Index

_

__add__() (mlptrain.configurations.configuration_set.ConfigurationSet method) __call__() (mlptrain.loss._base.LossFunction method) (mlptrain.loss.tau.TauCalculator method) (mlptrain.sampling._base.Function method) (mlptrain.sampling.bias.Bias method) (mlptrain.sampling.reaction_coord.ReactionCoordinate method) (mlptrain.training.selection.AbsDiffE method) (mlptrain.training.selection.AtomicEnvSimilarity method) (mlptrain.training.selection.SelectionMethod method) __eq__() (mlptrain.box.Box method) (mlptrain.configurations.configuration.Configuration method) __init__() (mlptrain.box.Box method) (mlptrain.configurations.configuration.Configuration method) (mlptrain.configurations.configuration_set.ConfigurationSet method) (mlptrain.configurations.trajectory.Trajectory method) (mlptrain.descriptor._base.Descriptor method) (mlptrain.descriptor.soap_descriptor.SoapDescriptor method) (mlptrain.energy.Energy method) (mlptrain.forces.Forces method) (mlptrain.loss._base.LossFunction method) (mlptrain.loss._base.LossValue method) (mlptrain.loss.tau.TauCalculator method) (mlptrain.potentials._base.MLPotential method) (mlptrain.potentials.mace.mace.MACE method) (mlptrain.sampling.bias.Bias method) (mlptrain.sampling.metadynamics.Metadynamics method) (mlptrain.sampling.plumed.PlumedAverageCV method) (mlptrain.sampling.plumed.PlumedBias method) (mlptrain.sampling.plumed.PlumedCNCV method) (mlptrain.sampling.plumed.PlumedCustomCV method) (mlptrain.sampling.plumed.PlumedDifferenceCV method) (mlptrain.sampling.reaction_coord.AverageDistance method) (mlptrain.sampling.reaction_coord.DifferenceDistance method) (mlptrain.sampling.umbrella.UmbrellaSampling method) (mlptrain.system.System method) (mlptrain.training.selection.AbsDiffE method) (mlptrain.training.selection.AtomicEnvDistance method) (mlptrain.training.selection.AtomicEnvSimilarity method) (mlptrain.training.selection.SelectionMethod method)

__repr__() (mlptrain.loss._base.LossValue method)

A

AbsDiffE (class in mlptrain.training.selection) ACE (class in mlptrain.potentials.ace.ace) add_molecule() (mlptrain.system.System method) add_molecules() (mlptrain.system.System method) adjust_forces() (mlptrain.sampling._base.ASEConstraint method) (mlptrain.sampling.bias.Bias method) (mlptrain.sampling.plumed.PlumedBias method) adjust_positions() (mlptrain.sampling._base.ASEConstraint method) (mlptrain.sampling.bias.Bias method) (mlptrain.sampling.plumed.PlumedBias method) adjust_potential_energy() (mlptrain.sampling._base.ASEConstraint method) (mlptrain.sampling.bias.Bias method) (mlptrain.sampling.plumed.PlumedBias method)

al_train() (mlptrain.potentials._base.MLPotential method) al_train_then_bias() (mlptrain.potentials._base.MLPotential method) append() (mlptrain.configurations.configuration_set.ConfigurationSet method) args (mlptrain.potentials.mace.mace.MACE property) ase_atoms (mlptrain.configurations.configuration.Configuration property) ase_calculator (mlptrain.potentials._base.MLPotential property) (mlptrain.potentials.ace.ace.ACE property) (mlptrain.potentials.mace.mace.MACE property) ASEConstraint (class in mlptrain.sampling._base) AtomicEnvDistance (class in mlptrain.training.selection) AtomicEnvSimilarity (class in mlptrain.training.selection) atoms (mlptrain.system.System property) AverageDistance (class in mlptrain.sampling.reaction_coord)

B

batch_size (mlptrain.potentials.mace.mace.MACE property) beta (mlptrain.sampling.umbrella.UmbrellaSampling property) Bias (class in mlptrain.sampling.bias)

bias_energies (mlptrain.configurations.configuration_set.ConfigurationSet property) biasfactor_setup (mlptrain.sampling.plumed.PlumedBias property) block_analysis() (mlptrain.sampling.metadynamics.Metadynamics method) Box (class in mlptrain.box)

C

calculate() (mlptrain.sampling.plumed.PlumedCalculator method) centroid (mlptrain.molecule.Molecule property) charge (mlptrain.system.System property) check (mlptrain.training.selection.AtomicEnvDistance property) (mlptrain.training.selection.SelectionMethod property) compare() (mlptrain.configurations.configuration_set.ConfigurationSet method) compute_energy_and_forces() (mlptrain.sampling.plumed.PlumedCalculator method) compute_fes() (mlptrain.sampling.metadynamics.Metadynamics method) compute_representation() (mlptrain.descriptor._base.Descriptor method) (mlptrain.descriptor.soap_descriptor.SoapDescriptor method)

Configuration (class in mlptrain.configurations.configuration) configuration (mlptrain.system.System property) ConfigurationSet (class in mlptrain.configurations.configuration_set) convert_ase_energy() (in module mlptrain.utils) convert_ase_time() (in module mlptrain.utils) convert_exponents() (in module mlptrain.utils) copy() (mlptrain.configurations.configuration.Configuration method) (mlptrain.potentials._base.MLPotential method) (mlptrain.training.selection.SelectionMethod method) cv_sequence (mlptrain.sampling.plumed.PlumedBias property)

D

delta (mlptrain.energy.Energy property) (mlptrain.forces.Forces property) Descriptor (class in mlptrain.descriptor._base)

descriptor (mlptrain.training.selection.AtomicEnvSimilarity attribute) DifferenceDistance (class in mlptrain.sampling.reaction_coord) DummyCoordinate (class in mlptrain.sampling.reaction_coord)

E

Energy (class in mlptrain.energy) error_force_histogram_per_elements() (in module mlptrain.configurations.plotting)

error_histogram() (in module mlptrain.configurations.plotting) error_histogram_index() (in module mlptrain.configurations.plotting) estimate_width() (mlptrain.sampling.metadynamics.Metadynamics method)

F

filename (mlptrain.potentials.mace.mace.MACE property) final_frame (mlptrain.configurations.trajectory.Trajectory property) Forces (class in mlptrain.forces) free_energies() (mlptrain.sampling.umbrella.UmbrellaSampling method) from_file (mlptrain.sampling.plumed.PlumedBias property) from_folder() (mlptrain.sampling.umbrella.UmbrellaSampling class method)

from_folders() (mlptrain.sampling.umbrella.UmbrellaSampling class method) from_orca_file() (mlptrain.configurations.configuration.Configuration class method) from_orca_files() (mlptrain.configurations.configuration_set.ConfigurationSet class method) from_xyz() (mlptrain.configurations.configuration.Configuration class method) (mlptrain.configurations.configuration_set.ConfigurationSet class method) Function (class in mlptrain.sampling._base)

G

get_colvar_filename() (in module mlptrain.sampling.plumed) get_E0s (mlptrain.potentials.mace.mace.MACE property) get_hills_filename() (in module mlptrain.sampling.plumed)

grad() (mlptrain.sampling._base.Function method) (mlptrain.sampling.bias.Bias method) (mlptrain.sampling.reaction_coord.ReactionCoordinate method)

H

has_a_none_energy (mlptrain.configurations.configuration_set.ConfigurationSet property)

has_zero_volume (mlptrain.box.Box property)

I

implemented_properties (mlptrain.sampling.plumed.PlumedCalculator attribute) inherited_bias_energies (mlptrain.configurations.configuration_set.ConfigurationSet property)

initialise_for_metad_al() (mlptrain.sampling.plumed.PlumedBias method) is_in_box() (mlptrain.molecule.Molecule method)

K

k_d_tree_insertion() (mlptrain.configurations.configuration.Configuration method) kbt (mlptrain.sampling.metadynamics.Metadynamics property)

kernel_vector() (mlptrain.descriptor._base.Descriptor method) (mlptrain.descriptor.soap_descriptor.SoapDescriptor method)

L

load() (mlptrain.configurations.configuration_set.ConfigurationSet method) (mlptrain.sampling.umbrella.UmbrellaSampling method) load_from_xyz() (mlptrain.configurations.configuration.Configuration method) load_mol_dict() (mlptrain.configurations.configuration.Configuration method) load_xyz() (mlptrain.configurations.configuration_set.ConfigurationSet method) loss_type (mlptrain.loss.mean_errors.MAD attribute) (mlptrain.loss.mean_errors.RMSE attribute)

LossFunction (class in mlptrain.loss._base) LossValue (class in mlptrain.loss._base) lowest_biased_energy (mlptrain.configurations.configuration_set.ConfigurationSet property) lowest_energy (mlptrain.configurations.configuration_set.ConfigurationSet property) lowest_inherited_biased_energy (mlptrain.configurations.configuration_set.ConfigurationSet property)

M

MACE (class in mlptrain.potentials.mace.mace) MAD (class in mlptrain.loss.mean_errors) MADValue (class in mlptrain.loss.mean_errors) metad_cv_sequence (mlptrain.sampling.plumed.PlumedBias property) metad_grid_setup (mlptrain.sampling.plumed.PlumedBias property) Metadynamics (class in mlptrain.sampling.metadynamics) metadynamics (mlptrain.sampling.plumed.PlumedBias property) midpoint (mlptrain.box.Box property) min_distance_to() (mlptrain.molecule.Molecule method) MLPotential (class in mlptrain.potentials._base) mlptrain.box module mlptrain.configurations.calculate module mlptrain.configurations.configuration module mlptrain.configurations.configuration_set module mlptrain.configurations.plotting module mlptrain.configurations.trajectory module mlptrain.descriptor._base module mlptrain.descriptor.soap_descriptor module mlptrain.energy module mlptrain.forces module mlptrain.loss._base module mlptrain.loss.mean_errors module mlptrain.loss.tau module mlptrain.molecule module mlptrain.potentials._base module mlptrain.potentials.ace.ace module mlptrain.potentials.mace.mace module mlptrain.sampling._base module mlptrain.sampling.bias module mlptrain.sampling.md module

mlptrain.sampling.md_openmm module mlptrain.sampling.metadynamics module mlptrain.sampling.plumed module mlptrain.sampling.reaction_coord module mlptrain.sampling.umbrella module mlptrain.system module mlptrain.training.active module mlptrain.training.selection module mlptrain.utils module module mlptrain.box mlptrain.configurations.calculate mlptrain.configurations.configuration mlptrain.configurations.configuration_set mlptrain.configurations.plotting mlptrain.configurations.trajectory mlptrain.descriptor._base mlptrain.descriptor.soap_descriptor mlptrain.energy mlptrain.forces mlptrain.loss._base mlptrain.loss.mean_errors mlptrain.loss.tau mlptrain.molecule mlptrain.potentials._base mlptrain.potentials.ace.ace mlptrain.potentials.mace.mace mlptrain.sampling._base mlptrain.sampling.bias mlptrain.sampling.md mlptrain.sampling.md_openmm mlptrain.sampling.metadynamics mlptrain.sampling.plumed mlptrain.sampling.reaction_coord mlptrain.sampling.umbrella mlptrain.system mlptrain.training.active mlptrain.training.selection mlptrain.utils Molecule (class in mlptrain.molecule) move_files() (in module mlptrain.utils) mult (mlptrain.system.System property)

N

n_backtrack (mlptrain.training.selection.AbsDiffE property) (mlptrain.training.selection.AtomicEnvDistance property) (mlptrain.training.selection.AtomicEnvSimilarity property) (mlptrain.training.selection.SelectionMethod property) n_cvs (mlptrain.sampling.metadynamics.Metadynamics property) (mlptrain.sampling.plumed.PlumedBias property)

n_eval (mlptrain.potentials._base.MLPotential property) n_metad_cvs (mlptrain.sampling.plumed.PlumedBias property) n_pairs (mlptrain.sampling.reaction_coord.AverageDistance property) n_train (mlptrain.potentials._base.MLPotential property)

O

optimise_solvent() (in module mlptrain.configurations.configuration)

P

parity_plot() (in module mlptrain.configurations.plotting) plot_cv1_and_cv2() (in module mlptrain.sampling.plumed) plot_cv_versus_time() (in module mlptrain.sampling.plumed) plot_fes() (mlptrain.sampling.metadynamics.Metadynamics method) plot_fes_convergence() (mlptrain.sampling.metadynamics.Metadynamics method) plot_gaussian_heights() (mlptrain.sampling.metadynamics.Metadynamics method) plumed_coordinates (mlptrain.configurations.configuration_set.ConfigurationSet property) plumed_setup() (in module mlptrain.sampling.plumed)

PlumedAverageCV (class in mlptrain.sampling.plumed) PlumedBias (class in mlptrain.sampling.plumed) PlumedCalculator (class in mlptrain.sampling.plumed) PlumedCNCV (class in mlptrain.sampling.plumed) PlumedCustomCV (class in mlptrain.sampling.plumed) PlumedDifferenceCV (class in mlptrain.sampling.plumed) predict() (mlptrain.potentials._base.MLPotential method) predicted_energies (mlptrain.configurations.configuration_set.ConfigurationSet property) predicted_forces (mlptrain.configurations.configuration_set.ConfigurationSet property)

R

random_configuration() (mlptrain.system.System method) random_configurations() (mlptrain.system.System method) random_normal_jiggle() (mlptrain.molecule.Molecule method) random_point (mlptrain.box.Box property) ReactionCoordinate (class in mlptrain.sampling.reaction_coord) remove_above_e() (mlptrain.configurations.configuration_set.ConfigurationSet method) remove_none_energy() (mlptrain.configurations.configuration_set.ConfigurationSet method) requires_atomic_energies (mlptrain.potentials._base.MLPotential property) (mlptrain.potentials.ace.ace.ACE property) (mlptrain.potentials.mace.mace.MACE property)

requires_non_zero_box_size (mlptrain.potentials._base.MLPotential property) (mlptrain.potentials.ace.ace.ACE property) (mlptrain.potentials.mace.mace.MACE property) RMSE (class in mlptrain.loss.mean_errors) RMSEValue (class in mlptrain.loss.mean_errors) run_autode() (in module mlptrain.configurations.calculate) run_metadynamics() (mlptrain.sampling.metadynamics.Metadynamics method) run_mlp_md() (in module mlptrain.sampling.md) run_mlp_md_openmm() (in module mlptrain.sampling.md_openmm) run_umbrella_sampling() (mlptrain.sampling.umbrella.UmbrellaSampling method)

S

save() (mlptrain.configurations.configuration_set.ConfigurationSet method) (mlptrain.sampling.umbrella.UmbrellaSampling method) save_mol_dict() (mlptrain.configurations.configuration.Configuration method) save_xyz() (mlptrain.configurations.configuration.Configuration method) (mlptrain.configurations.configuration_set.ConfigurationSet method) select (mlptrain.training.selection.AbsDiffE property) (mlptrain.training.selection.AtomicEnvDistance property) (mlptrain.training.selection.AtomicEnvSimilarity property) (mlptrain.training.selection.SelectionMethod property)

SelectionMethod (class in mlptrain.training.selection) set_atomic_energies() (mlptrain.potentials._base.MLPotential method) single_point() (mlptrain.configurations.configuration.Configuration method) (mlptrain.configurations.configuration_set.ConfigurationSet method) SoapDescriptor (class in mlptrain.descriptor.soap_descriptor) solvate() (mlptrain.configurations.configuration.Configuration method) statistic() (mlptrain.loss.mean_errors.MAD static method) (mlptrain.loss.mean_errors.RMSE static method) strip() (mlptrain.sampling.plumed.PlumedBias method) System (class in mlptrain.system)

T

t0 (mlptrain.configurations.trajectory.Trajectory property) t_min() (mlptrain.configurations.configuration_set.ConfigurationSet method) Tau (class in mlptrain.loss.tau) TauCalculator (class in mlptrain.loss.tau) too_large (mlptrain.training.selection.AbsDiffE property) (mlptrain.training.selection.AtomicEnvDistance property) (mlptrain.training.selection.AtomicEnvSimilarity property) (mlptrain.training.selection.SelectionMethod property)

train() (in module mlptrain.training.active) (mlptrain.potentials._base.MLPotential method) training_data (mlptrain.potentials._base.MLPotential property) Trajectory (class in mlptrain.configurations.trajectory) true_energies (mlptrain.configurations.configuration_set.ConfigurationSet property) true_forces (mlptrain.configurations.configuration_set.ConfigurationSet property) try_multiple_biasfactors() (mlptrain.sampling.metadynamics.Metadynamics method)

U

umbrella_integration() (mlptrain.sampling.umbrella.UmbrellaSampling method) UmbrellaSampling (class in mlptrain.sampling.umbrella)

unique_atomic_symbols (mlptrain.system.System property) unique_name() (in module mlptrain.utils) update_attr_from() (mlptrain.configurations.configuration.Configuration method)

V

valid_fraction (mlptrain.potentials.mace.mace.MACE property)

validate_mol_dict() (mlptrain.configurations.configuration.Configuration method) volume (mlptrain.box.Box property)

W

wham() (mlptrain.sampling.umbrella.UmbrellaSampling method) width_sequence (mlptrain.sampling.plumed.PlumedBias property)

work_in_dir() (in module mlptrain.utils) work_in_tmp_dir() (in module mlptrain.utils) write_cv_files() (mlptrain.sampling.plumed.PlumedBias method)

Z

zeta_refs (mlptrain.sampling.umbrella.UmbrellaSampling property)