#Nanoreactor package #### Authors: Lee-Ping Wang, Heejune Park, Robert McGibbon, Leah Isseroff Bendavid, Alexey Titov, Todd J. Martinez This is a script and library to analyze reactive MD (nanoreactor) simulations. It provides two main capabilities: ### 1) Reaction extraction and visualization. To analyze a simulation trajectory, run "LearnReactions.py traj.xyz". Use the "-h" argument to get help. It will generate reaction_123.xyz files that contain your chemical reactions, as well as bonds.dat, color.dat, charge.dat and spin.dat used to highlight your reactive MD trajectory. To view the highlighted trajectory, you need to install VMD and preferably be using a 3D-accelerated machine. Make sure reactions.vmd is in the same folder and run using: 'vmd -e reactions.vmd -args coors.xyz' ### 2) Energy refinement of extracted reactions. To convert a nanoreactor "reaction event" into a minimum energy path, run "Refine.py reaction.xyz". It will start a workflow which (1) optimizes the geometries of subsampled frames, (2) find frame pairs that contain chemically distinct species and construct a pathway connecting the energy basins, (3) smooth the pathway in internal coordinates, and (4) perform string method + transition state + intrinsic reaction coordinate calculations to locate the minimum energy path. Finally it will summarize the reaction as a PDF at the end. #### Installation: To install the package, run "python setup.py install". Make sure all dependencies are installed (below) - it's more challenging than installing the package itself. :) An example for LearnReactions.py is included. Examples for Refine.py are forthcoming. #### Dependencies (there are many, though I tried to keep the # down): - Python 2.7, 3.5 or above, and the Python packages numpy, scipy and networkx. The sklearn package is recommended but not required. These dependencies are satisfied if you get the Python distribution from Enthought Canopy or (I think) Anaconda. Note that future versions of sklearn (0.17) plan to deprecate the Hidden Markov Model so this dependency may need to be updated in the future. - The Cooperative Computing Tools (http://ccl.cse.nd.edu/software/) is recommended for rolling out a highly parallel energy refinement calculation of many pathways. Using the Work Queue library, hundreds to thousands of Q-Chem calculations may be run in parallel across any combination of available computing resources. - Q-Chem 4.2 is required for running the energy refinement calculations. MPI and OpenMP parallelism are both required, because the stability analysis only works with MPI and the other components work with OpenMP. IMPORTANT NOTE: The commercial version of Q-Chem is somewhat problematic for the intrinsic reaction coordinate part of the calculation, because the user has no way to set the IRC initial direction. I have modified the source code to make sure the rpath_direction rem variable works as intended; the Q-Chem binary on Fire has this change, and I submitted the updated source code to the Q-Chem repository. The following is required for drawing the summary PDF at the end of energy refinement: - Gnuplot for drawing the energy diagram. Make sure the SVG terminal is supported. - lxml (Python interface to libxml2) for parsing XML files. Comes with Anaconda and Enthought Canopy. If installing from scratch, you need to install libxml2 and libxslt first. - Openbabel (version from GitHub newer than September 26, 2014). Used for generating SVG images of molecules. As of September 26, 2014, the latest release contained bugs so please check out the code from GitHub (https://github.com/openbabel/openbabel) and build from source. Make sure to build with Python bindings enabled. Building Openbabel requires Eigen which is a pain, but it comes as a Ubuntu package. - rsvg-convert for converting SVG to PDF. SVG is a nice file format for editing vector graphics, but it may look different when viewed on different machines. This is part of the GNOME project and comes as a Ubuntu package; building from souce might be painful. Enjoy! - Lee-Ping License: This software uses the BSD license (except for nebterpolator which uses GNU GPL 3.0). See LICENSE and nebterpolator/LICENSE.