spirit.parameters.gneb module

Geodesic nudged elastic band (GNEB)

spirit.parameters.gneb.IMAGE_CLIMBING = 1

Climbing GNEB image type. Climbing images move towards maxima along the path.

spirit.parameters.gneb.IMAGE_FALLING = 2

Falling GNEB image type. Falling images move towards the closest minima.

spirit.parameters.gneb.IMAGE_NORMAL = 0

Regular GNEB image type.

spirit.parameters.gneb.IMAGE_STATIONARY = 3

Stationary GNEB image type. Stationary images are not influenced during a GNEB calculation.

spirit.parameters.gneb.get_climbing_falling(p_state, idx_image=-1, idx_chain=-1)

Returns the integer of whether an image is regular, climbing, falling, or stationary.

The integers are defined above.

spirit.parameters.gneb.get_convergence(p_state, idx_image=-1, idx_chain=-1)

Returns the convergence value.

spirit.parameters.gneb.get_equilibrium_delta_Rx(p_state, idx_chain=-1)

Return the equilibrium delta_Rx for the moving endpoints.

spirit.parameters.gneb.get_iterations(p_state, idx_image=-1, idx_chain=-1)

Returns the maximum number of iterations and the step size.

spirit.parameters.gneb.get_moving_endpoints(p_state, idx_chain=-1)

Return if moving endpoints are used.

spirit.parameters.gneb.get_n_energy_interpolations(p_state, idx_chain=-1)

Returns the number of energy values interpolated between images.

spirit.parameters.gneb.get_path_shortening_constant(p_state, idx_image=-1, idx_chain=-1)

Return the path shortening constant.

spirit.parameters.gneb.get_spring_force(p_state, idx_image=-1, idx_chain=-1)

Returns the spring force constant and Ratio of energy to reaction coordinate.

spirit.parameters.gneb.get_translating_endpoints(p_state, idx_chain=-1)

Return if translating endpoints are used.

spirit.parameters.gneb.set_climbing_falling(p_state, image_type, idx_image=-1, idx_chain=-1)

Set the GNEB image type (see the integers defined above).

spirit.parameters.gneb.set_convergence(p_state, convergence, idx_image=-1, idx_chain=-1)

Set the convergence limit.

When the maximum absolute component value of the force drops below this value, the calculation is considered converged and will stop.

spirit.parameters.gneb.set_equilibrium_delta_Rx(p_state, delta_Rx_left, delta_Rx_right, idx_chain=-1)

Set if moving endpoints should be used.

spirit.parameters.gneb.set_image_type_automatically(p_state, idx_chain=-1)

Automatically set GNEB image types.

Minima along the path will be set to falling, maxima to climbing and the rest to regular.

spirit.parameters.gneb.set_iterations(p_state, n_iterations, n_iterations_log, idx_image=-1, idx_chain=-1)

Set the number of iterations and how often to log and write output.

  • n_iterations: the maximum number of iterations

  • n_iterations_log: the number of iterations after which status is logged and output written

spirit.parameters.gneb.set_moving_endpoints(p_state, moving_endpoints, idx_chain=-1)

Set if moving endpoints should be used.

spirit.parameters.gneb.set_output_chain(p_state, step=False, filetype=3, idx_image=-1, idx_chain=-1)

Set whether to write chain output files.

  • step: whether to write a new file after each set of iterations

  • filetype: the format in which the data is written

spirit.parameters.gneb.set_output_energies(p_state, step=True, interpolated=True, divide_by_nos=True, add_readability_lines=True, idx_image=-1, idx_chain=-1)

Set whether to write energy output files.

  • step: whether to write a new file after each set of iterations

  • interpolated: whether to write a file containing interpolated reaction coordinate and energy values

  • divide_by_nos: whether to divide energies by the number of spins

  • add_readability_lines: whether to separate columns by lines

spirit.parameters.gneb.set_output_folder(p_state, folder, idx_image=-1, idx_chain=-1)

Set the folder, where output files are placed.

spirit.parameters.gneb.set_output_general(p_state, any=True, initial=False, final=False, idx_image=-1, idx_chain=-1)

Set whether to write any output files at all.

spirit.parameters.gneb.set_output_tag(p_state, tag, idx_image=-1, idx_chain=-1)

Set the tag placed in front of output file names.

If the tag is “<time>”, it will be the date-time of the creation of the state.

spirit.parameters.gneb.set_path_shortening_constant(p_state, shortening_constant, idx_image=-1, idx_chain=-1)

Set the path shortening constant.

spirit.parameters.gneb.set_spring_force(p_state, spring_constant=1, ratio=0, idx_image=-1, idx_chain=-1)

Set the spring force constant and the ratio between energy and reaction coordinate.

spirit.parameters.gneb.set_translating_endpoints(p_state, translating_endpoints, idx_chain=-1)

Set if attracting endpoints should be used.