Index

A

a1 (xnn.dnn.models.physnet.PhysNet property) a2 (xnn.dnn.models.physnet.PhysNet property) add_dispersion() (in module xnn.common.models.registry) AEV (class in xnn.dnn.featurizers.aev) aggregate_energy() (xnn.common.models.base.InteratomicPotential method) AgnesiDistanceTransform (class in xnn.gnn.featurizers.radial) Allegro (class in xnn.gnn.models.allegro) angle() (xnn.ffnn.common.frc.ForceField method) AngularSymmetryFunctions (class in xnn.dnn.featurizers.symmetry_functions) ANI (class in xnn.dnn.models.ani) ani1() (xnn.dnn.featurizers.aev.AEV class method) (xnn.dnn.models.ani.ANI class method) ANI1Builder (class in xnn.common.data.hub.ani1) ani1ccx() (xnn.dnn.models.ani.ANI class method) ANI1ccxBuilder (class in xnn.common.data.hub.ani1ccx) ani1x() (xnn.dnn.featurizers.aev.AEV class method) (xnn.dnn.models.ani.ANI class method)

ANI1xBuilder (class in xnn.common.data.hub.ani1x) ani2x() (xnn.dnn.featurizers.aev.AEV class method) (xnn.dnn.models.ani.ANI class method) ANI2xBuilder (class in xnn.common.data.hub.ani2x) apply_overrides() (in module xnn.common.config.loaders) apply_units() (in module xnn.common.benchmark.report) ArgonMDBuilder (class in xnn.common.data.hub.argon_md) assign_atom_types() (in module xnn.ffnn.common.typing) atom_types (xnn.ffnn.common.frc.ForceField property) atomic_number() (in module xnn.ffnn.common.elements) atomic_properties() (xnn.dnn.models.physnet.PhysNet method) AtomicDataset (class in xnn.common.data.dataset) AtomicGraph (class in xnn.common.data.atomic_data) atoms_to_structure() (in module xnn.common.data.ase_io) AtomTypingError available_metrics() (in module xnn.common.benchmark.metrics) available_models() (in module xnn.common.models.registry) available_writers() (in module xnn.common.benchmark.report)

B

BAMBOO (class in xnn.hybrid.models.bamboo) Benchmark (class in xnn.common.benchmark.runner) BenchmarkConfig (class in xnn.common.benchmark.config) BesselRBF (class in xnn.gnn.featurizers.radial) bond() (xnn.ffnn.common.frc.ForceField method) build_e0_lookup() (in module xnn.common.benchmark.energy)

build_model() (in module xnn.common.models.registry) build_neighbor_list() (in module xnn.common.data.neighborlist) build_neighbor_list_ts() (in module xnn.common.deploy.torchscript) build_triplets() (in module xnn.common.models.ops) builtin_data_dir() (in module xnn.ffnn.common.frc) builtin_library() (in module xnn.ffnn.models.oplslib)

C

c6_matrix() (in module xnn.common.models.d4) (xnn.common.models.d3.DFTD3 method) CACE (class in xnn.gnn.models.cace) calculate() (xnn.common.deploy.ase_calculator.XNNCalculator method) (xnn.common.deploy.mdi_engine.MDIEngine method) canonical_key() (in module xnn.ffnn.common.frc) CartesianAngularBasis (class in xnn.gnn.featurizers.cartesian) charge() (xnn.ffnn.common.frc.ForceField method) check_generators() (xnn.ffnn.models.dreiding.DreidingForceField method) cls() (xnn.ffnn.models.oplslib.OPLSLibrary method) coerce_per_species() (in module xnn.common.config.coerce) coerce_species() (in module xnn.common.config.coerce) collate() (in module xnn.common.data.dataset)

collect_predictions() (in module xnn.common.benchmark.metrics) columns() (in module xnn.common.benchmark.report) combination() (xnn.ffnn.common.frc.ForceField method) complete_hbonds() (in module xnn.ffnn.models.ffield) complete_off_diagonal() (in module xnn.ffnn.models.ffield) Config (class in xnn.common.config.schema) convert_units() (in module xnn.ffnn.common.frc) ConvNetLayer (class in xnn.gnn.models.nequip) coordination_numbers() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) CosineCutoff (class in xnn.common.featurizers.cutoff) coulomb_energy() (xnn.hybrid.models.bamboo.BAMBOO method) cutoff_table() (in module xnn.ffnn.models.ffield)

D

d3 (xnn.common.models.d3.D3Dispersion property) d3_c6ab (in module xnn.common.models.d3) d3_options_from_extra() (in module xnn.common.models.d3) d3_r2r4 (in module xnn.common.models.d3) d3_rcov (in module xnn.common.models.d3) D3CSODispersion (class in xnn.hybrid.models.dispersion) D3Dispersion (class in xnn.common.models.d3) d4 (xnn.common.models.d4.D4Dispersion property) d4_options_from_extra() (in module xnn.common.models.d4) D4Dispersion (class in xnn.common.models.d4) DataConfig (class in xnn.common.config.schema) dataset_structures() (in module xnn.common.benchmark.energy) DatasetBuilder (class in xnn.common.data.hub.base) DEBYE_EA (in module xnn.hybrid.models.bamboo)

dedup_torsion_types() (in module xnn.ffnn.models.ffield) default_pair_cutoff() (in module xnn.ffnn.models.ffield) Define (class in xnn.ffnn.common.frc) DescriptorPotential (class in xnn.dnn.models.base) DFTD3 (class in xnn.common.models.d3) DFTD4 (class in xnn.common.models.d4) dihedral_cos() (in module xnn.ffnn.models.geometry) dispersion() (xnn.common.models.dispersion.DispersionCorrection method) dispersion_energy_per_atom() (xnn.dnn.models.physnet.PhysNet method) DispersionCorrection (class in xnn.common.models.dispersion) Dreiding (class in xnn.ffnn.models.dreiding) DreidingForceField (class in xnn.ffnn.models.dreiding) DreidingLibrary (class in xnn.ffnn.models.dreidinglib) dynamic_polarizabilities() (xnn.common.models.d4.DFTD4 method)

E

edge_vectors() (xnn.common.data.atomic_data.AtomicGraph method) EdgeMultiheadAttention (class in xnn.transformer.attention) edisp() (in module xnn.common.models.d3) eeq_charges() (xnn.common.models.d4.DFTD4 method) ELE_FACTOR (in module xnn.hybrid.models.bamboo) electrostatic_energy_per_atom() (xnn.dnn.models.physnet.PhysNet method) element() (xnn.ffnn.models.dreidinglib.DreidingLibrary method) element_of() (in module xnn.ffnn.models.dreidinglib) embed() (xnn.gnn.featurizers.spherical.SphericalHarmonicEdgeEmbedding method) empty() (xnn.ffnn.common.frc.FrcFile class method) equivalent() (xnn.ffnn.common.frc.ForceField method) EquivariantGNN (class in xnn.gnn.models.base) evaluate() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) (xnn.common.train.trainer.Trainer method)

evaluate_on_graph() (in module xnn.common.models.dispersion) EwaldSummation (class in xnn.common.models.les) ExpNormalSmearing (class in xnn.transformer.featurizers.radial) export_library() (xnn.ffnn.models.dreiding.Dreiding method) (xnn.ffnn.models.dreiding.DreidingForceField method) (xnn.ffnn.models.opls.OPLS method) (xnn.ffnn.models.opls.OPLSForceField method) (xnn.ffnn.models.reaxff.ReaxFF method) export_to_lammps() (in module xnn.common.deploy.lammps) export_torchscript() (in module xnn.common.deploy.lammps) export_torchscript_potential() (in module xnn.common.deploy.torchscript)

F

Featurizer (class in xnn.common.featurizers.base) ff_form (xnn.ffnn.common.frc.ForceField property) FFieldLibrary (class in xnn.ffnn.models.ffield) find_forcefield() (in module xnn.ffnn.common.frc) fit() (xnn.common.train.trainer.Trainer method) fit_atomic_energies() (in module xnn.common.benchmark.energy) ForceField (class in xnn.ffnn.common.frc) forcefield() (xnn.ffnn.common.frc.FrcFile method) forcefields (xnn.ffnn.common.frc.FrcFile property) ForceStressOutput (class in xnn.common.models.outputs) format_table() (in module xnn.common.benchmark.report) forward() (xnn.cnn.models.schnet.SchNet method) (xnn.common.deploy.lammps.LAMMPSWrapper method) (xnn.common.deploy.torchscript.TorchScriptPotential method) (xnn.common.featurizers.base.Featurizer method) (xnn.common.featurizers.cutoff.CosineCutoff method) (xnn.common.featurizers.radial.GaussianRBF method) (xnn.common.models.base.InteratomicPotential method) (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) (xnn.common.models.dispersion.DispersionCorrection method) (xnn.common.models.les.EwaldSummation method) (xnn.common.models.les.LatentEwald method) (xnn.common.models.outputs.ForceStressOutput method) (xnn.dnn.featurizers.aev.AEV method) (xnn.dnn.featurizers.symmetry_functions.AngularSymmetryFunctions method) (xnn.dnn.featurizers.symmetry_functions.RadialSymmetryFunctions method) (xnn.dnn.models.base.DescriptorPotential method) (xnn.dnn.models.physnet.PhysNet method) (xnn.ffnn.models.dreiding.Dreiding method) (xnn.ffnn.models.opls.OPLS method) (xnn.ffnn.models.reaxff.ReaxFF method) (xnn.gnn.featurizers.cartesian.CartesianAngularBasis method) (xnn.gnn.featurizers.cutoff.PolynomialCutoff method) (xnn.gnn.featurizers.radial.AgnesiDistanceTransform method) (xnn.gnn.featurizers.radial.BesselRBF method) (xnn.gnn.featurizers.radial.IdentityDistanceTransform method) (xnn.gnn.featurizers.radial.SoftDistanceTransform method) (xnn.gnn.featurizers.spherical.SphericalHarmonicEdgeEmbedding method) (xnn.gnn.models.allegro.Allegro method) (xnn.gnn.models.blocks.ScalarActivation method) (xnn.gnn.models.cace.CACE method) (xnn.gnn.models.mace.MACE method) (xnn.gnn.models.mace.RealAgnosticDensityInteractionBlock method) (xnn.gnn.models.mace.RealAgnosticDensityResidualInteractionBlock method) (xnn.gnn.models.mace.RealAgnosticInteractionBlock method) (xnn.gnn.models.mace.RealAgnosticResidualInteractionBlock method) (xnn.gnn.models.mace.SymmetricContraction method) (xnn.gnn.models.nequip.ConvNetLayer method) (xnn.gnn.models.nequip.InteractionBlock method) (xnn.gnn.models.nequip.NequIP method) (xnn.hybrid.models.bamboo.BAMBOO method) (xnn.hybrid.models.bamboo.GETLayer method) (xnn.hybrid.models.dispersion.D3CSODispersion method) (xnn.transformer.attention.EdgeMultiheadAttention method) (xnn.transformer.featurizers.radial.ExpNormalSmearing method)

forward_lammps() (xnn.common.deploy.torchscript.TorchScriptPotential method) foundation_to_xnn() (in module xnn.gnn.models.mace_foundation) fourier_to_rb() (in module xnn.ffnn.models.oplslib) FRC_FORMAT_VERSION (in module xnn.ffnn.common.frc) FrcFile (class in xnn.ffnn.common.frc) from_argparse() (in module xnn.common.config.loaders) from_ase() (xnn.ffnn.models.topology.MolecularTopology class method) from_atoms() (xnn.common.data.dataset.AtomicDataset class method) (xnn.ffnn.models.dreiding.Dreiding class method) (xnn.ffnn.models.opls.OPLS class method) from_bonds() (xnn.ffnn.models.topology.MolecularTopology class method) from_checkpoint() (xnn.common.deploy.mdi_engine.MDIEngine class method) from_config() (xnn.cnn.models.schnet.SchNet class method) (xnn.common.models.base.InteratomicPotential class method) (xnn.common.models.d3.D3Dispersion class method) (xnn.common.models.d4.D4Dispersion class method) (xnn.common.models.les.LatentEwald class method) (xnn.dnn.models.ani.ANI class method) (xnn.dnn.models.hdnnp.HDNNP class method) (xnn.dnn.models.physnet.PhysNet class method) (xnn.ffnn.models.dreiding.Dreiding class method) (xnn.ffnn.models.opls.OPLS class method) (xnn.ffnn.models.reaxff.ReaxFF class method) (xnn.gnn.models.allegro.Allegro class method) (xnn.gnn.models.cace.CACE class method) (xnn.gnn.models.mace.MACE class method) (xnn.gnn.models.nequip.NequIP class method) (xnn.hybrid.models.bamboo.BAMBOO class method) from_dict() (in module xnn.common.benchmark.config) (in module xnn.common.config.loaders) from_ffield() (xnn.ffnn.models.reaxff.ReaxFF class method) from_file() (xnn.common.data.dataset.AtomicDataset class method) from_forcefield() (in module xnn.ffnn.models.ffield) (in module xnn.ffnn.models.oplslib) from_foundation() (xnn.gnn.models.mace.MACE class method) from_hydra() (in module xnn.common.config.loaders) from_mace_torch() (in module xnn.gnn.models.mace_foundation) from_yaml() (in module xnn.common.benchmark.config) (in module xnn.common.config.loaders)

G

gaussian_reference_weights() (in module xnn.common.models.dispersion) GaussianRBF (class in xnn.common.featurizers.radial) geometric_mean() (in module xnn.ffnn.models.geometry) get_builder() (in module xnn.common.data.hub.base)

get_metric() (in module xnn.common.benchmark.metrics) GETLayer (class in xnn.hybrid.models.bamboo) GNNPotential (class in xnn.gnn.models.base) guarded_exp() (in module xnn.ffnn.models.reaxff) guess_bonds() (in module xnn.ffnn.models.topology)

H

HARTREE_KCAL_MOL (in module xnn.hybrid.models.dispersion) HDNNP (class in xnn.dnn.models.hdnnp)

hidden_irreps() (in module xnn.gnn.models.blocks) hybrid() (xnn.ffnn.models.dreidinglib.DreidingLibrary method) hybridization() (in module xnn.ffnn.models.dreidinglib)

I

IdentityDistanceTransform (class in xnn.gnn.featurizers.radial) implemented_properties (xnn.common.deploy.ase_calculator.XNNCalculator attribute) improper() (xnn.ffnn.common.frc.ForceField method) improper_defined() (xnn.ffnn.models.opls.OPLSForceField method) improper_key() (in module xnn.ffnn.models.oplslib)

inner_graph() (xnn.common.models.dispersion.DispersionCorrection method) InteractionBlock (class in xnn.gnn.models.nequip) InteratomicPotential (class in xnn.common.models.base) is_acceptor() (xnn.ffnn.models.dreidinglib.DreidingLibrary method) is_nn (xnn.ffnn.models.ffield.FFieldLibrary property)

K

kinds_of() (xnn.ffnn.common.frc.ForceField method)

L

LAMMPSWrapper (class in xnn.common.deploy.lammps) LatentEwald (class in xnn.common.models.les) latest() (xnn.ffnn.common.frc.Section method) legacy_c6_table() (in module xnn.common.models.d3) list_datasets() (in module xnn.common.data.hub.base) list_forcefields() (in module xnn.ffnn.common.frc) load() (xnn.common.data.hub.ani1.ANI1Builder method) (xnn.common.data.hub.ani1ccx.ANI1ccxBuilder method) (xnn.common.data.hub.ani1x.ANI1xBuilder method) (xnn.common.data.hub.ani2x.ANI2xBuilder method) (xnn.common.data.hub.argon_md.ArgonMDBuilder method) (xnn.common.data.hub.base.DatasetBuilder method) (xnn.common.data.hub.lode_dimers.LODEDimersBuilder method) (xnn.common.data.hub.rmd17.RMD17Builder method)

load_custom_metric() (in module xnn.common.benchmark.metrics) load_dataset() (in module xnn.common.data.hub.base) load_foundation() (in module xnn.gnn.models.mace_foundation) load_structures() (in module xnn.common.data.ase_io) LODEDimersBuilder (class in xnn.common.data.hub.lode_dimers) lxlylz_list() (in module xnn.gnn.featurizers.cartesian)

M

MACE (class in xnn.gnn.models.mace) mae() (in module xnn.common.benchmark.metrics) main() (in module xnn.common.cli) (in module xnn.common.deploy.mdi_engine) make_section() (in module xnn.ffnn.common.frc) masses (xnn.ffnn.models.dreiding.Dreiding property) (xnn.ffnn.models.opls.OPLS property) MDIEngine (class in xnn.common.deploy.mdi_engine) ModelConfig (class in xnn.common.config.schema) ModelEntry (class in xnn.common.benchmark.config) modifier() (xnn.ffnn.common.frc.Section method) module xnn.cnn xnn.cnn.models xnn.cnn.models.schnet xnn.common xnn.common.benchmark xnn.common.benchmark.config xnn.common.benchmark.energy xnn.common.benchmark.metrics xnn.common.benchmark.report xnn.common.benchmark.runner xnn.common.cli xnn.common.config xnn.common.config.coerce xnn.common.config.loaders xnn.common.config.schema xnn.common.config.translate xnn.common.data xnn.common.data.ase_io xnn.common.data.atomic_data xnn.common.data.dataset xnn.common.data.hub xnn.common.data.hub.ani1 xnn.common.data.hub.ani1ccx xnn.common.data.hub.ani1x xnn.common.data.hub.ani2x xnn.common.data.hub.argon_md xnn.common.data.hub.base xnn.common.data.hub.lode_dimers xnn.common.data.hub.rmd17 xnn.common.data.neighborlist xnn.common.deploy xnn.common.deploy.ase_calculator xnn.common.deploy.lammps xnn.common.deploy.mdi_engine xnn.common.deploy.torchscript xnn.common.featurizers xnn.common.featurizers.base xnn.common.featurizers.cutoff xnn.common.featurizers.radial xnn.common.models xnn.common.models.base xnn.common.models.d3 xnn.common.models.d4 xnn.common.models.dispersion xnn.common.models.les xnn.common.models.ops xnn.common.models.outputs xnn.common.models.registry xnn.common.train xnn.common.train.losses xnn.common.train.trainer xnn.dnn xnn.dnn.featurizers xnn.dnn.featurizers.aev xnn.dnn.featurizers.symmetry_functions xnn.dnn.models xnn.dnn.models.ani xnn.dnn.models.base xnn.dnn.models.hdnnp xnn.dnn.models.physnet xnn.ffnn xnn.ffnn.common xnn.ffnn.common.elements xnn.ffnn.common.frc xnn.ffnn.common.typing xnn.ffnn.models xnn.ffnn.models.dreiding xnn.ffnn.models.dreidinglib xnn.ffnn.models.ffield xnn.ffnn.models.geometry xnn.ffnn.models.opls xnn.ffnn.models.oplslib xnn.ffnn.models.reaxff xnn.ffnn.models.topology xnn.gnn xnn.gnn.featurizers xnn.gnn.featurizers.cartesian xnn.gnn.featurizers.cutoff xnn.gnn.featurizers.radial xnn.gnn.featurizers.spherical xnn.gnn.models xnn.gnn.models.allegro xnn.gnn.models.base xnn.gnn.models.blocks xnn.gnn.models.cace xnn.gnn.models.mace xnn.gnn.models.mace_foundation xnn.gnn.models.nequip xnn.hybrid xnn.hybrid.models xnn.hybrid.models.bamboo xnn.hybrid.models.dispersion xnn.transformer xnn.transformer.attention xnn.transformer.featurizers xnn.transformer.featurizers.radial

module (xnn.common.train.trainer.Trainer property) MolecularTopology (class in xnn.ffnn.models.topology) mse() (in module xnn.common.benchmark.metrics) multinomial_coefficient() (in module xnn.gnn.featurizers.cartesian)

N

n_atoms (xnn.ffnn.models.topology.MolecularTopology property) n_lxlylz() (in module xnn.gnn.featurizers.cartesian) NequIP (class in xnn.gnn.models.nequip) nequip_hidden_irreps() (in module xnn.gnn.models.nequip) node_attr() (xnn.gnn.models.base.GNNPotential method) node_energy() (xnn.cnn.models.schnet.SchNet method) (xnn.gnn.models.allegro.Allegro method) (xnn.gnn.models.cace.CACE method) (xnn.gnn.models.mace.MACE method) (xnn.gnn.models.nequip.NequIP method)

node_features_energy() (xnn.cnn.models.schnet.SchNet method) (xnn.gnn.models.allegro.Allegro method) (xnn.gnn.models.cace.CACE method) (xnn.gnn.models.mace.MACE method) (xnn.gnn.models.nequip.NequIP method) nonbond() (xnn.ffnn.common.frc.ForceField method) nonbond_to_sigma_eps() (in module xnn.ffnn.common.frc) nonbonded_taper() (in module xnn.ffnn.models.reaxff) num_edges (xnn.common.data.atomic_data.AtomicGraph property) num_graphs (xnn.common.data.atomic_data.AtomicGraph property) num_nodes (xnn.common.data.atomic_data.AtomicGraph property)

O

OPLS (class in xnn.ffnn.models.opls) OPLSForceField (class in xnn.ffnn.models.opls) OPLSLibrary (class in xnn.ffnn.models.oplslib) OptimConfig (class in xnn.common.config.schema) options_from_extra() (in module xnn.common.models.dispersion) output_dim (xnn.common.featurizers.base.Featurizer property) (xnn.dnn.featurizers.aev.AEV property) (xnn.dnn.featurizers.symmetry_functions.AngularSymmetryFunctions property) (xnn.dnn.featurizers.symmetry_functions.RadialSymmetryFunctions property) (xnn.gnn.featurizers.spherical.SphericalHarmonicEdgeEmbedding property)

OutputConfig (class in xnn.common.benchmark.config) oxygen_column() (xnn.ffnn.models.dreidinglib.DreidingLibrary method)

P

pair_c6() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) pair_radius() (xnn.common.models.d3.DFTD3 method) pair_radius_table() (xnn.common.models.d4.DFTD4 method) pair_vectors() (in module xnn.ffnn.models.geometry) parse_header() (in module xnn.ffnn.common.frc)

parse_version() (in module xnn.ffnn.common.frc) PBE0_D3BJ (in module xnn.common.models.d3) perceive_bond_orders() (in module xnn.ffnn.common.typing) perceive_bonds() (in module xnn.ffnn.common.typing) PhysNet (class in xnn.dnn.models.physnet) PolynomialCutoff (class in xnn.gnn.featurizers.cutoff)

R

RadialSymmetryFunctions (class in xnn.dnn.featurizers.symmetry_functions) rb_to_fourier() (in module xnn.ffnn.models.oplslib) read_dreiding() (in module xnn.ffnn.models.dreidinglib) read_ffield() (in module xnn.ffnn.models.ffield) read_forcefield() (in module xnn.ffnn.common.frc) read_frc() (in module xnn.ffnn.common.frc) read_opls() (in module xnn.ffnn.models.oplslib) read_topology() (in module xnn.ffnn.models.topology) RealAgnosticDensityInteractionBlock (class in xnn.gnn.models.mace) RealAgnosticDensityResidualInteractionBlock (class in xnn.gnn.models.mace) RealAgnosticInteractionBlock (class in xnn.gnn.models.mace) RealAgnosticResidualInteractionBlock (class in xnn.gnn.models.mace) realspace() (xnn.common.models.les.EwaldSummation method) ReaxFF (class in xnn.ffnn.models.reaxff) reciprocal() (xnn.common.models.les.EwaldSummation method) Reference (class in xnn.ffnn.common.frc) REFERENCE_SETS (in module xnn.common.models.d3) reference_tables() (in module xnn.common.models.d3) reference_weights() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) references_used() (xnn.ffnn.common.frc.ForceField method) register_dataset() (in module xnn.common.data.hub.base) register_key_translation() (in module xnn.common.config.translate)

register_metric() (in module xnn.common.benchmark.metrics) register_model() (in module xnn.common.models.registry) register_section_schema() (in module xnn.ffnn.common.frc) register_writer() (in module xnn.common.benchmark.report) replicate() (xnn.ffnn.models.topology.MolecularTopology method) reset_parameters() (xnn.transformer.featurizers.radial.ExpNormalSmearing method) resolve_angle() (xnn.ffnn.models.opls.OPLSForceField method) resolve_angle_type() (in module xnn.ffnn.models.oplslib) resolve_bond() (xnn.ffnn.models.opls.OPLSForceField method) resolve_bond_type() (in module xnn.ffnn.models.oplslib) resolve_device() (in module xnn.common.train.trainer) resolve_dihedral() (xnn.ffnn.models.opls.OPLSForceField method) resolve_dihedral_type() (in module xnn.ffnn.models.oplslib) resolve_improper() (xnn.ffnn.models.opls.OPLSForceField method) resolve_improper_type() (in module xnn.ffnn.models.oplslib) resolve_torsion() (in module xnn.ffnn.models.ffield) reverse_edge_permutation() (in module xnn.ffnn.models.reaxff) RMD17Builder (class in xnn.common.data.hub.rmd17) rmse() (in module xnn.common.benchmark.metrics) Row (class in xnn.ffnn.common.frc) rows() (xnn.ffnn.common.frc.ForceField method) run() (xnn.common.benchmark.runner.Benchmark method) (xnn.common.deploy.mdi_engine.MDIEngine method) run_benchmark() (in module xnn.common.benchmark.runner)

S

s6 (xnn.dnn.models.physnet.PhysNet property) s8 (xnn.dnn.models.physnet.PhysNet property) save() (xnn.common.train.trainer.Trainer method) (xnn.ffnn.models.dreidinglib.DreidingLibrary method) (xnn.ffnn.models.ffield.FFieldLibrary method) (xnn.ffnn.models.oplslib.OPLSLibrary method) (xnn.ffnn.models.topology.MolecularTopology method) save_frc() (xnn.ffnn.models.oplslib.OPLSLibrary method) ScalarActivation (class in xnn.gnn.models.blocks) scaled_charges() (xnn.dnn.models.physnet.PhysNet method) scatter_sum() (in module xnn.common.models.ops) schema (xnn.ffnn.common.frc.Section property) SchNet (class in xnn.cnn.models.schnet) score() (in module xnn.common.benchmark.metrics) Section (class in xnn.ffnn.common.frc)

sections_for() (xnn.ffnn.common.frc.Define method) semi_orthogonal_glorot_weights() (in module xnn.dnn.models.physnet) set_atomic_energies() (xnn.cnn.models.schnet.SchNet method) (xnn.gnn.models.base.GNNPotential method) set_energy_scale_shift() (xnn.cnn.models.schnet.SchNet method) shifted_softplus() (in module xnn.common.models.ops) (in module xnn.gnn.models.blocks) SoftDistanceTransform (class in xnn.gnn.featurizers.radial) softplus_inverse() (in module xnn.dnn.models.physnet) species_irreps() (in module xnn.gnn.models.blocks) SphericalHarmonicEdgeEmbedding (class in xnn.gnn.featurizers.spherical) split_wrappers() (in module xnn.common.deploy.torchscript) structure_to_graph() (in module xnn.common.data.dataset) switching_function() (in module xnn.common.models.dispersion) SymmetricContraction (class in xnn.gnn.models.mace)

T

taper_down() (in module xnn.ffnn.models.reaxff) taper_up() (in module xnn.ffnn.models.reaxff) targets (xnn.common.benchmark.config.BenchmarkConfig property) template_library() (in module xnn.ffnn.models.ffield) terms (xnn.ffnn.common.frc.ForceField property) three_body_energy() (in module xnn.common.models.dispersion) to() (xnn.common.data.atomic_data.AtomicGraph method) to_config() (xnn.common.benchmark.config.ModelEntry method) to_forcefield() (in module xnn.ffnn.models.ffield) (in module xnn.ffnn.models.oplslib) to_rdkit() (in module xnn.ffnn.common.typing)

TorchScriptPotential (class in xnn.common.deploy.torchscript) torsion() (xnn.ffnn.common.frc.ForceField method) torsion_rule() (in module xnn.ffnn.models.dreidinglib) tp_out_irreps_with_instructions() (in module xnn.gnn.models.blocks) tp_path_exists() (in module xnn.gnn.models.blocks) Trainer (class in xnn.common.train.trainer) translate_model_keys() (in module xnn.common.config.translate) two_body_energy() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) type_index() (xnn.ffnn.models.dreiding.DreidingForceField method) (xnn.ffnn.models.opls.OPLSForceField method)

U

U_matrix_real() (in module xnn.gnn.models.mace)

unit_factor() (in module xnn.ffnn.common.frc) units() (xnn.ffnn.common.frc.Section method)

V

version_key (xnn.ffnn.common.frc.Row property)

W

weighted_loss() (in module xnn.common.train.losses) write() (in module xnn.common.benchmark.report) (xnn.ffnn.common.frc.FrcFile method) write_all() (in module xnn.common.benchmark.report)

write_csv() (in module xnn.common.benchmark.report) write_frc() (in module xnn.ffnn.common.frc) write_json() (in module xnn.common.benchmark.report) write_markdown() (in module xnn.common.benchmark.report)

X

xnn.cnn module xnn.cnn.models module xnn.cnn.models.schnet module xnn.common module xnn.common.benchmark module xnn.common.benchmark.config module xnn.common.benchmark.energy module xnn.common.benchmark.metrics module xnn.common.benchmark.report module xnn.common.benchmark.runner module xnn.common.cli module xnn.common.config module xnn.common.config.coerce module xnn.common.config.loaders module xnn.common.config.schema module xnn.common.config.translate module xnn.common.data module xnn.common.data.ase_io module xnn.common.data.atomic_data module xnn.common.data.dataset module xnn.common.data.hub module xnn.common.data.hub.ani1 module xnn.common.data.hub.ani1ccx module xnn.common.data.hub.ani1x module xnn.common.data.hub.ani2x module xnn.common.data.hub.argon_md module xnn.common.data.hub.base module xnn.common.data.hub.lode_dimers module xnn.common.data.hub.rmd17 module xnn.common.data.neighborlist module xnn.common.deploy module xnn.common.deploy.ase_calculator module xnn.common.deploy.lammps module xnn.common.deploy.mdi_engine module xnn.common.deploy.torchscript module xnn.common.featurizers module xnn.common.featurizers.base module xnn.common.featurizers.cutoff module xnn.common.featurizers.radial module xnn.common.models module xnn.common.models.base module xnn.common.models.d3 module xnn.common.models.d4 module xnn.common.models.dispersion module xnn.common.models.les module xnn.common.models.ops module xnn.common.models.outputs module xnn.common.models.registry module

xnn.common.train module xnn.common.train.losses module xnn.common.train.trainer module xnn.dnn module xnn.dnn.featurizers module xnn.dnn.featurizers.aev module xnn.dnn.featurizers.symmetry_functions module xnn.dnn.models module xnn.dnn.models.ani module xnn.dnn.models.base module xnn.dnn.models.hdnnp module xnn.dnn.models.physnet module xnn.ffnn module xnn.ffnn.common module xnn.ffnn.common.elements module xnn.ffnn.common.frc module xnn.ffnn.common.typing module xnn.ffnn.models module xnn.ffnn.models.dreiding module xnn.ffnn.models.dreidinglib module xnn.ffnn.models.ffield module xnn.ffnn.models.geometry module xnn.ffnn.models.opls module xnn.ffnn.models.oplslib module xnn.ffnn.models.reaxff module xnn.ffnn.models.topology module xnn.gnn module xnn.gnn.featurizers module xnn.gnn.featurizers.cartesian module xnn.gnn.featurizers.cutoff module xnn.gnn.featurizers.radial module xnn.gnn.featurizers.spherical module xnn.gnn.models module xnn.gnn.models.allegro module xnn.gnn.models.base module xnn.gnn.models.blocks module xnn.gnn.models.cace module xnn.gnn.models.mace module xnn.gnn.models.mace_foundation module xnn.gnn.models.nequip module xnn.hybrid module xnn.hybrid.models module xnn.hybrid.models.bamboo module xnn.hybrid.models.dispersion module xnn.transformer module xnn.transformer.attention module xnn.transformer.featurizers module xnn.transformer.featurizers.radial module XNNCalculator (class in xnn.common.deploy.ase_calculator)