Index

A

amp module Amp (class in amp) amp.analysis module amp.convert module amp.descriptor.bispectrum module amp.descriptor.cutoffs module amp.descriptor.example module amp.descriptor.gaussian module amp.descriptor.zernike module amp.model module

amp.model.neuralnetwork module amp.nft.activelearner module amp.preprocess.image_selection module amp.regression module amp.stats.bootstrap module amp.utilities module anneal() (amp.utilities.Annealer method) Annealer (class in amp.utilities) archive() (amp.utilities.FileDatabase method) archive_directory() (in module amp.stats.bootstrap) assign_cores() (in module amp.utilities) AtomCenteredExample (class in amp.descriptor.example) attach_model() (amp.model.LossFunction method) auto() (amp.utilities.Annealer method)

B

binomial() (in module amp.descriptor.bispectrum) (in module amp.descriptor.zernike)

Bispectrum (class in amp.descriptor.bispectrum) BootStrap (class in amp.stats.bootstrap) bootstrap() (in module amp.stats.bootstrap)

C

calc_rmse() (in module amp.analysis) calculate() (amp.Amp method) (amp.descriptor.bispectrum.FingerprintCalculator method) (amp.descriptor.bispectrum.NeighborlistCalculator method) (amp.descriptor.example.FingerprintCalculator method) (amp.descriptor.example.NeighborlistCalculator method) (amp.descriptor.gaussian.FingerprintCalculator method) (amp.descriptor.gaussian.FingerprintPrimeCalculator method) (amp.descriptor.gaussian.NeighborlistCalculator method) (amp.descriptor.zernike.FingerprintCalculator method) (amp.descriptor.zernike.FingerprintPrimeCalculator method) (amp.descriptor.zernike.NeighborlistCalculator method) calculate_atomic_energy() (amp.model.neuralnetwork.NeuralNetwork method) calculate_B() (in module amp.descriptor.bispectrum) calculate_c() (in module amp.descriptor.bispectrum) calculate_charge_fingerprints_range() (in module amp.model) calculate_charge_fp() (in module amp.model) calculate_charge_fpprime() (in module amp.model) calculate_dAtomicEnergy_dParameters() (amp.model.neuralnetwork.NeuralNetwork method) calculate_dEnergy_dParameters() (amp.model.Model method) calculate_dForce_dParameters() (amp.model.neuralnetwork.NeuralNetwork method) calculate_dForces_dParameters() (amp.model.Model method) calculate_dgcEnergy_dParameters() (amp.model.Model method) calculate_dgcForces_dParameters() (amp.model.Model method) calculate_dOutputs_dInputs() (in module amp.model.neuralnetwork) calculate_energy() (amp.model.Model method) calculate_fingerprints() (amp.descriptor.bispectrum.Bispectrum method) (amp.descriptor.example.AtomCenteredExample method) (amp.descriptor.gaussian.Gaussian method) (amp.descriptor.zernike.Zernike method) calculate_fingerprints_range() (in module amp.model) calculate_force() (amp.model.neuralnetwork.NeuralNetwork method)

calculate_forces() (amp.model.Model method) calculate_G2() (in module amp.descriptor.gaussian) calculate_G2_prime() (in module amp.descriptor.gaussian) calculate_G4() (in module amp.descriptor.gaussian) calculate_G4_prime() (in module amp.descriptor.gaussian) calculate_G5() (in module amp.descriptor.gaussian) calculate_G5_prime() (in module amp.descriptor.gaussian) calculate_gc_energy() (amp.model.Model method) calculate_gc_forces() (amp.model.Model method) calculate_items() (amp.utilities.Data method) calculate_loss() (amp.model.LossFunction method) calculate_nodal_outputs() (in module amp.model.neuralnetwork) calculate_numerical_dEnergy_dParameters() (amp.model.Model method) calculate_numerical_dForces_dParameters() (amp.model.Model method) calculate_numerical_dgcEnergy_dParameters() (amp.model.Model method) calculate_numerical_dgcForces_dParameters() (amp.model.Model method) calculate_ohat_D_delta() (in module amp.model.neuralnetwork) calculate_q() (in module amp.descriptor.zernike) calculate_R() (in module amp.descriptor.zernike) calculate_Z() (in module amp.descriptor.zernike) calculate_Z_prime() (in module amp.descriptor.zernike) CG() (in module amp.descriptor.bispectrum) check_convergence() (amp.model.LossFunction method) check_images() (in module amp.utilities) clear_all() (amp.utilities.EphemeralDatabase class method) close() (amp.utilities.Data method) (amp.utilities.EphemeralDatabase method) (amp.utilities.FileDatabase method) ConvergenceOccurred copy_state() (amp.utilities.Annealer method) copy_strategy (amp.utilities.Annealer attribute) cores (amp.Amp property) Cosine (class in amp.descriptor.cutoffs)

D

Data (class in amp.utilities) dCos_theta_ijk_dR_ml() (in module amp.descriptor.gaussian) default_parameters (amp.model.LossFunction attribute) der_position() (in module amp.descriptor.zernike)

descriptor (amp.Amp property) dict2cutoff() (in module amp.descriptor.cutoffs) distance() (amp.preprocess.image_selection.FurthestPointSampling method) dRij_dRml() (in module amp.descriptor.gaussian) dRij_dRml_vector() (in module amp.descriptor.gaussian)

E

enforce_magnetic_moments() (in module amp.utilities)

EphemeralDatabase (class in amp.utilities) extract_an_atomic_chunk() (in module amp.utilities)

F

FileDatabase (class in amp.utilities) FingerprintCalculator (class in amp.descriptor.bispectrum) (class in amp.descriptor.example) (class in amp.descriptor.gaussian) (class in amp.descriptor.zernike)

FingerprintPrimeCalculator (class in amp.descriptor.gaussian) (class in amp.descriptor.zernike) fit() (amp.model.neuralnetwork.NeuralNetwork method) forcetraining (amp.model.neuralnetwork.NeuralNetwork property) FurthestPointSampling (class in amp.preprocess.image_selection)

G

Gaussian (class in amp.descriptor.gaussian) generate_coefficients() (in module amp.descriptor.bispectrum) (in module amp.descriptor.zernike) get_amp_calc() (amp.stats.bootstrap.TrainingArchive method) get_atomic_energies() (amp.stats.bootstrap.BootStrap method) get_atomic_uncertainties() (in module amp.utilities) get_charges() (amp.stats.bootstrap.BootStrap method) get_excess_Ne() (amp.stats.bootstrap.BootStrap method) get_fingerprint() (amp.descriptor.bispectrum.FingerprintCalculator method) (amp.descriptor.example.FingerprintCalculator method) (amp.descriptor.gaussian.FingerprintCalculator method) (amp.descriptor.zernike.FingerprintCalculator method) get_fingerprintprime() (amp.descriptor.gaussian.FingerprintPrimeCalculator method) (amp.descriptor.zernike.FingerprintPrimeCalculator method)

get_forces() (amp.stats.bootstrap.BootStrap method) get_gc_hash() (in module amp.utilities) get_git_commit() (in module amp) get_Gs_indices() (in module amp.convert) get_hash() (in module amp.utilities) get_initial_scalings() (in module amp.model.neuralnetwork) get_loss() (amp.model.LossFunction method) (amp.model.neuralnetwork.NeuralNetwork method) (amp.utilities.Annealer method) get_overfit_mask() (in module amp.utilities) get_potential_energy() (amp.model.neuralnetwork.OffsetCalculator method) (amp.stats.bootstrap.BootStrap method) get_random_weights() (in module amp.model.neuralnetwork) get_trajectory() (amp.stats.bootstrap.TrainingArchive method)

H

hash_gc_images() (in module amp.utilities)

hash_images() (in module amp.utilities)

I

implemented_properties (amp.Amp attribute)

importer() (in module amp.utilities) importhelper() (in module amp)

K

keys() (amp.utilities.EphemeralDatabase method) (amp.utilities.FileDatabase method)

Kronecker() (in module amp.descriptor.gaussian) (in module amp.descriptor.zernike)

L

label (amp.Amp property) load() (amp.Amp class method) (amp.stats.bootstrap.BootStrap class method)

log (amp.model.Model property) Logger (class in amp.utilities) lossfunction (amp.model.neuralnetwork.NeuralNetwork property) LossFunction (class in amp.model)

M

m_values() (in module amp.descriptor.bispectrum) make_default_symmetry_functions() (in module amp.descriptor.gaussian) make_filename() (in module amp.utilities) make_sublists() (in module amp.utilities) make_symmetry_functions() (in module amp.descriptor.gaussian) MessageDictionary (class in amp.utilities) metadata (amp.utilities.MetaDict attribute) MetaDict (class in amp.utilities) MissingDataError model (amp.Amp property) Model (class in amp.model) module amp amp.analysis amp.convert amp.descriptor.bispectrum amp.descriptor.cutoffs amp.descriptor.example amp.descriptor.gaussian amp.descriptor.zernike amp.model amp.model.neuralnetwork amp.nft.activelearner amp.preprocess.image_selection amp.regression amp.stats.bootstrap amp.utilities

move() (amp.utilities.Annealer method)

N

NeighborlistCalculator (class in amp.descriptor.bispectrum) (class in amp.descriptor.example) (class in amp.descriptor.gaussian) (class in amp.descriptor.zernike)

NeuralNetwork (class in amp.model.neuralnetwork) NFT (class in amp.nft.activelearner) NodePlot (class in amp.model.neuralnetwork) now() (in module amp.utilities)

O

OffsetCalculator (class in amp.model.neuralnetwork) open() (amp.utilities.Data method) (amp.utilities.EphemeralDatabase class method) (amp.utilities.FileDatabase class method)

overwrite_file() (in module amp.convert)

P

parse_slurm_allocation() (in module amp.utilities) plot() (amp.model.neuralnetwork.NodePlot method) plot_convergence() (in module amp.analysis) plot_parity_and_error() (in module amp.analysis) plot_sensitivity() (in module amp.analysis)

Polynomial (class in amp.descriptor.cutoffs) prescale_intercepts() (amp.model.neuralnetwork.NeuralNetwork method) prime() (amp.descriptor.cutoffs.Cosine method) (amp.descriptor.cutoffs.Polynomial method) process_parallels() (amp.model.LossFunction method)

R

randomize() (amp.model.neuralnetwork.NeuralNetwork method) randomize_images() (in module amp.utilities) ravel_data() (in module amp.model) Raveler (class in amp.model.neuralnetwork) read_amp_log_status() (in module amp.utilities)

read_trainlog() (in module amp.analysis) regress() (amp.regression.Regressor method) Regressor (class in amp.regression) reset() (amp.model.LossFunction method) round_figures() (amp.utilities.Annealer static method) run() (amp.nft.activelearner.NFT method)

S

save() (amp.Amp method) save_state() (amp.utilities.Annealer method) save_state_on_exit (amp.utilities.Annealer attribute) save_to_n2p2() (in module amp.convert) save_to_n2p2_images_only() (in module amp.convert) save_to_openkim() (in module amp.convert) save_to_prophet() (in module amp.convert) search() (amp.preprocess.image_selection.FurthestPointSampling method)

send_data_to_fortran() (in module amp.model) set() (amp.Amp method) (amp.stats.bootstrap.BootStrap method) set_schedule() (amp.utilities.Annealer method) set_user_exit() (amp.utilities.Annealer method) setup_parallel() (in module amp.utilities) start_workers() (in module amp.utilities) steps (amp.utilities.Annealer attribute) string2dict() (in module amp.utilities)

T

tic() (amp.utilities.Logger method) time_string() (amp.utilities.Annealer static method) Tmax (amp.utilities.Annealer attribute) Tmin (amp.utilities.Annealer attribute) to_dicts() (amp.model.neuralnetwork.Raveler method) to_vector() (amp.model.neuralnetwork.Raveler method) todict() (amp.descriptor.cutoffs.Cosine method) (amp.descriptor.cutoffs.Polynomial method)

tostring() (amp.descriptor.bispectrum.Bispectrum method) (amp.descriptor.example.AtomCenteredExample method) (amp.descriptor.gaussian.Gaussian method) (amp.descriptor.zernike.Zernike method) (amp.model.Model method) train() (amp.Amp method) (amp.stats.bootstrap.BootStrap method) TrainingArchive (class in amp.stats.bootstrap) TrainingConvergenceError

U

U() (in module amp.descriptor.bispectrum) update() (amp.utilities.Annealer method) (amp.utilities.EphemeralDatabase method) (amp.utilities.FileDatabase method)

updates (amp.utilities.Annealer attribute) user_exit (amp.utilities.Annealer attribute)

V

values() (amp.utilities.FileDatabase method)

vector (amp.model.neuralnetwork.NeuralNetwork property)

W

WignerD() (in module amp.descriptor.bispectrum)

Z

Zernike (class in amp.descriptor.zernike)