RPMDrate - Bimolecular reaction rates via ring polymer molecular dynamics

About RPMDrate

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.

License

RPMDrate is distributed under the terms of the MIT license:

Copyright (c) 2012 by Joshua W. Allen (jwallen@mit.edu)
                      William H. Green (whgreen@mit.edu)
                      Yury V. Suleimanov (ysuleyma@mit.edu, ysuleyma@princeton.edu)

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.

Installation

Dependencies

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. gfortran, g95, ifort, etc.)

RPMDrate uses the f2py tool (bundled with NumPy) to expose its Fortran code to Python.

Getting RPMDrate

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 setup.py script:

$ 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).

Modification

Bug fix: zero variance would interrupt
Bug fix: r2r (real to real) FFT does not work. Replace with common complex FFT. Then combine real and complex parts manually.
Update: In main.py, :.4f -> :.8f, :.6f -> :.10f. Especially, the reaction coordinate ($xi$) would be written full.
Modify: max number of bead Nmax, 1024 -> 64. You should change this parameter in math.f90 if you perform a calculation with more than 64 beads.
Add: .xyz format of umbrella configurations
Add: free energy change (kcal/mol) in the rate file.
Add: Print last frame of each trajectory in xyz format, include bead umbrella_sampling_{0:.8f}_bead.xyz and centroid umbrella_sampling_{0:.8f}_centroid.xyz. The reaction coordinate, average energy, and centroid energy present in the title line. Coordinate is in Angstrom. In the bead trajectory file, the momentum (in atomic unit, scientific format 14.8e) and the gradient (in kcal/mol per Angstrom, float format 14.8f) present after the coordinate. In the centroid trajectory file, the gyration radius (in Angstrom) present after the coordinate.
Add: Print energy of last frame in each trajectory in umbrella_sampling_{0:.8f}_traj_info.dat.
- Column 1: evolved number of steps
- Below items are in one trajectory.
  
  Column 2: sum of xi
  
  Column 3: sum of xi squared
  
  Column 4: average of xi
  
  Column 5: variance of xi
- Below items are average energy of the last frame in one trajectories in kcal/mol.
  
  Column 6: potential energy of centroid
  
  Column 7: mean potential energy (Emean)
  
  Column 8: kinetic energy (Ek)
  
  Column 9: ring energy (Ering)
  
  Column 10: total energy (Emean, Ek, Ering)
- Next Nbeads columns are the energies of each copy / image / bead of the system.

wbfan95/RPMDrate