Move smalloc.h to utility/

One common header away from legacyheaders/.
Mostly mechanical replacement for the include paths, but removed a few
instances where the header was included more than once.  Also, reordered
the headers a bit, mainly in C++ files.

Part of #1415.

Change-Id: Ic438d501ebf5eccc285655a9e8f2f625eb12f1d1

diff --git a/src/contrib/anaf.c b/src/contrib/anaf.c
index b16b8c60203faa2baa0dc3150a256eff4f15c779..c71140f3b97bbb7020ea6489137e090e2eee1b71 100644 (file)
--- a/src/contrib/anaf.c
+++ b/src/contrib/anaf.c
@@ -49,7 +49,7 @@
 #include "gmx_fatal.h"
 #include "gromacs/fileio/xtcio.h"
 #include "gromacs/fileio/enxio.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/contrib/compnl.c b/src/contrib/compnl.c
index cf46200bc093f7106d3cd7ba4d96b383a3fabbd8..923319e4e3652e491783b1f930ce185d6578c08b 100644 (file)
--- a/src/contrib/compnl.c
+++ b/src/contrib/compnl.c
@@ -37,7 +37,7 @@
 #endif
 
 #include "ns.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "wnblist.h"
 #include "gromacs/fileio/futil.h"
 #include "macros.h"

diff --git a/src/contrib/do_multiprot.c b/src/contrib/do_multiprot.c
index aa82f0ead87d1cd68b2e231f0bdc1a69ce7a4421..23459e1c55ea603e7a8b287fbf7273bd105cbea4 100644 (file)
--- a/src/contrib/do_multiprot.c
+++ b/src/contrib/do_multiprot.c
@@ -42,7 +42,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "mshift.h"
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"

diff --git a/src/contrib/do_shift.c b/src/contrib/do_shift.c
index bcc227c353e7dc46abf3ce82d64bc579b2cf18a8..f48f5bac8c4ce1b9865ac10db8960ec1c18636ad 100644 (file)
--- a/src/contrib/do_shift.c
+++ b/src/contrib/do_shift.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "string2.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "mshift.h"
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"

diff --git a/src/contrib/ehanal.c b/src/contrib/ehanal.c
index e781f6331df96877495ac7343f717b600192f3c5..bd625ce29b4bd314c387cc1a63c527bce6168293 100644 (file)
--- a/src/contrib/ehanal.c
+++ b/src/contrib/ehanal.c
@@ -40,7 +40,7 @@
 #include <math.h>
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "random.h"

diff --git a/src/contrib/ehdata.c b/src/contrib/ehdata.c
index 0f9bec9cc18295ac50f93edb1a3ce741c4b63a58..f0f5d2c85ecb74896b7f3b5a9c31492635ff2342 100644 (file)
--- a/src/contrib/ehdata.c
+++ b/src/contrib/ehdata.c
@@ -39,7 +39,7 @@
 #include <stdlib.h>
 #include <math.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "random.h"

diff --git a/src/contrib/ehole.c b/src/contrib/ehole.c
index 740546cbcef63e1e23388b7d5268327f0ef5bd71..39ac52b22e92bec7f82bf2ac4c64f5aaa57c65b1 100644 (file)
--- a/src/contrib/ehole.c
+++ b/src/contrib/ehole.c
@@ -40,7 +40,7 @@
 #include <math.h>
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "copyrite.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/contrib/g_anavel.c b/src/contrib/g_anavel.c
index 263baad4c717cdc7f48026d8245a62a1ec45eab8..175b95cce4247bb8e7a5e6d5d8e4543d87447200 100644 (file)
--- a/src/contrib/g_anavel.c
+++ b/src/contrib/g_anavel.c
@@ -37,7 +37,7 @@
 #endif
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/commandline/pargs.h"
 #include "random.h"

diff --git a/src/contrib/gmx_sdf.c b/src/contrib/gmx_sdf.c
index e96e30dff591fc019799ba77ce583411a5b83f38..03bbf17d5c3f198aabf0765717ed3eacddd73ff2 100644 (file)
--- a/src/contrib/gmx_sdf.c
+++ b/src/contrib/gmx_sdf.c
@@ -31,7 +31,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "gstat.h"
 #include "gromacs/fileio/matio.h"

diff --git a/src/contrib/gmx_stats_test.c b/src/contrib/gmx_stats_test.c
index 1129db07af331f7e1c85fda7ebd1d6a1b1a8590c..1896bd00a6f4d6f65945cdc87265aaeaa239c7f6 100644 (file)
--- a/src/contrib/gmx_stats_test.c
+++ b/src/contrib/gmx_stats_test.c
@@ -1,6 +1,6 @@
 #include <stdio.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "gmx_random.h"
 #include "gmx_statistics.h"

diff --git a/src/contrib/hexamer.c b/src/contrib/hexamer.c
index fd9bd2e5427ce3f176bfed81529e33fe19c4e8e1..986044be95bc23e7408cf1c4f9c3bdd9eb98e4e5 100644 (file)
--- a/src/contrib/hexamer.c
+++ b/src/contrib/hexamer.c
@@ -42,10 +42,9 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
 #include "symtab.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "symtab.h"
 #include "macros.h"
-#include "smalloc.h"
 #include "copyrite.h"
 #include "gromacs/commandline/pargs.h"
 #include "index.h"

diff --git a/src/contrib/hrefify.c b/src/contrib/hrefify.c
index cec40f4f897d54370a36aed2f8f2f7256408de6c..769f2d99097839c4676a6ca345818721a955c156 100644 (file)
--- a/src/contrib/hrefify.c
+++ b/src/contrib/hrefify.c
@@ -39,7 +39,7 @@
 #include <math.h>
 #include <string.h> 
 #include <ctype.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "macros.h"
 #include "string2.h"

diff --git a/src/contrib/mkice.c b/src/contrib/mkice.c
index e89f8415f550d4bc8668b255f24b85a273ecb820..91fb0657ab5e47c6c73632dc3fd39700979405fd 100644 (file)
--- a/src/contrib/mkice.c
+++ b/src/contrib/mkice.c
@@ -44,7 +44,7 @@
 #include "gmx_fatal.h"
 #include "gromacs/fileio/pdbio.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "pbc.h"
 #include "physics.h"

diff --git a/src/contrib/pmetest.c b/src/contrib/pmetest.c
index 63d6ef14ff3d6a23ea2d6c78d4e30845508805ed..3f03bb7d067aab63d4fd6462a7546e23c470f901 100644 (file)
--- a/src/contrib/pmetest.c
+++ b/src/contrib/pmetest.c
@@ -38,7 +38,7 @@
 
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "copyrite.h"
 #include "main.h"
 #include "nrnb.h"

diff --git a/src/contrib/test.c b/src/contrib/test.c
index a4c1c7acab97fc78d47f4c3d1b8fbf5a3ebf1119..3bea84f5d96fe1da230d6d2de07681ea1d8b88b8 100644 (file)
--- a/src/contrib/test.c
+++ b/src/contrib/test.c
@@ -45,7 +45,7 @@
 #include "xvgr.h"
 #include "gromacs/fileio/pdbio.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "pbc.h"
 #include "physics.h"

diff --git a/src/contrib/testfft.c b/src/contrib/testfft.c
index 4c1c427714ce52eca6930c7500bb1134f51e6395..b97146db75b4b265a3a16d2621d00df88623c347 100644 (file)
--- a/src/contrib/testfft.c
+++ b/src/contrib/testfft.c
@@ -36,7 +36,7 @@
 #include <stdio.h>
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "xvgr.h"
 #include "complex.h"
 #include "fftgrid.h"

diff --git a/src/contrib/testlr.c b/src/contrib/testlr.c
index b0a519258bdb918644c87a632e1a2271282e7704..247a7cd85334864e48957f91a84cb3b002a57ef8 100644 (file)
--- a/src/contrib/testlr.c
+++ b/src/contrib/testlr.c
@@ -39,7 +39,7 @@
 #include "physics.h"
 #include "macros.h"
 #include "names.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/writeps.h"

diff --git a/src/contrib/testxml.c b/src/contrib/testxml.c
index 2130c2a5431bc8864d3b58a7aa7f070f418bfd2b..e9fc47e28ff6a2b5eada3b1985d075b810eba870 100644 (file)
--- a/src/contrib/testxml.c
+++ b/src/contrib/testxml.c
@@ -33,7 +33,7 @@
  * GROningen Mixture of Alchemy and Childrens' Stories
  */
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "xmlio.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/contrib/timefft.c b/src/contrib/timefft.c
index efc4404383e05b7de25e77db5b128646851e1387..017604b6152ea7f6c395fd08dc088bf84bfb32c0 100644 (file)
--- a/src/contrib/timefft.c
+++ b/src/contrib/timefft.c
@@ -38,7 +38,7 @@
 
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "xvgr.h"
 #include "copyrite.h"
 #include "mdrun.h"

diff --git a/src/gromacs/analysisdata/modules/displacement.cpp b/src/gromacs/analysisdata/modules/displacement.cpp
index c45f7e8e5103d70b7db30ec22261e8be282e6d31..52fd4193ed9a3e2a5022ba787098c4fff9b25376 100644 (file)
--- a/src/gromacs/analysisdata/modules/displacement.cpp
+++ b/src/gromacs/analysisdata/modules/displacement.cpp
@@ -41,14 +41,13 @@
  */
 #include "gromacs/analysisdata/modules/displacement.h"
 
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/math/utilities.h"
-
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datamodulemanager.h"
 #include "gromacs/analysisdata/modules/histogram.h"
+#include "gromacs/math/utilities.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/cmdlineinit.cpp b/src/gromacs/commandline/cmdlineinit.cpp
index aef6121bc39f3c44937840598a601c1df3812674..afac7d982bb1fde18f3e66903a6a769c7bcca724 100644 (file)
--- a/src/gromacs/commandline/cmdlineinit.cpp
+++ b/src/gromacs/commandline/cmdlineinit.cpp
@@ -46,7 +46,6 @@
 #include <boost/scoped_ptr.hpp>
 
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 
 #include "gromacs/commandline/cmdlinemodulemanager.h"
@@ -55,6 +54,7 @@
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/init.h"
 #include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/commandline/pargs.cpp b/src/gromacs/commandline/pargs.cpp
index 148f5a2217153c0d42efecd4806af8c8b2bb9150..d0595c1712e534a6acb58f25613a74738427a153 100644 (file)
--- a/src/gromacs/commandline/pargs.cpp
+++ b/src/gromacs/commandline/pargs.cpp
@@ -61,7 +61,6 @@
 #include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/string2.h"
 
 #include "gromacs/commandline/cmdlinehelpcontext.h"
@@ -75,6 +74,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 /* The source code in this file should be thread-safe.

diff --git a/src/gromacs/essentialdynamics/edsam.c b/src/gromacs/essentialdynamics/edsam.c
index b0c952e92c7ddf99bee77d8ea40de43526113339..39965c8aef3677c2b558594a3d8c5a22b95e5c89 100644 (file)
--- a/src/gromacs/essentialdynamics/edsam.c
+++ b/src/gromacs/essentialdynamics/edsam.c
@@ -44,7 +44,7 @@
 
 #include "typedefs.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "gromacs/fileio/confio.h"
 #include "txtdump.h"

diff --git a/src/gromacs/fft/fft5d.cpp b/src/gromacs/fft/fft5d.cpp
index 98f4a16087abb5fa23abec4bde6084560066369a..06e0826a7dd7de6484fe353a422e72537eb0558a 100644 (file)
--- a/src/gromacs/fft/fft5d.cpp
+++ b/src/gromacs/fft/fft5d.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014, 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.
@@ -65,7 +65,7 @@
 #include <float.h>
 #include <math.h>
 #include <assert.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifndef __FLT_EPSILON__
 #define __FLT_EPSILON__ FLT_EPSILON

diff --git a/src/gromacs/fft/parallel_3dfft.c b/src/gromacs/fft/parallel_3dfft.c
index 6f99351c735ca0280adec212a24243f66680360c..7312cbedc79309abdb6fb5b3b9fc31ac0ed91766 100644 (file)
--- a/src/gromacs/fft/parallel_3dfft.c
+++ b/src/gromacs/fft/parallel_3dfft.c
@@ -46,7 +46,7 @@
 #include "gromacs/math/gmxcomplex.h"
 #include "gromacs/utility/gmxmpi.h"
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 
 #include "fft5d.h"

diff --git a/src/gromacs/fileio/confio.c b/src/gromacs/fileio/confio.c
index f1cf0a76037878fd4adb00528ad8f07d75a678a1..71ade51cef58aac6730d4313876f2fe9e048e386 100644 (file)
--- a/src/gromacs/fileio/confio.c
+++ b/src/gromacs/fileio/confio.c
@@ -41,7 +41,7 @@
 #include <math.h>
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include <errno.h>
 #include "macros.h"

diff --git a/src/gromacs/fileio/enxio.c b/src/gromacs/fileio/enxio.c
index b40146d8596e870948e7873446eeb64363e7602a..1a7585f3fbaf2141c44f9bcf68682ade01a883d8 100644 (file)
--- a/src/gromacs/fileio/enxio.c
+++ b/src/gromacs/fileio/enxio.c
@@ -42,7 +42,7 @@
 
 #include "futil.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmxfio.h"
 #include "enxio.h"
 #include "vec.h"

diff --git a/src/gromacs/fileio/filenm.c b/src/gromacs/fileio/filenm.c
index eec919a98c89756026e797d454e219a760c4d2c5..516f082ceb00009ef8a629204b654bbc6e8d359a 100644 (file)
--- a/src/gromacs/fileio/filenm.c
+++ b/src/gromacs/fileio/filenm.c
@@ -47,7 +47,7 @@
 #include "futil.h"
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 #include "types/simple.h"
 #include "types/commrec.h"

diff --git a/src/gromacs/fileio/futil.cpp b/src/gromacs/fileio/futil.cpp
index 829f48c2885f1c333da8f5068c757d5bf109f007..629eb52c83ff259e7dcd4519c49effdf2790b074 100644 (file)
--- a/src/gromacs/fileio/futil.cpp
+++ b/src/gromacs/fileio/futil.cpp
@@ -70,13 +70,13 @@
 #include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/network.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/string2.h"
 
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/path.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 /* we keep a linked list of all files opened through pipes (i.e.

diff --git a/src/gromacs/fileio/gmxfio.c b/src/gromacs/fileio/gmxfio.c
index 4ba73a1f77101f9a54f8b4379cb84c1622d1df8f..a772655ba42edba59ced39427e5cae82086332a3 100644 (file)
--- a/src/gromacs/fileio/gmxfio.c
+++ b/src/gromacs/fileio/gmxfio.c
@@ -52,7 +52,7 @@
 
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "futil.h"
 #include "filenm.h"
 #include "string2.h"

diff --git a/src/gromacs/fileio/gmxfio_asc.c b/src/gromacs/fileio/gmxfio_asc.c
index d91856cbeae13b0f302da41766b5adcda3e1f67c..c869643866c765f145324589f30419614d8ebed5 100644 (file)
--- a/src/gromacs/fileio/gmxfio_asc.c
+++ b/src/gromacs/fileio/gmxfio_asc.c
@@ -50,7 +50,7 @@
 
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "futil.h"
 #include "filenm.h"
 #include "string2.h"

diff --git a/src/gromacs/fileio/gmxfio_bin.c b/src/gromacs/fileio/gmxfio_bin.c
index 7547fb8693f7a0e7f2aadf29e107e34a09418d07..0cb819533effae6c8cc22cedb5140e908092d1e0 100644 (file)
--- a/src/gromacs/fileio/gmxfio_bin.c
+++ b/src/gromacs/fileio/gmxfio_bin.c
@@ -47,7 +47,7 @@
 
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "futil.h"
 #include "filenm.h"
 #include "gmxfio.h"

diff --git a/src/gromacs/fileio/gmxfio_rw.c b/src/gromacs/fileio/gmxfio_rw.c
index 36eec3e16b7562d7827e2161118b0e71edc918ea..9705486a20ed3dbfc2a77b0a6a9c5f1267987dc8 100644 (file)
--- a/src/gromacs/fileio/gmxfio_rw.c
+++ b/src/gromacs/fileio/gmxfio_rw.c
@@ -46,7 +46,7 @@
 
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "futil.h"
 #include "filenm.h"
 #include "gmxfio.h"

diff --git a/src/gromacs/fileio/gmxfio_xdr.c b/src/gromacs/fileio/gmxfio_xdr.c
index 685b6b4b4022f6f207f4bdb5b83dc8c487bfdc05..47ad3ca59c3c9a37592d6a9293a37720caea027b 100644 (file)
--- a/src/gromacs/fileio/gmxfio_xdr.c
+++ b/src/gromacs/fileio/gmxfio_xdr.c
@@ -47,7 +47,7 @@
 
 #include "gmx_fatal.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "futil.h"
 #include "filenm.h"
 #include "gmxfio.h"

diff --git a/src/gromacs/fileio/matio.cpp b/src/gromacs/fileio/matio.cpp
index d32e4613c5c2eb50d8b6b8c1bf90c42d05da858e..96ca01c3751c33878d11b33eba90c5e517ea902e 100644 (file)
--- a/src/gromacs/fileio/matio.cpp
+++ b/src/gromacs/fileio/matio.cpp
@@ -47,7 +47,7 @@
 #include "futil.h"
 #include "string2.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "matio.h"
 #include "gmxfio.h"

diff --git a/src/gromacs/fileio/mdoutf.c b/src/gromacs/fileio/mdoutf.c
index d140e1dc6a80b232aa4a7e3469d074e5b6047dfb..bcbf75b11456e2d963db0db381419405c587bc8f 100644 (file)
--- a/src/gromacs/fileio/mdoutf.c
+++ b/src/gromacs/fileio/mdoutf.c
@@ -36,7 +36,6 @@
 
 #include "gromacs/legacyheaders/xvgr.h"
 #include "gromacs/legacyheaders/mdrun.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/types/commrec.h"
 #include "gromacs/legacyheaders/mvdata.h"
 #include "gromacs/legacyheaders/domdec.h"
@@ -47,6 +46,8 @@
 #include "checkpoint.h"
 #include "copyrite.h"
 
+#include "gromacs/utility/smalloc.h"
+
 struct gmx_mdoutf {
     t_fileio         *fp_trn;
     t_fileio         *fp_xtc;

diff --git a/src/gromacs/fileio/pdbio.c b/src/gromacs/fileio/pdbio.c
index de10f0adfc17da143c07ef0bebbca9ab3201d1ec..180e01049a4dea34d78ef33dccdc507812dc471c 100644 (file)
--- a/src/gromacs/fileio/pdbio.c
+++ b/src/gromacs/fileio/pdbio.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "string2.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "symtab.h"
 #include "pdbio.h"

diff --git a/src/gromacs/fileio/strdb.c b/src/gromacs/fileio/strdb.c
index b577c42457bfb009650f02ec0ac64de93a9a9b5c..995158ab2f3b8a0363769bffd1e6c64ba04bf24f 100644 (file)
--- a/src/gromacs/fileio/strdb.c
+++ b/src/gromacs/fileio/strdb.c
@@ -45,7 +45,7 @@
 #include <string.h>
 
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/fileio/tngio_for_tools.cpp b/src/gromacs/fileio/tngio_for_tools.cpp
index 04ac5169d6ea31292ee97650aa5671e1f5d0f675..3d7954d1365c6806f0eb337751d8eb532d5cf5a1 100644 (file)
--- a/src/gromacs/fileio/tngio_for_tools.cpp
+++ b/src/gromacs/fileio/tngio_for_tools.cpp
@@ -47,12 +47,13 @@
 #include "../../external/tng_io/include/tng_io.h"
 #endif
 
-#include "gromacs/utility/common.h"
 #include "gromacs/legacyheaders/types/atoms.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/physics.h"
 #include "gromacs/legacyheaders/gmx_fatal.h"
 
+#include "gromacs/utility/common.h"
+#include "gromacs/utility/smalloc.h"
+
 void gmx_prepare_tng_writing(const char              *filename,
                              char                     mode,
                              tng_trajectory_t        *input,

diff --git a/src/gromacs/fileio/tpxio.c b/src/gromacs/fileio/tpxio.c
index 40c41827cb5f5e4cbe96aedaa7e6d030252bc800..5ba1cd37bad37cabd12885f180c317403aa04203 100644 (file)
--- a/src/gromacs/fileio/tpxio.c
+++ b/src/gromacs/fileio/tpxio.c
@@ -43,7 +43,7 @@
 #include <string.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 #include "gmx_fatal.h"
 #include "macros.h"

diff --git a/src/gromacs/fileio/trajectory_writing.c b/src/gromacs/fileio/trajectory_writing.c
index 3cea7d40f9d97b99a8b446675c9769d60a36436d..699b482022db3bec73c038e07ff2bb36f5948d6b 100644 (file)
--- a/src/gromacs/fileio/trajectory_writing.c
+++ b/src/gromacs/fileio/trajectory_writing.c
@@ -37,7 +37,7 @@
 #endif
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "vec.h"
 #include "sim_util.h"

diff --git a/src/gromacs/fileio/trnio.c b/src/gromacs/fileio/trnio.c
index 23e76ea4a5c5ce3e2a8db2a74d9b4483b2755e49..91634ce09acf1d3074dec4a721fab2e2de0c54d4 100644 (file)
--- a/src/gromacs/fileio/trnio.c
+++ b/src/gromacs/fileio/trnio.c
@@ -2,8 +2,8 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * 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) 2001-2004, The GROMACS development team.
+ * 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 <string.h>
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "txtdump.h"
 #include "names.h"

diff --git a/src/gromacs/fileio/trxio.c b/src/gromacs/fileio/trxio.c
index fbc8f0fd88889ef72375e50c9634f893c70f849b..065bad2445ad1c9e40a5b3800a6300ebda72a3d3 100644 (file)
--- a/src/gromacs/fileio/trxio.c
+++ b/src/gromacs/fileio/trxio.c
@@ -48,7 +48,7 @@
 #ifdef GMX_USE_PLUGINS
 #include "vmdio.h"
 #endif
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 #include "gmxfio.h"
 #include "trxio.h"

diff --git a/src/gromacs/fileio/vmdio.c b/src/gromacs/fileio/vmdio.c
index 6d95d4f0631ef8a292fa50618d4f6aaf0eeb1ce9..3fd42702d2ac914a165b652f311adff74a5a00c2 100644 (file)
--- a/src/gromacs/fileio/vmdio.c
+++ b/src/gromacs/fileio/vmdio.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014, 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.
@@ -101,7 +101,7 @@
 #include <windows.h>
 #include <shlobj.h>
 #endif
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "futil.h"
 #include "vmdio.h"
 

diff --git a/src/gromacs/fileio/writeps.c b/src/gromacs/fileio/writeps.c
index 936667294f599748c96cbf18739b454f579f9cb7..dba6c5c15eb6dc57338160bd98eb033dc8bbf7fc 100644 (file)
--- a/src/gromacs/fileio/writeps.c
+++ b/src/gromacs/fileio/writeps.c
@@ -43,7 +43,7 @@
 #include <stdio.h>
 
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/fileio/xdrd.c b/src/gromacs/fileio/xdrd.c
index 1ce76a4a2c112e69cef85168db9b28bc906ccbfb..e48afd19bbe2acb1e05c82e3a6203aed8a4b88fe 100644 (file)
--- a/src/gromacs/fileio/xdrd.c
+++ b/src/gromacs/fileio/xdrd.c
@@ -2,8 +2,8 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * 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) 2001-2004, The GROMACS development team.
+ * 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 "typedefs.h"
 #include "xdrf.h"
 #include "gmx_fatal.h"
-#include "smalloc.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 d7a866597227015529072bb5c7cf59ba2ae29abb..da52ac6bc24cb12c78b909bc1f953158c3ef2ae7 100644 (file)
--- a/src/gromacs/fileio/xtcio.c
+++ b/src/gromacs/fileio/xtcio.c
@@ -2,8 +2,8 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * 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) 2001-2004, The GROMACS development team.
+ * 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 "xdrf.h"
 #include "gmxfio.h"
 #include "xtcio.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "futil.h"
 #include "gmx_fatal.h"

diff --git a/src/gromacs/gmxana/anadih.c b/src/gromacs/gmxana/anadih.c
index 8ae35c8ee16757aee2801d25434ebcedecbec3c6..72a027183ed0fadc664864326b4710a4c8eef1df 100644 (file)
--- a/src/gromacs/gmxana/anadih.c
+++ b/src/gromacs/gmxana/anadih.c
@@ -42,7 +42,7 @@
 #include <stdio.h>
 #include <string.h>
 #include "physics.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "txtdump.h"
 #include "bondf.h"

diff --git a/src/gromacs/gmxana/autocorr.c b/src/gromacs/gmxana/autocorr.c
index 4a92b63bcae3b1ab5e2b132decf8bb403bd89ae9..5aca984fc62c2d03de44757fb8fdc1ddba03964c 100644 (file)
--- a/src/gromacs/gmxana/autocorr.c
+++ b/src/gromacs/gmxana/autocorr.c
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "typedefs.h"
 #include "physics.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "xvgr.h"
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"

diff --git a/src/gromacs/gmxana/cmat.c b/src/gromacs/gmxana/cmat.c
index e8374fd547ec02d1e7af74bc2a9df64efffcc2f8..7eb7155eedb0134a0d6aedf22216045738260590 100644 (file)
--- a/src/gromacs/gmxana/cmat.c
+++ b/src/gromacs/gmxana/cmat.c
@@ -39,7 +39,7 @@
 #endif
 
 #include "cmat.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/correl.c b/src/gromacs/gmxana/correl.c
index a779cda9fee3bc61d4f89de4a112a1fd0ca08939..b4a2c9b47516863d2f2ec01e81730e26b9335c99 100644 (file)
--- a/src/gromacs/gmxana/correl.c
+++ b/src/gromacs/gmxana/correl.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, 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.
@@ -44,7 +44,7 @@
 #include <math.h>
 
 #include "gromacs/fft/fft.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "correl.h"
 
 #define SWAP(a, b) tempr = (a); (a) = (b); (b) = tempr

diff --git a/src/gromacs/gmxana/dens_filter.c b/src/gromacs/gmxana/dens_filter.c
index 29e52293cd03fb3500efddbfe50e6e7f0b43c969..585422bde3626d1b9389954ddc4129349bfd44b1 100644 (file)
--- a/src/gromacs/gmxana/dens_filter.c
+++ b/src/gromacs/gmxana/dens_filter.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2011,2013, by the GROMACS development team, led by
+ * Copyright (c) 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.
@@ -43,7 +43,7 @@
 #include <math.h>
 #include "typedefs.h"
 #include "dens_filter.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 
 #ifdef GMX_DOUBLE

diff --git a/src/gromacs/gmxana/dlist.c b/src/gromacs/gmxana/dlist.c
index 3901a7a694b2d29d115ff9e1931eb81911a2fc9c..11ee4eaea02e047789b1a88be26da662a4fa3cbc 100644 (file)
--- a/src/gromacs/gmxana/dlist.c
+++ b/src/gromacs/gmxana/dlist.c
@@ -41,7 +41,7 @@
 #include <stdlib.h>
 #include <string.h>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gstat.h"
 #include "gmx_fatal.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/edittop.c b/src/gromacs/gmxana/edittop.c
index 1efd40cad8d514eb94aca4286162e56304fd2858..973660bdc8654ad10f65c819274892ef285f93ec 100644 (file)
--- a/src/gromacs/gmxana/edittop.c
+++ b/src/gromacs/gmxana/edittop.c
@@ -38,7 +38,7 @@
 #include <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "symtab.h"
 

diff --git a/src/gromacs/gmxana/eigio.c b/src/gromacs/gmxana/eigio.c
index 75564f67a55f15b126859dd3e87b7dd2ad54e807..2d555dc274572e1d05f76e3bcb22e81e41b478b3 100644 (file)
--- a/src/gromacs/gmxana/eigio.c
+++ b/src/gromacs/gmxana/eigio.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.
@@ -38,7 +38,7 @@
 #include <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "eigio.h"
 #include "gromacs/fileio/trnio.h"

diff --git a/src/gromacs/gmxana/expfit.c b/src/gromacs/gmxana/expfit.c
index d566a5081832578621f6c5924a308bb398d39172..6c2d0caf9e7944954713c9e519652ad38458c8cf 100644 (file)
--- a/src/gromacs/gmxana/expfit.c
+++ b/src/gromacs/gmxana/expfit.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "xvgr.h"
 #include "gromacs/fileio/futil.h"
 #include "gstat.h"

diff --git a/src/gromacs/gmxana/fitahx.c b/src/gromacs/gmxana/fitahx.c
index 6b3789bd281fa1495aa43fa04d1d1454c93ee8c6..96b0376bed0418a5a56709a36c91201ad1438e87 100644 (file)
--- a/src/gromacs/gmxana/fitahx.c
+++ b/src/gromacs/gmxana/fitahx.c
@@ -40,7 +40,7 @@
 
 #include "fitahx.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "gromacs/math/do_fit.h"
 

diff --git a/src/gromacs/gmxana/geminate.c b/src/gromacs/gmxana/geminate.c
index f488a38ee76b1fddab30cd46077d5088ebe4b93b..c9be94d3749db4de9ea571938a436f384fb82666 100644 (file)
--- a/src/gromacs/gmxana/geminate.c
+++ b/src/gromacs/gmxana/geminate.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, 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.
@@ -49,7 +49,7 @@
 
 #include <math.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "geminate.h"
 

diff --git a/src/gromacs/gmxana/gmx_anadock.c b/src/gromacs/gmxana/gmx_anadock.c
index f55463217474114463f60aaeed3c1b13c6e63661..7a8209922f9d96442815d59f8b3942e0120d2e6a 100644 (file)
--- a/src/gromacs/gmxana/gmx_anadock.c
+++ b/src/gromacs/gmxana/gmx_anadock.c
@@ -44,7 +44,7 @@
 #include "copyrite.h"
 #include "gromacs/fileio/futil.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 #include "vec.h"
 #include "gromacs/statistics/statistics.h"

diff --git a/src/gromacs/gmxana/gmx_anaeig.c b/src/gromacs/gmxana/gmx_anaeig.c
index da221f6a90f3e53a04068ca878c7a0bbdf5146a7..f59b1130d807e8be4ecea627030dfd60ed670c1a 100644 (file)
--- a/src/gromacs/gmxana/gmx_anaeig.c
+++ b/src/gromacs/gmxana/gmx_anaeig.c
@@ -42,7 +42,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_analyze.c b/src/gromacs/gmxana/gmx_analyze.c
index 379574cc4fd641d923e15c37cefe3dec756feb17..494e19e3e0dca82b5429ccf6c1e89ebdb47c75f4 100644 (file)
--- a/src/gromacs/gmxana/gmx_analyze.c
+++ b/src/gromacs/gmxana/gmx_analyze.c
@@ -42,7 +42,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_angle.c b/src/gromacs/gmxana/gmx_angle.c
index 8d4d9111c67c3bfef3deba1f17d8e37f13d9d0a0..65bfad1cc58973aa04ece639ec9bfd9ca565ae55 100644 (file)
--- a/src/gromacs/gmxana/gmx_angle.c
+++ b/src/gromacs/gmxana/gmx_angle.c
@@ -43,7 +43,7 @@
 #include "sysstuff.h"
 #include "physics.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/commandline/pargs.h"
 #include "copyrite.h"

diff --git a/src/gromacs/gmxana/gmx_bar.c b/src/gromacs/gmxana/gmx_bar.c
index ea78714e94b609bc10e1508b92306d5ccf12925e..2a58d2210a41ab55f4281aaa5a268c3ec4788c82 100644 (file)
--- a/src/gromacs/gmxana/gmx_bar.c
+++ b/src/gromacs/gmxana/gmx_bar.c
@@ -44,7 +44,7 @@
 
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/commandline/pargs.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/gmx_bundle.c b/src/gromacs/gmxana/gmx_bundle.c
index 7ce5dc0edc6314ef8ce496702d32b0f33a58564f..7f839f74613050d66badabbf38b67cb3d6564e62 100644 (file)
--- a/src/gromacs/gmxana/gmx_bundle.c
+++ b/src/gromacs/gmxana/gmx_bundle.c
@@ -43,7 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/gmx_chi.c b/src/gromacs/gmxana/gmx_chi.c
index 62c14cbe6c83b55bff337a8202d653580ea098a9..9bee8377f24ecbbd44936ff34b3c8bef2c32b264 100644 (file)
--- a/src/gromacs/gmxana/gmx_chi.c
+++ b/src/gromacs/gmxana/gmx_chi.c
@@ -49,7 +49,7 @@
 #include "gromacs/math/utilities.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"
 #include <string.h>

diff --git a/src/gromacs/gmxana/gmx_cluster.c b/src/gromacs/gmxana/gmx_cluster.c
index 0929e4e73bf5aa1f01b93be5c6360d23eeda8e25..b3ae697dc76919df3d058294a65dae5deda2081e 100644 (file)
--- a/src/gromacs/gmxana/gmx_cluster.c
+++ b/src/gromacs/gmxana/gmx_cluster.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/gromacs/gmxana/gmx_clustsize.c b/src/gromacs/gmxana/gmx_clustsize.c
index 9091dc3d92861edb0ddfa959b5e692c4fd2e4a74..8a33f5e4523dc199819752b30853f110bed7ba0d 100644 (file)
--- a/src/gromacs/gmxana/gmx_clustsize.c
+++ b/src/gromacs/gmxana/gmx_clustsize.c
@@ -52,7 +52,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "calcgrid.h"
 #include "nrnb.h"
 #include "physics.h"

diff --git a/src/gromacs/gmxana/gmx_confrms.c b/src/gromacs/gmxana/gmx_confrms.c
index 075fe212bc02da1829377d920d8d93f681cbab65..4b9391fd1f6f8317cf888c12fbb32eeb8403c582 100644 (file)
--- a/src/gromacs/gmxana/gmx_confrms.c
+++ b/src/gromacs/gmxana/gmx_confrms.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "gromacs/fileio/filenm.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "typedefs.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_covar.c b/src/gromacs/gmxana/gmx_covar.c
index 4f2d1bbb0ec61017a0c25edc7461d4f6c96a6764..1b69798cc245fa3a4a122ec73f89605b18808072 100644 (file)
--- a/src/gromacs/gmxana/gmx_covar.c
+++ b/src/gromacs/gmxana/gmx_covar.c
@@ -49,7 +49,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_current.c b/src/gromacs/gmxana/gmx_current.c
index bd053807a9d061521aa1189eca765c8c33500f3b..030b4e7451d541a92cda40f7a4844891b7beea11 100644 (file)
--- a/src/gromacs/gmxana/gmx_current.c
+++ b/src/gromacs/gmxana/gmx_current.c
@@ -38,7 +38,7 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"

diff --git a/src/gromacs/gmxana/gmx_density.c b/src/gromacs/gmxana/gmx_density.c
index 33fac9beb00482e33b9132ba9cb9f4b8cfb6842f..f25d27ce603b9e783fd24c186d92893f97c068cc 100644 (file)
--- a/src/gromacs/gmxana/gmx_density.c
+++ b/src/gromacs/gmxana/gmx_density.c
@@ -44,7 +44,7 @@
 #include <string.h>
 #include "string2.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gstat.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_densmap.c b/src/gromacs/gmxana/gmx_densmap.c
index 0206280fa341b1ec74975d9ac9085184b47dfc34..7a885a72e79ae69c37cfe81ee480b601111cbb3a 100644 (file)
--- a/src/gromacs/gmxana/gmx_densmap.c
+++ b/src/gromacs/gmxana/gmx_densmap.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_densorder.cpp b/src/gromacs/gmxana/gmx_densorder.cpp
index b367dc0518125e792a2797f8a272b801eb70d147..8ceab74669a3dc1766e4bc303db882ef2c8e31b4 100644 (file)
--- a/src/gromacs/gmxana/gmx_densorder.cpp
+++ b/src/gromacs/gmxana/gmx_densorder.cpp
@@ -43,7 +43,7 @@
 #include "sysstuff.h"
 #include "string2.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gstat.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_dielectric.c b/src/gromacs/gmxana/gmx_dielectric.c
index 8071df4f469041c2cffe8ba216acf48f325bca29..13faf8be965e79c4c2a521c47af13d2ab36635d6 100644 (file)
--- a/src/gromacs/gmxana/gmx_dielectric.c
+++ b/src/gromacs/gmxana/gmx_dielectric.c
@@ -45,7 +45,7 @@
 #include "copyrite.h"
 #include "typedefs.h"
 #include "gstat.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "xvgr.h"
 #include "correl.h"

diff --git a/src/gromacs/gmxana/gmx_dipoles.cpp b/src/gromacs/gmxana/gmx_dipoles.cpp
index 0df6eaafeb49d9f41a1907006626410c8df13912..f1f6dc4aa8dcf0010257630978f924a62743c932 100644 (file)
--- a/src/gromacs/gmxana/gmx_dipoles.cpp
+++ b/src/gromacs/gmxana/gmx_dipoles.cpp
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "pbc.h"
 #include "bondf.h"

diff --git a/src/gromacs/gmxana/gmx_disre.c b/src/gromacs/gmxana/gmx_disre.c
index 24787db56a84bc7d054dd5b43d9c88de63aa766e..92a56928837fd5d60d6650a4be3c73e3c600da5d 100644 (file)
--- a/src/gromacs/gmxana/gmx_disre.c
+++ b/src/gromacs/gmxana/gmx_disre.c
@@ -46,7 +46,7 @@
 #include "xvgr.h"
 #include "vec.h"
 #include "gromacs/fileio/confio.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "disre.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_do_dssp.c b/src/gromacs/gmxana/gmx_do_dssp.c
index 77e143348029ee62715f134b4e2ddcf4ab57d8cf..b3b92fffd89055abdbc1bad039d6cd7f66e6e946 100644 (file)
--- a/src/gromacs/gmxana/gmx_do_dssp.c
+++ b/src/gromacs/gmxana/gmx_do_dssp.c
@@ -43,7 +43,7 @@
 #include "string2.h"
 #include "gromacs/fileio/strdb.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "mshift.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/pdbio.h"

diff --git a/src/gromacs/gmxana/gmx_dos.c b/src/gromacs/gmxana/gmx_dos.c
index f4f9a0932f6151602a7d57c8c001747abc521745..8d5438c3fb980ff29c877e8611eccd45b7229467 100644 (file)
--- a/src/gromacs/gmxana/gmx_dos.c
+++ b/src/gromacs/gmxana/gmx_dos.c
@@ -47,7 +47,7 @@
 #include "gromacs/math/utilities.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include <string.h>
 #include "sysstuff.h"

diff --git a/src/gromacs/gmxana/gmx_dyecoupl.c b/src/gromacs/gmxana/gmx_dyecoupl.c
index 9577dc895ab494dda0e3a262982af8905d1d3109..6542966e5434e03b4ac44edd0bcf17c68f0c43d5 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyecoupl.c
+++ b/src/gromacs/gmxana/gmx_dyecoupl.c
@@ -36,7 +36,7 @@
 #include "gromacs/fileio/filenm.h"
 #include "macros.h"
 #include "pbc.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "vec.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_dyndom.c b/src/gromacs/gmxana/gmx_dyndom.c
index e899ab122e817a5db74cd561a3f8478c5089551b..65de201a1b6284567932f364b18bb7a34d93fc47 100644 (file)
--- a/src/gromacs/gmxana/gmx_dyndom.c
+++ b/src/gromacs/gmxana/gmx_dyndom.c
@@ -40,7 +40,7 @@
 
 #include "gromacs/math/3dview.h"
 #include "gromacs/commandline/pargs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "index.h"
 #include "gromacs/fileio/confio.h"
 #include "gmx_fatal.h"

diff --git a/src/gromacs/gmxana/gmx_editconf.c b/src/gromacs/gmxana/gmx_editconf.c
index 729c94accc7ddc619455c0e452f78b8175148789..c0836aa442db80f24ceef005fb4d2af59d61e799 100644 (file)
--- a/src/gromacs/gmxana/gmx_editconf.c
+++ b/src/gromacs/gmxana/gmx_editconf.c
@@ -44,7 +44,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/confio.h"
 #include "symtab.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/strdb.h"

diff --git a/src/gromacs/gmxana/gmx_eneconv.c b/src/gromacs/gmxana/gmx_eneconv.c
index ced58e413372604523fb60fe4986243e6dac92ea..b0ad9f342eadd5d9d0658cb580608afe36ae8f55 100644 (file)
--- a/src/gromacs/gmxana/gmx_eneconv.c
+++ b/src/gromacs/gmxana/gmx_eneconv.c
@@ -41,7 +41,7 @@
 #include <math.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "disre.h"
 #include "names.h"

diff --git a/src/gromacs/gmxana/gmx_enemat.c b/src/gromacs/gmxana/gmx_enemat.c
index d2ff0eb9706d3f25511f799cc42abec7d7140b3b..572a804e4e8646e06b6e63a59a521b67f5d6ff3e 100644 (file)
--- a/src/gromacs/gmxana/gmx_enemat.c
+++ b/src/gromacs/gmxana/gmx_enemat.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "gmx_fatal.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/commandline/pargs.h"
 #include "names.h"

diff --git a/src/gromacs/gmxana/gmx_energy.c b/src/gromacs/gmxana/gmx_energy.c
index 23f88483588ff8ddbfb328ca59f772af0d8ddc3e..f5c6abfb18add16ec95ae0264076917f881e3e26 100644 (file)
--- a/src/gromacs/gmxana/gmx_energy.c
+++ b/src/gromacs/gmxana/gmx_energy.c
@@ -45,7 +45,7 @@
 #include "gmx_fatal.h"
 #include "vec.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/commandline/pargs.h"
 #include "names.h"

diff --git a/src/gromacs/gmxana/gmx_filter.c b/src/gromacs/gmxana/gmx_filter.c
index 414cd45d5d960d04416c4af6bb26f53479004f28..98c4c69a5d4aed4f688be5dfc6448bb0b69893af 100644 (file)
--- a/src/gromacs/gmxana/gmx_filter.c
+++ b/src/gromacs/gmxana/gmx_filter.c
@@ -43,7 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/gmx_genion.c b/src/gromacs/gmxana/gmx_genion.c
index 8cdb628b4ef76abed096d618b1bb0441fbf78228..0f1ea387cb87c07c58fc47fc3b9ce2195a62186d 100644 (file)
--- a/src/gromacs/gmxana/gmx_genion.c
+++ b/src/gromacs/gmxana/gmx_genion.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_genpr.c b/src/gromacs/gmxana/gmx_genpr.c
index bb56226e0b247b7e9cc7fa2133ecd0265e0e3a6e..6257f6a6742d7f6b081e5dc79d56268455531a77 100644 (file)
--- a/src/gromacs/gmxana/gmx_genpr.c
+++ b/src/gromacs/gmxana/gmx_genpr.c
@@ -42,7 +42,7 @@
 #include "sysstuff.h"
 #include "gromacs/commandline/pargs.h"
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/gmx_gyrate.c b/src/gromacs/gmxana/gmx_gyrate.c
index dca936d1c0bba759e763c64821ab32ba275508ce..42b54847719e7b3ede252a0f9a161550b5df71f1 100644 (file)
--- a/src/gromacs/gmxana/gmx_gyrate.c
+++ b/src/gromacs/gmxana/gmx_gyrate.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_h2order.c b/src/gromacs/gmxana/gmx_h2order.c
index 17a0bf5abcd1d50f0426c33abc208905d10ca437..f73644f4ff3422fc495e784bd4a8a2c03aec8f98 100644 (file)
--- a/src/gromacs/gmxana/gmx_h2order.c
+++ b/src/gromacs/gmxana/gmx_h2order.c
@@ -43,7 +43,7 @@
 #include "sysstuff.h"
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "princ.h"
 #include "rmpbc.h"

diff --git a/src/gromacs/gmxana/gmx_hbond.c b/src/gromacs/gmxana/gmx_hbond.c
index 15c8143e17fe8f59ad005f5f1b90560a3c6681a1..a5e87d1fef41a6e07132840cc69f137177eb1541 100644 (file)
--- a/src/gromacs/gmxana/gmx_hbond.c
+++ b/src/gromacs/gmxana/gmx_hbond.c
@@ -49,7 +49,7 @@
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "xvgr.h"
 #include "gstat.h"

diff --git a/src/gromacs/gmxana/gmx_helix.c b/src/gromacs/gmxana/gmx_helix.c
index a16875c31dbdbc84c64b2eab869b7b4a31037984..78a020004815d4aac163e3af608a195c1f9f4711 100644 (file)
--- a/src/gromacs/gmxana/gmx_helix.c
+++ b/src/gromacs/gmxana/gmx_helix.c
@@ -53,7 +53,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include <string.h>
 #include "sysstuff.h"

diff --git a/src/gromacs/gmxana/gmx_helixorient.c b/src/gromacs/gmxana/gmx_helixorient.c
index 4a46f6be37268bf5eec9f50b35f3b027214d3d41..981047233635dbfe8007f3317d04e3cc8b26a245 100644 (file)
--- a/src/gromacs/gmxana/gmx_helixorient.c
+++ b/src/gromacs/gmxana/gmx_helixorient.c
@@ -41,7 +41,7 @@
 #include <math.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "xvgr.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_hydorder.c b/src/gromacs/gmxana/gmx_hydorder.c
index 4ab042643423dce23a047181e40ecb878ca7f23b..a0e179ab6aa4a1fb68d37e7d0f81f402d655773c 100644 (file)
--- a/src/gromacs/gmxana/gmx_hydorder.c
+++ b/src/gromacs/gmxana/gmx_hydorder.c
@@ -43,7 +43,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "gromacs/commandline/pargs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gstat.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_kinetics.c b/src/gromacs/gmxana/gmx_kinetics.c
index aae29b9ca88b4646f0eab4287785a6665563cd21..2854ded64117b121f49ba1d993fe6d2859c10809 100644 (file)
--- a/src/gromacs/gmxana/gmx_kinetics.c
+++ b/src/gromacs/gmxana/gmx_kinetics.c
@@ -43,7 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_lie.c b/src/gromacs/gmxana/gmx_lie.c
index f838c87fbd694f382d2ebeee34426d62c6ac988b..a8279ef8f382b24d5b1aa5b24d0c86c7054edf7a 100644 (file)
--- a/src/gromacs/gmxana/gmx_lie.c
+++ b/src/gromacs/gmxana/gmx_lie.c
@@ -46,7 +46,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_make_edi.c b/src/gromacs/gmxana/gmx_make_edi.c
index 66a90d4f18d8505f2a98dcc86305381890be82ab..26f63c131743bfdc23925c653db122436770862d 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_edi.c
+++ b/src/gromacs/gmxana/gmx_make_edi.c
@@ -48,7 +48,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_make_ndx.c b/src/gromacs/gmxana/gmx_make_ndx.c
index 09ab0f4aae29d2cb99fd232ed658f6c08758734f..2250fc2b0dd772df9f79d4b69b66997a65cb1a3f 100644 (file)
--- a/src/gromacs/gmxana/gmx_make_ndx.c
+++ b/src/gromacs/gmxana/gmx_make_ndx.c
@@ -49,7 +49,7 @@
 #include "gromacs/fileio/confio.h"
 #include "typedefs.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "index.h"
 

diff --git a/src/gromacs/gmxana/gmx_mdmat.c b/src/gromacs/gmxana/gmx_mdmat.c
index 43a9f0d21d1e37d8d0bc3a4d7d24b12ce8002b94..09900e1ff4e0dafcc67534f0c320cf13f5593c42 100644 (file)
--- a/src/gromacs/gmxana/gmx_mdmat.c
+++ b/src/gromacs/gmxana/gmx_mdmat.c
@@ -49,7 +49,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/futil.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/matio.h"
 #include "xvgr.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/gmx_mindist.c b/src/gromacs/gmxana/gmx_mindist.c
index c7cec72b8642e6d64069d5a3284e1149fdfd2b0b..2ec58643ef35908043df659bd21c36d58905c1b3 100644 (file)
--- a/src/gromacs/gmxana/gmx_mindist.c
+++ b/src/gromacs/gmxana/gmx_mindist.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_mk_angndx.c b/src/gromacs/gmxana/gmx_mk_angndx.c
index 01aab35199ec4ea86a7e9ce2283271842710a678..9e684f300d7c22f945d9aebbe6c5d2b4b99a1e07 100644 (file)
--- a/src/gromacs/gmxana/gmx_mk_angndx.c
+++ b/src/gromacs/gmxana/gmx_mk_angndx.c
@@ -40,7 +40,7 @@
 
 #include <math.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "macros.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/gmx_morph.c b/src/gromacs/gmxana/gmx_morph.c
index 0df463205521c1d9e73cccca848ef6449b9843e5..38c4fa11439ee8deb11101120d57e5306eade527 100644 (file)
--- a/src/gromacs/gmxana/gmx_morph.c
+++ b/src/gromacs/gmxana/gmx_morph.c
@@ -39,7 +39,7 @@
 #endif
 
 #include "gromacs/commandline/pargs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/fileio/confio.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_msd.c b/src/gromacs/gmxana/gmx_msd.c
index 10f9dfbac69d373ece8be5e71eaed13055f5416f..26dcabd24ac9edc3de4d86b6c697f939aa5990a7 100644 (file)
--- a/src/gromacs/gmxana/gmx_msd.c
+++ b/src/gromacs/gmxana/gmx_msd.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/gmxana/gmx_nmeig.c b/src/gromacs/gmxana/gmx_nmeig.c
index 597377aec0383ecd0a5151d2caf692894fbe69b2..1d7d786c6dc1150be9215e2ea498d2326354fdfc 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmeig.c
+++ b/src/gromacs/gmxana/gmx_nmeig.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_nmens.c b/src/gromacs/gmxana/gmx_nmens.c
index de293f16d23c8b5b3624ead10eb1cc1c3865ad9b..e41ca0dd41494a0095702e31118ce9e64660c8fa 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmens.c
+++ b/src/gromacs/gmxana/gmx_nmens.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_nmtraj.c b/src/gromacs/gmxana/gmx_nmtraj.c
index 7995a9d6dbaed4df7a72a77271f0972475a1c233..10ec827609d8e295166074f68aa8fb1e33bdd460 100644 (file)
--- a/src/gromacs/gmxana/gmx_nmtraj.c
+++ b/src/gromacs/gmxana/gmx_nmtraj.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_order.c b/src/gromacs/gmxana/gmx_order.c
index dae0c8cfabd94067e3175e77a57f274b55b6d140..d1bb842d4a3b22cd1fb651d39edbfc3f73eadbb9 100644 (file)
--- a/src/gromacs/gmxana/gmx_order.c
+++ b/src/gromacs/gmxana/gmx_order.c
@@ -43,7 +43,7 @@
 
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gstat.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_pme_error.cpp b/src/gromacs/gmxana/gmx_pme_error.cpp
index 78df42f53bbd11276a67f5895c8bb9b775babdb2..7db07ee9109ddf3168a89837bd38ae4d8a25ec52 100644 (file)
--- a/src/gromacs/gmxana/gmx_pme_error.cpp
+++ b/src/gromacs/gmxana/gmx_pme_error.cpp
@@ -37,7 +37,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "copyrite.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/gromacs/gmxana/gmx_polystat.c b/src/gromacs/gmxana/gmx_polystat.c
index 91c75f676b08ffd12b9731f7ce7939c765c141e9..b9bbcffbe992cd415bc7d2b39cade2261340932f 100644 (file)
--- a/src/gromacs/gmxana/gmx_polystat.c
+++ b/src/gromacs/gmxana/gmx_polystat.c
@@ -43,7 +43,7 @@
 #include "sysstuff.h"
 #include "physics.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/commandline/pargs.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_potential.c b/src/gromacs/gmxana/gmx_potential.c
index 3ccb728231983ac22965afc4641ddc5e858eab22..4fc33a99e050b1cf3e4150823148ae58f36b6b83 100644 (file)
--- a/src/gromacs/gmxana/gmx_potential.c
+++ b/src/gromacs/gmxana/gmx_potential.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "princ.h"
 #include "rmpbc.h"

diff --git a/src/gromacs/gmxana/gmx_principal.c b/src/gromacs/gmxana/gmx_principal.c
index 7fe4c3c5b109f5456a367a1c1c9a0d0e723d9f2d..daa2425c231d8ddea331bf33dcb93994e8b6ba10 100644 (file)
--- a/src/gromacs/gmxana/gmx_principal.c
+++ b/src/gromacs/gmxana/gmx_principal.c
@@ -44,7 +44,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_rama.c b/src/gromacs/gmxana/gmx_rama.c
index 8e2a74d0c75bed6ac47eb95ba6d8494d3ce58547..b544a6a897dbb0878ddcbc914edab0a3f583fabd 100644 (file)
--- a/src/gromacs/gmxana/gmx_rama.c
+++ b/src/gromacs/gmxana/gmx_rama.c
@@ -42,7 +42,7 @@
 #include "sysstuff.h"
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_rdf.c b/src/gromacs/gmxana/gmx_rdf.c
index 83a5cd4af125c52cc553bfe69d56ad8352d9e5bf..579cd2728946ce6d86122245e22e912b7db9c963 100644 (file)
--- a/src/gromacs/gmxana/gmx_rdf.c
+++ b/src/gromacs/gmxana/gmx_rdf.c
@@ -53,7 +53,7 @@
 #include "gromacs/fileio/trxio.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "calcgrid.h"
 #include "nrnb.h"
 #include "coulomb.h"

diff --git a/src/gromacs/gmxana/gmx_rms.c b/src/gromacs/gmxana/gmx_rms.c
index 217bb3e33e7c7f1368f9c4f1a76fda1680404fdb..13aeb6c807a88773a68b382568b3ee7dbaf598c3 100644 (file)
--- a/src/gromacs/gmxana/gmx_rms.c
+++ b/src/gromacs/gmxana/gmx_rms.c
@@ -38,7 +38,7 @@
 #include <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include <math.h>
 #include "macros.h"
 #include "typedefs.h"

diff --git a/src/gromacs/gmxana/gmx_rmsdist.c b/src/gromacs/gmxana/gmx_rmsdist.c
index 117ec105fbf05c3a9767a250e57a11dce658a57d..a28f241f45b269f66febead85eca4fa465c415e0 100644 (file)
--- a/src/gromacs/gmxana/gmx_rmsdist.c
+++ b/src/gromacs/gmxana/gmx_rmsdist.c
@@ -41,7 +41,7 @@
 #include <math.h>
 
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "names.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxana/gmx_rmsf.c b/src/gromacs/gmxana/gmx_rmsf.c
index 30d2d061ff56ce538eafe8b58bba8dc167d8e15b..399de70d06546e577162833bb3644a823614b3f6 100644 (file)
--- a/src/gromacs/gmxana/gmx_rmsf.c
+++ b/src/gromacs/gmxana/gmx_rmsf.c
@@ -38,7 +38,7 @@
 #include <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include <math.h>
 #include "macros.h"
 #include "typedefs.h"

diff --git a/src/gromacs/gmxana/gmx_rotacf.c b/src/gromacs/gmxana/gmx_rotacf.c
index 18c9972e93a81ace01648b77693ed48bc910dcad..b540f38d2c3dd96fb9387c4de40b4e5256c5b379 100644 (file)
--- a/src/gromacs/gmxana/gmx_rotacf.c
+++ b/src/gromacs/gmxana/gmx_rotacf.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.
@@ -43,7 +43,7 @@
 #include "sysstuff.h"
 #include "physics.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/commandline/pargs.h"
 #include "index.h"

diff --git a/src/gromacs/gmxana/gmx_rotmat.c b/src/gromacs/gmxana/gmx_rotmat.c
index c35a066dddff3e938214174e4ab0f2314e35ada2..891a3bf9f5e8d4760c35998385062c3e1491e851 100644 (file)
--- a/src/gromacs/gmxana/gmx_rotmat.c
+++ b/src/gromacs/gmxana/gmx_rotmat.c
@@ -42,7 +42,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_saltbr.c b/src/gromacs/gmxana/gmx_saltbr.c
index a9cd92383da3ad7d6ef9af851e32b14f9966c6b9..7c262e74cb34f228f966a95d13da74021d51a044 100644 (file)
--- a/src/gromacs/gmxana/gmx_saltbr.c
+++ b/src/gromacs/gmxana/gmx_saltbr.c
@@ -49,7 +49,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/futil.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 #include "xvgr.h"
 #include "gmx_ana.h"

diff --git a/src/gromacs/gmxana/gmx_sans.c b/src/gromacs/gmxana/gmx_sans.c
index 9ad63094b3477afc88652f54c8745deb7864dea3..b57e9f1a2e282f3ee3a49d764679bf58753cde2e 100644 (file)
--- a/src/gromacs/gmxana/gmx_sans.c
+++ b/src/gromacs/gmxana/gmx_sans.c
@@ -37,7 +37,7 @@
 #include <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxana/gmx_saxs.c b/src/gromacs/gmxana/gmx_saxs.c
index 075020ece069196e276147e551ff4b7ed052ba6d..5f35524e1c8439ea7e656c480639f3a17564e927 100644 (file)
--- a/src/gromacs/gmxana/gmx_saxs.c
+++ b/src/gromacs/gmxana/gmx_saxs.c
@@ -53,7 +53,7 @@
 #include "gromacs/fileio/tpxio.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "calcgrid.h"
 #include "nrnb.h"
 #include "coulomb.h"

diff --git a/src/gromacs/gmxana/gmx_sham.c b/src/gromacs/gmxana/gmx_sham.c
index aceaff417449031443c5d37cc511845b059f860b..9d670c4897bb8706eb4941b82417df63a7f84a7a 100644 (file)
--- a/src/gromacs/gmxana/gmx_sham.c
+++ b/src/gromacs/gmxana/gmx_sham.c
@@ -42,7 +42,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxana/gmx_sigeps.c b/src/gromacs/gmxana/gmx_sigeps.c
index 8a2b36050a18d9525182ad33deca152d0b1e1d3e..458e1271d934d96e3458e3cc723ee41480d3c646 100644 (file)
--- a/src/gromacs/gmxana/gmx_sigeps.c
+++ b/src/gromacs/gmxana/gmx_sigeps.c
@@ -46,7 +46,7 @@
 #include "xvgr.h"
 #include "gromacs/fileio/pdbio.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "pbc.h"
 #include "physics.h"

diff --git a/src/gromacs/gmxana/gmx_sorient.c b/src/gromacs/gmxana/gmx_sorient.c
index d9675030991b602739ef4fbfa055151169fa8e54..2ecd08ca92440813cf27d11e8caac36ad3b27f94 100644 (file)
--- a/src/gromacs/gmxana/gmx_sorient.c
+++ b/src/gromacs/gmxana/gmx_sorient.c
@@ -40,7 +40,7 @@
 
 #include "macros.h"
 #include "gromacs/commandline/pargs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gstat.h"
 #include "vec.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_spatial.c b/src/gromacs/gmxana/gmx_spatial.c
index 93354fa7d3ffdd91966ab9961fd38797e231871e..32d2fefc36a505d920248932576fae3736b94d4d 100644 (file)
--- a/src/gromacs/gmxana/gmx_spatial.c
+++ b/src/gromacs/gmxana/gmx_spatial.c
@@ -40,7 +40,7 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"

diff --git a/src/gromacs/gmxana/gmx_spol.c b/src/gromacs/gmxana/gmx_spol.c
index 5c5eb710a12673a4d8eb47e6f3064fdab7561150..3f1ab9d5b823405def2af9d1a05cf8529c7d71b0 100644 (file)
--- a/src/gromacs/gmxana/gmx_spol.c
+++ b/src/gromacs/gmxana/gmx_spol.c
@@ -40,7 +40,7 @@
 
 #include "macros.h"
 #include "gromacs/commandline/pargs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gstat.h"
 #include "vec.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_tcaf.c b/src/gromacs/gmxana/gmx_tcaf.c
index 6177bba7d128e9655beec1565dd8a5182b27df1e..15738d8c4fbce2b48742d28e6df2fcd8844ffa42 100644 (file)
--- a/src/gromacs/gmxana/gmx_tcaf.c
+++ b/src/gromacs/gmxana/gmx_tcaf.c
@@ -48,7 +48,7 @@
 #include "gromacs/math/utilities.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include <string.h>
 #include "sysstuff.h"

diff --git a/src/gromacs/gmxana/gmx_traj.c b/src/gromacs/gmxana/gmx_traj.c
index 63628b3c8cc0f4b01f5f887e70f13eefcc88c3fa..a2de81721e2e89caeeb404df523f35736d7d45db 100644 (file)
--- a/src/gromacs/gmxana/gmx_traj.c
+++ b/src/gromacs/gmxana/gmx_traj.c
@@ -43,7 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_trjcat.c b/src/gromacs/gmxana/gmx_trjcat.c
index f6d5c085dec9afee409017eb39c5270c86e7c0ca..8ce1deea3d5ce3bd14ca282556b0b19e70ce61c7 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjcat.c
+++ b/src/gromacs/gmxana/gmx_trjcat.c
@@ -42,7 +42,7 @@
 #include <math.h>
 #include "macros.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/gromacs/gmxana/gmx_trjconv.c b/src/gromacs/gmxana/gmx_trjconv.c
index a6ec21d9421f1e751b8e9dc28a8be577e4cf0966..8ddc50c37ba57214541d787f58a06e8daec98df5 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjconv.c
+++ b/src/gromacs/gmxana/gmx_trjconv.c
@@ -44,7 +44,7 @@
 #include "copyrite.h"
 #include "macros.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/gromacs/gmxana/gmx_trjorder.c b/src/gromacs/gmxana/gmx_trjorder.c
index b16b4fc01cc86554cc17842ffc7af281620e2df6..d2d4d47039afdc012c9a144857e957c397743f78 100644 (file)
--- a/src/gromacs/gmxana/gmx_trjorder.c
+++ b/src/gromacs/gmxana/gmx_trjorder.c
@@ -43,7 +43,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxana/gmx_tune_pme.c b/src/gromacs/gmxana/gmx_tune_pme.c
index ac6a6e779e59fa23ec01b3230269bde98b6d8dc3..631c94c8269cdd30cfe421eaa21e5af30cf8c405 100644 (file)
--- a/src/gromacs/gmxana/gmx_tune_pme.c
+++ b/src/gromacs/gmxana/gmx_tune_pme.c
@@ -47,7 +47,7 @@
 #include "gromacs/commandline/pargs.h"
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "copyrite.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/gromacs/gmxana/gmx_vanhove.c b/src/gromacs/gmxana/gmx_vanhove.c
index 04a93a50cc60d35bc76fcfc2fe9faf407af3deaf..e3f14fa84fa94deca5bf347e6039391ae87c9dc7 100644 (file)
--- a/src/gromacs/gmxana/gmx_vanhove.c
+++ b/src/gromacs/gmxana/gmx_vanhove.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/gmxana/gmx_velacc.c b/src/gromacs/gmxana/gmx_velacc.c
index 69ffd7b372b742410f06126dd4e08b2029d9a0b5..77fe30fc3a0dad877bacc0708b4d3c7067f21b5b 100644 (file)
--- a/src/gromacs/gmxana/gmx_velacc.c
+++ b/src/gromacs/gmxana/gmx_velacc.c
@@ -48,7 +48,7 @@
 #include "gromacs/math/utilities.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include <string.h>
 #include "sysstuff.h"

diff --git a/src/gromacs/gmxana/gmx_wham.cpp b/src/gromacs/gmxana/gmx_wham.cpp
index 57c01be040f5cac727f8b4d71142d1f8bc7dc5de..3c31096fb590fefb1ed376cf533d5467b1bb3857 100644 (file)
--- a/src/gromacs/gmxana/gmx_wham.cpp
+++ b/src/gromacs/gmxana/gmx_wham.cpp
@@ -54,7 +54,7 @@
 
 #include "gromacs/commandline/pargs.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "copyrite.h"
 #include "gromacs/fileio/tpxio.h"

diff --git a/src/gromacs/gmxana/gmx_wheel.c b/src/gromacs/gmxana/gmx_wheel.c
index cdfb0332e28b25752e16874c2882a8622ab3f06d..d33ebf1abb97f20850c8e1fe4ab65deb113729f3 100644 (file)
--- a/src/gromacs/gmxana/gmx_wheel.c
+++ b/src/gromacs/gmxana/gmx_wheel.c
@@ -46,7 +46,7 @@
 #include "sysstuff.h"
 #include "physics.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "xvgr.h"

diff --git a/src/gromacs/gmxana/gmx_xpm2ps.c b/src/gromacs/gmxana/gmx_xpm2ps.c
index 9740dee44db908789436181ed43bac3255133020..064e667c3c4806806378c1011f6440aae18874f3 100644 (file)
--- a/src/gromacs/gmxana/gmx_xpm2ps.c
+++ b/src/gromacs/gmxana/gmx_xpm2ps.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "macros.h"
 #include "gmx_fatal.h"
-#include "smalloc.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 b9e80ba90a5c0a9f5edb6148053be0fb12f58939..99d636ede1bb0c8820de57be49ffc0c1d8178ba3 100644 (file)
--- a/src/gromacs/gmxana/hxprops.c
+++ b/src/gromacs/gmxana/hxprops.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.
@@ -47,7 +47,7 @@
 #include "vec.h"
 #include "index.h"
 #include "hxprops.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "bondf.h"
 
 real ellipticity(int nres, t_bb bb[])

diff --git a/src/gromacs/gmxana/nrama.c b/src/gromacs/gmxana/nrama.c
index 1693702de4ab3dfe20bd2b56925b03c6b40ee6e5..e20501f7df862fff4bd2ab67b033f9be9cadede3 100644 (file)
--- a/src/gromacs/gmxana/nrama.c
+++ b/src/gromacs/gmxana/nrama.c
@@ -41,7 +41,7 @@
 #include "nrama.h"
 #include <math.h>
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "bondf.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/nsfactor.c b/src/gromacs/gmxana/nsfactor.c
index c1efd9d807ec12cb9a4a1e43b075cf4712ef82c7..dddd87b22632c6b67dbb1f30a38ab52f25198e9e 100644 (file)
--- a/src/gromacs/gmxana/nsfactor.c
+++ b/src/gromacs/gmxana/nsfactor.c
@@ -39,7 +39,7 @@
 #include <string.h>
 
 #include "gromacs/random/random.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "vec.h"
 #include "nsfactor.h"

diff --git a/src/gromacs/gmxana/powerspect.c b/src/gromacs/gmxana/powerspect.c
index 277d33fa020783b84e3b0d5ecea3c433ed9575b2..06e7d94caec5060d51609446ea6d4de20e574489 100644 (file)
--- a/src/gromacs/gmxana/powerspect.c
+++ b/src/gromacs/gmxana/powerspect.c
@@ -37,7 +37,7 @@
 #include <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fft/fft.h"
 #include "gmx_fatal.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxana/pp2shift.c b/src/gromacs/gmxana/pp2shift.c
index a5284e1569a792f174a3fe5171147f92e3f6ac7f..85e29ac4eb8f10c3d4c00e5f63ba1b0d9e6afc7c 100644 (file)
--- a/src/gromacs/gmxana/pp2shift.c
+++ b/src/gromacs/gmxana/pp2shift.c
@@ -44,7 +44,7 @@
 #include "gromacs/fileio/futil.h"
 #include "macros.h"
 #include "physics.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gstat.h"
 #include "gromacs/fileio/matio.h"
 #include "copyrite.h"

diff --git a/src/gromacs/gmxlib/atomprop.c b/src/gromacs/gmxlib/atomprop.c
index 60e3bdb728546dbf019523f88fabdca39af599b9..7d8d01c7c95c71cc6b6615317019cf67f937c05e 100644 (file)
--- a/src/gromacs/gmxlib/atomprop.c
+++ b/src/gromacs/gmxlib/atomprop.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 #include "gmx_fatal.h"
 #include "atomprop.h"

diff --git a/src/gromacs/gmxlib/bondfree.c b/src/gromacs/gmxlib/bondfree.c
index ca0110552e2309426f289c650eea3c0bf2d9e6b6..6d696e93f7ade05a3c9d51543dcef58109ea999e 100644 (file)
--- a/src/gromacs/gmxlib/bondfree.c
+++ b/src/gromacs/gmxlib/bondfree.c
@@ -45,7 +45,7 @@
 #include "gromacs/math/utilities.h"
 #include "txtdump.h"
 #include "bondf.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 #include "ns.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxlib/calcgrid.c b/src/gromacs/gmxlib/calcgrid.c
index 15ee221fbbcc1c9cef9c688e769a8e7e18464393..3d1e70d909ef0bb0932bbd80df9cd12976c46120 100644 (file)
--- a/src/gromacs/gmxlib/calcgrid.c
+++ b/src/gromacs/gmxlib/calcgrid.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.
@@ -41,7 +41,7 @@
 #include <math.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "calcgrid.h"
 

diff --git a/src/gromacs/gmxlib/chargegroup.c b/src/gromacs/gmxlib/chargegroup.c
index 6265c7836d5ecbd84bab086ab2bdd6cb1f439102..93df8e1a1d9587037fa45c8f4ed4f10f8f3ac9df 100644 (file)
--- a/src/gromacs/gmxlib/chargegroup.c
+++ b/src/gromacs/gmxlib/chargegroup.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.
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "vec.h"
 #include "pbc.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "chargegroup.h"
 

diff --git a/src/gromacs/gmxlib/checkpoint.c b/src/gromacs/gmxlib/checkpoint.c
index 9582494722b24bee9f011d8390869280c64f148b..35ef97686392340102fc751860cb693048beacbf 100644 (file)
--- a/src/gromacs/gmxlib/checkpoint.c
+++ b/src/gromacs/gmxlib/checkpoint.c
@@ -62,7 +62,7 @@
 #include "names.h"
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "txtdump.h"
 #include "vec.h"
 #include "network.h"

diff --git a/src/gromacs/gmxlib/copyrite.cpp b/src/gromacs/gmxlib/copyrite.cpp
index e3f3033ca1ecafba3ef08e2565730ec645dfd37e..c7f57f68cd32ecfdfaa2d7eb2fe0307a5548a89a 100644 (file)
--- a/src/gromacs/gmxlib/copyrite.cpp
+++ b/src/gromacs/gmxlib/copyrite.cpp
@@ -58,18 +58,18 @@
 /* This file is completely threadsafe - keep it that way! */
 
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/random/random.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/string2.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/fft/fft.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/strdb.h"
+#include "gromacs/random/random.h"
 #include "gromacs/utility/baseversion.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "buildinfo.h"
 

diff --git a/src/gromacs/gmxlib/cuda_tools/cudautils.cu b/src/gromacs/gmxlib/cuda_tools/cudautils.cu
index e8f32b2332b685f763bfd8f80e81d7289e495934..7682148bae5ed275361c21896bc2d1971addf999 100644 (file)
--- a/src/gromacs/gmxlib/cuda_tools/cudautils.cu
+++ b/src/gromacs/gmxlib/cuda_tools/cudautils.cu
@@ -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.
@@ -36,7 +36,7 @@
 #include <stdlib.h>
 
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "cudautils.cuh"
 

diff --git a/src/gromacs/gmxlib/disre.c b/src/gromacs/gmxlib/disre.c
index b792c2240a5e1a8657983622bcb0df4a22a17320..061521d9f218c6ed4c6766fcf01866ec7001ec42 100644 (file)
--- a/src/gromacs/gmxlib/disre.c
+++ b/src/gromacs/gmxlib/disre.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxlib/ewald_util.c b/src/gromacs/gmxlib/ewald_util.c
index 8b811323080fd1f3796852b06839faf1d6a91063..b6af0d607b11b4d92bb2851d7ddc6183be666d0f 100644 (file)
--- a/src/gromacs/gmxlib/ewald_util.c
+++ b/src/gromacs/gmxlib/ewald_util.c
@@ -45,7 +45,7 @@
 #include "types/commrec.h"
 #include "vec.h"
 #include "coulomb.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "txtdump.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxlib/gmx_detect_hardware.c b/src/gromacs/gmxlib/gmx_detect_hardware.c
index 986f9ccb05bb5b77f8181f66a3951624d7b3b839..f262dcc584526d0ae034ad9fc12db2cfec4955ba 100644 (file)
--- a/src/gromacs/gmxlib/gmx_detect_hardware.c
+++ b/src/gromacs/gmxlib/gmx_detect_hardware.c
@@ -52,7 +52,7 @@
 #include "gmx_fatal_collective.h"
 #include "md_logging.h"
 #include "gmx_cpuid.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gpu_utils.h"
 #include "copyrite.h"
 #include "gmx_detect_hardware.h"

diff --git a/src/gromacs/gmxlib/gmx_fatal.c b/src/gromacs/gmxlib/gmx_fatal.c
index c7bab505dbd2d128b1e708b92d3a85c3241f1dd0..4c580b6bb273fec2fcf57846fc6a60aeab39e85d 100644 (file)
--- a/src/gromacs/gmxlib/gmx_fatal.c
+++ b/src/gromacs/gmxlib/gmx_fatal.c
@@ -52,7 +52,7 @@
 #include "copyrite.h"
 #include "macros.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "gromacs/fileio/futil.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
index 828ad082e4f95c1d8bd88a8c4a2da40e8ad23988..d626214d5cfee2055eb4ed53757c4b38629b4558 100644 (file)
--- a/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
+++ b/src/gromacs/gmxlib/gpu_utils/gpu_utils.cu
@@ -37,7 +37,7 @@
 #include <stdlib.h>
 #include <assert.h>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/hw_info.h"
 
 #include "gpu_utils.h"

diff --git a/src/gromacs/gmxlib/index.c b/src/gromacs/gmxlib/index.c
index b74db0c59543d912d616d9ca8a0578a3cc1cb38e..fc80ac92bc5afba35addf29f9fe38b53cd0248c9 100644 (file)
--- a/src/gromacs/gmxlib/index.c
+++ b/src/gromacs/gmxlib/index.c
@@ -47,7 +47,7 @@
 #include "string2.h"
 #include "main.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "invblock.h"
 #include "macros.h"
 #include "index.h"

diff --git a/src/gromacs/gmxlib/invblock.c b/src/gromacs/gmxlib/invblock.c
index 646cf70311ed64647438dca68eea83e4dfd41176..235a1f6c2a4768c9b35fefb5ead9e16bf908e1ea 100644 (file)
--- a/src/gromacs/gmxlib/invblock.c
+++ b/src/gromacs/gmxlib/invblock.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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 @@
 #endif
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "invblock.h"
 #include "gmx_fatal.h"
 

diff --git a/src/gromacs/gmxlib/main.cpp b/src/gromacs/gmxlib/main.cpp
index 4b4d75855e2afa4cc000f63944b757f8a4158430..862dbdcae643b93c5be154997ea3f70470f750d3 100644 (file)
--- a/src/gromacs/gmxlib/main.cpp
+++ b/src/gromacs/gmxlib/main.cpp
@@ -48,7 +48,7 @@
 #include <sys/time.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "gmx_fatal.h"
 #include "network.h"

diff --git a/src/gromacs/gmxlib/mshift.c b/src/gromacs/gmxlib/mshift.c
index 0b688298b2af178f46cbab22ed999922c7676f53..6b6ad831a216389af6ef77e2d2aa5557b398382f 100644 (file)
--- a/src/gromacs/gmxlib/mshift.c
+++ b/src/gromacs/gmxlib/mshift.c
@@ -39,7 +39,7 @@
 #endif
 
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "macros.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxlib/mtop_util.c b/src/gromacs/gmxlib/mtop_util.c
index a2199582a14484eb5033ce404e4e5cb4ea376d55..83c615634ea71e672df443ae5ac7fb5d144d4c93 100644 (file)
--- a/src/gromacs/gmxlib/mtop_util.c
+++ b/src/gromacs/gmxlib/mtop_util.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2008,2009,2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2008,2009,2010,2012,2013,2014, 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.
@@ -38,7 +38,7 @@
 #endif
 
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "mtop_util.h"
 #include "topsort.h"

diff --git a/src/gromacs/gmxlib/mvdata.c b/src/gromacs/gmxlib/mvdata.c
index 7fad00743d224516026e9fc689fadadeb2a44195..62b88991556b53c4ed3f7f836941cec56736f78b 100644 (file)
--- a/src/gromacs/gmxlib/mvdata.c
+++ b/src/gromacs/gmxlib/mvdata.c
@@ -46,7 +46,7 @@
 #include "mvdata.h"
 #include "types/commrec.h"
 #include "network.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "symtab.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxlib/network.c b/src/gromacs/gmxlib/network.c
index f850de4e92e587e14917153f5c24ccb44f288eb8..06780b90c72b71dcae40a6bb2663ff17bdbe7a06 100644 (file)
--- a/src/gromacs/gmxlib/network.c
+++ b/src/gromacs/gmxlib/network.c
@@ -41,7 +41,7 @@
 #include <string.h>
 #include "gmx_fatal.h"
 #include "main.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "network.h"
 #include "copyrite.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel.c b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
index 91906ea13a9fffe8561d6f03b2153392c94ed6d7..f9e5cab32cbcf8a4d55298c36d9c7dd78676d8e6 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel.c
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * 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.
@@ -41,7 +41,7 @@
 #include <string.h>
 
 #include "nb_kernel.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 #include "gmx_fatal.h"
 

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
index 2ab4d928d143df5fa013f77d7d15bdde7a79cee9..6eae3017090abfbc46c8f0f1dc966027f8d88c3d 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsall.c
@@ -43,7 +43,7 @@
 #include "types/simple.h"
 
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "nb_kernel_allvsall.h"
 #include "nrnb.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
index 6101ae0523eb609db4f6522078e85c741fa8aee4..532702ebb8768e22739dd1b3cb478506955370b5 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
+++ b/src/gromacs/gmxlib/nonbonded/nb_kernel_c/nb_kernel_allvsallgb.c
@@ -43,7 +43,7 @@
 #include "types/simple.h"
 
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "nb_kernel_allvsallgb.h"
 #include "nrnb.h"

diff --git a/src/gromacs/gmxlib/nonbonded/nonbonded.c b/src/gromacs/gmxlib/nonbonded/nonbonded.c
index d85fecec8bfb6eb4452d9d0a3790f521c2ad80c3..10d5dafa7be8751785603dbee66ae6d4d3c71640 100644 (file)
--- a/src/gromacs/gmxlib/nonbonded/nonbonded.c
+++ b/src/gromacs/gmxlib/nonbonded/nonbonded.c
@@ -45,7 +45,7 @@
 
 #include "typedefs.h"
 #include "txtdump.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "ns.h"
 #include "vec.h"
 #include "gromacs/math/utilities.h"
@@ -60,7 +60,6 @@
 #include "force.h"
 #include "bondf.h"
 #include "nrnb.h"
-#include "smalloc.h"
 #include "nonbonded.h"
 #include "gromacs/simd/simd.h"
 

diff --git a/src/gromacs/gmxlib/nrnb.c b/src/gromacs/gmxlib/nrnb.c
index 9fd76c22d7d4c5fc7a8d142c97731501872f9b25..1d0143866ded176f1972c1a9131d2bc799c44ea5 100644 (file)
--- a/src/gromacs/gmxlib/nrnb.c
+++ b/src/gromacs/gmxlib/nrnb.c
@@ -46,7 +46,7 @@
 #include "macros.h"
 #include "nrnb.h"
 #include "main.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 typedef struct {
     const char *name;

diff --git a/src/gromacs/gmxlib/oenv.cpp b/src/gromacs/gmxlib/oenv.cpp
index d38a037800ec3a8fe7c2c2b21a7d8708815bbbc6..ebe3d156da1961303144cfc9460121b2a3cef3d4 100644 (file)
--- a/src/gromacs/gmxlib/oenv.cpp
+++ b/src/gromacs/gmxlib/oenv.cpp
@@ -36,7 +36,7 @@
  */
 #include "oenv.h"
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "gromacs/utility/programcontext.h"
 #include "gromacs/utility/exceptions.h"

diff --git a/src/gromacs/gmxlib/orires.c b/src/gromacs/gmxlib/orires.c
index 583cd409b9663c4a45db2091d33e66e496153f25..11c970949fadd0e3e44e9b986e61ff8fe4dd90d4 100644 (file)
--- a/src/gromacs/gmxlib/orires.c
+++ b/src/gromacs/gmxlib/orires.c
@@ -39,7 +39,7 @@
 #endif
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "types/commrec.h"
 #include "network.h"

diff --git a/src/gromacs/gmxlib/pbc.c b/src/gromacs/gmxlib/pbc.c
index 514c680a73a8f8ac4fe18adeef77ab50cbcdb563..c96eba4f063ba40dcfd3ca446584b0442838406b 100644 (file)
--- a/src/gromacs/gmxlib/pbc.c
+++ b/src/gromacs/gmxlib/pbc.c
@@ -48,7 +48,7 @@
 #include "gromacs/math/utilities.h"
 #include "main.h"
 #include "pbc.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "txtdump.h"
 #include "gmx_fatal.h"
 #include "names.h"

diff --git a/src/gromacs/gmxlib/princ.c b/src/gromacs/gmxlib/princ.c
index 73ca01221d68c82301c180fb0f90729f6cdc6d73..19cc04844d313ee73cc81564c0019ea9419425d3 100644 (file)
--- a/src/gromacs/gmxlib/princ.c
+++ b/src/gromacs/gmxlib/princ.c
@@ -41,7 +41,7 @@
 
 #include "typedefs.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "txtdump.h"
 #include "princ.h"
 

diff --git a/src/gromacs/gmxlib/rbin.c b/src/gromacs/gmxlib/rbin.c
index 047bb9f4d4b6c0a348d77f4c87438833dee37cba..35435d663207d19a2702e09624e9be9be03c8d76 100644 (file)
--- a/src/gromacs/gmxlib/rbin.c
+++ b/src/gromacs/gmxlib/rbin.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2010, by the GROMACS development team, led by
+ * Copyright (c) 2010,2014, 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 "main.h"
 #include "network.h"
 #include "rbin.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 t_bin *mk_bin(void)
 {

diff --git a/src/gromacs/gmxlib/readinp.c b/src/gromacs/gmxlib/readinp.c
index cd665652b46af74e6b86a895ab0cd93d140622d0..80b63e0bb9f05387a619e40a9e964bb86eb529fc 100644 (file)
--- a/src/gromacs/gmxlib/readinp.c
+++ b/src/gromacs/gmxlib/readinp.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "string2.h"
 #include "gromacs/fileio/futil.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "readinp.h"
 #include "macros.h"
 #include "gromacs/fileio/gmxfio.h"

diff --git a/src/gromacs/gmxlib/restcbt.c b/src/gromacs/gmxlib/restcbt.c
index 8e38db9dc160d0c706926659b53262c447e6a0a7..919d5ea42614216625a04a54d05da2eec4e5c7f0 100644 (file)
--- a/src/gromacs/gmxlib/restcbt.c
+++ b/src/gromacs/gmxlib/restcbt.c
@@ -42,7 +42,7 @@
 #include "gromacs/math/utilities.h"
 #include "txtdump.h"
 #include "bondf.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 #include "ns.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxlib/rmpbc.c b/src/gromacs/gmxlib/rmpbc.c
index aeb3d7ddebbff43582e6aaba29d15fa71fce9f88..7f9c06ab17663a526006ee35ac3ac4a3f4409e41 100644 (file)
--- a/src/gromacs/gmxlib/rmpbc.c
+++ b/src/gromacs/gmxlib/rmpbc.c
@@ -40,7 +40,7 @@
 
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "mshift.h"
 #include "pbc.h"
 #include "rmpbc.h"

diff --git a/src/gromacs/gmxlib/sfactor.c b/src/gromacs/gmxlib/sfactor.c
index ff684f2716e753fdbd0216045574990674d83e28..1684a5490b16f91b920c60cba5c0e5fa688bee5b 100644 (file)
--- a/src/gromacs/gmxlib/sfactor.c
+++ b/src/gromacs/gmxlib/sfactor.c
@@ -39,7 +39,7 @@
 #endif
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "gromacs/math/utilities.h"
 #include "gmx_fatal.h"

diff --git a/src/gromacs/gmxlib/splitter.c b/src/gromacs/gmxlib/splitter.c
index 2abd2656e060f5a42cc98b097c58fd66c1a172a6..1d98dc2c8d2319c5a8b8a570b4c77305bfd3df06 100644 (file)
--- a/src/gromacs/gmxlib/splitter.c
+++ b/src/gromacs/gmxlib/splitter.c
@@ -43,7 +43,7 @@
 #include <assert.h>
 #include <string.h>
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "mshift.h"
 #include "gmx_fatal.h"
 

diff --git a/src/gromacs/gmxlib/string2.c b/src/gromacs/gmxlib/string2.c
index 84433ce74c44e50071d9a193935342e270986c7f..9b2d6f844a5522e24ae5d8f0a5beebeabc5f9283 100644 (file)
--- a/src/gromacs/gmxlib/string2.c
+++ b/src/gromacs/gmxlib/string2.c
@@ -62,7 +62,7 @@
 #include <assert.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "macros.h"
 #include "main.h"

diff --git a/src/gromacs/gmxlib/symtab.c b/src/gromacs/gmxlib/symtab.c
index cde0af579b09f73bb0707ce8b2e4e03159a899e9..7e9d65a450b934208623da5b242bad61e4cb1756 100644 (file)
--- a/src/gromacs/gmxlib/symtab.c
+++ b/src/gromacs/gmxlib/symtab.c
@@ -43,7 +43,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "txtdump.h"
 #include "symtab.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxlib/topsort.c b/src/gromacs/gmxlib/topsort.c
index c51ce064b5bdf0ab1be8e3adcf866b8ad397a5fc..7d1f5e5fb33530cbe0878876bb62aede35cac87f 100644 (file)
--- a/src/gromacs/gmxlib/topsort.c
+++ b/src/gromacs/gmxlib/topsort.c
@@ -41,7 +41,7 @@
 
 #include "typedefs.h"
 #include "topsort.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.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 769a237d9a5567cb2e1367c9963c9d87d8220396..5325bd88fe1e21fc9ef85acbc1c2e27dae5e85f0 100644 (file)
--- a/src/gromacs/gmxlib/txtdump.c
+++ b/src/gromacs/gmxlib/txtdump.c
@@ -41,7 +41,7 @@
 /* This file is completely threadsafe - please keep it that way! */
 
 #include <stdio.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "names.h"

diff --git a/src/gromacs/gmxlib/typedefs.c b/src/gromacs/gmxlib/typedefs.c
index a550ee4789f866ff3244b85add08f45ab269e64e..81eab1b2ebf765d19b7f0090a4ae24f106cbb140 100644 (file)
--- a/src/gromacs/gmxlib/typedefs.c
+++ b/src/gromacs/gmxlib/typedefs.c
@@ -41,7 +41,7 @@
 
 #include "thread_mpi/threads.h"
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "symtab.h"
 #include "vec.h"
 #include "pbc.h"

diff --git a/src/gromacs/gmxlib/warninp.c b/src/gromacs/gmxlib/warninp.c
index 3a1b6602f11ed9f69f4a8a9ea5f5ae7bb7ed0a76..9da44c99d9a03af5c52bd647eaa815ff034ce64a 100644 (file)
--- a/src/gromacs/gmxlib/warninp.c
+++ b/src/gromacs/gmxlib/warninp.c
@@ -40,7 +40,7 @@
 
 #include <string.h>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "copyrite.h"
 #include "string2.h"
 #include "gmx_fatal.h"

diff --git a/src/gromacs/gmxlib/xvgr.cpp b/src/gromacs/gmxlib/xvgr.cpp
index dcd73a14d853a0b9cbe346606f227ac15ce19168..21d0f2d21b56bcf24a26e8411e5bb08a90983b01 100644 (file)
--- a/src/gromacs/gmxlib/xvgr.cpp
+++ b/src/gromacs/gmxlib/xvgr.cpp
@@ -51,7 +51,7 @@
 #include "gromacs/fileio/futil.h"
 #include "copyrite.h"
 #include "oenv.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "xvgr.h"
 #include "viewit.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/add_par.c b/src/gromacs/gmxpreprocess/add_par.c
index 430f912b2e529843bd2c992cff20f4e172dbd353..4bf607634abcd15b28b50790d622370b1a05243d 100644 (file)
--- a/src/gromacs/gmxpreprocess/add_par.c
+++ b/src/gromacs/gmxpreprocess/add_par.c
@@ -41,7 +41,7 @@
 
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "grompp-impl.h"
 #include "macros.h"
 #include "toputil.h"

diff --git a/src/gromacs/gmxpreprocess/addconf.c b/src/gromacs/gmxpreprocess/addconf.c
index 68b80f19c74b8254e1d02885fcce6eed96d99f4f..e2d7a17e619ec75431ee630e49a3932dc65eb00a 100644 (file)
--- a/src/gromacs/gmxpreprocess/addconf.c
+++ b/src/gromacs/gmxpreprocess/addconf.c
@@ -44,7 +44,7 @@
 #include <string.h>
 #include "vec.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "force.h"
 #include "names.h"

diff --git a/src/gromacs/gmxpreprocess/calc_verletbuf.c b/src/gromacs/gmxpreprocess/calc_verletbuf.c
index 5862d61b9ea59f2fa3410b04a603dae14ff8b0d3..a96bd0679e12189f7deb961679b78280de87c349 100644 (file)
--- a/src/gromacs/gmxpreprocess/calc_verletbuf.c
+++ b/src/gromacs/gmxpreprocess/calc_verletbuf.c
@@ -42,7 +42,7 @@
 #include <math.h>
 #include "typedefs.h"
 #include "physics.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "macros.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/convparm.c b/src/gromacs/gmxpreprocess/convparm.c
index 7747fe46a49ead1428eec949768a64acd03ff5de..fb97126e251b77bac8d21c24c8a1aa72bd01df57 100644 (file)
--- a/src/gromacs/gmxpreprocess/convparm.c
+++ b/src/gromacs/gmxpreprocess/convparm.c
@@ -45,7 +45,7 @@
 #include "sysstuff.h"
 #include "physics.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "gmx_fatal.h"
 #include "topio.h"

diff --git a/src/gromacs/gmxpreprocess/fflibutil.cpp b/src/gromacs/gmxpreprocess/fflibutil.cpp
index 4b6bfda70b3793c2b62d7b2ff7b6471784ba7812..f1cdf02aa3c7e75105f37a756caaa48e76d2b68c 100644 (file)
--- a/src/gromacs/gmxpreprocess/fflibutil.cpp
+++ b/src/gromacs/gmxpreprocess/fflibutil.cpp
@@ -45,7 +45,7 @@
 #include "sysstuff.h"
 #include "network.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>

diff --git a/src/gromacs/gmxpreprocess/gen_ad.c b/src/gromacs/gmxpreprocess/gen_ad.c
index d6778871b5f88b753b639f9e979e5a837f4d597a..9ce949b56fe3b62e3f46d4b22c9b8fac6bf0710e 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_ad.c
+++ b/src/gromacs/gmxpreprocess/gen_ad.c
@@ -45,7 +45,7 @@
 
 #include "sysstuff.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 #include "gromacs/fileio/confio.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
index d25a75a2d95f02e901b82f2fec0b07fa938d0d0b..73326ac08fab1d321db7962b213803cac3c75571 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
+++ b/src/gromacs/gmxpreprocess/gen_maxwell_velocities.c
@@ -41,7 +41,7 @@
 #include <math.h>
 #include "gromacs/random/random.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "typedefs.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/gen_vsite.c b/src/gromacs/gmxpreprocess/gen_vsite.c
index dade614bbb45eb868957eb75f2463f3e86ff7743..2d9f0d1828bb1c11bb7bbc05d7808ca316c53e05 100644 (file)
--- a/src/gromacs/gmxpreprocess/gen_vsite.c
+++ b/src/gromacs/gmxpreprocess/gen_vsite.c
@@ -43,7 +43,7 @@
 #include <math.h>
 #include <string.h>
 #include "gen_vsite.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "resall.h"
 #include "add_par.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/genconf.c b/src/gromacs/gmxpreprocess/genconf.c
index f5af537de7c899aa49a2e0ac45c1ed8f1f60d82e..65ee7a85b522f42197ca1fd2c513a3df0cc8e13d 100644 (file)
--- a/src/gromacs/gmxpreprocess/genconf.c
+++ b/src/gromacs/gmxpreprocess/genconf.c
@@ -38,7 +38,7 @@
 
 #include "gromacs/math/utilities.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "gromacs/fileio/confio.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/gromacs/gmxpreprocess/genhydro.c b/src/gromacs/gmxpreprocess/genhydro.c
index 1dffeba8fb978a32f3ab06cb6384de96f14e7b56..afcadb43b4b09b5f96df7d4f074426171ccc133f 100644 (file)
--- a/src/gromacs/gmxpreprocess/genhydro.c
+++ b/src/gromacs/gmxpreprocess/genhydro.c
@@ -43,7 +43,7 @@
 
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/confio.h"
 #include "symtab.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/gmxcpp.c b/src/gromacs/gmxpreprocess/gmxcpp.c
index f66f0d1838a3fadeee260114c3d1ce70120ca734..a6c69d1e4126f07eeefdeead02ad647d903b992c 100644 (file)
--- a/src/gromacs/gmxpreprocess/gmxcpp.c
+++ b/src/gromacs/gmxpreprocess/gmxcpp.c
@@ -48,7 +48,7 @@
 #include <ctype.h>
 
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "macros.h"
 #include "gmx_fatal.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_atomtype.c b/src/gromacs/gmxpreprocess/gpp_atomtype.c
index 78aa58c0defca8a05a9e738e9903e674f5e7f887..31a39aec157e9438ef17b08ee9464b8bdc2fb43b 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_atomtype.c
+++ b/src/gromacs/gmxpreprocess/gpp_atomtype.c
@@ -41,7 +41,7 @@
 #include <math.h>
 #include <string.h>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "macros.h"
 #include "topdirs.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
index c8b82d91be85450c404b508d859d707dcf56454a..91faf37e12057242fce35b65ac126997c8b3d835 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
+++ b/src/gromacs/gmxpreprocess/gpp_bond_atomtype.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2011, by the GROMACS development team, led by
+ * Copyright (c) 2011,2014, 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 <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "macros.h"
 #include "symtab.h"

diff --git a/src/gromacs/gmxpreprocess/gpp_nextnb.c b/src/gromacs/gmxpreprocess/gpp_nextnb.c
index 3fc2cddb37c54a25858b59531ade267f07934448..b90c82274286efc4b578f09df67a01f91fa47809 100644 (file)
--- a/src/gromacs/gmxpreprocess/gpp_nextnb.c
+++ b/src/gromacs/gmxpreprocess/gpp_nextnb.c
@@ -40,7 +40,7 @@
 #endif
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 /* #define DEBUG_NNB */
 #include "gpp_nextnb.h"

diff --git a/src/gromacs/gmxpreprocess/grompp.c b/src/gromacs/gmxpreprocess/grompp.c
index 5c280c73ea7e4d7ec5ccba3e6c50c364cbdd2bb4..872c670990c99807997386445ec424ecab86cc7e 100644 (file)
--- a/src/gromacs/gmxpreprocess/grompp.c
+++ b/src/gromacs/gmxpreprocess/grompp.c
@@ -48,7 +48,7 @@
 #include <assert.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "readir.h"
 #include "toputil.h"

diff --git a/src/gromacs/gmxpreprocess/h_db.c b/src/gromacs/gmxpreprocess/h_db.c
index 4bd2e5f06752fcaaab3059e372f88848e6b00451..8998c8ba36fc6b36b62880b2551fc6d4dcb3b751 100644 (file)
--- a/src/gromacs/gmxpreprocess/h_db.c
+++ b/src/gromacs/gmxpreprocess/h_db.c
@@ -42,7 +42,7 @@
 #include <string.h>
 #include "string2.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "symtab.h"
 #include "h_db.h"

diff --git a/src/gromacs/gmxpreprocess/hackblock.c b/src/gromacs/gmxpreprocess/hackblock.c
index 3ce0598904247ce5cbaabb0582f77559a68f33c2..262e308f72da17defb1fbe9bf05a35514b361571 100644 (file)
--- a/src/gromacs/gmxpreprocess/hackblock.c
+++ b/src/gromacs/gmxpreprocess/hackblock.c
@@ -41,7 +41,7 @@
 
 #include <string.h>
 #include "hackblock.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "macros.h"
 

diff --git a/src/gromacs/gmxpreprocess/hizzie.c b/src/gromacs/gmxpreprocess/hizzie.c
index 5f7011b34191c99c6f721d0a757e8bc5afe945b3..5e612361605df48c2165a59bbae5d3ad442ef1fa 100644 (file)
--- a/src/gromacs/gmxpreprocess/hizzie.c
+++ b/src/gromacs/gmxpreprocess/hizzie.c
@@ -43,7 +43,7 @@
 #include <string.h>
 #include "typedefs.h"
 #include "gromacs/fileio/pdbio.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "physics.h"
 #include "toputil.h"

diff --git a/src/gromacs/gmxpreprocess/insert-molecules.cpp b/src/gromacs/gmxpreprocess/insert-molecules.cpp
index 61f143ca2784c8698682747fa5cb976b272de00c..c60b4d0d03c2678e25e7db81d38669ecabc3905d 100644 (file)
--- a/src/gromacs/gmxpreprocess/insert-molecules.cpp
+++ b/src/gromacs/gmxpreprocess/insert-molecules.cpp
@@ -43,7 +43,7 @@
 
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/math/utilities.h"
 #include "gromacs/fileio/confio.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxpreprocess/nm2type.c b/src/gromacs/gmxpreprocess/nm2type.c
index a37bf2926e79672619250d2010087d9f3c23c27e..fc96d5656d66e7958b071dd74268223292972128 100644 (file)
--- a/src/gromacs/gmxpreprocess/nm2type.c
+++ b/src/gromacs/gmxpreprocess/nm2type.c
@@ -45,7 +45,7 @@
 #include "macros.h"
 #include "bondf.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "gromacs/fileio/confio.h"
 #include "physics.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2gmx.c b/src/gromacs/gmxpreprocess/pdb2gmx.c
index 2ed370e43ba6964dc7494b43ebb4bf128a9dcc27..6aa39c7dcd51cf72aa1177dbd3c0126e958c745e 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2gmx.c
+++ b/src/gromacs/gmxpreprocess/pdb2gmx.c
@@ -47,7 +47,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "copyrite.h"
 #include "string2.h"
 #include "gromacs/fileio/confio.h"

diff --git a/src/gromacs/gmxpreprocess/pdb2top.cpp b/src/gromacs/gmxpreprocess/pdb2top.cpp
index baba4b46255df1c5ab8dbc125c25e4bbad4f9ab7..8237afc812014136921b2cbb3612658eb737e193 100644 (file)
--- a/src/gromacs/gmxpreprocess/pdb2top.cpp
+++ b/src/gromacs/gmxpreprocess/pdb2top.cpp
@@ -43,7 +43,7 @@
 #include <ctype.h>
 
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "symtab.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxpreprocess/protonate.c b/src/gromacs/gmxpreprocess/protonate.c
index 818e8cff7dfd0c3ddb234c5991f510cad83269fe..3293f2b7431d0d1a2ad360d2840e338582d3c872 100644 (file)
--- a/src/gromacs/gmxpreprocess/protonate.c
+++ b/src/gromacs/gmxpreprocess/protonate.c
@@ -44,7 +44,7 @@
 #include "string2.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/commandline/pargs.h"
 #include "gromacs/fileio/confio.h"
 #include "genhydro.h"

diff --git a/src/gromacs/gmxpreprocess/read-conformation.cpp b/src/gromacs/gmxpreprocess/read-conformation.cpp
index cfb4718c79033ceafe97863ba2a4013735727c74..64fa909de44387d358105fd555d18b4a8936c54d 100644 (file)
--- a/src/gromacs/gmxpreprocess/read-conformation.cpp
+++ b/src/gromacs/gmxpreprocess/read-conformation.cpp
@@ -38,7 +38,7 @@
 #include "atomprop.h"
 #include "types/simple.h"
 #include "types/atoms.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 real *makeExclusionDistances(const t_atoms *a, gmx_atomprop_t aps,
                              real defaultDistance, real scaleFactor)

diff --git a/src/gromacs/gmxpreprocess/readadress.c b/src/gromacs/gmxpreprocess/readadress.c
index 494305749f64be4f15457141655e6c03881998e0..58b6baf53f6e843de50fa3aa897922de5e00a504 100644 (file)
--- a/src/gromacs/gmxpreprocess/readadress.c
+++ b/src/gromacs/gmxpreprocess/readadress.c
@@ -38,7 +38,7 @@
 #include "string2.h"
 #include "readir.h"
 #include "names.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 
 #define MAXPTR 254

diff --git a/src/gromacs/gmxpreprocess/readir.c b/src/gromacs/gmxpreprocess/readir.c
index ff641f450efd1ea5dac8f957c005cec8135e9755..6e27071e3d9059bd37f8cb9c3cc66d60aeb959b7 100644 (file)
--- a/src/gromacs/gmxpreprocess/readir.c
+++ b/src/gromacs/gmxpreprocess/readir.c
@@ -42,7 +42,7 @@
 #include <stdlib.h>
 #include <limits.h>
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "physics.h"
 #include "names.h"

diff --git a/src/gromacs/gmxpreprocess/readpull.c b/src/gromacs/gmxpreprocess/readpull.c
index 2099d1d8fb4bdcc67f832da9f7f5343f26bc2e99..76faad9af15a8adebb40b43a6e70a962b3352f10 100644 (file)
--- a/src/gromacs/gmxpreprocess/readpull.c
+++ b/src/gromacs/gmxpreprocess/readpull.c
@@ -46,7 +46,7 @@
 #include "princ.h"
 #include "gromacs/fileio/futil.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "names.h"
 #include "gmx_fatal.h"

diff --git a/src/gromacs/gmxpreprocess/readrot.c b/src/gromacs/gmxpreprocess/readrot.c
index 468f5f8116338d0d6422cbfe1b6b86985f74aa34..56e0daac662500f748cda1c70dce9dd45cbf86bf 100644 (file)
--- a/src/gromacs/gmxpreprocess/readrot.c
+++ b/src/gromacs/gmxpreprocess/readrot.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.
@@ -39,7 +39,7 @@
 #endif
 
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "readir.h"
 #include "names.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxpreprocess/resall.c b/src/gromacs/gmxpreprocess/resall.c
index 465e64b7dfd4d99633fd4d467d37c11b4553e048..de0ee8a44c1917f22fb27e13813c9e379c7bc03f 100644 (file)
--- a/src/gromacs/gmxpreprocess/resall.c
+++ b/src/gromacs/gmxpreprocess/resall.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "string2.h"
 #include "gromacs/fileio/futil.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "symtab.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxpreprocess/solvate.cpp b/src/gromacs/gmxpreprocess/solvate.cpp
index 9496b687c0b1e5e25a35706ff3e2b9bc453720fb..857c4985a6622d2d30cbf47fe53c6d359ce6f23c 100644 (file)
--- a/src/gromacs/gmxpreprocess/solvate.cpp
+++ b/src/gromacs/gmxpreprocess/solvate.cpp
@@ -44,7 +44,7 @@
 
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "string2.h"
 #include "gromacs/fileio/confio.h"
 #include "macros.h"

diff --git a/src/gromacs/gmxpreprocess/sortwater.c b/src/gromacs/gmxpreprocess/sortwater.c
index 0766d69bd9fe140ab686c036a33b5ee10cce2e81..63834a92585c7fac628a66f597d1c901aecb487d 100644 (file)
--- a/src/gromacs/gmxpreprocess/sortwater.c
+++ b/src/gromacs/gmxpreprocess/sortwater.c
@@ -40,7 +40,7 @@
 
 #include "typedefs.h"
 #include "gromacs/random/random.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "sortwater.h"
 

diff --git a/src/gromacs/gmxpreprocess/specbond.c b/src/gromacs/gmxpreprocess/specbond.c
index 99747dce2283aa8eb2797068b685045abd6d9e92..6aadf9027442f71039ebbe3cb31ba64058dd1d29 100644 (file)
--- a/src/gromacs/gmxpreprocess/specbond.c
+++ b/src/gromacs/gmxpreprocess/specbond.c
@@ -46,7 +46,7 @@
 #include "gromacs/fileio/pdbio.h"
 #include "gromacs/fileio/strdb.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "specbond.h"
 #include "pdb2top.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/ter_db.c b/src/gromacs/gmxpreprocess/ter_db.c
index f45eabe2b9ca2e208ac372947a2afb9045457e41..94b61f0b75d1a0bf2eec0b9e281f4488d91d1351 100644 (file)
--- a/src/gromacs/gmxpreprocess/ter_db.c
+++ b/src/gromacs/gmxpreprocess/ter_db.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "symtab.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/gmxpreprocess/tomorse.c b/src/gromacs/gmxpreprocess/tomorse.c
index be4894438400730995c32623a8d96f488d6f1fbf..7e78facf5d6a599bd369c0e226be3ca4a1788aab 100644 (file)
--- a/src/gromacs/gmxpreprocess/tomorse.c
+++ b/src/gromacs/gmxpreprocess/tomorse.c
@@ -48,7 +48,7 @@
 #include "string2.h"
 #include "grompp-impl.h"
 #include "gromacs/fileio/futil.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "toputil.h"
 #include "gmx_fatal.h"
 #include "gpp_atomtype.h"

diff --git a/src/gromacs/gmxpreprocess/topdirs.c b/src/gromacs/gmxpreprocess/topdirs.c
index 8742bc5b8b9f6bf1427416b4db0068dc37c0c192..32c55af47c426281feb16786b4259c258040252a 100644 (file)
--- a/src/gromacs/gmxpreprocess/topdirs.c
+++ b/src/gromacs/gmxpreprocess/topdirs.c
@@ -42,7 +42,7 @@
 #include <stdarg.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "string2.h"
 #include "gmx_fatal.h"

diff --git a/src/gromacs/gmxpreprocess/topio.c b/src/gromacs/gmxpreprocess/topio.c
index 70bba75b1c5d2da4ee257ded66ee1430f58f0895..8ff26c24ea9d29ae959f2ca341953ac98ab3dfd1 100644 (file)
--- a/src/gromacs/gmxpreprocess/topio.c
+++ b/src/gromacs/gmxpreprocess/topio.c
@@ -49,7 +49,7 @@
 #include "gromacs/fileio/futil.h"
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "txtdump.h"

diff --git a/src/gromacs/gmxpreprocess/toppush.c b/src/gromacs/gmxpreprocess/toppush.c
index 841c446731a3fce093d73457a4600470156e7cfe..241eed73d9f8daca4848d45df6a7daacd729e928 100644 (file)
--- a/src/gromacs/gmxpreprocess/toppush.c
+++ b/src/gromacs/gmxpreprocess/toppush.c
@@ -43,7 +43,7 @@
 #include <assert.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "string2.h"
 #include "names.h"

diff --git a/src/gromacs/gmxpreprocess/topshake.c b/src/gromacs/gmxpreprocess/topshake.c
index 68911eb5acabf2c738e3b1d3b47f61ca737ec49d..fa00694a6e534e1e702638c33f48149e94a06d4a 100644 (file)
--- a/src/gromacs/gmxpreprocess/topshake.c
+++ b/src/gromacs/gmxpreprocess/topshake.c
@@ -51,7 +51,7 @@
 #include "toppush.h"
 #include "toputil.h"
 #include "topdirs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 
 static void copy_bond (t_params *pr, int to, int from)

diff --git a/src/gromacs/gmxpreprocess/toputil.c b/src/gromacs/gmxpreprocess/toputil.c
index 80ce3b68d3b1bcbfc61dd4879004eb59ede1c261..33db83ee49aa90a11fe2897cea52118e38fdcfef 100644 (file)
--- a/src/gromacs/gmxpreprocess/toputil.c
+++ b/src/gromacs/gmxpreprocess/toputil.c
@@ -41,7 +41,7 @@
 #include <math.h>
 #include <string.h>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "macros.h"
 #include "topdirs.h"

diff --git a/src/gromacs/gmxpreprocess/vsite_parm.c b/src/gromacs/gmxpreprocess/vsite_parm.c
index eaa35b09a16a9f33157100bf109948fbd7b773e5..36c56a8ae1cda9f24759e6b7f2806bc89124318e 100644 (file)
--- a/src/gromacs/gmxpreprocess/vsite_parm.c
+++ b/src/gromacs/gmxpreprocess/vsite_parm.c
@@ -43,7 +43,7 @@
 #include <assert.h>
 #include <string.h>
 #include "vsite_parm.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "resall.h"
 #include "add_par.h"
 #include "vec.h"

diff --git a/src/gromacs/gmxpreprocess/x2top.c b/src/gromacs/gmxpreprocess/x2top.c
index b3d051cb1273a3edb81f271b3907dcb5f6662943..4f4084974184213f03e188f3b124b04b52d4e27e 100644 (file)
--- a/src/gromacs/gmxpreprocess/x2top.c
+++ b/src/gromacs/gmxpreprocess/x2top.c
@@ -48,7 +48,7 @@
 #include "bondf.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "gromacs/fileio/confio.h"
 #include "physics.h"

diff --git a/src/gromacs/gmxpreprocess/xlate.c b/src/gromacs/gmxpreprocess/xlate.c
index fed4c8b73e3a2ac05767ede79bdbb1a36ee5658f..53a88e05011269fbd35952781bf734fb8d64cd3a 100644 (file)
--- a/src/gromacs/gmxpreprocess/xlate.c
+++ b/src/gromacs/gmxpreprocess/xlate.c
@@ -42,7 +42,7 @@
 #include <string.h>
 #include "typedefs.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "symtab.h"
 #include "index.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/imd/imd.c b/src/gromacs/imd/imd.c
index 9347a22b69df9c97af24044675ffbf9bcaffb651..fb73ce7fc436dd520c00d50de9d23e237b45fd82 100644 (file)
--- a/src/gromacs/imd/imd.c
+++ b/src/gromacs/imd/imd.c
@@ -53,7 +53,7 @@
 
 #include "imd.h"
 #include "imdsocket.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "network.h"
 #include "mdrun.h"
 #include "sighandler.h"

diff --git a/src/gromacs/imd/imdsocket.c b/src/gromacs/imd/imdsocket.c
index 82c6804f1ae7dcb0ef1af59f95881963989692a0..6febf83e55b57d45d739bb681b2bf49d3275e7dc 100644 (file)
--- a/src/gromacs/imd/imdsocket.c
+++ b/src/gromacs/imd/imdsocket.c
@@ -52,7 +52,7 @@
 
 
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "imdsocket.h"
 #include "imd.h"

diff --git a/src/gromacs/legacyheaders/gmx_ga2la.h b/src/gromacs/legacyheaders/gmx_ga2la.h
index c6f9ca34ded3d372983c879f0e9b06d2f58bce8f..e5820421df81734d326c9e2e096b7fcbcbc8d9cb 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_ga2la.h
+++ b/src/gromacs/legacyheaders/gmx_ga2la.h
@@ -39,7 +39,7 @@
 
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #ifdef __cplusplus
 extern "C" {

diff --git a/src/gromacs/legacyheaders/gmx_hash.h b/src/gromacs/legacyheaders/gmx_hash.h
index 0be911727681cc40c727ddb6b1ae535216c8801a..a241ee0def4f5f4695784237dd20dc978fc3dfe6 100644 (file)
--- a/src/gromacs/legacyheaders/gmx_hash.h
+++ b/src/gromacs/legacyheaders/gmx_hash.h
@@ -36,7 +36,7 @@
 #define _gmx_hash_h
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 
 #ifdef __cplusplus

diff --git a/src/gromacs/linearalgebra/eigensolver.c b/src/gromacs/linearalgebra/eigensolver.c
index e4d81c172e0f17c5aca9088a0e9f2081b37e4639..a0221be3c7a95407a2eb791659687c6223aaa21f 100644 (file)
--- a/src/gromacs/linearalgebra/eigensolver.c
+++ b/src/gromacs/linearalgebra/eigensolver.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.
@@ -38,9 +38,10 @@
 
 #include "gromacs/legacyheaders/types/simple.h"
 #include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/smalloc.h"
 
 #include "gromacs/linearalgebra/sparsematrix.h"
+#include "gromacs/utility/smalloc.h"
+
 #include "gmx_lapack.h"
 #include "gmx_arpack.h"
 

diff --git a/src/gromacs/linearalgebra/matrix.c b/src/gromacs/linearalgebra/matrix.c
index 0d78627b552bd662fa5855f4e9df792b2e7bc7b3..ccbd22ec19a4e4b248ee3ad7ac60a8498040cf28 100644 (file)
--- a/src/gromacs/linearalgebra/matrix.c
+++ b/src/gromacs/linearalgebra/matrix.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, 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.
@@ -43,9 +43,10 @@
 #include <stdio.h>
 
 #include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
+#include "gromacs/utility/smalloc.h"
+
 #include "gmx_lapack.h"
 
 double **alloc_matrix(int n, int m)

diff --git a/src/gromacs/linearalgebra/mtxio.c b/src/gromacs/linearalgebra/mtxio.c
index 69e562e24b07f9a1a0fcce2822e68356f9f03f13..0a82d271c600941c7e831ddf2e527162977fc9d0 100644 (file)
--- a/src/gromacs/linearalgebra/mtxio.c
+++ b/src/gromacs/linearalgebra/mtxio.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.
@@ -48,10 +48,10 @@
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/gmx_fatal.h"
 #include "gromacs/fileio/gmxfio.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/fileio/xdrf.h"
 #include "gromacs/linearalgebra/sparsematrix.h"
 
+#include "gromacs/utility/smalloc.h"
 
 /* Just a number to identify our file type */
 #define GMX_MTXIO_MAGIC_NUMBER  0x34ce8fd2

diff --git a/src/gromacs/linearalgebra/nrjac.c b/src/gromacs/linearalgebra/nrjac.c
index 49d685106618fae9098b63c616af65b4b54d6ed9..b5cf7066b4612f26ce79b0962fa8621b6c8a9329 100644 (file)
--- a/src/gromacs/linearalgebra/nrjac.c
+++ b/src/gromacs/linearalgebra/nrjac.c
@@ -40,7 +40,7 @@
 #include <math.h>
 
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 static gmx_inline
 void do_rotate(double **a, int i, int j, int k, int l, double tau, double s)

diff --git a/src/gromacs/linearalgebra/sparsematrix.c b/src/gromacs/linearalgebra/sparsematrix.c
index 52187a35c47782e708dfd5217eda418084ccf6a5..d2bb9495f4bc84340a2637f0df45305830b10f93 100644 (file)
--- a/src/gromacs/linearalgebra/sparsematrix.c
+++ b/src/gromacs/linearalgebra/sparsematrix.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.
@@ -40,10 +40,7 @@
 #include <stdlib.h>
 #include <stdio.h>
 
-#include "gromacs/legacyheaders/smalloc.h"
-
-
-
+#include "gromacs/utility/smalloc.h"
 
 gmx_sparsematrix_t *
 gmx_sparsematrix_init(int                    nrow)

diff --git a/src/gromacs/math/3dview.c b/src/gromacs/math/3dview.c
index 4ca8016ab7f7c039b09c94609da24b3c5aa937f3..895c423a92381c9359e2dab3bb202319bfc0a67f 100644 (file)
--- a/src/gromacs/math/3dview.c
+++ b/src/gromacs/math/3dview.c
@@ -42,7 +42,7 @@
 
 #include <math.h>
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "physics.h"
 #include "pbc.h"

diff --git a/src/gromacs/math/do_fit.c b/src/gromacs/math/do_fit.c
index 7d4b471ec9dbf6a2d90e46ee675573eec4c6cde4..db483c8f41316a7c5c938ef189667f98b1d9bbe8 100644 (file)
--- a/src/gromacs/math/do_fit.c
+++ b/src/gromacs/math/do_fit.c
@@ -41,7 +41,7 @@
 #include "typedefs.h"
 #include "vec.h"
 #include "txtdump.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "gromacs/linearalgebra/nrjac.h"
 

diff --git a/src/gromacs/mdlib/clincs.c b/src/gromacs/mdlib/clincs.c
index 0476d241518aed33759ebab9a56736f34407082b..6ac3d2f81a86ddd8947002fcd4cd84dbbe1fab26 100644 (file)
--- a/src/gromacs/mdlib/clincs.c
+++ b/src/gromacs/mdlib/clincs.c
@@ -46,7 +46,7 @@
 #include "physics.h"
 #include "vec.h"
 #include "pbc.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "mdrun.h"
 #include "nrnb.h"
 #include "domdec.h"

diff --git a/src/gromacs/mdlib/constr.c b/src/gromacs/mdlib/constr.c
index a237a084579c8b3c12f249d89c95abdd4ac2a9f0..716c65d54356a6ed6974b0dfd8635ad3dd6b8c8b 100644 (file)
--- a/src/gromacs/mdlib/constr.c
+++ b/src/gromacs/mdlib/constr.c
@@ -46,7 +46,7 @@
 #include "main.h"
 #include "mdrun.h"
 #include "nrnb.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "physics.h"
 #include "names.h"

diff --git a/src/gromacs/mdlib/coupling.c b/src/gromacs/mdlib/coupling.c
index d5e4d9d3ff1a90fbdf95400690f107f7449a9bda..c0ca0111489f07271b62b622fcd873924eca4c7a 100644 (file)
--- a/src/gromacs/mdlib/coupling.c
+++ b/src/gromacs/mdlib/coupling.c
@@ -41,7 +41,7 @@
 
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "update.h"
 #include "vec.h"
 #include "macros.h"

diff --git a/src/gromacs/mdlib/csettle.c b/src/gromacs/mdlib/csettle.c
index 5f89dbdb7a42ce1dba20052fa8747a272307393d..281f3973c2aa9721df5bf717be24d554b3d9a474 100644 (file)
--- a/src/gromacs/mdlib/csettle.c
+++ b/src/gromacs/mdlib/csettle.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.
@@ -43,7 +43,7 @@
 #include "vec.h"
 #include "constr.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 
 typedef struct

diff --git a/src/gromacs/mdlib/domdec.c b/src/gromacs/mdlib/domdec.c
index 3ec4f8120b970de18d9fc3d406f5f4937b55481f..fc82a2d455ba1a7e9ec7e49cf7e08f658a221404 100644 (file)
--- a/src/gromacs/mdlib/domdec.c
+++ b/src/gromacs/mdlib/domdec.c
@@ -45,7 +45,7 @@
 #include <assert.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "gmx_fatal_collective.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/domdec_con.c b/src/gromacs/mdlib/domdec_con.c
index 417992bfc9e17703215d9aef190700445cf54314..d7233bdf311616f74e11321e934d65f5a66de60a 100644 (file)
--- a/src/gromacs/mdlib/domdec_con.c
+++ b/src/gromacs/mdlib/domdec_con.c
@@ -38,7 +38,7 @@
 #endif
 #include <assert.h>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "constr.h"
 #include "types/commrec.h"

diff --git a/src/gromacs/mdlib/domdec_setup.c b/src/gromacs/mdlib/domdec_setup.c
index 8e39f16daa9dc21ab8ce23c2f4227e2ba9aff738..d8001ea9dabaaa52c91f565e5daecc8c73a5628e 100644 (file)
--- a/src/gromacs/mdlib/domdec_setup.c
+++ b/src/gromacs/mdlib/domdec_setup.c
@@ -44,7 +44,7 @@
 #include "network.h"
 #include "perf_est.h"
 #include "physics.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "vec.h"
 #include "names.h"

diff --git a/src/gromacs/mdlib/domdec_top.c b/src/gromacs/mdlib/domdec_top.c
index 1503d9d963df1fd415a2977bfbcddff0738dd2d6..9b69e69d035d4f48f4c56e69e79334dc2fed2d67 100644 (file)
--- a/src/gromacs/mdlib/domdec_top.c
+++ b/src/gromacs/mdlib/domdec_top.c
@@ -39,7 +39,7 @@
 
 #include <string.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "domdec.h"
 #include "domdec_network.h"

diff --git a/src/gromacs/mdlib/ebin.c b/src/gromacs/mdlib/ebin.c
index ab3eb58a026d2f7611e6290d9baad9d8987feb84..4760fcf32e1ea8d2397a16551d0b29c3200d42b9 100644 (file)
--- a/src/gromacs/mdlib/ebin.c
+++ b/src/gromacs/mdlib/ebin.c
@@ -42,7 +42,7 @@
 #include <math.h>
 #include <string.h>
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "gmx_fatal.h"
 #include "ebin.h"

diff --git a/src/gromacs/mdlib/ewald.c b/src/gromacs/mdlib/ewald.c
index 740ad32e989f086afde9a2f114cafd6b97beb699..9a12d41e884c51b9c52b1573aba8762d46010cb4 100644 (file)
--- a/src/gromacs/mdlib/ewald.c
+++ b/src/gromacs/mdlib/ewald.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "physics.h"
 #include "coulomb.h"

diff --git a/src/gromacs/mdlib/expanded.c b/src/gromacs/mdlib/expanded.c
index ea23df3babb72620df96a38f26dc61f6b816a93d..64116f96d65c93b891f4176deaa9b0a2480acc38 100644 (file)
--- a/src/gromacs/mdlib/expanded.c
+++ b/src/gromacs/mdlib/expanded.c
@@ -39,7 +39,7 @@
 #include <stdio.h>
 #include <math.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "gromacs/fileio/confio.h"
 #include "txtdump.h"

diff --git a/src/gromacs/mdlib/force.c b/src/gromacs/mdlib/force.c
index d16e1a3c86e4885a9c620c649384b793b96aff4e..c54d56ebcb561ae25dfb1cda7a38b27af8bd66ad 100644 (file)
--- a/src/gromacs/mdlib/force.c
+++ b/src/gromacs/mdlib/force.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "physics.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/forcerec.c b/src/gromacs/mdlib/forcerec.c
index 019a6826f07ff41dbd3f364676dcccc172bd3b67..44cd7c4c5d84e5be682fe9501a83ff3da063dc0d 100644 (file)
--- a/src/gromacs/mdlib/forcerec.c
+++ b/src/gromacs/mdlib/forcerec.c
@@ -47,7 +47,7 @@
 #include "vec.h"
 #include "gromacs/math/utilities.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gmx_fatal.h"
 #include "gmx_fatal_collective.h"

diff --git a/src/gromacs/mdlib/genborn.c b/src/gromacs/mdlib/genborn.c
index edd78818a70ca30d2ad3964d75d309c8e65c2772..6c20080c5f8a5ee44823975b91a53f776c416eb8 100644 (file)
--- a/src/gromacs/mdlib/genborn.c
+++ b/src/gromacs/mdlib/genborn.c
@@ -44,7 +44,7 @@
 
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "genborn.h"
 #include "vec.h"
 #include "gromacs/fileio/pdbio.h"

diff --git a/src/gromacs/mdlib/genborn_allvsall.c b/src/gromacs/mdlib/genborn_allvsall.c
index aa5134379afd7a453d4e605a86267f6da8ac8c65..766341efad9b0621674a83d2bb1903ad6f3ce8c5 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall.c
+++ b/src/gromacs/mdlib/genborn_allvsall.c
@@ -42,7 +42,7 @@
 #include "types/simple.h"
 
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "network.h"
 #include "physics.h"

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
index 27c87c65aa46b6b08b0ffed87ca2429027971283..ff2c3aefd44dfae96f25155b54b0d9d7ea1dabe0 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_double.c
@@ -42,7 +42,7 @@
 #include "types/simple.h"
 
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "network.h"
 #include "physics.h"

diff --git a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
index a5aa598c2fa1b2b008174bd7c1323e6dc6c208b7..1f17f499aa55341f0c0341282f6f30034a4a3517 100644 (file)
--- a/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_allvsall_sse2_single.c
@@ -42,7 +42,7 @@
 #include "types/simple.h"
 
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "network.h"
 #include "physics.h"

diff --git a/src/gromacs/mdlib/genborn_sse2_double.c b/src/gromacs/mdlib/genborn_sse2_double.c
index e756484dba2ca03e034e84d50690ec0b372ce916..7e71bf8ba437977065a6fd0ada88a1917f1c0bec 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_double.c
+++ b/src/gromacs/mdlib/genborn_sse2_double.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "genborn.h"
 #include "vec.h"
 #include "gromacs/fileio/pdbio.h"

diff --git a/src/gromacs/mdlib/genborn_sse2_single.c b/src/gromacs/mdlib/genborn_sse2_single.c
index 93978cd230cc76658581d30b43bb9f422e0e5342..95fa0cdc40a9fe2927aa548b790fa60ab3669f08 100644 (file)
--- a/src/gromacs/mdlib/genborn_sse2_single.c
+++ b/src/gromacs/mdlib/genborn_sse2_single.c
@@ -42,7 +42,7 @@
 #include <string.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "genborn.h"
 #include "vec.h"
 #include "gromacs/fileio/pdbio.h"

diff --git a/src/gromacs/mdlib/groupcoord.c b/src/gromacs/mdlib/groupcoord.c
index 770d8af7c44ea263e4239a21cea44d3dd272cbbc..dae82018af8c037e07534b8e8a2fbd14593ee52a 100644 (file)
--- a/src/gromacs/mdlib/groupcoord.c
+++ b/src/gromacs/mdlib/groupcoord.c
@@ -43,7 +43,7 @@
 #include "network.h"
 #include "pbc.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_ga2la.h"
 
 #define MIN(a, b) (((a) < (b)) ? (a) : (b))

diff --git a/src/gromacs/mdlib/init.c b/src/gromacs/mdlib/init.c
index 38bf4401f017c82f0002765a09596326e9609b70..95516341f8b957d79e02e317f8f7cdd55f6db0c4 100644 (file)
--- a/src/gromacs/mdlib/init.c
+++ b/src/gromacs/mdlib/init.c
@@ -41,7 +41,7 @@
 #include <stdio.h>
 #include "typedefs.h"
 #include "gromacs/fileio/tpxio.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "main.h"
 #include "mvdata.h"

diff --git a/src/gromacs/mdlib/md_support.c b/src/gromacs/mdlib/md_support.c
index 0050afe87d3ddce5209ce5a197495e5aa5213aef..ba42efe4ca46f4d6b733fe8148de49d852589758 100644 (file)
--- a/src/gromacs/mdlib/md_support.c
+++ b/src/gromacs/mdlib/md_support.c
@@ -40,7 +40,7 @@
 
 #include "typedefs.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "mdrun.h"
 #include "domdec.h"
 #include "mtop_util.h"

diff --git a/src/gromacs/mdlib/mdatom.c b/src/gromacs/mdlib/mdatom.c
index b3d6475c531fe5b6e9cae6b2a1d78c853ae28bbf..9c0c5943d54f139e40b6629a308b2d59955a2734 100644 (file)
--- a/src/gromacs/mdlib/mdatom.c
+++ b/src/gromacs/mdlib/mdatom.c
@@ -42,7 +42,7 @@
 
 #include "typedefs.h"
 #include "mdatoms.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "main.h"
 #include "qmmm.h"
 #include "mtop_util.h"

diff --git a/src/gromacs/mdlib/mdebin.c b/src/gromacs/mdlib/mdebin.c
index a0bd5b1cd8bbdb48e7a631909e5300173124afc8..5ef8b7d79a98ca52491ca4e5782f34fc8ac3ea24 100644 (file)
--- a/src/gromacs/mdlib/mdebin.c
+++ b/src/gromacs/mdlib/mdebin.c
@@ -42,7 +42,7 @@
 #include <float.h>
 #include "typedefs.h"
 #include "mdebin.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "gromacs/fileio/enxio.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/mdebin_bar.c b/src/gromacs/mdlib/mdebin_bar.c
index 236e867dae3bb1cfd26f26d760a612f120eff9c0..9f057bd6fd4126dda7848c64f8149e4a3c01f354 100644 (file)
--- a/src/gromacs/mdlib/mdebin_bar.c
+++ b/src/gromacs/mdlib/mdebin_bar.c
@@ -44,7 +44,7 @@
 #include "typedefs.h"
 #include "gmx_fatal.h"
 #include "mdebin.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/enxio.h"
 #include "gromacs/fileio/gmxfio.h"
 #include "mdebin_bar.h"

diff --git a/src/gromacs/mdlib/minimize.c b/src/gromacs/mdlib/minimize.c
index 6af2bca9d91cecf41e3e665be800600b5f4a919b..130a87f573d44dbb21b2169b01c1f1381d6922af 100644 (file)
--- a/src/gromacs/mdlib/minimize.c
+++ b/src/gromacs/mdlib/minimize.c
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "string2.h"
 #include "network.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "main.h"
 #include "force.h"

diff --git a/src/gromacs/mdlib/nbnxn_atomdata.c b/src/gromacs/mdlib/nbnxn_atomdata.c
index 36c5b2c565ea1a269cc98518ec88a8992acbcf94..68365412121494b5daeab85794965ca63608977c 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_atomdata.c
+++ b/src/gromacs/mdlib/nbnxn_atomdata.c
@@ -40,7 +40,7 @@
 #include <math.h>
 #include <string.h>
 #include <assert.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "vec.h"
 #include "nbnxn_consts.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 32dc486a4ba96a84fa1a963b5175268337381d01..fb437c37a7efe2850a5635efa0192e3c0627c83c 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 "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "tables.h"
 #include "typedefs.h"
 #include "types/enums.h"

diff --git a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
index 3a04cb57538b48c7957cc540d8775f23922a4677..0be4be644d987e9eecf22b6a64f4457644cfe755 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
+++ b/src/gromacs/mdlib/nbnxn_kernels/nbnxn_kernel_ref.c
@@ -41,7 +41,7 @@
 
 #include "typedefs.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "force.h"
 #include "gmx_omp_nthreads.h"
 #include "nbnxn_kernel_ref.h"

diff --git a/src/gromacs/mdlib/nbnxn_search.c b/src/gromacs/mdlib/nbnxn_search.c
index 5466bb5288ed738503dfa0e73bfac4e35b6c9d75..a2fe52a902444d28aed1f1bfde137d8bde2082a6 100644 (file)
--- a/src/gromacs/mdlib/nbnxn_search.c
+++ b/src/gromacs/mdlib/nbnxn_search.c
@@ -42,7 +42,7 @@
 #include <assert.h>
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"

diff --git a/src/gromacs/mdlib/ns.c b/src/gromacs/mdlib/ns.c
index 491d53ee0eba9a28364940caf12ff13974cdc7cf..6558e2be9cfe51e3347fb4c7b8f180169c34144f 100644 (file)
--- a/src/gromacs/mdlib/ns.c
+++ b/src/gromacs/mdlib/ns.c
@@ -41,7 +41,7 @@
 #include <math.h>
 #include <string.h>
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "gromacs/math/utilities.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/nsgrid.c b/src/gromacs/mdlib/nsgrid.c
index fe8eb6591317eca4da225ff11a582ff71adf6594..137b06f25559d6ef13d92f79586b1e2e76dc9a69 100644 (file)
--- a/src/gromacs/mdlib/nsgrid.c
+++ b/src/gromacs/mdlib/nsgrid.c
@@ -45,7 +45,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "nsgrid.h"
 #include "gmx_fatal.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/pme.c b/src/gromacs/mdlib/pme.c
index bd2a5a6a591f721293ee8f86c3ddcb913aea2082..17eb6482d157f672699247b292b494a0eaf78cd6 100644 (file)
--- a/src/gromacs/mdlib/pme.c
+++ b/src/gromacs/mdlib/pme.c
@@ -68,7 +68,7 @@
 #include "typedefs.h"
 #include "txtdump.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "coulomb.h"
 #include "gmx_fatal.h"
 #include "pme.h"

diff --git a/src/gromacs/mdlib/pme_pp.c b/src/gromacs/mdlib/pme_pp.c
index 5ea913e7b55f07b5072cbf0482354a894698c4b6..7ed29b31171710a7b1ec89178562095287f6c32f 100644 (file)
--- a/src/gromacs/mdlib/pme_pp.c
+++ b/src/gromacs/mdlib/pme_pp.c
@@ -45,7 +45,7 @@
 #include <math.h>
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "vec.h"
 #include "pme.h"

diff --git a/src/gromacs/mdlib/qm_gamess.c b/src/gromacs/mdlib/qm_gamess.c
index 4fb34c20791ad0c682562c6b76164a9739f5883a..d3ba4ac4ab0a17e6b6f851d9f22f35cdfcd21cd9 100644 (file)
--- a/src/gromacs/mdlib/qm_gamess.c
+++ b/src/gromacs/mdlib/qm_gamess.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.
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "macros.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/qm_gaussian.c b/src/gromacs/mdlib/qm_gaussian.c
index e0d749c0fcf6bff78fdda4056b305fccf5530007..8e96ec739ab7874a63550927b66485e8ec13c657 100644 (file)
--- a/src/gromacs/mdlib/qm_gaussian.c
+++ b/src/gromacs/mdlib/qm_gaussian.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.
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "macros.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/qm_mopac.c b/src/gromacs/mdlib/qm_mopac.c
index a35c541f43f30227a7dbb0eb827ed04caade1e62..760e4e00589779fbf2ca03dca0be1ae3e384b7bf 100644 (file)
--- a/src/gromacs/mdlib/qm_mopac.c
+++ b/src/gromacs/mdlib/qm_mopac.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.
@@ -44,7 +44,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "macros.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/qm_orca.c b/src/gromacs/mdlib/qm_orca.c
index f9f87ce69c01aeb3f16fc85d77af5e50a3d0f9b2..db48238ff0e49722e742b0722a1ebaee3a54ee09 100644 (file)
--- a/src/gromacs/mdlib/qm_orca.c
+++ b/src/gromacs/mdlib/qm_orca.c
@@ -3,7 +3,7 @@
  *
  * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
  * Copyright (c) 2001-2008, 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.
@@ -42,7 +42,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "macros.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/qmmm.c b/src/gromacs/mdlib/qmmm.c
index b4fca75f1fd9b934ffdb0a088bb0b255f0370474..ad0b66e387d61550cb38c4e338b684b08ac5ecbb 100644 (file)
--- a/src/gromacs/mdlib/qmmm.c
+++ b/src/gromacs/mdlib/qmmm.c
@@ -43,7 +43,7 @@
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "macros.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/shakef.c b/src/gromacs/mdlib/shakef.c
index 950c45a1b56cc4d58555a331d8f15fb7c84b4359..ab09ea47b7afd7b1bd1f84b23cce2f622d93eaf2 100644 (file)
--- a/src/gromacs/mdlib/shakef.c
+++ b/src/gromacs/mdlib/shakef.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 <math.h>
 #include "sysstuff.h"
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "pbc.h"
 #include "txtdump.h"
 #include "vec.h"

diff --git a/src/gromacs/mdlib/shellfc.c b/src/gromacs/mdlib/shellfc.c
index 4cb1bb5a2f62bfe76b5b3f4a4bf6f23f97d92356..531b88b61673dc519f888287f881b43600db2a5b 100644 (file)
--- a/src/gromacs/mdlib/shellfc.c
+++ b/src/gromacs/mdlib/shellfc.c
@@ -41,7 +41,7 @@
 #include <string.h>
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "vec.h"
 #include "txtdump.h"

diff --git a/src/gromacs/mdlib/sim_util.c b/src/gromacs/mdlib/sim_util.c
index 77f958f204bd642d12f9ff7588ad9050f7f91f38..682f302775daa1511baf5c97fab203f5e9b4706f 100644 (file)
--- a/src/gromacs/mdlib/sim_util.c
+++ b/src/gromacs/mdlib/sim_util.c
@@ -48,7 +48,7 @@
 
 #include "typedefs.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "txtdump.h"
 #include "pbc.h"

diff --git a/src/gromacs/mdlib/stat.c b/src/gromacs/mdlib/stat.c
index f09e9ed4cad124330d3f8905e8dda1662c5df45f..393e4fe8840720bc125847f1e4196e5db61ff350 100644 (file)
--- a/src/gromacs/mdlib/stat.c
+++ b/src/gromacs/mdlib/stat.c
@@ -53,7 +53,7 @@
 #include "main.h"
 #include "force.h"
 #include "vcm.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "network.h"
 #include "rbin.h"

diff --git a/src/gromacs/mdlib/tables.c b/src/gromacs/mdlib/tables.c
index 61f69e2cff6837909ffc75ff854761180bdcbf42..ff73a90e89e5452f64cc7feb7d4f570675ac2011 100644 (file)
--- a/src/gromacs/mdlib/tables.c
+++ b/src/gromacs/mdlib/tables.c
@@ -42,7 +42,7 @@
 #include "gromacs/math/utilities.h"
 #include "typedefs.h"
 #include "names.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "gromacs/fileio/futil.h"
 #include "xvgr.h"

diff --git a/src/gromacs/mdlib/tgroup.c b/src/gromacs/mdlib/tgroup.c
index f56fd36d24d2a0a94539cf6e03d5de7fc72ea283..cd32b2477b56b8e75e481b042602e96f3e0ad10f 100644 (file)
--- a/src/gromacs/mdlib/tgroup.c
+++ b/src/gromacs/mdlib/tgroup.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.
@@ -43,12 +43,11 @@
 #include <math.h>
 #include "macros.h"
 #include "main.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "tgroup.h"
 #include "vec.h"
 #include "network.h"
-#include "smalloc.h"
 #include "update.h"
 #include "rbin.h"
 #include "mtop_util.h"

diff --git a/src/gromacs/mdlib/tpi.c b/src/gromacs/mdlib/tpi.c
index f5b67ad6788a8cdeedb62127d53a7d79e9291286..72a6901f9e221778df7c9781305f0ddf1b7bf3d0 100644 (file)
--- a/src/gromacs/mdlib/tpi.c
+++ b/src/gromacs/mdlib/tpi.c
@@ -43,7 +43,7 @@
 #include <math.h>
 #include "sysstuff.h"
 #include "network.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "main.h"
 #include "chargegroup.h"

diff --git a/src/gromacs/mdlib/update.c b/src/gromacs/mdlib/update.c
index 07dff61a036add354cdf83647e84d95972a195fb..0f96a357777491f7a468907277b86a1426224cfd 100644 (file)
--- a/src/gromacs/mdlib/update.c
+++ b/src/gromacs/mdlib/update.c
@@ -44,7 +44,7 @@
 
 #include "types/commrec.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "nrnb.h"
 #include "physics.h"

diff --git a/src/gromacs/mdlib/vcm.c b/src/gromacs/mdlib/vcm.c
index 91c9d9160e45accf1de4f6cb8686b172fe33139f..3be1995d4071a9cc1e0677a35076cafb999a908a 100644 (file)
--- a/src/gromacs/mdlib/vcm.c
+++ b/src/gromacs/mdlib/vcm.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.
@@ -42,7 +42,7 @@
 #include "macros.h"
 #include "vcm.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "txtdump.h"
 #include "network.h"

diff --git a/src/gromacs/mdlib/vsite.c b/src/gromacs/mdlib/vsite.c
index 220c6e91889f6a293c3e440291a8043edf5143cb..7ad217f4a5cae44f14ecd28358ec664185f51b3e 100644 (file)
--- a/src/gromacs/mdlib/vsite.c
+++ b/src/gromacs/mdlib/vsite.c
@@ -42,7 +42,7 @@
 #include "typedefs.h"
 #include "vsite.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "nrnb.h"
 #include "vec.h"
 #include "network.h"

diff --git a/src/gromacs/mdlib/wall.c b/src/gromacs/mdlib/wall.c
index ccfef14d44af0ab50c770b1e2e0176f3cc59ecf3..85a74eb4aef035394a95ba6b97b3be308294bca1 100644 (file)
--- a/src/gromacs/mdlib/wall.c
+++ b/src/gromacs/mdlib/wall.c
@@ -45,7 +45,7 @@
 #include "sysstuff.h"
 #include "typedefs.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "force.h"
 #include "gromacs/fileio/filenm.h"
 #include "nrnb.h"

diff --git a/src/gromacs/mdlib/wnblist.c b/src/gromacs/mdlib/wnblist.c
index cd0991201112c7ab900471f5568e7aadabf377a1..eb99f7a3a4491854facafbfd6f8c1a2ae35bfc67 100644 (file)
--- a/src/gromacs/mdlib/wnblist.c
+++ b/src/gromacs/mdlib/wnblist.c
@@ -42,7 +42,7 @@
 #include <stdio.h>
 #include <string.h>
 #include "force.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "ns.h"
 #include "nrnb.h"

diff --git a/src/gromacs/pulling/pull.c b/src/gromacs/pulling/pull.c
index 58dbd60c58e648c89cae7b127dfaab53750da48d..b2200918f8fc8212fee8b46725a698c495e10d00 100644 (file)
--- a/src/gromacs/pulling/pull.c
+++ b/src/gromacs/pulling/pull.c
@@ -51,7 +51,7 @@
 #include "network.h"
 #include "gromacs/fileio/filenm.h"
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "pull.h"
 #include "xvgr.h"
 #include "names.h"

diff --git a/src/gromacs/pulling/pull_rotation.c b/src/gromacs/pulling/pull_rotation.c
index 1fcd90ad47746b7be2b57df58490303272d143eb..cdee91efff60099565e5ec362f87bbdbe65d522b 100644 (file)
--- a/src/gromacs/pulling/pull_rotation.c
+++ b/src/gromacs/pulling/pull_rotation.c
@@ -43,7 +43,7 @@
 #include <string.h>
 
 #include "domdec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "network.h"
 #include "pbc.h"
 #include "mdrun.h"

diff --git a/src/gromacs/pulling/pullutil.c b/src/gromacs/pulling/pullutil.c
index 5ffc05787b454f39676ea1c85b623a78d49b93b3..6b30d111b12822545200731016531e58ac677176 100644 (file)
--- a/src/gromacs/pulling/pullutil.c
+++ b/src/gromacs/pulling/pullutil.c
@@ -44,7 +44,7 @@
 #include "princ.h"
 #include "gromacs/fileio/futil.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "types/commrec.h"
 #include "names.h"

diff --git a/src/gromacs/selection/compiler.cpp b/src/gromacs/selection/compiler.cpp
index 3d9ff0ba5a41b2effb151c05d6b905efe25c3721..2cc7655e150458f3219d01c6f28dad56a788dd0d 100644 (file)
--- a/src/gromacs/selection/compiler.cpp
+++ b/src/gromacs/selection/compiler.cpp
@@ -276,7 +276,6 @@
 #include <math.h>
 #include <stdarg.h>
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/selection/indexutil.h"
@@ -284,6 +283,7 @@
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "evaluate.h"

diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp
index 4339884d010e1093349e24b73afcaeb6cb72716d..0d67bb0c2d622f7bb622c530b916d6c4fcf72140 100644 (file)
--- a/src/gromacs/selection/evaluate.cpp
+++ b/src/gromacs/selection/evaluate.cpp
@@ -52,7 +52,6 @@
  */
 #include <string.h>
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/math/utilities.h"
@@ -62,6 +61,7 @@
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "evaluate.h"
 #include "mempool.h"

diff --git a/src/gromacs/selection/indexutil.cpp b/src/gromacs/selection/indexutil.cpp
index 770c4a9c082a4e8781c963771137214449f756c4..084577d365ca97fb3adacbec2a720a4327e17809 100644 (file)
--- a/src/gromacs/selection/indexutil.cpp
+++ b/src/gromacs/selection/indexutil.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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.
@@ -48,9 +48,9 @@
 
 #include "gromacs/legacyheaders/index.h"
 #include "gromacs/legacyheaders/gmx_fatal.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 
+#include "gromacs/utility/smalloc.h"
 
 /********************************************************************
  * gmx_ana_indexgrps_t functions

diff --git a/src/gromacs/selection/mempool.cpp b/src/gromacs/selection/mempool.cpp
index 13e90aad50f76c8fd5e5504107cf951946b6478e..177ff0f77bd7ab7993d622992e7dbff89d1fee1a 100644 (file)
--- a/src/gromacs/selection/mempool.cpp
+++ b/src/gromacs/selection/mempool.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2014, 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.
@@ -43,11 +43,10 @@
 
 #include <new>
 
-#include "gromacs/legacyheaders/smalloc.h"
-
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "mempool.h"
 

diff --git a/src/gromacs/selection/nbsearch.cpp b/src/gromacs/selection/nbsearch.cpp
index ffa113817f029e381c5792602b987b3394dedfd7..06ecbe62a37e417ebd5118ecff94f79711fd84c8 100644 (file)
--- a/src/gromacs/selection/nbsearch.cpp
+++ b/src/gromacs/selection/nbsearch.cpp
@@ -64,7 +64,6 @@
 
 #include "thread_mpi/mutex.h"
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/pbc.h"
 #include "gromacs/legacyheaders/vec.h"
@@ -72,6 +71,7 @@
 #include "gromacs/selection/position.h"
 #include "gromacs/utility/arrayref.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/params.cpp b/src/gromacs/selection/params.cpp
index f4cc64a6ca8c54abe4d4003d52fffd9f7ce2de91..28686b059e50a5495ae39271fd832b176240516c 100644 (file)
--- a/src/gromacs/selection/params.cpp
+++ b/src/gromacs/selection/params.cpp
@@ -42,7 +42,6 @@
 #include <algorithm>
 #include <string>
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/selection/position.h"
@@ -51,6 +50,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "parsetree.h"

diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp
index d7bb436172f8e6559e5a5227085df8cf2b3c747c..7f4566923dc45d57f5ac53fdb56a28945cc19063 100644 (file)
--- a/src/gromacs/selection/parsetree.cpp
+++ b/src/gromacs/selection/parsetree.cpp
@@ -226,14 +226,13 @@
 #include <boost/shared_ptr.hpp>
 
 #include "gromacs/fileio/futil.h"
-#include "gromacs/legacyheaders/smalloc.h"
-
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"

diff --git a/src/gromacs/selection/poscalc.cpp b/src/gromacs/selection/poscalc.cpp
index bceff0039ee5acbcba0a9269a767b94458ac3835..1f1757237605121e7c9819415a433fc178f5d83c 100644 (file)
--- a/src/gromacs/selection/poscalc.cpp
+++ b/src/gromacs/selection/poscalc.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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.
@@ -61,7 +61,6 @@
  */
 #include <string.h>
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/pbc.h"
 #include "gromacs/legacyheaders/vec.h"
@@ -72,6 +71,7 @@
 #include "gromacs/selection/position.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/position.cpp b/src/gromacs/selection/position.cpp
index 4521730fec93285d3c18acea3d8e3d9ab67fb7a1..fe89b9ff6a99c253ee686b372b184fa8bbe2e67f 100644 (file)
--- a/src/gromacs/selection/position.cpp
+++ b/src/gromacs/selection/position.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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.
@@ -43,12 +43,12 @@
 
 #include <string.h>
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 gmx_ana_pos_t::gmx_ana_pos_t()
 {

diff --git a/src/gromacs/selection/scanner_internal.cpp b/src/gromacs/selection/scanner_internal.cpp
index c26f8759be52acca3f8b1e73a3df6b3a6388b5d6..0c982d99a1abb3cd742ea463aa3b233fa62ac6d6 100644 (file)
--- a/src/gromacs/selection/scanner_internal.cpp
+++ b/src/gromacs/selection/scanner_internal.cpp
@@ -57,12 +57,12 @@
 #include <string>
 
 #include "gromacs/legacyheaders/typedefs.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/string2.h"
 
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "parsetree.h"

diff --git a/src/gromacs/selection/selectioncollection.cpp b/src/gromacs/selection/selectioncollection.cpp
index 18bcff9838d8ce7afd5d42ea9e512f54b3bf4334..09f24e03c5faf90968ef74b3c38fd6c1801f57a8 100644 (file)
--- a/src/gromacs/selection/selectioncollection.cpp
+++ b/src/gromacs/selection/selectioncollection.cpp
@@ -50,7 +50,6 @@
 #include <boost/shared_ptr.hpp>
 
 #include "gromacs/legacyheaders/oenv.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/xvgr.h"
 
 #include "gromacs/onlinehelp/helpmanager.h"
@@ -62,6 +61,7 @@
 #include "gromacs/utility/file.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/messagestringcollector.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "compiler.h"

diff --git a/src/gromacs/selection/selelem.cpp b/src/gromacs/selection/selelem.cpp
index 804ce7d726a666c2c930cf45ff8cd02da955ba99..01d7c6f77a6adf7bccec8536245294753a908358 100644 (file)
--- a/src/gromacs/selection/selelem.cpp
+++ b/src/gromacs/selection/selelem.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2011,2012,2013,2014, 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.
@@ -41,14 +41,13 @@
  */
 #include <cstring>
 
-#include "gromacs/legacyheaders/smalloc.h"
-
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "keywords.h"

diff --git a/src/gromacs/selection/selvalue.cpp b/src/gromacs/selection/selvalue.cpp
index 9d7905a8716eed22631f389b1b040b3db48708a4..18a51f0a2601bc87256a454ab87ffc6642aa5df5 100644 (file)
--- a/src/gromacs/selection/selvalue.cpp
+++ b/src/gromacs/selection/selvalue.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2009,2010,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2009,2010,2012,2013,2014, 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.
@@ -39,12 +39,11 @@
  * \author Teemu Murtola <teemu.murtola@gmail.com>
  * \ingroup module_selection
  */
-#include "gromacs/legacyheaders/smalloc.h"
-
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selvalue.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 /*!
  * \param[out] val  Output structure

diff --git a/src/gromacs/selection/sm_compare.cpp b/src/gromacs/selection/sm_compare.cpp
index 79a827060e3496c8d3e2eca087db2c6072ceac04..7c12dd9a5fe0caf3413f7f17ea57ddfeecd7be54 100644 (file)
--- a/src/gromacs/selection/sm_compare.cpp
+++ b/src/gromacs/selection/sm_compare.cpp
@@ -42,12 +42,12 @@
 #include <cmath>
 
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
 
 #include "gromacs/math/utilities.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
 
 /** Defines the comparison operator for comparison expressions. */
 typedef enum

diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp
index 51afaddf5e2a805ceb3dba90e9d64ca2e089e0ed..f9b8e736f739ee9a516a8074eec8043237229cfe 100644 (file)
--- a/src/gromacs/selection/sm_insolidangle.cpp
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -119,7 +119,6 @@
 #include "gromacs/legacyheaders/macros.h"
 #include "gromacs/legacyheaders/pbc.h"
 #include "gromacs/legacyheaders/physics.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/math/utilities.h"
@@ -128,6 +127,7 @@
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "selelem.h"
 

diff --git a/src/gromacs/selection/sm_keywords.cpp b/src/gromacs/selection/sm_keywords.cpp
index e2c9e23e8164d947324591d3fbbcb8fc30dc4507..11e458090c91a6205e9e7c4a3260ed6956992eb6 100644 (file)
--- a/src/gromacs/selection/sm_keywords.cpp
+++ b/src/gromacs/selection/sm_keywords.cpp
@@ -48,7 +48,6 @@
 #include <boost/shared_ptr.hpp>
 
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/string2.h"
 
 #include "gromacs/selection/selmethod.h"
@@ -56,6 +55,7 @@
 #include "gromacs/utility/gmxregex.h"
 #include "gromacs/utility/messagestringcollector.h"
 #include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/selection/sm_merge.cpp b/src/gromacs/selection/sm_merge.cpp
index a55202528186393d73c1ac6dc320808190cfbe90..258dc85d1f3cc14e608e8493e80f8ede49744286 100644 (file)
--- a/src/gromacs/selection/sm_merge.cpp
+++ b/src/gromacs/selection/sm_merge.cpp
@@ -40,13 +40,13 @@
  * \ingroup module_selection
  */
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/common.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
 
 /*! \internal \brief
  * Data structure for the merging selection modifiers.

diff --git a/src/gromacs/selection/sm_permute.cpp b/src/gromacs/selection/sm_permute.cpp
index 553eea3e217acfb06218123cdae44c843f6822b3..b9a194d0f33720908a6a4d89217dce21f121e58c 100644 (file)
--- a/src/gromacs/selection/sm_permute.cpp
+++ b/src/gromacs/selection/sm_permute.cpp
@@ -40,12 +40,12 @@
  * \ingroup module_selection
  */
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 /*! \internal \brief

diff --git a/src/gromacs/selection/sm_position.cpp b/src/gromacs/selection/sm_position.cpp
index f0b6fb1a6847d4c0449224b799542f546866bb73..01be21a972d7b6613bddb8406d684dab59decd4f 100644 (file)
--- a/src/gromacs/selection/sm_position.cpp
+++ b/src/gromacs/selection/sm_position.cpp
@@ -40,13 +40,13 @@
  * \ingroup module_selection
  */
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/string2.h"
 
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "keywords.h"
 #include "selelem.h"

diff --git a/src/gromacs/selection/sm_same.cpp b/src/gromacs/selection/sm_same.cpp
index a7d073f0c4f8a8cf7dd33dde3afe7917a270ff43..71192b842d9c01eece0ef71422dcae99891840aa 100644 (file)
--- a/src/gromacs/selection/sm_same.cpp
+++ b/src/gromacs/selection/sm_same.cpp
@@ -42,10 +42,10 @@
 #include <stdlib.h>
 
 #include "gromacs/legacyheaders/macros.h"
-#include "gromacs/legacyheaders/smalloc.h"
 
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/selection/tests/nbsearch.cpp b/src/gromacs/selection/tests/nbsearch.cpp
index 6782ab8a599c74c5a090a72f2fd6b0a000b5d72a..0ecf04b6e1af0738ea1d3b092d59a8c752412aff 100644 (file)
--- a/src/gromacs/selection/tests/nbsearch.cpp
+++ b/src/gromacs/selection/tests/nbsearch.cpp
@@ -52,12 +52,12 @@
 #include <set>
 #include <vector>
 
-#include "gromacs/random/random.h"
 #include "gromacs/legacyheaders/pbc.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/selection/nbsearch.h"
+#include "gromacs/random/random.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "testutils/testasserts.h"
 

diff --git a/src/gromacs/selection/tests/poscalc.cpp b/src/gromacs/selection/tests/poscalc.cpp
index 177912e487a67f6b3af3c40182b82a0dedc42a3f..ba2b25d52f41f3a40b27e17e10a944cd82cfafbb 100644 (file)
--- a/src/gromacs/selection/tests/poscalc.cpp
+++ b/src/gromacs/selection/tests/poscalc.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * 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.
@@ -43,13 +43,13 @@
 
 #include <vector>
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/uniqueptr.h"
 
 #include "testutils/refdata.h"

diff --git a/src/gromacs/selection/tests/toputils.cpp b/src/gromacs/selection/tests/toputils.cpp
index b9d2a52e85e883a5a596cbb158152f051474e4a0..1e55142ee2bb5b49d6395e0646cbcc9f4a6b81cc 100644 (file)
--- a/src/gromacs/selection/tests/toputils.cpp
+++ b/src/gromacs/selection/tests/toputils.cpp
@@ -43,13 +43,13 @@
 
 #include <cstring>
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/typedefs.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/fileio/tpxio.h"
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "testutils/testfilemanager.h"
 

diff --git a/src/gromacs/statistics/statistics.c b/src/gromacs/statistics/statistics.c
index 0a984ae462b79e398e52101184cee6e0bbb1d226..21fadecf2f13e076923e3d68d25f0bdca3c5b7ba 100644 (file)
--- a/src/gromacs/statistics/statistics.c
+++ b/src/gromacs/statistics/statistics.c
@@ -40,7 +40,7 @@
 #endif
 #include <math.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 
 static int gmx_dnint(double x)

diff --git a/src/gromacs/statistics/statistics_test.c b/src/gromacs/statistics/statistics_test.c
index c5fee43be9f429a4a3b789b897c317cc70d8ce52..6d31816c4cd195691dbed9ccf422a7e63fcfcf11 100644 (file)
--- a/src/gromacs/statistics/statistics_test.c
+++ b/src/gromacs/statistics/statistics_test.c
@@ -40,7 +40,7 @@
 
 #include <stdio.h>
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "vec.h"
 #include "gromacs/random/random.h"
 #include "statistics.h"

diff --git a/src/gromacs/swap/swapcoords.c b/src/gromacs/swap/swapcoords.c
index 196023248061cea0d5309974d5b4f7139ebad90a..4a0816757581f4cc6778e6d92bd1277dd2237be8 100644 (file)
--- a/src/gromacs/swap/swapcoords.c
+++ b/src/gromacs/swap/swapcoords.c
@@ -49,7 +49,7 @@
 #include <time.h>
 #include "typedefs.h"
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/mdlib/groupcoord.h"
 #include "mtop_util.h"
 #include "macros.h"

diff --git a/src/gromacs/timing/wallcycle.c b/src/gromacs/timing/wallcycle.c
index 5b6c93161ac714a0701a53d2185fed99c7c815b6..2be9d858606c710f7e649706309ed4fc8aa5f087 100644 (file)
--- a/src/gromacs/timing/wallcycle.c
+++ b/src/gromacs/timing/wallcycle.c
@@ -42,7 +42,7 @@
 
 #include <string.h>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "md_logging.h"
 #include "string2.h"

diff --git a/src/gromacs/timing/walltime_accounting.c b/src/gromacs/timing/walltime_accounting.c
index b52d3e979a396ebf9d4382e33a1fcedbe2b33b09..ec256b22730656de4a25d9f39352d96410aab715 100644 (file)
--- a/src/gromacs/timing/walltime_accounting.c
+++ b/src/gromacs/timing/walltime_accounting.c
@@ -2,7 +2,7 @@
  * This file is part of the GROMACS molecular simulation package.
  *
  * Copyright (c) 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.
@@ -39,9 +39,6 @@
 #include <config.h>
 #endif
 
-#include "gromacs/legacyheaders/smalloc.h"
-#include "gromacs/legacyheaders/types/simple.h"
-
 #include <time.h>
 #ifdef HAVE_UNISTD_H
 #include <unistd.h>
@@ -50,6 +47,10 @@
 #include <sys/time.h>
 #endif
 
+#include "gromacs/legacyheaders/types/simple.h"
+
+#include "gromacs/utility/smalloc.h"
+
 /* TODO in future: convert gmx_walltime_accounting to a class,
  * resolve who should have responsibility for recording the number of
  * steps done, consider whether parts of finish_time, print_perf,

diff --git a/src/gromacs/tools/check.c b/src/gromacs/tools/check.c
index 9ff46e19782f3fc433322e8f847055f674b3f953..3d166cf465bba208a69497e52796fc7230842e95 100644 (file)
--- a/src/gromacs/tools/check.c
+++ b/src/gromacs/tools/check.c
@@ -53,7 +53,7 @@
 #include "pbc.h"
 #include "physics.h"
 #include "index.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "mtop_util.h"
 #include "gromacs/fileio/futil.h"

diff --git a/src/gromacs/tools/compare.c b/src/gromacs/tools/compare.c
index cef2d70117b6d040895c7055adab9fbb0d05fbce..9f027e732ee3e7f239398f06780c4c42a7f1d439 100644 (file)
--- a/src/gromacs/tools/compare.c
+++ b/src/gromacs/tools/compare.c
@@ -44,7 +44,7 @@
 #include <string.h>
 #include "main.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/fileio/futil.h"
 #include "sysstuff.h"
 #include "txtdump.h"

diff --git a/src/gromacs/tools/convert_tpr.c b/src/gromacs/tools/convert_tpr.c
index 40df603bfb72842757ddd5064cf67059e08e27b4..08c264e97e52a5198f92611c8f09f08fa1092d44 100644 (file)
--- a/src/gromacs/tools/convert_tpr.c
+++ b/src/gromacs/tools/convert_tpr.c
@@ -42,7 +42,7 @@
 #include "index.h"
 #include "gmx_fatal.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "names.h"
 #include "typedefs.h"

diff --git a/src/gromacs/tools/dump.c b/src/gromacs/tools/dump.c
index 452f2c5e3995d52414b4379b52a333b53b4eebc8..ad94ac7162c9f21f836d86af3e408af44d8f6251 100644 (file)
--- a/src/gromacs/tools/dump.c
+++ b/src/gromacs/tools/dump.c
@@ -48,7 +48,7 @@
 #include "sysstuff.h"
 #include "txtdump.h"
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "names.h"
 #include "txtdump.h"
 #include "gromacs/gmxpreprocess/gmxcpp.h"

diff --git a/src/gromacs/trajectoryanalysis/analysissettings.cpp b/src/gromacs/trajectoryanalysis/analysissettings.cpp
index bd362034812e74837b183ba0839b06f5a9ebfbbf..6cfc1d20d7597ea7b3a883045afc3c9b20851036 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysissettings.cpp
+++ b/src/gromacs/trajectoryanalysis/analysissettings.cpp
@@ -1,7 +1,7 @@
 /*
  * This file is part of the GROMACS molecular simulation package.
  *
- * Copyright (c) 2010,2011,2012,2013, by the GROMACS development team, led by
+ * Copyright (c) 2010,2011,2012,2013,2014, 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.
@@ -41,11 +41,11 @@
  */
 #include "analysissettings.h"
 
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/fileio/trxio.h"
 #include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "analysissettings-impl.h"
 

diff --git a/src/gromacs/trajectoryanalysis/modules/nsc.c b/src/gromacs/trajectoryanalysis/modules/nsc.c
index df89b3989449cdffb3730f2aa81019fe3899d118..ab27dae4e32c7c477d252bd4f56c224a28dd3290 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/nsc.c
+++ b/src/gromacs/trajectoryanalysis/modules/nsc.c
@@ -47,7 +47,7 @@
 #include "pbc.h"
 #include "macros.h"
 #include "vec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "nsc.h"
 
 #define TEST_NSC 0

diff --git a/src/gromacs/trajectoryanalysis/modules/sasa.cpp b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
index d20fd2f3eb59c132badb00aecc8a56204d7cb295..eb7a3d3e69b215282c4ae987ce4151b690ec0e30 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/sasa.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/sasa.cpp
@@ -51,7 +51,6 @@
 #include "gromacs/legacyheaders/copyrite.h"
 #include "gromacs/legacyheaders/pbc.h"
 #include "gromacs/legacyheaders/physics.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/symtab.h"
 #include "gromacs/legacyheaders/vec.h"
 
@@ -70,6 +69,7 @@
 #include "gromacs/trajectoryanalysis/analysissettings.h"
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/scoped_ptr_sfree.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "nsc.h"

diff --git a/src/gromacs/trajectoryanalysis/modules/select.cpp b/src/gromacs/trajectoryanalysis/modules/select.cpp
index ea00c6732ce37db93bfb33a71d440cd641433bce..fc8f592e93ebcd19a2a9773d47d53fd283222abe 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/select.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/select.cpp
@@ -49,8 +49,6 @@
 #include <string>
 #include <vector>
 
-#include "gromacs/legacyheaders/smalloc.h"
-
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datamodule.h"
@@ -69,6 +67,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/scoped_ptr_sfree.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 namespace gmx

diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp
index 62793a6e932919cb743d58a3acd95eced41effae..b69fe77f497b1676beff499c601919d9977dc5be 100644 (file)
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -49,7 +49,6 @@
 
 #include "gromacs/legacyheaders/oenv.h"
 #include "gromacs/legacyheaders/rmpbc.h"
-#include "gromacs/legacyheaders/smalloc.h"
 #include "gromacs/legacyheaders/vec.h"
 
 #include "gromacs/fileio/timecontrol.h"
@@ -65,6 +64,7 @@
 #include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/programcontext.h"
+#include "gromacs/utility/smalloc.h"
 #include "gromacs/utility/stringutil.h"
 
 #include "analysissettings-impl.h"

diff --git a/src/gromacs/utility/CMakeLists.txt b/src/gromacs/utility/CMakeLists.txt
index def7b9691be7e5c6a0a9b530a6429446d4e9b005..17bfe7391782b32582df96ce56bf271ccd916e96 100644 (file)
--- a/src/gromacs/utility/CMakeLists.txt
+++ b/src/gromacs/utility/CMakeLists.txt
@@ -50,6 +50,7 @@ set(UTILITY_PUBLIC_HEADERS
     gmxassert.h
     init.h
     programcontext.h
+    smalloc.h
     stringutil.h
     uniqueptr.h)
 gmx_install_headers(utility ${UTILITY_PUBLIC_HEADERS})

diff --git a/src/gromacs/utility/scoped_ptr_sfree.h b/src/gromacs/utility/scoped_ptr_sfree.h
index 1fd0fa3369d98d2d08f54a5b2249a9133564e5b8..3c1077ccaea4f97b63fcf114a972ed4ad3f0fe7b 100644 (file)
--- a/src/gromacs/utility/scoped_ptr_sfree.h
+++ b/src/gromacs/utility/scoped_ptr_sfree.h
@@ -43,8 +43,8 @@
 #ifndef GMX_UTILITY_SCOPED_PTR_SFREE_H
 #define GMX_UTILITY_SCOPED_PTR_SFREE_H
 
-#include "../legacyheaders/smalloc.h"
 #include "common.h"
+#include "gromacs/utility/smalloc.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/gmxlib/smalloc.c b/src/gromacs/utility/smalloc.c
similarity index 98%
rename from src/gromacs/gmxlib/smalloc.c
rename to src/gromacs/utility/smalloc.c
index 70c709b16c08a6e2306ef876f56e2df04c0d98da..13e782f1b58953205b36db9f1e8acba2ae8f8c53 100644 (file)
--- a/src/gromacs/gmxlib/smalloc.c
+++ b/src/gromacs/utility/smalloc.c
@@ -34,24 +34,26 @@
  * 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 "gromacs/utility/smalloc.h"
+
 #ifdef HAVE_CONFIG_H
 #include <config.h>
 #endif
 
-/* This file is completely threadsafe - keep it that way! */
-
-#include "gromacs/utility/gmxmpi.h"
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "gmx_fatal.h"
-#include "smalloc.h"
-#include "main.h"
+
 #ifdef WITH_DMALLOC
 #include <dmalloc.h>
 #endif
 
+#include "gromacs/legacyheaders/gmx_fatal.h"
+
+#ifdef PRINT_ALLOC_KB
+#include "gromacs/utility/gmxmpi.h"
+#endif
+
 #ifdef DEBUG
 #include "thread_mpi/threads.h"
 

diff --git a/src/gromacs/legacyheaders/smalloc.h b/src/gromacs/utility/smalloc.h
similarity index 99%
rename from src/gromacs/legacyheaders/smalloc.h
rename to src/gromacs/utility/smalloc.h
index 87d04017df5fe94a0068ead15b29a663c42a8045..0d1aa3aaed042c91c9cd19a63b34a6d88dbbceaa 100644 (file)
--- a/src/gromacs/legacyheaders/smalloc.h
+++ b/src/gromacs/utility/smalloc.h
@@ -66,9 +66,10 @@
  * \endif
  *
  * \inpublicapi
+ * \ingroup module_utility
  */
-#ifndef _smalloc_h
-#define _smalloc_h
+#ifndef GMX_UTILITY_SMALLOC_H
+#define GMX_UTILITY_SMALLOC_H
 
 #include <stddef.h>
 
@@ -281,7 +282,7 @@ void gmx_snew_aligned_impl(const char *name, const char *file, int line,
  * \param[in]  size Number of bytes to allocate.
  *
  * Allocates memory for \p size bytes and sets this to \p ptr.
- * The allocated memory is not initialized.
+ * The allocated memory is initialized to zero.
  *
  * \hideinitializer
  */

diff --git a/src/programs/mdrun/md.c b/src/programs/mdrun/md.c
index f6b41af0d0d88c5e5ce3000f4a0fe0dd669849e7..2aece97cba26e17530ee416bd5bf7c0a4220e7a5 100644 (file)
--- a/src/programs/mdrun/md.c
+++ b/src/programs/mdrun/md.c
@@ -39,7 +39,7 @@
 #endif
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "vec.h"
 #include "vcm.h"

diff --git a/src/programs/mdrun/membed.c b/src/programs/mdrun/membed.c
index 5f64e5d84e29b97537d4f31c035ad263f0f0430e..8082ac764dffaf8dcb9869e3116ba13983b4ed1f 100644 (file)
--- a/src/programs/mdrun/membed.c
+++ b/src/programs/mdrun/membed.c
@@ -40,7 +40,7 @@
 #include <stdlib.h>
 #include "typedefs.h"
 #include "types/commrec.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "vec.h"
 #include "macros.h"

diff --git a/src/programs/mdrun/pme_loadbal.c b/src/programs/mdrun/pme_loadbal.c
index 1caf80e26d77bf8885d6c9b84dff56e19147f1f5..e88b4b3b457fe17cb9c598bbe287a48dff591e82 100644 (file)
--- a/src/programs/mdrun/pme_loadbal.c
+++ b/src/programs/mdrun/pme_loadbal.c
@@ -36,7 +36,7 @@
 #include <config.h>
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "types/commrec.h"
 #include "network.h"
 #include "calcgrid.h"

diff --git a/src/programs/mdrun/repl_ex.c b/src/programs/mdrun/repl_ex.c
index 21a5426c09d761362e74ffae0e66585fdc79a85c..d52bf5b95f9b250afb598d4f027ca04d3d6a275b 100644 (file)
--- a/src/programs/mdrun/repl_ex.c
+++ b/src/programs/mdrun/repl_ex.c
@@ -42,7 +42,7 @@
 #include "repl_ex.h"
 #include "network.h"
 #include "gromacs/random/random.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "physics.h"
 #include "copyrite.h"
 #include "macros.h"

diff --git a/src/programs/mdrun/runner.c b/src/programs/mdrun/runner.c
index f40e4c8422a476781a8c911149682e91ddc079a6..a0d7b7f8a4eb3f811424b7b5416f01511a03fa71 100644 (file)
--- a/src/programs/mdrun/runner.c
+++ b/src/programs/mdrun/runner.c
@@ -46,7 +46,7 @@
 #include <assert.h>
 
 #include "typedefs.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "copyrite.h"
 #include "force.h"

diff --git a/src/programs/view/buttons.cpp b/src/programs/view/buttons.cpp
index e734b0d2320381c4bcce576541c1cbcafaa7d488..3d5d76145c9cfeaa411bbe90a196d16fa6c12317 100644 (file)
--- a/src/programs/view/buttons.cpp
+++ b/src/programs/view/buttons.cpp
@@ -43,7 +43,7 @@
 #include <algorithm>
 
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 
 #include "x11.h"

diff --git a/src/programs/view/dialogs.cpp b/src/programs/view/dialogs.cpp
index 7ec4b24e9bf545d71217b58ca4c99adf57001d8f..d6927223409e578ae62bedb7591465e1ca4f5f38 100644 (file)
--- a/src/programs/view/dialogs.cpp
+++ b/src/programs/view/dialogs.cpp
@@ -42,7 +42,7 @@
 #include <unistd.h> // for fork()
 #endif
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "sysstuff.h"
 #include "macros.h"
 #include "string2.h"

diff --git a/src/programs/view/fgrid.cpp b/src/programs/view/fgrid.cpp
index 3c77f0d0954085d21624f22042c45ac6c00684b4..5228af0f619e69589ec410f6e5399cc9e8b5f379 100644 (file)
--- a/src/programs/view/fgrid.cpp
+++ b/src/programs/view/fgrid.cpp
@@ -43,7 +43,7 @@
 #include <string.h>
 #include <ctype.h>
 #include "string2.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "fgrid.h"
 #include "gromacs/fileio/futil.h"
 

diff --git a/src/programs/view/filter.cpp b/src/programs/view/filter.cpp
index b030d043c7f866a7cbeeb48d5255cc525be104d7..1acaa8c42bad028d95ddb069292e39c5f60dc865 100644 (file)
--- a/src/programs/view/filter.cpp
+++ b/src/programs/view/filter.cpp
@@ -44,7 +44,7 @@
 
 #include "sysstuff.h"
 #include "gromacs/fileio/futil.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "index.h"
 #include "xdlghi.h"

diff --git a/src/programs/view/logo.cpp b/src/programs/view/logo.cpp
index 38c29f835f1f343c3f55ac7ae051f6b9fb9a2038..11ef88b9664d9632fb8110304b8fb994e45fbbba 100644 (file)
--- a/src/programs/view/logo.cpp
+++ b/src/programs/view/logo.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.
@@ -42,7 +42,7 @@
 #include "macros.h"
 #include "xutil.h"
 #include "Xstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "copyrite.h"
 #include "logo.h"
 

diff --git a/src/programs/view/manager.cpp b/src/programs/view/manager.cpp
index 7a061ee417ed495e059abaa31af5f9a6dbeb7dc0..3d51c31aa22dc730086a34357624e7b6009938c2 100644 (file)
--- a/src/programs/view/manager.cpp
+++ b/src/programs/view/manager.cpp
@@ -46,9 +46,8 @@
 #endif
 
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
-#include "smalloc.h"
 #include "macros.h"
 #include "atomprop.h"
 #include "names.h"

diff --git a/src/programs/view/molps.cpp b/src/programs/view/molps.cpp
index 37e64ba8c87f320ff6cac423b520f4967ba84d8a..e947a0ed50c89f8f4ea37f27fe18c74f6d198eba 100644 (file)
--- a/src/programs/view/molps.cpp
+++ b/src/programs/view/molps.cpp
@@ -41,7 +41,7 @@
 #include <math.h>
 #include "sysstuff.h"
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "xutil.h"
 #include "gmx_fatal.h"

diff --git a/src/programs/view/nleg.cpp b/src/programs/view/nleg.cpp
index 307b5c347e561e458b48b076435a0e698dbe1ad5..61a643610fa751a1ccba2fe397e3988c9eda19a0 100644 (file)
--- a/src/programs/view/nleg.cpp
+++ b/src/programs/view/nleg.cpp
@@ -43,7 +43,7 @@
 #include <algorithm>
 
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "buttons.h"
 #include "nleg.h"

diff --git a/src/programs/view/nmol.cpp b/src/programs/view/nmol.cpp
index 2155810c8d64d4299555db8f6da7ff9c670ed73d..5a6866fff4de98517d193ea23c2011a2f06b35c0 100644 (file)
--- a/src/programs/view/nmol.cpp
+++ b/src/programs/view/nmol.cpp
@@ -41,7 +41,7 @@
 #include <math.h>
 #include "sysstuff.h"
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "xutil.h"
 #include "gromacs/math/3dview.h"

diff --git a/src/programs/view/popup.cpp b/src/programs/view/popup.cpp
index d608e37a6e49f9467593fda63b3f4814e43d2919..0f5ec8cd6c1ff523dd86fdf9e1e28591d819c2d6 100644 (file)
--- a/src/programs/view/popup.cpp
+++ b/src/programs/view/popup.cpp
@@ -44,7 +44,7 @@
 #include <algorithm>
 
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 
 #include "x11.h"
 #include "xutil.h"

diff --git a/src/programs/view/pulldown.cpp b/src/programs/view/pulldown.cpp
index f09ddb02ae60b13267e7f3dd297500d5e1f6f7f6..4034e6ae2937272f534e57512e508892153f3dbd 100644 (file)
--- a/src/programs/view/pulldown.cpp
+++ b/src/programs/view/pulldown.cpp
@@ -42,7 +42,7 @@
 
 #include <algorithm>
 
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 
 #include "x11.h"

diff --git a/src/programs/view/view.cpp b/src/programs/view/view.cpp
index 7766574c8cc664c5c75bf2cf1edaa94d5b052241..2408ced16fa1bf4253f79a751ca7d277ba49e647 100644 (file)
--- a/src/programs/view/view.cpp
+++ b/src/programs/view/view.cpp
@@ -43,7 +43,7 @@
 
 #include "sysstuff.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "gmx_fatal.h"
 #include "typedefs.h"
 #include "gromacs/commandline/pargs.h"

diff --git a/src/programs/view/x11.cpp b/src/programs/view/x11.cpp
index 09dfa370c7ef7b31312b986a2653e6371ca5c199..e30b6f1a8d8330a54798b55681e42090e53bcbd2 100644 (file)
--- a/src/programs/view/x11.cpp
+++ b/src/programs/view/x11.cpp
@@ -41,7 +41,7 @@
 #include <string.h>
 #include "typedefs.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "Xstuff.h"
 #include "x11.h"
 

diff --git a/src/programs/view/xdlg.cpp b/src/programs/view/xdlg.cpp
index 0e3b76dec3095374a44b63e4cfffdd1e4b55e33e..31321d0904560e4906d08c2332dad81f04f6febd 100644 (file)
--- a/src/programs/view/xdlg.cpp
+++ b/src/programs/view/xdlg.cpp
@@ -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.
@@ -43,7 +43,7 @@
 #include <string.h>
 #include "string2.h"
 #include "macros.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "Xstuff.h"
 #include "xutil.h"
 #include "xdlg.h"

diff --git a/src/programs/view/xdlghi.cpp b/src/programs/view/xdlghi.cpp
index 367dcacbb5002d03feab69757d78d0f83c99a751..252a65db0aa2d6c1ef10486fd7c1ecded2c1c9e0 100644 (file)
--- a/src/programs/view/xdlghi.cpp
+++ b/src/programs/view/xdlghi.cpp
@@ -45,7 +45,7 @@
 #include "gmx_fatal.h"
 #include "string2.h"
 #include "sysstuff.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "xutil.h"
 #include "xdlghi.h"

diff --git a/src/programs/view/xdlgitem.cpp b/src/programs/view/xdlgitem.cpp
index ecadf2ca1318cb7ba684d9f1f5ddc055f59a341d..590bf733240a7e36d2c6167af45cc258f0730a7c 100644 (file)
--- a/src/programs/view/xdlgitem.cpp
+++ b/src/programs/view/xdlgitem.cpp
@@ -46,7 +46,7 @@
 #include <algorithm>
 
 #include "gmx_fatal.h"
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "macros.h"
 #include "Xstuff.h"
 #include "xdlgitem.h"

diff --git a/src/programs/view/xutil.cpp b/src/programs/view/xutil.cpp
index ceb474be19ab88f5414e56b1e7da1d8bb988cb21..6402306be9ce42a6d90d06bf92856e3c40e0c85e 100644 (file)
--- a/src/programs/view/xutil.cpp
+++ b/src/programs/view/xutil.cpp
@@ -41,7 +41,7 @@
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
-#include "smalloc.h"
+#include "gromacs/utility/smalloc.h"
 #include "typedefs.h"
 #include "xutil.h"
 #include "Xstuff.h"