Index

_

__init__() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) (tfep.io.dataset.dict.DictDataset method) (tfep.io.dataset.merged.MergedDataset method) (tfep.io.dataset.traj.TrajectoryDataset method) (tfep.io.dataset.traj.TrajectorySubset method) (tfep.io.log.TFEPLogger method) (tfep.io.sampler.StatefulBatchSampler method) (tfep.loss.BoltzmannKLDivLoss method) (tfep.nn.conditioners.conditioner.Conditioner method) (tfep.nn.conditioners.made.MADE method) (tfep.nn.dynamics.egnn.EGNNDynamics method) (tfep.nn.embeddings.mafembed.FlipInvariantEmbedding method) (tfep.nn.embeddings.mafembed.MAFEmbedding method) (tfep.nn.embeddings.mafembed.MixedEmbedding method) (tfep.nn.embeddings.mafembed.PeriodicEmbedding method) (tfep.nn.embeddings.radial.BehlerParrinelloRadialExpansion method) (tfep.nn.embeddings.radial.GaussianBasisExpansion method) (tfep.nn.flows.autoregressive.AutoregressiveFlow method) (tfep.nn.flows.centroid.CenteredCentroidFlow method) (tfep.nn.flows.continuous.ContinuousFlow method) (tfep.nn.flows.maf.MAF method) (tfep.nn.flows.oriented.OrientedFlow method) (tfep.nn.flows.partial.PartialFlow method) (tfep.nn.flows.pca.PCAWhitenedFlow method) (tfep.nn.flows.sequential.SequentialFlow method) (tfep.nn.graph.FixedGraph method) (tfep.nn.masked.MaskedLinear method) (tfep.nn.masked.MaskedLinearFunc method) (tfep.nn.masked.MaskedWeightNorm method) (tfep.nn.transformers.affine.AffineTransformer method) (tfep.nn.transformers.affine.VolumePreservingShiftTransformer method) (tfep.nn.transformers.mixed.MixedTransformer method) (tfep.nn.transformers.moebius.MoebiusTransformer method) (tfep.nn.transformers.moebius.SymmetrizedMoebiusTransformer method) (tfep.nn.transformers.quatprod.QuaternionProductTransformer method) (tfep.nn.transformers.sos.SOSPolynomialTransformer method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc method) (tfep.nn.transformers.spline.NeuralSplineTransformer method) (tfep.nn.transformers.transformer.MAFTransformer method) (tfep.nn.transformers.transformer.Transformer method) (tfep.potentials.ase.ASEPotential method) (tfep.potentials.ase.ASEPotentialEnergyFunc method) (tfep.potentials.base.PotentialBase method) (tfep.potentials.gromacs.GmxGrompp method) (tfep.potentials.gromacs.GmxMdrun method) (tfep.potentials.gromacs.GmxTraj method) (tfep.potentials.gromacs.GROMACSPotential method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc method) (tfep.potentials.mimic.Cpmd method) (tfep.potentials.mimic.MiMiCPotential method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc method) (tfep.potentials.openmm.OpenMMPotential method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc method) (tfep.potentials.psi4.Psi4Potential method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc method) (tfep.potentials.tblite.TBLitePotential method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc method) (tfep.tests.MockPotential method) (tfep.utils.cli.launcher.Launcher method) (tfep.utils.cli.launcher.SRunLauncher method) (tfep.utils.cli.launcher.SRunTool method) (tfep.utils.cli.tool.AbsolutePathOption method) (tfep.utils.cli.tool.CLIOption method) (tfep.utils.cli.tool.CLITool method) (tfep.utils.cli.tool.FlagOption method) (tfep.utils.cli.tool.KeyValueOption method) (tfep.utils.parallel.ParallelizationStrategy method) (tfep.utils.parallel.ProcessPoolStrategy method) (tfep.utils.parallel.SerialStrategy method) (tfep.utils.plumed.auxreader.PLUMEDAuxReader method)

A

AbsolutePathOption (class in tfep.utils.cli.tool) affine_transformer() (in module tfep.nn.transformers.affine) affine_transformer_inverse() (in module tfep.nn.transformers.affine) AffineTransformer (class in tfep.nn.transformers.affine) append() (tfep.nn.flows.sequential.SequentialFlow method) are_axes_atoms_mapped() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method)

ase_potential_energy() (in module tfep.potentials.ase) ASEPotential (class in tfep.potentials.ase) ASEPotentialEnergyFunc (class in tfep.potentials.ase) atom_to_flattened() (in module tfep.utils.misc) atom_to_flattened_indices() (in module tfep.utils.misc) attach_auxiliary() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) AutoregressiveFlow (class in tfep.nn.flows.autoregressive)

B

backward() (tfep.nn.masked.MaskedLinearFunc static method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc static method) (tfep.potentials.ase.ASEPotentialEnergyFunc static method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc static method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc static method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc static method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc static method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc static method) batch_autograd_jacobian() (in module tfep.utils.math)

batch_autograd_log_abs_det_J() (in module tfep.utils.math) batch_size (tfep.io.log.TFEPLogger property) (tfep.io.sampler.StatefulBatchSampler property) batchwise_dot() (in module tfep.utils.math) batchwise_outer() (in module tfep.utils.math) batchwise_rotate() (in module tfep.utils.geometry) behler_parrinello_cosine_switching_function() (in module tfep.nn.embeddings.radial) BehlerParrinelloRadialExpansion (class in tfep.nn.embeddings.radial) benzoic_acid_universe() (in module tfep.tests) BoltzmannKLDivLoss (class in tfep.loss)

C

calc_representative() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) cartesian_to_polar() (in module tfep.utils.geometry) CartesianMAFMap (class in tfep.app.cartesianmaf) CenteredCentroidFlow (class in tfep.nn.flows.centroid) check_atom_groups() (in module tfep.tests.app) check_autoregressive_property() (in module tfep.tests.nn) check_independent() (in module tfep.app.mixedmaf) check_plumed_is_installed() (in module tfep.utils.plumed) CLIOption (class in tfep.utils.cli.tool) CLITool (class in tfep.utils.cli.tool) compute_edge_distances() (in module tfep.nn.graph) Conditioner (class in tfep.nn.conditioners.conditioner) configure_flow() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) configure_optimizers() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method)

configure_psi4() (in module tfep.potentials.psi4) constant_dt (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) ContinuousFlow (class in tfep.nn.flows.continuous) copy() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) cov() (in module tfep.utils.math) Cpmd (class in tfep.potentials.mimic) create_autoregressive_mask() (in module tfep.nn.masked) create_dataset() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) create_partial_flow() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) create_psi4_molecule() (in module tfep.potentials.psi4) create_random_input() (in module tfep.tests.nn) create_universe() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method)

D

data_selector (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) dataset (tfep.app.base.TFEPMapBase attribute) (tfep.app.cartesianmaf.CartesianMAFMap attribute) (tfep.app.mixedmaf.MixedMAFMap attribute) DEFAULT_ENERGY_UNIT (tfep.potentials.ase.ASEPotential attribute) (tfep.potentials.base.PotentialBase attribute) (tfep.potentials.gromacs.GROMACSPotential attribute) (tfep.potentials.mimic.MiMiCPotential attribute) (tfep.potentials.openmm.OpenMMPotential attribute) (tfep.potentials.psi4.Psi4Potential attribute) (tfep.potentials.tblite.TBLitePotential attribute) (tfep.tests.MockPotential attribute) default_energy_unit() (tfep.potentials.ase.ASEPotential class method) (tfep.potentials.base.PotentialBase class method) (tfep.potentials.gromacs.GROMACSPotential class method) (tfep.potentials.mimic.MiMiCPotential class method) (tfep.potentials.openmm.OpenMMPotential class method) (tfep.potentials.psi4.Psi4Potential class method) (tfep.potentials.tblite.TBLitePotential class method) (tfep.tests.MockPotential class method) DEFAULT_POSITIONS_UNIT (tfep.potentials.ase.ASEPotential attribute) (tfep.potentials.base.PotentialBase attribute) (tfep.potentials.gromacs.GROMACSPotential attribute) (tfep.potentials.mimic.MiMiCPotential attribute) (tfep.potentials.openmm.OpenMMPotential attribute) (tfep.potentials.psi4.Psi4Potential attribute) (tfep.potentials.tblite.TBLitePotential attribute) (tfep.tests.MockPotential attribute)

default_positions_unit() (tfep.potentials.ase.ASEPotential class method) (tfep.potentials.base.PotentialBase class method) (tfep.potentials.gromacs.GROMACSPotential class method) (tfep.potentials.mimic.MiMiCPotential class method) (tfep.potentials.openmm.OpenMMPotential class method) (tfep.potentials.psi4.Psi4Potential class method) (tfep.potentials.tblite.TBLitePotential class method) (tfep.tests.MockPotential class method) degree_polynomials (tfep.nn.transformers.sos.SOSPolynomialTransformer property) determine_atom_indices() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) DictDataset (class in tfep.io.dataset.dict) dimension_in (tfep.nn.conditioners.made.MADE property) dimension_out (tfep.nn.conditioners.made.MADE property) dimensions_hidden (tfep.nn.conditioners.made.MADE property) drop_last (tfep.io.sampler.StatefulBatchSampler property) dt (tfep.utils.plumed.auxreader.PLUMEDAuxReader property)

E

EGNNDynamics (class in tfep.nn.dynamics.egnn) embedding_dimension (tfep.nn.embeddings.mafembed.FlipInvariantEmbedding property) energies_array_to_tensor() (in module tfep.utils.misc) energy() (tfep.potentials.mimic.MiMiCPotential method) (tfep.potentials.psi4.Psi4Potential method) energy_unit (tfep.potentials.ase.ASEPotential property) (tfep.potentials.base.PotentialBase property) (tfep.potentials.gromacs.GROMACSPotential property) (tfep.potentials.mimic.MiMiCPotential property) (tfep.potentials.openmm.OpenMMPotential property) (tfep.potentials.psi4.Psi4Potential property) (tfep.potentials.tblite.TBLitePotential property) (tfep.tests.MockPotential property)

ensure_tensor_sequence() (in module tfep.utils.misc) executable_path (tfep.potentials.gromacs.GmxGrompp property) (tfep.potentials.gromacs.GmxMdrun property) (tfep.potentials.gromacs.GmxTraj property) (tfep.potentials.mimic.Cpmd property) (tfep.utils.cli.launcher.SRunTool property) (tfep.utils.cli.tool.CLITool property) extra_repr() (tfep.nn.masked.MaskedLinear method)

F

fep_estimator() (in module tfep.analysis.estimator) fix_node_indices_batch_size() (in module tfep.nn.graph) FixedGraph (class in tfep.nn.graph) FlagOption (class in tfep.utils.cli.tool) flattened_to_atom() (in module tfep.utils.misc) FlipInvariantEmbedding (class in tfep.nn.embeddings.mafembed) flow (tfep.nn.flows.centroid.CenteredCentroidFlow attribute) (tfep.nn.flows.oriented.OrientedFlow attribute) (tfep.nn.flows.partial.PartialFlow attribute) force() (tfep.potentials.mimic.MiMiCPotential method) (tfep.potentials.psi4.Psi4Potential method) forces_array_to_tensor() (in module tfep.utils.misc) forward() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) (tfep.loss.BoltzmannKLDivLoss method) (tfep.nn.conditioners.conditioner.Conditioner method) (tfep.nn.conditioners.made.MADE method) (tfep.nn.dynamics.egnn.EGNNDynamics method) (tfep.nn.embeddings.mafembed.FlipInvariantEmbedding method) (tfep.nn.embeddings.mafembed.MixedEmbedding method) (tfep.nn.embeddings.mafembed.PeriodicEmbedding method) (tfep.nn.embeddings.radial.BehlerParrinelloRadialExpansion method) (tfep.nn.embeddings.radial.GaussianBasisExpansion method) (tfep.nn.flows.autoregressive.AutoregressiveFlow method) (tfep.nn.flows.centroid.CenteredCentroidFlow method) (tfep.nn.flows.continuous.ContinuousFlow method) (tfep.nn.flows.maf.MAF method) (tfep.nn.flows.oriented.OrientedFlow method) (tfep.nn.flows.partial.PartialFlow method) (tfep.nn.flows.pca.PCAWhitenedFlow method) (tfep.nn.flows.sequential.SequentialFlow method) (tfep.nn.masked.MaskedLinear method) (tfep.nn.masked.MaskedLinearFunc static method) (tfep.nn.transformers.affine.AffineTransformer method) (tfep.nn.transformers.affine.VolumePreservingShiftTransformer method) (tfep.nn.transformers.mixed.MixedTransformer method) (tfep.nn.transformers.moebius.MoebiusTransformer method) (tfep.nn.transformers.moebius.SymmetrizedMoebiusTransformer method) (tfep.nn.transformers.quatprod.QuaternionProductTransformer method) (tfep.nn.transformers.sos.SOSPolynomialTransformer method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc static method) (tfep.nn.transformers.spline.NeuralSplineTransformer method) (tfep.nn.transformers.transformer.MAFTransformer method) (tfep.nn.transformers.transformer.Transformer method) (tfep.potentials.ase.ASEPotential method) (tfep.potentials.ase.ASEPotentialEnergyFunc static method) (tfep.potentials.gromacs.GROMACSPotential method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc static method) (tfep.potentials.mimic.MiMiCPotential method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc static method) (tfep.potentials.openmm.OpenMMPotential method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc static method) (tfep.potentials.psi4.Psi4Potential method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc static method) (tfep.potentials.tblite.TBLitePotential method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc static method) (tfep.tests.MockPotential method)

from_filter() (tfep.io.dataset.traj.TrajectorySubset class method) from_range() (tfep.nn.embeddings.radial.BehlerParrinelloRadialExpansion class method) (tfep.nn.embeddings.radial.GaussianBasisExpansion class method)

G

GaussianBasisExpansion (class in tfep.nn.embeddings.radial) generate_degrees() (in module tfep.nn.conditioners.made) get_all_edges() (in module tfep.nn.graph) get_axis_from_name() (in module tfep.utils.geometry) get_column_idx() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) get_conditioning_indices() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) get_degrees_out() (tfep.nn.embeddings.mafembed.FlipInvariantEmbedding method) (tfep.nn.embeddings.mafembed.MAFEmbedding method) (tfep.nn.embeddings.mafembed.MixedEmbedding method) (tfep.nn.embeddings.mafembed.PeriodicEmbedding method) (tfep.nn.transformers.affine.AffineTransformer method) (tfep.nn.transformers.affine.VolumePreservingShiftTransformer method) (tfep.nn.transformers.mixed.MixedTransformer method) (tfep.nn.transformers.moebius.MoebiusTransformer method) (tfep.nn.transformers.moebius.SymmetrizedMoebiusTransformer method) (tfep.nn.transformers.quatprod.QuaternionProductTransformer method) (tfep.nn.transformers.sos.SOSPolynomialTransformer method) (tfep.nn.transformers.spline.NeuralSplineTransformer method) (tfep.nn.transformers.transformer.MAFTransformer method) get_description() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) get_edges() (tfep.nn.dynamics.egnn.EGNNDynamics method) (tfep.nn.graph.FixedGraph method) get_identity_parameters() (tfep.nn.transformers.affine.AffineTransformer method) (tfep.nn.transformers.affine.VolumePreservingShiftTransformer method) (tfep.nn.transformers.mixed.MixedTransformer method) (tfep.nn.transformers.moebius.MoebiusTransformer method) (tfep.nn.transformers.moebius.SymmetrizedMoebiusTransformer method) (tfep.nn.transformers.quatprod.QuaternionProductTransformer method) (tfep.nn.transformers.sos.SOSPolynomialTransformer method) (tfep.nn.transformers.spline.NeuralSplineTransformer method) (tfep.nn.transformers.transformer.MAFTransformer method) (tfep.nn.transformers.transformer.Transformer method)

get_mapped_indices() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) get_nonfixed_indices() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) get_reference_atoms_indices() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) get_sos_poly_coefficients() (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc static method) get_subsampled_indices() (in module tfep.io.dataset.traj) get_timestep() (tfep.io.dataset.traj.TrajectoryDataset method) (tfep.io.dataset.traj.TrajectorySubset method) get_transformer_parameters() (tfep.nn.flows.autoregressive.AutoregressiveFlow method) (tfep.nn.flows.maf.MAF method) global_context_cache (in module tfep.potentials.openmm) GmxGrompp (class in tfep.potentials.gromacs) GmxMdrun (class in tfep.potentials.gromacs) GmxTraj (class in tfep.potentials.gromacs) gromacs_potential_energy() (in module tfep.potentials.gromacs) GROMACSPotential (class in tfep.potentials.gromacs) GROMACSPotentialEnergyFunc (class in tfep.potentials.gromacs)

H

has_fixed_indices (tfep.nn.flows.autoregressive.AutoregressiveFlow property) (tfep.nn.flows.maf.MAF property)

I

ignore_nan (tfep.loss.BoltzmannKLDivLoss attribute) initial_time (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) inverse() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) (tfep.nn.flows.autoregressive.AutoregressiveFlow method) (tfep.nn.flows.centroid.CenteredCentroidFlow method) (tfep.nn.flows.maf.MAF method) (tfep.nn.flows.oriented.OrientedFlow method) (tfep.nn.transformers.affine.AffineTransformer method) (tfep.nn.transformers.affine.VolumePreservingShiftTransformer method) (tfep.nn.transformers.mixed.MixedTransformer method) (tfep.nn.transformers.moebius.MoebiusTransformer method) (tfep.nn.transformers.moebius.SymmetrizedMoebiusTransformer method) (tfep.nn.transformers.quatprod.QuaternionProductTransformer method) (tfep.nn.transformers.sos.SOSPolynomialTransformer method) (tfep.nn.transformers.spline.NeuralSplineTransformer method) (tfep.nn.transformers.transformer.MAFTransformer method) (tfep.nn.transformers.transformer.Transformer method)

is_collinear() (in module tfep.app.mixedmaf) iterate_as_timestep() (tfep.io.dataset.traj.TrajectoryDataset method) (tfep.io.dataset.traj.TrajectorySubset method)

J

jvp() (tfep.nn.masked.MaskedLinearFunc static method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc static method) (tfep.potentials.ase.ASEPotentialEnergyFunc static method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc static method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc static method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc static method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc static method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc static method)

K

KeyValueOption (class in tfep.utils.cli.tool)

L

Launcher (class in tfep.utils.cli.launcher)

load_state_dict() (tfep.io.sampler.StatefulBatchSampler method)

M

MADE (class in tfep.nn.conditioners.made) MAF (class in tfep.nn.flows.maf) MAFEmbedding (class in tfep.nn.embeddings.mafembed) MAFTransformer (class in tfep.nn.transformers.transformer) mark_dirty() (tfep.nn.masked.MaskedLinearFunc method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc method) (tfep.potentials.ase.ASEPotentialEnergyFunc method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc method) mark_non_differentiable() (tfep.nn.masked.MaskedLinearFunc method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc method) (tfep.potentials.ase.ASEPotentialEnergyFunc method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc method) masked_weight_norm() (in module tfep.nn.masked) MaskedLinear (class in tfep.nn.masked) MaskedLinearFunc (class in tfep.nn.masked) MaskedWeightNorm (class in tfep.nn.masked) MergedDataset (class in tfep.io.dataset.merged) method (tfep.potentials.tblite.TBLitePotential attribute) mimic_potential_energy() (in module tfep.potentials.mimic) MiMiCPotential (class in tfep.potentials.mimic) MiMiCPotentialEnergyFunc (class in tfep.potentials.mimic) MixedEmbedding (class in tfep.nn.embeddings.mafembed) MixedMAFMap (class in tfep.app.mixedmaf) MixedTransformer (class in tfep.nn.transformers.mixed) MockPotential (class in tfep.tests) module tfep tfep.analysis tfep.analysis.bootstrap tfep.analysis.estimator tfep.app tfep.app.base tfep.app.cartesianmaf tfep.app.mixedmaf tfep.io tfep.io.dataset tfep.io.dataset.dict tfep.io.dataset.merged tfep.io.dataset.traj tfep.io.log tfep.io.sampler tfep.loss tfep.nn tfep.nn.conditioners tfep.nn.conditioners.conditioner tfep.nn.conditioners.made tfep.nn.dynamics tfep.nn.dynamics.egnn tfep.nn.embeddings tfep.nn.embeddings.mafembed tfep.nn.embeddings.radial tfep.nn.flows tfep.nn.flows.autoregressive tfep.nn.flows.centroid tfep.nn.flows.continuous tfep.nn.flows.maf tfep.nn.flows.oriented tfep.nn.flows.partial tfep.nn.flows.pca tfep.nn.flows.sequential tfep.nn.graph tfep.nn.masked tfep.nn.transformers tfep.nn.transformers.affine tfep.nn.transformers.mixed tfep.nn.transformers.moebius tfep.nn.transformers.quatprod tfep.nn.transformers.sos tfep.nn.transformers.spline tfep.nn.transformers.transformer tfep.potentials tfep.potentials.ase tfep.potentials.base tfep.potentials.gromacs tfep.potentials.mimic tfep.potentials.openmm tfep.potentials.psi4 tfep.potentials.tblite tfep.tests tfep.tests.app tfep.tests.io tfep.tests.nn tfep.tests.nn.conditioners tfep.tests.nn.embeddings tfep.tests.nn.flows tfep.tests.nn.transformers tfep.tests.potentials tfep.tests.utils tfep.tests.utils.plumed tfep.utils tfep.utils.cli tfep.utils.cli.launcher tfep.utils.cli.tool tfep.utils.geometry tfep.utils.math tfep.utils.misc tfep.utils.parallel tfep.utils.plumed tfep.utils.plumed.auxreader tfep.utils.plumed.io tfep.utils.plumed.plot tfep.utils.plumed.sumhills

moebius_transformer() (in module tfep.nn.transformers.moebius) MoebiusTransformer (class in tfep.nn.transformers.moebius) move_to_ts() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) multiprog (tfep.utils.cli.launcher.SRunLauncher attribute) multiprog_config_file_path (tfep.utils.cli.launcher.SRunLauncher attribute)

N

n_atoms (tfep.io.dataset.traj.TrajectoryDataset property) (tfep.io.dataset.traj.TrajectorySubset property) n_batches_per_epoch (tfep.io.log.TFEPLogger property) n_conditioning_atoms (tfep.app.base.TFEPMapBase property) (tfep.app.cartesianmaf.CartesianMAFMap property) (tfep.app.mixedmaf.MixedMAFMap property) n_conditioning_dofs (tfep.app.base.TFEPMapBase property) (tfep.app.cartesianmaf.CartesianMAFMap property) (tfep.app.mixedmaf.MixedMAFMap property) n_edges (tfep.nn.dynamics.egnn.EGNNDynamics property) (tfep.nn.graph.FixedGraph property) n_fixed_atoms (tfep.app.base.TFEPMapBase property) (tfep.app.cartesianmaf.CartesianMAFMap property) (tfep.app.mixedmaf.MixedMAFMap property) n_mapped_atoms (tfep.app.base.TFEPMapBase property) (tfep.app.cartesianmaf.CartesianMAFMap property) (tfep.app.mixedmaf.MixedMAFMap property) n_mapped_dofs (tfep.app.base.TFEPMapBase property) (tfep.app.cartesianmaf.CartesianMAFMap property) (tfep.app.mixedmaf.MixedMAFMap property) n_nodes (tfep.nn.dynamics.egnn.EGNNDynamics property) (tfep.nn.graph.FixedGraph property) n_nonfixed_atoms (tfep.app.base.TFEPMapBase property) (tfep.app.cartesianmaf.CartesianMAFMap property) (tfep.app.mixedmaf.MixedMAFMap property)

n_nonfixed_dofs (tfep.app.base.TFEPMapBase property) (tfep.app.cartesianmaf.CartesianMAFMap property) (tfep.app.mixedmaf.MixedMAFMap property) n_parameters() (tfep.nn.conditioners.made.MADE method) (tfep.nn.flows.centroid.CenteredCentroidFlow method) (tfep.nn.flows.maf.MAF method) (tfep.nn.flows.oriented.OrientedFlow method) (tfep.nn.flows.partial.PartialFlow method) (tfep.nn.flows.pca.PCAWhitenedFlow method) (tfep.nn.flows.sequential.SequentialFlow method) (tfep.nn.masked.MaskedLinear method) n_parameters_per_feature (tfep.nn.transformers.sos.SOSPolynomialTransformer property) (tfep.nn.transformers.spline.NeuralSplineTransformer property) n_samples_per_epoch (tfep.io.log.TFEPLogger property) n_steps (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) n_tasks (tfep.utils.cli.launcher.SRunLauncher attribute) neural_spline_transformer() (in module tfep.nn.transformers.spline) neural_spline_transformer_inverse() (in module tfep.nn.transformers.spline) NeuralSplineTransformer (class in tfep.nn.transformers.spline) next() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) next_nonempty_frame() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) numbers (tfep.potentials.tblite.TBLitePotential attribute)

O

on_load_checkpoint() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) on_save_checkpoint() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method)

openmm_potential_energy() (in module tfep.potentials.openmm) OpenMMPotential (class in tfep.potentials.openmm) OpenMMPotentialEnergyFunc (class in tfep.potentials.openmm) OrientedFlow (class in tfep.nn.flows.oriented)

P

parallelization_strategy (tfep.potentials.openmm.OpenMMPotential attribute) (tfep.potentials.tblite.TBLitePotential attribute) ParallelizationStrategy (class in tfep.utils.parallel) parameters_per_polynomial (tfep.nn.transformers.sos.SOSPolynomialTransformer property) PartialFlow (class in tfep.nn.flows.partial) PCAWhitenedFlow (class in tfep.nn.flows.pca) pdist() (in module tfep.utils.geometry) PeriodicEmbedding (class in tfep.nn.embeddings.mafembed) platform (tfep.potentials.openmm.OpenMMPotential attribute) plot_trajectory() (in module tfep.utils.plumed.plot) PLUMEDAuxReader (class in tfep.utils.plumed.auxreader) polar_to_cartesian() (in module tfep.utils.geometry) positions_unit (tfep.potentials.ase.ASEPotential property) (tfep.potentials.base.PotentialBase property) (tfep.potentials.gromacs.GROMACSPotential property) (tfep.potentials.mimic.MiMiCPotential property) (tfep.potentials.openmm.OpenMMPotential property) (tfep.potentials.psi4.Psi4Potential property) (tfep.potentials.tblite.TBLitePotential property) (tfep.tests.MockPotential property)

PotentialBase (class in tfep.potentials.base) precompute_gradient (tfep.potentials.openmm.OpenMMPotential attribute) (tfep.potentials.tblite.TBLitePotential attribute) ProcessPoolStrategy (class in tfep.utils.parallel) proper_dihedral_angle() (in module tfep.utils.geometry) prune_long_edges() (in module tfep.nn.graph) psi4_potential_energy() (in module tfep.potentials.psi4) Psi4Potential (class in tfep.potentials.psi4) Psi4PotentialEnergyFunc (class in tfep.potentials.psi4)

Q

QuaternionProductTransformer (class in tfep.nn.transformers.quatprod)

R

read_all_times() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) read_eval_tensors() (tfep.io.log.TFEPLogger method) read_table() (in module tfep.utils.plumed.io) read_table_field_names() (in module tfep.utils.plumed.io) read_table_n_rows() (in module tfep.utils.plumed.io) read_train_tensors() (tfep.io.log.TFEPLogger method) read_ts() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) reference_frame_rotation_matrix() (in module tfep.utils.geometry) remove_and_shift_sorted_indices() (in module tfep.utils.misc) remove_masked_weight_norm() (in module tfep.nn.masked) represent_ts_as (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) return_dataset_sample_index (tfep.io.dataset.traj.TrajectorySubset property)

return_partial (tfep.nn.flows.centroid.CenteredCentroidFlow attribute) (tfep.nn.flows.oriented.OrientedFlow attribute) (tfep.nn.flows.partial.PartialFlow attribute) return_trajectory_sample_index (tfep.io.dataset.traj.TrajectorySubset property) rewind() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) rotate_back (tfep.nn.flows.oriented.OrientedFlow attribute) rotation_matrix_3d() (in module tfep.utils.geometry) run() (tfep.utils.cli.launcher.Launcher method) (tfep.utils.cli.launcher.SRunLauncher method) (tfep.utils.parallel.ParallelizationStrategy method) (tfep.utils.parallel.ProcessPoolStrategy method) (tfep.utils.parallel.SerialStrategy method) run_plumed_sum_hills() (in module tfep.utils.plumed.sumhills)

S

save_dir_path (tfep.io.log.TFEPLogger property) save_eval_tensors() (tfep.io.log.TFEPLogger method) save_for_backward() (tfep.nn.masked.MaskedLinearFunc method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc method) (tfep.potentials.ase.ASEPotentialEnergyFunc method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc method) save_for_forward() (tfep.nn.masked.MaskedLinearFunc method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc method) (tfep.potentials.ase.ASEPotentialEnergyFunc method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc method) save_train_tensors() (tfep.io.log.TFEPLogger method) select_atoms() (tfep.io.dataset.traj.TrajectoryDataset method) (tfep.io.dataset.traj.TrajectorySubset method) SequentialFlow (class in tfep.nn.flows.sequential) SerialStrategy (class in tfep.utils.parallel) set_materialize_grads() (tfep.nn.masked.MaskedLinearFunc method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc method) (tfep.potentials.ase.ASEPotentialEnergyFunc method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc method)

set_output() (tfep.nn.conditioners.conditioner.Conditioner method) (tfep.nn.conditioners.made.MADE method) setup() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) setup_context() (tfep.nn.masked.MaskedLinearFunc static method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc static method) (tfep.potentials.ase.ASEPotentialEnergyFunc static method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc static method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc static method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc static method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc static method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc static method) shuffle (tfep.io.sampler.StatefulBatchSampler property) SOSPolynomialTransformer (class in tfep.nn.transformers.sos) SOSPolynomialTransformerFunc (class in tfep.nn.transformers.sos) space_dimension (tfep.nn.flows.centroid.CenteredCentroidFlow property) srun_kwargs (tfep.utils.cli.launcher.SRunLauncher attribute) SRunLauncher (class in tfep.utils.cli.launcher) SRunTool (class in tfep.utils.cli.launcher) state_dict() (tfep.io.sampler.StatefulBatchSampler method) StatefulBatchSampler (class in tfep.io.sampler) step (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) step_to_frame() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) step_to_time() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method) subsample() (tfep.io.dataset.traj.TrajectoryDataset method) symmetrized_moebius_transformer() (in module tfep.nn.transformers.moebius) symmetrized_moebius_transformer_inverse() (in module tfep.nn.transformers.moebius) SymmetrizedMoebiusTransformer (class in tfep.nn.transformers.moebius) system (tfep.potentials.openmm.OpenMMPotential attribute) system_name (tfep.potentials.openmm.OpenMMPotential attribute)

T

tblite_potential_energy() (in module tfep.potentials.tblite) TBLitePotential (class in tfep.potentials.tblite) TBLitePotentialEnergyFunc (class in tfep.potentials.tblite) temporary_cd() (in module tfep.utils.misc) tfep module tfep.analysis module tfep.analysis.bootstrap module tfep.analysis.estimator module tfep.app module tfep.app.base module tfep.app.cartesianmaf module tfep.app.mixedmaf module tfep.io module tfep.io.dataset module tfep.io.dataset.dict module tfep.io.dataset.merged module tfep.io.dataset.traj module tfep.io.log module tfep.io.sampler module tfep.loss module tfep.nn module tfep.nn.conditioners module tfep.nn.conditioners.conditioner module tfep.nn.conditioners.made module tfep.nn.dynamics module tfep.nn.dynamics.egnn module tfep.nn.embeddings module tfep.nn.embeddings.mafembed module tfep.nn.embeddings.radial module tfep.nn.flows module tfep.nn.flows.autoregressive module tfep.nn.flows.centroid module tfep.nn.flows.continuous module tfep.nn.flows.maf module tfep.nn.flows.oriented module tfep.nn.flows.partial module tfep.nn.flows.pca module tfep.nn.flows.sequential module tfep.nn.graph module tfep.nn.masked module tfep.nn.transformers module tfep.nn.transformers.affine module tfep.nn.transformers.mixed module tfep.nn.transformers.moebius module tfep.nn.transformers.quatprod module tfep.nn.transformers.sos module tfep.nn.transformers.spline module

tfep.nn.transformers.transformer module tfep.potentials module tfep.potentials.ase module tfep.potentials.base module tfep.potentials.gromacs module tfep.potentials.mimic module tfep.potentials.openmm module tfep.potentials.psi4 module tfep.potentials.tblite module tfep.tests module tfep.tests.app module tfep.tests.io module tfep.tests.nn module tfep.tests.nn.conditioners module tfep.tests.nn.embeddings module tfep.tests.nn.flows module tfep.tests.nn.transformers module tfep.tests.potentials module tfep.tests.utils module tfep.tests.utils.plumed module tfep.utils module tfep.utils.cli module tfep.utils.cli.launcher module tfep.utils.cli.tool module tfep.utils.geometry module tfep.utils.math module tfep.utils.misc module tfep.utils.parallel module tfep.utils.plumed module tfep.utils.plumed.auxreader module tfep.utils.plumed.io module tfep.utils.plumed.plot module tfep.utils.plumed.sumhills module TFEPLogger (class in tfep.io.log) TFEPMapBase (class in tfep.app.base) time (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) time_selector (tfep.utils.plumed.auxreader.PLUMEDAuxReader property) to_subprocess() (tfep.potentials.gromacs.GmxGrompp method) (tfep.potentials.gromacs.GmxMdrun method) (tfep.potentials.gromacs.GmxTraj method) (tfep.potentials.mimic.Cpmd method) (tfep.utils.cli.launcher.SRunTool method) (tfep.utils.cli.tool.AbsolutePathOption method) (tfep.utils.cli.tool.CLIOption method) (tfep.utils.cli.tool.CLITool method) (tfep.utils.cli.tool.FlagOption method) (tfep.utils.cli.tool.KeyValueOption method) train_dataloader() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) trainer (tfep.io.sampler.StatefulBatchSampler attribute) training_step() (tfep.app.base.TFEPMapBase method) (tfep.app.cartesianmaf.CartesianMAFMap method) (tfep.app.mixedmaf.MixedMAFMap method) trajectory_sample_indices (tfep.io.dataset.traj.TrajectorySubset property) TrajectoryDataset (class in tfep.io.dataset.traj) TrajectorySubset (class in tfep.io.dataset.traj) Transformer (class in tfep.nn.transformers.transformer)

U

universe (tfep.io.dataset.traj.TrajectorySubset property)

unsorted_segment_sum() (in module tfep.nn.graph) update_ts() (tfep.utils.plumed.auxreader.PLUMEDAuxReader method)

V

vector_dimension (tfep.nn.embeddings.mafembed.FlipInvariantEmbedding property) vector_plane_angle() (in module tfep.utils.geometry) vector_vector_angle() (in module tfep.utils.geometry) vjp() (tfep.nn.masked.MaskedLinearFunc static method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc static method) (tfep.potentials.ase.ASEPotentialEnergyFunc static method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc static method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc static method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc static method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc static method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc static method)

vmap() (tfep.nn.masked.MaskedLinearFunc static method) (tfep.nn.transformers.sos.SOSPolynomialTransformerFunc static method) (tfep.potentials.ase.ASEPotentialEnergyFunc static method) (tfep.potentials.gromacs.GROMACSPotentialEnergyFunc static method) (tfep.potentials.mimic.MiMiCPotentialEnergyFunc static method) (tfep.potentials.openmm.OpenMMPotentialEnergyFunc static method) (tfep.potentials.psi4.Psi4PotentialEnergyFunc static method) (tfep.potentials.tblite.TBLitePotentialEnergyFunc static method) volume_preserving_shift_transformer() (in module tfep.nn.transformers.affine) volume_preserving_shift_transformer_inverse() (in module tfep.nn.transformers.affine) VolumePreservingShiftTransformer (class in tfep.nn.transformers.affine)

W

water_universe() (in module tfep.tests)

weight_norm (tfep.nn.conditioners.made.MADE property) write_table() (in module tfep.utils.plumed.io)