CDE: Chemistry discovery engine
CDE is a set of fortran routines which implements several different calculation types associated with chemical reaction-path analysis.
CDE can perform several types of calculations, including:
- Single-ended Graph-driven sampling for chemical reactions,
- Double-ended mechanism searching,
- Generation of initial approximate MEPs connecting user-defined reactant and product structures using a variety of methods, including linear interpolation and image-dependent pair potential (IDPP) method.
- Nudged elastic band calculations for refinement of chemical reaction paths.
CDE interfaces with several external programs to perform energy evaluations and geometry optimization, including:
- ORCA
- Psi-4
- LAMMPS
- DFTB+
- Molpro
- xTB
- FHI-aims
The graph-driven sampling of reaction-paths implemented in CDE is initially described in the following articles:
- Sampling reactive pathways with random walks in chemical space: Applications to molecular dissociation and catalysis, S Habershon, Journal of chemical physics 143 (9), 094106 (2015)
- Automated prediction of catalytic mechanism and rate law using graph-based reaction path sampling, S. Habershon, Journal of chemical theory and computation 12 (4), 1786-1798 (2016)
- Automatic proposal of multistep reaction mechanisms using a graph-driven search, I. Ismail, H. B. V. A. Stuttaford-Fowler, C. Ochan Ashok, C. Robertson, and S. Habershon, Journal of Physical Chemistry A, 123, 3407-3417 (2019)