Merge fatalerror into utility.

Also adjusted a few includes from <...> to "..." in the touched files.

Closes #906, see the issue for details.

Change-Id: I291bfc6a004f6a3b9c3f8c1de8f724320591a5c6

diff --git a/src/gromacs/CMakeLists.txt b/src/gromacs/CMakeLists.txt
index 5b586a19c7da2ad04875ddb237c3495bcbd957e4..aedc5a11802a0bec1d19a9963a78e488b6159cae 100644 (file)
--- a/src/gromacs/CMakeLists.txt
+++ b/src/gromacs/CMakeLists.txt
@@ -5,7 +5,6 @@ add_subdirectory(gmxlib)
 add_subdirectory(mdlib)
 add_subdirectory(gmxpreprocess)
 add_subdirectory(analysisdata)
-add_subdirectory(fatalerror)
 add_subdirectory(options)
 add_subdirectory(selection)
 add_subdirectory(trajectoryanalysis)

diff --git a/src/gromacs/analysisdata/abstractdata.cpp b/src/gromacs/analysisdata/abstractdata.cpp
index 6b412e34bcc3e7685dbd51f0211822617370fece..d1260cd23774afb7c5236f497d9782bc4d8da2c4 100644 (file)
--- a/src/gromacs/analysisdata/abstractdata.cpp
+++ b/src/gromacs/analysisdata/abstractdata.cpp
@@ -37,8 +37,8 @@
  */
 #include "gromacs/analysisdata/abstractdata.h"
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "abstractdata-impl.h"
 #include "dataframe.h"

diff --git a/src/gromacs/analysisdata/analysisdata.cpp b/src/gromacs/analysisdata/analysisdata.cpp
index 6a92df2766b5c35f4925cc2c45e67803f3b97c87..73fdc91c93875677006f9c2c203bbc24ef13d33a 100644 (file)
--- a/src/gromacs/analysisdata/analysisdata.cpp
+++ b/src/gromacs/analysisdata/analysisdata.cpp
@@ -40,8 +40,8 @@
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datastorage.h"
 #include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "analysisdata-impl.h"
 

diff --git a/src/gromacs/analysisdata/arraydata.cpp b/src/gromacs/analysisdata/arraydata.cpp
index 05c3a087b13dc75656eac00abeb38378bc0ef83e..30326e9ab9ef859fbe723329624b4c0abf6f5930 100644 (file)
--- a/src/gromacs/analysisdata/arraydata.cpp
+++ b/src/gromacs/analysisdata/arraydata.cpp
@@ -40,8 +40,8 @@
 #include <algorithm>
 
 #include "gromacs/analysisdata/dataframe.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/arraydata.h b/src/gromacs/analysisdata/arraydata.h
index 056e0097fd9c5f07b16a95016f9f1a39346da572..cc336b2031cef0002c1bd012afeebf6b5f6aa170 100644 (file)
--- a/src/gromacs/analysisdata/arraydata.h
+++ b/src/gromacs/analysisdata/arraydata.h
@@ -41,7 +41,7 @@
 
 #include <vector>
 
-#include "../fatalerror/gmxassert.h"
+#include "../utility/gmxassert.h"
 
 #include "abstractdata.h"
 #include "dataframe.h"

diff --git a/src/gromacs/analysisdata/dataframe.cpp b/src/gromacs/analysisdata/dataframe.cpp
index 45ca1a90ff2e1a50099b1e3c5062412c3a3809bc..88fb15296ada676feeb0050e69a8bb502a73d81e 100644 (file)
--- a/src/gromacs/analysisdata/dataframe.cpp
+++ b/src/gromacs/analysisdata/dataframe.cpp
@@ -37,7 +37,7 @@
  */
 #include "dataframe.h"
 
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/dataframe.h b/src/gromacs/analysisdata/dataframe.h
index 8208be6134a17119c74e7bac47301e28447cf24b..3cd87b29a796eaaae58d8baf935c01a4bcdb9a87 100644 (file)
--- a/src/gromacs/analysisdata/dataframe.h
+++ b/src/gromacs/analysisdata/dataframe.h
@@ -43,9 +43,9 @@
 
 #include "../legacyheaders/types/simple.h"
 
-#include "../fatalerror/gmxassert.h"
 #include "../utility/arrayref.h"
 #include "../utility/flags.h"
+#include "../utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/dataproxy.cpp b/src/gromacs/analysisdata/dataproxy.cpp
index b7ed9b53331af1621e7070615f5804eafda20c17..c46e446a1206c5b589a2336667cd8ae3af43fd73 100644 (file)
--- a/src/gromacs/analysisdata/dataproxy.cpp
+++ b/src/gromacs/analysisdata/dataproxy.cpp
@@ -38,7 +38,7 @@
 #include "dataproxy.h"
 
 #include "gromacs/analysisdata/dataframe.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/analysisdata/datastorage.cpp b/src/gromacs/analysisdata/datastorage.cpp
index 04059fed9da1566485bb99234e9f64da1bc04440..a356fefce8f90fba852ca8e163e31b6bc3dd426d 100644 (file)
--- a/src/gromacs/analysisdata/datastorage.cpp
+++ b/src/gromacs/analysisdata/datastorage.cpp
@@ -42,8 +42,8 @@
 #include "gromacs/analysisdata/abstractdata.h"
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "datastorage-impl.h"
 

diff --git a/src/gromacs/analysisdata/datastorage.h b/src/gromacs/analysisdata/datastorage.h
index 6893e4c6d619917f6e51a84fb3b0c69a712ff224..21c7789598635213da5bc42400fec4f1e8374f80 100644 (file)
--- a/src/gromacs/analysisdata/datastorage.h
+++ b/src/gromacs/analysisdata/datastorage.h
@@ -43,8 +43,8 @@
 
 #include "../legacyheaders/types/simple.h"
 
-#include "../fatalerror/gmxassert.h"
 #include "../utility/common.h"
+#include "../utility/gmxassert.h"
 
 #include "dataframe.h"
 

diff --git a/src/gromacs/analysisdata/modules/displacement.cpp b/src/gromacs/analysisdata/modules/displacement.cpp
index 9c3722154bba5d74782b5ad6dba69a98fd49cd34..4d5727548b67006542a03276ba24f39c929bfb70 100644 (file)
--- a/src/gromacs/analysisdata/modules/displacement.cpp
+++ b/src/gromacs/analysisdata/modules/displacement.cpp
@@ -46,8 +46,8 @@
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/modules/histogram.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "displacement-impl.h"
 

diff --git a/src/gromacs/analysisdata/modules/histogram.cpp b/src/gromacs/analysisdata/modules/histogram.cpp
index aafd293be5814d08dee47498828c2a76efce49ad..542f28198a38c0b18e816456d9650eba5ba6d041 100644 (file)
--- a/src/gromacs/analysisdata/modules/histogram.cpp
+++ b/src/gromacs/analysisdata/modules/histogram.cpp
@@ -43,8 +43,8 @@
 
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datastorage.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "histogram-impl.h"
 

diff --git a/src/gromacs/analysisdata/modules/plot.cpp b/src/gromacs/analysisdata/modules/plot.cpp
index 92fe367b0986ecb2ceee8c0713f92eddeb6ad62b..4160b6cbaa4ea8348118e6806b950c2187b83c86 100644 (file)
--- a/src/gromacs/analysisdata/modules/plot.cpp
+++ b/src/gromacs/analysisdata/modules/plot.cpp
@@ -59,10 +59,10 @@
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/timeunitmanager.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/selection/selectioncollection.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "plot-impl.h"
 

diff --git a/src/gromacs/analysisdata/tests/analysisdata.cpp b/src/gromacs/analysisdata/tests/analysisdata.cpp
index 8ff03f355a3ccd5f71c73fcdc9d8ccfef8bb2de3..9a7446e1dd49d2631124e620928d59c8005e2205 100644 (file)
--- a/src/gromacs/analysisdata/tests/analysisdata.cpp
+++ b/src/gromacs/analysisdata/tests/analysisdata.cpp
@@ -46,7 +46,7 @@
 
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/fatalerror/exceptions.h"
+#include "gromacs/utility/exceptions.h"
 
 #include "datatest.h"
 #include "mock_module.h"

diff --git a/src/gromacs/analysisdata/tests/datatest.cpp b/src/gromacs/analysisdata/tests/datatest.cpp
index 3bda6eb8ea799284b3ed1227c9e569e35c41258d..246be19c7e0abba9f7e982044c90cd280a1eb787 100644 (file)
--- a/src/gromacs/analysisdata/tests/datatest.cpp
+++ b/src/gromacs/analysisdata/tests/datatest.cpp
@@ -42,8 +42,8 @@
 
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/utility/format.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "testutils/refdata.h"
 

diff --git a/src/gromacs/analysisdata/tests/datatest.h b/src/gromacs/analysisdata/tests/datatest.h
index ce75e0060e3068179e0f538b3a77db61981b4905..2f775dc5237a31c28b78887599063f6cd5f64259 100644 (file)
--- a/src/gromacs/analysisdata/tests/datatest.h
+++ b/src/gromacs/analysisdata/tests/datatest.h
@@ -45,7 +45,8 @@
 #include <gtest/gtest.h>
 
 #include "gromacs/legacyheaders/types/simple.h"
-#include "gromacs/fatalerror/gmxassert.h"
+
+#include "gromacs/utility/gmxassert.h"
 
 #include "testutils/refdata.h"
 

diff --git a/src/gromacs/analysisdata/tests/mock_module.cpp b/src/gromacs/analysisdata/tests/mock_module.cpp
index aecca90b697e750086d3b8f105302a530b3de231..7b50839e11ab62b0c2147afda2a1d789b3c1a55b 100644 (file)
--- a/src/gromacs/analysisdata/tests/mock_module.cpp
+++ b/src/gromacs/analysisdata/tests/mock_module.cpp
@@ -42,8 +42,8 @@
 
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/dataframe.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/utility/format.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "testutils/refdata.h"
 

diff --git a/src/gromacs/fatalerror/CMakeLists.txt b/src/gromacs/fatalerror/CMakeLists.txt
deleted file mode 100644 (file)
index 19efdfb..0000000
--- a/src/gromacs/fatalerror/CMakeLists.txt
+++ /dev/null
@@ -1,8 +0,0 @@
-file(GLOB FATALERROR_SOURCES *.cpp)
-set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${FATALERROR_SOURCES} PARENT_SCOPE)
-
-set(FATALERROR_PUBLIC_HEADERS
-    errorcodes.h exceptions.h gmxassert.h)
-install(FILES ${FATALERROR_PUBLIC_HEADERS}
-        DESTINATION ${INCL_INSTALL_DIR}/gromacs/fatalerror
-        COMPONENT development)

diff --git a/src/gromacs/options/abstractoption.cpp b/src/gromacs/options/abstractoption.cpp
index 6dc97bfea9f52f2acec3ffb9869005acc2d52a1b..696f853eb4e238eb5f2a4664e21b8de89089833a 100644 (file)
--- a/src/gromacs/options/abstractoption.cpp
+++ b/src/gromacs/options/abstractoption.cpp
@@ -37,10 +37,10 @@
  */
 #include "gromacs/options/abstractoption.h"
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/options/abstractoptionstorage.h"
 #include "gromacs/options/optionflags.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "basicoptionstorage.h"
 

diff --git a/src/gromacs/options/basicoptions.cpp b/src/gromacs/options/basicoptions.cpp
index cc63721f81605787abc425d83b2660fd249a9e9d..e32013b7e17f3ac84e4192afedb850c34c73b9ff 100644 (file)
--- a/src/gromacs/options/basicoptions.cpp
+++ b/src/gromacs/options/basicoptions.cpp
@@ -43,9 +43,9 @@
 #include <string>
 #include <vector>
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/basicoptioninfo.h"
 #include "gromacs/options/options.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
 
 #include "basicoptionstorage.h"

diff --git a/src/gromacs/options/basicoptions.h b/src/gromacs/options/basicoptions.h
index 48b0bbdce4a3aef3b74a08eefb3f1c959d7ff872..a2db12f37fe41b22ac1eafe7c40f09d876b53318 100644 (file)
--- a/src/gromacs/options/basicoptions.h
+++ b/src/gromacs/options/basicoptions.h
@@ -44,7 +44,7 @@
 
 #include <string>
 
-#include "../fatalerror/gmxassert.h"
+#include "../utility/gmxassert.h"
 
 #include "abstractoption.h"
 #include "optionfiletype.h"

diff --git a/src/gromacs/options/cmdlineparser.cpp b/src/gromacs/options/cmdlineparser.cpp
index 27c2f862135c639aac99f68b2999a34e2a75826e..3ab7e2afc857b53ed980a6703b520264790e2cea 100644 (file)
--- a/src/gromacs/options/cmdlineparser.cpp
+++ b/src/gromacs/options/cmdlineparser.cpp
@@ -39,9 +39,9 @@
 
 #include <cctype>
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
 #include "gromacs/options/optionsassigner.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "cmdlineparser-impl.h"
 

diff --git a/src/gromacs/options/options.cpp b/src/gromacs/options/options.cpp
index 08b9709a538fec9b599ef41e79b5033c8bd7c9ef..b8be800fc4be44ef4cd2bfca332d12e3aed33348 100644 (file)
--- a/src/gromacs/options/options.cpp
+++ b/src/gromacs/options/options.cpp
@@ -40,11 +40,11 @@
 #include <cctype>
 #include <cstring>
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
 #include "gromacs/options/abstractoption.h"
 #include "gromacs/options/abstractoptionstorage.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "options-impl.h"
 

diff --git a/src/gromacs/options/optionsassigner.cpp b/src/gromacs/options/optionsassigner.cpp
index 6019fbd5b1c268c66685334c7e050d4261b1c7e3..144702bbad1b88fae75225323daa649b12de8045 100644 (file)
--- a/src/gromacs/options/optionsassigner.cpp
+++ b/src/gromacs/options/optionsassigner.cpp
@@ -39,10 +39,10 @@
 
 #include <deque>
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/options/abstractoptionstorage.h"
 #include "gromacs/options/options.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "optionsassigner-impl.h"
 #include "options-impl.h"

diff --git a/src/gromacs/options/optionstoragetemplate.h b/src/gromacs/options/optionstoragetemplate.h
index 3544f3724105afb110b48f15f278b5ff3ed8782c..f97397818916e2bb6d87df1fc6f83ebc09bcf9b4 100644 (file)
--- a/src/gromacs/options/optionstoragetemplate.h
+++ b/src/gromacs/options/optionstoragetemplate.h
@@ -44,8 +44,8 @@
 
 #include <boost/scoped_ptr.hpp>
 
-#include "../fatalerror/exceptions.h"
-#include "../fatalerror/gmxassert.h"
+#include "../utility/exceptions.h"
+#include "../utility/gmxassert.h"
 
 #include "abstractoption.h"
 #include "abstractoptionstorage.h"

diff --git a/src/gromacs/options/tests/abstractoptionstorage.cpp b/src/gromacs/options/tests/abstractoptionstorage.cpp
index 0c88cfd6c4da1c877384c351faf71a074c920d24..3e6499889ded788225e161cf053d536c1f6a8031 100644 (file)
--- a/src/gromacs/options/tests/abstractoptionstorage.cpp
+++ b/src/gromacs/options/tests/abstractoptionstorage.cpp
@@ -44,11 +44,11 @@
 #include <gmock/gmock.h>
 #include <gtest/gtest.h>
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/abstractoption.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionstoragetemplate.h"
 #include "gromacs/options/optionsassigner.h"
+#include "gromacs/utility/exceptions.h"
 #include "testutils/testexceptions.h"
 
 namespace

diff --git a/src/gromacs/options/tests/option.cpp b/src/gromacs/options/tests/option.cpp
index b3e2cfab2cce96a17a3e6d4f308b64506d7e1f59..928af8dd21b47d75ee50dbc6ae3617310327c327 100644 (file)
--- a/src/gromacs/options/tests/option.cpp
+++ b/src/gromacs/options/tests/option.cpp
@@ -43,9 +43,9 @@
 
 #include <gtest/gtest.h>
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
+#include "gromacs/utility/exceptions.h"
 
 namespace
 {

diff --git a/src/gromacs/options/tests/optionsassigner.cpp b/src/gromacs/options/tests/optionsassigner.cpp
index 10f563ade4a132c270f2560042acafe2923a702c..6ae3ac4ebca700f7a25d070ffd58bc223a40e600 100644 (file)
--- a/src/gromacs/options/tests/optionsassigner.cpp
+++ b/src/gromacs/options/tests/optionsassigner.cpp
@@ -45,10 +45,10 @@
 
 #include <gtest/gtest.h>
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionsassigner.h"
+#include "gromacs/utility/exceptions.h"
 
 namespace
 {

diff --git a/src/gromacs/options/timeunitmanager.cpp b/src/gromacs/options/timeunitmanager.cpp
index a86f72fb399a3a1415f903bd96be667d90604456..47c282a869de849c3291f92cd50173184e44c902 100644 (file)
--- a/src/gromacs/options/timeunitmanager.cpp
+++ b/src/gromacs/options/timeunitmanager.cpp
@@ -37,11 +37,11 @@
  */
 #include "gromacs/options/timeunitmanager.h"
 
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/options/basicoptioninfo.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionsvisitor.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/options/timeunitmanager.h b/src/gromacs/options/timeunitmanager.h
index 181158a243fb7066d7ab07aa49e7f7857e37747a..6f6f485632045237fed25a5abca85234cead8214 100644 (file)
--- a/src/gromacs/options/timeunitmanager.h
+++ b/src/gromacs/options/timeunitmanager.h
@@ -39,7 +39,7 @@
 #ifndef GMX_OPTIONS_TIMEUNITMANAGER_H
 #define GMX_OPTIONS_TIMEUNITMANAGER_H
 
-#include "../fatalerror/gmxassert.h"
+#include "../utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/compiler.cpp b/src/gromacs/selection/compiler.cpp
index c7b353104618a1e1d32ca7eb0b7b1cd15c553b93..160deb9c0ffa96260f5127fc210430a3e79f3968 100644 (file)
--- a/src/gromacs/selection/compiler.cpp
+++ b/src/gromacs/selection/compiler.cpp
@@ -273,15 +273,15 @@
 #include <math.h>
 #include <stdarg.h>
 
-#include <smalloc.h>
-#include <string2.h>
-#include <vec.h>
+#include "smalloc.h"
+#include "string2.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
 
 #include "evaluate.h"

diff --git a/src/gromacs/selection/evaluate.cpp b/src/gromacs/selection/evaluate.cpp
index 822d5218d12c7bd3b426a84fde0808c22480172d..4aecec699c829424e135614a9647ffed8e222a0c 100644 (file)
--- a/src/gromacs/selection/evaluate.cpp
+++ b/src/gromacs/selection/evaluate.cpp
@@ -52,16 +52,16 @@
 
 #include <string.h>
 
-#include <maths.h>
-#include <smalloc.h>
-#include <vec.h>
+#include "maths.h"
+#include "smalloc.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "evaluate.h"
 #include "mempool.h"

diff --git a/src/gromacs/selection/mempool.cpp b/src/gromacs/selection/mempool.cpp
index e6a1fec306594963c3231dbd8edd9aa2ee016db2..18a30f2385598aae485b0bc7c6fe624857511824 100644 (file)
--- a/src/gromacs/selection/mempool.cpp
+++ b/src/gromacs/selection/mempool.cpp
@@ -43,11 +43,11 @@
 
 #include <new>
 
-#include <smalloc.h>
+#include "smalloc.h"
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/selection/indexutil.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "mempool.h"
 

diff --git a/src/gromacs/selection/params.cpp b/src/gromacs/selection/params.cpp
index 88a019401e1eb7a4875f48778baa9e7de5c1b195..f3dd0d784430951399f63b6f5bdb0ee07db69fe8 100644 (file)
--- a/src/gromacs/selection/params.cpp
+++ b/src/gromacs/selection/params.cpp
@@ -41,17 +41,17 @@
 
 #include <algorithm>
 
-#include <smalloc.h>
-#include <string2.h>
-#include <vec.h>
+#include "smalloc.h"
+#include "string2.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/errorcodes.h"
-#include "gromacs/fatalerror/gmxassert.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
 #include "gromacs/selection/selparam.h"
+#include "gromacs/utility/errorcodes.h"
 #include "gromacs/utility/format.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "parsetree.h"
 #include "position.h"

diff --git a/src/gromacs/selection/parsetree.cpp b/src/gromacs/selection/parsetree.cpp
index be3c1501855e70595f492e7fa1d85d052f63289b..910af34a9f20e5304f977df0b7259e104754acc7 100644 (file)
--- a/src/gromacs/selection/parsetree.cpp
+++ b/src/gromacs/selection/parsetree.cpp
@@ -216,16 +216,16 @@
 #include <stdio.h>
 #include <stdarg.h>
 
-#include <futil.h>
-#include <smalloc.h>
-#include <string2.h>
+#include "futil.h"
+#include "smalloc.h"
+#include "string2.h"
 
-#include "gromacs/fatalerror/errorcodes.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/selection/poscalc.cpp b/src/gromacs/selection/poscalc.cpp
index 027fbbe3f3434f134892cdd1137e3de33790f837..6ff036342c77f6fbcd2a6f7356b2ad81a7dd7dba 100644 (file)
--- a/src/gromacs/selection/poscalc.cpp
+++ b/src/gromacs/selection/poscalc.cpp
@@ -61,18 +61,17 @@
 
 #include <string.h>
 
-#include <macros.h>
-#include <smalloc.h>
-#include <typedefs.h>
-#include <pbc.h>
-#include <vec.h>
-
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "smalloc.h"
+#include "typedefs.h"
+#include "pbc.h"
+#include "vec.h"
+
 #include "gromacs/selection/centerofmass.h"
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/position.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/selection/position.cpp b/src/gromacs/selection/position.cpp
index c24fc9d67661af32fe92b056dc9834796fb6fdae..8293d9c682bbf5a4c29d3077fbf87c2436954349 100644 (file)
--- a/src/gromacs/selection/position.cpp
+++ b/src/gromacs/selection/position.cpp
@@ -41,13 +41,13 @@
 
 #include <string.h>
 
-#include <smalloc.h>
-#include <typedefs.h>
-#include <vec.h>
+#include "smalloc.h"
+#include "typedefs.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/position.h"
+#include "gromacs/utility/gmxassert.h"
 
 /*!
  * \param[out] pos      Output structure.

diff --git a/src/gromacs/selection/scanner_internal.cpp b/src/gromacs/selection/scanner_internal.cpp
index 1fe024b2f1a7e8fd345e09dfc36cf4bf117bf4e9..833c65cf1aa4b68e94f479c978e75332a2e261a7 100644 (file)
--- a/src/gromacs/selection/scanner_internal.cpp
+++ b/src/gromacs/selection/scanner_internal.cpp
@@ -50,22 +50,21 @@
 #endif
 
 #include <stdlib.h>
-#include <typedefs.h>
-#include <smalloc.h>
 #include <string.h>
 
+#include "typedefs.h"
+#include "smalloc.h"
 #include "string2.h"
 
-#include "gromacs/fatalerror/errorcodes.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
-
-#include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "parsetree.h"
 #include "selectioncollection-impl.h"
 #include "selelem.h"
+#include "selmethod.h"
 #include "symrec.h"
 
 #include "parser.h"

diff --git a/src/gromacs/selection/selection.h b/src/gromacs/selection/selection.h
index a7c8541873402b6849aeab49bc1e3508cf978300..19b90395205d70f804081453f36b9b878a77cf68 100644 (file)
--- a/src/gromacs/selection/selection.h
+++ b/src/gromacs/selection/selection.h
@@ -44,9 +44,9 @@
 
 #include "../legacyheaders/typedefs.h"
 
-#include "../fatalerror/gmxassert.h"
 #include "../utility/arrayref.h"
 #include "../utility/common.h"
+#include "../utility/gmxassert.h"
 
 #include "position.h"
 #include "indexutil.h"

diff --git a/src/gromacs/selection/selectioncollection.cpp b/src/gromacs/selection/selectioncollection.cpp
index e5f9d94e3769c90a1dfea8be462dc74f24d8295b..32dd0144afd4e550e27c32a7c58aa7e805e85b28 100644 (file)
--- a/src/gromacs/selection/selectioncollection.cpp
+++ b/src/gromacs/selection/selectioncollection.cpp
@@ -46,13 +46,13 @@
 #include "smalloc.h"
 #include "xvgr.h"
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectioncollection.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "compiler.h"
 #include "mempool.h"

diff --git a/src/gromacs/selection/selectionoption.cpp b/src/gromacs/selection/selectionoption.cpp
index d5a87b0a3bfe036af4b76ebce0affc167d871788..056e8795ce74396a68cda37dc326076a24ff7a15 100644 (file)
--- a/src/gromacs/selection/selectionoption.cpp
+++ b/src/gromacs/selection/selectionoption.cpp
@@ -40,14 +40,14 @@
 #include <string>
 #include <vector>
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionsvisitor.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selectionoptioninfo.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "selectioncollection-impl.h"
 #include "selectionoptionstorage.h"

diff --git a/src/gromacs/selection/selelem.cpp b/src/gromacs/selection/selelem.cpp
index 1d9fdd84c74e2ac27578722538eb70a4ca047ab3..55b8a5e53f292a637bd5ecbcf1ca682dc878b021 100644 (file)
--- a/src/gromacs/selection/selelem.cpp
+++ b/src/gromacs/selection/selelem.cpp
@@ -39,14 +39,14 @@
 #include <config.h>
 #endif
 
-#include <smalloc.h>
-#include <gmx_fatal.h>
+#include "gmx_fatal.h"
+#include "smalloc.h"
 
-#include "gromacs/fatalerror/exceptions.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 "keywords.h"
 #include "mempool.h"

diff --git a/src/gromacs/selection/sm_compare.cpp b/src/gromacs/selection/sm_compare.cpp
index defbf421b8e83c2fe161a25f47f76bebb97d6c2a..4a8281e733ce36a0063d0810e0d7437b4cd7bb18 100644 (file)
--- a/src/gromacs/selection/sm_compare.cpp
+++ b/src/gromacs/selection/sm_compare.cpp
@@ -39,12 +39,12 @@
 #include <config.h>
 #endif
 
-#include <maths.h>
-#include <macros.h>
-#include <smalloc.h>
+#include "maths.h"
+#include "macros.h"
+#include "smalloc.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
 
 /** Defines the comparison operator for comparison expressions. */
 typedef enum

diff --git a/src/gromacs/selection/sm_distance.cpp b/src/gromacs/selection/sm_distance.cpp
index 8c6da795f9bf21dc2347c414ee039f907a79c80c..5c269a2958ac3d28ea1c28b60b720652a9151415 100644 (file)
--- a/src/gromacs/selection/sm_distance.cpp
+++ b/src/gromacs/selection/sm_distance.cpp
@@ -42,15 +42,15 @@
 #include <config.h>
 #endif
 
-#include <macros.h>
-#include <pbc.h>
-#include <smalloc.h>
-#include <vec.h>
+#include "macros.h"
+#include "pbc.h"
+#include "smalloc.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/selection/nbsearch.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
 
 /*! \internal \brief
  * Data structure for distance-based selection method.

diff --git a/src/gromacs/selection/sm_insolidangle.cpp b/src/gromacs/selection/sm_insolidangle.cpp
index 19bae2e65335373f4b900cdd44a89b771576a941..3f0c683e682e889c99f61a3e1324e95ae5dcdde0 100644 (file)
--- a/src/gromacs/selection/sm_insolidangle.cpp
+++ b/src/gromacs/selection/sm_insolidangle.cpp
@@ -115,18 +115,18 @@
 
 #include <math.h>
 
-#include <macros.h>
-#include <maths.h>
-#include <pbc.h>
-#include <physics.h>
-#include <smalloc.h>
-#include <vec.h>
-
-#include "gromacs/fatalerror/exceptions.h"
+#include "macros.h"
+#include "maths.h"
+#include "pbc.h"
+#include "physics.h"
+#include "smalloc.h"
+#include "vec.h"
+
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
 
 #include "selelem.h"
 

diff --git a/src/gromacs/selection/sm_keywords.cpp b/src/gromacs/selection/sm_keywords.cpp
index e936be3bba387620153cc3e637dbaa9ea8a8b8dd..9c777e21b47ced5466bb173052568754df76d663 100644 (file)
--- a/src/gromacs/selection/sm_keywords.cpp
+++ b/src/gromacs/selection/sm_keywords.cpp
@@ -49,13 +49,13 @@
 #define USE_REGEX
 #endif
 
-#include <macros.h>
-#include <smalloc.h>
-#include <string2.h>
+#include "macros.h"
+#include "smalloc.h"
+#include "string2.h"
 
-#include "gromacs/fatalerror/errorcodes.h"
-#include "gromacs/fatalerror/messagestringcollector.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/selection/sm_merge.cpp b/src/gromacs/selection/sm_merge.cpp
index 05eea6f93e06f3f348ea82668bcf26ba7d53ae41..05700e79214426878fde9ba7dc1e7d6051e64058 100644 (file)
--- a/src/gromacs/selection/sm_merge.cpp
+++ b/src/gromacs/selection/sm_merge.cpp
@@ -39,13 +39,13 @@
 #include <config.h>
 #endif
 
-#include <macros.h>
-#include <smalloc.h>
-#include <vec.h>
+#include "macros.h"
+#include "smalloc.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.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 4b08ca9048092084cb37537da3adcc3cf8f07ac8..2964a2f21fd2cc57ecd4f2b5623a50abb5c4a878 100644 (file)
--- a/src/gromacs/selection/sm_permute.cpp
+++ b/src/gromacs/selection/sm_permute.cpp
@@ -39,13 +39,13 @@
 #include <config.h>
 #endif
 
-#include <macros.h>
-#include <smalloc.h>
-#include <vec.h>
+#include "macros.h"
+#include "smalloc.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
 
 /*! \internal \brief

diff --git a/src/gromacs/selection/sm_same.cpp b/src/gromacs/selection/sm_same.cpp
index 9094ef8eceaf4c169bed218f548d8c8e8d968f0e..5a497de1068b4c91b54399eed57ca4732f4baf66 100644 (file)
--- a/src/gromacs/selection/sm_same.cpp
+++ b/src/gromacs/selection/sm_same.cpp
@@ -41,12 +41,12 @@
 
 #include <stdlib.h>
 
-#include <macros.h>
-#include <smalloc.h>
-#include <string2.h>
+#include "macros.h"
+#include "smalloc.h"
+#include "string2.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
 
 #include "keywords.h"
 #include "parsetree.h"

diff --git a/src/gromacs/selection/sm_simple.cpp b/src/gromacs/selection/sm_simple.cpp
index 30369fa6d6218a23761bd5786ee67dc7457ada8c..a7ff1d43500f95c29ffc53ac55cdc958953838d7 100644 (file)
--- a/src/gromacs/selection/sm_simple.cpp
+++ b/src/gromacs/selection/sm_simple.cpp
@@ -39,9 +39,9 @@
 #include <config.h>
 #endif
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/selection/position.h"
 #include "gromacs/selection/selmethod.h"
+#include "gromacs/utility/exceptions.h"
 
 /** Evaluates the \p all selection keyword. */
 static void

diff --git a/src/gromacs/selection/tests/selectioncollection.cpp b/src/gromacs/selection/tests/selectioncollection.cpp
index f4390d4518577a3be7d8a06c86944edc983115b5..c2dea66e92bc5166126272290762633c195cc579 100644 (file)
--- a/src/gromacs/selection/tests/selectioncollection.cpp
+++ b/src/gromacs/selection/tests/selectioncollection.cpp
@@ -46,12 +46,12 @@
 #include "tpxio.h"
 #include "vec.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/poscalc.h"
 #include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selection.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/flags.h"
 #include "gromacs/utility/format.h"
 

diff --git a/src/gromacs/selection/tests/selectionoption.cpp b/src/gromacs/selection/tests/selectionoption.cpp
index 705080b58151eae5934f0a28b67240a2b930f0d4..7eba71cc527cfdc0396be859fddeaea3bf7c2823 100644 (file)
--- a/src/gromacs/selection/tests/selectionoption.cpp
+++ b/src/gromacs/selection/tests/selectionoption.cpp
@@ -37,13 +37,13 @@
  */
 #include <gtest/gtest.h>
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/options/optionsassigner.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectioncollection.h"
 #include "gromacs/selection/selectionoption.h"
 #include "gromacs/selection/selectionoptioninfo.h"
+#include "gromacs/utility/exceptions.h"
 
 namespace
 {

diff --git a/src/gromacs/trajectoryanalysis.h b/src/gromacs/trajectoryanalysis.h
index 26d3d083c6938358ae418154a294eba48ac413e5..58ecb9e0431abcde069215d76874b2acf7bd26df 100644 (file)
--- a/src/gromacs/trajectoryanalysis.h
+++ b/src/gromacs/trajectoryanalysis.h
@@ -78,10 +78,10 @@
 #include "options.h"
 #include "selection.h"
 
-#include "fatalerror/exceptions.h"
 #include "trajectoryanalysis/analysismodule.h"
 #include "trajectoryanalysis/analysissettings.h"
 #include "trajectoryanalysis/cmdlinerunner.h"
 #include "trajectoryanalysis/nbsearch.h"
+#include "utility/exceptions.h"
 
 #endif

diff --git a/src/gromacs/trajectoryanalysis/analysismodule.cpp b/src/gromacs/trajectoryanalysis/analysismodule.cpp
index d2099899b399b4babf66d59dcc17eaa350cddaec..d850f32714df4981ab899f65d482fd89db2214e1 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysismodule.cpp
+++ b/src/gromacs/trajectoryanalysis/analysismodule.cpp
@@ -40,9 +40,9 @@
 #include <utility>
 
 #include "gromacs/analysisdata/analysisdata.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/selection/selection.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "analysismodule-impl.h"
 

diff --git a/src/gromacs/trajectoryanalysis/analysissettings.cpp b/src/gromacs/trajectoryanalysis/analysissettings.cpp
index cd7d71bc939a592e4a3e9d5d77668423216d5364..89a4515bd0969b078583cdc66047c0f916e3b0d6 100644 (file)
--- a/src/gromacs/trajectoryanalysis/analysissettings.cpp
+++ b/src/gromacs/trajectoryanalysis/analysissettings.cpp
@@ -39,12 +39,12 @@
 #include <config.h>
 #endif
 
-#include <smalloc.h>
-#include <statutil.h>
-#include <vec.h>
+#include "smalloc.h"
+#include "statutil.h"
+#include "vec.h"
 
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
 
 #include "analysissettings-impl.h"
 

diff --git a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
index a39f6a4182958387b044f7beaee9f1ef950c2b21..c3865f7f21dadd577cdf27d51a84bf59b8b22c5f 100644 (file)
--- a/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
+++ b/src/gromacs/trajectoryanalysis/cmdlinerunner.cpp
@@ -39,14 +39,12 @@
 #include <config.h>
 #endif
 
-#include <copyrite.h>
-#include <pbc.h>
-#include <rmpbc.h>
-#include <statutil.h>
+#include "copyrite.h"
+#include "pbc.h"
+#include "rmpbc.h"
+#include "statutil.h"
 
 #include "gromacs/analysisdata/paralleloptions.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/options/asciihelpwriter.h"
 #include "gromacs/options/cmdlineparser.h"
 #include "gromacs/options/options.h"
@@ -56,6 +54,8 @@
 #include "gromacs/trajectoryanalysis/analysissettings.h"
 #include "gromacs/trajectoryanalysis/cmdlinerunner.h"
 #include "gromacs/trajectoryanalysis/runnercommon.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules.cpp b/src/gromacs/trajectoryanalysis/modules.cpp
index 075e3e976ff67f70122b7e307d724de85472fc20..258876fe869897ba4870cbe534398cf974c54966 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules.cpp
+++ b/src/gromacs/trajectoryanalysis/modules.cpp
@@ -37,9 +37,9 @@
  */
 #include "gromacs/trajectoryanalysis/modules.h"
 
-#include <string2.h>
+#include "string2.h"
 
-#include "gromacs/fatalerror/exceptions.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
 
 #include "modules/angle.h"

diff --git a/src/gromacs/trajectoryanalysis/modules/angle.cpp b/src/gromacs/trajectoryanalysis/modules/angle.cpp
index 6c1a5812656e603d328cc9101ce6eb39c0abdddc..6749665eaef6c43d44b6ad590bd53b06242ad457 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/angle.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/angle.cpp
@@ -41,20 +41,20 @@
 #include <config.h>
 #endif
 
-#include <pbc.h>
-#include <vec.h>
+#include "pbc.h"
+#include "vec.h"
 
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/modules/plot.h"
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectionoption.h"
 #include "gromacs/selection/selectionoptioninfo.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules/distance.cpp b/src/gromacs/trajectoryanalysis/modules/distance.cpp
index 6d313607582edaa1b2a0ac0a0545820ae5d552e7..f3ff84fbf78ea4cb945264463665a8a1e948af23 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/distance.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/distance.cpp
@@ -41,17 +41,17 @@
 #include <config.h>
 #endif
 
-#include <pbc.h>
-#include <vec.h>
+#include "pbc.h"
+#include "vec.h"
 
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/modules/plot.h"
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectionoption.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/trajectoryanalysis/modules/select.cpp b/src/gromacs/trajectoryanalysis/modules/select.cpp
index 246fc8669ecc34315122908ffd889e9121ea4923..3b6221df31c4039af6a1106be4f6e575c193c0bc 100644 (file)
--- a/src/gromacs/trajectoryanalysis/modules/select.cpp
+++ b/src/gromacs/trajectoryanalysis/modules/select.cpp
@@ -46,18 +46,18 @@
 #include <string>
 #include <vector>
 
-#include <gmxfio.h>
+#include "gmxfio.h"
 
 #include "gromacs/analysisdata/analysisdata.h"
 #include "gromacs/analysisdata/dataframe.h"
 #include "gromacs/analysisdata/datamodule.h"
 #include "gromacs/analysisdata/modules/plot.h"
-#include "gromacs/fatalerror/exceptions.h"
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/selection.h"
 #include "gromacs/selection/selectionoption.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
 
 namespace gmx

diff --git a/src/gromacs/trajectoryanalysis/runnercommon.cpp b/src/gromacs/trajectoryanalysis/runnercommon.cpp
index c75f960587e014dfd47d245377fb37479f933e05..e7713886165f5857e436b3d90a86003500519b8a 100644 (file)
--- a/src/gromacs/trajectoryanalysis/runnercommon.cpp
+++ b/src/gromacs/trajectoryanalysis/runnercommon.cpp
@@ -41,21 +41,21 @@
 
 #include <string.h>
 
-#include <rmpbc.h>
-#include <smalloc.h>
-#include <statutil.h>
-#include <tpxio.h>
-#include <vec.h>
-
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "rmpbc.h"
+#include "smalloc.h"
+#include "statutil.h"
+#include "tpxio.h"
+#include "vec.h"
+
 #include "gromacs/options/basicoptions.h"
 #include "gromacs/options/options.h"
 #include "gromacs/selection/indexutil.h"
 #include "gromacs/selection/selectioncollection.h"
 #include "gromacs/trajectoryanalysis/analysissettings.h"
 #include "gromacs/trajectoryanalysis/runnercommon.h"
+#include "gromacs/utility/exceptions.h"
 #include "gromacs/utility/format.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "analysissettings-impl.h"
 

diff --git a/src/gromacs/trajectoryanalysis/tests/test_selection.cpp b/src/gromacs/trajectoryanalysis/tests/test_selection.cpp
index e0281dfdd1e0eeadde84db352bf0df34565b7840..6c8d3d0b3160193d5e564da3f56d3c83123070c0 100644 (file)
--- a/src/gromacs/trajectoryanalysis/tests/test_selection.cpp
+++ b/src/gromacs/trajectoryanalysis/tests/test_selection.cpp
@@ -37,7 +37,6 @@
 #include <config.h>
 #endif
 
-#include <gromacs/fatalerror/exceptions.h>
 #include <gromacs/options/basicoptions.h>
 #include <gromacs/options/options.h>
 #include <gromacs/selection/selection.h>
@@ -45,6 +44,7 @@
 #include <gromacs/trajectoryanalysis/analysismodule.h>
 #include <gromacs/trajectoryanalysis/analysissettings.h>
 #include <gromacs/trajectoryanalysis/cmdlinerunner.h>
+#include <gromacs/utility/exceptions.h>
 
 namespace gmx
 {

diff --git a/src/gromacs/fatalerror.h b/src/gromacs/utility.h
similarity index 88%
rename from src/gromacs/fatalerror.h
rename to src/gromacs/utility.h
index 6e1fd11cb11d031037da3961ea8656a885366433..7325a629f806cc0a413bab0d2d60ebfe1bf940be 100644 (file)
--- a/src/gromacs/fatalerror.h
+++ b/src/gromacs/utility.h
@@ -28,10 +28,12 @@
  *
  * For more info, check our website at http://www.gromacs.org
  */
-/*! \defgroup module_fatalerror Handling of Fatal Errors
+/*! \defgroup module_utility Low-level Utility Module
  * \ingroup group_utilitymodules
  * \brief
- * Provides functions for handling fatal errors.
+ * Provides various low-level utilities.
+ *
+ * <H3>Handling fatal errors</H3>
  *
  * Exception classes used in the library are defined in the exceptions.h header
  * file.  This header also declares a ::GMX_THROW macro that should be used for
@@ -56,17 +58,17 @@
  */
 /*! \file
  * \brief
- * Public API convenience header for fatal error handling.
+ * Public API convenience header for low-level utilities.
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  * \inpublicapi
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#ifndef GMX_FATALERROR_H
-#define GMX_FATALERROR_H
+#ifndef GMX_UTILITY_H
+#define GMX_UTILITY_H
 
-#include "fatalerror/errorcodes.h"
-#include "fatalerror/exceptions.h"
-#include "fatalerror/gmxassert.h"
+#include "utility/errorcodes.h"
+#include "utility/exceptions.h"
+#include "utility/gmxassert.h"
 
 #endif

diff --git a/src/gromacs/utility/CMakeLists.txt b/src/gromacs/utility/CMakeLists.txt
index f57408e2eab39b52820b06aae9726c3c8fadf6a6..0e25ccfe64061448c5194c2517d5da9a405fcdfd 100644 (file)
--- a/src/gromacs/utility/CMakeLists.txt
+++ b/src/gromacs/utility/CMakeLists.txt
@@ -2,7 +2,14 @@ file(GLOB UTILITY_SOURCES *.cpp)
 set(LIBGROMACS_SOURCES ${LIBGROMACS_SOURCES} ${UTILITY_SOURCES} PARENT_SCOPE)
 
 set(UTILITY_PUBLIC_HEADERS
-    arrayref.h common.h flags.h format.h uniqueptr.h)
+    arrayref.h
+    common.h
+    errorcodes.h
+    exceptions.h
+    flags.h
+    format.h
+    gmxassert.h
+    uniqueptr.h)
 install(FILES ${UTILITY_PUBLIC_HEADERS}
         DESTINATION ${INCL_INSTALL_DIR}/gromacs/utility
         COMPONENT development)

diff --git a/src/gromacs/utility/arrayref.h b/src/gromacs/utility/arrayref.h
index f232f072fe0335b86c9698f9065b3fe91a8453c4..0d51aef57b0268417604d78f579b67eb7cbc5b2a 100644 (file)
--- a/src/gromacs/utility/arrayref.h
+++ b/src/gromacs/utility/arrayref.h
@@ -46,7 +46,7 @@
 #include <utility>
 #include <vector>
 
-#include "../fatalerror/gmxassert.h"
+#include "gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/fatalerror/errorcodes.cpp b/src/gromacs/utility/errorcodes.cpp
similarity index 96%
rename from src/gromacs/fatalerror/errorcodes.cpp
rename to src/gromacs/utility/errorcodes.cpp
index bdfdd2fee49b949841cb02cc1aad50977513ba6e..ecb79cfd5656ab53a6e3f87bbe48f0d5a332f40f 100644 (file)
--- a/src/gromacs/fatalerror/errorcodes.cpp
+++ b/src/gromacs/utility/errorcodes.cpp
@@ -33,9 +33,9 @@
  * Implements functions in errorcodes.h.
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#include "gromacs/fatalerror/errorcodes.h"
+#include "gromacs/utility/errorcodes.h"
 
 #include <cstdarg>
 #include <cstdio>
@@ -43,7 +43,7 @@
 
 #include "errorformat.h"
 
-// This has to match the enum in fatalerror.h
+// This has to match the enum in errorcodes.h
 static const char *const error_names[] =
 {
     "No error",

diff --git a/src/gromacs/fatalerror/errorcodes.h b/src/gromacs/utility/errorcodes.h
similarity index 97%
rename from src/gromacs/fatalerror/errorcodes.h
rename to src/gromacs/utility/errorcodes.h
index 366afa4b1210dfac6f7149fcea081c5c23ceff33..5c8387546a8779e4048c1baf175bdb7f54a0580d 100644 (file)
--- a/src/gromacs/fatalerror/errorcodes.h
+++ b/src/gromacs/utility/errorcodes.h
@@ -34,10 +34,10 @@
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  * \inpublicapi
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#ifndef GMX_FATALERROR_ERRORCODES_H
-#define GMX_FATALERROR_ERRORCODES_H
+#ifndef GMX_UTILITY_ERRORCODES_H
+#define GMX_UTILITY_ERRORCODES_H
 
 namespace gmx
 {
@@ -159,7 +159,7 @@ namespace internal
  * Should not be called directly, but instead through ::GMX_ERROR or
  * ::GMX_ERROR_NORET.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 void fatalError(int retcode, const char *msg, const char *file, int line);
 

diff --git a/src/gromacs/fatalerror/errorformat.cpp b/src/gromacs/utility/errorformat.cpp
similarity index 97%
rename from src/gromacs/fatalerror/errorformat.cpp
rename to src/gromacs/utility/errorformat.cpp
index 2647e56dbf2c6f5a485da58e565a57eeb6e6a962..4c8ebe814bf569507eafcf2c7a9e3d72fd2bebcf 100644 (file)
--- a/src/gromacs/fatalerror/errorformat.cpp
+++ b/src/gromacs/utility/errorformat.cpp
@@ -33,9 +33,9 @@
  * Implements functions declared in errorformat.h.
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#include "gromacs/fatalerror/errorformat.h"
+#include "gromacs/utility/errorformat.h"
 
 #include <string>
 

diff --git a/src/gromacs/fatalerror/errorformat.h b/src/gromacs/utility/errorformat.h
similarity index 93%
rename from src/gromacs/fatalerror/errorformat.h
rename to src/gromacs/utility/errorformat.h
index 547df7ea66400add6c66d9505d80e9da8d0d1c24..bee75fb4882e777fb11370ddfa9c0e92fc1515ad 100644 (file)
--- a/src/gromacs/fatalerror/errorformat.h
+++ b/src/gromacs/utility/errorformat.h
@@ -33,10 +33,10 @@
  * Declares an internal helper function for formatting standard error messages.
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#ifndef GMX_FATALERROR_ERRORFORMAT_H
-#define GMX_FATALERROR_ERRORFORMAT_H
+#ifndef GMX_UTILITY_ERRORFORMAT_H
+#define GMX_UTILITY_ERRORFORMAT_H
 
 #include <string>
 
@@ -50,7 +50,7 @@ namespace internal
 /*! \internal \brief
  * Formats common headers and footers for error messages.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 std::string formatFatalError(const char *title, const char *details,
                              const char *func, const char *file, int line);

diff --git a/src/gromacs/fatalerror/exceptions.cpp b/src/gromacs/utility/exceptions.cpp
similarity index 96%
rename from src/gromacs/fatalerror/exceptions.cpp
rename to src/gromacs/utility/exceptions.cpp
index 3925af0b33f550ec5652b87fe0b08f20a72d9e74..510297162febcdd24b84a4a5e972be64da150da2 100644 (file)
--- a/src/gromacs/fatalerror/exceptions.cpp
+++ b/src/gromacs/utility/exceptions.cpp
@@ -33,13 +33,13 @@
  * Implements classes and functions in exceptions.h.
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#include "gromacs/fatalerror/exceptions.h"
+#include "gromacs/utility/exceptions.h"
 
 #include <boost/exception/get_error_info.hpp>
 
-#include "gromacs/fatalerror/errorcodes.h"
+#include "gromacs/utility/errorcodes.h"
 
 #include "errorformat.h"
 

diff --git a/src/gromacs/fatalerror/exceptions.h b/src/gromacs/utility/exceptions.h
similarity index 95%
rename from src/gromacs/fatalerror/exceptions.h
rename to src/gromacs/utility/exceptions.h
index c622c7422c9b35a1a6ac6c7bfe8dc3178a7bbc5e..2cf437663c46767c20e4baee294282ae5d7e12b0 100644 (file)
--- a/src/gromacs/fatalerror/exceptions.h
+++ b/src/gromacs/utility/exceptions.h
@@ -34,10 +34,10 @@
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  * \inpublicapi
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#ifndef GMX_FATALERROR_EXCEPTIONS_H
-#define GMX_FATALERROR_EXCEPTIONS_H
+#ifndef GMX_UTILITY_EXCEPTIONS_H
+#define GMX_UTILITY_EXCEPTIONS_H
 
 #include <exception>
 #include <string>
@@ -77,7 +77,7 @@ typedef boost::error_info<struct errinfo_message_, std::string> errinfo_message;
  * -# Because the constructor takes an argument, virtual inheritance would
  *    complicate any classes that inherit indirectly from this class.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class GromacsException : public std::exception, public boost::exception
 {
@@ -105,7 +105,7 @@ class GromacsException : public std::exception, public boost::exception
 /*! \brief
  * Exception class for file I/O errors.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class FileIOError : public GromacsException
 {
@@ -127,7 +127,7 @@ class FileIOError : public GromacsException
  * Derived classes should be used to indicate the nature of the error instead
  * of throwing this class directly.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class UserInputError : public GromacsException
 {
@@ -140,7 +140,7 @@ class UserInputError : public GromacsException
 /*! \brief
  * Exception class for situations where user input cannot be parsed/understood.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class InvalidInputError : public UserInputError
 {
@@ -155,7 +155,7 @@ class InvalidInputError : public UserInputError
 /*! \brief
  * Exception class for situations where user input is inconsistent.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class InconsistentInputError : public UserInputError
 {
@@ -170,7 +170,7 @@ class InconsistentInputError : public UserInputError
 /*! \brief
  * Exception class for simulation instabilities.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class SimulationInstabilityError : public GromacsException
 {
@@ -185,7 +185,7 @@ class SimulationInstabilityError : public GromacsException
 /*! \brief
  * Exception class for internal errors.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class InternalError : public GromacsException
 {
@@ -200,7 +200,7 @@ class InternalError : public GromacsException
 /*! \brief
  * Exception class for incorrect use of an API.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class APIError : public GromacsException
 {
@@ -215,7 +215,7 @@ class APIError : public GromacsException
 /*! \brief
  * Exception class for use of an unimplemented feature.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class NotImplementedError : public APIError
 {

diff --git a/src/gromacs/fatalerror/gmxassert.cpp b/src/gromacs/utility/gmxassert.cpp
similarity index 96%
rename from src/gromacs/fatalerror/gmxassert.cpp
rename to src/gromacs/utility/gmxassert.cpp
index d8058570803633a32e71002961afe96376b03d41..6a2c2dc36c582ba1e0b6ce555082629e9058351b 100644 (file)
--- a/src/gromacs/fatalerror/gmxassert.cpp
+++ b/src/gromacs/utility/gmxassert.cpp
@@ -33,9 +33,9 @@
  * Implements assertion handlers.
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include <cstdio>
 #include <cstdlib>

diff --git a/src/gromacs/fatalerror/gmxassert.h b/src/gromacs/utility/gmxassert.h
similarity index 95%
rename from src/gromacs/fatalerror/gmxassert.h
rename to src/gromacs/utility/gmxassert.h
index 55c3d12da219732b277533e30fc5b5ecfd5bb86b..7e0c8695a6a76ae8cec6baa4e7d297d968b3fb9e 100644 (file)
--- a/src/gromacs/fatalerror/gmxassert.h
+++ b/src/gromacs/utility/gmxassert.h
@@ -34,10 +34,10 @@
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  * \inpublicapi
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#ifndef GMX_FATALERROR_GMXASSERT_H
-#define GMX_FATALERROR_GMXASSERT_H
+#ifndef GMX_UTILITY_GMXASSERT_H
+#define GMX_UTILITY_GMXASSERT_H
 
 #include <boost/current_function.hpp>
 #include <boost/exception/detail/attribute_noreturn.hpp>
@@ -90,7 +90,7 @@ namespace internal
  * Should not be called directly, but instead through ::GMX_ASSERT or
  * ::GMX_RELEASE_ASSERT.
  *
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 BOOST_ATTRIBUTE_NORETURN
 void assertHandler(const char *condition, const char *msg,

diff --git a/src/gromacs/fatalerror/messagestringcollector.cpp b/src/gromacs/utility/messagestringcollector.cpp
similarity index 96%
rename from src/gromacs/fatalerror/messagestringcollector.cpp
rename to src/gromacs/utility/messagestringcollector.cpp
index 3d9abd19b0dcaf84b882536dedb8d99df8edaa3c..d377f369f5509bfbe7b2b58922ed0f18fc4323ff 100644 (file)
--- a/src/gromacs/fatalerror/messagestringcollector.cpp
+++ b/src/gromacs/utility/messagestringcollector.cpp
@@ -33,13 +33,13 @@
  * Implements gmx::MessageStringCollector.
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#include "gromacs/fatalerror/messagestringcollector.h"
+#include "gromacs/utility/messagestringcollector.h"
 
 #include <vector>
 
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 
 namespace gmx
 {

diff --git a/src/gromacs/fatalerror/messagestringcollector.h b/src/gromacs/utility/messagestringcollector.h
similarity index 96%
rename from src/gromacs/fatalerror/messagestringcollector.h
rename to src/gromacs/utility/messagestringcollector.h
index 6ddda7070b3f5bf0bf4c88e4d5d2f9836ca9d913..05f08fc4ef57f5ba1e3751e2ab34f72ea00202f4 100644 (file)
--- a/src/gromacs/fatalerror/messagestringcollector.h
+++ b/src/gromacs/utility/messagestringcollector.h
@@ -34,10 +34,10 @@
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  * \inlibraryapi
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
-#ifndef GMX_FATALERROR_MESSAGESTRINGCOLLECTOR_H
-#define GMX_FATALERROR_MESSAGESTRINGCOLLECTOR_H
+#ifndef GMX_UTILITY_MESSAGESTRINGCOLLECTOR_H
+#define GMX_UTILITY_MESSAGESTRINGCOLLECTOR_H
 
 #include <string>
 
@@ -53,7 +53,7 @@ namespace gmx
  * string for, e.g., printing out or for including in an exception.
  *
  * \inlibraryapi
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class MessageStringCollector
 {
@@ -139,7 +139,7 @@ bool function(::gmx::MessageStringCollector *errors)
  *
  * \see MessageStringCollector
  * \inlibraryapi
- * \ingroup module_fatalerror
+ * \ingroup module_utility
  */
 class MessageStringContext
 {

diff --git a/src/gromacs/utility/uniqueptr.h b/src/gromacs/utility/uniqueptr.h
index b3a754fa60ccb140cbc884d69da2946a5e442c76..40eb4b9012da17cd670d4de65182e19d614700b3 100644 (file)
--- a/src/gromacs/utility/uniqueptr.h
+++ b/src/gromacs/utility/uniqueptr.h
@@ -82,7 +82,6 @@ typedef gmx_unique_ptr<ExampleClass>::type ExampleClassPointer;
  * For C++11 gmx::move is the std::move, for non-C++11 compilers, the
  * move operation is a no-op.
  *
- * \ingroup module_utility
  * \inlibraryapi
  */
 #ifdef HAVE_CXX11 // C++11 Compiler

diff --git a/src/programs/g_ana/g_ana.cpp b/src/programs/g_ana/g_ana.cpp
index 3f41c9d8700579e408ab388018dd88bd36d0ef2a..762640ff671cbdc1562eb9e7d448d9f1b3f19993 100644 (file)
--- a/src/programs/g_ana/g_ana.cpp
+++ b/src/programs/g_ana/g_ana.cpp
@@ -33,12 +33,12 @@
  *
  * \author Teemu Murtola <teemu.murtola@cbr.su.se>
  */
-#include <copyrite.h>
+#include "gromacs/legacyheaders/copyrite.h"
 
-#include "gromacs/fatalerror.h"
 #include "gromacs/trajectoryanalysis/analysismodule.h"
 #include "gromacs/trajectoryanalysis/cmdlinerunner.h"
 #include "gromacs/trajectoryanalysis/modules.h"
+#include "gromacs/utility/exceptions.h"
 
 int
 main(int argc, char *argv[])

diff --git a/src/testutils/datapath.cpp b/src/testutils/datapath.cpp
index 771fec09733a802aaad1bec88a676d5b4a797010..c72aa32c1d8d1c4f9ca271c17fc12febf951893e 100644 (file)
--- a/src/testutils/datapath.cpp
+++ b/src/testutils/datapath.cpp
@@ -37,7 +37,7 @@
  */
 #include "datapath.h"
 
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/path.h"
 
 static const char *g_testDataPath = NULL;

diff --git a/src/testutils/refdata.cpp b/src/testutils/refdata.cpp
index 75dd1ff7dec5c8486ac3713bdbf4f45fd2670120..39dccc9251694fe721180d4e5e3723017931e3ea 100644 (file)
--- a/src/testutils/refdata.cpp
+++ b/src/testutils/refdata.cpp
@@ -46,8 +46,8 @@
 #include <libxml/parser.h>
 #include <libxml/xmlmemory.h>
 
-#include "gromacs/fatalerror/exceptions.h"
-#include "gromacs/fatalerror/gmxassert.h"
+#include "gromacs/utility/exceptions.h"
+#include "gromacs/utility/gmxassert.h"
 #include "gromacs/utility/path.h"
 #include "gromacs/utility/format.h"
 #include "testutils/testexceptions.h"

diff --git a/src/testutils/testexceptions.h b/src/testutils/testexceptions.h
index afc3da7abf670068ce7cbfa89de25e340d51d342..dfd339f87e158ac3de09c87ef4892a7556964a13 100644 (file)
--- a/src/testutils/testexceptions.h
+++ b/src/testutils/testexceptions.h
@@ -41,7 +41,7 @@
 
 #include <string>
 
-#include "gromacs/fatalerror/exceptions.h"
+#include "gromacs/utility/exceptions.h"
 
 namespace gmx
 {

diff --git a/src/testutils/testoptions.cpp b/src/testutils/testoptions.cpp
index db930dc42bb81a3b913c48c52975da48400cd16b..6950931836e6a3f3985f8e33ef407d2d0c889e50 100644 (file)
--- a/src/testutils/testoptions.cpp
+++ b/src/testutils/testoptions.cpp
@@ -46,10 +46,10 @@
 
 #include <boost/scoped_ptr.hpp>
 
-#include "gromacs/fatalerror/errorcodes.h"
-#include "gromacs/fatalerror/gmxassert.h"
 #include "gromacs/options/cmdlineparser.h"
 #include "gromacs/options/options.h"
+#include "gromacs/utility/errorcodes.h"
+#include "gromacs/utility/gmxassert.h"
 
 #include "datapath.h"
 #include "refdata.h"