Index

A

a1 (xnn.dnn.models.physnet.PhysNet property) a2 (xnn.dnn.models.physnet.PhysNet property) ACTIVATIONS (in module xnn.dnn.common.runner) adapted_weight() (xnn.common.finetune.lora.LoRAAdapter method) (xnn.common.finetune.lora.LoRAEquivariantLinear method) 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) AIMNet2 (class in xnn.gnn.models.aimnet2) ALIASES (in module xnn.gnn.models.aimnet2_foundation) all_gather_cat() (in module xnn.common.distributed) all_pairs() (in module xnn.common.models.electrostatics) all_reduce_sum() (in module xnn.common.distributed) Allegro (class in xnn.gnn.models.allegro) analyze() (xnn.cnn.models.spherical.S2Transform method) (xnn.cnn.models.spherical.SO3Transform method) angle() (xnn.ffnn.common.frc.ForceField method) angular() (xnn.gnn.featurizers.spherical_bessel.SphericalBesselBasis method) angular_kernel_basis() (in module xnn.cnn.models.steerable) 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_differentiable() (xnn.common.models.dispersion_fast.eeq.FastEEQSystem method) (xnn.common.models.eeq.EEQSystem method) 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) assemble() (xnn.common.models.eeq.EEQSystem method) assign_atom_types() (in module xnn.ffnn.common.typing) atm_energy() (in module xnn.common.models.dispersion_fast.atm) ATMConstants (class in xnn.common.models.dispersion_fast.atm) atom_types (xnn.ffnn.common.frc.ForceField property) AtomCenteredSymmetryFunctions (class in xnn.dnn.featurizers.acsf) atomic_energies() (xnn.common.finetune.heads.MultiHead method) ATOMIC_MASSES (in module xnn.common.models.ops) atomic_number() (in module xnn.common.data.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 AUTO_LARGE_PERIODIC (in module xnn.common.models.d4) AUTO_POLICY (in module xnn.common.models.dispersion_fast) (in module xnn.common.models.les) (in module xnn.gnn.fast) auto_triplet_chunk() (in module xnn.common.models.dispersion) AutoPolicy (class in xnn.common.models.fast) available_metrics() (in module xnn.common.benchmark.metrics) available_models() (in module xnn.common.models.registry) available_writers() (in module xnn.common.benchmark.report) average_atomic_energies() (in module xnn.common.finetune.reference) axis_table() (xnn.common.models.reciprocal.PhaseColumns method)

B

BAMBOO (class in xnn.hybrid.models.bamboo) BANDLIMITS (in module xnn.cnn.models.steerable) barrier() (in module xnn.common.distributed) Benchmark (class in xnn.common.benchmark.runner) BenchmarkConfig (class in xnn.common.benchmark.config) BesselRBF (class in xnn.gnn.featurizers.radial) BLOCK (in module xnn.common.models.dispersion_fast.atm) blocks() (xnn.common.models.reciprocal.PhaseColumns method) BOHR_TO_ANGSTROM (in module xnn.common.data.hub.units) bond() (xnn.ffnn.common.frc.ForceField method) bonded_fragments() (in module xnn.common.models.charge_solve)

bspline_moduli() (in module xnn.common.models.pme) bspline_weights() (in module xnn.common.models.pme) build_e0_lookup() (in module xnn.common.benchmark.energy) build_loggers() (in module xnn.common.train.loggers) 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_potential() (in module xnn.common.models.hub.checkpoint) 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) Callback (class in xnn.common.train.callbacks) canonical_key() (in module xnn.ffnn.common.frc) CartesianAngularBasis (class in xnn.gnn.featurizers.cartesian) cell_volume() (in module xnn.common.models.ops) center_of_mass() (in module xnn.common.models.ops) CG_TOL (in module xnn.common.models.eeq) CG_TOL_FLOAT32 (in module xnn.common.models.dispersion_fast.eeq) channel_index() (xnn.cnn.featurizers.spherical.SphericalGrid method) (xnn.cnn.featurizers.voxel.VoxelGrid method) channel_totals() (xnn.gnn.models.aimnet2.AIMNet2 method) charge() (xnn.ffnn.common.frc.ForceField method) charge_energy() (in module xnn.common.models.charge_solve) charge_input() (xnn.dnn.models.hdnnp.HDNNP method) charges_and_parameters() (xnn.dnn.models.hdnnp.HDNNP method) check_generators() (xnn.ffnn.models.dreiding.DreidingForceField method) check_state() (xnn.common.deploy.ase_calculator.XNNCalculator method) Checkpoint (class in xnn.common.models.hub.checkpoint) choose() (in module xnn.common.models.hub.zenodo) citation() (in module xnn.common.models.hub.zenodo) cls() (xnn.ffnn.models.oplslib.OPLSLibrary method) CNN3D (class in xnn.cnn.models.cnn3d) 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) column_table() (xnn.common.models.reciprocal.PhaseColumns method) column_units() (in module xnn.common.benchmark.runner) 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) complex_dtype() (in module xnn.common.models.reciprocal)

composition_matrix() (in module xnn.common.finetune.reference) Config (class in xnn.common.config.schema) config_to_dict() (in module xnn.common.models.hub.checkpoint) conjugate_gradient() (xnn.common.models.dispersion_fast.eeq.FastEEQSystem method) (xnn.common.models.eeq.EEQSystem method) ConsoleLogger (class in xnn.common.train.loggers) constrain() (xnn.common.models.les.LatentEwald method) conv() (xnn.gnn.fast.conv.ConvTensorProduct method) Conv3dBlock (class in xnn.cnn.models.cnn3d) convert_artifact() (in module xnn.gnn.models.aimnet2_foundation) convert_units() (in module xnn.ffnn.common.frc) ConvNetLayer (class in xnn.gnn.models.nequip) ConvTensorProduct (class in xnn.gnn.fast.conv) coordination_numbers() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) core_model() (in module xnn.common.models.hub.checkpoint) (in module xnn.common.models.registry) CosineCutoff (class in xnn.common.featurizers.cutoff) COULOMB_CONSTANT (in module xnn.common.models.electrostatics) coulomb_direct() (in module xnn.common.models.electrostatics) coulomb_dsf() (in module xnn.common.models.electrostatics) coulomb_energy() (xnn.hybrid.models.bamboo.BAMBOO method) coulomb_ewald() (in module xnn.common.models.electrostatics) coulomb_matrices() (xnn.dnn.models.hdnnp.HDNNP method) coulomb_matrix() (in module xnn.common.models.charge_solve) (xnn.common.models.les.EwaldSummation method) coulomb_matvec() (in module xnn.common.models.dispersion_fast.coulomb) COULOMB_METHODS (in module xnn.gnn.models.aimnet2) COULOMB_OPTIONS (in module xnn.gnn.models.aimnet2) coulomb_pme() (in module xnn.common.models.electrostatics) count_parameters() (in module xnn.common.finetune.freeze) COVALENT_RADII (in module xnn.dnn.models.hdnnp) covalent_radii() (in module xnn.common.models.charge_solve) CSVLogger (class in xnn.common.train.loggers) cutoff_function() (in module xnn.dnn.featurizers.acsf) CUTOFF_KINDS (in module xnn.dnn.featurizers.acsf) cutoff_table() (in module xnn.ffnn.models.ffield) CUTOFFS (in module xnn.dnn.common.runner)

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) deactivate() (in module xnn.common.models.fast) DEBYE_EA (in module xnn.hybrid.models.bamboo) decide() (xnn.common.models.fast.AutoPolicy method) dedup_torsion_types() (in module xnn.ffnn.models.ffield) DEFAULT_ALPHA (in module xnn.common.finetune.lora) DEFAULT_COLUMNS (in module xnn.common.data.runner_io) DEFAULT_CUTOFF_EEQ (in module xnn.common.models.d4) default_fields() (in module xnn.cnn.models.base) default_gaussian_widths() (in module xnn.dnn.models.hdnnp) DEFAULT_INIT_STD (in module xnn.common.finetune.lora) default_model_cache_dir() (in module xnn.common.models.hub.cache) default_pair_cutoff() (in module xnn.ffnn.models.ffield) DEFAULT_RANK (in module xnn.common.finetune.lora) default_schedule() (in module xnn.cnn.models.spherical)

default_strides() (in module xnn.cnn.models.base) default_symmetry_functions() (in module xnn.dnn.models.hdnnp) Define (class in xnn.ffnn.common.frc) delta() (xnn.common.finetune.lora.LoRAAdapter method) (xnn.common.finetune.lora.LoRAEquivariantLinear method) DENSE_REUSE_MAX_ATOMS (in module xnn.common.models.eeq) deployment_config() (in module xnn.common.models.registry) DescriptorPotential (class in xnn.dnn.models.base) destroy_process_group() (in module xnn.common.distributed) detect_artifact() (in module xnn.gnn.models.aimnet2_foundation) detect_format() (in module xnn.common.models.hub.formats) DFTD3 (class in xnn.common.models.d3) DFTD4 (class in xnn.common.models.d4) dielectric (xnn.common.models.les.LatentEwald property) dihedral_cos() (in module xnn.ffnn.models.geometry) DimeNet (class in xnn.gnn.models.dimenet) DimeNetPP (class in xnn.gnn.models.dimenet) dipole() (xnn.common.models.les.LatentEwald method) directed_triplets() (in module xnn.gnn.models.dimenet) dispersion() (xnn.common.models.dispersion.DispersionCorrection method) dispersion_energy_per_atom() (xnn.dnn.models.physnet.PhysNet method) DispersionCorrection (class in xnn.common.models.dispersion) downloadable (xnn.common.models.hub.card.ModelCard property) 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

E_ANGSTROM_TO_DEBYE (in module xnn.common.data.hub.units) EarlyStopping (class in xnn.common.train.callbacks) EDGE_BLOCK (in module xnn.common.data.atomic_data) edge_cell_shifts() (in module xnn.common.models.dispersion) 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) eeq_charges_large() (in module xnn.common.models.eeq) EEQReuse (class in xnn.common.models.eeq) EEQSystem (class in xnn.common.models.eeq) ELE_FACTOR (in module xnn.hybrid.models.bamboo) electron_configurations() (in module xnn.hybrid.models.spookynet) electrostatic_energy() (xnn.dnn.models.hdnnp.HDNNP method) electrostatic_energy_per_atom() (xnn.dnn.models.physnet.PhysNet method) element() (xnn.ffnn.models.dreidinglib.DreidingLibrary method) element_filter() (in module xnn.common.finetune.replay) element_of() (in module xnn.ffnn.models.dreidinglib) eligible() (in module xnn.gnn.fast.symmetric_contraction) embed() (xnn.gnn.featurizers.spherical.SphericalHarmonicEdgeEmbedding method) empty() (xnn.ffnn.common.frc.FrcFile class method) enable_eeq_reuse() (in module xnn.common.models.d4) (xnn.common.models.d4.DFTD4 method) energy_labelled() (in module xnn.common.data.dataset) equilibrate() (xnn.gnn.models.aimnet2.AIMNet2 method) equivalent() (xnn.ffnn.common.frc.ForceField method) EquivariantGNN (class in xnn.gnn.models.base) estimate_atomic_energies() (in module xnn.common.finetune.reference) EthanolResponseBuilder (class in xnn.common.data.hub.ethanol_response) euler_to_matrix() (in module xnn.cnn.models.spherical) eval_module (xnn.common.train.trainer.Trainer property) 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) ewald_alpha() (in module xnn.common.models.eeq) ewald_corrections() (in module xnn.common.models.electrostatics) EWALD_EPS (in module xnn.common.models.eeq) ewald_mesh_sizes() (in module xnn.common.models.electrostatics) ewald_parameters() (in module xnn.common.models.electrostatics) ewald_real() (in module xnn.common.models.electrostatics) ewald_reciprocal() (in module xnn.common.models.electrostatics) EwaldSummation (class in xnn.common.models.les) exact_constants() (xnn.gnn.featurizers.radial.BesselRBF method) (xnn.hybrid.featurizers.radial.ExponentialBernsteinRBF method) exact_float64_constants() (in module xnn.gnn.constants) experiment (xnn.common.train.loggers.TensorBoardLogger property) ExpNormalSmearing (class in xnn.transformer.featurizers.radial) ExponentialBernsteinRBF (class in xnn.hybrid.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) extra_repr() (xnn.cnn.featurizers.spherical.SphericalGrid method) (xnn.cnn.featurizers.voxel.VoxelGrid method) (xnn.cnn.models.spherical.S2Convolution method) (xnn.cnn.models.spherical.SO3Convolution method) (xnn.cnn.models.steerable.SteerableConv3d method) (xnn.common.finetune.lora.LoRAAdapter method) (xnn.common.finetune.lora.LoRAEquivariantLinear method)

F

FAST_BLOCK_ENTRIES (in module xnn.common.models.les) FAST_LU_MAX_ATOMS (in module xnn.common.models.dispersion_fast.eeq) fast_modules() (in module xnn.common.models.fast) fast_supported() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) (xnn.common.models.fast.FastPathModule method) (xnn.common.models.les.EwaldSummation method) (xnn.gnn.fast.conv.ConvTensorProduct method) (xnn.gnn.models.mace.SymmetricContraction method) FastEEQSystem (class in xnn.common.models.dispersion_fast.eeq) FastPathModule (class in xnn.common.models.fast) FastPathPrecisionWarning Featurizer (class in xnn.common.featurizers.base) fetch_model() (in module xnn.common.models.hub.loader) fetch_record() (in module xnn.common.models.hub.zenodo) ff_form (xnn.ffnn.common.frc.ForceField property) FFieldLibrary (class in xnn.ffnn.models.ffield) field_dim() (in module xnn.cnn.models.base) field_slices() (in module xnn.cnn.models.steerable) file_references() (in module xnn.common.models.hub.checkpoint) files() (in module xnn.common.models.hub.zenodo) filter_spectrum() (xnn.cnn.models.spherical.S2Convolution method) (xnn.cnn.models.spherical.SO3Convolution method) finalize() (xnn.common.train.loggers.Logger method) (xnn.common.train.loggers.TensorBoardLogger method) find_forcefield() (in module xnn.ffnn.common.frc) find_multihead() (in module xnn.common.finetune.heads) FINETUNE_KEYS (in module xnn.common.models.registry) fit() (xnn.common.train.trainer.Trainer method) fit_atomic_energies() (in module xnn.common.benchmark.energy) fit_basis_map() (in module xnn.gnn.fast.symmetric_contraction) fit_scaling() (xnn.dnn.featurizers.acsf.AtomCenteredSymmetryFunctions method) (xnn.dnn.models.hdnnp.HDNNP method) (xnn.dnn.models.hdnnp.NNP1G method) fit_scaling_factors() (xnn.gnn.models.gemnet.GemNet method) float_dtype() (in module xnn.common.models.hub.checkpoint) 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.featurizers.spherical.SphericalGrid method) (xnn.cnn.featurizers.voxel.VoxelGrid method) (xnn.cnn.models.base.VoxelPotential method) (xnn.cnn.models.cnn3d.Conv3dBlock method) (xnn.cnn.models.spherical.S2Convolution method) (xnn.cnn.models.spherical.SO3Convolution method) (xnn.cnn.models.spherical.SphericalCNN method) (xnn.cnn.models.spherical.SphericalResBlock method) (xnn.cnn.models.steerable.GatedBlock method) (xnn.cnn.models.steerable.SteerableBatchNorm method) (xnn.cnn.models.steerable.SteerableConv3d 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.cutoff.MollifierCutoff method) (xnn.common.featurizers.radial.GaussianRBF method) (xnn.common.finetune.heads.MultiHead method) (xnn.common.finetune.lora.LoRAAdapter method) (xnn.common.finetune.lora.LoRAEquivariantLinear 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.ops.GaussianActivation method) (xnn.common.models.ops.ScaledTanh method) (xnn.common.models.ops.ShiftedSoftplus method) (xnn.common.models.ops.Softplus method) (xnn.common.models.ops.Square method) (xnn.common.models.outputs.ForceStressOutput method) (xnn.dnn.featurizers.acsf.AtomCenteredSymmetryFunctions 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.hdnnp.HDNNP method) (xnn.dnn.models.hdnnp.NNP1G 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.featurizers.spherical_bessel.SphericalBesselBasis method) (xnn.gnn.models.aimnet2.AIMNet2 method) (xnn.gnn.models.aimnet2.ShellConvolution method) (xnn.gnn.models.allegro.Allegro method) (xnn.gnn.models.blocks.RadialNet method) (xnn.gnn.models.blocks.ScalarActivation method) (xnn.gnn.models.cace.CACE method) (xnn.gnn.models.dimenet.DimeNet method) (xnn.gnn.models.gemnet.GemNet method) (xnn.gnn.models.gemnet.ScaleFactor 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.gnn.models.painn.GatedEquivariantBlock method) (xnn.gnn.models.painn.PaiNN method) (xnn.gnn.models.schnet.SchNet method) (xnn.hybrid.featurizers.radial.ExponentialBernsteinRBF method) (xnn.hybrid.models.bamboo.BAMBOO method) (xnn.hybrid.models.bamboo.GETLayer method) (xnn.hybrid.models.dispersion.D3CSODispersion method) (xnn.hybrid.models.spookynet.SpookyNet method) (xnn.hybrid.models.spookynet.Swish method) (xnn.transformer.attention.EdgeMultiheadAttention method) (xnn.transformer.featurizers.radial.ExpNormalSmearing method)

forward_lammps() (xnn.common.deploy.torchscript.TorchScriptPotential method) FOUNDATION_MODELS (in module xnn.gnn.models.aimnet2_foundation) foundation_to_xnn() (in module xnn.gnn.models.aimnet2_foundation) (in module xnn.gnn.models.mace_foundation) fourier_to_rb() (in module xnn.ffnn.models.oplslib) fragment_targets() (in module xnn.common.models.charge_solve) FRC_FORMAT_VERSION (in module xnn.ffnn.common.frc) FrcFile (class in xnn.ffnn.common.frc) freeze_parameters() (in module xnn.common.finetune.freeze) from_aimnet_artifact() (in module xnn.gnn.models.aimnet2_foundation) 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.cnn3d.CNN3D class method) (xnn.cnn.models.spherical.SphericalCNN class method) (xnn.cnn.models.steerable.SteerableCNN class method) (xnn.common.finetune.heads.MultiHead 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.hdnnp.NNP1G 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.aimnet2.AIMNet2 class method) (xnn.gnn.models.allegro.Allegro class method) (xnn.gnn.models.cace.CACE class method) (xnn.gnn.models.dimenet.DimeNet class method) (xnn.gnn.models.dimenet.DimeNetPP class method) (xnn.gnn.models.gemnet.GemNet class method) (xnn.gnn.models.mace.MACE class method) (xnn.gnn.models.nequip.NequIP class method) (xnn.gnn.models.painn.PaiNN class method) (xnn.gnn.models.schnet.SchNet class method) (xnn.hybrid.models.bamboo.BAMBOO class method) (xnn.hybrid.models.spookynet.SpookyNet class method) from_dict() (in module xnn.common.benchmark.config) (in module xnn.common.config.loaders) (xnn.common.models.hub.card.ModelCard class method) 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.aimnet2.AIMNet2 class method) (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_pretrained() (in module xnn.common.models.hub.loader) (xnn.common.deploy.ase_calculator.XNNCalculator class method) (xnn.common.models.base.InteratomicPotential class method) from_reference_checkpoint() (xnn.hybrid.models.spookynet.SpookyNet class method) from_yaml() (in module xnn.common.benchmark.config) (in module xnn.common.config.loaders)

G

gamma (xnn.hybrid.featurizers.radial.ExponentialBernsteinRBF property) GatedBlock (class in xnn.cnn.models.steerable) GatedEquivariantBlock (class in xnn.gnn.models.painn) gaussian_coulomb_matrix() (in module xnn.common.models.charge_solve) gaussian_reference_weights() (in module xnn.common.models.dispersion) GaussianActivation (class in xnn.common.models.ops) GaussianRBF (class in xnn.common.featurizers.radial) GemNet (class in xnn.gnn.models.gemnet) geometric_mean() (in module xnn.ffnn.models.geometry) get_atomic_energies() (in module xnn.common.finetune.reference) get_builder() (in module xnn.common.data.hub.base)

get_card() (in module xnn.common.models.hub.registry) get_format() (in module xnn.common.models.hub.formats) get_metric() (in module xnn.common.benchmark.metrics) GETLayer (class in xnn.hybrid.models.bamboo) global_average_pool() (in module xnn.cnn.models.base) glorot_orthogonal_() (in module xnn.common.models.ops) GNNPotential (class in xnn.gnn.models.base) grid_coordinates() (in module xnn.cnn.models.base) grid_size (xnn.cnn.featurizers.spherical.SphericalGrid property) (xnn.cnn.models.base.VoxelPotential property) guarded_exp() (in module xnn.ffnn.models.reaxff) guess_bonds() (in module xnn.ffnn.models.topology)

H

half_space() (in module xnn.common.models.reciprocal) hardness_of() (xnn.common.models.les.LatentEwald method) HARTREE_KCAL_MOL (in module xnn.hybrid.models.dispersion) HARTREE_TO_EV (in module xnn.common.data.hub.units) has_dispersion() (in module xnn.common.models.hub.checkpoint) has_electrostatics() (in module xnn.common.models.registry) has_lora() (in module xnn.common.finetune.lora) HDNNP (class in xnn.dnn.models.hdnnp)

HDNNP4GBuilder (class in xnn.common.data.hub.hdnnp4g) he_orthogonal_() (in module xnn.gnn.models.gemnet) head_dir() (in module xnn.common.models.hub.cache) head_module_names() (in module xnn.common.finetune.heads) head_names() (in module xnn.common.finetune.heads) head_options() (in module xnn.common.finetune.heads) 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) index() (xnn.common.finetune.heads.MultiHead method) init_process_group() (in module xnn.common.distributed) inject_lora() (in module xnn.common.finetune.lora) inner_graph() (xnn.common.models.dispersion.DispersionCorrection method) inputs() (xnn.dnn.models.hdnnp.NNP1G method) InteractionBlock (class in xnn.gnn.models.nequip) InteratomicPotential (class in xnn.common.models.base)

intra_structure_pairs() (in module xnn.common.models.les) ion_charge_table() (in module xnn.common.models.charge_solve) ION_CHARGES (in module xnn.common.models.charge_solve) is_acceptor() (xnn.ffnn.models.dreidinglib.DreidingLibrary method) is_archive() (in module xnn.common.models.hub.formats) is_cache_key() (in module xnn.common.models.hub.cache) is_distributed() (in module xnn.common.distributed) is_doi() (in module xnn.common.models.hub.zenodo) is_main() (in module xnn.common.distributed) is_nn (xnn.ffnn.models.ffield.FFieldLibrary property) is_ready() (in module xnn.common.models.hub.cache) iter_fast_capable() (in module xnn.common.models.fast) iter_runner_data() (in module xnn.common.data.runner_io)

K

k_set() (xnn.common.models.les.EwaldSummation method) KCAL_MOL_TO_EV (in module xnn.common.data.hub.units) keep_structure_factors (xnn.common.models.dispersion_fast.eeq.FastEEQSystem attribute) (xnn.common.models.eeq.EEQSystem attribute)

kernel() (xnn.cnn.models.steerable.SteerableConv3d method) kinds_of() (xnn.ffnn.common.frc.ForceField method)

L

label() (xnn.common.finetune.heads.MultiHead method) label_head() (in module xnn.common.finetune.heads) lammps_pair_parameters() (in module xnn.ffnn.models.ffield) LAMMPSWrapper (class in xnn.common.deploy.lammps) LATENT_CHARGE_PER_E (in module xnn.common.models.les) LatentEwald (class in xnn.common.models.les) latest() (xnn.ffnn.common.frc.Section method) legacy_c6_table() (in module xnn.common.models.d3) license_id() (in module xnn.common.models.hub.zenodo) list_datasets() (in module xnn.common.data.hub.base) list_forcefields() (in module xnn.ffnn.common.frc) list_models() (in module xnn.common.models.hub.registry) LIVE_BUDGET (in module xnn.common.models.dispersion_fast.eeq) 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.ethanol_response.EthanolResponseBuilder method) (xnn.common.data.hub.hdnnp4g.HDNNP4GBuilder method) (xnn.common.data.hub.lode_dimers.LODEDimersBuilder method) (xnn.common.data.hub.qm7.QM7Builder method) (xnn.common.data.hub.rmd17.RMD17Builder method) (xnn.common.data.hub.spookynet_states.SpookyNetStatesBuilder method) (xnn.common.models.hub.card.ModelCard class method) load_artifact() (in module xnn.gnn.models.aimnet2_foundation) load_checkpoint() (in module xnn.common.models.hub.checkpoint) 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_pretrained() (in module xnn.common.models.hub.loader) load_runner_model() (in module xnn.dnn.common.runner) load_scaling_factors() (xnn.gnn.models.gemnet.GemNet method) load_structures() (in module xnn.common.data.ase_io) LODEDimersBuilder (class in xnn.common.data.hub.lode_dimers) log_hyperparams() (xnn.common.train.loggers.CSVLogger method) (xnn.common.train.loggers.Logger method) (xnn.common.train.loggers.TensorBoardLogger method) log_metrics() (xnn.common.train.loggers.ConsoleLogger method) (xnn.common.train.loggers.CSVLogger method) (xnn.common.train.loggers.Logger method) (xnn.common.train.loggers.TensorBoardLogger method) (xnn.common.train.trainer.Trainer method) Logger (class in xnn.common.train.loggers) LOGGERS (in module xnn.common.train.loggers) LONG_RANGE_METHODS (in module xnn.gnn.models.aimnet2) lora_modules() (in module xnn.common.finetune.lora) lora_options() (in module xnn.common.finetune.lora) lora_parameters() (in module xnn.common.finetune.lora) LoRAAdapter (class in xnn.common.finetune.lora) LoRAEquivariantLinear (class in xnn.common.finetune.lora) LOW_K_VECTORS (in module xnn.common.models.dispersion_fast.eeq) low_pass_filter() (in module xnn.cnn.models.base) LU_MAX_ATOMS (in module xnn.common.models.eeq) lu_solve_implicit() (in module xnn.common.models.eeq) lu_solve_refined() (in module xnn.common.models.eeq) 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) (in module xnn.common.models.hub.cli) make_activation() (in module xnn.common.models.ops) make_section() (in module xnn.ffnn.common.frc) masses (xnn.ffnn.models.dreiding.Dreiding property) (xnn.ffnn.models.opls.OPLS property) match_torsion() (in module xnn.ffnn.models.ffield) matrix_to_euler() (in module xnn.cnn.models.spherical) matvec() (xnn.common.models.dispersion_fast.eeq.FastEEQSystem method) (xnn.common.models.eeq.EEQSystem method) MAX_Z (in module xnn.hybrid.models.spookynet) MDIEngine (class in xnn.common.deploy.mdi_engine) merge() (xnn.common.finetune.lora.LoRAAdapter method) (xnn.common.finetune.lora.LoRAEquivariantLinear method) merge_dicts() (in module xnn.common.distributed) merge_lora() (in module xnn.common.finetune.lora) merge_parts() (in module xnn.common.benchmark.runner) mesh_wavevectors() (in module xnn.common.models.pme) model_card() (in module xnn.common.models.hub.registry) model_dtype (xnn.common.data.atomic_data.AtomicGraph property) ModelCard (class in xnn.common.models.hub.card) ModelCheckpoint (class in xnn.common.train.callbacks) ModelConfig (class in xnn.common.config.schema) ModelEntry (class in xnn.common.benchmark.config) ModelFormat (class in xnn.common.models.hub.formats) modifier() (xnn.ffnn.common.frc.Section method) module xnn.cnn xnn.cnn.featurizers xnn.cnn.featurizers.spherical xnn.cnn.featurizers.voxel xnn.cnn.models xnn.cnn.models.base xnn.cnn.models.cnn3d xnn.cnn.models.spherical xnn.cnn.models.steerable 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.elements 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.ethanol_response xnn.common.data.hub.hdnnp4g xnn.common.data.hub.lode_dimers xnn.common.data.hub.noncovalent xnn.common.data.hub.qm7 xnn.common.data.hub.rmd17 xnn.common.data.hub.spookynet_states xnn.common.data.hub.units xnn.common.data.neighborlist xnn.common.data.runner_io xnn.common.deploy xnn.common.deploy.ase_calculator xnn.common.deploy.lammps xnn.common.deploy.mdi_engine xnn.common.deploy.torchscript xnn.common.distributed xnn.common.featurizers xnn.common.featurizers.base xnn.common.featurizers.cutoff xnn.common.featurizers.radial xnn.common.finetune xnn.common.finetune.freeze xnn.common.finetune.heads xnn.common.finetune.lora xnn.common.finetune.reference xnn.common.finetune.replay xnn.common.models xnn.common.models.base xnn.common.models.charge_solve xnn.common.models.d3 xnn.common.models.d4 xnn.common.models.dispersion xnn.common.models.dispersion_fast xnn.common.models.dispersion_fast.atm xnn.common.models.dispersion_fast.coulomb xnn.common.models.dispersion_fast.eeq xnn.common.models.eeq xnn.common.models.electrostatics xnn.common.models.fast xnn.common.models.hub xnn.common.models.hub.cache xnn.common.models.hub.card xnn.common.models.hub.checkpoint xnn.common.models.hub.cli xnn.common.models.hub.formats xnn.common.models.hub.loader xnn.common.models.hub.registry xnn.common.models.hub.zenodo xnn.common.models.les xnn.common.models.ops xnn.common.models.outputs xnn.common.models.pme xnn.common.models.reciprocal xnn.common.models.recompute xnn.common.models.registry xnn.common.train xnn.common.train.callbacks xnn.common.train.loggers xnn.common.train.losses xnn.common.train.trainer xnn.dnn xnn.dnn.common xnn.dnn.common.runner xnn.dnn.featurizers xnn.dnn.featurizers.acsf 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.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.constants xnn.gnn.fast xnn.gnn.fast.conv xnn.gnn.fast.symmetric_contraction xnn.gnn.featurizers xnn.gnn.featurizers.cartesian xnn.gnn.featurizers.cutoff xnn.gnn.featurizers.radial xnn.gnn.featurizers.spherical xnn.gnn.featurizers.spherical_bessel xnn.gnn.models xnn.gnn.models.aimnet2 xnn.gnn.models.aimnet2_foundation xnn.gnn.models.allegro xnn.gnn.models.base xnn.gnn.models.blocks xnn.gnn.models.cace xnn.gnn.models.dimenet xnn.gnn.models.gemnet xnn.gnn.models.mace xnn.gnn.models.mace_foundation xnn.gnn.models.nequip xnn.gnn.models.painn xnn.gnn.models.schnet xnn.hybrid xnn.hybrid.featurizers xnn.hybrid.featurizers.radial xnn.hybrid.models xnn.hybrid.models.bamboo xnn.hybrid.models.dispersion xnn.hybrid.models.spookynet 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) MollifierCutoff (class in xnn.common.featurizers.cutoff) monitored_value() (in module xnn.common.train.callbacks) mse() (in module xnn.common.benchmark.metrics) MultiHead (class in xnn.common.finetune.heads) multinomial_coefficient() (in module xnn.gnn.featurizers.cartesian)

N

n_atoms (xnn.ffnn.models.topology.MolecularTopology property) n_basis_kernels() (in module xnn.cnn.models.steerable) n_channels (xnn.cnn.featurizers.spherical.SphericalGrid property) (xnn.cnn.featurizers.voxel.VoxelGrid property) (xnn.cnn.models.base.VoxelPotential 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) NNP1G (class in xnn.dnn.models.hdnnp) node_attr() (xnn.gnn.models.base.GNNPotential method) node_energy() (xnn.gnn.models.allegro.Allegro method) (xnn.gnn.models.cace.CACE method) (xnn.gnn.models.dimenet.DimeNet method) (xnn.gnn.models.gemnet.GemNet method) (xnn.gnn.models.mace.MACE method) (xnn.gnn.models.nequip.NequIP method) (xnn.gnn.models.painn.PaiNN method) (xnn.gnn.models.schnet.SchNet method)

node_features_energy() (xnn.cnn.models.base.VoxelPotential method) (xnn.gnn.models.allegro.Allegro method) (xnn.gnn.models.cace.CACE method) (xnn.gnn.models.dimenet.DimeNet method) (xnn.gnn.models.gemnet.GemNet method) (xnn.gnn.models.mace.MACE method) (xnn.gnn.models.nequip.NequIP method) (xnn.gnn.models.painn.PaiNN method) (xnn.gnn.models.schnet.SchNet method) node_features_energy_charges() (xnn.gnn.models.aimnet2.AIMNet2 method) (xnn.hybrid.models.spookynet.SpookyNet 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) normalize_subtracted_dispersion() (in module xnn.common.config.schema) NQE_EPSILON (in module xnn.gnn.models.aimnet2) 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

offline() (in module xnn.common.models.hub.cache) on_epoch_end() (xnn.common.train.callbacks.Callback method) (xnn.common.train.callbacks.EarlyStopping method) (xnn.common.train.callbacks.ModelCheckpoint method) (xnn.common.train.callbacks.ProgressBar method) on_fit_end() (xnn.common.train.callbacks.Callback method) on_fit_start() (xnn.common.train.callbacks.Callback method) (xnn.common.train.callbacks.EarlyStopping method) (xnn.common.train.callbacks.ModelCheckpoint method) on_train_batch_end() (xnn.common.train.callbacks.Callback method) (xnn.common.train.callbacks.ProgressBar method) on_train_end() (xnn.common.train.callbacks.Callback method) (xnn.common.train.callbacks.ModelCheckpoint method) on_train_epoch_start() (xnn.common.train.callbacks.Callback method) (xnn.common.train.callbacks.ProgressBar method) 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) orthogonal_random_features() (in module xnn.hybrid.models.spookynet) out_channels (xnn.cnn.models.steerable.GatedBlock property) output_dim (xnn.cnn.featurizers.spherical.SphericalGrid property) (xnn.cnn.featurizers.voxel.VoxelGrid property) (xnn.common.featurizers.base.Featurizer property) (xnn.dnn.featurizers.acsf.AtomCenteredSymmetryFunctions 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) (xnn.gnn.featurizers.spherical_bessel.SphericalBesselBasis attribute) OutputConfig (class in xnn.common.benchmark.config) oxygen_column() (xnn.ffnn.models.dreidinglib.DreidingLibrary method)

P

PaiNN (class in xnn.gnn.models.painn) pair_c6() (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) pair_edge_keys() (in module xnn.common.models.dispersion) 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() (in module xnn.common.models.hub.zenodo) parse_header() (in module xnn.ffnn.common.frc) parse_input_nn() (in module xnn.dnn.common.runner) parse_version() (in module xnn.ffnn.common.frc) part_tag() (in module xnn.common.benchmark.runner) path (xnn.common.train.loggers.CSVLogger property) 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) periodic_structures() (in module xnn.common.models.les)

PhaseColumns (class in xnn.common.models.reciprocal) phases() (xnn.common.models.reciprocal.PhaseColumns static method) PhysNet (class in xnn.dnn.models.physnet) plan_triplets() (in module xnn.common.models.dispersion_fast.atm) pme_mesh() (in module xnn.common.models.pme) (xnn.common.models.les.EwaldSummation method) pme_reciprocal() (in module xnn.common.models.pme) pme_weighted_sum() (in module xnn.common.models.pme) POINT_BLOCK (in module xnn.cnn.featurizers.spherical) PolynomialCutoff (class in xnn.gnn.featurizers.cutoff) potential() (xnn.cnn.featurizers.spherical.SphericalGrid method) precondition() (xnn.common.models.dispersion_fast.eeq.FastEEQSystem method) predict_energies() (in module xnn.common.finetune.reference) prediction_pairs() (in module xnn.common.benchmark.metrics) prepare_model() (in module xnn.common.models.registry) PretrainedModel (class in xnn.common.models.hub.loader) ProgressBar (class in xnn.common.train.callbacks) pseudolabel() (in module xnn.common.finetune.replay)

Q

QM7Builder (class in xnn.common.data.hub.qm7)

quadrature_weights() (in module xnn.cnn.models.spherical)

R

radial() (xnn.gnn.featurizers.spherical_bessel.SphericalBesselBasis method) RadialNet (class in xnn.gnn.models.blocks) RadialSymmetryFunctions (class in xnn.dnn.featurizers.symmetry_functions) rank() (in module xnn.common.distributed) raw() (xnn.dnn.featurizers.acsf.AtomCenteredSymmetryFunctions method) rb_to_fourier() (in module xnn.ffnn.models.oplslib) read_config() (in module xnn.common.models.hub.checkpoint) 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_runner_data() (in module xnn.common.data.runner_io) read_safetensors() (in module xnn.gnn.models.aimnet2_foundation) read_topology() (in module xnn.ffnn.models.topology) real_spherical_harmonics() (in module xnn.gnn.featurizers.spherical_bessel) 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) realspace_batch() (xnn.common.models.les.EwaldSummation method) realspace_single() (xnn.common.models.les.EwaldSummation method) ReaxFF (class in xnn.ffnn.models.reaxff) reciprocal() (xnn.common.models.les.EwaldSummation method) RECIPROCAL_BUDGET (in module xnn.common.models.electrostatics) reciprocal_fast() (xnn.common.models.les.EwaldSummation method) reciprocal_lattice() (in module xnn.common.models.electrostatics) reciprocal_pme() (xnn.common.models.les.EwaldSummation method) reciprocal_vectors() (in module xnn.common.models.eeq) reciprocal_weights() (in module xnn.common.models.eeq) recompute() (in module xnn.common.models.recompute) RECOMPUTE_MIN_EDGES (in module xnn.gnn.models.blocks) recorded_dispersion() (in module xnn.common.models.registry) Reference (class in xnn.ffnn.common.frc) REFERENCE_MARKERS (in module xnn.common.finetune.reference) reference_markers() (in module xnn.common.finetune.reference) REFERENCE_SETS (in module xnn.common.models.d3) reference_state_dict() (in module xnn.hybrid.models.spookynet) reference_tables() (in module xnn.common.models.d3) reference_weights() (in module xnn.gnn.fast.symmetric_contraction) (xnn.common.models.d3.DFTD3 method) (xnn.common.models.d4.DFTD4 method) references_used() (xnn.ffnn.common.frc.ForceField method)

register_constant() (in module xnn.gnn.constants) register_dataset() (in module xnn.common.data.hub.base) register_format() (in module xnn.common.models.hub.formats) register_key_translation() (in module xnn.common.config.translate) register_lora_target() (in module xnn.common.finetune.lora) register_metric() (in module xnn.common.benchmark.metrics) register_model() (in module xnn.common.models.registry) register_pretrained() (in module xnn.common.models.hub.registry) register_section_schema() (in module xnn.ffnn.common.frc) register_writer() (in module xnn.common.benchmark.report) registered_cards() (in module xnn.common.models.hub.registry) replace_module() (in module xnn.common.models.registry) REPLAY_FILTERS (in module xnn.common.finetune.replay) replicate() (xnn.ffnn.models.topology.MolecularTopology method) representation() (xnn.gnn.models.painn.PaiNN method) reset() (xnn.common.models.eeq.EEQReuse 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_cache_dir() (in module xnn.common.models.hub.cache) 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_dispersion() (in module xnn.common.models.registry) 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) resolve_use_fast() (in module xnn.common.models.fast) restore_exact() (in module xnn.gnn.constants) reverse_edge_permutation() (in module xnn.ffnn.models.reaxff) reverse_edges() (in module xnn.gnn.models.gemnet) RMD17Builder (class in xnn.common.data.hub.rmd17) rmse() (in module xnn.common.benchmark.metrics) rotate_fields() (in module xnn.cnn.models.steerable) rotate_voxels() (in module xnn.cnn.models.base) Row (class in xnn.ffnn.common.frc) ROW_CHUNK (in module xnn.common.models.eeq) 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) run_parallel() (in module xnn.common.benchmark.runner) runner_feature_key() (in module xnn.dnn.common.runner)

S

s2_equatorial_grid() (in module xnn.cnn.models.spherical) s2_grid_points() (in module xnn.cnn.models.spherical) s2_kernel_basis() (in module xnn.cnn.models.spherical) s2_near_identity_grid() (in module xnn.cnn.models.spherical) s2_rotate() (in module xnn.cnn.models.spherical) S2Convolution (class in xnn.cnn.models.spherical) S2Transform (class in xnn.cnn.models.spherical) s6 (xnn.dnn.models.physnet.PhysNet property) s8 (xnn.dnn.models.physnet.PhysNet property) sanitize() (in module xnn.common.models.hub.cache) save() (xnn.common.models.hub.card.ModelCard method) (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) save_pretrained() (in module xnn.common.models.hub.checkpoint) (xnn.common.train.trainer.Trainer method) ScalarActivation (class in xnn.gnn.models.blocks) scale_factors() (xnn.gnn.models.gemnet.GemNet method) scaled_charges() (xnn.dnn.models.physnet.PhysNet method) ScaledTanh (class in xnn.common.models.ops) ScaleFactor (class in xnn.gnn.models.gemnet) scaling() (xnn.dnn.featurizers.acsf.AtomCenteredSymmetryFunctions method) SCALING_MODES (in module xnn.dnn.featurizers.acsf) scan() (in module xnn.common.models.hub.cache) scatter() (xnn.common.models.reciprocal.PhaseColumns method) scatter_sum() (in module xnn.common.models.ops) schema (xnn.ffnn.common.frc.Section property) SchNet (class in xnn.gnn.models.schnet) score() (in module xnn.common.benchmark.metrics) screened() (xnn.common.models.les.LatentEwald method) Section (class in xnn.ffnn.common.frc) sections_for() (xnn.ffnn.common.frc.Define method) segment_sum() (in module xnn.common.models.ops) select() (in module xnn.common.models.fast) (xnn.common.finetune.heads.MultiHead method) select_entries() (in module xnn.common.benchmark.runner) select_regime() (xnn.common.models.d4.DFTD4 method) select_replay() (in module xnn.common.finetune.replay) semi_orthogonal_glorot_weights() (in module xnn.dnn.models.physnet) set_atomic_energies() (in module xnn.common.finetune.reference) (xnn.cnn.models.base.VoxelPotential method) (xnn.common.finetune.heads.MultiHead method) (xnn.gnn.models.base.GNNPotential method) (xnn.gnn.models.dimenet.DimeNet method) (xnn.gnn.models.gemnet.GemNet method) (xnn.gnn.models.painn.PaiNN method) (xnn.gnn.models.schnet.SchNet method) (xnn.hybrid.models.spookynet.SpookyNet method) set_energy_scale_shift() (xnn.cnn.models.base.VoxelPotential method) (xnn.gnn.models.painn.PaiNN method) (xnn.gnn.models.schnet.SchNet method) set_recompute_radial() (in module xnn.gnn.models.blocks) set_use_fast() (in module xnn.common.models.fast) (xnn.common.finetune.heads.MultiHead method) (xnn.common.models.dispersion.DispersionCorrection method) (xnn.common.models.les.LatentEwald method) (xnn.gnn.models.base.EquivariantGNN method)

setup() (xnn.common.train.loggers.CSVLogger method) (xnn.common.train.loggers.Logger method) (xnn.common.train.loggers.TensorBoardLogger method) SF_BUDGET (in module xnn.common.models.eeq) shard_indices() (in module xnn.common.distributed) shell_bandlimits() (in module xnn.cnn.models.steerable) ShellConvolution (class in xnn.gnn.models.aimnet2) shifted_softplus() (in module xnn.common.models.ops) (in module xnn.gnn.models.blocks) ShiftedSoftplus (class in xnn.common.models.ops) smooth_size() (in module xnn.common.models.les) smooth_switch() (in module xnn.hybrid.models.spookynet) so3_alphas() (in module xnn.cnn.models.spherical) so3_betas() (in module xnn.cnn.models.spherical) so3_equatorial_grid() (in module xnn.cnn.models.spherical) so3_integrate() (in module xnn.cnn.models.spherical) so3_kernel_basis() (in module xnn.cnn.models.spherical) so3_near_identity_grid() (in module xnn.cnn.models.spherical) so3_rotate() (in module xnn.cnn.models.spherical) SO3Convolution (class in xnn.cnn.models.spherical) SO3Transform (class in xnn.cnn.models.spherical) SoftDistanceTransform (class in xnn.gnn.featurizers.radial) Softplus (class in xnn.common.models.ops) softplus_inverse() (in module xnn.common.models.ops) solve() (xnn.common.models.eeq.EEQReuse method) solve_augmented() (xnn.common.models.dispersion_fast.eeq.FastEEQSystem method) (xnn.common.models.eeq.EEQSystem method) solve_charges() (in module xnn.common.models.charge_solve) (xnn.common.models.les.LatentEwald method) species (xnn.common.finetune.heads.MultiHead property) species_irreps() (in module xnn.gnn.models.blocks) species_of() (in module xnn.common.finetune.reference) spherical_bessel_jn() (in module xnn.gnn.featurizers.spherical_bessel) spherical_bessel_zeros() (in module xnn.gnn.featurizers.spherical_bessel) SphericalBesselBasis (class in xnn.gnn.featurizers.spherical_bessel) SphericalCNN (class in xnn.cnn.models.spherical) SphericalGrid (class in xnn.cnn.featurizers.spherical) SphericalHarmonicEdgeEmbedding (class in xnn.gnn.featurizers.spherical) SphericalResBlock (class in xnn.cnn.models.spherical) spline_moduli() (in module xnn.common.models.pme) split_wrappers() (in module xnn.common.deploy.torchscript) SpookyNet (class in xnn.hybrid.models.spookynet) SpookyNetStatesBuilder (class in xnn.common.data.hub.spookynet_states) spread_charges() (in module xnn.common.models.pme) Square (class in xnn.common.models.ops) SR_ENVELOPES (in module xnn.gnn.models.aimnet2) steerable_kernel_basis() (in module xnn.cnn.models.steerable) SteerableBatchNorm (class in xnn.cnn.models.steerable) SteerableCNN (class in xnn.cnn.models.steerable) SteerableConv3d (class in xnn.cnn.models.steerable) structure_factors() (in module xnn.common.models.reciprocal) structure_sum() (in module xnn.common.models.ops) structure_to_graph() (in module xnn.common.data.dataset) subset() (xnn.common.data.atomic_data.AtomicGraph method) suffixes() (in module xnn.common.models.hub.formats) Swish (class in xnn.hybrid.models.spookynet) switching_function() (in module xnn.common.models.dispersion) SymmetricContraction (class in xnn.gnn.models.mace) SymmetricContractionKernel (class in xnn.gnn.fast.symmetric_contraction) synthesize() (xnn.cnn.models.spherical.S2Transform method) (xnn.cnn.models.spherical.SO3Transform method)

T

TABLE_BUDGET (in module xnn.common.models.dispersion_fast.eeq) tail_energy() (xnn.common.models.d4.DFTD4 method) tail_integrals() (xnn.common.models.d4.DFTD4 method) 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) TensorBoardLogger (class in xnn.common.train.loggers) terms (xnn.ffnn.common.frc.ForceField property) three_body_energy() (in module xnn.common.models.dispersion) three_body_energy_chunked() (in module xnn.common.models.dispersion) threshold() (xnn.common.models.fast.AutoPolicy method) to() (xnn.common.data.atomic_data.AtomicGraph method) to_config() (xnn.common.benchmark.config.ModelEntry method) to_dict() (xnn.common.models.hub.card.ModelCard 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) TrainerConfig (class in xnn.common.config.schema) translate_model_keys() (in module xnn.common.config.translate) triplet_cache_budget() (in module xnn.common.models.dispersion) triplet_energy() (in module xnn.common.models.dispersion) TripletPlan (class in xnn.common.models.dispersion_fast.atm) triplets() (in module xnn.gnn.models.gemnet) trunk() (xnn.cnn.models.base.VoxelPotential method) (xnn.cnn.models.cnn3d.CNN3D method) (xnn.cnn.models.spherical.SphericalCNN method) (xnn.cnn.models.steerable.SteerableCNN method) 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() (in module xnn.common.models.reciprocal) unit_factor() (in module xnn.ffnn.common.frc)

units() (xnn.ffnn.common.frc.Section method) url_slot() (in module xnn.common.models.hub.cache) using() (xnn.common.finetune.heads.MultiHead method)

V

validate() (xnn.common.config.schema.TrainerConfig method) version_key (xnn.ffnn.common.frc.Row property) VOXEL_BLOCK (in module xnn.cnn.featurizers.voxel)

VoxelGrid (class in xnn.cnn.featurizers.voxel) voxelize() (xnn.cnn.featurizers.voxel.VoxelGrid method) VoxelPotential (class in xnn.cnn.models.base)

W

warn_float32_once() (in module xnn.common.models.fast) weighted_loss() (in module xnn.common.train.losses) wigner_D() (in module xnn.cnn.models.spherical) wigner_d() (in module xnn.cnn.models.spherical) wigner_d_table() (in module xnn.cnn.models.spherical) world_size() (in module xnn.common.distributed) wrapped_state_dict() (in module xnn.common.models.hub.checkpoint) write() (in module xnn.common.benchmark.report) (xnn.ffnn.common.frc.FrcFile method)

write_all() (in module xnn.common.benchmark.report) write_config() (in module xnn.common.models.hub.checkpoint) write_csv() (in module xnn.common.benchmark.report) write_ffield() (in module xnn.ffnn.models.ffield) write_frc() (in module xnn.ffnn.common.frc) write_json() (in module xnn.common.benchmark.report) write_markdown() (in module xnn.common.benchmark.report) write_part() (in module xnn.common.benchmark.runner) write_report() (in module xnn.common.benchmark.runner) write_runner_data() (in module xnn.common.data.runner_io)

X

xnn.cnn module xnn.cnn.featurizers module xnn.cnn.featurizers.spherical module xnn.cnn.featurizers.voxel module xnn.cnn.models module xnn.cnn.models.base module xnn.cnn.models.cnn3d module xnn.cnn.models.spherical module xnn.cnn.models.steerable 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.elements 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.ethanol_response module xnn.common.data.hub.hdnnp4g module xnn.common.data.hub.lode_dimers module xnn.common.data.hub.noncovalent module xnn.common.data.hub.qm7 module xnn.common.data.hub.rmd17 module xnn.common.data.hub.spookynet_states module xnn.common.data.hub.units module xnn.common.data.neighborlist module xnn.common.data.runner_io 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.distributed module xnn.common.featurizers module xnn.common.featurizers.base module xnn.common.featurizers.cutoff module xnn.common.featurizers.radial module xnn.common.finetune module xnn.common.finetune.freeze module xnn.common.finetune.heads module xnn.common.finetune.lora module xnn.common.finetune.reference module xnn.common.finetune.replay module xnn.common.models module xnn.common.models.base module xnn.common.models.charge_solve module xnn.common.models.d3 module xnn.common.models.d4 module xnn.common.models.dispersion module xnn.common.models.dispersion_fast module xnn.common.models.dispersion_fast.atm module xnn.common.models.dispersion_fast.coulomb module xnn.common.models.dispersion_fast.eeq module xnn.common.models.eeq module xnn.common.models.electrostatics module xnn.common.models.fast module xnn.common.models.hub module xnn.common.models.hub.cache module xnn.common.models.hub.card module xnn.common.models.hub.checkpoint module xnn.common.models.hub.cli module

xnn.common.models.hub.formats module xnn.common.models.hub.loader module xnn.common.models.hub.registry module xnn.common.models.hub.zenodo module xnn.common.models.les module xnn.common.models.ops module xnn.common.models.outputs module xnn.common.models.pme module xnn.common.models.reciprocal module xnn.common.models.recompute module xnn.common.models.registry module xnn.common.train module xnn.common.train.callbacks module xnn.common.train.loggers module xnn.common.train.losses module xnn.common.train.trainer module xnn.dnn module xnn.dnn.common module xnn.dnn.common.runner module xnn.dnn.featurizers module xnn.dnn.featurizers.acsf 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.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.constants module xnn.gnn.fast module xnn.gnn.fast.conv module xnn.gnn.fast.symmetric_contraction 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.featurizers.spherical_bessel module xnn.gnn.models module xnn.gnn.models.aimnet2 module xnn.gnn.models.aimnet2_foundation module xnn.gnn.models.allegro module xnn.gnn.models.base module xnn.gnn.models.blocks module xnn.gnn.models.cace module xnn.gnn.models.dimenet module xnn.gnn.models.gemnet module xnn.gnn.models.mace module xnn.gnn.models.mace_foundation module xnn.gnn.models.nequip module xnn.gnn.models.painn module xnn.gnn.models.schnet module xnn.hybrid module xnn.hybrid.featurizers module xnn.hybrid.featurizers.radial module xnn.hybrid.models module xnn.hybrid.models.bamboo module xnn.hybrid.models.dispersion module xnn.hybrid.models.spookynet 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)

Z

zonal_harmonics() (in module xnn.gnn.featurizers.spherical_bessel)