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.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method)

build_grid_3b() (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel 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_ef_loc() (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_2body_confs() (in module mff.configurations) carve_3body_confs() (in module mff.configurations) carve_confs() (in module mff.configurations) carve_from_snapshot() (in module mff.configurations) CombinedSingleSpeciesModel (class in mff.models.combined) CombinedTwoSpeciesModel (class in mff.models.combined) compile_theano() (mff.kernels.threebodykernel.ThreeBodySingleSpeciesKernel static method) (mff.kernels.threebodykernel.ThreeBodyTwoSpeciesKernel static method) (mff.kernels.twobodykernel.TwoBodySingleSpeciesKernel static method) (mff.kernels.twobodykernel.TwoBodyTwoSpeciesKernel static method) Configurations (class in mff.configurations) ConfsTwoBodySingleForces (class in mff.configurations) ConfsTwoForces (class in mff.configurations)

E

elements (mff.advanced_sampling.Sampling attribute) (mff.calculators.ThreeBodyTwoSpecies attribute) (mff.calculators.TwoBodyTwoSpecies attribute)

Energies (class in mff.configurations)

F

fit() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method) fit_energy() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method) fit_force_and_energy() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method)

fit_update() (mff.gp.GaussianProcess method) fit_update_energy() (mff.gp.GaussianProcess method) fit_update_single() (mff.gp.GaussianProcess method) fit_update_single_energy() (mff.gp.GaussianProcess method) Forces (class in mff.configurations) from_json() (mff.models.combined.CombinedSingleSpeciesModel class method) (mff.models.combined.CombinedTwoSpeciesModel class method) (mff.models.threebody.ThreeBodyTwoSpeciesModel class method) (mff.models.twobody.TwoBodySingleSpeciesModel class method) (mff.models.twobody.TwoBodyTwoSpeciesModel class method)

G

GaussianProcess (class in mff.gp) generate_triplets() (mff.models.combined.CombinedSingleSpeciesModel static method) (mff.models.threebody.ThreeBodySingleSpeciesModel static method) generate_triplets_all() (mff.models.combined.CombinedTwoSpeciesModel static method) (mff.models.threebody.ThreeBodyTwoSpeciesModel static method) generate_triplets_with_permutation_invariance() (mff.models.threebody.ThreeBodyTwoSpeciesModel static method) gp (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.threebody.ThreeBodyTwoSpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyTwoSpeciesModel attribute) gp_2b (mff.models.combined.CombinedSingleSpeciesModel attribute) (mff.models.combined.CombinedTwoSpeciesModel attribute) gp_3b (mff.models.combined.CombinedSingleSpeciesModel attribute) (mff.models.combined.CombinedTwoSpeciesModel attribute) grid (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.threebody.ThreeBodyTwoSpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyTwoSpeciesModel attribute) grid_2b (mff.calculators.TwoBodySingleSpecies attribute) (mff.models.combined.CombinedSingleSpeciesModel attribute) (mff.models.combined.CombinedTwoSpeciesModel attribute), [1]

grid_3b (mff.calculators.ThreeBodySingleSpecies attribute) (mff.models.combined.CombinedSingleSpeciesModel attribute) grid_num (mff.models.combined.CombinedSingleSpeciesModel attribute) (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.threebody.ThreeBodyTwoSpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyTwoSpeciesModel attribute) grid_num_2b (mff.models.combined.CombinedTwoSpeciesModel attribute) grid_num_3b (mff.models.combined.CombinedTwoSpeciesModel attribute) grid_start (mff.models.combined.CombinedSingleSpeciesModel attribute) (mff.models.combined.CombinedTwoSpeciesModel attribute) (mff.models.threebody.ThreeBodySingleSpeciesModel attribute) (mff.models.threebody.ThreeBodyTwoSpeciesModel attribute) (mff.models.twobody.TwoBodySingleSpeciesModel attribute) (mff.models.twobody.TwoBodyTwoSpeciesModel attribute) grids_2b (mff.calculators.TwoBodyTwoSpecies attribute) grids_3b (mff.calculators.ThreeBodyTwoSpecies attribute)

K

K (mff.gp.GaussianProcess attribute) K2 (mff.advanced_sampling.Sampling attribute) k2_ee (mff.kernels.twobodykernel.BaseTwoBody attribute) k2_ef (mff.kernels.twobodykernel.BaseTwoBody attribute) k2_ef_loc (mff.kernels.twobodykernel.BaseTwoBody attribute)

k2_ff (mff.kernels.twobodykernel.BaseTwoBody attribute) K3 (mff.advanced_sampling.Sampling 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() (mff.gp.GaussianProcess method) load_gp() (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel 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.threebody (module) mff.models.twobody (module) MissingData

N

natoms (mff.advanced_sampling.Sampling attribute)

P

predict() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method) predict_energy() (mff.gp.GaussianProcess method) (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method)

predict_energy_map() (mff.gp.GaussianProcess method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method) predict_energy_single() (mff.gp.GaussianProcess method) predict_energy_single_map() (mff.gp.GaussianProcess method) predict_single() (mff.gp.GaussianProcess method) pseudo_log_likelihood() (mff.gp.GaussianProcess method)

R

rep_alpha (mff.calculators.TwoBodySingleSpecies attribute) (mff.calculators.TwoBodyTwoSpecies attribute) results (mff.calculators.ThreeBodySingleSpecies attribute) (mff.calculators.ThreeBodyTwoSpecies attribute) (mff.calculators.TwoBodySingleSpecies attribute) (mff.calculators.TwoBodyTwoSpecies attribute)

S

save() (mff.gp.GaussianProcess method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method) save_combined() (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method)

save_gp() (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method)

T

ThreeBodySingleSpeciesGP (class in mff.gp) ThreeBodySingleSpeciesKernel (class in mff.kernels.threebodykernel) ThreeBodySingleSpeciesModel (class in mff.models.threebody) ThreeBodyTwoSpeciesKernel (class in mff.kernels.threebodykernel) ThreeBodyTwoSpeciesModel (class in mff.models.threebody)

TwoBodySingleSpeciesGP (class in mff.gp) TwoBodySingleSpeciesKernel (class in mff.kernels.twobodykernel) TwoBodySingleSpeciesModel (class in mff.models.twobody) TwoBodyTwoSpeciesKernel (class in mff.kernels.twobodykernel) TwoBodyTwoSpeciesModel (class in mff.models.twobody)

U

update_energy() (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method)

update_force() (mff.models.combined.CombinedSingleSpeciesModel method) (mff.models.combined.CombinedTwoSpeciesModel method) (mff.models.threebody.ThreeBodySingleSpeciesModel method) (mff.models.threebody.ThreeBodyTwoSpeciesModel method) (mff.models.twobody.TwoBodySingleSpeciesModel method) (mff.models.twobody.TwoBodyTwoSpeciesModel method)

X

X_train_ (mff.gp.GaussianProcess attribute)