Ultra-Fast Forcefields
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B
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C
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D
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E
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F
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G
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I
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K
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L
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M
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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
analyze_hdf_tables() (in module uf3.data.io)
apply_weighted_gram() (in module uf3.regression.least_squares)
apply_weights() (in module uf3.regression.least_squares)
arrange_3b() (in module uf3.representation.angles)
arrange_coefficients() (in module uf3.regression.least_squares)
arrange_deriv_3b() (in module uf3.representation.angles)
arrange_features_dataframe() (BasisFeaturizer method)
atoms_from_df() (in module uf3.data.io)
B
band_structure() (UFCalculator method)
(UFLammps method)
BasicLinearModel (class in uf3.regression.least_squares)
BasisFeaturizer (class in uf3.representation.process)
batch_relax() (in module uf3.forcefield.lammps)
batch_submit() (in module uf3.util.parallel)
batched_energy_and_forces() (in module uf3.forcefield.lammps)
batched_moore_penrose() (in module uf3.regression.least_squares)
batched_predict() (WeightedLinearModel method)
batched_prediction() (in module uf3.regression.least_squares)
BSplineBasis (class in uf3.representation.bspline)
C
cache_data() (in module uf3.data.io)
calculate() (UFCalculator method)
(UFLammps method)
calculate_numerical_forces() (UFCalculator method)
(UFLammps method)
calculate_numerical_stress() (UFCalculator method)
(UFLammps method)
calculate_properties() (UFCalculator method)
(UFLammps method)
calculation_required() (UFCalculator method)
check_state() (UFCalculator method)
(UFLammps method)
ChemicalSystem (class in uf3.data.composition)
coefficient_counts_from_knots() (in module uf3.representation.angles)
coefficients_by_interaction() (in module uf3.forcefield.calculator)
combine_regularizer_matrices() (in module uf3.regression.regularize)
combine_weighted_gram() (WeightedLinearModel method)
CompactJSONEncoder (class in uf3.util.json_io)
compute_direction_cosines() (in module uf3.representation.distances)
concat_dataframes() (in module uf3.data.io)
consistency_check() (in module uf3.util.user_config)
consolidate() (DataCoordinator method)
construct_pair_potentials() (in module uf3.forcefield.calculator)
CONTAINER_TYPES (CompactJSONEncoder attribute)
D
DataCoordinator (class in uf3.data.io)
dataframe_batch_loader() (in module uf3.data.io)
dataframe_from_lammps_run() (DataCoordinator method)
dataframe_from_lists() (DataCoordinator method)
dataframe_from_trajectory() (DataCoordinator method)
dataframe_from_vasprun() (DataCoordinator method)
dataframe_from_xyz() (DataCoordinator method)
dataframe_to_training_tuples() (in module uf3.representation.process)
dataframe_to_tuples() (in module uf3.regression.least_squares)
decode_interaction_map() (in module uf3.util.json_io)
default() (CompactJSONEncoder method)
density_estimation() (in module uf3.util.plotting)
density_scatter() (in module uf3.util.plotting)
derivatives_by_interaction() (in module uf3.representation.distances)
df_from_tsv_text() (in module uf3.data.io)
distances_by_interaction() (in module uf3.representation.distances)
distances_from_geometry() (in module uf3.representation.distances)
dump() (WeightedLinearModel method)
dump_interaction_map() (in module uf3.util.json_io)
E
encode() (CompactJSONEncoder method)
encode_interaction_map() (in module uf3.util.json_io)
evaluate() (BasisFeaturizer method)
evaluate_basis_functions() (in module uf3.representation.bspline)
evaluate_configuration() (BasisFeaturizer method)
evaluate_energy_3b() (in module uf3.forcefield.calculator)
evaluate_forces_3b() (in module uf3.forcefield.calculator)
evaluate_parallel() (BasisFeaturizer method)
evaluate_triplet_derivatives() (in module uf3.representation.angles)
evaluate_triplet_distances() (in module uf3.representation.angles)
export_tabulated_potential() (in module uf3.forcefield.lammps)
F
farthest_point_sampling() (in module uf3.util.subsample)
featurize_energy_2B() (BasisFeaturizer method)
featurize_energy_3B() (BasisFeaturizer method)
featurize_energy_3b() (in module uf3.representation.angles)
featurize_force_2B() (BasisFeaturizer method)
(in module uf3.representation.bspline)
featurize_force_3B() (BasisFeaturizer method)
featurize_force_3b() (in module uf3.representation.angles)
find_pair_potential_well() (in module uf3.regression.least_squares)
find_spline_indices() (in module uf3.representation.bspline)
fit() (BasicLinearModel method)
(WeightedLinearModel method)
fit_from_file() (WeightedLinearModel method)
fit_spline_1d() (in module uf3.representation.bspline)
fit_with_gram() (WeightedLinearModel method)
flatten_by_interactions() (in module uf3.representation.process)
freeze_columns() (in module uf3.regression.least_squares)
freeze_regularizer() (in module uf3.regression.least_squares)
from_config() (BasisFeaturizer static method)
(BSplineBasis static method)
(ChemicalSystem static method)
(DataCoordinator static method)
G
gather_and_merge() (in module uf3.util.parallel)
generate_basis_functions() (in module uf3.representation.bspline)
generate_displacements_from_forces() (in module uf3.data.geometry)
generate_geometric_knots() (in module uf3.representation.bspline)
generate_handlers() (in module uf3.util.user_config)
generate_inv_knots() (in module uf3.representation.bspline)
generate_lammps_knots() (in module uf3.representation.bspline)
generate_triplets() (in module uf3.representation.angles)
generate_uniform_knots() (in module uf3.representation.bspline)
get_composition_tuple() (ChemicalSystem method)
get_distance_derivatives() (in module uf3.representation.distances)
get_distance_matrix() (in module uf3.representation.distances)
get_elastic_constants() (UFCalculator method)
(UFLammps method)
get_electronegativity_sort() (in module uf3.data.composition)
get_element_combinations() (in module uf3.data.composition)
get_element_tuple() (in module uf3.util.user_config)
get_feature_partition_sizes() (BSplineBasis method)
get_forces() (UFCalculator method)
get_freezing_mask() (in module uf3.regression.least_squares)
get_interaction_hashes() (ChemicalSystem method)
get_interactions_list() (ChemicalSystem method)
get_interactions_map() (ChemicalSystem method)
get_knot_spacer() (in module uf3.representation.bspline)
get_knot_subintervals() (in module uf3.representation.bspline)
get_magnetic_moments() (UFCalculator method)
(UFLammps method)
get_penalty_matrix_2D() (in module uf3.regression.regularize)
get_penalty_matrix_3D() (in module uf3.regression.regularize)
get_phonon_data() (UFCalculator method)
(UFLammps method)
get_potential_energy() (UFCalculator method)
get_property() (UFCalculator method)
(UFLammps method)
get_regularization_matrix() (BSplineBasis method)
get_regularizer_matrix() (in module uf3.regression.regularize)
get_stress() (UFCalculator method)
get_stresses() (UFCalculator method)
(UFLammps method)
get_subsets() (in module uf3.util.plotting)
get_supercell() (in module uf3.data.geometry)
get_supercell_factors() (in module uf3.data.geometry)
get_symmetry_weights() (in module uf3.representation.angles)
get_szudzik_hash() (in module uf3.data.composition)
get_training_tuples() (BasisFeaturizer method)
gram_from_df() (WeightedLinearModel method)
I
identify_ij() (in module uf3.representation.angles)
identify_paths() (in module uf3.data.io)
initialize_gram_ordinate() (WeightedLinearModel method)
iterencode() (CompactJSONEncoder method)
K
knot_sequence_from_points() (in module uf3.representation.bspline)
kronecker_delta() (in module uf3.representation.distances)
kronecker_vectorized() (in module uf3.representation.distances)
L
lammpsbc() (UFLammps method)
legacy_generate_triplets() (in module uf3.representation.angles)
legacy_load_feature_db() (in module uf3.representation.process)
linear_least_squares() (in module uf3.regression.least_squares)
load() (WeightedLinearModel method)
load_dataframe() (DataCoordinator method)
load_feature_db() (in module uf3.representation.process)
load_interaction_map() (in module uf3.util.json_io)
lu_factorization() (in module uf3.regression.least_squares)
M
mae_metric() (in module uf3.regression.least_squares)
mask_matrix_by_pair_interaction() (in module uf3.representation.distances)
mask_supercell_with_radius() (in module uf3.representation.distances)
module
uf3
uf3.data
uf3.data.composition
uf3.data.geometry
uf3.data.io
uf3.forcefield
uf3.forcefield.calculator
uf3.forcefield.lammps
uf3.regression
uf3.regression.least_squares
uf3.regression.regularize
uf3.representation
uf3.representation.angles
uf3.representation.bspline
uf3.representation.distances
uf3.representation.process
uf3.util
uf3.util.json_io
uf3.util.parallel
uf3.util.plotting
uf3.util.subsample
uf3.util.user_config
moore_penrose_components() (in module uf3.regression.least_squares)
P
parse_knots_file() (in module uf3.representation.bspline)
parse_lammps_dump() (in module uf3.data.io)
parse_lammps_log() (in module uf3.data.io)
parse_lammps_outputs() (in module uf3.data.io)
parse_trajectory() (in module uf3.data.io)
parse_with_subsampling() (in module uf3.data.io)
postprocess_coefficients_2b() (in module uf3.regression.least_squares)
predict() (BasicLinearModel method)
(WeightedLinearModel method)
prepare_dataframe_from_lists() (in module uf3.data.io)
progress_iter() (in module uf3.util.parallel)
ProgressText (class in uf3.util.parallel)
propagate() (UFLammps method)
R
read() (UFCalculator method)
(UFLammps method)
read_config() (in module uf3.util.user_config)
read_database() (in module uf3.data.io)
read_vasp_pressure() (in module uf3.data.io)
regenerate_coefficients() (in module uf3.forcefield.calculator)
relax() (UFLammps method)
relax_fmax() (UFCalculator method)
reset() (UFCalculator method)
(UFLammps method)
resolve_name_conflict() (in module uf3.data.io)
revert_frozen_coefficients() (in module uf3.regression.least_squares)
rmse_metric() (in module uf3.regression.least_squares)
round_lims() (in module uf3.util.plotting)
S
save() (WeightedLinearModel method)
save_feature_db() (in module uf3.representation.process)
score() (BasicLinearModel method)
(WeightedLinearModel method)
select_wait_function() (in module uf3.util.parallel)
set() (UFCalculator method)
(UFLammps method)
set_flatten_template_3B() (BSplineBasis method)
set_label() (UFCalculator method)
(UFLammps method)
set_params() (WeightedLinearModel method)
sort_image_indices() (in module uf3.data.geometry)
sort_interaction_map() (in module uf3.data.composition)
sort_interaction_symbols() (in module uf3.data.composition)
split_dataframe() (in module uf3.util.parallel)
split_zip() (in module uf3.util.parallel)
subset_prediction() (in module uf3.regression.least_squares)
summarize_distances() (in module uf3.representation.distances)
symmetrize_3B() (in module uf3.representation.angles)
szudzik_pair() (in module uf3.data.composition)
szudzik_unpair() (in module uf3.data.composition)
T
type_check() (in module uf3.util.user_config)
U
uf3
module
uf3.data
module
uf3.data.composition
module
uf3.data.geometry
module
uf3.data.io
module
uf3.forcefield
module
uf3.forcefield.calculator
module
uf3.forcefield.lammps
module
uf3.regression
module
uf3.regression.least_squares
module
uf3.regression.regularize
module
uf3.representation
module
uf3.representation.angles
module
uf3.representation.bspline
module
uf3.representation.distances
module
uf3.representation.process
module
uf3.util
module
uf3.util.json_io
module
uf3.util.parallel
module
uf3.util.plotting
module
uf3.util.subsample
module
uf3.util.user_config
module
UFCalculator (class in uf3.forcefield.calculator)
UFLammps (class in uf3.forcefield.lammps)
unpack_szudzik_hash() (in module uf3.data.composition)
update() (VarianceRecorder method)
update_dataframe_from_geometries() (in module uf3.data.io)
update_geometries_from_calc() (in module uf3.data.io)
update_geometries_from_dataframe() (in module uf3.data.io)
update_with_components() (VarianceRecorder method)
V
validate_regularizer() (in module uf3.regression.least_squares)
VarianceRecorder (class in uf3.regression.least_squares)
visualize_splines() (in module uf3.util.plotting)
W
wait_progress() (in module uf3.util.parallel)
weighted_least_squares() (in module uf3.regression.least_squares)
WeightedLinearModel (class in uf3.regression.least_squares)
write_lammps_data() (in module uf3.forcefield.lammps)
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