Merge commit 'astyle-master~1' into pamm

.astyle.options

@@ -0,0 +1 @@
+-n --indent=spaces=2 --keep-one-line-statements --keep-one-line-blocks

.gitignore

@@ -10,6 +10,8 @@
 *.dll
 *.sw?
 *.exe
+*.gcda
+*.gcno
 a.out
 makefile.dep
 /Makefile.conf

.travis.yml

@@ -4,10 +4,12 @@ matrix:
 # list of configurations to be attempted:
 # MPI + doc
 # this is the "master" one, it is going to update the manual if log contains [makedoc]
+# Variable PLUMED_ALL_TESTS=yes ensures that all the regtests can be run.
+# If some of them is not enabled, the whole suite will fail.
   - os: linux
     dist: trusty
     sudo: required
-    env: PLUMED_CC=mpicc PLUMED_CXX=mpic++ MAKEDOC=yes
+    env: PLUMED_CC=mpicc PLUMED_CXX=mpic++ MAKEDOC=yes PLUMED_ALL_TESTS=yes CONFIG_FLAGS=--enable-cxx-exceptions
 # the following are with debug flags
   - os: linux
     dist: trusty
@@ -22,43 +24,43 @@ matrix:
   - os: linux
     dist: trusty
     sudo: required
-    env: CPPCHECK=yes CPPCHECK_VERSION=1.71
-  - os: linux
-    dist: trusty
-    sudo: required
-    env: CPPCHECK=yes CPPCHECK_VERSION=1.74
+    env: CPPCHECK=yes CPPCHECK_VERSION=1.78
 # then check with different optimization flags
   - os: linux
     dist: trusty
     sudo: required
     env: PLUMED_CC=gcc   PLUMED_CXX=g++     PLUMED_CXXFLAGS=-O3 LAPACK=yes
-# then I try serial compiler on UBUNTU precise
-  - os: linux
-    dist: precise
-    sudo: required
-    env: PLUMED_CC=gcc   PLUMED_CXX=g++
 # test using external blas with internal lapack
   - os: linux
     dist: trusty
     sudo: required
     env: PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3 LAPACK=yes CONFIG_FLAGS="--disable-external-lapack"
 # osx serial
   - os: osx
+    osx_image: xcode7.3
     env: PLUMED_CC=clang PLUMED_CXX=clang++ PLUMED_CXXFLAGS=-O3
 # osx parallel
   - os: osx
+    osx_image: xcode7.3
     env: PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3
 # osx serial macports
   - os: osx
+    osx_image: xcode7.3
     env: PLUMED_MACPORTS="plumed"
 # osx serial macports debug variant
   - os: osx
-    env: PLUMED_MACPORTS="plumed +crystallization +manyrestraints +adjmat"
+    osx_image: xcode7.3
+    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
-  allow_failures:
-# I allow this to fail temporarily
-    - env: CPPCHECK=yes CPPCHECK_VERSION=1.74
-# Possible additional variables:
+## This command can be used to allow failures:
+##  allow_failures:
+## # I allow this to fail temporarily
+##    - env: CPPCHECK=yes CPPCHECK_VERSION=1.74
+## Possible additional variables:
 #   VALGRIND=yes to make valgrind tests, only when log contains string [valgrind]
 install:
 # setup environment to allow install on the home directory
@@ -69,7 +71,8 @@ install:
   - export LD_LIBRARY_PATH="$HOME/opt/lib:$LD_LIBRARY_PATH"
 # build the manual, only if log contains string [makedoc]
   - export PLUMED_NUM_THREADS=2
-  - ./.travis/check.log makedoc  || MAKEDOC=no
+# accept both [makedoc] and [makedocs] as an option
+  - ./.travis/check.log makedoc  || ./.travis/check.log makedocs || MAKEDOC=no
   - ./.travis/check.log valgrind || VALGRIND=no
 # update packages
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && test -z "$PLUMED_MACPORTS" ; then brew update > /dev/null ; fi
@@ -80,37 +83,46 @@ install:
 # cppcheck:
 # 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 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
   - if test "$PLUMED_CXX" == "mpic++" -a "$TRAVIS_OS_NAME" == "osx" ;   then brew install openmpi ; fi
   - if test "$MAKEDOC" == yes ; then sudo apt-get install -y graphviz            ; fi
 # install doxygen-latex
   - if test "$MAKEDOC" == yes ; then sudo apt-get install -y doxygen-latex ; fi
+# install lcov
+  - if test "$MAKEDOC" == yes ; then sudo apt-get install -y lcov ; fi
 # then replace doxygen with the desided version
 # I use 1.8.10 instead of 1.8.11 since it looks like 1.8.11 have troubles with
 # non case sensitive files (it writes capitalized filenames)
-  - if test "$MAKEDOC" == yes ; then ./.travis/install.doxygen Release_1_8_10 ; 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 stty rows 40 columns 80 ; fi
-  - 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
-  - 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:pamm"
+# 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
@@ -121,12 +133,13 @@ script:
   - if test "$PLUMED_CXX" ; then make install prefix="$HOME/opt" ; fi
 
 # build using macports
-  - 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 "$VALGRIND" == yes ; then OPT=valgrind ; else OPT="" ; fi
   - if test "$PLUMED_CXX" || test -n "$PLUMED_MACPORTS" ; then make -C regtest $OPT ; fi
   - if test "$MAKEDOC" == yes ; then make -C regtest copytodoc ; fi
+  - if test "$MAKEDOC" == yes ; then make -C developer-doc coverage ; fi
   - if test "$MAKEDOC" == yes ; then make doc >/dev/null ; fi
   - if test "$PLUMED_CXX" || test -n "$PLUMED_MACPORTS" ; then make -C regtest checkfail ; fi
 
@@ -135,6 +148,8 @@ script:
 # notice that this is done automatically in build
   - if test "$CPPCHECK" == yes ; then make -C src/lib/ dirslinks ; fi
 # then we do cppcheck
-  - if test "$CPPCHECK" == yes ; then make cppcheck ; fi
+# notice that with make codecheck we also run the maketools/plumedcheck
+# script which check if coding policies are satisfied
+  - if test "$CPPCHECK" == yes ; then make codecheck ; fi
 after_success:
   - if test "$MAKEDOC" == yes ; then ./.travis/pushdoc ; fi 

.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

@@ -0,0 +1,27 @@
+#! /bin/bash
+
+set -e
+set -x
+
+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
+

.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 ../
 

.travis/pushdoc

@@ -15,6 +15,7 @@ cp -R $root/user-doc/{html,manual.pdf} user-doc/
 test -d $root/user-doc/regtests && cp -R $root/user-doc/regtests user-doc/ || true
 mkdir developer-doc
 cp -R $root/developer-doc/html developer-doc/
+test -d $root/developer-doc/coverage && cp -R $root/developer-doc/coverage developer-doc || true
 
 # This file should be here, it is needed otherwise
 # files beginning with _ are skipped
@@ -45,13 +46,16 @@ cat > README.md << EOF
 Precompiled manual for PLUMED ${TRAVIS_BRANCH}
 -----------------------------
 
-This repository hosts a precompiled manual
-for PLUMED ${TRAVIS_BRANCH}, git revision $hash, on $(date).
+This repository hosts a precompiled manual for [PLUMED](http://www.plumed.org) ${TRAVIS_BRANCH},
+git revision [$hash](https://github.com/plumed/plumed2/commit/$hash).
 
-This manual has been compiled on [travis](http://travis-ci.org/plumed/plumed2).
+This manual has been compiled on [travis](http://travis-ci.org/plumed/plumed2) on $(date).
 
 To browse the manual you should go [here](http://plumed.github.io/doc-${TRAVIS_BRANCH}).
 
+You can also download a full copy of the manual for offline access
+at [this link](http://github.com/plumed/doc-${TRAVIS_BRANCH}/archive/gh-pages.zip).
+
 EOF
 git add --all .
 git commit -m "Update to plumed/plumed2@$hash"

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

@@ -165,16 +165,33 @@ 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 
 - GSL library is now treated by `./configure` in the same way as other libraries, that is `-lgsl -lgslcblas` are only
   added if necessary.
+- Fix a bug in \ref METAD when using INTERVAL and ADAPTIVE gaussians at the same time
+- 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.
+
 */