RPMDrate - Bimolecular reaction rates via ring polymer molecular dynamics
RPMDrate is a free, open-source software package for using ring polymer molecular dynamics simulations to compute properties of chemical systems, including, but not limited to, chemical reaction rates.
RPMDrate is distributed under the terms of the MIT license:
Copyright (c) 2012 by Joshua W. Allen (email@example.com) William H. Green (firstname.lastname@example.org) Yury V. Suleimanov (email@example.com, firstname.lastname@example.org) 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.
RPMDrate depends on several other packages in order to provide its full functional capabilities. The following dependencies are required to compile and run RPMD:
- Python (version 2.5.x or later, including any version of Python 3, is recommended)
- NumPy (version 1.5.0 or later is recommended)
- FFTW (version 3.3 or later is recommended)
- A standard Fortran 90/95 compiler (e.g.
RPMDrate uses the
f2py tool (bundled with NumPy) to expose its Fortran code
The best way to obtain a copy of the repository is to clone it using git:
$ git clone git://github.com/GreenGroup/RPMDrate.git
This enables you to easy update your local clone with the latest changes. If you intend to contribute, you should fork the project on GitHub first, and clone from your fork.
Compiling from Source
RPMDrate is installed by invoking the
$ python setup.py install
This will compile the Fortran source and Python wrapper code, which may take some time. Note that you may need administrator privileges to install RPMD.
If you wish to use RPMDrate without installing, simply add the folder containing
this file to your
PYTHONPATH environment variable and compile the source
code in-place using the command
$ python setup.py build_ext --inplace
A Makefile that wraps these commands has been provided. The Makefile also provides a clean target for deleting all files created during compilation.
Running the Unit Tests
RPMDrate comes with a large suite of unit tests that ensure functionality is working as intended. To run these tests, first install RPMDrate or compile it from source in-place using the directions above. Then, simply invoke the entire suite of unit tests using
$ python setup.py test
This will run all of the unit tests in sequence, which may take some time. If one or more unit tests fail, please report them on the GitHub issue tracker (if they aren't already reported).