This module implements the Nudged Elastic Band (NEB) method for identification of minimum energy path (MEP) between two minima. By default, the improved version is used.
The initial estimate of the path should be provided by the user as a series of geometries connecting the reactant and product. LBFGS optimzer is used because optimizing all the points at the same time leads to large number of optimized variables.
With the NEB method, it is not possible to achieve very tight convergence because the optimizer can not use the total energy of the system which is not defined. Set the convergence thresholds accordingly.
The following examples, along with all other files needed to run them, can be found in the directory cuby4/protocols/neb/examples
#=============================================================================== # Nudged Elatic Band protocol example 1 #=============================================================================== # Minimum energy path optimization for rotation of bond in propane molecule job: neb # The initial series of geometries was built by interpolating z-matrices of # an initial and rotated state geometry: propane_scan.xyz # Force constant connecting the images - it controls the spacing of the points # along the MEP but the calculation is not very sensitive to it neb_fconst: 10.0 # Optimize also the initial and final state - can be disabled if the geometries # had been optimized already neb_optimize_endpoints: yes # Calculate four images in parallel cuby_threads: 4 calculation: interface: mopac method: pm6 charge: 0