Updated to PLUMED 2.4. Implemented CSE and renamed modules according …

…to paper R2.

.github/CONTRIBUTING.md

@@ -13,18 +13,16 @@ your code in the future.  Consequently, please  be ready to answer to specific q
 Finally, we are very happy to accept contributions to the documentation.
 
 Notice that when you open a pull request you
-*implictly agree to transfer the copyright of your code to the PLUMED developers*.
+*implictly agree to transfer the copyright of your code to the PLUMED developers* (or to the authors
+of the code that you are modifying).
 We understand that you might think this unfair.  However, we want to be 100% sure that in the
 future we can make drastic changes to the code, including changes to the  license and that we will not have to 
 contact all the developers that contributed a small number of lines when doing so.
 
-If you want to contribute some large change, notice that
-we prefer not to include your code directly in PLUMED. Large external contributions are difficult for us to maintain.
-To be more specific, a contribution can be considered small (and maintainable) only if one
-of the current PLUMED developers is able to read every single line of it and understand what it does.
-We have, however, put considerable effort into making the code modular.  Consequently, adding a new collective variable is often a single matter of including one additional
-file. We would therefore suggest that, one option you might consider is putting your extra files on the web in some way.
-In other words, you can just distribute a single cpp file together with instructions on how to include this with PLUMED.
-Alternatively, and this is the option we would recommend, you can distribution a separate fork of the full PLUMED with your added code inside.  Creating such forks is relatively straightforward if you use github.
-In addition, if you use this second object people will be able to download a fully validated version of plumed with your extra feature,
-and will, furthermore, be able to merge the latest changes of the code.  On a final note, we are more than happy to put a link to your webpage/repository/whatever in the PLUMED manual so as to make it is visible to our community of users.
+If you want to contribute some large change, please consider adding a new module.
+Documentation about adding new modules is still limited, but you can get inspiration
+from the existing ones. This procedure will allow you to keep the ownership on your code.
+On the other hand, we expect that you will maintain it in the future.
+
+Finally, notice that you can always share modified versions of PLUMED with your changes.
+We are happy if you want to host on github a fork of PLUMED with additional features.

.github/PULL_REQUEST_TEMPLATE.md

@@ -1,5 +1,34 @@
+##### Description
+
+<!-- describe here your pull request -->
+
+##### Target release
+
+<!-- please tell us where you would like your code to appear (e.g. v2.4): -->
+I would like my code to appear in release __XXXXX__
+
+##### Type of contribution
+
+<!--
+  Please select the type of your contribution among these:
+  (Change [ ] to [X] to tick an option)
+-->
+- [ ] changes to code or doc authored by PLUMED developers
+- [ ] changes to a module not authored by you
+- [ ] new module contribution or edit of a module authored by you
+
+##### Copyright
+
+<!--
+  In case you picked one of the first two choices
+  MAKE SURE TO TICK ALSO THE FOLLOWING BOX
+-->
+
+- [ ] I agree to transfer the copyright of the code I have written to the PLUMED developers or to the author of the code I am modifying.
+
+##### Tests
+
 Make sure these boxes are checked before submitting your pull request:
 
 - [ ] I added a new regtest or modified an existing regtest to validate my changes.
-- [ ] I verified that all regtests are passed succesfully on Travis.
-- [ ] I agree to transfer the copyright of the code I have written to the PLUMED developers.
+- [ ] I verified that all regtests are passed successfully on Travis-CI.

.gitignore

@@ -1,6 +1,7 @@
 .DS_Store
 *~
 *.o
+*.a
 *.d
 *.cppdep
 *.cdep

.gitmodules

@@ -1,4 +1,4 @@
 [submodule "src/stanmath/math"]
-	path = src/stanmath/math
+	path = src/curvature_autodiff/math
 	url = http://github.com/stan-dev/math.git
 	branch = origin/v2.16.0

.travis.yml

@@ -4,7 +4,7 @@ matrix:
   include:
 # list of configurations to be attempted:
 # MPI + doc
-# this is the "master" one, it is going to update the manual if log contains [makedoc]
+# this is the "master" one, it is going to update the manual every time
 # 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
@@ -25,29 +25,27 @@ matrix:
   - os: linux
     dist: trusty
     sudo: required
-    env: CPPCHECK=yes CPPCHECK_VERSION=1.79
+    env: CPPCHECK=yes CPPCHECK_VERSION=1.81
 # 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++
+    env: PLUMED_CC=mpicc   PLUMED_CXX=mpic++     PLUMED_CXXFLAGS=-O3 LAPACK=yes
 # test using external blas with internal lapack
   - os: linux
+    if: branch =~ ^test- OR type IN(pull_request)
     dist: trusty
     sudo: required
     env: PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3 LAPACK=yes CONFIG_FLAGS="--disable-external-lapack"
 # test using docker image.
 # currently it means ubuntu 17, with gcc6
   - sudo: required
+    if: branch =~ ^test- OR type IN(pull_request)
     services: docker
     env: PLUMED_DOCKER=yes
 # osx serial
   - os: osx
+    if: branch =~ ^test- OR type IN(pull_request)
     osx_image: xcode7.3
     env: PLUMED_CC=clang PLUMED_CXX=clang++ PLUMED_CXXFLAGS=-O3
 # this should not be required. I add it since it looks like with OSX it does not work otherwise
@@ -56,6 +54,7 @@ matrix:
       - $HOME/.ccache
 # osx parallel
   - os: osx
+    if: branch =~ ^test- OR type IN(pull_request)
     osx_image: xcode7.3
     env: PLUMED_CC=mpicc PLUMED_CXX=mpic++  PLUMED_CXXFLAGS=-O3
 # this should not be required. I add it since it looks like with OSX it does not work otherwise
@@ -64,30 +63,32 @@ matrix:
       - $HOME/.ccache
 # osx serial macports
   - os: osx
+    if: branch =~ ^test- OR type IN(pull_request)
     osx_image: xcode7.3
     env: PLUMED_MACPORTS="plumed"
     cache:
       directories:
       - $HOME/.macports-ci-ccache
 # osx serial macports debug variant
   - os: osx
+    if: branch =~ ^test- OR type IN(pull_request)
     osx_image: xcode7.3
     env: PLUMED_MACPORTS="plumed +allmodules"
     cache:
       directories:
       - $HOME/.macports-ci-ccache
 # osx serial macports debug variant
   - os: osx
-    osx_image: xcode8.2
+    osx_image: xcode8.3
     env: PLUMED_MACPORTS="plumed +allmodules"
     cache:
       directories:
       - $HOME/.macports-ci-ccache
 # I don't put any mpi variant with macports since it takes too long to compile
 ## This command can be used to allow failures:
-##  allow_failures:
-## # I allow this to fail temporarily
-##    - env: CPPCHECK=yes CPPCHECK_VERSION=1.74
+  allow_failures:
+# I allow this to fail temporarily
+  - env: PLUMED_DOCKER=yes
 ## Possible additional variables:
 #   VALGRIND=yes to make valgrind tests, only when log contains string [valgrind]
 install:
@@ -97,19 +98,19 @@ install:
   - export INCLUDE="$HOME/opt/include:$INCLUDE"
   - export LIBRARY_PATH="$HOME/opt/lib:$LIBRARY_PATH"
   - export LD_LIBRARY_PATH="$HOME/opt/lib:$LD_LIBRARY_PATH"
-# build the manual, only if log contains string [makedoc]
+# on travis, better dump stack trace in case there is an error
+  - export PLUMED_STACK_TRACE=yes
   - export PLUMED_NUM_THREADS=2
-# accept both [makedoc] and [makedocs] as an option
-  - ./.travis/check.log makedoc  || ./.travis/check.log makedocs || MAKEDOC=no
   - ./.travis/check.log valgrind || VALGRIND=no
 # update packages
   - if [[ "$TRAVIS_OS_NAME" == "osx" ]] && test -z "$PLUMED_MACPORTS" ; then
       brew update > /dev/null ;
       brew install ccache ;
+      export PLUMED_MPIRUN="mpirun --oversubscribe" ;
     fi
   - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get update -qq ; fi
 # install some package - these are fast, we install them anyway
-  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y libmatheval-dev libfftw3-dev gsl-bin libgsl0-dev ; fi
+  - if [[ "$TRAVIS_OS_NAME" == "linux" ]]; then sudo apt-get install -y libmatheval-dev libfftw3-dev gsl-bin libgsl0-dev  libboost-serialization-dev ; fi
   - if test "$PLUMED_CXX" ; then ./.travis/install.xdrfile ; fi
 # cppcheck:
 # I use 1.71 since 1.72 seems to report a lot of false positive
@@ -153,6 +154,8 @@ script:
   - CONFIG_FLAGS="$CONFIG_FLAGS --enable-modules=all"
 # we enable fftw, which is off by default
   - CONFIG_FLAGS="$CONFIG_FLAGS --enable-fftw"
+# enable boost_serialization to test drr module
+  - CONFIG_FLAGS="$CONFIG_FLAGS --enable-boost_serialization"
   - 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
@@ -170,7 +173,8 @@ script:
 
 # build using macports
   - if test -n "$PLUMED_MACPORTS" ; then
-      sudo port -N install $PLUMED_MACPORTS ;
+      sudo port -N -k install $PLUMED_MACPORTS ;
+      plumed config show
       ./macports-ci ccache --save ;
     fi
 
@@ -179,7 +183,8 @@ script:
 
 # TEST:
   - if test "$VALGRIND" == yes ; then OPT=valgrind ; else OPT="" ; fi
-  - if test "$PLUMED_CXX" || test -n "$PLUMED_MACPORTS" ; then make -C regtest $OPT ; fi
+# --no-print-directory make it more silent
+  - if test "$PLUMED_CXX" ; then make --no-print-directory -C regtest $OPT ; fi
 
 # test with gcc6
   - if test "$PLUMED_DOCKER" = yes ; then docker run -v "$PWD/regtest":/home/plumed/regtest -it plumed /bin/bash -c "make -C regtest" ; fi
@@ -188,7 +193,8 @@ script:
   - 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 "$PLUMED_MACPORTS" ; then make -C regtest checkfail ; fi
+  - if test "$PLUMED_CXX" ; then make -C regtest checkfail ; fi
+  - if test -n "$PLUMED_MACPORTS" ; then sudo port -N -d test $PLUMED_MACPORTS ; fi
 
 # CPPCHECK:
 # this is required so as to have all the include files inplace:

.travis/install.cppcheck

@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 git clone https://github.com/danmar/cppcheck.git
 cd cppcheck
@@ -16,8 +16,13 @@ else
   version=$(git tag | tail -n 1)
 fi
 
+# pick native architecture
+native="$($CC -march=native -Q --help=target | grep march= | awk '{print $2}')"
+# this is required so that when running the job on a different architecture ccache understand
+# the object file should not be recycled
+
 git checkout $version
-make -j 4 install CFGDIR="$HOME/opt/share/cppcheck/" CXXFLAGS="-O2 -march=native -mtune=native -Wunreachable-code" PREFIX="$HOME/opt"
+make -j 4 install CFGDIR="$HOME/opt/share/cppcheck/" CXXFLAGS="-O2 -march="$native" -mtune="$native" -Wunreachable-code" PREFIX="$HOME/opt"
 cd ../
 
 cppcheck --version

.travis/install.doxygen

@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 git clone https://github.com/doxygen/doxygen.git
 

.travis/install.gawk

@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 version=4.1.4
 

.travis/install.lcov

@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 git clone https://github.com/linux-test-project/lcov.git
 

.travis/install.xdrfile

@@ -3,7 +3,7 @@
 set -e
 set -x
 
-cd "$(mktemp -d)"
+cd "$(mktemp -dt plumed.XXXXXX)"
 
 echo "installing xdrfile library"
 # wget ftp://ftp.gromacs.org/pub/contrib/xdrfile-1.1.4.tar.gz

.travis/pushdoc

@@ -3,16 +3,22 @@
 set -e
 set -x
 
-if [[ "$TRAVIS_BRANCH" =~ ^v2\.[0-9]+$ ]] ; then
-# TODO: this should be made automatic by reading the CHANGES/*.txt files:
-  if [ "$TRAVIS_BRANCH" = v2.0 ] || [ "$TRAVIS_BRANCH" = v2.1 ] || [ "$TRAVIS_BRANCH" = v2.2 ] ; then
-    branchtype=unsupported
+GIT_OWNER=$(  echo $TRAVIS_REPO_SLUG | sed "s/\/.*$//" )
+GIT_REPO=$(   echo $TRAVIS_REPO_SLUG | sed "s/^.*\///" )
+
+if [ "$GIT_OWNER" = plumed ] ; then
+  if [[ "$TRAVIS_BRANCH" =~ ^v2\.[0-9]+$ ]] ; then
+    if test -f CHANGES/"$TRAVIS_BRANCH".md && grep -q plumednotmaintained CHANGES/"$TRAVIS_BRANCH".md ; then
+      branchtype=unsupported
+    else
+      branchtype=official
+    fi
+  elif [ "$TRAVIS_BRANCH" = master ] ; then
+    branchtype=master
   else
-    branchtype=official
+    branchtype=unofficial
   fi
-elif [ "$TRAVIS_BRANCH" = master ] ; then
-  branchtype=master
-else
+else 
   branchtype=unofficial
 fi
 
@@ -47,34 +53,44 @@ This is an auto redirect page.
 </html>
 EOF
 
+if test -z "${GIT_BOT}"
+then
+  export GIT_BOT=plumedbot
+fi
+
+if test -z "${GIT_BOT_EMAIL}"
+then
+  export GIT_BOT_EMAIL=giovanni.bussi+plumedbot@gmail.com
+fi
+
 git init
-git config user.email "giovanni.bussi+plumedbot@gmail.com"
-git config user.name "plumedbot"
+git config user.email "${GIT_BOT_EMAIL}"
+git config user.name "${GIT_BOT}"
 git checkout -b gh-pages
 # this is not to show the GIT_TOKEN on Travis log
 set +x
-git remote add doc https://plumedbot:$GIT_TOKEN@github.com/plumed/doc-${TRAVIS_BRANCH}.git
+git remote add doc https://${GIT_BOT}:$GIT_TOKEN@github.com/$GIT_OWNER/doc-${TRAVIS_BRANCH}.git
 set -x
 cat > README.md << EOF
 Precompiled manual for PLUMED ${TRAVIS_BRANCH}
 -----------------------------
 
 This repository hosts a precompiled manual for [PLUMED](http://www.plumed.org) ${TRAVIS_BRANCH},
-git revision [$hash](https://github.com/plumed/plumed2/commit/$hash).
+git revision [$hash](https://github.com/${GIT_OWNER}/${GIT_REPO}/commit/$hash).
 
-This manual has been compiled on [travis](http://travis-ci.org/plumed/plumed2) on $(date).
+This manual has been compiled on [travis](http://travis-ci.org/${GIT_OWNER}/${GIT_REPO}) on $(date).
 
-To browse the manual you should go [here](http://plumed.github.io/doc-${TRAVIS_BRANCH}).
+To browse the manual you should go [here](http://${GIT_OWNER}.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-${TRAVIS_BRANCH}/archive/gh-pages.zip).
+at [this link](http://github.com/${GIT_OWNER}/doc-${TRAVIS_BRANCH}/archive/gh-pages.zip).
 
 EOF
 
 case "$branchtype" in
 (official)    echo "This is the manual for an official and supported PLUMED branch." >> README.md ;;
 (unsupported) echo "This is the manual for an official but unsupported PLUMED branch. It will not appear on search engines." >> README.md ;;
-(master)      echo "This is the manual for an the development PLUMED branch." >> README.md ;;
+(master)      echo "This is the manual for the development PLUMED branch." >> README.md ;;
 (unofficial)  echo "This is the manual for an unofficial PLUMED branch. It will not appear on search engines." >> README.md ;;
 esac
 
@@ -99,6 +115,7 @@ set -x
 esac
 
 git add --all .
-git commit -m "Update to plumed/plumed2@$hash"
+# >/dev/null to avoid excessive noise on travis log
+git commit -m "Update to ${GIT_OWNER}/${GIT_REPO}@$hash" >/dev/null
 # -q and 2> is not to show the GIT_TOKEN on Travis log
 git push -q -f doc gh-pages 2> /dev/null