structopt.common.individual.fitnesses¶
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class
structopt.common.individual.fitnesses.
Fitnesses
(parameters)¶ Bases:
object
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calculate_fitness
(individual)¶ Perform the fitness calculations on an individual.
- Args:
- individual (Individual): the individual to evaluate
(@parallel) Designed to run code that runs differently on different cores. The MPI functionality should be implemented inside these functions.
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post_processing
()¶
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class
structopt.common.individual.fitnesses.
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. Note for fitness values, the last two values are set to 0, so no relaxation is done. 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.
- reference (dict) – Reference energies of the particle. These are values to subtract from the values returned by LAMMPS. Given as a dictionary of {sym : E} pairs, where sym is a str denoating the the element, while E is the value to be subtracted per sym. This is typically the pure component formation energy calculated with LAMMPS. Note since this is merely a fixed subtraction, should not change the performance in constant composition runs.
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calculate_fitness
(individual)¶
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get_command
(individual)¶
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normalize
(E, individual)¶
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reference
(E, individual)¶ References the energy of the cluster to a reference energy
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class
structopt.common.individual.fitnesses.
FEMSIM
(parameters)¶ Bases:
object
Contains parameters and functions for running FEMSIM through Python.
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chi2
(vk)¶
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get_spawn_args
(individual)¶ Returns a dictionary of arguments to be passed to MPI.COMM_SELF.Spawn which will be collected for all structures and concatenated into MPI.COMM_SELF.Spawn_multiple: https://github.com/mpi4py/mpi4py/blob/2acfc552c42846628304e54a3b87e2bf3a59af07/src/mpi4py/MPI/Comm.pyx#L1555
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get_vk_data
()¶
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read_inputs
(parameters)¶
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setup_individual_evaluation
(individual)¶
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update_parameters
(**kwargs)¶
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write_paramfile
(individual)¶
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