automaticTransitionState

automaticTransitionState(neb, final_max_forces=None, initial_max_forces=None, neb_preoptimization_calculator=None, climbing_image=None, dimer=None, trajectory_filename_prefix=None, log_filename_prefix=None, spring_constant=None, spring_skew=None, preoptimization=None, optimizer_method=None, relax_dimer_parameters=None, dimer_separation=None)

Automatically determine the transition state using NEB and Dimer methods. Up to a total of four optimization steps are performed in following order:

  1. OptimizeNudgedElasticBand with a pre-optimization calculator

  2. OptimizeNudgedElasticBand without climbing image

  3. OptimizeNudgedElasticBand with climbing image

  4. DimerRelaxation

The NEB pre-optimization is optional and can be used to prepare the NEB for the subsequent optimization steps. The NEB optimization without climbing image is always performed and can be followed by a climbing image optimization. The Dimer relaxation can be used to further optimize the transition state.

Parameters:

  • neb (NudgedElasticBand) – The NudgedElasticBand object serving as the initial guess for the transition state.

  • final_max_forces (PhysicalQuantity of type force) – The maximum forces for the final optimization steps.
    Default: 0.05 eV/Ang

  • initial_max_forces (PhysicalQuantity of type force) – The maximum forces for the initial optimization steps.
    Default: Five times larger than the final max forces

  • neb_preoptimization_calculator (Calculator) – The calculator to use for pre-optimizing the complete NEB. This parameter is mutually exclusive with the preoptimization parameter used to optimize the endpoints.
    Default: No pre-optimization

  • climbing_image (bool) – Whether to use the climbing image method for the NEB optimization. A regular NEB optimization is always performed before the climbing image optimization.
    Default: False

  • dimer (bool) – Whether to perform a Dimer relaxation after the NEB optimization. The Dimer relaxation is performed on the transition state image obtained from the NEB optimization.
    Default: False

  • trajectory_filename_prefix (str) – The prefix used for the trajectory filenames.
    Default: No trajectory files are written

  • log_filename_prefix (str) – The prefix used for the log filenames.
    Default: Log is written to the standard output

  • spring_constant (PhysicalQuantity of type force/length) – The spring constant used for the NEB optimizations.
    Default: 5.0*(eV/Ang**2)

  • spring_skew (float) – Ratio between the distances of the optimized lower and higher energy neighbor. A value larger than 1.0 will skew an image towards the neighbor with the higher energy. As a result images are spaced closer around transition states, which can improve convergence of the NEB optimization. Works with climbing image NEB.

  • preoptimization (bool) – Flag indicating if the endpoints should be optimized before the NEB optimization. Preoptimization is disabled when restarting.
    Default: False.

  • optimizer_method (FIRE | LBFGS | VelocityProjectionOptimization) – The optimizer method used for the NEB optimizations.
    Default: LBFGS.

  • relax_dimer_parameters (RelaxDimerParameters) –

    The parameters used for the Dimer relaxation.

    The following parameters are also applied to the NEB optimizations: * max_steps * max_step_length * constraints * trajectory_interval * restart_strategy

    The following parameters are ignored: * max_forces * trajectory_filename * log_filename_prefix * trajectory_object_id

  • dimer_separation (PhysicalQuantity of type length) – The distance separating the displaced dimer images from the central image.
    Default: 1e-4 Angstrom

Returns:

An NEB object and a Dimer configuration.

Return type:

(NudgedElasticBand, DimerConfiguration)