Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W | X | Y | Z _ _ (IMLCV.implementations.tensorflow.CvDiscovery.hkFunBase attribute) (verlet.NVE attribute) _3d_muller_brown_cvs() (in module IMLCV.examples.example_systems) __add__() (IMLCV.base.bias.EnergyResult method) (IMLCV.base.CV.CV method) (IMLCV.base.CV.CvMetric method) (IMLCV.base.CV.CvTrans method) (IMLCV.base.CV.NeighbourList method) (IMLCV.base.CV.SystemParams method) (IMLCV.base.MdEngine.TrajectoryInfo method) (IMLCV.base.rounds.DataLoaderOutput method) __call__() (IMLCV.implementations.CvDiscovery.Decoder method) (IMLCV.implementations.CvDiscovery.Encoder method) (IMLCV.implementations.CvDiscovery.VAE method) (IMLCV.tools._rbf_interp.RBFInterpolator method) (iterative.Hook method) (npt.TBCombination method) (verlet.NVE method) (verlet.VerletHook method) __div__() (IMLCV.base.CV.CV method) __eq__() (IMLCV.tools.tools.HashableArrayWrapper method) __getattribute__() (IMLCV.tools.tools.HashableArrayWrapper method) __getitem__() (IMLCV.base.CV.CollectiveVariable method) (IMLCV.base.CV.CV method) (IMLCV.base.CV.CvMetric method) (IMLCV.base.CV.NeighbourList method) (IMLCV.base.CV.SystemParams method) (IMLCV.base.MdEngine.TrajectoryInfo method) (IMLCV.tools.tools.HashableArrayWrapper method) __getstate__() (IMLCV.base.bias.Bias method) (IMLCV.base.bias.BiasModify method) (IMLCV.base.CV.CollectiveVariable method) (IMLCV.base.CV.CV method) (IMLCV.base.CV.CvFunBase method) (IMLCV.base.CV.CvMetric method) (IMLCV.base.CV.CvTrans method) (IMLCV.base.CV.NeighbourList method) (IMLCV.base.CV.NeighbourListInfo method) (IMLCV.base.CV.NeighbourListUpdate method) (IMLCV.base.MdEngine.MDEngine method) (IMLCV.base.rounds.Rounds method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method) (IMLCV.implementations.energy.MACEASE method) (IMLCV.implementations.energy.OpenMmEnergy method) (IMLCV.implementations.tensorflow.CV.KerasFunBase method) (IMLCV.implementations.tensorflow.CV.tfl_module method) (IMLCV.tools._rbf_interp.RBFInterpolator method) __hash__() (IMLCV.tools.tools.HashableArrayWrapper method) __init_subclass__() (IMLCV.base.datastructures.MyPyTreeNode class method) __iter__() (IMLCV.base.CV.CV method) (IMLCV.base.CV.SystemParams method) __matmul__() (IMLCV.base.CV.CV method) __mul__() (IMLCV.base.CV.CV method) (IMLCV.base.CV.CvTrans method) (IMLCV.base.CVDiscovery.Transformer method) __periodic_wrap() (IMLCV.base.CV.CvMetric method) __post_init__() (IMLCV.base.MdEngine.StaticMdInfo method) (nvt.NHChain method) __radd__() (IMLCV.base.CV.CV method) __rmatmul__() (IMLCV.base.CV.CV method) __rmul__() (IMLCV.base.CV.CV method) __rsub__() (IMLCV.base.CV.CV method) __setitem__() (IMLCV.tools.tools.HashableArrayWrapper method) __setstate__() (IMLCV.base.bias.Bias method) (IMLCV.base.bias.BiasModify method) (IMLCV.base.CV.CollectiveVariable method) (IMLCV.base.CV.CV method) (IMLCV.base.CV.CvFunBase method) (IMLCV.base.CV.CvMetric method) (IMLCV.base.CV.CvTrans method) (IMLCV.base.CV.NeighbourList method) (IMLCV.base.CV.NeighbourListInfo method) (IMLCV.base.CV.NeighbourListUpdate method) (IMLCV.base.MdEngine.MDEngine method) (IMLCV.base.rounds.Rounds method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method) (IMLCV.implementations.energy.MACEASE method) (IMLCV.implementations.energy.OpenMmEnergy method) (IMLCV.implementations.tensorflow.CV.KerasFunBase method) (IMLCV.implementations.tensorflow.CV.tfl_module method) (IMLCV.tools._rbf_interp.RBFInterpolator method) __sub__() (IMLCV.base.CV.CV method) __update_CV() (IMLCV.base.rounds.Rounds method) _add_1() (IMLCV.base.rounds.KoopmanModel static method) _affine_trans() (in module IMLCV.implementations.CV) _append_trans() (in module IMLCV.implementations.CV) _apply() (IMLCV.base.rounds.DataLoaderOutput static method) _apply_bias() (IMLCV.base.rounds.DataLoaderOutput static method) _arr (IMLCV.base.MdEngine.StaticMdInfo attribute) _attr (IMLCV.base.MdEngine.StaticMdInfo attribute) _besseljn_backward_recurrence() (in module IMLCV.tools.bessel_jn) _besseljn_forward_recurrence() (in module IMLCV.tools.bessel_jn) _besseljn_power_series() (in module IMLCV.tools.bessel_jn) _c_vals() (IMLCV.base.rounds.Rounds method) _calc() (IMLCV.implementations.tensorflow.CV.KerasFunBase method) (IMLCV.implementations.tensorflow.CvDiscovery.hkFunBase method) _calculator() (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method) (IMLCV.implementations.energy.MACEASE method) _capacity (IMLCV.base.MdEngine.TrajectoryInfo attribute) _cell (IMLCV.base.MdEngine.TrajectoryInfo attribute) _charges (IMLCV.base.MdEngine.TrajectoryInfo attribute) _clip() (in module IMLCV.implementations.bias) _coeffs (IMLCV.tools._rbf_interp.RBFInterpolator attribute) _combine_dims (IMLCV.base.CV.CV attribute) _compute() (IMLCV.base.bias.Bias method) (IMLCV.base.bias.BiasF method) (IMLCV.base.bias.BiasModify method) (IMLCV.base.bias.CompositeBias method) (IMLCV.implementations.bias.BiasMTD method) (IMLCV.implementations.bias.GridBias method) (IMLCV.implementations.bias.HarmonicBias method) (IMLCV.implementations.bias.RbfBias method) _compute_angular_tensor() (npt.TadmorBarostat method) _compute_coor() (IMLCV.base.bias.Energy method) (IMLCV.base.bias.EnergyFn method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.OpenMmEnergy method) _compute_cv() (IMLCV.base.CV._ParralelCvTrans method) (IMLCV.base.CV._SerialCvTrans method) (IMLCV.base.CV.CvFun method) (IMLCV.base.CV.CvFunBase method) _compute_ekin() (verlet.VerletIntegrator method) _compute_ekin_baro() (npt.MTKBarostat method) (npt.PRBarostat method) (npt.TadmorBarostat method) _cons_err_tracker (verlet.VerletIntegrator attribute) _constant() (in module IMLCV.base.bias) _copy_from_previous_round() (IMLCV.base.rounds.Rounds method) _cv (IMLCV.base.MdEngine.TrajectoryInfo attribute) _cv_index() (in module IMLCV.implementations.CV) _cv_orig (IMLCV.base.MdEngine.TrajectoryInfo attribute) _cv_slice() (in module IMLCV.implementations.CV) _dihedral() (in module IMLCV.implementations.CV) _distance() (in module IMLCV.implementations.CV) _distance_line_from_origin() (in module IMLCV.external.hsluv) _e_bias (IMLCV.base.MdEngine.TrajectoryInfo attribute) _e_pot (IMLCV.base.MdEngine.TrajectoryInfo attribute) _ener_3d_muller_brown() (in module IMLCV.examples.example_systems) _epsilon (in module IMLCV.external.hsluv) _err (IMLCV.base.MdEngine.TrajectoryInfo attribute) _expand_capacity() (IMLCV.base.MdEngine.TrajectoryInfo method) _fes_nd_thermolib() (IMLCV.base.Observable.Observable static method) _fes_nd_weights() (IMLCV.base.Observable.Observable static method) _finished (IMLCV.base.MdEngine.TrajectoryInfo attribute) _fit() (IMLCV.base.CVDiscovery.CombineTransformer method) (IMLCV.base.CVDiscovery.CvTransTransformer method) (IMLCV.base.CVDiscovery.IdentityTransformer method) (IMLCV.base.CVDiscovery.Transformer method) (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder method) (IMLCV.implementations.CvDiscovery.TransformerMAF method) (IMLCV.implementations.CvDiscovery.TransoformerLDA method) (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP method) _from_linear() (in module IMLCV.external.hsluv) _get_bounds() (in module IMLCV.external.hsluv) _get_color_data() (IMLCV.base.CVDiscovery.Transformer static method) _get_fes_bias_from_weights() (IMLCV.base.rounds.DataLoaderOutput static method) _get_init() (IMLCV.base.rounds.Rounds static method) _get_neighbour_list() (IMLCV.base.CV.SystemParams method) _get_simul() (IMLCV.implementations.energy.OpenMmEnergy method) _grid_spec_iterator() (IMLCV.base.CVDiscovery.Transformer static method) _handle_exception() (IMLCV.base.bias.Energy method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method) _histogram() (IMLCV.base.rounds.DataLoaderOutput static method) _hpluv_to_rgb() (in module IMLCV.external.hsluv) _hsluv_to_rgb() (in module IMLCV.external.hsluv) _i_vals() (IMLCV.base.rounds.Rounds method) _identity_trans() (in module IMLCV.implementations.CV) _inv_sigma_weighing() (in module IMLCV.implementations.CV) _invalid (IMLCV.base.MdEngine.TrajectoryInfo attribute) _items_scal (IMLCV.base.MdEngine.TrajectoryInfo attribute) _items_vec (IMLCV.base.MdEngine.TrajectoryInfo attribute) _kappa (in module IMLCV.external.hsluv) _l_to_y() (in module IMLCV.external.hsluv) _lattice_invariants() (in module IMLCV.implementations.CV) _lattice_invariants_2() (in module IMLCV.implementations.CV) _lax_const (in module IMLCV.tools.spherical_bessel) _LDA_rescale() (in module IMLCV.implementations.CvDiscovery) _LDA_trans() (in module IMLCV.implementations.CvDiscovery) _length_of_ray_until_intersect() (in module IMLCV.external.hsluv) _load() (IMLCV.base.MdEngine.StaticMdInfo static method) (IMLCV.base.MdEngine.TrajectoryInfo static method) _m (in module IMLCV.external.hsluv) _m_inv (in module IMLCV.external.hsluv) _macro_chunk_map() (in module IMLCV.base.CV) _max_chroma_for_lh() (in module IMLCV.external.hsluv) _max_safe_chroma_for_l() (in module IMLCV.external.hsluv) _n_pad() (in module IMLCV.base.CV) _n_unpad() (in module IMLCV.base.CV) _name_bias() (IMLCV.base.rounds.Rounds method) _name_md() (IMLCV.base.rounds.Rounds method) _nl (IMLCV.base.bias.EnergyFn attribute) _normalize() (in module IMLCV.implementations.CV) _normalize_output() (in module IMLCV.external.hsluv) _num_vals() (IMLCV.base.rounds.Rounds method) _P (IMLCV.base.MdEngine.TrajectoryInfo attribute) _padding_bools (IMLCV.base.CV.NeighbourList attribute) _ParralelCvTrans (class in IMLCV.base.CV) _plot_1d() (IMLCV.base.CVDiscovery.Transformer static method) _plot_2d() (IMLCV.base.CVDiscovery.Transformer static method) _plot_3d() (IMLCV.base.CVDiscovery.Transformer static method) _position_index() (in module IMLCV.implementations.CV) _positions (IMLCV.base.MdEngine.TrajectoryInfo attribute) _project_distances() (in module IMLCV.implementations.CV) _quad_nd() (in module IMLCV.external.quadrature) _r_vals() (IMLCV.base.rounds.Rounds method) _ref_u (in module IMLCV.external.hsluv) _ref_v (in module IMLCV.external.hsluv) _ref_y (in module IMLCV.external.hsluv) _relative() (IMLCV.implementations.energy.Cp2kEnergy static method) _remove_mean() (in module IMLCV.implementations.CV) _restore_function() (IMLCV.Unpickler method) _restore_object_instance_variables() (IMLCV.Unpickler method) _rho (IMLCV.base.MdEngine.TrajectoryInfo attribute) (IMLCV.base.rounds.DataLoaderOutput attribute) _rho_t (IMLCV.base.rounds.DataLoaderOutput attribute) _rotate_2d() (in module IMLCV.implementations.CV) _round_information() (IMLCV.base.rounds.Rounds method) _run() (IMLCV.base.MdEngine.MDEngine method) (IMLCV.implementations.MdEngine.AseEngine method) (IMLCV.implementations.MdEngine.NewYaffEngine method) _save() (IMLCV.base.MdEngine.StaticMdInfo method) (IMLCV.base.MdEngine.TrajectoryInfo method) _sb_descriptor() (in module IMLCV.implementations.CV) _scale_cv_trans() (in module IMLCV.implementations.CV) _scale_trans() (in module IMLCV.implementations.CvDiscovery) _SerialCvTrans (class in IMLCV.base.CV) _setup_verlet() (IMLCV.implementations.MdEngine.AseEngine method) (IMLCV.implementations.MdEngine.NewYaffEngine method) _shard() (in module IMLCV.base.CV) _shard_out() (in module IMLCV.base.CV) _shrink_capacity() (IMLCV.base.MdEngine.TrajectoryInfo method) _simul (IMLCV.implementations.energy.OpenMmEnergy attribute) _sinkhorn_divergence_trans_2() (in module IMLCV.implementations.CV) _size (IMLCV.base.MdEngine.TrajectoryInfo attribute) _soap_descriptor() (in module IMLCV.implementations.CV) _sp (IMLCV.base.bias.EnergyFn attribute) _spb1_maclaurin() (in module IMLCV.tools.spherical_bessel) _spb1_maclaurin_jvp() (in module IMLCV.tools.spherical_bessel) _stack() (IMLCV.base.MdEngine.TrajectoryInfo method) _stack_dims (IMLCV.base.CV.CV attribute) _stack_reduce() (in module IMLCV.implementations.CV) _T (IMLCV.base.MdEngine.TrajectoryInfo attribute) _t (IMLCV.base.MdEngine.TrajectoryInfo attribute) _to_linear() (in module IMLCV.external.hsluv) _toy_periodic_cvs() (in module IMLCV.examples.example_systems) _trajectory_information() (IMLCV.base.rounds.Rounds method) _transform() (IMLCV.base.rounds.DataLoaderOutput static method) _trunc_svd() (in module IMLCV.implementations.CV) _un_atomize() (in module IMLCV.implementations.CV) _unstack_weights() (IMLCV.base.rounds.DataLoaderOutput static method) _update_bias() (IMLCV.base.bias.Bias method) _update_CV() (IMLCV.base.rounds.Rounds static method) _verlet (IMLCV.implementations.MdEngine.AseEngine attribute) (IMLCV.implementations.MdEngine.NewYaffEngine attribute) _verlet_initialized (IMLCV.implementations.MdEngine.AseEngine attribute) (IMLCV.implementations.MdEngine.NewYaffEngine attribute) _Volume() (in module IMLCV.implementations.CV) _w (IMLCV.base.MdEngine.TrajectoryInfo attribute) _weights (IMLCV.base.rounds.DataLoaderOutput attribute) _weights_t (IMLCV.base.rounds.DataLoaderOutput attribute) _y_to_l() (in module IMLCV.external.hsluv) _yaff_ener (IMLCV.implementations.MdEngine.NewYaffEngine attribute) _zero_cv_flow() (in module IMLCV.implementations.CV) _zero_cv_trans() (in module IMLCV.implementations.CV) _zero_fun() (in module IMLCV.base.bias) A a_p (nvt.GLEThermostat attribute) acc (verlet.VerletIntegrator attribute) add_1 (IMLCV.base.rounds.KoopmanModel attribute), [1] add_cv() (IMLCV.base.rounds.Rounds method), [1] add_press_cont() (npt.MTKBarostat method) (npt.PRBarostat method) (npt.TadmorBarostat method) add_round() (IMLCV.base.rounds.Rounds method), [1] affine_2d() (in module IMLCV.implementations.CV), [1] alanine_dipeptide_openmm() (in module IMLCV.examples.example_systems) alanine_dipeptide_refs() (in module IMLCV.examples.example_systems) amp (npt.McDonaldBarostat attribute) ampere (in module IMLCV.base.UnitsConstants) amu (in module IMLCV.base.UnitsConstants) AndersenThermostat (class in nvt) angles() (IMLCV.base.CV.SystemParams method), [1] angstrom (in module IMLCV.base.UnitsConstants) angular_moment() (in module IMLCV.new_yaff.utils) (in module utils) angular_velocity() (in module IMLCV.new_yaff.utils) (in module utils) anisotropic (npt.BerendsenBarostat attribute) (npt.LangevinBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) annealing (nvt.AndersenThermostat attribute) append_trans() (in module IMLCV.implementations.CV), [1] apply() (IMLCV.base.bias.Bias method), [1] apply_bias() (IMLCV.base.rounds.DataLoaderOutput method), [1] apply_canonicalize() (IMLCV.base.CV.SystemParams method), [1] apply_cv() (IMLCV.base.rounds.DataLoaderOutput static method), [1] apply_fun_neighbour() (IMLCV.base.CV.NeighbourList method), [1] apply_fun_neighbour_pair() (IMLCV.base.CV.NeighbourList method), [1] apply_minkowski_reduction() (IMLCV.base.CV.SystemParams method), [1] apply_rotation() (IMLCV.base.CV.SystemParams method), [1] apply_wrap() (IMLCV.base.CV.SystemParams method), [1] argmask (IMLCV.base.rounds.KoopmanModel attribute), [1] AseEnergy (class in IMLCV.implementations.energy), [1] AseEngine (class in IMLCV.implementations.MdEngine) atm (in module IMLCV.base.UnitsConstants) atom_indices (IMLCV.base.CV.NeighbourList attribute), [1] atomic (IMLCV.base.CV.CV attribute), [1] atomic_numbers (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] atoms (IMLCV.implementations.energy.AseEnergy attribute) (IMLCV.implementations.energy.Cp2kEnergy attribute) attr (npt.MTKAttributeStateItem attribute) (nvt.NHCAttributeStateItem attribute) AttributeStateItem (class in IMLCV.new_yaff.iterative) (class in iterative) au (in module IMLCV.base.UnitsConstants) avogadro (in module IMLCV.base.UnitsConstants) axis (IMLCV.base.CV.ShmapKwargs attribute), [1] axis_name (IMLCV.base.CV.ShmapKwargs attribute), [1] B backward (IMLCV.base.CV.CvFun attribute), [1] bar (in module IMLCV.base.UnitsConstants) baro() (npt.LangevinBarostat method) (npt.MTKBarostat method) (npt.PRBarostat method) (npt.TadmorBarostat method) baro_expects_call (npt.TBCombination attribute) baro_ndof (verlet.BarostatHook attribute) baro_thermo (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) barostat (IMLCV.base.MdEngine.StaticMdInfo property), [1] (npt.TBCombination attribute) BarostatHook (class in verlet) bash_app_python() (in module IMLCV.configs.bash_app_python), [1] batch() (IMLCV.base.CV.CV method), [1] (IMLCV.base.CV.NeighbourList method), [1] (IMLCV.base.CV.SystemParams method), [1] batch_dim (IMLCV.base.CV.CV property), [1] (IMLCV.base.CV.NeighbourList property), [1] (IMLCV.base.CV.SystemParams property), [1] batch_size (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder attribute), [1] batched (IMLCV.base.CV.CV property), [1] (IMLCV.base.CV.NeighbourList property), [1] (IMLCV.base.CV.SystemParams property), [1] BerendsenBarostat (class in npt) BerendsenThermostat (class in nvt) bessel_jn() (in module IMLCV.tools.bessel_jn) besseljn_backward_recurrence_cutoff() (in module IMLCV.tools.bessel_jn), [1] besseljn_jvp() (in module IMLCV.tools.bessel_jn), [1] beta (npt.BerendsenBarostat attribute) Bias (class in IMLCV.base.bias), [1] bias (IMLCV.base.bias.BiasModify attribute), [1] (IMLCV.base.MdEngine.MDEngine attribute), [1] (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.scheme.Scheme property), [1] BiasError, [1] biases (IMLCV.base.bias.CompositeBias attribute), [1] BiasF (class in IMLCV.base.bias), [1] BiasModify (class in IMLCV.base.bias), [1] BiasMTD (class in IMLCV.implementations.bias), [1] bin_counts (IMLCV.base.rounds.WeightOutput attribute), [1] boltzmann (in module IMLCV.base.UnitsConstants) bounding_box (IMLCV.base.CV.CvMetric attribute), [1] bounds (IMLCV.implementations.bias.GridBias attribute), [1] bounds_from_bias() (IMLCV.base.bias.Bias method), [1] bounds_from_cv() (IMLCV.base.CV.CvMetric static method), [1] bwd (IMLCV.implementations.tensorflow.CV.KerasFunBase attribute) bwd_kwargs (IMLCV.implementations.tensorflow.CvDiscovery.hkFunBase attribute), [1] bwd_params (IMLCV.implementations.tensorflow.CvDiscovery.hkFunBase attribute), [1] C C00 (IMLCV.base.rounds.Covariances property), [1] C01 (IMLCV.base.rounds.Covariances property), [1] C10 (IMLCV.base.rounds.Covariances property), [1] C11 (IMLCV.base.rounds.Covariances property), [1] c_p (nvt.GLEThermostat attribute) calc_neighbours() (IMLCV.base.rounds.DataLoaderOutput method), [1] calc_pi (IMLCV.base.rounds.KoopmanModel attribute), [1] call_hooks() (verlet.VerletIntegrator method) calorie (in module IMLCV.base.UnitsConstants) canonicalize() (IMLCV.base.CV.SystemParams method), [1] canonicalized_sp() (IMLCV.base.CV.NeighbourList method), [1] cell (IMLCV.base.bias.Energy property), [1] (IMLCV.base.bias.EnergyFn property), [1] (IMLCV.base.CV.SystemParams attribute), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.implementations.energy.AseEnergy property), [1] (IMLCV.new_yaff.system.YaffSys attribute) (npt.BerendsenBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) (system.YaffSys attribute) cell_lower() (in module IMLCV.new_yaff.utils) (in module utils) cell_symmetrize() (in module IMLCV.new_yaff.utils) (in module utils) cellinv0 (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) CellStateItem (class in IMLCV.new_yaff.iterative) (class in iterative) centimeter (in module IMLCV.base.UnitsConstants) chain (nvt.NHCThermostat attribute) chainvel0 (npt.TBCombination attribute) charges (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.new_yaff.system.YaffSys attribute) (system.YaffSys attribute) check_w() (IMLCV.base.rounds.DataLoaderOutput static method), [1] clean_momenta() (in module IMLCV.new_yaff.utils) (in module utils) collective_variable (IMLCV.base.bias.Bias attribute), [1] (IMLCV.base.Observable.Observable attribute), [1] (IMLCV.base.rounds.DataLoaderOutput attribute), [1] CollectiveVariable (class in IMLCV.base.CV), [1] combine() (IMLCV.base.CV.CV static method), [1] combine_dims (IMLCV.base.CV.CV property), [1] CombineTransformer (class in IMLCV.base.CVDiscovery), [1] common_bias (IMLCV.base.Observable.Observable attribute), [1] CompositeBias (class in IMLCV.base.bias), [1] compute() (ff.YaffFF method) (IMLCV.new_yaff.ff.YaffFF method) compute_cv() (IMLCV.base.CV.CollectiveVariable method), [1] (IMLCV.base.CV.CvFunBase method), [1] (IMLCV.base.CV.CvTrans method), [1] compute_from_cv() (IMLCV.base.bias.Bias method), [1] compute_from_system_params() (IMLCV.base.bias.Bias method), [1] (IMLCV.base.bias.Energy method), [1] compute_properties() (verlet.VerletIntegrator method) config() (in module IMLCV.configs.config_general), [1] (in module IMLCV.configs.hpc_ugent), [1] cons_err (verlet.VerletIntegrator attribute) ConsErrStateItem (class in IMLCV.new_yaff.iterative) (class in iterative) ConsErrTracker (class in verlet) constant_threshold (IMLCV.base.rounds.KoopmanModel attribute), [1] continue_run() (IMLCV.base.rounds.Rounds method), [1] coordinates (IMLCV.base.bias.Energy property), [1] (IMLCV.base.bias.EnergyFn property), [1] (IMLCV.base.CV.SystemParams attribute), [1] (IMLCV.implementations.energy.AseEnergy property), [1] correlation_whiten (IMLCV.base.rounds.KoopmanModel attribute), [1] coulomb (in module IMLCV.base.UnitsConstants) counter (verlet.ConsErrTracker attribute) (verlet.VerletIntegrator attribute) cov (IMLCV.base.rounds.KoopmanModel attribute), [1] Covariances (class in IMLCV.base.rounds), [1] cp2k (IMLCV.configs.config_general.ReferenceCommands attribute), [1] cp2k_inp (IMLCV.implementations.energy.Cp2kEnergy attribute) Cp2kEnergy (class in IMLCV.implementations.energy), [1] create() (ff.YaffFF static method) (IMLCV.base.bias.Bias static method), [1] (IMLCV.base.bias.BiasF static method), [1] (IMLCV.base.bias.BiasModify class method), [1] (IMLCV.base.bias.CompositeBias class method), [1] (IMLCV.base.bias.NoneBias static method), [1] (IMLCV.base.CV.CV static method), [1] (IMLCV.base.CV.CvMetric class method), [1] (IMLCV.base.CV.NeighbourList static method), [1] (IMLCV.base.CV.NeighbourListInfo static method), [1] (IMLCV.base.CV.NeighbourListUpdate static method), [1] (IMLCV.base.CV.ShmapKwargs static method), [1] (IMLCV.base.CVDiscovery.CombineTransformer static method), [1] (IMLCV.base.MdEngine.MDEngine class method), [1] (IMLCV.base.MdEngine.TrajectoryInfo static method), [1] (IMLCV.base.Observable.Observable static method), [1] (IMLCV.base.rounds.Covariances static method), [1] (IMLCV.base.rounds.KoopmanModel static method), [1] (IMLCV.base.rounds.Rounds static method), [1] (IMLCV.implementations.bias.BiasMTD class method), [1] (IMLCV.implementations.bias.GridBias class method), [1] (IMLCV.implementations.bias.HarmonicBias static method), [1] (IMLCV.implementations.bias.MinBias class method), [1] (IMLCV.implementations.bias.RbfBias class method), [1] (IMLCV.implementations.MdEngine.AseEngine static method) (IMLCV.implementations.MdEngine.NewYaffEngine static method) (IMLCV.implementations.tensorflow.CV.KerasFunBase static method) (IMLCV.new_yaff.ff.YaffFF static method) (IMLCV.new_yaff.system.YaffCell static method) (IMLCV.new_yaff.system.YaffSys static method) (IMLCV.tools._rbf_interp.RBFInterpolator class method) (system.YaffCell static method) (system.YaffSys static method) (verlet.VerletIntegrator static method) CsPbI3_MACE() (in module IMLCV.examples.example_systems) CsPbI3_MACE_lattice() (in module IMLCV.examples.example_systems) CsPbI3_refs() (in module IMLCV.examples.example_systems) csphjy() (in module IMLCV.tools.spherical_bessel) csphjy_jvp() (in module IMLCV.tools.spherical_bessel), [1] CSVRThermostat (class in nvt) cubic() (in module IMLCV.tools._rbfinterp_pythran) custom_jvp_decorator() (in module IMLCV.base.datastructures), [1] CV (class in IMLCV.base.CV), [1] cv (IMLCV.base.CV.CV attribute), [1] CV (IMLCV.base.MdEngine.TrajectoryInfo property), [1] cv (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.Rounds property), [1] (verlet.VerletIntegrator attribute) cv_0 (IMLCV.base.rounds.KoopmanModel attribute), [1] cv_norm() (in module IMLCV.tools._rbfinterp_pythran) CV_orig (IMLCV.base.MdEngine.TrajectoryInfo property), [1] cv_orig (IMLCV.base.MdEngine.TrajectoryInfo property), [1] cv_round (IMLCV.base.Observable.Observable attribute), [1] cv_t (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] cv_vals() (in module IMLCV.tools._rbf_interp) (in module IMLCV.tools._rbfinterp_pythran) CvFun (class in IMLCV.base.CV), [1] CvFunBase (class in IMLCV.base.CV), [1] CvMetric (class in IMLCV.base.CV), [1] CvTrans (class in IMLCV.base.CV), [1] CvTransTransformer (class in IMLCV.base.CVDiscovery), [1] D d (IMLCV.tools._rbf_interp.RBFInterpolator attribute) d_dtype (IMLCV.tools._rbf_interp.RBFInterpolator attribute) d_shape (IMLCV.tools._rbf_interp.RBFInterpolator attribute) data_loader() (IMLCV.base.rounds.Rounds method), [1] DATA_ROOT (in module IMLCV.examples.example_systems) DataLoaderOutput (class in IMLCV.base.rounds), [1] debye (in module IMLCV.base.UnitsConstants) decimeter (in module IMLCV.base.UnitsConstants) Decoder (class in IMLCV.implementations.CvDiscovery), [1] decoder (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP attribute), [1] decompose() (IMLCV.base.rounds.Covariances method), [1] default (IMLCV.configs.config_general.Executors attribute), [1] default_parameters (IMLCV.implementations.energy.Cp2kEnergy attribute), [1] deg (in module IMLCV.base.UnitsConstants) 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(IMLCV.base.MdEngine.TrajectoryInfo property), [1] econs (verlet.VerletIntegrator attribute) econs_correction (verlet.NVE attribute) (verlet.VerletHook attribute) econs_m (verlet.ConsErrTracker attribute) econs_s (verlet.ConsErrTracker attribute) ekin (verlet.VerletIntegrator attribute) ekin_m (verlet.ConsErrTracker attribute) ekin_new (verlet.VerletIntegrator attribute) ekin_s (verlet.ConsErrTracker attribute) electronvolt (in module IMLCV.base.UnitsConstants) encode() (IMLCV.implementations.CvDiscovery.VAE method), [1] Encoder (class in IMLCV.implementations.CvDiscovery), [1] Energy (class in IMLCV.base.bias), [1] energy (IMLCV.base.bias.EnergyResult attribute), [1] (IMLCV.base.MdEngine.MDEngine attribute), [1] EnergyError, [1] EnergyFn (class in IMLCV.base.bias), [1] EnergyResult (class in IMLCV.base.bias), [1] envj() (in module IMLCV.tools.spherical_bessel), [1] epot (verlet.VerletIntegrator attribute) eps (IMLCV.base.rounds.KoopmanModel attribute), [1] (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] eps_pre (IMLCV.base.rounds.KoopmanModel attribute), [1] (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] epsilon (IMLCV.tools._rbf_interp.RBFInterpolator attribute) equilibration (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] err (IMLCV.base.MdEngine.TrajectoryInfo property), [1] etot (verlet.VerletIntegrator attribute) eval_kernel_matrix() (in module IMLCV.tools._rbfinterp_pythran) eval_polynomial_matrix() (in module IMLCV.tools._rbfinterp_pythran) evaluate_system() (in module IMLCV.tools._rbfinterp_pythran) Executors (class in IMLCV.configs.config_general), [1] expects_call() (IMLCV.new_yaff.iterative.Hook method) (iterative.Hook method) explicit_shmap (IMLCV.base.CV.ShmapKwargs attribute), [1] external_callback (IMLCV.base.bias.Energy attribute), [1] (IMLCV.base.bias.EnergyFn attribute), [1] F f (IMLCV.base.bias.EnergyFn attribute), [1] (IMLCV.base.CV.CollectiveVariable attribute), [1] f() (IMLCV.base.rounds.KoopmanModel method), [1] f_3d_Muller_Brown() (in module IMLCV.examples.example_systems) f_toy_periodic() (in module IMLCV.examples.example_systems) femtosecond (in module IMLCV.base.UnitsConstants) FES_bias (IMLCV.base.rounds.WeightOutput attribute), [1] fes_bias() (IMLCV.base.Observable.Observable method), [1] FES_bias_std (IMLCV.base.rounds.WeightOutput attribute), [1] fes_nd_thermolib() (IMLCV.base.Observable.Observable method), [1] fes_nd_weights() (IMLCV.base.Observable.Observable method), [1] FESBias() (IMLCV.scheme.Scheme method), [1] ff module ff (verlet.VerletIntegrator attribute) field (in module IMLCV.base.datastructures) filter_nans() (IMLCV.base.rounds.DataLoaderOutput method), [1] finalize() (verlet.VerletIntegrator method) finalized (IMLCV.base.bias.Bias attribute), [1] finish_data() (IMLCV.base.rounds.Rounds method), [1] finished (IMLCV.base.rounds.TrajectoryInformation attribute), [1] fit() (IMLCV.base.CVDiscovery.Transformer method), [1] flatten() (IMLCV.JaxHandler method), [1] folder (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.Rounds attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] forcefield_name (IMLCV.implementations.energy.OpenMmEnergy attribute), [1] forward (IMLCV.base.CV.CvFun attribute), [1] from_cv_function() (IMLCV.base.CV.CvTrans static method), [1] from_refs() (IMLCV.scheme.Scheme static method), [1] full_path() (IMLCV.base.rounds.Rounds method), [1] fun (IMLCV.base.bias.BiasModify attribute), [1] (IMLCV.base.bias.CompositeBias attribute), [1] fun() (in module IMLCV.configs.bash_app_python), [1] fwd (IMLCV.implementations.tensorflow.CV.KerasFunBase attribute) fwd_kwargs (IMLCV.implementations.tensorflow.CvDiscovery.hkFunBase attribute), [1] fwd_params (IMLCV.implementations.tensorflow.CvDiscovery.hkFunBase attribute), [1] G g (IMLCV.base.bias.BiasF attribute) g() (IMLCV.base.bias.BiasF method) (IMLCV.base.rounds.KoopmanModel method), [1] G1_add (npt.TBCombination attribute) gaussian() (in module IMLCV.tools._rbfinterp_pythran) generate_bessel() (in module IMLCV.tools.bessel_callback), [1] get() (verlet.ConsErrTracker method) get_bias() (IMLCV.base.MdEngine.MDEngine method), [1] (IMLCV.base.rounds.RoundInformation method), [1] (IMLCV.base.rounds.Rounds method), [1] (IMLCV.base.rounds.TrajectoryInformation method), [1] get_bincount() (IMLCV.base.rounds.DataLoaderOutput method), [1] get_collective_variable() (IMLCV.base.rounds.Rounds method), [1] get_config() (IMLCV.implementations.tensorflow.CV.tfl_module method) (in module IMLCV.configs.local_threadpool), [1] get_d() (in module IMLCV.tools._rbfinterp_pythran) get_econs_correction() (nvt.NHChain method) get_energy() (IMLCV.base.MdEngine.MDEngine method), [1] get_engine() (IMLCV.base.rounds.RoundInformation method), [1] (IMLCV.base.rounds.Rounds method), [1] get_feature_cov() (in module IMLCV.implementations.CV), [1] get_fes_bias_from_weights() (IMLCV.base.rounds.DataLoaderOutput method), [1] get_histo() (IMLCV.base.rounds.DataLoaderOutput static method), [1] get_info() (IMLCV.implementations.energy.OpenMmEnergy method), [1] get_inv_sigma_weighing() (in module IMLCV.implementations.CV), [1] get_n() (IMLCV.base.CV.CvMetric static method), [1] get_n_skip() (IMLCV.base.rounds.KoopmanModel method), [1] get_ndof_baro() (in module IMLCV.new_yaff.utils) (in module utils) get_ndof_internal_md() (in module IMLCV.new_yaff.utils) (in module utils) get_neighbour_list() (IMLCV.base.CV.SystemParams method), [1] get_non_constant_trans() (in module IMLCV.implementations.CV), [1] get_normalize_trans() (in module IMLCV.implementations.CV), [1] get_platform() (in module IMLCV.configs.config_general), [1] get_point() (IMLCV.base.rounds.DataLoaderOutput method), [1] get_random_vel() (in module IMLCV.new_yaff.utils) (in module utils) get_random_vel_press() (in module IMLCV.new_yaff.utils) (in module utils) get_random_vel_therm() (nvt.NHChain method) get_remove_mean_trans() (in module IMLCV.implementations.CV), [1] get_round() (IMLCV.base.rounds.Rounds method), [1] get_sinkhorn_divergence_2() (in module IMLCV.implementations.CV), [1] get_slurm_provider() (in module IMLCV.configs.hpc_ugent), [1] get_static_trajectory_info() (IMLCV.base.rounds.Rounds method), [1] get_trajectory() (IMLCV.base.MdEngine.MDEngine method), [1] get_transformed_fes() (IMLCV.base.rounds.DataLoaderOutput method), [1] get_value() (IMLCV.new_yaff.iterative.AttributeStateItem method) (IMLCV.new_yaff.iterative.CellStateItem method) (IMLCV.new_yaff.iterative.ConsErrStateItem method) (IMLCV.new_yaff.iterative.PosStateItem method) (IMLCV.new_yaff.iterative.StateItem method) (iterative.AttributeStateItem method) (iterative.CellStateItem method) (iterative.ConsErrStateItem method) (iterative.PosStateItem method) (iterative.StateItem method) (npt.MTKAttributeStateItem method) (nvt.NHCAttributeStateItem method) (verlet.TemperatureStateItem method) get_vtens_finite_difference() (IMLCV.base.bias.Energy 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(in module IMLCV.external.hsluv), [1] hpluv_to_rgb (in module IMLCV.external.hsluv) hpluv_to_rgb() (in module IMLCV.external.hsluv) hsluv_to_lch() (in module IMLCV.external.hsluv), [1] hsluv_to_rgb() (in module IMLCV.external.hsluv), [1] I i_recurrence() (in module IMLCV.tools.bessel_callback), [1] identity_trans (in module IMLCV.implementations.CV) IdentityTransformer (class in IMLCV.base.CVDiscovery), [1] ie_n() (in module IMLCV.tools.bessel_callback) ie_n_jvp() (in module IMLCV.tools.bessel_callback), [1] ie_n_recurrence_pattern() (in module IMLCV.tools.bessel_callback), [1] ie_n_recurrence_pattern_unstalbe() (in module IMLCV.tools.bessel_callback), [1] ijk_indices (IMLCV.base.CV.NeighbourList attribute), [1] IMLCV module, [1] IMLCV.base module, [1] IMLCV.base.bias module, [1] IMLCV.base.CV module, [1] IMLCV.base.CVDiscovery module, [1] IMLCV.base.datastructures module, [1] IMLCV.base.MdEngine module, [1] IMLCV.base.Observable module, [1] IMLCV.base.rounds module, [1] IMLCV.base.UnitsConstants module, [1] IMLCV.configs module, [1] IMLCV.configs.bash_app_python module, [1] IMLCV.configs.config_general module, [1] IMLCV.configs.hpc_ugent module, [1] IMLCV.configs.local_threadpool module, [1] IMLCV.examples module, [1] IMLCV.examples.example_systems module IMLCV.external module, [1] IMLCV.external.hsluv module, [1] IMLCV.external.quadrature module, [1] IMLCV.external.tf2jax module IMLCV.implementations module, [1] IMLCV.implementations.bias module, [1] IMLCV.implementations.CV module, [1] IMLCV.implementations.CvDiscovery module, [1] IMLCV.implementations.energy module, [1] IMLCV.implementations.MdEngine module IMLCV.implementations.tensorflow module, [1] IMLCV.implementations.tensorflow.CV module IMLCV.implementations.tensorflow.CvDiscovery module, [1] IMLCV.new_yaff module IMLCV.new_yaff.ff module IMLCV.new_yaff.iterative module IMLCV.new_yaff.system module IMLCV.new_yaff.utils module IMLCV.scheme module, [1] IMLCV.tools module, [1] IMLCV.tools._rbf_interp module IMLCV.tools._rbfinterp_pythran module IMLCV.tools.bessel_callback module, [1] IMLCV.tools.bessel_jn module, [1] IMLCV.tools.soap_kernel module, [1] IMLCV.tools.spherical_bessel module, [1] IMLCV.tools.tools module, [1] inertia_tensor() (in module IMLCV.new_yaff.utils) (in module utils) info (IMLCV.base.CV.NeighbourList attribute), [1] init() (npt.BerendsenBarostat method) (npt.LangevinBarostat method) (npt.McDonaldBarostat method) (npt.MTKBarostat method) (npt.PRBarostat method) (npt.TadmorBarostat method) (npt.TBCombination method) (nvt.AndersenThermostat method) (nvt.BerendsenThermostat method) (nvt.CSVRThermostat method) (nvt.GLEThermostat method) (nvt.LangevinThermostat method) (nvt.NHCThermostat method) (verlet.NVE method) (verlet.VerletHook method) inner_loop() (IMLCV.scheme.Scheme method), [1] input_kwargs (IMLCV.implementations.energy.Cp2kEnergy attribute) invalid (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] invalidate_data() (IMLCV.base.rounds.Rounds method), [1] inverse_multiquadric() (in module IMLCV.tools._rbfinterp_pythran) inverse_quadratic() (in module IMLCV.tools._rbfinterp_pythran) is_finished() (IMLCV.base.rounds.Rounds method), [1] is_valid() (IMLCV.base.rounds.Rounds method), [1] is_zipped() (IMLCV.base.rounds.Rounds method), [1] iter() (IMLCV.base.rounds.Rounds method), [1] iter_ase_atoms() (IMLCV.base.rounds.Rounds method), [1] iterative module iv (in module IMLCV.tools.bessel_callback) ive (in module IMLCV.tools.bessel_callback) J j0() (in module IMLCV.tools.bessel_jn) j0_large() (in module IMLCV.tools.bessel_jn), [1] j0_small() (in module IMLCV.tools.bessel_jn), [1] j1() (in module IMLCV.tools.bessel_jn) j1_large() (in module IMLCV.tools.bessel_jn), [1] j1_small() (in module IMLCV.tools.bessel_jn), [1] jac (IMLCV.base.CV.CollectiveVariable attribute) jac() (IMLCV.base.CV.CollectiveVariable method) JaxHandler (class in IMLCV), [1] jint() (in module IMLCV.tools.spherical_bessel), [1] jit_decorator() (in module IMLCV.base.datastructures), [1] joule (in module IMLCV.base.UnitsConstants) jv (in module IMLCV.tools.bessel_callback) K K (IMLCV.implementations.bias.BiasMTD attribute), [1] k (IMLCV.implementations.bias.HarmonicBias attribute), [1] k_max (IMLCV.implementations.bias.HarmonicBias attribute), [1] kcalmol (in module IMLCV.base.UnitsConstants) kelvin (in module IMLCV.base.UnitsConstants) KerasFunBase (class in IMLCV.implementations.tensorflow.CV) kernel (IMLCV.implementations.CvDiscovery.TransoformerLDA attribute), [1] (IMLCV.tools._rbf_interp.RBFInterpolator attribute) kernel_dist() (in module IMLCV.implementations.CV), [1] key (IMLCV.new_yaff.iterative.CellStateItem attribute) (IMLCV.new_yaff.iterative.PosStateItem attribute) (IMLCV.new_yaff.iterative.StateItem attribute) KEY (in module IMLCV) key (iterative.CellStateItem attribute) (iterative.PosStateItem attribute) (iterative.StateItem attribute) (npt.LangevinBarostat attribute) (npt.McDonaldBarostat attribute) (npt.MTKAttributeStateItem attribute) (npt.MTKBarostat attribute) (npt.TadmorBarostat attribute) (nvt.CSVRThermostat attribute) (nvt.GLEThermostat attribute) (nvt.LangevinThermostat attribute) (nvt.NHChain attribute) kilogram (in module IMLCV.base.UnitsConstants) kin (nvt.CSVRThermostat attribute) (nvt.GLEThermostat attribute) kind (IMLCV.new_yaff.iterative.Hook attribute) (iterative.Hook attribute) (npt.BerendsenBarostat attribute) (npt.LangevinBarostat attribute) (npt.McDonaldBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) (nvt.AndersenThermostat attribute) (nvt.BerendsenThermostat attribute) (nvt.CSVRThermostat attribute) (nvt.GLEThermostat attribute) (nvt.LangevinThermostat attribute) (nvt.NHCThermostat attribute) kjmol (in module IMLCV.base.UnitsConstants) kl_divergence() (IMLCV.base.bias.Bias method), [1] koopman_model() (IMLCV.base.rounds.DataLoaderOutput method), [1] koopman_weight() (IMLCV.base.rounds.DataLoaderOutput method), [1] (IMLCV.base.rounds.KoopmanModel method), [1] KoopmanModel (class in IMLCV.base.rounds), [1] Ks (IMLCV.implementations.bias.BiasMTD attribute), [1] kv (in module IMLCV.tools.bessel_callback) kve (in module IMLCV.tools.bessel_callback) kwargs (IMLCV.base.bias.BiasF attribute), [1] (IMLCV.base.bias.BiasModify attribute), [1] (IMLCV.base.bias.EnergyFn attribute), [1] (IMLCV.base.CV.CvFunBase attribute), [1] (IMLCV.implementations.energy.Cp2kEnergy attribute) L labels (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.WeightOutput attribute), [1] langevin (IMLCV.implementations.MdEngine.AseEngine attribute) LangevinBarostat (class in npt) LangevinThermostat (class in nvt) latents (IMLCV.implementations.CvDiscovery.Decoder attribute), [1] (IMLCV.implementations.CvDiscovery.Encoder attribute), [1] (IMLCV.implementations.CvDiscovery.VAE attribute), [1] LatticeInvariants (in module IMLCV.implementations.CV) LatticeInvariants2 (in module IMLCV.implementations.CV) layers (IMLCV.implementations.CvDiscovery.Decoder attribute), [1] (IMLCV.implementations.CvDiscovery.Encoder attribute), [1] (IMLCV.implementations.CvDiscovery.VAE attribute), [1] lch_to_hpluv() (in module IMLCV.external.hsluv), [1] lch_to_hsluv() (in module IMLCV.external.hsluv), [1] lch_to_luv() (in module IMLCV.external.hsluv), [1] lch_to_rgb() (in module IMLCV.external.hsluv), [1] legendre() (in module IMLCV.tools.soap_kernel) legendre_l() (in module IMLCV.tools.soap_kernel) length (nvt.NHChain attribute) lightspeed (in module IMLCV.base.UnitsConstants) linear() (in module IMLCV.tools._rbfinterp_pythran) liter (in module IMLCV.base.UnitsConstants) load() (IMLCV.base.bias.Bias static method), [1] (IMLCV.base.bias.Energy static method), [1] (IMLCV.base.CV.CollectiveVariable static method), [1] (IMLCV.base.MdEngine.MDEngine static method), [1] (IMLCV.base.MdEngine.StaticMdInfo static method), [1] (IMLCV.base.MdEngine.TrajectoryInfo static method), [1] (IMLCV.implementations.MdEngine.NewYaffEngine static method) (in module IMLCV.configs.bash_app_python), [1] log_exp_slice (IMLCV.base.bias.Bias attribute), [1] logger (in module IMLCV.configs.hpc_ugent) loop_batcher() (in module IMLCV.external.tf2jax) lr (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder attribute), [1] luv_to_lch() (in module IMLCV.external.hsluv), [1] luv_to_xyz() (in module IMLCV.external.hsluv), [1] M MACEASE (class in IMLCV.implementations.energy), [1] macro_chunk_map() (in module IMLCV.base.CV), [1] macro_chunk_map_fun() (in module IMLCV.base.CV), [1] manual_vtens (IMLCV.base.bias.Energy attribute), [1] map() (IMLCV.base.CV.CvMetric method), [1] mapped (IMLCV.base.CV.CV attribute), [1] mask() (IMLCV.base.rounds.Covariances method), [1] mass_press (npt.BerendsenBarostat attribute) (npt.LangevinBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) masses (IMLCV.base.MdEngine.StaticMdInfo property), [1] (IMLCV.new_yaff.system.YaffSys attribute) (nvt.NHChain attribute) (system.YaffSys attribute) (verlet.VerletIntegrator attribute) max_features (IMLCV.base.rounds.KoopmanModel attribute), [1] (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] max_features_pre (IMLCV.base.rounds.KoopmanModel attribute), [1] (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] max_grad (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] max_iterations (IMLCV.implementations.CvDiscovery.TransoformerLDA attribute), [1] McDonaldBarostat (class in npt) md (IMLCV.scheme.Scheme property), [1] md_engine (ff.YaffFF attribute) (IMLCV.new_yaff.ff.YaffFF attribute) MDEngine (class in IMLCV.base.MdEngine), [1] mesh (IMLCV.base.CV.ShmapKwargs attribute), [1] meter (in module IMLCV.base.UnitsConstants) method (IMLCV.implementations.CvDiscovery.TransoformerLDA attribute), [1] (IMLCV.new_yaff.iterative.Hook attribute) (iterative.Hook attribute) (npt.BerendsenBarostat attribute) (npt.LangevinBarostat attribute) (npt.McDonaldBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) (nvt.AndersenThermostat attribute) (nvt.BerendsenThermostat attribute) (nvt.CSVRThermostat attribute) (nvt.GLEThermostat attribute) (nvt.LangevinThermostat attribute) (nvt.NHCThermostat attribute) metric (IMLCV.base.CV.CollectiveVariable attribute), [1] (IMLCV.tools._rbf_interp.RBFInterpolator attribute) micrometer (in module IMLCV.base.UnitsConstants) miligram (in module IMLCV.base.UnitsConstants) milimeter (in module IMLCV.base.UnitsConstants) min_cv() (IMLCV.base.CV.CvMetric method), [1] min_distance() (IMLCV.base.CV.SystemParams method), [1] min_gradient_norm (IMLCV.implementations.CvDiscovery.TransoformerLDA attribute), [1] min_step_size (IMLCV.implementations.CvDiscovery.TransoformerLDA attribute), [1] min_t_frac (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] MinBias (class in IMLCV.implementations.bias), [1] minkowski_reduce() (IMLCV.base.CV.SystemParams method), [1] mod (IMLCV.implementations.tensorflow.CV.tfl_module attribute) module ff IMLCV, [1] IMLCV.base, [1] IMLCV.base.bias, [1] IMLCV.base.CV, [1] IMLCV.base.CVDiscovery, [1] IMLCV.base.datastructures, [1] IMLCV.base.MdEngine, [1] IMLCV.base.Observable, [1] IMLCV.base.rounds, [1] IMLCV.base.UnitsConstants, [1] IMLCV.configs, [1] IMLCV.configs.bash_app_python, [1] IMLCV.configs.config_general, [1] IMLCV.configs.hpc_ugent, [1] IMLCV.configs.local_threadpool, [1] IMLCV.examples, [1] IMLCV.examples.example_systems IMLCV.external, [1] IMLCV.external.hsluv, [1] IMLCV.external.quadrature, [1] IMLCV.external.tf2jax IMLCV.implementations, [1] IMLCV.implementations.bias, [1] IMLCV.implementations.CV, [1] IMLCV.implementations.CvDiscovery, [1] IMLCV.implementations.energy, [1] IMLCV.implementations.MdEngine IMLCV.implementations.tensorflow, [1] IMLCV.implementations.tensorflow.CV IMLCV.implementations.tensorflow.CvDiscovery, [1] IMLCV.new_yaff IMLCV.new_yaff.ff IMLCV.new_yaff.iterative IMLCV.new_yaff.system IMLCV.new_yaff.utils IMLCV.scheme, [1] IMLCV.tools, [1] IMLCV.tools._rbf_interp IMLCV.tools._rbfinterp_pythran IMLCV.tools.bessel_callback, [1] IMLCV.tools.bessel_jn, [1] IMLCV.tools.soap_kernel, [1] IMLCV.tools.spherical_bessel, [1] IMLCV.tools.tools, [1] iterative npt nvt system utils verlet mol (in module IMLCV.base.UnitsConstants) moved_functions (in module IMLCV) msta1() (in module IMLCV.tools.spherical_bessel), [1] msta2() (in module IMLCV.tools.spherical_bessel), [1] MTKAttributeStateItem (class in npt) MTKBarostat (class in npt) multiquadric() (in module IMLCV.tools._rbfinterp_pythran) MyPyTreeNode (class in IMLCV.base.datastructures), [1] N n (IMLCV.base.CV.CollectiveVariable property), [1] (IMLCV.implementations.bias.GridBias attribute), [1] n() (IMLCV.base.rounds.Rounds method), [1] n_atoms (nvt.GLEThermostat attribute) n_devices (IMLCV.base.CV.ShmapKwargs attribute), [1] n_neighbors (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP attribute), [1] name (IMLCV.implementations.CvDiscovery.Decoder attribute) (IMLCV.implementations.CvDiscovery.Encoder attribute) (IMLCV.implementations.CvDiscovery.VAE attribute) (IMLCV.new_yaff.iterative.Hook attribute) (iterative.Hook attribute) (npt.BerendsenBarostat attribute) (npt.LangevinBarostat attribute) (npt.McDonaldBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) (npt.TBCombination attribute) (nvt.AndersenThermostat attribute) (nvt.BerendsenThermostat attribute) (nvt.CSVRThermostat attribute) (nvt.GLEThermostat attribute) (nvt.LangevinThermostat attribute) (nvt.NHCThermostat attribute) name_bias (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] name_md (IMLCV.base.rounds.RoundInformation attribute), [1] NAME_TO_FUNC (in module IMLCV.tools._rbfinterp_pythran) nanometer (in module IMLCV.base.UnitsConstants) nanosecond (in module IMLCV.base.UnitsConstants) natom (IMLCV.new_yaff.system.YaffSys property) (system.YaffSys property) ndim (IMLCV.base.CV.CvMetric property), [1] ndof (nvt.NHChain attribute) (verlet.VerletIntegrator attribute) needs_calculation (IMLCV.base.CV.NeighbourList property), [1] needs_update() (IMLCV.base.CV.NeighbourList method), [1] neighbour_list_info (IMLCV.base.MdEngine.StaticMdInfo property), [1] neighbour_pos() (IMLCV.base.CV.NeighbourList method), [1] NeighbourList (class in IMLCV.base.CV), [1] NeighbourListInfo (class in IMLCV.base.CV), [1] NeighbourListUpdate (class in IMLCV.base.CV), [1] new_bias() (IMLCV.base.MdEngine.MDEngine method), [1] newton (in module IMLCV.base.UnitsConstants) NewYaffEngine (class in IMLCV.implementations.MdEngine) NHCAttributeStateItem (class in nvt) NHChain (class in nvt) NHCThermostat (class in nvt) nl (IMLCV.base.bias.Energy property), [1] (IMLCV.base.bias.EnergyFn property), [1] (IMLCV.base.MdEngine.MDEngine attribute), [1] (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] nl_split_z() (IMLCV.base.CV.NeighbourList method), [1] (IMLCV.base.CV.NeighbourListInfo method), [1] nl_t (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] nlayers (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder attribute), [1] (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP attribute), [1] nneighs() (IMLCV.base.CV.NeighbourList method), [1] NoneBias (class in IMLCV.base.bias), [1] NoneCV() (in module IMLCV.implementations.CV), [1] norm() (IMLCV.base.CV.CvMetric method), [1] norm_w() (IMLCV.base.rounds.DataLoaderOutput static method), [1] npt module ns (nvt.GLEThermostat attribute) num (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] num_epochs (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder attribute), [1] num_neighs (IMLCV.base.CV.NeighbourListUpdate attribute), [1] num_vals (IMLCV.base.rounds.RoundInformation attribute), [1] num_z_unique (IMLCV.base.CV.NeighbourListInfo attribute), [1] numbers (IMLCV.new_yaff.system.YaffSys attribute) (system.YaffSys attribute) nunits (IMLCV.implementations.CvDiscovery.Decoder attribute), [1] (IMLCV.implementations.CvDiscovery.Encoder attribute), [1] (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder attribute), [1] (IMLCV.implementations.CvDiscovery.VAE attribute), [1] (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP attribute), [1] NVE (class in verlet) nvec (IMLCV.new_yaff.system.YaffCell property) (system.YaffCell property) nvt module nxyz (IMLCV.base.CV.NeighbourListUpdate attribute), [1] O Observable (class in IMLCV.base.Observable), [1] offset (IMLCV.implementations.bias.RbfBias attribute), [1] only_diag (IMLCV.base.rounds.Covariances attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] op_cell (IMLCV.base.CV.NeighbourList attribute), [1] op_center (IMLCV.base.CV.NeighbourList attribute), [1] op_coor (IMLCV.base.CV.NeighbourList attribute), [1] OpenMmEnergy (class in IMLCV.implementations.energy), [1] optimizer (IMLCV.implementations.CvDiscovery.TransoformerLDA attribute), [1] order (IMLCV.implementations.bias.GridBias attribute), [1] ORDER (in module IMLCV.tools.bessel_callback) other_hooks (verlet.VerletIntegrator attribute) out_axes (IMLCV.base.CV.ShmapKwargs attribute), [1] out_dim (IMLCV.base.rounds.KoopmanModel attribute), [1] outdim (IMLCV.base.CVDiscovery.Transformer attribute), [1] P P (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.base.rounds.Rounds property), [1] (in module IMLCV.base.CV), [1] (in module IMLCV.base.datastructures) (in module IMLCV.configs.bash_app_python) (in module IMLCV.external.quadrature) (in module IMLCV.tools.soap_kernel) (npt.PRBarostat attribute) P2 (in module IMLCV.base.CV) (in module IMLCV.base.datastructures) p_i() (in module IMLCV.tools.soap_kernel), [1] p_inl_sb() (in module IMLCV.tools.soap_kernel), [1] p_innl_soap() (in module IMLCV.tools.soap_kernel), [1] p_select (IMLCV.base.rounds.WeightOutput attribute), [1] padded_shard_map() (in module IMLCV.base.CV), [1] padded_vmap() (in module IMLCV.base.CV), [1] padding_bools (IMLCV.base.CV.NeighbourList property), [1] parametric (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP attribute), [1] parent (IMLCV.implementations.CvDiscovery.Decoder attribute) (IMLCV.implementations.CvDiscovery.Encoder attribute) (IMLCV.implementations.CvDiscovery.VAE attribute) parser (in module IMLCV.configs.bash_app_python) PARSL_DICT (in module IMLCV.configs.config_general) Partial_decorator() (in module IMLCV.base.datastructures), [1] pascal (in module IMLCV.base.UnitsConstants) path() (IMLCV.base.rounds.Rounds method), [1] pdb (IMLCV.implementations.energy.OpenMmEnergy attribute), [1] periodic_wrap() (IMLCV.base.CV.CvMetric method), [1] periodicities (IMLCV.base.CV.CvMetric attribute), [1] pi_0 (IMLCV.base.rounds.Covariances property), [1] pi_1 (IMLCV.base.rounds.Covariances property), [1] pi_s_0 (IMLCV.base.rounds.Covariances attribute), [1] pi_s_1 (IMLCV.base.rounds.Covariances attribute), [1] picometer (in module IMLCV.base.UnitsConstants) picosecond (in module IMLCV.base.UnitsConstants) PIO4 (in module IMLCV.tools.bessel_jn) planck (in module IMLCV.base.UnitsConstants) plot() (IMLCV.base.bias.Bias method), [1] plot_app() (IMLCV.base.CVDiscovery.Transformer static method), [1] plot_cv_discovery() (IMLCV.base.rounds.Rounds method), [1] plot_md_run() (IMLCV.base.rounds.Rounds static method), [1] plot_round() (IMLCV.base.rounds.Rounds method), [1] PlumedEnerg (class in IMLCV.base.bias), [1] pmap (IMLCV.base.CV.ShmapKwargs attribute), [1] pos (IMLCV.new_yaff.system.YaffSys attribute) (nvt.NHChain attribute) (system.YaffSys attribute) (verlet.VerletIntegrator attribute) pos0 (nvt.NHChain attribute) pos_old (verlet.VerletIntegrator attribute) position_index() (in module IMLCV.implementations.CV), [1] positions (IMLCV.base.MdEngine.TrajectoryInfo property), [1] PosStateItem (class in IMLCV.new_yaff.iterative) (class in iterative) post() (npt.BerendsenBarostat method) (npt.LangevinBarostat method) (npt.McDonaldBarostat method) (npt.MTKBarostat method) (npt.PRBarostat method) (npt.TadmorBarostat method) (npt.TBCombination method) (nvt.AndersenThermostat method) (nvt.BerendsenThermostat method) (nvt.CSVRThermostat method) (nvt.GLEThermostat method) (nvt.LangevinThermostat method) (nvt.NHCThermostat method) (verlet.BarostatHook method) (verlet.NVE method) (verlet.ThermostatHook method) (verlet.VerletHook method) post_scale (IMLCV.base.CVDiscovery.Transformer attribute), [1] powers (IMLCV.tools._rbf_interp.RBFInterpolator attribute) PP0 (in module IMLCV.tools.bessel_jn) PP1 (in module IMLCV.tools.bessel_jn) PQ0 (in module IMLCV.tools.bessel_jn) PQ1 (in module IMLCV.tools.bessel_jn) PRBarostat (class in npt) pre() (npt.BerendsenBarostat method) (npt.LangevinBarostat method) (npt.McDonaldBarostat method) (npt.MTKBarostat method) (npt.PRBarostat method) (npt.TadmorBarostat method) (npt.TBCombination method) (nvt.AndersenThermostat method) (nvt.BerendsenThermostat method) (nvt.CSVRThermostat method) (nvt.GLEThermostat method) (nvt.LangevinThermostat method) (nvt.NHCThermostat method) (verlet.BarostatHook method) (verlet.NVE method) (verlet.ThermostatHook method) (verlet.VerletHook method) pre_fit() (IMLCV.base.CVDiscovery.Transformer method), [1] pre_scale (IMLCV.base.CVDiscovery.Transformer attribute), [1] press (npt.TBCombination attribute) (verlet.BarostatHook attribute) (verlet.VerletIntegrator attribute) project_distances() (in module IMLCV.implementations.CV), [1] propagate() (verlet.VerletIntegrator method) ptens (verlet.VerletIntegrator attribute) py_env (in module IMLCV.configs.config_general) pytreenode_equal() (in module IMLCV), [1] Q q0 (IMLCV.implementations.bias.HarmonicBias attribute), [1] q0s (IMLCV.implementations.bias.BiasMTD attribute), [1] QP0 (in module IMLCV.tools.bessel_jn) QP1 (in module IMLCV.tools.bessel_jn) QQ0 (in module IMLCV.tools.bessel_jn) QQ1 (in module IMLCV.tools.bessel_jn) quad() (in module IMLCV.external.quadrature), [1] quad_bounds() (in module IMLCV.external.quadrature), [1] quintic() (in module IMLCV.tools._rbfinterp_pythran) R r0 (IMLCV.implementations.bias.HarmonicBias attribute), [1] r_cut (IMLCV.base.CV.NeighbourListInfo attribute), [1] (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] r_skin (IMLCV.base.CV.NeighbourListInfo attribute), [1] (IMLCV.base.MdEngine.MDEngine attribute), [1] rad (in module IMLCV.base.UnitsConstants) rbf (IMLCV.implementations.bias.RbfBias attribute), [1] RbfBias (class in IMLCV.implementations.bias), [1] RBFInterpolator (class in IMLCV.tools._rbf_interp) recalc() (IMLCV.base.rounds.DataLoaderOutput method), [1] reference (IMLCV.configs.config_general.Executors attribute), [1] REFERENCE_COMMANDS (in module IMLCV.configs.config_general) ReferenceCommands (class in IMLCV.configs.config_general), [1] rel_path() (IMLCV.base.rounds.Rounds method), [1] remove_angular_moment() (in module IMLCV.new_yaff.utils) (in module utils) remove_com_moment() (in module IMLCV.new_yaff.utils) (in module utils) reparameterize() (IMLCV.implementations.CvDiscovery.VAE class method), [1] replace() (IMLCV.base.bias.Bias method) (IMLCV.base.bias.BiasF method) (IMLCV.base.bias.BiasModify method) (IMLCV.base.bias.CompositeBias method) (IMLCV.base.bias.EnergyFn method) (IMLCV.base.bias.EnergyResult method) (IMLCV.base.bias.NoneBias method) (IMLCV.base.CV.CollectiveVariable method) (IMLCV.base.CV.CV method) (IMLCV.base.CV.CvFun method) (IMLCV.base.CV.CvFunBase method) (IMLCV.base.CV.CvMetric method) (IMLCV.base.CV.CvTrans method) (IMLCV.base.CV.NeighbourList method) (IMLCV.base.CV.NeighbourListInfo method) (IMLCV.base.CV.NeighbourListUpdate method) (IMLCV.base.CV.ShmapKwargs method) (IMLCV.base.CV.SystemParams method) (IMLCV.base.CVDiscovery.CombineTransformer method) (IMLCV.base.CVDiscovery.CvTransTransformer method) (IMLCV.base.CVDiscovery.IdentityTransformer method) (IMLCV.base.CVDiscovery.Transformer method) (IMLCV.base.datastructures.MyPyTreeNode method), [1] (IMLCV.base.MdEngine.TrajectoryInfo method) (IMLCV.base.rounds.Covariances method) (IMLCV.base.rounds.DataLoaderOutput method) (IMLCV.base.rounds.KoopmanModel method) (IMLCV.base.rounds.WeightOutput method) (IMLCV.implementations.bias.BiasMTD method) (IMLCV.implementations.bias.GridBias method) (IMLCV.implementations.bias.HarmonicBias method) (IMLCV.implementations.bias.MinBias method) (IMLCV.implementations.bias.RbfBias method) (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder method) (IMLCV.implementations.CvDiscovery.TransformerMAF method) (IMLCV.implementations.CvDiscovery.TransoformerLDA method) (IMLCV.implementations.tensorflow.CvDiscovery.hkFunBase method) (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP method) (IMLCV.new_yaff.ff.YaffFF method) (IMLCV.new_yaff.iterative.AttributeStateItem method) (IMLCV.new_yaff.iterative.CellStateItem method) (IMLCV.new_yaff.iterative.ConsErrStateItem method) (IMLCV.new_yaff.iterative.Hook method) (IMLCV.new_yaff.iterative.PosStateItem method) (IMLCV.new_yaff.iterative.StateItem method) (IMLCV.new_yaff.system.YaffCell method) (IMLCV.new_yaff.system.YaffSys method) resample() (IMLCV.base.bias.Bias method), [1] RESOURCES_DICT (in module IMLCV.configs.config_general) restart_pos (nvt.NHChain attribute) restart_vel (nvt.NHChain attribute) restore() (IMLCV.JaxHandler method), [1] rgb_to_hpluv() (in module IMLCV.external.hsluv), [1] rgb_to_hsluv() (in module IMLCV.external.hsluv), [1] rgb_to_lch() (in module IMLCV.external.hsluv), [1] rgb_to_xyz() (in module IMLCV.external.hsluv), [1] rho (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] rho_00 (IMLCV.base.rounds.Covariances attribute), [1] rho_01 (IMLCV.base.rounds.Covariances attribute), [1] rho_10 (IMLCV.base.rounds.Covariances attribute), [1] rho_11 (IMLCV.base.rounds.Covariances attribute), [1] rho_t (IMLCV.base.rounds.KoopmanModel attribute), [1] rigid_body_angular_velocities() (in module IMLCV.new_yaff.utils) (in module utils) rmsd_delta (verlet.VerletIntegrator attribute) rmsd_gpos (verlet.VerletIntegrator attribute) rmsd_gpos_bias (verlet.VerletIntegrator attribute) rnd (IMLCV.base.Observable.Observable attribute), [1] ROOT_DIR (in module IMLCV.configs.config_general) (in module IMLCV.configs.hpc_ugent) rotate_2d() (in module IMLCV.implementations.CV), [1] rotate_cell() (IMLCV.base.CV.SystemParams method), [1] round (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.Rounds property), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] RoundInformation (class in IMLCV.base.rounds), [1] Rounds (class in IMLCV.base.rounds), [1] rounds (IMLCV.base.Observable.Observable attribute), [1] (IMLCV.scheme.Scheme attribute), [1] rp (IMLCV.implementations.energy.Cp2kEnergy attribute) RP0 (in module IMLCV.tools.bessel_jn) RP1 (in module IMLCV.tools.bessel_jn) RQ0 (in module IMLCV.tools.bessel_jn) RQ1 (in module IMLCV.tools.bessel_jn) run() (IMLCV.base.MdEngine.MDEngine method), [1] (IMLCV.base.rounds.Rounds method), [1] (verlet.VerletIntegrator method) run_md() (IMLCV.base.rounds.Rounds static method), [1] run_par() (IMLCV.base.rounds.Rounds method), [1] rvecs (IMLCV.new_yaff.system.YaffCell attribute) (system.YaffCell attribute) (verlet.VerletIntegrator attribute) rydberg (in module IMLCV.base.UnitsConstants) S s (IMLCV.base.rounds.KoopmanModel attribute), [1] S (in module IMLCV.base.CV) (nvt.GLEThermostat attribute) S_ani (npt.PRBarostat attribute) save() (IMLCV.base.bias.Bias method), [1] (IMLCV.base.bias.Energy method), [1] (IMLCV.base.CV.CollectiveVariable method), [1] (IMLCV.base.MdEngine.MDEngine method), [1] (IMLCV.base.MdEngine.StaticMdInfo method), [1] (IMLCV.base.MdEngine.TrajectoryInfo method), [1] save_step() (IMLCV.base.MdEngine.MDEngine method), [1] sb_descriptor() (in module IMLCV.implementations.CV), [1] scale_cv_trans() (in module IMLCV.implementations.CV), [1] scaled_tau (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] Scheme (class in IMLCV.scheme), [1] scope (IMLCV.implementations.CvDiscovery.Decoder attribute) (IMLCV.implementations.CvDiscovery.Encoder attribute) (IMLCV.implementations.CvDiscovery.VAE attribute) screen_log (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] second (in module IMLCV.base.UnitsConstants) select (nvt.AndersenThermostat attribute) set_ndof() (nvt.NHChain method) setup() (IMLCV.implementations.CvDiscovery.VAE method), [1] shape (IMLCV.base.CV.CV property), [1] (IMLCV.base.CV.NeighbourList property), [1] (IMLCV.base.CV.SystemParams property), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] ShmapKwargs (class in IMLCV.base.CV), [1] Sigma (npt.PRBarostat attribute) sigma_0 (IMLCV.base.rounds.Covariances attribute), [1] sigma_0_inv (IMLCV.base.rounds.Covariances property), [1] sigma_1 (IMLCV.base.rounds.Covariances attribute), [1] sigma_1_inv (IMLCV.base.rounds.Covariances property), [1] sigmas (IMLCV.implementations.bias.BiasMTD attribute), [1] sinkhorn_divergence_2() (in module IMLCV.implementations.CV), [1] size (IMLCV.base.CV.CV property), [1] slice() (IMLCV.base.bias.Bias method), [1] slice_exponent (IMLCV.base.bias.Bias attribute), [1] slice_mean (IMLCV.base.bias.Bias attribute), [1] smoothing (IMLCV.tools._rbf_interp.RBFInterpolator attribute) soap_descriptor() (in module IMLCV.implementations.CV), [1] solver (IMLCV.implementations.CvDiscovery.TransoformerLDA attribute), [1] sp (IMLCV.base.bias.Energy property), [1] (IMLCV.base.bias.EnergyFn property), [1] (IMLCV.base.MdEngine.MDEngine attribute), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.new_yaff.system.YaffSys property) (system.YaffSys property) sp_orig (IMLCV.base.CV.NeighbourList attribute), [1] sp_t (IMLCV.base.rounds.DataLoaderOutput attribute), [1] spb1() (in module IMLCV.tools.spherical_bessel), [1] spherical_jn() (in module IMLCV.tools.bessel_callback) spherical_jn_b (in module IMLCV.tools.bessel_callback) spherical_jn_jvp() (in module IMLCV.tools.bessel_callback), [1] spherical_jn_recurrence() (in module IMLCV.tools.bessel_callback), [1] spherical_jn_recurrence_pattern() (in module IMLCV.tools.bessel_callback), [1] spherical_jn_recurrence_pattern_unstable() (in module IMLCV.tools.bessel_callback), [1] spherical_yn (in module IMLCV.tools.bessel_callback) split() (IMLCV.base.CV.CV method), [1] SQ2OPI (in module IMLCV.tools.bessel_jn) stabilized_cholesky_decomp() (in module IMLCV.new_yaff.utils) (in module utils) stack() (IMLCV.base.CV.CV static method), [1] (IMLCV.base.CV.NeighbourList static method), [1] (IMLCV.base.CV.SystemParams static method), [1] stack_dims (IMLCV.base.CV.CV property), [1] (IMLCV.base.CV.NeighbourList property), [1] (IMLCV.base.CV.NeighbourListUpdate attribute), [1] stack_reduce() (in module IMLCV.implementations.CV), [1] start (IMLCV.base.bias.Bias attribute), [1] (IMLCV.new_yaff.iterative.Hook attribute) (iterative.Hook attribute) StateItem (class in IMLCV.new_yaff.iterative) (class in iterative) static_fit() (IMLCV.base.CVDiscovery.Transformer static method), [1] static_kwargs (IMLCV.base.bias.BiasF attribute), [1] (IMLCV.base.bias.BiasModify attribute), [1] (IMLCV.base.bias.EnergyFn attribute), [1] (IMLCV.base.CV.CvFunBase attribute), [1] static_trajectory_info (IMLCV.base.MdEngine.MDEngine attribute), [1] static_trajectory_information() (IMLCV.base.rounds.Rounds method), [1] StaticMdInfo (class in IMLCV.base.MdEngine), [1] step (IMLCV.base.bias.Bias attribute), [1] (IMLCV.base.MdEngine.MDEngine attribute), [1] (IMLCV.new_yaff.iterative.Hook attribute) (iterative.Hook attribute) step_baro (npt.TBCombination attribute) step_thermo (npt.TBCombination attribute) sti (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.scheme.Scheme property), [1] Strans (npt.TadmorBarostat attribute) super_cell() (IMLCV.base.CV.SystemParams method), [1] sym (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] symmetric (IMLCV.base.rounds.Covariances attribute), [1] symmetrize() (IMLCV.base.rounds.Covariances method), [1] system module system (ff.YaffFF attribute) (IMLCV.new_yaff.ff.YaffFF attribute) SystemParams (class in IMLCV.base.CV), [1] T T (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] t (IMLCV.base.MdEngine.TrajectoryInfo property), [1] T (IMLCV.base.rounds.Rounds property), [1] (in module IMLCV.base.CV), [1], [2] (in module IMLCV.base.datastructures) (in module IMLCV.configs.bash_app_python) (in module IMLCV.external.quadrature) (in module IMLCV.tools.tools) t (nvt.GLEThermostat attribute) T1 (in module IMLCV.tools.soap_kernel) T2 (in module IMLCV.tools.soap_kernel) T_scale (IMLCV.base.rounds.KoopmanModel attribute), [1] (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] TadmorBarostat (class in npt) tau (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] TBCombination (class in npt) temp (npt.TBCombination attribute) (nvt.NHChain attribute) (verlet.BarostatHook attribute) (verlet.NVE attribute) (verlet.ThermostatHook attribute) (verlet.VerletIntegrator attribute) TemperatureStateItem (class in verlet) tempering (IMLCV.implementations.bias.BiasMTD attribute), [1] tfl_module (class in IMLCV.implementations.tensorflow.CV) thermo() (nvt.GLEThermostat method) (nvt.LangevinThermostat method) thermo_expects_call (npt.TBCombination attribute) thermostat (IMLCV.base.MdEngine.StaticMdInfo property), [1] (npt.TBCombination attribute) ThermostatHook (class in verlet) thin_plate_spline() (in module IMLCV.tools._rbfinterp_pythran) THPIO4 (in module IMLCV.tools.bessel_jn) threadpool (IMLCV.configs.config_general.Executors attribute), [1] ti (IMLCV.base.rounds.DataLoaderOutput attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] ti_t (IMLCV.base.rounds.DataLoaderOutput attribute), [1] tic (IMLCV.base.rounds.RoundInformation attribute), [1] time (verlet.VerletIntegrator attribute) time0 (IMLCV.base.MdEngine.MDEngine attribute), [1] time_per_bin (IMLCV.base.Observable.Observable attribute), [1] time_scaling (IMLCV.base.rounds.WeightOutput attribute), [1] time_series (IMLCV.base.rounds.DataLoaderOutput attribute), [1] timecon (npt.LangevinBarostat attribute) (npt.MTKBarostat attribute) (nvt.BerendsenThermostat attribute) (nvt.CSVRThermostat attribute) (nvt.GLEThermostat attribute) (nvt.LangevinThermostat attribute) (nvt.NHChain attribute) timecon_baro (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] timecon_press (npt.BerendsenBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) timecon_thermo (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] timescales() (IMLCV.base.rounds.KoopmanModel method), [1] timestep (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] (nvt.NHChain attribute) (verlet.VerletIntegrator attribute) timestep_press (npt.LangevinBarostat attribute) TNode (in module IMLCV.base.datastructures) to_absolute() (IMLCV.base.CV.SystemParams method), [1] to_ase() (IMLCV.base.CV.SystemParams method), [1] to_jax_vec() (IMLCV.implementations.energy.OpenMmEnergy static method), [1] to_relative() (IMLCV.base.CV.SystemParams method), [1] tot_trans (IMLCV.base.rounds.KoopmanModel property), [1] toy_1d() (in module IMLCV.examples.example_systems) toy_periodic_phase_trans() (in module IMLCV.examples.example_systems) training (IMLCV.configs.config_general.Executors attribute), [1] trajectory_file (IMLCV.base.MdEngine.MDEngine attribute), [1] trajectory_info (IMLCV.base.MdEngine.MDEngine attribute), [1] TrajectoryInfo (class in IMLCV.base.MdEngine), [1] TrajectoryInformation (class in IMLCV.base.rounds), [1] TranformerAutoEncoder (class in IMLCV.implementations.CvDiscovery), [1] TranformerUMAP (class in IMLCV.implementations.tensorflow.CvDiscovery), [1] trans (IMLCV.base.CV._ParralelCvTrans attribute) (IMLCV.base.CV._SerialCvTrans attribute) (IMLCV.base.CV.CvTrans attribute), [1] (IMLCV.base.CVDiscovery.CvTransTransformer attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] trans_f (IMLCV.base.rounds.Covariances attribute), [1] trans_g (IMLCV.base.rounds.Covariances attribute), [1] transform_CV() (IMLCV.base.rounds.Rounds method), [1] (IMLCV.scheme.Scheme method), [1] transform_FES() (IMLCV.base.rounds.DataLoaderOutput method), [1] Transformer (class in IMLCV.base.CVDiscovery), [1] TransformerMAF (class in IMLCV.implementations.CvDiscovery), [1] transformers (IMLCV.base.CVDiscovery.CombineTransformer attribute), [1] TransoformerLDA (class in IMLCV.implementations.CvDiscovery), [1] trunc_svd() (in module IMLCV.implementations.CV), [1] U umap_encoder() (in module IMLCV.implementations.tensorflow.CvDiscovery), [1] umap_function() (in module IMLCV.implementations.tensorflow.CvDiscovery), [1] un_atomize (in module IMLCV.implementations.CV) unbatch() (IMLCV.base.CV.CV method), [1] (IMLCV.base.CV.SystemParams method), [1] unified (in module IMLCV.base.UnitsConstants) unmap() (IMLCV.base.CV.CvMetric method), [1] Unpickler (class in IMLCV), [1] unpickler (in module IMLCV) unstack() (IMLCV.base.CV.CV method), [1] (IMLCV.base.CV.NeighbourList method), [1] unzip_cv() (IMLCV.base.rounds.Rounds method), [1] unzip_cv_round() (IMLCV.base.rounds.Rounds method), [1] update (IMLCV.base.CV.NeighbourList attribute), [1] update() (IMLCV.new_yaff.iterative.StateItem method) (iterative.StateItem method) (nvt.NHChain method) (verlet.ConsErrTracker method) update_bias() (IMLCV.base.bias.Bias method), [1] (IMLCV.base.bias.BiasModify method), [1] (IMLCV.base.bias.CompositeBias method), [1] (IMLCV.implementations.bias.BiasMTD method), [1] update_CV() (IMLCV.base.rounds.Rounds method), [1] (IMLCV.scheme.Scheme method), [1] update_nl() (IMLCV.base.CV.NeighbourList method), [1] (IMLCV.base.MdEngine.MDEngine method), [1] update_sp() (IMLCV.implementations.MdEngine.AseEngine method) use_w (IMLCV.implementations.CvDiscovery.TransformerMAF attribute), [1] utils module V VAE (class in IMLCV.implementations.CvDiscovery), [1] val (IMLCV.tools.tools.HashableArrayWrapper attribute) valid (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] validate_data() (IMLCV.base.rounds.Rounds method), [1] vals (IMLCV.implementations.bias.GridBias attribute), [1] value (IMLCV.new_yaff.iterative.StateItem attribute) (iterative.StateItem attribute) vel (nvt.NHChain attribute) (verlet.VerletIntegrator attribute) vel0 (nvt.NHChain attribute) vel_press (npt.LangevinBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) verbose (IMLCV.base.CV.ShmapKwargs attribute), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] verify() (npt.TBCombination method) verlet module verlet_hook (verlet.VerletIntegrator attribute) VerletHook (class in verlet) VerletIntegrator (class in verlet) visible_devices (in module IMLCV.implementations.tensorflow) vmap_decorator() (in module IMLCV.base.datastructures), [1] vol0 (npt.PRBarostat attribute) Vol0 (npt.TadmorBarostat attribute) vol_constraint (npt.BerendsenBarostat attribute) (npt.LangevinBarostat attribute) (npt.MTKBarostat attribute) (npt.PRBarostat attribute) (npt.TadmorBarostat attribute) volume (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.new_yaff.system.YaffCell property) Volume (in module IMLCV.implementations.CV) volume (system.YaffCell property) volume() (IMLCV.base.CV.SystemParams method), [1] vtens (IMLCV.base.bias.EnergyResult attribute), [1] (verlet.VerletIntegrator attribute) W w (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.base.rounds.KoopmanModel attribute), [1] W0 (IMLCV.base.rounds.KoopmanModel attribute), [1] W1 (IMLCV.base.rounds.KoopmanModel attribute), [1] W_0 (IMLCV.base.rounds.Covariances attribute), [1] W_1 (IMLCV.base.rounds.Covariances attribute), [1] w_t (IMLCV.base.rounds.KoopmanModel attribute), [1] weighted_model() (IMLCV.base.rounds.KoopmanModel method), [1] WeightOutput (class in IMLCV.base.rounds), [1] weights (IMLCV.base.rounds.WeightOutput attribute), [1] wham_weight() (IMLCV.base.rounds.DataLoaderOutput method), [1] whiten_rho() (IMLCV.base.rounds.Covariances method), [1] wrap_positions() (IMLCV.base.CV.SystemParams method), [1] write_step (IMLCV.base.MdEngine.StaticMdInfo attribute), [1] write_xyz() (IMLCV.base.rounds.Rounds method), [1] X X (in module IMLCV.base.CV) (in module IMLCV.base.rounds) X2 (in module IMLCV.base.CV) (in module IMLCV.base.rounds) xyz_to_luv() (in module IMLCV.external.hsluv), [1] xyz_to_rgb() (in module IMLCV.external.hsluv), [1] Y y (IMLCV.tools._rbf_interp.RBFInterpolator attribute) y0 (IMLCV.implementations.bias.HarmonicBias attribute), [1] YaffCell (class in IMLCV.new_yaff.system) (class in system) YaffFF (class in ff) (class in IMLCV.new_yaff.ff) YaffSys (class in IMLCV.new_yaff.system) (class in system) YP0 (in module IMLCV.tools.bessel_jn) YP1 (in module IMLCV.tools.bessel_jn) YQ0 (in module IMLCV.tools.bessel_jn) YQ1 (in module IMLCV.tools.bessel_jn) yv (in module IMLCV.tools.bessel_callback) Z Z1 (in module IMLCV.tools.bessel_jn) Z2 (in module IMLCV.tools.bessel_jn) z_array (IMLCV.base.CV.NeighbourListInfo attribute), [1] z_unique (IMLCV.base.CV.NeighbourListInfo attribute), [1] zero_flow (in module IMLCV.implementations.CV) zero_trans (in module IMLCV.implementations.CV) zip_cv() (IMLCV.base.rounds.Rounds method), [1] zip_cv_round() (IMLCV.base.rounds.Rounds method), [1] zip_cv_rounds() (IMLCV.base.rounds.Rounds method), [1]