single.c b/src/gromacs/mdlib/genborn_sse2_single.c
index 95fa0cdc40a9fe2927aa548b790fa60ab3669f08..8e1b69bc89588514936dc862efd32c8ecb864506 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_sse2_single.c
@@ -50,7 +50,7 @@
 #include "physics.h"
 #include "domdec.h"
 #include "network.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "mtop_util.h"
 #include "genborn.h"
 

diff --git a/src/gromacs/mdlib/init.c b/src/gromacs/mdlib/init.c
index 95516341f8b957d79e02e317f8f7cdd55f6db0c4..2dcc481b8b0610f0a23c5a963193f9cad0931924 100644 (file)
--- a/src/gromacs/mdlib/init.c
+++ b/src/gromacs/mdlib/init.c
@@ -45,7 +45,7 @@
 #include "vec.h"
 #include "main.h"
 #include "mvdata.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "symtab.h"
 #include "txtdump.h"
 #include "mdatoms.h"

diff --git a/src/gromacs/mdlib/iteratedconstraints.c b/src/gromacs/mdlib/iteratedconstraints.c
index 5c3529f0f028162abfec9edef6ee5f94873659a1..f3f37a40eba2f7d0afc9c86bc5b3cc679434bb95 100644 (file)
--- a/src/gromacs/mdlib/iteratedconstraints.c
+++ b/src/gromacs/mdlib/iteratedconstraints.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -40,7 +40,7 @@
 
 #include <math.h>
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "mdrun.h"
 #include "md_support.h"
 #include "md_logging.h"

diff --git a/src/gromacs/mdlib/mdebin_bar.c b/src/gromacs/mdlib/mdebin_bar.c
index 9f057bd6fd4126dda7848c64f8149e4a3c01f354..84b602cf809d074bd6197f1760b3c242aee9cb76 100644 (file)
--- a/src/gromacs/mdlib/mdebin_bar.c
+++ b/src/gromacs/mdlib/mdebin_bar.c
@@ -42,7 +42,7 @@
 #include <float.h>
 #include <math.h>
 #include "typedefs.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "mdebin.h"
 #include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/enxio.h"

diff --git a/src/gromacs/mdlib/minimize.c b/src/gromacs/mdlib/minimize.c
index 213c05d27a74d10192374449bcc24cd27ee9efc7..ca94eb1beec71b543ea692bbda76e09c6be27689 100644 (file)
--- a/src/gromacs/mdlib/minimize.c
+++ b/src/gromacs/mdlib/minimize.c
@@ -50,7 +50,7 @@
 #include "force.h"
 #include "macros.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "txtdump.h"
 #include "typedefs.h"
 #include "update.h"

diff --git a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
index 4ba5acfb23c5d6a3ff582f928661b4c2843611cf..9212e11fbd64b9436561b434601ca90b1705de1b 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
+++ b/src/gromacs/mdlib/nbnxn_cuda/nbnxn_cuda_data_mgmt.cu
@@ -43,7 +43,7 @@
 
 #include <cuda.h>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "tables.h"
 #include "typedefs.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
index 1ac1bf54197b72c8f86bb80d24bd711d9cd5d26e..ed2ffcdc22e14c3f0cff8e089013c8e19eacd69b 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_file_generator/nbnxn_kernel_simd_template.c.pre
@@ -49,7 +49,7 @@
 #include "../nbnxn_kernel_common.h"
 #include "gmx_omp_nthreads.h"
 #include "types/force_flags.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
  */
@@ -116,7 +116,7 @@ reduce_group_energies(int ng, int ng_2log,
 
 #else /* {0} */
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #endif /* {0} */
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
index 45f09bc4621d64d900ba6c9fc66effead4372743..ffb0670fa59c9469a821d48f7f3e257f6d6e0fa5 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_2xnn/nbnxn_kernel_simd_2xnn.c
@@ -59,7 +59,7 @@
 #include "../nbnxn_kernel_common.h"
 #include "gmx_omp_nthreads.h"
 #include "types/force_flags.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
  */
@@ -252,7 +252,7 @@ reduce_group_energies(int ng, int ng_2log,
 
 #else /* GMX_NBNXN_SIMD_2XNN */
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #endif /* GMX_NBNXN_SIMD_2XNN */
 

diff --git a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
index 17608af2e7037a7fa46f647413d213f09036ada8..3cd1cce93b74de3f91a4e0b3c6041d780f2b7a30 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/simd_4xn/nbnxn_kernel_simd_4xn.c
@@ -57,7 +57,7 @@
 #include "../nbnxn_kernel_common.h"
 #include "gmx_omp_nthreads.h"
 #include "types/force_flags.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /*! \brief Kinds of electrostatic treatments in SIMD Verlet kernels
  */
@@ -250,7 +250,7 @@ reduce_group_energies(int ng, int ng_2log,
 
 #else /* GMX_NBNXN_SIMD_4XN */
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #endif /* GMX_NBNXN_SIMD_4XN */
 

diff --git a/src/gromacs/mdlib/nlistheuristics.c b/src/gromacs/mdlib/nlistheuristics.c
index d2f7401295fbf079611ea9d8730ab62e14c789d6..f5266aace7b40ddcf4014bb010657e119f019ee4 100644 (file)
--- a/src/gromacs/mdlib/nlistheuristics.c
+++ b/src/gromacs/mdlib/nlistheuristics.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2012,2013,2014, 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.
@@ -40,7 +40,7 @@
 
 #include "typedefs.h"
 #include "types/nlistheuristics.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 
 void reset_nlistheuristics(gmx_nlheur_t *nlh, gmx_int64_t step)

diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 6558e2be9cfe51e3347fb4c7b8f180169c34144f..4e68fcc5f47aa6a9012ec0c5df8212461d4d688b 100644 (file)
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -53,7 +53,7 @@
 #include "ns.h"
 #include "pbc.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "nrnb.h"
 #include "txtdump.h"
 #include "mtop_util.h"

diff --git a/src/gromacs/mdlib/nsgrid.c b/src/gromacs/mdlib/nsgrid.c
index 137b06f25559d6ef13d92f79586b1e2e76dc9a69..7fbf8900cdf7be2b60a5522292e7e2b24a122e64 100644 (file)
--- a/src/gromacs/mdlib/nsgrid.c
+++ b/src/gromacs/mdlib/nsgrid.c
@@ -47,7 +47,7 @@
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
 #include "nsgrid.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "network.h"
 #include "domdec.h"

diff --git a/src/gromacs/mdlib/pme.c b/src/gromacs/mdlib/pme.c
index 17eb6482d157f672699247b292b494a0eaf78cd6..a832a389ef1fa5f805073f8559ba1737a0057c94 100644 (file)
--- a/src/gromacs/mdlib/pme.c
+++ b/src/gromacs/mdlib/pme.c
@@ -70,7 +70,7 @@
 #include "vec.h"
 #include "gromacs/utility/smalloc.h"
 #include "coulomb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "pme.h"
 #include "network.h"
 #include "physics.h"

diff --git a/src/gromacs/mdlib/pme_pp.c b/src/gromacs/mdlib/pme_pp.c
index 7ed29b31171710a7b1ec89178562095287f6c32f..ddaeba64aceda71512d0fef44e107bf4922aa179 100644 (file)
--- a/src/gromacs/mdlib/pme_pp.c
+++ b/src/gromacs/mdlib/pme_pp.c
@@ -46,7 +46,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "pme.h"
 #include "network.h"

diff --git a/src/gromacs/mdlib/qm_gamess.c b/src/gromacs/mdlib/qm_gamess.c
index d3ba4ac4ab0a17e6b6f851d9f22f35cdfcd21cd9..f3e69193a35e089a1dbe4bd347ef21b67c1bf214 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.c
+++ b/src/gromacs/mdlib/qm_gamess.c
@@ -62,7 +62,7 @@
 #include "qmmm.h"
 #include <stdio.h>
 #include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
 #include <stdlib.h>
 

diff --git a/src/gromacs/mdlib/qm_gaussian.c b/src/gromacs/mdlib/qm_gaussian.c
index 8e96ec739ab7874a63550927b66485e8ec13c657..d984e0e1b63ac39f91b5930e877e3d889897a8da 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.c
+++ b/src/gromacs/mdlib/qm_gaussian.c
@@ -62,7 +62,7 @@
 #include "qmmm.h"
 #include <stdio.h>
 #include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
 #include <stdlib.h>
 

diff --git a/src/gromacs/mdlib/qm_mopac.c b/src/gromacs/mdlib/qm_mopac.c
index 760e4e00589779fbf2ca03dca0be1ae3e384b7bf..20b8c0d2968b73eb6edd5ce4d5e5f4a7d467093e 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.c
+++ b/src/gromacs/mdlib/qm_mopac.c
@@ -62,7 +62,7 @@
 #include "qmmm.h"
 #include <stdio.h>
 #include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
 #include <stdlib.h>
 

diff --git a/src/gromacs/mdlib/qm_orca.c b/src/gromacs/mdlib/qm_orca.c
index db48238ff0e49722e742b0722a1ebaee3a54ee09..af2b8a80cba19b35961c4247b0f70e5fe6e9fd7d 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.c
+++ b/src/gromacs/mdlib/qm_orca.c
@@ -60,7 +60,7 @@
 #include "qmmm.h"
 #include <stdio.h>
 #include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
 #include <stdlib.h>
 

diff --git a/src/gromacs/mdlib/qmmm.c b/src/gromacs/mdlib/qmmm.c
index ad0b66e387d61550cb38c4e338b684b08ac5ecbb..a1584deb37175aa5d503302503d912308d787cb7 100644 (file)
--- a/src/gromacs/mdlib/qmmm.c
+++ b/src/gromacs/mdlib/qmmm.c
@@ -61,7 +61,7 @@
 #include "qmmm.h"
 #include <stdio.h>
 #include <string.h>
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
 #include <stdlib.h>
 #include "mtop_util.h"

diff --git a/src/gromacs/mdlib/shellfc.c b/src/gromacs/mdlib/shellfc.c
index 531b88b61673dc519f888287f881b43600db2a5b..caca5722993eb84183c3671cc9544411acde50e5 100644 (file)
--- a/src/gromacs/mdlib/shellfc.c
+++ b/src/gromacs/mdlib/shellfc.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "vec.h"
 #include "txtdump.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/stat.c b/src/gromacs/mdlib/stat.c
index 393e4fe8840720bc125847f1e4196e5db61ff350..f001d28a3bc4cbe2ae3bab277da3c418c8f90c70 100644 (file)
--- a/src/gromacs/mdlib/stat.c
+++ b/src/gromacs/mdlib/stat.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "sysstuff.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "network.h"
 #include "txtdump.h"
 #include "names.h"

diff --git a/src/gromacs/mdlib/tables.c b/src/gromacs/mdlib/tables.c
index ff73a90e89e5452f64cc7feb7d4f570675ac2011..b558d267cd0ab2d655f967c75ee5b5fd6c770373 100644 (file)
--- a/src/gromacs/mdlib/tables.c
+++ b/src/gromacs/mdlib/tables.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "names.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/fileio/futil.h"
 #include "xvgr.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index 72a6901f9e221778df7c9781305f0ddf1b7bf3d0..df285c1c24970f67808b6a91c4e3416423e9915f 100644 (file)
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -50,7 +50,7 @@
 #include "force.h"
 #include "macros.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "txtdump.h"
 #include "typedefs.h"
 #include "update.h"

diff --git a/src/gromacs/mdlib/wnblist.c b/src/gromacs/mdlib/wnblist.c
index eb99f7a3a4491854facafbfd6f8c1a2ae35bfc67..076be3819c08473d0ae25fa18e20f13d6c6389a3 100644 (file)
--- a/src/gromacs/mdlib/wnblist.c
+++ b/src/gromacs/mdlib/wnblist.c
@@ -46,7 +46,7 @@
 #include "types/commrec.h"
 #include "ns.h"
 #include "nrnb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "gromacs/fileio/futil.h"
 #include "names.h"

diff --git a/src/gromacs/pulling/pullutil.c b/src/gromacs/pulling/pullutil.c
index 6b30d111b12822545200731016531e58ac677176..3adcf1eb0b2d64816c0c474c622b78b96a14b62b 100644 (file)
--- a/src/gromacs/pulling/pullutil.c
+++ b/src/gromacs/pulling/pullutil.c
@@ -48,7 +48,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "names.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "macros.h"
 #include "symtab.h"
 #include "index.h"

diff --git a/src/gromacs/selection/indexutil.cpp b/src/gromacs/selection/indexutil.cpp
index 084577d365ca97fb3adacbec2a720a4327e17809..52b467e2dc81227b01f80efc7e4ec2495828f729 100644 (file)
--- a/src/gromacs/selection/indexutil.cpp
+++ b/src/gromacs/selection/indexutil.cpp
@@ -47,9 +47,9 @@
 #include <vector>
 
 #include "gromacs/legacyheaders/index.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/typedefs.h"
 
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/smalloc.h"
 
 /********************************************************************
@@ -844,7 +844,7 @@ gmx_ana_index_make_block(t_blocka *t, t_topology *top, gmx_ana_index_t *g,
                         break;
 
                     default: /* Should not be reached */
-                        gmx_bug("internal error");
+                        GMX_RELEASE_ASSERT(false, "Unreachable code was reached");
                         break;
                 }
             }

diff --git a/src/gromacs/simd/impl_reference/impl_reference.h b/src/gromacs/simd/impl_reference/impl_reference.h
index 5269fa14e5e403e94814336ca80b6ffb3e9bcbfb..c4f6f776caa1aa353d1ae14dcd62b1a75be866aa 100644 (file)
--- a/src/gromacs/simd/impl_reference/impl_reference.h
+++ b/src/gromacs/simd/impl_reference/impl_reference.h
@@ -48,7 +48,7 @@
 
 #include <math.h>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 /*! \cond libapi */
 /*! \addtogroup module_simd */

diff --git a/src/gromacs/timing/wallcycle.c b/src/gromacs/timing/wallcycle.c
index 03f726d9d5b5645b1a60269b5188b887727b7e85..ccecbe8ca4e2d217df2d49f11422d1e61946afc7 100644 (file)
--- a/src/gromacs/timing/wallcycle.c
+++ b/src/gromacs/timing/wallcycle.c
@@ -43,7 +43,7 @@
 #include <string.h>
 
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "md_logging.h"
 #include "gromacs/utility/cstringutil.h"
 

diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index 3d166cf465bba208a69497e52796fc7230842e95..404c0560455130bd70fa49cd7a3568ef7743571c 100644 (file)
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -47,7 +47,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "atomprop.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.c
index 24ad49bab7c581586be4f5cce08308988a77484a..dc7f6aac987230b84d78da1b795c337f5650c430 100644 (file)
--- a/src/gromacs/tools/compare.c
+++ b/src/gromacs/tools/compare.c
@@ -48,7 +48,7 @@
 #include "gromacs/fileio/futil.h"
 #include "sysstuff.h"
 #include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "names.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"

diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.c
index 08c264e97e52a5198f92611c8f09f08fa1092d44..32495dbe7b8ecd4f14d683f8beb8b9cdf0dcae0a 100644 (file)
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.c
@@ -40,7 +40,7 @@
 
 #include <math.h>
 #include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "sysstuff.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"

diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.c
index ad94ac7162c9f21f836d86af3e408af44d8f6251..f31811dd573bfb0ce8d0d0718adaddb8795518c7 100644 (file)
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.c
@@ -47,7 +47,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "txtdump.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "txtdump.h"

diff --git a/src/gromacs/utility/CMakeLists.txt b/src/gromacs/utility/CMakeLists.txt
index ae59513caa0dca83540b68296f4f735f97699cdb..b0871b57c892f21c47634ef1acc84121138a9af6 100644 (file)
--- a/src/gromacs/utility/CMakeLists.txt
+++ b/src/gromacs/utility/CMakeLists.txt
@@ -45,6 +45,7 @@ set(UTILITY_PUBLIC_HEADERS
     common.h
     errorcodes.h
     exceptions.h
+    fatalerror.h
     file.h
     flags.h
     gmx_header_config.h

diff --git a/src/gromacs/utility/cstringutil.c b/src/gromacs/utility/cstringutil.c
index 71c22d38387a854a419ff5f019a4f60f09821ac2..230c92a5cfd252f991d94ddae67e60ab63170010 100644 (file)
--- a/src/gromacs/utility/cstringutil.c
+++ b/src/gromacs/utility/cstringutil.c
@@ -60,10 +60,10 @@
 #endif
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/main.h"
 
 #include "gromacs/fileio/futil.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 
 int continuing(char *s)

diff --git a/src/gromacs/gmxlib/gmx_fatal.c b/src/gromacs/utility/fatalerror.c
similarity index 97%
rename from src/gromacs/gmxlib/gmx_fatal.c
rename to src/gromacs/utility/fatalerror.c
index 837abe06d7197d179cf1b782408e4ba9f800b9ec..2c1171ef67ced6bbfa35ba530e87948f1b96cefc 100644 (file)
--- a/src/gromacs/gmxlib/gmx_fatal.c
+++ b/src/gromacs/utility/fatalerror.c
@@ -34,8 +34,8 @@
  * To help us fund GROMACS development, we humbly ask that you cite
  * the research papers on the package. Check out http://www.gromacs.org.
  */
-#include "gmx_fatal.h"
-#include "gmx_fatal_collective.h"
+#include "fatalerror.h"
+#include "gromacs/legacyheaders/gmx_fatal_collective.h"
 
 #ifdef HAVE_CONFIG_H
 #include <config.h>
@@ -44,15 +44,15 @@
 #include <ctype.h>
 #include <errno.h>
 #include <stdarg.h>
+#include <stdlib.h>
 #include <string.h>
 
 #include "thread_mpi/threads.h"
 
-#include "main.h"
-#include "types/commrec.h"
-#include "network.h"
-#include "copyrite.h"
-#include "macros.h"
+#include "gromacs/legacyheaders/types/commrec.h"
+#include "gromacs/legacyheaders/copyrite.h"
+#include "gromacs/legacyheaders/macros.h"
+#include "gromacs/legacyheaders/network.h"
 
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/legacyheaders/gmx_fatal.h b/src/gromacs/utility/fatalerror.h
similarity index 98%
rename from src/gromacs/legacyheaders/gmx_fatal.h
rename to src/gromacs/utility/fatalerror.h
index 8bf145b35e8f997bbbf0e83dbcc9639ce92891d9..8e8c0912f426ec201e531f5cf5316902e41f4efb 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_fatal.h
+++ b/src/gromacs/utility/fatalerror.h
@@ -39,13 +39,14 @@
  * Declares fatal error handling and debugging routines for C code.
  *
  * \inpublicapi
+ * \ingroup module_utility
  */
-#ifndef _fatal_h
-#define _fatal_h
+#ifndef GMX_UTILITY_FATALERROR_H
+#define GMX_UTILITY_FATALERROR_H
 
 #include <stdio.h>
 
-#include "types/simple.h"
+#include "../legacyheaders/types/simple.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/utility/gmxomp.cpp b/src/gromacs/utility/gmxomp.cpp
index 9e6469b3a442fb02d6400a33ab106a586e7d7fb8..a258481f237af32ebe944ae79c5aa14395adb8f1 100644 (file)
--- a/src/gromacs/utility/gmxomp.cpp
+++ b/src/gromacs/utility/gmxomp.cpp
@@ -49,11 +49,11 @@
 #endif
 
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/md_logging.h"
 
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/cstringutil.h"
+#include "gromacs/utility/fatalerror.h"
 
 int gmx_omp_get_max_threads(void)
 {

diff --git a/src/gromacs/utility/smalloc.c b/src/gromacs/utility/smalloc.c
index 85ae9d0b1412082f7c32be90ef37dee1e30f21ea..54145246890fe1092ddc90470bf543796cdb54e5 100644 (file)
--- a/src/gromacs/utility/smalloc.c
+++ b/src/gromacs/utility/smalloc.c
@@ -49,8 +49,7 @@
 #include <dmalloc.h>
 #endif
 
-#include "gromacs/legacyheaders/gmx_fatal.h"
-
+#include "gromacs/utility/fatalerror.h"
 #ifdef PRINT_ALLOC_KB
 #include "gromacs/utility/gmxmpi.h"
 #endif

diff --git a/src/programs/mdrun/mdrun.cpp b/src/programs/mdrun/mdrun.cpp
index ca96aadcfb6bb6bf4e91d48e5ec0af0bc454013f..a783c3505453e6ffe3218743980743497caf48c4 100644 (file)
--- a/src/programs/mdrun/mdrun.cpp
+++ b/src/programs/mdrun/mdrun.cpp
@@ -44,7 +44,6 @@
 
 #include "gromacs/legacyheaders/checkpoint.h"
 #include "gromacs/legacyheaders/copyrite.h"
-#include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/main.h"
 #include "gromacs/legacyheaders/mdrun.h"
@@ -55,6 +54,7 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/filenm.h"
+#include "gromacs/utility/fatalerror.h"
 
 int gmx_mdrun(int argc, char *argv[])
 {

diff --git a/src/programs/view/dialogs.cpp b/src/programs/view/dialogs.cpp
index e4ba670a4c7127e398949bc854aa0039c9837cf7..6aee5b5ef6b97cbd413f54417082f9012cfac338 100644 (file)
--- a/src/programs/view/dialogs.cpp
+++ b/src/programs/view/dialogs.cpp
@@ -54,7 +54,7 @@
 #include "nmol.h"
 #include "manager.h"
 #include "gromacs/fileio/futil.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 #define MBFLAGS /* MB_APPLMODAL | */ MB_DONTSHOW
 

diff --git a/src/programs/view/filter.cpp b/src/programs/view/filter.cpp
index 1acaa8c42bad028d95ddb069292e39c5f60dc865..15affb3fd077eca61be8757ba4b30de9a1eb937e 100644 (file)
--- a/src/programs/view/filter.cpp
+++ b/src/programs/view/filter.cpp
@@ -50,7 +50,7 @@
 #include "xdlghi.h"
 #include "dialogs.h"
 #include "index.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 
 t_filter *init_filter(t_atoms *atoms, const char *fn, int natom_trx)
 {

diff --git a/src/programs/view/nmol.cpp b/src/programs/view/nmol.cpp
index 5a6866fff4de98517d193ea23c2011a2f06b35c0..28086732d1b262c0f33d1d37ed8029841316726c 100644 (file)
--- a/src/programs/view/nmol.cpp
+++ b/src/programs/view/nmol.cpp
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "xutil.h"
 #include "gromacs/math/3dview.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "buttons.h"
 #include "manager.h"
 #include "nmol.h"

diff --git a/src/programs/view/view.cpp b/src/programs/view/view.cpp
index 2408ced16fa1bf4253f79a751ca7d277ba49e647..0d0c823172b7bf6a829221da7609857d8103d78c 100644 (file)
--- a/src/programs/view/view.cpp
+++ b/src/programs/view/view.cpp
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "macros.h"
 #include "gromacs/utility/smalloc.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "typedefs.h"
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"

diff --git a/src/programs/view/xdlg.cpp b/src/programs/view/xdlg.cpp
index dc4e0b6e4e661970ce433a0570e590e1adae7985..997ad2255a4c346fa0d464ff61008f40c6462c5a 100644 (file)
--- a/src/programs/view/xdlg.cpp
+++ b/src/programs/view/xdlg.cpp
@@ -48,7 +48,7 @@
 #include "xutil.h"
 #include "xdlg.h"
 #include "xmb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 /*****************************
  *
  * Helpful routines

diff --git a/src/programs/view/xdlghi.cpp b/src/programs/view/xdlghi.cpp
index 5d280fc75d32db67fac7cb661943bc4f51d146cc..6ebf21adc0048c5183a32477f370591af02a6cf1 100644 (file)
--- a/src/programs/view/xdlghi.cpp
+++ b/src/programs/view/xdlghi.cpp
@@ -42,7 +42,7 @@
 
 #include <algorithm>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/cstringutil.h"
 #include "sysstuff.h"
 #include "gromacs/utility/smalloc.h"

diff --git a/src/programs/view/xdlgitem.cpp b/src/programs/view/xdlgitem.cpp
index 590bf733240a7e36d2c6167af45cc258f0730a7c..09bf122b13daf39a160475933fc25f3f8a2a16ae 100644 (file)
--- a/src/programs/view/xdlgitem.cpp
+++ b/src/programs/view/xdlgitem.cpp
@@ -45,7 +45,7 @@
 
 #include <algorithm>
 
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "Xstuff.h"

diff --git a/src/programs/view/xmb.cpp b/src/programs/view/xmb.cpp
index 2b747ded6d549f7b208634ac52288d8dc6aec6bc..8e08a7b2668ca909661a96e63d3df4b06c7d705d 100644 (file)
--- a/src/programs/view/xmb.cpp
+++ b/src/programs/view/xmb.cpp
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2013, The GROMACS development team.
- * Copyright (c) 2013, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014, 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.
@@ -49,7 +49,7 @@
 #include "xutil.h"
 #include "xdlg.h"
 #include "xmb.h"
-#include "gmx_fatal.h"
+#include "gromacs/utility/fatalerror.h"
 #include "gromacs.bm"
 #include "stop.bm"
 #include "info.bm"