structopt.common.individual.relaxations

class structopt.common.individual.relaxations.Relaxations(parameters)

Bases: object

post_processing()
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.

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.
get_command(individual)
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.

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.

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.

relax(individual)

Relaxes the individual using a hard-sphere cutoff method. :param individual: the individual to relax :type individual: Individual