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structopt
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Index
A
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B
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C
|
E
|
F
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G
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H
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I
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K
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L
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M
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N
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P
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R
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S
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T
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U
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V
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W
A
add() (structopt.common.population.Population method)
adsorbate_info (structopt.common.individual.Individual attribute)
allgather() (in module structopt.tools.parallel)
(structopt.common.population.Population method)
append() (structopt.common.individual.Individual method)
apply_fingerprinters() (structopt.common.population.Population method)
B
bcast() (structopt.common.population.Population method)
best() (in module structopt.common.population.predators)
(in module structopt.common.population.selections)
(structopt.common.population.predators.Predators static method)
(structopt.common.population.selections.Selections static method)
C
calc (structopt.common.individual.Individual attribute)
calculate_fitness() (structopt.common.individual.fitnesses.Fitnesses method)
(structopt.common.individual.Individual method)
(structopt.common.individual.fitnesses.LAMMPS method)
calculate_fitnesses() (structopt.common.population.fitnesses.Fitnesses method)
(structopt.common.population.Population method)
cell (structopt.common.individual.Individual attribute)
center() (structopt.common.individual.Individual method)
chi2() (structopt.common.individual.fitnesses.FEMSIM method)
clear() (structopt.common.individual.Individual method)
(structopt.common.population.Population method)
constraints (structopt.common.individual.Individual attribute)
copy() (structopt.common.individual.Individual method)
(structopt.common.population.Population method)
crossover() (structopt.common.population.crossovers.Crossovers method)
(structopt.common.population.Population method)
Crossovers (class in structopt.common.population.crossovers)
E
edit() (structopt.common.individual.Individual method)
ellipsoid() (in module structopt.cluster.individual.generators)
enrich_bulk() (in module structopt.cluster.individual.mutations)
enrich_surface() (in module structopt.cluster.individual.mutations)
enrich_surface_defects() (in module structopt.cluster.individual.mutations)
enrich_surface_facets() (in module structopt.cluster.individual.mutations)
euler_rotate() (structopt.common.individual.Individual method)
extend() (structopt.common.individual.Individual method)
(structopt.common.population.Population method)
F
fcc() (in module structopt.cluster.individual.generators)
FEMSIM (class in structopt.common.individual.fitnesses)
fitness (structopt.common.individual.Individual attribute)
fitness() (in module structopt.common.population.fitnesses.FEMSIM)
(in module structopt.common.population.fitnesses.LAMMPS)
Fitnesses (class in structopt.common.individual.fitnesses)
(class in structopt.common.population.fitnesses)
fits (structopt.common.individual.Individual attribute)
fromkeys() (structopt.common.population.Population method)
fuss() (in module structopt.common.population.predators)
(structopt.common.population.predators.Predators static method)
G
generate() (structopt.common.individual.Individual method)
get() (structopt.common.population.Population method)
get_all_distances() (structopt.common.individual.Individual method)
get_angle() (structopt.common.individual.Individual method)
get_angular_momentum() (structopt.common.individual.Individual method)
get_array() (structopt.common.individual.Individual method)
get_atom_indices_within_distance_of_atom() (structopt.common.individual.Individual method)
get_atomic_numbers() (structopt.common.individual.Individual method)
get_by_position() (structopt.common.population.Population method)
get_calculator() (structopt.common.individual.Individual method)
get_cell() (structopt.common.individual.Individual method)
get_cell_lengths_and_angles() (structopt.common.individual.Individual method)
get_celldisp() (structopt.common.individual.Individual method)
get_center_of_mass() (structopt.common.individual.Individual method)
get_charges() (structopt.common.individual.Individual method)
get_chemical_formula() (structopt.common.individual.Individual method)
get_chemical_symbols() (structopt.common.individual.Individual method)
get_command() (structopt.common.individual.fitnesses.LAMMPS method)
(structopt.common.individual.relaxations.LAMMPS method)
get_dihedral() (structopt.common.individual.Individual method)
get_dipole_moment() (structopt.common.individual.Individual method)
get_distance() (structopt.common.individual.Individual method)
get_distances() (structopt.common.individual.Individual method)
get_forces() (structopt.common.individual.Individual method)
get_initial_charges() (structopt.common.individual.Individual method)
get_initial_magnetic_moments() (structopt.common.individual.Individual method)
get_kinetic_energy() (structopt.common.individual.Individual method)
get_magnetic_moment() (structopt.common.individual.Individual method)
get_magnetic_moments() (structopt.common.individual.Individual method)
get_masses() (structopt.common.individual.Individual method)
get_momenta() (structopt.common.individual.Individual method)
get_moments_of_inertia() (structopt.common.individual.Individual method)
get_nearest_atom_indices() (structopt.common.individual.Individual method)
get_new_id() (structopt.common.population.Population method)
get_number_of_atoms() (structopt.common.individual.Individual method)
get_pbc() (structopt.common.individual.Individual method)
get_positions() (structopt.common.individual.Individual method)
get_potential_energies() (structopt.common.individual.Individual method)
get_potential_energy() (structopt.common.individual.Individual method)
get_reciprocal_cell() (structopt.common.individual.Individual method)
get_scaled_positions() (structopt.common.individual.Individual method)
get_spawn_args() (structopt.common.individual.fitnesses.FEMSIM method)
get_stress() (structopt.common.individual.Individual method)
get_stresses() (structopt.common.individual.Individual method)
get_tags() (structopt.common.individual.Individual method)
get_temperature() (structopt.common.individual.Individual method)
get_total_energy() (structopt.common.individual.Individual method)
get_velocities() (structopt.common.individual.Individual method)
get_vk_data() (structopt.common.individual.fitnesses.FEMSIM method)
get_volume() (structopt.common.individual.Individual method)
H
hard_sphere_cutoff (class in structopt.common.individual.relaxations)
has() (structopt.common.individual.Individual method)
I
Individual (class in structopt.common.individual)
items() (structopt.common.population.Population method)
K
keys() (structopt.common.population.Population method)
kill() (structopt.common.population.Population method)
(structopt.common.population.predators.Predators method)
L
LAMMPS (class in structopt.common.individual.fitnesses)
,
[1]
(class in structopt.common.individual.relaxations)
,
[1]
load_modules() (structopt.common.individual.Individual method)
(structopt.common.population.Population method)
logger_utils() (in module structopt.io)
M
move_atoms() (in module structopt.cluster.individual.mutations)
(structopt.common.individual.mutations.Mutations static method)
move_surface_atoms() (in module structopt.cluster.individual.mutations)
move_surface_defects() (in module structopt.cluster.individual.mutations)
mutate() (structopt.common.individual.Individual method)
(structopt.common.individual.mutations.Mutations method)
(structopt.common.population.Population method)
(structopt.common.population.mutations.Mutations method)
Mutations (class in structopt.common.individual.mutations)
(class in structopt.common.population.mutations)
N
new_array() (structopt.common.individual.Individual method)
normalize() (structopt.common.individual.fitnesses.LAMMPS method)
number_of_lattice_vectors (structopt.common.individual.Individual attribute)
numbers (structopt.common.individual.Individual attribute)
P
parallel() (in module structopt.tools.parallel)
parameters() (in module structopt.io)
pbc (structopt.common.individual.Individual attribute)
permutation() (in module structopt.common.individual.mutations)
(structopt.common.individual.mutations.Mutations static method)
poor2rich() (in module structopt.cluster.individual.mutations)
pop() (structopt.common.individual.Individual method)
(structopt.common.population.Population method)
popitem() (structopt.common.population.Population method)
Population (class in structopt.common.population)
position() (structopt.common.population.Population method)
positions (structopt.common.individual.Individual attribute)
post_processing() (structopt.common.individual.fitnesses.Fitnesses method)
(structopt.common.individual.mutations.Mutations method)
(structopt.common.individual.relaxations.Relaxations method)
(structopt.common.population.crossovers.Crossovers method)
(structopt.common.population.fitnesses.Fitnesses method)
(structopt.common.population.mutations.Mutations method)
(structopt.common.population.predators.Predators method)
(structopt.common.population.relaxations.Relaxations method)
(structopt.common.population.selections.Selections method)
Predators (class in structopt.common.population.predators)
R
random_selection() (in module structopt.common.population.selections)
(structopt.common.population.selections.Selections static method)
rank() (in module structopt.common.population.predators)
(in module structopt.common.population.selections)
(structopt.common.population.predators.Predators static method)
(structopt.common.population.selections.Selections static method)
rattle() (in module structopt.common.individual.mutations)
(structopt.common.individual.Individual method)
(structopt.common.individual.mutations.Mutations static method)
read_inputs() (structopt.common.individual.fitnesses.FEMSIM method)
read_xyz() (in module structopt.common.individual.generators)
(in module structopt.io)
reference() (structopt.common.individual.fitnesses.LAMMPS method)
relax() (in module structopt.common.population.relaxations.hard_sphere_cutoff)
(in module structopt.common.population.relaxations.LAMMPS)
(structopt.common.individual.Individual method)
(structopt.common.individual.relaxations.LAMMPS method)
(structopt.common.individual.relaxations.Relaxations method)
(structopt.common.individual.relaxations.hard_sphere_cutoff method)
(structopt.common.population.Population method)
(structopt.common.population.relaxations.Relaxations method)
Relaxations (class in structopt.common.individual.relaxations)
(class in structopt.common.population.relaxations)
remove() (structopt.common.population.Population method)
repair() (structopt.common.individual.relaxations.LAMMPS method)
repeat() (structopt.common.individual.Individual method)
replace() (structopt.common.population.Population method)
rich2poor() (in module structopt.cluster.individual.mutations)
root() (in module structopt.tools.parallel)
rotate() (in module structopt.cluster.population.crossovers)
(structopt.common.individual.Individual method)
(structopt.common.population.crossovers.Crossovers static method)
rotate_all() (in module structopt.common.individual.mutations)
(structopt.common.individual.mutations.Mutations static method)
rotate_atoms() (in module structopt.common.individual.mutations)
(structopt.common.individual.mutations.Mutations static method)
rotate_cluster() (in module structopt.cluster.individual.mutations)
(structopt.common.individual.mutations.Mutations static method)
rotate_dihedral() (structopt.common.individual.Individual method)
rotate_euler() (structopt.common.individual.Individual method)
roulette() (in module structopt.common.population.predators)
(in module structopt.common.population.selections)
(structopt.common.population.predators.Predators static method)
(structopt.common.population.selections.Selections static method)
run_pso_moves() (structopt.common.population.Population method)
S
select() (structopt.common.population.Population method)
(structopt.common.population.selections.Selections method)
select_crossover() (structopt.common.population.crossovers.Crossovers method)
select_mutation() (structopt.common.individual.mutations.Mutations method)
select_predator() (structopt.common.population.predators.Predators method)
select_selection() (structopt.common.population.selections.Selections method)
Selections (class in structopt.common.population.selections)
set_angle() (structopt.common.individual.Individual method)
set_array() (structopt.common.individual.Individual method)
set_atomic_numbers() (structopt.common.individual.Individual method)
set_calculator() (structopt.common.individual.Individual method)
set_cell() (structopt.common.individual.Individual method)
set_celldisp() (structopt.common.individual.Individual method)
set_chemical_symbols() (structopt.common.individual.Individual method)
set_constraint() (structopt.common.individual.Individual method)
set_dihedral() (structopt.common.individual.Individual method)
set_distance() (structopt.common.individual.Individual method)
set_initial_charges() (structopt.common.individual.Individual method)
set_initial_magnetic_moments() (structopt.common.individual.Individual method)
set_masses() (structopt.common.individual.Individual method)
set_momenta() (structopt.common.individual.Individual method)
set_pbc() (structopt.common.individual.Individual method)
set_positions() (structopt.common.individual.Individual method)
set_scaled_positions() (structopt.common.individual.Individual method)
set_tags() (structopt.common.individual.Individual method)
set_velocities() (structopt.common.individual.Individual method)
setdefault() (structopt.common.population.Population method)
setup_individual_evaluation() (structopt.common.individual.fitnesses.FEMSIM method)
single_core() (in module structopt.tools.parallel)
sphere() (in module structopt.cluster.individual.generators)
swap_core_shell() (in module structopt.cluster.individual.mutations)
swap_positions() (in module structopt.common.individual.mutations)
(structopt.common.individual.mutations.Mutations static method)
swap_species() (in module structopt.common.individual.mutations)
(structopt.common.individual.mutations.Mutations static method)
T
tournament() (in module structopt.common.population.predators)
(in module structopt.common.population.selections)
(structopt.common.population.predators.Predators static method)
(structopt.common.population.selections.Selections static method)
translate() (structopt.common.individual.Individual method)
twist() (in module structopt.cluster.individual.mutations)
U
update() (structopt.common.population.Population method)
update_parameters() (structopt.common.individual.fitnesses.FEMSIM method)
V
values() (structopt.common.population.Population method)
velocities (structopt.common.individual.Individual attribute)
W
wrap() (structopt.common.individual.Individual method)
write() (structopt.common.individual.Individual method)
write_paramfile() (structopt.common.individual.fitnesses.FEMSIM method)
write_xyz() (in module structopt.io)
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