structopt.common.individual.relaxations¶
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class
structopt.common.individual.relaxations.
Relaxations
(parameters)¶ Bases:
object
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post_processing
()¶
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relax
(individual, generation=None)¶ Relax an individual.
- Args:
- individual (Individual): the individual to relax
(@parallel) Designed to run code that runs differently on different cores. The MPI functionality should be implemented inside these functions.
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class
structopt.common.individual.relaxations.
LAMMPS
(parameters)¶ Bases:
object
LAMMPS class for running LAMMPS on a single individual. Takes a dictionary, where the key: value are the parameters for running LAMMPs.
Parameters: - min_style (str) – The minimization scheme for running LAMMPS. See LAMMPS doc.
- min_modify (str) – Parameters for min_style energy minimization algorithm. See LAMMPS doc.
- minimize (str) – Convergence criteria for minimization algorithm. See LAMMPS doc.
- pair_style (str) – Type of potential used. See LAMMPS doc.
- potential_file (str) – The path to the potential_file. Should be absolute.
- thermo_steps (int) – How much output to print of thermodynamic information. If set to 0, only the last step is printed.See LAMMPS doc.
- keep_file (bool) – Will keep all of the LAMMPS input and output files for each individual. Use with caution.
- repair (bool) – Determines whether to run an algorithm to make sure no atoms are in “space”. Atoms can be in space due to a mutation or crossover that results in a large force that shoots the atom outside of the particle.
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get_command
(individual)¶
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relax
(individual)¶ Relax an individual.
- Args:
- individual (Individual): the individual to relax
(@parallel) Designed to run code that runs differently on different cores. The MPI functionality should be implemented inside these functions.
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repair
(individual, generation)¶ - Repairs an individual. Currently takes isolated atoms moves them next to
- a non-isolated atom
(@parallel) Designed to run code that runs differently on different cores. The MPI functionality should be implemented inside these functions.
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class
structopt.common.individual.relaxations.
hard_sphere_cutoff
(parameters, cutoff=0.7)¶ Bases:
object
A relaxation module to ensure atoms in an individual are not too close together. This is often a preliminary relaxation before LAMMPS for VASP to ensure the models do not explode.
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relax
(individual)¶ Relaxes the individual using a hard-sphere cutoff method. :param individual: the individual to relax :type individual: Individual
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