Geodesic nudged elastic band (GNEB)¶
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spirit.parameters.gneb.
IMAGE_CLIMBING
= 1¶ Climbing GNEB image type. Climbing images move towards maxima along the path.
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spirit.parameters.gneb.
IMAGE_FALLING
= 2¶ Falling GNEB image type. Falling images move towards the closest minima.
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spirit.parameters.gneb.
IMAGE_NORMAL
= 0¶ Regular GNEB image type.
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spirit.parameters.gneb.
IMAGE_STATIONARY
= 3¶ Stationary GNEB image type. Stationary images are not influenced during a GNEB calculation.
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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.
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spirit.parameters.gneb.
get_convergence
(p_state, idx_image=-1, idx_chain=-1)¶ Returns the convergence value.
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spirit.parameters.gneb.
get_iterations
(p_state, idx_image=-1, idx_chain=-1)¶ Returns the maximum number of iterations and the step size.
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spirit.parameters.gneb.
get_n_energy_interpolations
(p_state, idx_chain=-1)¶ Returns the number of energy values interpolated between images.
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spirit.parameters.gneb.
get_path_shortening_constant
(p_state, idx_image=-1, idx_chain=-1)¶ Return the path shortening constant.
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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.
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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).
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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.
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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.
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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
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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
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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
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spirit.parameters.gneb.
set_output_folder
(p_state, folder, idx_image=-1, idx_chain=-1)¶ Set the folder, where output files are placed.
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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.
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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.
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spirit.parameters.gneb.
set_path_shortening_constant
(p_state, shortening_constant, idx_image=-1, idx_chain=-1)¶ Set the path shortening constant.
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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.