Transition state barrier

static_barrier_string.static_barrier(pos, inputs, calc_en_f, name=None, log_propagate=True, debug=False)

Compute the transition state barrier of a rigid cluster between two points of the substrate.

The barrier is computed using the string algorithm [DOI: 10.1063/1.2720838].

Inputs: - pos: position of particles in rigid cluster - inputs: dictionary defining the syste. Must contain the start (p0) and end (p1) of the initial path. Optionally, the number of points in the string (Npt=100) and number of iterations (Nsteps=3000)

Returns the positions of the relaxed path, along with energy, force and torque evaluated along it.

Molecular Dynamics of rigid cluster

MD_rigid_rototrasl.MD_rigid(inputs, outstream=<_io.TextIOWrapper name='<stdout>' mode='w' encoding='utf-8'>, name=None, log_propagate=False, debug=False)

Overdamped (1st order differential equaltion) Langevin Molecular Dynamics of rigid cluster over a substrate.

Input parameters are passaed as directly as dictionary or read from a JSON file (if inputs is a string). Position of particles in cluster is given as .hex or .npy filename. Info about run are written in name+’info.json’

MD output is printed on sys stdout.