stko.CollapserMC
- class stko.CollapserMC(output_dir, step_size, target_bond_length, num_steps, bond_epsilon=50, nonbond_epsilon=20, nonbond_sigma=1.2, nonbond_mu=3, beta=2, random_seed=None)[source]
Bases:
CollapserCollapse molecule to decrease enlarged bonds using MC algorithm.
It is recommended to use the MCHammer version of this code with
MCHammer[1], where a much cleaner version is written. The utilities get_long_bond_ids will help generate sub units.Smarter optimisation than Collapser using simple Monte Carlo algorithm to perform rigid translations of building blocks.
- Parameters:
output_dir (Path | str) – The name of the directory into which files generated during the calculation are written.
step_size (float) – The relative size of the step to take during step.
target_bond_length (float) – Target equilibrium bond length for long bonds to minimize to.
num_steps (int) – Number of MC moves to perform.
bond_epsilon (float) – Value of epsilon used in the bond potential in MC moves. Determines strength of the bond potential. Defaults to 50.
nonbond_epsilon (float) – Value of epsilon used in the nonbond potential in MC moves. Determines strength of the nonbond potential. Defaults to 20.
nonbond_sigma (float) – Value of sigma used in the nonbond potential in MC moves. Defaults to 1.2.
nonbond_mu (float) – Value of mu used in the nonbond potential in MC moves. Determines the steepness of the nonbond potential. Defaults to 3.
beta (float) – Value of beta used in the in MC moves. Beta takes the place of the inverse boltzmann temperature. Defaults to 2.
random_seed (int | None) – Random seed to use for MC algorithm. Should only be set if exactly reproducible results are required, otherwise a system-based random seed should be used for proper sampling.
References
Methods
Optimize mol.