Index

A

alpha_ (mff.gp.GaussianProcess attribute)

B

BaseThreeBody (class in mff.kernels.threebodykernel) BaseTwoBody (class in mff.kernels.twobodykernel) build_grid() (mff.gp.ThreeBodySingleSpeciesGP method) (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method)

build_grid_3b() (mff.models.combined.CombinedManySpeciesModel method) (mff.models.threebody.ThreeBodyManySpeciesModel method)

C

calc() (mff.kernels.threebodykernel.BaseThreeBody method) (mff.kernels.twobodykernel.BaseTwoBody method) calc_ee() (mff.kernels.threebodykernel.BaseThreeBody method) (mff.kernels.twobodykernel.BaseTwoBody method) calc_ef() (mff.kernels.threebodykernel.BaseThreeBody method) (mff.kernels.twobodykernel.BaseTwoBody method) calc_gram() (mff.kernels.threebodykernel.BaseThreeBody method) (mff.kernels.twobodykernel.BaseTwoBody method) calc_gram_e() (mff.kernels.threebodykernel.BaseThreeBody method) (mff.kernels.twobodykernel.BaseTwoBody method)

calc_gram_ee() (mff.gp.GaussianProcess method) calc_gram_ef() (mff.kernels.threebodykernel.BaseThreeBody method) (mff.kernels.twobodykernel.BaseTwoBody method) calc_gram_ff() (mff.gp.GaussianProcess method) carve_from_snapshot() (in module mff.configurations) CombinedManySpeciesModel (class in mff.models.combined) CombinedSingleSpeciesModel (class in mff.models.combined) compile_theano() (mff.kernels.threebodykernel.ThreeBodyManySpeciesKernel static method) (mff.kernels.threebodykernel.ThreeBodySingleSpeciesKernel static method) (mff.kernels.twobodykernel.TwoBodyManySpeciesKernel static method) (mff.kernels.twobodykernel.TwoBodySingleSpeciesKernel static method)

D

default() (mff.models.combined.NpEncoder method) (mff.models.eam.NpEncoder method), [1] (mff.models.threebody.NpEncoder method) (mff.models.twobody.NpEncoder method) dummy_calc_ee() (in module mff.kernels.threebodykernel) (in module mff.kernels.twobodykernel)

dummy_calc_ef() (in module mff.kernels.threebodykernel) (in module mff.kernels.twobodykernel) dummy_calc_ff() (in module mff.kernels.threebodykernel) (in module mff.kernels.twobodykernel)

E

EamManySpeciesModel (class in mff.models.eam), [1] EamSingleSpeciesModel (class in mff.models.eam), [1]

elements (mff.calculators.ThreeBodyManySpecies attribute) (mff.calculators.TwoBodyManySpecies attribute)

F

fit() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) fit_energy() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method)

fit_force_and_energy() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) from_json() (mff.models.combined.CombinedManySpeciesModel class method) (mff.models.combined.CombinedSingleSpeciesModel class method) (mff.models.eam.EamManySpeciesModel class method), [1] (mff.models.eam.EamSingleSpeciesModel class method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel class method) (mff.models.threebody.ThreeBodySingleSpeciesModel class method) (mff.models.twobody.TwoBodyManySpeciesModel class method) (mff.models.twobody.TwoBodySingleSpeciesModel class method)

G

GaussianProcess (class in mff.gp) generate() (in module mff.configurations) generate_and_save() (in module mff.configurations) generate_triplets() (mff.models.combined.CombinedSingleSpeciesModel static method) (mff.models.threebody.ThreeBodySingleSpeciesModel static method) generate_triplets_all() (mff.models.combined.CombinedManySpeciesModel static method) (mff.models.threebody.ThreeBodyManySpeciesModel static method) generate_triplets_with_permutation_invariance() (mff.models.threebody.ThreeBodyManySpeciesModel static method) gp (mff.models.eam.EamManySpeciesModel attribute), [1] (mff.models.eam.EamSingleSpeciesModel attribute), [1] (mff.models.threebody.ThreeBodyManySpeciesModel attribute) (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyManySpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) gp_2b (mff.models.combined.CombinedManySpeciesModel attribute) (mff.models.combined.CombinedSingleSpeciesModel attribute) gp_3b (mff.models.combined.CombinedManySpeciesModel attribute) (mff.models.combined.CombinedSingleSpeciesModel attribute) grid (mff.models.eam.EamManySpeciesModel attribute), [1] (mff.models.eam.EamSingleSpeciesModel attribute), [1] (mff.models.threebody.ThreeBodyManySpeciesModel attribute) (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyManySpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) grid_2b (mff.calculators.TwoBodySingleSpecies attribute) (mff.models.combined.CombinedManySpeciesModel attribute), [1] (mff.models.combined.CombinedSingleSpeciesModel attribute)

grid_3b (mff.calculators.ThreeBodySingleSpecies attribute) (mff.models.combined.CombinedSingleSpeciesModel attribute) grid_eam (mff.calculators.EamManySpecies attribute) (mff.calculators.EamSingleSpecies attribute) grid_end (mff.models.eam.EamManySpeciesModel attribute), [1] (mff.models.eam.EamSingleSpeciesModel attribute), [1] grid_num (mff.models.combined.CombinedSingleSpeciesModel attribute) (mff.models.eam.EamManySpeciesModel attribute), [1] (mff.models.eam.EamSingleSpeciesModel attribute), [1] (mff.models.threebody.ThreeBodyManySpeciesModel attribute) (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyManySpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) grid_num_2b (mff.models.combined.CombinedManySpeciesModel attribute) grid_num_3b (mff.models.combined.CombinedManySpeciesModel attribute) grid_start (mff.models.combined.CombinedManySpeciesModel attribute) (mff.models.combined.CombinedSingleSpeciesModel attribute) (mff.models.eam.EamManySpeciesModel attribute), [1] (mff.models.eam.EamSingleSpeciesModel attribute), [1] (mff.models.threebody.ThreeBodyManySpeciesModel attribute) (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyManySpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) grids_2b (mff.calculators.TwoBodyManySpecies attribute) grids_3b (mff.calculators.ThreeBodyManySpecies attribute)

K

K (mff.gp.GaussianProcess attribute) k2_ee (mff.kernels.twobodykernel.BaseTwoBody attribute) k2_ef (mff.kernels.twobodykernel.BaseTwoBody attribute) k2_ff (mff.kernels.twobodykernel.BaseTwoBody attribute)

k3_ee (mff.kernels.threebodykernel.BaseThreeBody attribute) k3_ef (mff.kernels.threebodykernel.BaseThreeBody attribute) k3_ef_loc (mff.kernels.threebodykernel.BaseThreeBody attribute) k3_ff (mff.kernels.threebodykernel.BaseThreeBody attribute)

L

L_ (mff.gp.GaussianProcess attribute) load() (in module mff.configurations) (mff.gp.GaussianProcess method) load_and_unpack() (in module mff.configurations) load_gp() (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method)

log_marginal_likelihood() (mff.gp.GaussianProcess method)

M

mff.configurations (module) mff.gp (module) mff.kernels.threebodykernel (module) mff.kernels.twobodykernel (module)

mff.models.combined (module) mff.models.eam (module), [1] mff.models.threebody (module) mff.models.twobody (module) MissingData

N

NpEncoder (class in mff.models.combined) (class in mff.models.eam), [1] (class in mff.models.threebody) (class in mff.models.twobody)

P

predict() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method)

predict_energy() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) pseudo_log_likelihood() (mff.gp.GaussianProcess method)

R

results (mff.calculators.EamManySpecies attribute) (mff.calculators.EamSingleSpecies attribute) (mff.calculators.ThreeBodyManySpecies attribute) (mff.calculators.ThreeBodySingleSpecies attribute) (mff.calculators.TwoBodyManySpecies attribute) (mff.calculators.TwoBodySingleSpecies attribute)

S

save() (in module mff.configurations) (mff.gp.GaussianProcess method) (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method)

save_gp() (mff.models.combined.CombinedManySpeciesModel method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.eam.EamManySpeciesModel method), [1] (mff.models.eam.EamSingleSpeciesModel method), [1] (mff.models.threebody.ThreeBodyManySpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyManySpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method)

T

ThreeBodyManySpeciesKernel (class in mff.kernels.threebodykernel) ThreeBodyManySpeciesModel (class in mff.models.threebody) ThreeBodySingleSpeciesGP (class in mff.gp) ThreeBodySingleSpeciesKernel (class in mff.kernels.threebodykernel) ThreeBodySingleSpeciesModel (class in mff.models.threebody)

TwoBodyManySpeciesKernel (class in mff.kernels.twobodykernel) TwoBodyManySpeciesModel (class in mff.models.twobody) TwoBodySingleSpeciesGP (class in mff.gp) TwoBodySingleSpeciesKernel (class in mff.kernels.twobodykernel) TwoBodySingleSpeciesModel (class in mff.models.twobody)

U

unpack() (in module mff.configurations)

update_energy() (mff.models.threebody.ThreeBodyManySpeciesModel method) update_force() (mff.models.threebody.ThreeBodyManySpeciesModel method)

X

X_train_ (mff.gp.GaussianProcess attribute)