Index _ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ __init__() (enerzyme.data.datahub.DataHub method) (enerzyme.data.datahub.FieldDataset method) (enerzyme.data.datahub.SingleDataHub method) (enerzyme.data.supplier.PickleSupplier method) (enerzyme.data.supplier.SDFSupplier method) (enerzyme.data.supplier.Supplier method) (enerzyme.data.transform.AtomicEnergyTransform method) (enerzyme.data.transform.BaseTransform method) (enerzyme.data.transform.NegativeGradientTransform method) (enerzyme.data.transform.TotalEnergyNormalization method) (enerzyme.data.transform.Transform method) (enerzyme.models.activation.BaseScaledTemperedActivation method) (enerzyme.models.activation.ShiftedSoftplus method) (enerzyme.models.activation.Swish method) (enerzyme.models.blocks.attention.Attention method) (enerzyme.models.blocks.mlp.DenseLayer method) (enerzyme.models.blocks.mlp.NeuronLayer method) (enerzyme.models.blocks.mlp.ResidualLayer method) (enerzyme.models.blocks.mlp.ResidualMLP method) (enerzyme.models.blocks.mlp.ResidualStack method) (enerzyme.models.ff.BaseFFLauncher method) (enerzyme.models.ff.FF_committee method) (enerzyme.models.ff.FF_single method) (enerzyme.models.ff.FFDataset method) (enerzyme.models.ff.MetaStateDict method) (enerzyme.models.irreps_tools.reshape_irreps method) (enerzyme.models.layers.atom_embedding.BaseAtomEmbedding method) (enerzyme.models.layers.atom_embedding.NuclearEmbedding method) (enerzyme.models.layers.atom_embedding.RandomAtomEmbedding method) (enerzyme.models.layers.denormalize.AtomicAffineLayer method) (enerzyme.models.layers.dispersion.grimme_d3.GrimmeD3EnergyLayer method) (enerzyme.models.layers.dispersion.grimme_d4.GrimmeD4EnergyLayer method) (enerzyme.models.layers.electron_embedding.BaseElectronEmbedding method) (enerzyme.models.layers.electron_embedding.ElectronicEmbedding method) (enerzyme.models.layers.electron_embedding.NonlinearElectronicEmbedding method) (enerzyme.models.layers.electrostatics.AtomicCharge2DipoleLayer method) (enerzyme.models.layers.electrostatics.ChargeConservationLayer method) (enerzyme.models.layers.electrostatics.ElectrostaticEnergyLayer method) (enerzyme.models.layers.gather_embedding.GatherAtomEmbedding method) (enerzyme.models.layers.geometry.DistanceLayer method) (enerzyme.models.layers.geometry.RadiusGraphLayer method) (enerzyme.models.layers.geometry.RangeSeparationLayer method) (enerzyme.models.layers.gradient.EnergyVarianceGradientLayer method) (enerzyme.models.layers.gradient.ForceLayer method) (enerzyme.models.layers.rbf.BaseRBF method) (enerzyme.models.layers.rbf.BernsteinRBFLayer method) (enerzyme.models.layers.rbf.BesselRBFLayer method) (enerzyme.models.layers.rbf.ExponentialBernsteinRBFLayer method) (enerzyme.models.layers.rbf.ExponentialGaussianRBFLayer method) (enerzyme.models.layers.rbf.ExponentialRBF method) (enerzyme.models.layers.rbf.GaussianRBFLayer method) (enerzyme.models.layers.rbf.GaussianSmearing method) (enerzyme.models.layers.rbf.SincRBFLayer method) (enerzyme.models.layers.reduce.EnergyReduceLayer method) (enerzyme.models.layers.reduce.ShallowEnsembleReduceLayer method) (enerzyme.models.layers.scalar_embedding.ScalarDenseEmbedding method) (enerzyme.models.layers.scalar_embedding.ScalarEmbedding method) (enerzyme.models.layers.scalar_embedding.ScalarResidualMLPEmbedding method) (enerzyme.models.layers.zbl.ZBLRepulsionEnergyLayer method) (enerzyme.models.leftnet.core.aggregate_pos method) (enerzyme.models.leftnet.core.EquiMessagePassing method) (enerzyme.models.leftnet.core.EquiOutput method) (enerzyme.models.leftnet.core.FTE method) (enerzyme.models.leftnet.core.GatedEquivariantBlock method) (enerzyme.models.leftnet.core.LEFTNet method) (enerzyme.models.leftnet.core.NeighborEmb method) (enerzyme.models.leftnet.core.rbf_emb method) (enerzyme.models.leftnet.core.S_vector method) (enerzyme.models.loss.CRPSLoss method) (enerzyme.models.loss.L2Penalty method) (enerzyme.models.loss.MAELoss method) (enerzyme.models.loss.MSELoss method) (enerzyme.models.loss.NLLLoss method) (enerzyme.models.loss.NLLLossVarOnly method) (enerzyme.models.loss.RMSELoss method) (enerzyme.models.loss.WeightedLoss method) (enerzyme.models.mace.core.MACECore method) (enerzyme.models.mace.core.MACEWrapper method) (enerzyme.models.mace.interaction.AgnosticNonlinearInteractionBlock method) (enerzyme.models.mace.interaction.Contraction method) (enerzyme.models.mace.interaction.EquivariantProductBasisBlock method) (enerzyme.models.mace.interaction.InteractionBlock method) (enerzyme.models.mace.interaction.LinearReadoutBlock method) (enerzyme.models.mace.interaction.NonLinearReadoutBlock method) (enerzyme.models.mace.interaction.RealAgnosticAttResidualInteractionBlock method) (enerzyme.models.mace.interaction.RealAgnosticInteractionBlock method) (enerzyme.models.mace.interaction.RealAgnosticResidualInteractionBlock method) (enerzyme.models.mace.interaction.ResidualElementDependentInteractionBlock method) (enerzyme.models.mace.interaction.SymmetricContraction method) (enerzyme.models.mace.interaction.TensorProductWeightsBlock method) (enerzyme.models.modelhub.ModelHub method) (enerzyme.models.nequip.core.NequIPWrapper method) (enerzyme.models.physnet.core.PhysNetCore method) (enerzyme.models.physnet.interaction.InteractionBlock method) (enerzyme.models.physnet.interaction.InteractionLayer method) (enerzyme.models.physnet.loss.NHLoss method) (enerzyme.models.schnet.core.SchNetCore method) (enerzyme.models.schnet.interaction.CFConv method) (enerzyme.models.schnet.interaction.InteractionBlock method) (enerzyme.models.spookynet.core.SpookyNetCore method) (enerzyme.models.spookynet.interaction.InteractionModule method) (enerzyme.models.spookynet.interaction.LocalInteraction method) (enerzyme.models.spookynet.interaction.NonlocalInteraction method) (enerzyme.models.xpainn.core.XPaiNNWrapper method) (enerzyme.qm.qm_driver.QMDriver method) (enerzyme.qm.qm_driver.TeraChemDriver method) (enerzyme.tasks.calculator.ASECalculator method) (enerzyme.tasks.extractor.Extractor method) (enerzyme.tasks.lightning_utils.CollectOutputCallback method) (enerzyme.tasks.lightning_utils.EMACallback method) (enerzyme.tasks.lightning_utils.LightningModel method) (enerzyme.tasks.lightning_utils.MonitorCallback method) (enerzyme.tasks.metrics.Metrics method) (enerzyme.tasks.monitor.Monitor method) (enerzyme.tasks.server.Server method) (enerzyme.tasks.simulator.Simulation method) (enerzyme.tasks.splitter.RandomSplit method) (enerzyme.tasks.splitter.Splitter method) (enerzyme.tasks.trainer.Trainer method) (enerzyme.utils.base_logger.Logger method) (enerzyme.utils.config_handler.YamlHandler method) A activation_fn() (enerzyme.models.activation.BaseScaledTemperedActivation method) (enerzyme.models.activation.ShiftedSoftplus method) (enerzyme.models.activation.Swish method) active_learn() (enerzyme.models.ff.BaseFFLauncher method) addict2dict() (in module enerzyme.utils.config_handler) aggregate() (enerzyme.models.leftnet.core.EquiMessagePassing method) aggregate_pos (class in enerzyme.models.leftnet.core) AgnosticNonlinearInteractionBlock (class in enerzyme.models.mace.interaction) AgnosticResidualNonlinearInteractionBlock (class in enerzyme.models.mace.interaction) array_padding() (in module enerzyme.data.datahub) ASECalculator (class in enerzyme.tasks.calculator) AtomicAffineLayer (class in enerzyme.models.layers.denormalize) AtomicCharge2DipoleLayer (class in enerzyme.models.layers.electrostatics) AtomicEnergyTransform (class in enerzyme.data.transform) Attention (class in enerzyme.models.blocks.attention) B BaseAtomEmbedding (class in enerzyme.models.layers.atom_embedding) BaseElectronEmbedding (class in enerzyme.models.layers.electron_embedding) BaseFFLauncher (class in enerzyme.models.ff) BaseRBF (class in enerzyme.models.layers.rbf) BaseScaledTemperedActivation (class in enerzyme.models.activation) BaseTransform (class in enerzyme.data.transform) BernsteinRBFLayer (class in enerzyme.models.layers.rbf) BesselRBFLayer (class in enerzyme.models.layers.rbf) bias_default() (in module enerzyme.models.physnet.interaction) bond_with_template() (in module enerzyme.bond.bond) build() (enerzyme.models.leftnet.core.LEFTNet method) (enerzyme.models.mace.core.MACECore method) (enerzyme.models.mace.core.MACEWrapper method) (enerzyme.models.nequip.core.NequIPWrapper method) (enerzyme.models.physnet.core.PhysNetCore method) (enerzyme.models.schnet.core.SchNetCore method) (enerzyme.models.spookynet.core.SpookyNetCore method) (enerzyme.models.xpainn.core.XPaiNNWrapper method) build_affine() (enerzyme.models.layers.denormalize.AtomicAffineLayer method) build_Fa_picking() (in module enerzyme.tasks.picker) build_fragment() (enerzyme.tasks.extractor.Extractor method) build_layer() (in module enerzyme.models.ff) build_model() (in module enerzyme.models.ff) build_single_metric() (in module enerzyme.tasks.metrics) bump_transition() (in module enerzyme.models.cutoff) C cal_judge_score() (enerzyme.tasks.metrics.Metrics method) cal_metric() (enerzyme.tasks.metrics.Metrics method) cal_single_metric() (enerzyme.tasks.metrics.Metrics method) calculate() (enerzyme.tasks.calculator.ASECalculator method) (enerzyme.tasks.server.Server method) CFConv (class in enerzyme.models.schnet.interaction) ChargeConservationLayer (class in enerzyme.models.layers.electrostatics) check_and_reshape_cell() (in module enerzyme.models.leftnet.core) collect() (enerzyme.tasks.monitor.Monitor method) collect_results() (enerzyme.qm.qm_driver.QMDriver method) (enerzyme.qm.qm_driver.TeraChemDriver method) CollectOutputCallback (class in enerzyme.tasks.lightning_utils) compare_path() (in module enerzyme.models.modelhub) configure_callbacks() (enerzyme.tasks.lightning_utils.LightningModel method) configure_optimizers() (enerzyme.tasks.lightning_utils.LightningModel method) Contraction (class in enerzyme.models.mace.interaction) copy_files() (enerzyme.qm.qm_driver.QMDriver method) count_parameters() (enerzyme.models.ff.BaseFFLauncher method) CRPSLoss (class in enerzyme.models.loss) D DataHub (class in enerzyme.data.datahub) decorate_batch_input() (enerzyme.tasks.trainer.Trainer method) decorate_batch_output() (enerzyme.tasks.trainer.Trainer method) DenseLayer (class in enerzyme.models.blocks.mlp) DenseLayer() (in module enerzyme.models.physnet.interaction) DistanceLayer (class in enerzyme.models.layers.geometry) dump() (enerzyme.models.ff.BaseFFLauncher method) (enerzyme.models.ff.MetaStateDict method) dump_results() (enerzyme.qm.qm_driver.QMDriver method) E edisp() (in module enerzyme.models.layers.dispersion.grimme_d3) ElectronicEmbedding (class in enerzyme.models.layers.electron_embedding) ElectrostaticEnergyLayer (class in enerzyme.models.layers.electrostatics) EMACallback (class in enerzyme.tasks.lightning_utils) EnergyReduceLayer (class in enerzyme.models.layers.reduce) EnergyVarianceGradientLayer (class in enerzyme.models.layers.gradient) enerzyme.bond module enerzyme.bond.bond module enerzyme.data module enerzyme.data.datahub module enerzyme.data.datatype module enerzyme.data.neighbor_list module enerzyme.data.supplier module enerzyme.data.transform module enerzyme.models module enerzyme.models.activation module enerzyme.models.blocks module enerzyme.models.blocks.attention module enerzyme.models.blocks.mlp module enerzyme.models.cutoff module enerzyme.models.ff module enerzyme.models.functional module enerzyme.models.init module enerzyme.models.irreps_tools module enerzyme.models.layers module enerzyme.models.layers.atom_embedding module enerzyme.models.layers.denormalize module enerzyme.models.layers.dispersion module enerzyme.models.layers.dispersion.grimme_d3 module enerzyme.models.layers.dispersion.grimme_d4 module enerzyme.models.layers.electron_embedding module enerzyme.models.layers.electrostatics module enerzyme.models.layers.gather_embedding module enerzyme.models.layers.geometry module enerzyme.models.layers.gradient module enerzyme.models.layers.rbf module enerzyme.models.layers.reduce module enerzyme.models.layers.scalar_embedding module enerzyme.models.layers.zbl module enerzyme.models.leftnet module enerzyme.models.leftnet.core module enerzyme.models.loss module enerzyme.models.mace module enerzyme.models.mace.core module enerzyme.models.mace.interaction module enerzyme.models.modelhub module enerzyme.models.nequip module enerzyme.models.nequip.core module enerzyme.models.physnet module enerzyme.models.physnet.core module enerzyme.models.physnet.interaction module enerzyme.models.physnet.loss module enerzyme.models.schnet module enerzyme.models.schnet.core module enerzyme.models.schnet.interaction module enerzyme.models.special module enerzyme.models.spookynet module enerzyme.models.spookynet.core module enerzyme.models.spookynet.interaction module enerzyme.models.xpainn module enerzyme.models.xpainn.core module enerzyme.qm module enerzyme.qm.qm_driver module enerzyme.tasks module enerzyme.tasks.batch module enerzyme.tasks.calculator module enerzyme.tasks.extractor module enerzyme.tasks.lightning_utils module enerzyme.tasks.metrics module enerzyme.tasks.monitor module enerzyme.tasks.optimizer module enerzyme.tasks.picker module enerzyme.tasks.server module enerzyme.tasks.simulator module enerzyme.tasks.splitter module enerzyme.tasks.trainer module enerzyme.utils module enerzyme.utils.base_logger module enerzyme.utils.config_handler module enerzyme.utils.util module EquiMessagePassing (class in enerzyme.models.leftnet.core) EquiOutput (class in enerzyme.models.leftnet.core) EquivariantProductBasisBlock (class in enerzyme.models.mace.interaction) evaluate() (enerzyme.models.ff.BaseFFLauncher method) expand_with_indices() (enerzyme.models.ff.FFDataset method) ExponentialBernsteinRBFLayer (class in enerzyme.models.layers.rbf) ExponentialGaussianRBFLayer (class in enerzyme.models.layers.rbf) ExponentialRBF (class in enerzyme.models.layers.rbf) extract_submol() (in module enerzyme.tasks.extractor) extract_submol_with_center() (in module enerzyme.tasks.extractor) Extractor (class in enerzyme.tasks.extractor) F features (enerzyme.data.datahub.DataHub property) (enerzyme.data.datahub.SingleDataHub property) FF_committee (class in enerzyme.models.ff) FF_single (class in enerzyme.models.ff) FFDataset (class in enerzyme.models.ff) FieldDataset (class in enerzyme.data.datahub) filter() (enerzyme.utils.base_logger.PackagePathFilter method) fit_predict() (enerzyme.tasks.trainer.Trainer method) ForceLayer (class in enerzyme.models.layers.gradient) forward() (enerzyme.models.activation.BaseScaledTemperedActivation method) (enerzyme.models.blocks.attention.Attention method) (enerzyme.models.blocks.mlp.DenseLayer method) (enerzyme.models.blocks.mlp.ResidualLayer method) (enerzyme.models.blocks.mlp.ResidualMLP method) (enerzyme.models.blocks.mlp.ResidualStack method) (enerzyme.models.irreps_tools.reshape_irreps method) (enerzyme.models.leftnet.core.aggregate_pos method) (enerzyme.models.leftnet.core.EquiMessagePassing method) (enerzyme.models.leftnet.core.EquiOutput method) (enerzyme.models.leftnet.core.FTE method) (enerzyme.models.leftnet.core.GatedEquivariantBlock method) (enerzyme.models.leftnet.core.NeighborEmb method) (enerzyme.models.leftnet.core.rbf_emb method) (enerzyme.models.leftnet.core.S_vector method) (enerzyme.models.mace.interaction.AgnosticNonlinearInteractionBlock method) (enerzyme.models.mace.interaction.AgnosticResidualNonlinearInteractionBlock method) (enerzyme.models.mace.interaction.Contraction method) (enerzyme.models.mace.interaction.EquivariantProductBasisBlock method) (enerzyme.models.mace.interaction.InteractionBlock method) (enerzyme.models.mace.interaction.LinearReadoutBlock method) (enerzyme.models.mace.interaction.NonLinearReadoutBlock method) (enerzyme.models.mace.interaction.RealAgnosticAttResidualInteractionBlock method) (enerzyme.models.mace.interaction.RealAgnosticInteractionBlock method) (enerzyme.models.mace.interaction.RealAgnosticResidualInteractionBlock method) (enerzyme.models.mace.interaction.ResidualElementDependentInteractionBlock method) (enerzyme.models.mace.interaction.SymmetricContraction method) (enerzyme.models.mace.interaction.TensorProductWeightsBlock method) (enerzyme.models.physnet.interaction.InteractionBlock method) (enerzyme.models.physnet.interaction.InteractionLayer method) (enerzyme.models.schnet.interaction.CFConv method) (enerzyme.models.schnet.interaction.InteractionBlock method) (enerzyme.models.spookynet.interaction.InteractionModule method) (enerzyme.models.spookynet.interaction.LocalInteraction method) (enerzyme.models.spookynet.interaction.NonlocalInteraction method) FTE (class in enerzyme.models.leftnet.core) full_neighbor_list() (in module enerzyme.data.neighbor_list) G GatedEquivariantBlock (class in enerzyme.models.leftnet.core) gather_nd() (in module enerzyme.models.functional) GatherAtomEmbedding (class in enerzyme.models.layers.gather_embedding) GaussianRBFLayer (class in enerzyme.models.layers.rbf) GaussianSmearing (class in enerzyme.models.layers.rbf) get_activation_fn() (in module enerzyme.models.activation) get_all_possible_paths() (in module enerzyme.models.modelhub) get_all_possible_paths_with_rank() (in module enerzyme.models.modelhub) get_atom_embedding() (enerzyme.models.layers.atom_embedding.BaseAtomEmbedding method) get_atom_map() (in module enerzyme.bond.bond) get_berstein_coefficient() (in module enerzyme.models.special) get_bond_lengths() (in module enerzyme.tasks.extractor) get_calculator() (in module enerzyme.tasks.calculator) get_E_disp_a() (enerzyme.models.layers.dispersion.grimme_d3.GrimmeD3EnergyLayer method) (enerzyme.models.layers.dispersion.grimme_d4.GrimmeD4EnergyLayer method) get_E_ele_a() (enerzyme.models.layers.electrostatics.ElectrostaticEnergyLayer method) get_E_var_grad() (enerzyme.models.layers.gradient.EnergyVarianceGradientLayer method) get_E_zbl_a() (enerzyme.models.layers.zbl.ZBLRepulsionEnergyLayer method) get_Ea() (enerzyme.models.layers.denormalize.AtomicAffineLayer method) get_electron_embedding() (enerzyme.models.layers.electron_embedding.BaseElectronEmbedding method) (enerzyme.models.layers.electron_embedding.ElectronicEmbedding method) (enerzyme.models.layers.electron_embedding.NonlinearElectronicEmbedding method) get_embedding() (enerzyme.models.layers.atom_embedding.BaseAtomEmbedding method) (enerzyme.models.layers.atom_embedding.NuclearEmbedding method) (enerzyme.models.layers.atom_embedding.RandomAtomEmbedding method) get_Fa() (enerzyme.models.layers.gradient.ForceLayer method) get_ff_core() (in module enerzyme.models.ff) get_handle() (enerzyme.data.datahub.SingleDataHub method) get_logger() (enerzyme.utils.base_logger.Logger method) get_M2() (enerzyme.models.layers.electrostatics.AtomicCharge2DipoleLayer method) get_max_neighbors_mask() (in module enerzyme.models.leftnet.core) get_model_str() (in module enerzyme.models.modelhub) get_optimizer() (in module enerzyme.tasks.optimizer) (in module enerzyme.tasks.simulator) get_optimizer_config() (in module enerzyme.tasks.optimizer) get_output() (enerzyme.models.layers.electrostatics.ChargeConservationLayer method) (enerzyme.models.layers.gather_embedding.GatherAtomEmbedding method) (enerzyme.models.layers.geometry.DistanceLayer method) (enerzyme.models.layers.geometry.RadiusGraphLayer method) (enerzyme.models.layers.geometry.RangeSeparationLayer method) (enerzyme.models.layers.reduce.EnergyReduceLayer method) (enerzyme.models.layers.reduce.ShallowEnsembleReduceLayer method) (enerzyme.models.layers.scalar_embedding.ScalarEmbedding method) (enerzyme.models.leftnet.core.LEFTNet method) (enerzyme.models.mace.core.MACECore method) (enerzyme.models.mace.core.MACEWrapper method) (enerzyme.models.nequip.core.NequIPWrapper method) (enerzyme.models.physnet.core.PhysNetCore method) (enerzyme.models.schnet.core.SchNetCore method) (enerzyme.models.spookynet.core.SpookyNetCore method) (enerzyme.models.xpainn.core.XPaiNNWrapper method) get_package() (enerzyme.data.supplier.Supplier method) get_pbc_distances() (in module enerzyme.models.leftnet.core) get_pretrain_path() (in module enerzyme.models.modelhub) get_Qa() (enerzyme.models.layers.denormalize.AtomicAffineLayer method) get_rbf() (enerzyme.models.layers.rbf.BaseRBF method) (enerzyme.models.layers.rbf.GaussianSmearing method) get_relevant_input_fields() (enerzyme.models.layers.gather_embedding.GatherAtomEmbedding method) (enerzyme.models.layers.reduce.EnergyReduceLayer method) get_split() (enerzyme.tasks.splitter.Splitter method) get_supplier() (in module enerzyme.data.supplier) get_tensor_rank() (in module enerzyme.data.datatype) GrimmeD3EnergyLayer (class in enerzyme.models.layers.dispersion.grimme_d3) GrimmeD4EnergyLayer (class in enerzyme.models.layers.dispersion.grimme_d4) H hash_model_name() (in module enerzyme.utils.util) I implemented_properties (enerzyme.tasks.calculator.ASECalculator attribute) inner_fn() (enerzyme.models.layers.rbf.ExponentialBernsteinRBFLayer method) (enerzyme.models.layers.rbf.ExponentialGaussianRBFLayer method) (enerzyme.models.layers.rbf.ExponentialRBF method) InteractionBlock (class in enerzyme.models.mace.interaction) (class in enerzyme.models.physnet.interaction) (class in enerzyme.models.schnet.interaction) InteractionLayer (class in enerzyme.models.physnet.interaction) InteractionModule (class in enerzyme.models.spookynet.interaction) inverse_transform() (enerzyme.data.transform.BaseTransform method) (enerzyme.data.transform.Transform method) invoke_qm() (enerzyme.qm.qm_driver.QMDriver method) (enerzyme.qm.qm_driver.TeraChemDriver method) is_atomic() (in module enerzyme.data.datatype) is_grad() (in module enerzyme.data.datatype) is_idx() (in module enerzyme.data.datatype) is_int() (in module enerzyme.data.datatype) is_rounded() (in module enerzyme.data.datatype) is_target() (in module enerzyme.data.datatype) is_target_uq() (in module enerzyme.data.datatype) items() (enerzyme.data.datahub.FieldDataset method) K keys() (enerzyme.data.datahub.FieldDataset method) L l2loss() (enerzyme.models.blocks.mlp.DenseLayer method) L2Penalty (class in enerzyme.models.loss) LEFTNet (class in enerzyme.models.leftnet.core) LightningModel (class in enerzyme.tasks.lightning_utils) linear_out_irreps() (in module enerzyme.models.irreps_tools) LinearReadoutBlock (class in enerzyme.models.mace.interaction) load() (enerzyme.models.ff.MetaStateDict method) load_atomic_energy() (in module enerzyme.data.transform) load_from_pickle() (in module enerzyme.data.datahub) load_state_dict() (enerzyme.tasks.lightning_utils.EMACallback method) (enerzyme.tasks.trainer.Trainer method) load_subset() (enerzyme.data.datahub.FieldDataset method) loc() (enerzyme.data.datahub.FieldDataset method) LocalInteraction (class in enerzyme.models.spookynet.interaction) Logger (class in enerzyme.utils.base_logger) loss_fn() (enerzyme.models.loss.CRPSLoss method) (enerzyme.models.loss.MAELoss method) (enerzyme.models.loss.MSELoss method) (enerzyme.models.loss.NLLLoss method) (enerzyme.models.loss.NLLLossVarOnly method) (enerzyme.models.loss.RMSELoss method) (enerzyme.models.loss.WeightedLoss method) M MACECore (class in enerzyme.models.mace.core) MACEWrapper (class in enerzyme.models.mace.core) MAELoss (class in enerzyme.models.loss) make_input() (enerzyme.qm.qm_driver.QMDriver method) (enerzyme.qm.qm_driver.TeraChemDriver method) make_xyz_block() (in module enerzyme.tasks.extractor) message() (enerzyme.models.leftnet.core.EquiMessagePassing method) (enerzyme.models.leftnet.core.NeighborEmb method) (enerzyme.models.leftnet.core.S_vector method) (enerzyme.models.schnet.interaction.CFConv method) MetaStateDict (class in enerzyme.models.ff) Metrics (class in enerzyme.tasks.metrics) model_name_generation() (in module enerzyme.utils.util) ModelHub (class in enerzyme.models.modelhub) module enerzyme.bond enerzyme.bond.bond enerzyme.data enerzyme.data.datahub enerzyme.data.datatype enerzyme.data.neighbor_list enerzyme.data.supplier enerzyme.data.transform enerzyme.models enerzyme.models.activation enerzyme.models.blocks enerzyme.models.blocks.attention enerzyme.models.blocks.mlp enerzyme.models.cutoff enerzyme.models.ff enerzyme.models.functional enerzyme.models.init enerzyme.models.irreps_tools enerzyme.models.layers enerzyme.models.layers.atom_embedding enerzyme.models.layers.denormalize enerzyme.models.layers.dispersion enerzyme.models.layers.dispersion.grimme_d3 enerzyme.models.layers.dispersion.grimme_d4 enerzyme.models.layers.electron_embedding enerzyme.models.layers.electrostatics enerzyme.models.layers.gather_embedding enerzyme.models.layers.geometry enerzyme.models.layers.gradient enerzyme.models.layers.rbf enerzyme.models.layers.reduce enerzyme.models.layers.scalar_embedding enerzyme.models.layers.zbl enerzyme.models.leftnet enerzyme.models.leftnet.core enerzyme.models.loss enerzyme.models.mace enerzyme.models.mace.core enerzyme.models.mace.interaction enerzyme.models.modelhub enerzyme.models.nequip enerzyme.models.nequip.core enerzyme.models.physnet enerzyme.models.physnet.core enerzyme.models.physnet.interaction enerzyme.models.physnet.loss enerzyme.models.schnet enerzyme.models.schnet.core enerzyme.models.schnet.interaction enerzyme.models.special enerzyme.models.spookynet enerzyme.models.spookynet.core enerzyme.models.spookynet.interaction enerzyme.models.xpainn enerzyme.models.xpainn.core enerzyme.qm enerzyme.qm.qm_driver enerzyme.tasks enerzyme.tasks.batch enerzyme.tasks.calculator enerzyme.tasks.extractor enerzyme.tasks.lightning_utils enerzyme.tasks.metrics enerzyme.tasks.monitor enerzyme.tasks.optimizer enerzyme.tasks.picker enerzyme.tasks.server enerzyme.tasks.simulator enerzyme.tasks.splitter enerzyme.tasks.trainer enerzyme.utils enerzyme.utils.base_logger enerzyme.utils.config_handler enerzyme.utils.util Monitor (class in enerzyme.tasks.monitor) MonitorCallback (class in enerzyme.tasks.lightning_utils) MSELoss (class in enerzyme.models.loss) N name (enerzyme.data.supplier.Supplier attribute) NegativeGradientTransform (class in enerzyme.data.transform) NeighborEmb (class in enerzyme.models.leftnet.core) NequIPWrapper (class in enerzyme.models.nequip.core) NeuronLayer (class in enerzyme.models.blocks.mlp) NHLoss (class in enerzyme.models.physnet.loss) NLLLoss (class in enerzyme.models.loss) NLLLossVarOnly (class in enerzyme.models.loss) NonlinearElectronicEmbedding (class in enerzyme.models.layers.electron_embedding) NonLinearReadoutBlock (class in enerzyme.models.mace.interaction) NonlocalInteraction (class in enerzyme.models.spookynet.interaction) NuclearEmbedding (class in enerzyme.models.layers.atom_embedding) num_params (enerzyme.models.leftnet.core.LEFTNet property) O on_test_batch_end() (enerzyme.tasks.lightning_utils.CollectOutputCallback method) (enerzyme.tasks.lightning_utils.MonitorCallback method) on_test_epoch_end() (enerzyme.tasks.lightning_utils.CollectOutputCallback method) (enerzyme.tasks.lightning_utils.EMACallback method) (enerzyme.tasks.lightning_utils.MonitorCallback method) on_test_epoch_start() (enerzyme.tasks.lightning_utils.EMACallback method) on_train_batch_end() (enerzyme.tasks.lightning_utils.EMACallback method) on_validation_batch_end() (enerzyme.tasks.lightning_utils.CollectOutputCallback method) (enerzyme.tasks.lightning_utils.MonitorCallback method) on_validation_epoch_end() (enerzyme.tasks.lightning_utils.CollectOutputCallback method) (enerzyme.tasks.lightning_utils.EMACallback method) (enerzyme.tasks.lightning_utils.MonitorCallback method) on_validation_epoch_start() (enerzyme.tasks.lightning_utils.EMACallback method) ORCADriver (class in enerzyme.qm.qm_driver) OutputBlock() (in module enerzyme.models.physnet.interaction) P PackagePathFilter (class in enerzyme.utils.base_logger) parse_Za() (in module enerzyme.data.transform) path_resolve() (in module enerzyme.models.modelhub) pdb2mol() (in module enerzyme.bond.bond) PhysNetCore (class in enerzyme.models.physnet.core) PickleSupplier (class in enerzyme.data.supplier) polynomial_transition() (in module enerzyme.models.cutoff) predict() (enerzyme.tasks.trainer.Trainer method) preload_data() (enerzyme.data.datahub.SingleDataHub method) preload_path (enerzyme.data.datahub.DataHub property) preload_split() (enerzyme.tasks.splitter.Splitter method) print_fingerprint() (in module enerzyme.models.leftnet.core) Psi4Driver (class in enerzyme.qm.qm_driver) PySCFDriver (class in enerzyme.qm.qm_driver) Q QMDriver (class in enerzyme.qm.qm_driver) R radius_graph_pbc() (in module enerzyme.models.leftnet.core) RadiusGraphLayer (class in enerzyme.models.layers.geometry) random_picking() (in module enerzyme.tasks.picker) RandomAtomEmbedding (class in enerzyme.models.layers.atom_embedding) RandomSplit (class in enerzyme.tasks.splitter) RangeSeparationLayer (class in enerzyme.models.layers.geometry) raw_data() (enerzyme.data.supplier.Supplier method) rbf_emb (class in enerzyme.models.leftnet.core) read_yaml() (enerzyme.utils.config_handler.YamlHandler method) RealAgnosticAttResidualInteractionBlock (class in enerzyme.models.mace.interaction) RealAgnosticInteractionBlock (class in enerzyme.models.mace.interaction) RealAgnosticResidualInteractionBlock (class in enerzyme.models.mace.interaction) register_data_type() (in module enerzyme.data.datatype) requires_grad() (in module enerzyme.data.datatype) reset_handle() (enerzyme.data.datahub.SingleDataHub method) reset_parameters() (enerzyme.models.layers.atom_embedding.NuclearEmbedding method) (enerzyme.models.layers.dispersion.grimme_d4.GrimmeD4EnergyLayer method) (enerzyme.models.layers.electron_embedding.ElectronicEmbedding method) (enerzyme.models.layers.electron_embedding.NonlinearElectronicEmbedding method) (enerzyme.models.layers.zbl.ZBLRepulsionEnergyLayer method) (enerzyme.models.leftnet.core.EquiMessagePassing method) (enerzyme.models.leftnet.core.EquiOutput method) (enerzyme.models.leftnet.core.FTE method) (enerzyme.models.leftnet.core.GatedEquivariantBlock method) (enerzyme.models.leftnet.core.LEFTNet method) (enerzyme.models.leftnet.core.rbf_emb method) (enerzyme.models.schnet.core.SchNetCore method) (enerzyme.models.schnet.interaction.CFConv method) (enerzyme.models.schnet.interaction.InteractionBlock method) (enerzyme.models.spookynet.interaction.LocalInteraction method) reshape_irreps (class in enerzyme.models.irreps_tools) ResidualElementDependentInteractionBlock (class in enerzyme.models.mace.interaction) ResidualLayer (class in enerzyme.models.blocks.mlp) ResidualMLP (class in enerzyme.models.blocks.mlp) ResidualMLP() (in module enerzyme.models.layers.electron_embedding) ResidualStack (class in enerzyme.models.blocks.mlp) ResidualStack() (in module enerzyme.models.physnet.interaction) (in module enerzyme.models.spookynet.interaction) RMSELoss (class in enerzyme.models.loss) run() (enerzyme.qm.qm_driver.QMDriver method) (enerzyme.tasks.simulator.Simulation method) S S_vector (class in enerzyme.models.leftnet.core) save_state_dict() (enerzyme.tasks.trainer.Trainer method) ScalarDenseEmbedding (class in enerzyme.models.layers.scalar_embedding) ScalarEmbedding (class in enerzyme.models.layers.scalar_embedding) ScalarResidualMLPEmbedding (class in enerzyme.models.layers.scalar_embedding) scale() (in module enerzyme.models.cutoff) SchNetCore (class in enerzyme.models.schnet.core) SDFSupplier (class in enerzyme.data.supplier) segment_sum_coo() (in module enerzyme.models.functional) semi_orthogonal_glorot_weights() (in module enerzyme.models.init) semi_orthogonal_matrix() (in module enerzyme.models.init) Server (class in enerzyme.tasks.server) set_cutoff() (enerzyme.models.layers.dispersion.grimme_d4.GrimmeD4EnergyLayer method) setup() (enerzyme.tasks.lightning_utils.EMACallback method) ShallowEnsembleReduceLayer (class in enerzyme.models.layers.reduce) ShiftedSoftplus (class in enerzyme.models.activation) simple_activation_fn() (enerzyme.models.activation.BaseScaledTemperedActivation method) (enerzyme.models.activation.ShiftedSoftplus method) (enerzyme.models.activation.Swish method) Simulation (class in enerzyme.tasks.simulator) sinc() (in module enerzyme.models.special) SincRBFLayer (class in enerzyme.models.layers.rbf) single_inverse_transform() (enerzyme.data.transform.AtomicEnergyTransform method) (enerzyme.data.transform.BaseTransform method) (enerzyme.data.transform.NegativeGradientTransform method) (enerzyme.data.transform.TotalEnergyNormalization method) single_run() (enerzyme.qm.qm_driver.QMDriver method) SingleDataHub (class in enerzyme.data.datahub) smooth_transition() (in module enerzyme.models.cutoff) softplus_inverse() (in module enerzyme.models.functional) split() (enerzyme.tasks.splitter.RandomSplit method) Splitter (class in enerzyme.tasks.splitter) SpookyNetCore (class in enerzyme.models.spookynet.core) square_orthogonal_matrix() (in module enerzyme.models.init) state_dict() (enerzyme.tasks.lightning_utils.EMACallback method) summary() (enerzyme.tasks.monitor.Monitor method) suppl() (enerzyme.data.supplier.PickleSupplier method) (enerzyme.data.supplier.SDFSupplier method) (enerzyme.data.supplier.Supplier method) Supplier (class in enerzyme.data.supplier) Swish (class in enerzyme.models.activation) swish() (in module enerzyme.models.leftnet.core) SymmetricContraction (class in enerzyme.models.mace.interaction) T targets (enerzyme.data.datahub.DataHub property) (enerzyme.data.datahub.SingleDataHub property) TensorProductWeightsBlock (class in enerzyme.models.mace.interaction) TeraChemDriver (class in enerzyme.qm.qm_driver) test_step() (enerzyme.tasks.lightning_utils.LightningModel method) to_device() (enerzyme.tasks.trainer.Trainer method) TotalEnergyNormalization (class in enerzyme.data.transform) tp_out_irreps_with_instructions() (in module enerzyme.models.irreps_tools) train() (enerzyme.models.ff.BaseFFLauncher method) (enerzyme.models.layers.atom_embedding.NuclearEmbedding method) Trainer (class in enerzyme.tasks.trainer) training_step() (enerzyme.tasks.lightning_utils.LightningModel method) Transform (class in enerzyme.data.transform) transform (enerzyme.data.datahub.DataHub property) transform() (enerzyme.data.transform.AtomicEnergyTransform method) (enerzyme.data.transform.NegativeGradientTransform method) (enerzyme.data.transform.TotalEnergyNormalization method) (enerzyme.data.transform.Transform method) U U_matrix_real() (in module enerzyme.models.irreps_tools) U_tensors() (enerzyme.models.mace.interaction.Contraction method) update() (enerzyme.models.ff.MetaStateDict method) (enerzyme.models.leftnet.core.EquiMessagePassing method) V validation_step() (enerzyme.tasks.lightning_utils.LightningModel method) values() (enerzyme.data.datahub.FieldDataset method) W weight (enerzyme.models.layers.atom_embedding.RandomAtomEmbedding property) weight_default() (in module enerzyme.models.physnet.interaction) WeightedLoss (class in enerzyme.models.loss) with_vector_on() (enerzyme.models.layers.geometry.DistanceLayer method) write_yaml() (enerzyme.utils.config_handler.YamlHandler method) X XPaiNNWrapper (class in enerzyme.models.xpainn.core) Y YamlHandler (class in enerzyme.utils.config_handler) Z ZBLRepulsionEnergyLayer (class in enerzyme.models.layers.zbl)