Development version of plumed 2
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.github Update PULL_REQUEST_TEMPLATE.md Jun 18, 2018
.travis arrayfire: modifies installation folder, removed sudos Oct 16, 2018
CHANGES Merge branch 'v2.4' into v2.5 Nov 14, 2018
astyle astyle 3 -> 3.1 Feb 11, 2018
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python Fix #402 Oct 31, 2018
regtest Small consistency fix in wrapper Nov 13, 2018
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src astyle Nov 13, 2018
test ./configure is not anymore run when using make clean Apr 7, 2016
user-doc mention to OPS Nov 9, 2018
vim vim syntax for __FILL__ Apr 3, 2018
.astyle.options Added astyle script Apr 21, 2017
.codecov.yml Added support for codecov Apr 6, 2018
.gitignore Install libplumedWrapper.a Sep 29, 2017
.travis.yml Merge branch 'v2.4' into v2.5 Nov 7, 2018
COPYING.LESSER Initial commit, just containing the LGPL license Apr 6, 2011
Makefile Merge branch 'v2.4' Oct 30, 2017
Makefile.conf.in Using CXX compiler as a linker, including CXXFLAGS Oct 8, 2018
PEOPLE A few fixes to be more clear on licence Jan 20, 2014
README.md README: docker added Oct 11, 2018
VERSION master version Oct 5, 2018
configure Removed leftover comment Nov 9, 2018
configure.ac Removed leftover comment Nov 9, 2018
release.sh Merge branch 'v2.3' into v2.4 Sep 29, 2017
sourceme.sh.in stop setting DYLD_LIBRARY_PATH Feb 20, 2018
stamp-h.in Added automatic reconfigure Oct 16, 2015

README.md

Homepage Homepage codecov License: LGPL v3 Github Releases Twitter Follow

Packaging status

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.

In addition, the repository contains a number of other branches related to specific features. Please contact the developers that are committing on those branches before basing your work there, since they might contain temporary work and might be rebased later. For instance, branch testdoc is setup so as to push a test copy of the manual and is often force pushed.

To report problems found on beta or official releases, use the normal plumed-users@googlegroups.com mailing list. Please state exactly which version you are using. To report problems found on master branch, use the plumed2-git@googlegroups.com 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

Below you find the status on Travis-CI for the release branches.

Branch Status First stable release (year) Still supported
master Build Status 2019 (expected) /
v2.5 Build Status 2018 (expected) /
v2.4 Build Status 2017 yes
v2.3 Build Status 2016 yes
v2.2 Build Status 2015 no
v2.1 Build Status 2014 no
v2.0 Not available 2013 no

Content

Here's a description of the content of each file and directory in the root PLUMED directory.

CHANGES          : change log
COPYING.LESSER   : license
Makefile         : makefile
Makefile.conf.in : template configuration makefile
PEOPLE           : list of authors
README.md        : this file
VERSION          : version file
astyle           : a local version of astyle, used to format code
configure        : configuration script
configure.ac     : configuration script (autoconf)
developer-doc    : developer documentation
docker           : directory where Docker is generated
macports         : directory where Portfiles are generated
patches          : patch scripts
regtest          : regression tests, including reference results
release.sh       : developer utility to publish releases
scripts          : shell tools
sourceme.sh.in   : template configuration script
src              : source code
test             : examples
user-doc         : user documentation
vim              : directory where vim syntax is generated

Required software

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):

  • MPI library to run parallel simulations. It should be the same library used by your MD code.
  • Optimized blas and lapack libraries. They are automatically replaced by an internal version if not available.
  • VMD molfile plugins to read arbitrary file formats. They are automatically replaced by an internal version supporting a few formats if not available.
  • Zlib library to use compressed data files.
  • Xdrfile library to have read/write access to gromacs trajectory files.
  • Doxygen to build user manual. Doxygen might need the following packages:
    • Latex to build the pdf user manual.
    • Graphviz to show class hierarchy in developer manual.

Quick compilation instructions

Extensive installation instructions are in the user documentation. Quick instructions:

./configure --prefix=$HOME/opt
make
make doc # optional

User documentation can be found at user-doc/html/index.html. Developer documentation can be found at developer-doc/html/index.html. Pre-compiled documentation is available online, so this is only required if you are working with a modified version of the code!

In order to run PLUMED without installing it you should type source sourceme.sh. However, we recomment installing PLUMED. To install it in $HOME/opt (directory should be set during ./configure):

umask 022
make install

Now you will be able to run plumed using e.g.

plumed help

If you compiled your own documentation, paths to the installed documentation can be found with command plumed info --user-doc.

A sample modulefile with environment variable will be placed in $HOME/opt/lib/plumed/src/lib/modulefile. This can be useful if you want to install multiple PLUMED versions side by side and select them with env modules.