Merge commit 'astyle-v2.3~1' into v2.3-maxent

.astyle.options

+-n --indent=spaces=2 --keep-one-line-statements --keep-one-line-blocks

.travis.yml

@@ -24,7 +24,7 @@ matrix:
   - os: linux
     dist: trusty
     sudo: required
-    env: CPPCHECK=yes CPPCHECK_VERSION=1.75
+    env: CPPCHECK=yes CPPCHECK_VERSION=1.78
 # then check with different optimization flags
   - os: linux
     dist: trusty
@@ -55,7 +55,11 @@ matrix:
 # osx serial macports debug variant
   - os: osx
     osx_image: xcode7.3
-    env: PLUMED_MACPORTS="plumed +crystallization +manyrestraints +adjmat"
+    env: PLUMED_MACPORTS="plumed +allmodules"
+# osx serial macports debug variant
+  - os: osx
+    osx_image: xcode8.2
+    env: PLUMED_MACPORTS="plumed +allmodules"
 # I don't put any mpi variant with macports since it takes too long to compile
 ## This command can be used to allow failures:
 ##  allow_failures:
@@ -85,7 +89,7 @@ install:
 # I use 1.71 since 1.72 seems to report a lot of false positive
   - if test "$CPPCHECK" == yes ; then  ./.travis/install.cppcheck $CPPCHECK_VERSION ; fi
 # for plumedcheck I need latest gawk
-  - if test "$CPPCHECK" == yes ; then  ./.travis/install.gawk ; fi
+  - if test "$CPPCHECK" == yes ; then  ./.travis/install.gawk 4.1.4 ; fi
 # installation of these packages takes a lot of time
 # we do it only when needed
   - if test "$PLUMED_CXX" == "mpic++" -a "$TRAVIS_OS_NAME" == "linux" ; then sudo apt-get install -y libopenmpi-dev openmpi-bin ; fi
@@ -98,32 +102,32 @@ install:
 # then replace doxygen with the desided version
 # I use 1.8.10 instead of 1.8.11 since it looks like 1.8.11 have troubles with
 # non case sensitive files (it writes capitalized filenames)
-  - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_12 ; fi
+  - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_13 ; fi
   - if test "$VALGRIND" == yes ; then sudo apt-get install -y valgrind           ; fi
   - if test "$LAPACK" == yes ; then sudo apt-get -y install libatlas-base-dev      ; fi
 # moreover, we hardcode path to dynamic library, required for xdrfile to link properly
 # I do it only when LD_LIBRARY_PATH is non blank, since otherwise clang gives problems
   - if test -n "$LD_LIBRARY_PATH" ; then PLUMED_LDFLAGS="-Wl,-rpath,$LD_LIBRARY_PATH" ; fi
 # macports related stuff
-  - if test -n "$PLUMED_MACPORTS" ; then export COLUMNS=80 ; fi
-# install macports from source:
-#  - if test -n "$PLUMED_MACPORTS" ; then wget https://distfiles.macports.org/MacPorts/MacPorts-2.3.4.tar.bz2 && tar xvfj MacPorts-2.3.4.tar.bz2 ; fi
-#  - if test -n "$PLUMED_MACPORTS" ; then cd MacPorts-2.3.4 && ./configure && sudo make install && cd - && sudo rm -fr MacPorts-2.3.4 ; fi
-# install macports from binary (faster):
-  - if test -n "$PLUMED_MACPORTS" ; then wget https://distfiles.macports.org/MacPorts/MacPorts-2.3.4-10.11-ElCapitan.pkg ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then sudo installer -pkg MacPorts-2.3.4-10.11-ElCapitan.pkg -target / ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then export PATH=/opt/local/bin:$PATH ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then sudo port -v selfupdate ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then make macports ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then ./.travis/config.macports.sh ; fi
-
+# configure macports
+  - if test -n "$PLUMED_MACPORTS" ; then
+      export COLUMNS=80 ;
+      wget https://raw.githubusercontent.com/GiovanniBussi/macports-ci/master/macports-ci ;
+      chmod +x ./macports-ci ;
+      ./macports-ci install ;
+      PATH="/opt/local/bin:$PATH" ;
+      make macports ;
+      ./macports-ci localports macports ;
+    fi
 script:
-# we enable crystallization and manyrestraints modules
-  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-modules=crystallization:manyrestraints:adjmat"
+# make sure all modules are enabled
+  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-modules=all"
 # we enable fftw, which is off by default
   - CONFIG_FLAGS="$CONFIG_FLAGS --enable-fftw"
   - if test "$MAKEDOC" == yes ; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-pdfdoc" ; fi
   - if test "$MAKEDOC" == yes ; then CONFIG_FLAGS="$CONFIG_FLAGS --enable-gcov" ; fi
+# when running lcov plumed should be compiled with -O0
+  - if test "$MAKEDOC" == yes ; then PLUMED_CXXFLAGS=-O0 ; fi
 
 # BUILD:
 # this is done only if PLUMED_CXX is defined
@@ -134,9 +138,7 @@ script:
   - if test "$PLUMED_CXX" ; then make install prefix="$HOME/opt" ; fi
 
 # build using macports
-# this is required for some misterious reason:
-  - if test -n "$PLUMED_MACPORTS" ; then sudo port install flex +universal ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then sudo port install $PLUMED_MACPORTS ; fi
+  - if test -n "$PLUMED_MACPORTS" ; then sudo port -N install $PLUMED_MACPORTS ; fi
 
 # TEST:
   - if test "$VALGRIND" == yes ; then OPT=valgrind ; else OPT="" ; fi

.travis/config.macports.sh

-#! /bin/bash
-
-set -e
-set -x
-
-cd macports
-
-cp /opt/local/etc/macports/sources.conf $$
-awk -v repo="file://$PWD" '{if($NF=="[default]") print repo; print}' $$ > $$.new
-sudo mv -f $$.new /opt/local/etc/macports/sources.conf
-echo "** NEW SOURCES"
-cat /opt/local/etc/macports/sources.conf
-echo "** END NEW SOURCES"
-rm -f $$
-portindex
-

.travis/install.cppcheck

@@ -3,6 +3,7 @@
 set -e
 set -x
 
+cd "$(mktemp -d)"
 
 git clone https://github.com/danmar/cppcheck.git
 cd cppcheck
@@ -15,12 +16,9 @@ else
   version=$(git tag | tail -n 1)
 fi
 
-
 git checkout $version
 make -j 4 install CFGDIR="$HOME/opt/share/cppcheck/" CXXFLAGS="-O2 -march=native -mtune=native -Wunreachable-code" PREFIX="$HOME/opt"
 cd ../
 
 cppcheck --version
 
-
-

.travis/install.doxygen

@@ -3,6 +3,8 @@
 set -e
 set -x
 
+cd "$(mktemp -d)"
+
 git clone https://github.com/doxygen/doxygen.git
 
 cd doxygen

.travis/install.gawk

@@ -3,12 +3,25 @@
 set -e
 set -x
 
-echo "installing latest gawk"
-wget http://git.savannah.gnu.org/cgit/gawk.git/snapshot/gawk-4.1.4.tar.gz
-tar xzf gawk-4.1.4.tar.gz
-cd gawk-4.1.4
+cd "$(mktemp -d)"
+
+version=4.1.4
+
+if [ -n "$1" ] ; then
+  version=$1
+fi
+
+echo "installing gawk $version"
+
+wget http://git.savannah.gnu.org/cgit/gawk.git/snapshot/gawk-$version.tar.gz
+
+tar xzf gawk-$version.tar.gz
+
+cd gawk-$version
+
 ./configure --prefix="$HOME/opt"
+
 make -j 4
+
 make install
-cd ../
 

.travis/install.xdrfile

@@ -3,16 +3,25 @@
 set -e
 set -x
 
+cd "$(mktemp -d)"
+
 echo "installing xdrfile library"
 # wget ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz
 # xdrfile was removed from gromacs ftp
 # as a workaround I added a copy to people.sissa.it/~bussi/plumed
 # this complies with its license
+
 wget people.sissa.it/~bussi/plumed/xdrfile-1.1.4.tar.gz
+
 tar xzf xdrfile-1.1.4.tar.gz
+
 cd xdrfile-1.1.4
+
 ./configure --enable-shared --prefix="$HOME/opt"
+
 make
+
 make install
+
 cd ../
 

CHANGES/v2.1.txt

@@ -30,7 +30,7 @@ character now has a special usage in component names.
   if these libraries are not installed.
 - New actions:
   - \ref SPRINT topological collective variables.
-  - \ref CH3SHIFTS collective variable.
+  - CH3SHIFTS collective variable.
   - \ref POSITION collective variable.
   - \ref FIT_TO_TEMPLATE.
   - \ref COMMITTOR analysis.

CHANGES/v2.2.txt

@@ -165,9 +165,8 @@ For developers:
 - Tentative port files are now available at [this link](http://github.com/plumed/ports). 
   They can be used to install PLUMED using MacPorts.
 
-Version 2.2.4
+Version 2.2.4 (Dec 12, 2016)
 -------------
-See branch \branch{v2.2} on git repository.
 
 For users:
 - Fix a bug in \ref PBMETAD when biasing periodic and not periodic collective variables at the same time 
@@ -177,8 +176,22 @@ For users:
 - Updated gromacs patch for 5.1.x to 5.1.4
 - Fix a performance regression in the calculate loop where derivatives and forces were set to zero even if an action
   was not active, this is relevant for postprocessing and for the on-the-fly analysis
+- Torsion calculation has been made slightly faster and improved so as to provide correct
+  derivatives even for special angles (e.g. +pi/2 and -pi/2).
 
 For developers:
 - Macports portile is now tested on travis at every plumed push.
 
+Version 2.2.5 (Mar 31, 2017)
+-------------
+
+Notice that branch 2.2 will not be longer maintained! All users are invited to switch to version 2.3.
+
+For users:
+- Fixed a problem with large step numbers in driver (see \issue{209}).
+- Fixed a problem leading to crashes when using switching functions without cutoff with some compiler (see \issue{210}).
+- Fixed a bug when using \ref FIT_TO_TEMPLATE and domain decomposition (see \issue{214}).
+- Added an automatic flush of HILLS files when using \ref METAD with file-based multiple walkers.
+- Root dir is logged to allow easier debugging of problems.
+
 */

CHANGES/v2.3.txt

@@ -2,7 +2,7 @@
 
 @page CHANGES-2-3 Version 2.3
 
-Version 2.3 (Jun 30, 2016)
+Version 2.3 (Dec 12, 2016)
 ----------------------------
 
 Version
@@ -43,6 +43,7 @@ Changes from version 2.2 which are relevant for users:
   - \ref CS2BACKBONE, \ref NOE, \ref RDC, removed the keyword ENSEMBLE: now ensemble averages can only be calculated using \ref ENSEMBLE
   - \ref RDC, syntax changes
   - It is not possible anymore to select modules using `modulename.on` and `modulename.off` files. Use `./configure --enable-modules` instead.
+  - Removed IMD modules. In case someone is interested in restoring it, please contact the PLUMED developers.
 - New actions:
   - \ref FIXEDATOM
   - \ref HBOND_MATRIX
@@ -72,14 +73,18 @@ Changes from version 2.2 which are relevant for users:
   - \ref LOCALENSEMBLE
   - \ref FRET
   - \ref RESET_CELL
+  - \ref JCOUPLING
+  - \ref ERMSD
 - New features in MD patches (require repatch):
   - Patch for amber 14 now passes charges with appropriate units (fixes \issue{165}). Notice that
     the patch is still backward compatible with older PLUMED version, but the charges will only be passed
     when using PLUMED 2.3 or later.
   - Patch for GROMACS 5.1 incorporates Hamiltonian replica exchange, see \ref hrex
   - Gromacs 2016, 5.1.x, 5.0.x, flush the plumed output files upon checkpointing
-  - Added patch for Gromacs 2016
+  - Added patch for Gromacs 2016.1
+  - gromacs 5.1.x patch updated to 5.1.4
   - Removed the patch for Gromacs 4.6.x 
+  - LAMMPS patch updated to support multiple walkers and report plumed bias to LAMMPS (thanks to Pablo Piaggi).
 - New features for existing actions:
   - The SPECIES and SPECIESA keyword in MultiColvars can now take a multicolvar as input.  This allows one
     to calculate quantities such as the Q4 parameters for those atoms that have a coordination number greater
@@ -91,16 +96,25 @@ Changes from version 2.2 which are relevant for users:
   - \ref driver now allows --trajectory-stride to be set to zero when reading with --ixtc/--itrr. In this case, step number is read from the trajectory file.
   - \ref METAD and \ref PBMETAD can now be restarted from a GRID 
   - Added keywords TARGET and DAMPFACTOR in \ref METAD
+  - When using \ref METAD with file-based multple walkers and parallel jobs (i.e. mpirun) extra suffix is not added (thanks to Marco De La Pierre).
   - \ref ENSEMBLE added keywords for weighted averages, and calculation of higher momenta
   - \ref MOLINFO now allows single atoms to be picked by name.
   - \ref FIT_TO_TEMPLATE now supports optimal alignment.
   - \ref CONSTANT added the possibility of storing more values as components with or without derivatives
+  - \ref PUCKERING now supports 6 membered rings.
+  - Extended checkpoint infrastracture, now \ref METAD and \ref PBMETAD will write GRIDS also on checkpoint step (only the GROMACS patch
+    is currently using the checkpointing interface)
 - Other features:
   - Added a plumed-config command line tool. Can be used to inspect configuration also when cross compiling.
   - Added a `--mpi` option to `plumed`, symmetric to `--no-mpi`. Currently, it has no effect (MPI is initialized by default when available).
   - PLUMED now generate a VIM syntax file, see \ref VimSyntax
   - The backward cycle is now parallelised in MPI/OpenMP in case many collective variables are used.
+  - GSL library is now searched by default during `./configure`.
+  - Tutorials have been (partially) updated to reflect some of the changes in the syntax
+  - Parser now reports errors when passing numbers that cannot be parsed instead of silently replacing their default value. See \issue{104}.
   - More and more documentation
+- Bug fixes:
+- Fixed a bug in \ref PBMETAD that was preventing the writing of GRIDS if a hill was not added in that same step 
 
 For developers:
 - IMPORTANT: BIAS can now be BIASED as well, this changes can lead to some incompatibility: now the "bias" component is always defined automatically
@@ -109,29 +123,44 @@ For developers:
 - Added new strings for plumed cmd: setMDMassUnits, setMDChargeUnits, readInputLine, performCalcNoUpdate, update and doCheckPoint.
 - Easier to add actions with multiple arguments
 - New functions to access local quantities in domain decomposition
+- Active modules to enable regtests are chosen using `plumed config`.
+- A script is available to check if source code complies plumed standard. Notice that this script is run together with cppcheck on travis-ci.
+- Cppcheck on travis-ci has been updated to 1.75. Several small issues triggering errors on 1.75 were fixed (e.g. structures passed by value
+   are now passed by const ref) and false positives marked as such.
+- Added coverage scan.
 
-Fixes in beta
+Version 2.3.1 (Mar 31, 2017)
 -------------
 
-Fixes since 2.3b. Relevant things could be merged in the changelog above when we release 2.3.0
+- Fix to FIT_TO_TEMPLATE as in 2.2.5. Notice that in 2.3.0 also the case with TYPE=OPTIMAL was affected. This is fixed now.
+- small change in \ref CS2BACKBONE to symmetrise the ring current contribution with respect to ring rotations (also faster)
+- fixed `plumed-config` that was not working.
+- log file points to the `config.txt` files to allow users to check which features were available in that compiled version.
+- `make clean` in root dir now also cleans `vim` subdirectory.
+- Updated gromacs patch to version 2016.3 
+
+For developers:
+- Cppcheck on travis-ci has been updated to 1.77.
+- Doxygen on travis-ci has been updated to 1.8.13
+
+Version 2.3.2
+-------------
+See branch \branch{v2.3} on git repository.
+
+- New flag `--disable-libsearch` for `configure`, allowing an easier control of linked libraries when installing PLUMED
+  with a package manager such as MacPorts.
+- Resolved problem with nan in \ref SMAC with SPECIESA and SPECIESB involving molecules that are the same
+- PDB reader is now able to read files with dos newlines (see \issue{223}).
+- Fixed bug in \ref CS2BACKBONE (v2.3.1) related to ring currents of HIS and TRP
+- Fixed bug in if condition in \ref PCAVARS so that you can run with only one eigenvector defined in input 
+- Fixed bug with timers in \ref sum_hills \issue{194}.
+- Fixed bug when using \ref MOVINGRESTRAINT with periodic variables such as \ref TORSION \issue{225}.
+- Fixed bug in \ref HBONDS that used to apear when you used DONORNS and ACCEPTORS with same numbers of atoms 
+- Fixed bug in \ref DISTANCES that appears when using BETWEEN and link cells.
+- Prevented users from causing segfaults by storing derivatives without LOWMEM flag.  In these caess PLUMED crashes with meaningful errors.
+- Fixed bug in \ref HISTOGRAM that causes nans when using KERNEL=DISCRETE option
+
+For developers:
+- plumedcheck validation has been made stricter. All the checks are now described in the developer manual.
 
-- Fixed critical pragma in openmp of Colvar. This could have lead to wrong virial accumulation.
-- Extended checkpoint infrastracture, now \ref METAD and \ref PBMETAD will write GRIDS also on checkpoint step (only the GROMACS patch
-  is currently using the checkpointing interface)
-- Fixed a bug in \ref PBMETAD that was preventing the writing of GRIDS if a hill was not added in that same step 
-- GSL library is now searched by default during `./configure`.
-- Removed IMD modules. In case someone is interested in restoring it, please contact the PLUMED developers.
-- (for developers) Active modules to enable regtests are chosen using `plumed config`.
-- New CV: \ref JCOUPLING
-- New CV: \ref ERMSD
-- \ref PUCKERING now supports 6 membered rings.
-- Tutorials have been (partially) updated to reflect some of the changes in the syntax
-- gromacs 5.1.x patch updated to 5.1.4
-- LAMMPS patch updated to support multiple walkers and report plumed bias to LAMMPS (thanks to Pablo Piaggi).
-- When using \ref METAD with file-based multple walkers and parallel jobs (i.e. mpirun) extra suffix is not added (thanks to Marco De La Pierre).
-- Parser now reports errors when passing numbers that cannot be parsed instead of silently replacing their default value. See \issue{104}.
-- (for developers) A script is available to check if source code complies plumed standard. Notice that this script is run together with cppcheck on travis-ci.
-- (for developers) Cppcheck on travis-ci has been updated to 1.75. Several small issues triggering errors on 1.75 were fixed (e.g. structures passed by value
-   are now passed by const ref) and false positives marked as such.
-- (for developers) Added coverage scan.
 */

Makefile

@@ -4,12 +4,12 @@ endif
 
 
 SRCDIRS := src test
-SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest macports
+SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest macports vim astyle
 
 SUBDIRSCLEAN:=$(addsuffix .clean,$(SUBDIRS))
 
      
-.PHONY: all lib clean $(SRCDIRS) doc docclean check cppcheck distclean all_plus_docs macports codecheck plumedcheck
+.PHONY: all lib clean $(SRCDIRS) doc docclean check cppcheck distclean all_plus_docs macports codecheck plumedcheck astyle
 
 # if machine dependent configuration has been found:
 ifdef GCCDEP
@@ -111,5 +111,8 @@ stamp-h: sourceme.sh.in Makefile.conf.in config.status
 config.status: configure
 	./config.status --recheck
 
+astyle:
+	$(MAKE) -C astyle
+	$(MAKE) -C src astyle
 
 

README

@@ -5,7 +5,6 @@ COPYING.LESSER  : license
 Makefile        : makefile
 PEOPLE          : list of authors
 README          : this file
-README.git      : quick reference for git
 configurations/ : template configuration files
 configure       : configuration script
 developer-doc   : developer documentation

VERSION

@@ -5,4 +5,4 @@
 # (this is same as gromacs)
 # Notice that "plumed --version" will return only 2.X
 # and "plumed --long-version" will return the full string
-2.3b
+2.3.1

astyle/.gitignore

+astyle

astyle/LICENSE.md

+### MIT License
+
+Copyright (c) 2017 by Jim Pattee <jimp03@email.com>.
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

astyle/Makefile

+.PHONY: astyle
+
+astyle:
+	$(MAKE) -C build/gcc
+	ln -fs build/gcc/bin/astyle .
+
+clean:
+	$(MAKE) -C build/gcc clean
+	rm -f astyle

astyle/README.md

+Instructions for using Artistic Style are included in the *doc* directory.
+
+The file **install.html** contains instructions for compiling and
+installing Artistic Style.
+
+The file **astyle.html**' contains information on using Artistic Style.
+
+The files **news.html** and **notes.html** contain information on changes
+made to the various releases.

astyle/build/cb-clang/Clang AStyle A.cbp

+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<CodeBlocks_project_file>
+	<FileVersion major="1" minor="6" />
+	<Project>
+		<Option title="Clang AStyle A" />
+		<Option pch_mode="2" />
+		<Option compiler="clang" />
+		<Build>
+			<Target title="Debug">
+				<Option output="bin/astyled" prefix_auto="1" extension_auto="1" />
+				<Option working_dir="" />
+				<Option object_output="objA/Debug/" />
+				<Option type="2" />
+				<Option compiler="clang" />
+				<Option createDefFile="1" />
+				<Compiler>
+					<Add option="-Weverything" />
+					<Add option="-Wall" />
+					<Add option="-std=c++11" />
+					<Add option="-g" />
+					<Add option="-Wextra" />
+					<Add option="-fno-rtti" />
+					<Add option="-fno-exceptions" />
+					<Add option="-Wno-c++98-compat" />
+					<Add option="-Wno-exit-time-destructors" />
+					<Add option="-Wno-global-constructors" />
+					<Add option="-Wno-missing-variable-declarations" />
+					<Add option="-Wno-old-style-cast" />
+					<Add option="-Wno-padded" />
+					<Add option="-Wno-shorten-64-to-32" />
+					<Add option="-Wno-sign-conversion" />
+					<Add option="-Wno-weak-vtables" />
+					<Add option="-DASTYLE_LIB" />
+				</Compiler>
+			</Target>
+			<Target title="Release">
+				<Option output="bin/astyle" prefix_auto="1" extension_auto="1" />
+				<Option working_dir="" />
+				<Option object_output="objA/Release/" />
+				<Option type="2" />
+				<Option compiler="clang" />
+				<Option createDefFile="1" />
+				<Compiler>
+					<Add option="-O3" />
+					<Add option="-Weverything" />
+					<Add option="-Wall" />
+					<Add option="-std=c++11" />
+					<Add option="-Wextra" />
+					<Add option="-fno-rtti" />
+					<Add option="-fno-exceptions" />
+					<Add option="-Wno-c++98-compat" />
+					<Add option="-Wno-exit-time-destructors" />
+					<Add option="-Wno-global-constructors" />
+					<Add option="-Wno-missing-variable-declarations" />
+					<Add option="-Wno-old-style-cast" />
+					<Add option="-Wno-padded" />
+					<Add option="-Wno-shorten-64-to-32" />
+					<Add option="-Wno-sign-conversion" />
+					<Add option="-Wno-weak-vtables" />
+					<Add option="-DNDEBUG" />
+					<Add option="-DASTYLE_LIB" />
+				</Compiler>
+				<Linker>
+					<Add option="-s" />
+				</Linker>
+			</Target>
+		</Build>
+		<Unit filename="../../src/ASBeautifier.cpp" />
+		<Unit filename="../../src/ASEnhancer.cpp" />
+		<Unit filename="../../src/ASFormatter.cpp" />
+		<Unit filename="../../src/ASResource.cpp" />
+		<Unit filename="../../src/astyle.h" />
+		<Unit filename="../../src/astyle_main.cpp" />
+		<Unit filename="../../src/astyle_main.h" />
+		<Extensions>
+			<code_completion />
+			<envvars />
+			<debugger />
+		</Extensions>
+	</Project>
+</CodeBlocks_project_file>

astyle/build/cb-clang/Clang AStyle All.workspace

+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<CodeBlocks_workspace_file>
+	<Workspace title="Clang (GCC) AStyle All">
+		<Project filename="Clang AStyle.cbp" />
+		<Project filename="Clang AStyle So.cbp" />
+		<Project filename="Clang AStyle Java.cbp" />
+		<Project filename="Clang AStyle A.cbp" />
+	</Workspace>
+</CodeBlocks_workspace_file>

astyle/build/cb-clang/Clang AStyle Java.cbp

+<?xml version="1.0" encoding="UTF-8" standalone="yes" ?>
+<CodeBlocks_project_file>
+	<FileVersion major="1" minor="6" />
+	<Project>
+		<Option title="Clang AStyle Java" />
+		<Option pch_mode="2" />
+		<Option compiler="clang" />
+		<Build>
+			<Target title="Debug">
+				<Option output="bin/libastylejd.so.$(SOLIBVER)" prefix_auto="0" extension_auto="0" />
+				<Option object_output="objJ/Debug/" />
+				<Option type="3" />
+				<Option compiler="clang" />
+				<Compiler>
+					<Add option="-Weverything" />
+					<Add option="-Wall" />
+					<Add option="-std=c++11" />
+					<Add option="-g" />
+					<Add option="-Wextra" />
+					<Add option="-fno-rtti" />
+					<Add option="-fno-exceptions" />
+					<Add option="-fPIC" />
+					<Add option="-Wno-c++98-compat" />
+					<Add option="-Wno-exit-time-destructors" />
+					<Add option="-Wno-global-constructors" />
+					<Add option="-Wno-missing-variable-declarations" />
+					<Add option="-Wno-old-style-cast" />
+					<Add option="-Wno-padded" />
+					<Add option="-Wno-reserved-id-macro" />
+					<Add option="-Wno-shorten-64-to-32" />
+					<Add option="-Wno-sign-conversion" />
+					<Add option="-Wno-weak-vtables" />
+					<Add option="-Wno-unknown-warning-option" />
+					<Add option="-DASTYLE_JNI" />
+					<Add directory="/usr/lib/jvm/default-java/include" />
+					<Add directory="/usr/lib/jvm/default-java/include/linux" />
+				</Compiler>
+				<Linker>
+					<Add option="-Wl,-soname,libastylejd.so.$(MAJORVER)" />
+				</Linker>
+			</Target>
+			<Target title="Release">
+				<Option output="bin/libastylej.so.$(SOLIBVER)" prefix_auto="0" extension_auto="0" />
+				<Option object_output="objJ/Release/" />
+				<Option type="3" />
+				<Option compiler="clang" />
+				<Compiler>
+					<Add option="-O3" />
+					<Add option="-Weverything" />
+					<Add option="-Wall" />
+					<Add option="-std=c++11" />
+					<Add option="-Wextra" />
+					<Add option="-fno-rtti" />
+					<Add option="-fno-exceptions" />
+					<Add option="-fPIC" />
+					<Add option="-Wno-c++98-compat" />
+					<Add option="-Wno-exit-time-destructors" />
+					<Add option="-Wno-global-constructors" />
+					<Add option="-Wno-missing-variable-declarations" />
+					<Add option="-Wno-old-style-cast" />
+					<Add option="-Wno-padded" />
+					<Add option="-Wno-reserved-id-macro" />
+					<Add option="-Wno-shorten-64-to-32" />
+					<Add option="-Wno-sign-conversion" />
+					<Add option="-Wno-weak-vtables" />
+					<Add option="-Wno-unknown-warning-option" />
+					<Add option="-DASTYLE_JNI" />
+					<Add option="-DNDEBUG" />
+					<Add directory="/usr/lib/jvm/default-java/include" />
+					<Add directory="/usr/lib/jvm/default-java/include/linux" />
+				</Compiler>
+				<Linker>
+					<Add option="-s" />
+					<Add option="-Wl,-soname,libastylej.so.$(MAJORVER)" />
+				</Linker>
+			</Target>
+			<Environment>
+				<Variable name="MAJORVER" value="3" />
+				<Variable name="MINORVER" value="0" />
+				<Variable name="PATCHVER" value="0" />
+				<Variable name="SOLIBVER" value="$(MAJORVER).$(MINORVER).$(PATCHVER)" />
+			</Environment>
+		</Build>
+		<Unit filename="../../src/ASBeautifier.cpp" />
+		<Unit filename="../../src/ASEnhancer.cpp" />
+		<Unit filename="../../src/ASFormatter.cpp" />
+		<Unit filename="../../src/ASResource.cpp" />
+		<Unit filename="../../src/astyle.h" />
+		<Unit filename="../../src/astyle_main.cpp" />
+		<Unit filename="../../src/astyle_main.h" />
+		<Extensions>
+			<code_completion />
+			<debugger />
+			<envvars />
+		</Extensions>
+	</Project>
+</CodeBlocks_project_file>