Merge commit 'astyle-master~1' into topology-matrix

.astyle.options

@@ -0,0 +1 @@
+-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=1.77
+    env: CPPCHECK=yes CPPCHECK_VERSION=1.78
 # then check with different optimization flags
   - os: linux
     dist: trusty
@@ -104,22 +104,16 @@ install:
 # 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 OSX_VERSION="$(sw_vers -productVersion | sed 's/\.[^\.]*$//')" ; fi
-  - MACPORTS_PKG=MacPorts-2.4.1-10.11-ElCapitan.pkg
-  - if test "$OSX_VERSION" == 10.12 ; then MACPORTS_PKG=MacPorts-2.4.1-10.12-Sierra.pkg ; fi
-  - echo "$MACPORTS_PKG"
-  - if test -n "$PLUMED_MACPORTS" ; then wget https://distfiles.macports.org/MacPorts/$MACPORTS_PKG ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then sudo installer -pkg $MACPORTS_PKG -target / ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then export PATH=/opt/local/bin:$PATH ; fi
-  - if test -n "$PLUMED_MACPORTS" ; then sudo port -N -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:
 # make sure all modules are enabled
   - CONFIG_FLAGS="$CONFIG_FLAGS --enable-modules=all"

CHANGES/v2.3.txt

@@ -131,7 +131,6 @@ For developers:
 
 Version 2.3.1 (Mar 31, 2017)
 -------------
-See branch \branch{v2.3} on git repository.
 
 - 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)
@@ -144,4 +143,24 @@ 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.
+
 */

Makefile

@@ -4,12 +4,12 @@ endif
 
 
 SRCDIRS := src test
-SUBDIRS := $(SRCDIRS) user-doc developer-doc regtest macports vim
+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.md

@@ -0,0 +1,124 @@
+
+Content
+-------
+
+    CHANGES/         : change log
+    COPYING.LESSER   : license
+    Makefile         : makefile
+    Makefile.conf.in : template configuration makefile
+    PEOPLE           : list of authors
+    README           : this file
+    VERSION          : version file
+    configurations/  : template configuration files
+    configure        : configuration script
+    configure.ac     : configuration script (autoconf)
+    developer-doc    : developer documentation
+    include          : symbolic link for include files
+    macports         : directory where Portfiles are generated
+    patches          : patch scripts
+    release.sh       : developer utility to publish releases
+    regtest          : regression tests, including reference results
+    scripts          : shell tools
+    src              : source code
+    sourceme.sh      : template configuration script
+    test             : examples
+    user-doc         : user documentation
+    vim              : directory where vim syntax is generated
+
+Install
+-------
+
+Extensive installation instructions are in the user documentation.
+Links to precompiled versions of the documentation can be found [here](http://www.plumed.org/documentation).
+
+Required software:
+
+* GNU make
+* C/c++ compiler (c++11 support is required as of version 2.4).
+* A modern version of the `patch` command line tool
+* Support for POSIX library `dirent.h`
+* `xxd` (present in most unix distributions)
+
+Suggested software (libraries are checked by `./configure` and enabled if available):
+
+* Optimized blas and lapack libraries. Can be replaced by an internal version if not available.
+* MPI library to run parallel simulations. It should be the same library used by your MD code.
+* [VMD molfile plugins](http://www.ks.uiuc.edu/Research/vmd/plugins) to read arbitrary file formats. Can be replaced by an internal version supporting a few formats if not available.
+* [Matheval library](http://www.gnu.org/software/libmatheval) to use algebraic collective variables.
+* [Zlib library](http://zlib.net/) to use compressed data files.
+* [Xdrfile library](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library) to have read/write access to gromacs
+  trajectory files.
+* [Doxygen](http:://www.doxygen.org) to build user manual. Doxygen might need the following packages:
+  * Latex to build the pdf user manual.
+  * [Graphviz](http://www.graphviz.org) to show class hierarchy in
+    developer manual.
+
+Quick compilation instructions
+------------------------------
+
+Configure for your system
+
+    ./configure --prefix=$HOME/opt
+
+
+If necessary, edit `Makefile.conf`. 
+Configure your environment
+
+    source ./sourceme.sh
+
+Compile plumed
+
+    make
+
+The `plumed` executable should be now in your execution path
+
+    plumed help
+
+Compile the manuals (pre-compiled manual is available online):
+
+    make doc
+
+User documentation can be found at `user-doc/html/index.html`.
+Developer documentation can be found at `developer-doc/html/index.html`.
+
+Install PLUMED in `$HOME/opt` (directory should be set during `./configure`):
+
+    umask 022
+    make install
+
+A sample modulefile with environment variable will be placed in
+`$HOME/opt/lib/plumed/src/lib/modulefile`. Path to the installed documentation can be found with command `plumed info --user-doc`.
+
+
+Branches and releases
+---------------------
+
+Several branches and tags are stored on the git repository.
+
+Branches named `v2.X` correspond to release branches.
+
+Master branch may contain non tested features and is not expected to be used by non-developers.
+It typically contains features that will be available on the next release.
+
+Tags named `v2.XbY` correspond to beta releases, use it with care.
+Tags named `v2.X.Y` correspond to official releases, use the latest available.
+
+To report problems found on beta or official releases, use the normal `[email protected]`
+mailing list. Just state exactly which version you are using.
+
+To report problems found on `master` branch, use the `[email protected]` mailing list.
+This is also the correct place for discussions about new features etc.
+When reporting please provide the git hash (you can obtain it with `git rev-parse HEAD`).
+
+Status
+------
+
+| Branch   |      Status   | Supported |
+|:--------:|:-------------:|:--------:|
+| master   | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=master)](https://travis-ci.org/plumed/plumed2) | yes |
+| v2.3     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.3)](https://travis-ci.org/plumed/plumed2) | yes |
+| v2.2     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.3)](https://travis-ci.org/plumed/plumed2) | no |
+| v2.1     | [![Build Status](https://travis-ci.org/plumed/plumed2.svg?branch=v2.2)](https://travis-ci.org/plumed/plumed2) | no |
+| v2.0     | Not available | no |
+
+

astyle/.gitignore

@@ -0,0 +1 @@
+astyle

astyle/LICENSE.md

@@ -0,0 +1,21 @@
+### MIT License
+
+Copyright (c) 2017 by Jim Pattee <[email protected]>.
+
+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

@@ -0,0 +1,9 @@
+.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

@@ -0,0 +1,9 @@
+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.