Index

_

_ (IMLCV.base.CV.CvFunBase attribute) (IMLCV.implementations.CV.DistraxRealNVP attribute) (IMLCV.implementations.CV.RealNVP attribute) __add__() (IMLCV.base.bias.EnergyResult method) (IMLCV.base.CV.CV method) (IMLCV.base.CV.CvFlow 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) __call__() (IMLCV.implementations.CvDiscovery.Decoder method) (IMLCV.implementations.CvDiscovery.Encoder method) (IMLCV.implementations.CvDiscovery.VAE method) (IMLCV.implementations.MdEngine.YaffEngine method) (IMLCV.tools._rbf_interp.RBFInterpolator method) __div__() (IMLCV.base.CV.CV method) __eq__() (IMLCV.tools.tools.HashableArrayWrapper method) __getattribute__() (IMLCV.tools.tools.HashableArrayWrapper method) __getitem__() (IMLCV.base.CV.CV method) (IMLCV.base.CV.NeighbourList method) (IMLCV.base.CV.SystemParams method) (IMLCV.base.MdEngine.TrajectoryInfo method) (IMLCV.tools.tools.HashableArrayWrapper method) __getstate__() (IMLCV.base.MdEngine.MDEngine method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method) (IMLCV.implementations.energy.YaffEnergy method) (IMLCV.implementations.tensorflow.CV.KerasFunBase method) __hash__() (IMLCV.tools.tools.HashableArrayWrapper 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.CvFlow method) (IMLCV.base.CV.CvTrans method) (IMLCV.base.CV.CvTransNN method) __periodic_wrap() (IMLCV.base.CV.CvMetric method) __post_init__() (IMLCV.base.bias.EnergyResult method) (IMLCV.base.CV.SystemParams method) (IMLCV.base.MdEngine.MDEngine.YaffSys method) (IMLCV.base.MdEngine.StaticTrajectoryInfo method) (IMLCV.base.MdEngine.TrajectoryInfo method) __radd__() (IMLCV.base.CV.CV method) __rdiv__() (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.MdEngine.MDEngine method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method) (IMLCV.implementations.energy.YaffEnergy method) (IMLCV.implementations.tensorflow.CV.KerasFunBase method) __str__() (IMLCV.base.bias.EnergyResult method) (IMLCV.base.CV.SystemParams method) __sub__() (IMLCV.base.CV.CV method) _append_bias() (IMLCV.base.bias.CompositeBias method) _arr (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute) _attr (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute) _build_evaluation_coefficients() (in module IMLCV.tools._rbfinterp_pythran) _build_system() (in module IMLCV.tools._rbfinterp_pythran) _calc() (IMLCV.base.CV.CvFun method) (IMLCV.base.CV.CvFunBase method) (IMLCV.base.CV.CvFunDistrax method) (IMLCV.base.CV.CvFunNn method) (IMLCV.implementations.tensorflow.CV.KerasFunBase method) _calculator() (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method)

_capacity (IMLCV.base.MdEngine.TrajectoryInfo attribute) _cell (IMLCV.base.MdEngine.TrajectoryInfo attribute) _charges (IMLCV.base.MdEngine.TrajectoryInfo attribute) _chunk_evaluator() (IMLCV.tools._rbf_interp.RBFInterpolator method) _combine_dims (IMLCV.base.CV.CV attribute) _compute() (IMLCV.base.bias.Bias method) (IMLCV.base.bias.BiasF 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_coor() (IMLCV.base.bias.Energy method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.YaffEnergy method) _cv (IMLCV.base.MdEngine.TrajectoryInfo attribute) _e_bias (IMLCV.base.MdEngine.TrajectoryInfo attribute) _e_bias_gpos (IMLCV.base.MdEngine.TrajectoryInfo attribute) _e_bias_vtens (IMLCV.base.MdEngine.TrajectoryInfo attribute) _e_pot (IMLCV.base.MdEngine.TrajectoryInfo attribute) _e_pot_gpos (IMLCV.base.MdEngine.TrajectoryInfo attribute) _e_pot_vtens (IMLCV.base.MdEngine.TrajectoryInfo attribute) _ener (IMLCV.base.MdEngine.MDEngine.YaffSys attribute) (IMLCV.base.MdEngine.MDEngine.YaffSys.YaffCell attribute) _err (IMLCV.base.MdEngine.TrajectoryInfo attribute) _expand_capacity() (IMLCV.base.MdEngine.TrajectoryInfo method) _FES_mg() (IMLCV.base.Observable.ThermoLIB method) _fit() (IMLCV.base.CVDiscovery.Transformer method) (IMLCV.implementations.CvDiscovery.TranformerAutoEncoder method) (IMLCV.implementations.CvDiscovery.TransoformerLDA method) (IMLCV.implementations.tensorflow.CvDiscovery.TranformerUMAP method) _get_attr() (IMLCV.base.rounds.Rounds method) _get_neighbour_list() (IMLCV.base.CV.SystemParams method) _handle_exception() (IMLCV.base.bias.Energy method) (IMLCV.implementations.energy.AseEnergy method) (IMLCV.implementations.energy.Cp2kEnergy method) _internal_compute() (IMLCV.implementations.bias.PlumedBias method) (IMLCV.implementations.MdEngine.YaffEngine.YaffFF method) _items_scal (IMLCV.base.MdEngine.TrajectoryInfo attribute) _items_vec (IMLCV.base.MdEngine.TrajectoryInfo attribute) _jit_df() (IMLCV.base.CV.CollectiveVariable method) _jit_f() (IMLCV.base.CV.CollectiveVariable method) _load() (IMLCV.base.MdEngine.StaticTrajectoryInfo static method) (IMLCV.base.MdEngine.TrajectoryInfo static method) _log_Jf() (IMLCV.base.CV.CombinedCvFun method) (IMLCV.base.CV.CvFunBase method) (IMLCV.base.CV.CvFunDistrax method) _make_file() (IMLCV.base.rounds.Rounds method) _P (IMLCV.base.MdEngine.TrajectoryInfo attribute) _polynomial_matrix() (in module IMLCV.tools._rbfinterp_pythran) _pos() (IMLCV.base.CV.NeighbourList method) _positions (IMLCV.base.MdEngine.TrajectoryInfo attribute) _run() (IMLCV.base.MdEngine.MDEngine method) (IMLCV.implementations.MdEngine.YaffEngine method) _save() (IMLCV.base.MdEngine.StaticTrajectoryInfo method) (IMLCV.base.MdEngine.TrajectoryInfo method) _set_attr() (IMLCV.base.rounds.Rounds method) _setup_verlet() (IMLCV.implementations.MdEngine.YaffEngine method) _shrink_capacity() (IMLCV.base.MdEngine.TrajectoryInfo method) _size (IMLCV.base.MdEngine.TrajectoryInfo attribute) _stack_dims (IMLCV.base.CV.CV attribute) _status() (IMLCV.configs.hpc_ugent.SlurmProviderVSC method) _T (IMLCV.base.MdEngine.TrajectoryInfo attribute) _t (IMLCV.base.MdEngine.TrajectoryInfo attribute) _tic (IMLCV.base.MdEngine.MDEngine.YaffSys attribute) _update_bias() (IMLCV.base.bias.Bias method) _wrap_pos() (IMLCV.base.CV.SystemParams static method)

A

add_md() (IMLCV.base.rounds.Rounds method), [1] add_round() (IMLCV.base.rounds.Rounds method), [1] add_round_from_md() (IMLCV.base.rounds.Rounds method), [1] alanine_dipeptide_yaff() (in module IMLCV.examples.example_systems), [1] angles() (IMLCV.base.CV.SystemParams method), [1]

apply_fun_neighbour() (IMLCV.base.CV.NeighbourList method), [1] apply_fun_neighbour_pair() (IMLCV.base.CV.NeighbourList method), [1] AseEnergy (class in IMLCV.implementations.energy), [1] atom_indices (IMLCV.base.CV.NeighbourList attribute), [1] atomic (IMLCV.base.CV.CV attribute), [1] atomic_numbers (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1]

B

backward (IMLCV.base.CV.CvFun attribute), [1] backward() (IMLCV.base.CV.CvFunNn method), [1] (IMLCV.implementations.CV.RealNVP method), [1] barostat (IMLCV.base.MdEngine.StaticTrajectoryInfo property), [1] bash_app_python() (in module IMLCV.configs.bash_app_python), [1] batch() (IMLCV.base.CV.CV method), [1] (IMLCV.base.CV.SystemParams method), [1] batch_dim (IMLCV.base.CV.CV property), [1]

batched (IMLCV.base.CV.CV property), [1] (IMLCV.base.CV.NeighbourList property), [1] (IMLCV.base.CV.SystemParams property), [1] BC (class in IMLCV.base.bias), [1] Bias (class in IMLCV.base.bias), [1] BiasError, [1] BiasF (class in IMLCV.base.bias), [1] BiasMTD (class in IMLCV.implementations.bias), [1] bijector (IMLCV.base.CV.CvFunDistrax attribute), [1]

C

calc() (IMLCV.base.CV.CombinedCvFun method), [1] (IMLCV.base.CV.CvFunBase method), [1] (IMLCV.base.CV.NormalizingFlow method), [1] call() (IMLCV.implementations.tensorflow.CV.PeriodicLayer method), [1] cancel() (IMLCV.configs.hpc_ugent.SlurmProviderVSC method), [1] canoncialize() (IMLCV.base.CV.SystemParams method), [1] cell (IMLCV.base.bias.Energy property), [1] (IMLCV.base.CV.SystemParams attribute), [1] (IMLCV.base.MdEngine.MDEngine.YaffSys property), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.implementations.energy.AseEnergy property), [1] (IMLCV.implementations.energy.YaffEnergy property), [1] charges (IMLCV.base.MdEngine.MDEngine.YaffSys property), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] classes (IMLCV.base.CV.CombinedCvFun attribute), [1] CollectiveVariable (class in IMLCV.base.CV), [1] combine() (IMLCV.base.CV.CV static method), [1] (IMLCV.base.CV.CvFunInput method), [1] combine_dims (IMLCV.base.CV.CV property), [1] CombinedCvFun (class in IMLCV.base.CV), [1] CompositeBias (class in IMLCV.base.bias), [1] compute() (IMLCV.base.CVDiscovery.CVDiscovery method), [1] compute_cv() (IMLCV.base.CV.CollectiveVariable method), [1] compute_cv_flow() (IMLCV.base.CV.CvFlow method), [1] compute_cv_trans() (IMLCV.base.CV.CvTrans method), [1] (IMLCV.base.CV.CvTransNN 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]

conditioners (IMLCV.base.CV.CvFunInput attribute), [1] config() (in module IMLCV.configs.config_general), [1] (in module IMLCV.configs.hpc_ugent), [1] coordinates (IMLCV.base.bias.Energy property), [1] (IMLCV.base.CV.SystemParams attribute), [1] (IMLCV.implementations.energy.AseEnergy property), [1] (IMLCV.implementations.energy.YaffEnergy property), [1] Cp2kEnergy (class in IMLCV.implementations.energy), [1] CsPbI3() (in module IMLCV.examples.example_systems), [1] cubic() (in module IMLCV.tools._rbfinterp_pythran) 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] cv_input (IMLCV.base.CV.CvFunBase attribute), [1] (IMLCV.implementations.CV.RealNVP attribute) cv_norm() (in module IMLCV.tools._rbfinterp_pythran) cv_vals() (in module IMLCV.tools._rbf_interp) (in module IMLCV.tools._rbfinterp_pythran) CVDiscovery (class in IMLCV.base.CVDiscovery), [1] CvFlow (class in IMLCV.base.CV), [1] CvFun (class in IMLCV.base.CV), [1] CvFunBase (class in IMLCV.base.CV), [1] CvFunDistrax (class in IMLCV.base.CV), [1] CvFunInput (class in IMLCV.base.CV), [1] CvFunNn (class in IMLCV.base.CV), [1] CvMetric (class in IMLCV.base.CV), [1] CvTrans (class in IMLCV.base.CV), [1] CvTransNN (class in IMLCV.base.CV), [1]

D

data_loader() (IMLCV.base.CVDiscovery.CVDiscovery method), [1] Decoder (class in IMLCV.implementations.CvDiscovery), [1] default_parameters (IMLCV.implementations.energy.Cp2kEnergy attribute), [1] difference() (IMLCV.base.CV.CvMetric method), [1] dihedral() (in module IMLCV.implementations.CV), [1] dim (IMLCV.base.CV.CV property), [1] (IMLCV.implementations.CvDiscovery.Decoder attribute), [1] (IMLCV.implementations.CvDiscovery.Encoder attribute), [1] (IMLCV.implementations.CvDiscovery.VAE attribute), [1]

dist_name (in module IMLCV) distance_descriptor() (in module IMLCV.implementations.CV), [1] DistraxRealNVP (class in IMLCV.implementations.CV), [1]

E

e_bias (IMLCV.base.MdEngine.TrajectoryInfo property), [1] e_bias_gpos (IMLCV.base.MdEngine.TrajectoryInfo property), [1] e_bias_vtens (IMLCV.base.MdEngine.TrajectoryInfo property), [1] e_pot (IMLCV.base.MdEngine.TrajectoryInfo property), [1] e_pot_gpos (IMLCV.base.MdEngine.TrajectoryInfo property), [1] e_pot_vtens (IMLCV.base.MdEngine.TrajectoryInfo property), [1] 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] EnergyError, [1] EnergyResult (class in IMLCV.base.bias), [1] equilibration (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] err (IMLCV.base.MdEngine.TrajectoryInfo property), [1]

F

f() (in module IMLCV.examples.replot) features (IMLCV.implementations.CV.RealNVP attribute), [1] fes_bias() (IMLCV.base.Observable.ThermoLIB method), [1] fes_nd_thermolib() (IMLCV.base.Observable.ThermoLIB method), [1] FESBias() (IMLCV.scheme.Scheme method), [1] finalize() (IMLCV.base.bias.Bias method), [1] (IMLCV.base.bias.CompositeBias method), [1] find_sp() (IMLCV.base.CV.CvFlow method), [1] fit() (IMLCV.base.CVDiscovery.Transformer method), [1] flow (IMLCV.base.CV.NormalizingFlow attribute), [1]

folder (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] forward (IMLCV.base.CV.CvFun attribute), [1] forward() (IMLCV.base.CV.CvFunNn method), [1] (IMLCV.implementations.CV.RealNVP method), [1] from_array_function() (IMLCV.base.CV.CvTrans static method), [1] from_cv_fun() (IMLCV.base.CV.CvTrans static method), [1] from_cv_function() (IMLCV.base.CV.CvTrans static method), [1] from_function() (IMLCV.base.CV.CvFlow static method), [1] from_rounds() (IMLCV.scheme.Scheme static method), [1] full_path() (IMLCV.base.rounds.Rounds method), [1]

G

gaussian() (in module IMLCV.tools._rbfinterp_pythran) generate_bessel() (in module IMLCV.tools.bessel_callback), [1] get_args() (IMLCV.base.bias.Bias method), [1] (IMLCV.base.bias.BiasF method), [1] (IMLCV.base.bias.CompositeBias method), [1] (IMLCV.implementations.bias.BiasMTD method), [1] (IMLCV.implementations.bias.GridBias method), [1] (IMLCV.implementations.bias.HarmonicBias method), [1] (IMLCV.implementations.bias.RbfBias method), [1] 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_collective_variable() (IMLCV.base.rounds.Rounds method), [1] get_config() (IMLCV.implementations.tensorflow.CV.PeriodicLayer method), [1] (in module IMLCV.configs.local_htex), [1] (in module IMLCV.configs.local_threadpool), [1]

get_cp2k() (in module IMLCV.configs.config_general), [1] get_energy() (IMLCV.base.MdEngine.MDEngine method), [1] get_engine() (IMLCV.base.rounds.RoundInformation method), [1] (IMLCV.base.rounds.Rounds method), [1] get_neighbour_list() (IMLCV.base.CV.SystemParams method), [1] get_platform() (in module IMLCV.configs.config_general), [1] get_sinkhorn_divergence() (in module IMLCV.implementations.CV), [1] get_slurm_provider() (in module IMLCV.configs.hpc_ugent), [1] get_trajectory() (IMLCV.base.MdEngine.MDEngine method), [1] get_trajectory_information() (IMLCV.base.rounds.Rounds method), [1] gpos (IMLCV.base.bias.EnergyResult attribute), [1] grid() (IMLCV.base.CV.CvMetric method), [1] grid_umbrella() (IMLCV.scheme.Scheme method), [1] GridBias (class in IMLCV.implementations.bias), [1]

H

h5file_name (IMLCV.base.rounds.Rounds property), [1] h5filelock_name (IMLCV.base.rounds.Rounds property), [1] hankel1 (in module IMLCV.tools.bessel_callback)

hankel2 (in module IMLCV.tools.bessel_callback) HarmonicBias (class in IMLCV.implementations.bias), [1] HashableArrayWrapper (class in IMLCV.tools.tools), [1] hyperTorus (class in IMLCV.implementations.CV), [1]

I

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.MdEngine module, [1] IMLCV.base.Observable module, [1] IMLCV.base.rounds 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_htex module, [1] IMLCV.configs.local_threadpool module, [1] IMLCV.examples module, [1] IMLCV.examples.example_systems module, [1] IMLCV.examples.replot module, [1] IMLCV.examples.simul module, [1] IMLCV.external module, [1] IMLCV.external.tf2jax module, [1]

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, [1] IMLCV.implementations.tensorflow module, [1] IMLCV.implementations.tensorflow.CV module, [1] IMLCV.implementations.tensorflow.CvDiscovery module, [1] 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.soap_kernel module, [1] IMLCV.tools.tools module, [1] inner_loop() (IMLCV.scheme.Scheme method), [1] input (IMLCV.base.CV.CvFunInput 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_valid() (IMLCV.base.rounds.Rounds method), [1] iter() (IMLCV.base.rounds.Rounds method), [1] iter_ase_atoms() (IMLCV.base.rounds.Rounds method), [1] iv (in module IMLCV.tools.bessel_callback) ive (in module IMLCV.tools.bessel_callback)

J

jv (in module IMLCV.tools.bessel_callback)

K

keras (in module IMLCV.implementations.tensorflow.CV) KerasFunBase (class in IMLCV.implementations.tensorflow.CV), [1] kernel_matrix() (in module IMLCV.tools._rbfinterp_pythran) kernel_vector() (in module IMLCV.tools._rbfinterp_pythran)

KEY (in module IMLCV) keys (IMLCV.base.MdEngine.MDEngine attribute), [1] kv (in module IMLCV.tools.bessel_callback) kve (in module IMLCV.tools.bessel_callback)

L

latent_dim (IMLCV.implementations.CV.DistraxRealNVP attribute), [1] latents (IMLCV.implementations.CvDiscovery.Decoder attribute), [1] (IMLCV.implementations.CvDiscovery.Encoder attribute), [1] (IMLCV.implementations.CvDiscovery.VAE attribute), [1] layers (IMLCV.implementations.CvDiscovery.Decoder attribute), [1] (IMLCV.implementations.CvDiscovery.Encoder attribute), [1] (IMLCV.implementations.CvDiscovery.VAE attribute), [1] legendre() (in module IMLCV.tools.soap_kernel), [1] lengendre_l() (in module IMLCV.tools.soap_kernel), [1] linear() (in module IMLCV.tools._rbfinterp_pythran) load() (IMLCV.base.bias.BC static method), [1] (IMLCV.base.bias.Bias static method), [1] (IMLCV.base.bias.Energy static method), [1] (IMLCV.base.MdEngine.MDEngine static method), [1] (IMLCV.base.MdEngine.StaticTrajectoryInfo static method), [1] (IMLCV.base.MdEngine.TrajectoryInfo static method), [1] (IMLCV.base.rounds.Rounds static method), [1] (IMLCV.implementations.MdEngine.YaffEngine static method), [1] (IMLCV.scheme.Scheme class method), [1]

logger (in module IMLCV.configs.hpc_ugent) LOGLEVEL (in module IMLCV) loop_batcher() (in module IMLCV.external.tf2jax), [1]

M

map() (IMLCV.base.CV.CvMetric method), [1] mapped (IMLCV.base.CV.CV attribute), [1] masses (IMLCV.base.MdEngine.MDEngine.YaffSys property), [1] (IMLCV.base.MdEngine.StaticTrajectoryInfo property), [1] match_kernel() (IMLCV.base.CV.NeighbourList static method), [1] max_grad (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] MDEngine (class in IMLCV.base.MdEngine), [1] MDEngine.YaffSys (class in IMLCV.base.MdEngine), [1] MDEngine.YaffSys.YaffCell (class in IMLCV.base.MdEngine), [1] metric() (IMLCV.implementations.tensorflow.CV.PeriodicLayer method), [1] MetricUMAP (class in IMLCV.implementations.CV), [1] mil53_yaff() (in module IMLCV.examples.example_systems), [1] min_cv() (IMLCV.base.CV.CvMetric method), [1] min_distance() (IMLCV.base.CV.SystemParams method), [1] MinBias (class in IMLCV.implementations.bias), [1] minkowski_reduce() (IMLCV.base.CV.SystemParams method), [1] module IMLCV, [1] IMLCV.base, [1] IMLCV.base.bias, [1] IMLCV.base.CV, [1] IMLCV.base.CVDiscovery, [1] IMLCV.base.MdEngine, [1] IMLCV.base.Observable, [1] IMLCV.base.rounds, [1] IMLCV.configs, [1] IMLCV.configs.bash_app_python, [1] IMLCV.configs.config_general, [1] IMLCV.configs.hpc_ugent, [1] IMLCV.configs.local_htex, [1] IMLCV.configs.local_threadpool, [1] IMLCV.examples, [1] IMLCV.examples.example_systems, [1] IMLCV.examples.replot, [1] IMLCV.examples.simul, [1] IMLCV.external, [1] IMLCV.external.tf2jax, [1] IMLCV.implementations, [1] IMLCV.implementations.bias, [1] IMLCV.implementations.CV, [1] IMLCV.implementations.CvDiscovery, [1] IMLCV.implementations.energy, [1] IMLCV.implementations.MdEngine, [1] IMLCV.implementations.tensorflow, [1] IMLCV.implementations.tensorflow.CV, [1] IMLCV.implementations.tensorflow.CvDiscovery, [1] IMLCV.scheme, [1] IMLCV.tools, [1] IMLCV.tools._rbf_interp IMLCV.tools._rbfinterp_pythran IMLCV.tools.bessel_callback, [1] IMLCV.tools.soap_kernel, [1] IMLCV.tools.tools, [1]

MTDBias() (IMLCV.scheme.Scheme method), [1] multiquadric() (in module IMLCV.tools._rbfinterp_pythran)

N

n (IMLCV.base.CV.CollectiveVariable property), [1] n() (IMLCV.base.rounds.Rounds method), [1] name (IMLCV.base.CV.CvFunDistrax attribute) (IMLCV.base.CV.CvFunNn attribute) (IMLCV.base.CV.CvTransNN attribute) (IMLCV.base.CV.NormalizingFlow attribute) (IMLCV.implementations.CV.DistraxRealNVP attribute) (IMLCV.implementations.CV.RealNVP attribute) (IMLCV.implementations.CvDiscovery.Decoder attribute) (IMLCV.implementations.CvDiscovery.Encoder attribute) (IMLCV.implementations.CvDiscovery.VAE 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) natom (IMLCV.base.MdEngine.MDEngine.YaffSys property), [1] ndim (IMLCV.base.CV.CvMetric property), [1] NeighbourList (class in IMLCV.base.CV), [1] new_bias() (IMLCV.base.MdEngine.MDEngine method), [1]

new_metric() (IMLCV.base.Observable.ThermoLIB method), [1] (IMLCV.scheme.Scheme method), [1] nl (IMLCV.base.MdEngine.MDEngine property), [1] nl_split_z() (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] NormalizingFlow (class in IMLCV.base.CV), [1] num (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] num_neigh (IMLCV.base.CV.NeighbourList property), [1] num_vals (IMLCV.base.rounds.RoundInformation attribute), [1] num_z_unique (IMLCV.base.CV.NeighbourList attribute), [1] numbers (IMLCV.base.MdEngine.MDEngine.YaffSys property), [1] nunits (IMLCV.implementations.CvDiscovery.Decoder attribute), [1] (IMLCV.implementations.CvDiscovery.Encoder attribute), [1] (IMLCV.implementations.CvDiscovery.VAE attribute), [1] nvec (IMLCV.base.MdEngine.MDEngine.YaffSys.YaffCell property), [1] nxyz (IMLCV.base.CV.NeighbourList attribute), [1]

O

op_cell (IMLCV.base.CV.NeighbourList attribute), [1]

op_center (IMLCV.base.CV.NeighbourList attribute), [1] op_coor (IMLCV.base.CV.NeighbourList attribute), [1]

P

P (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.base.rounds.Rounds property), [1] 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] parent (IMLCV.base.CV.CvFunDistrax attribute) (IMLCV.base.CV.CvFunNn attribute) (IMLCV.base.CV.CvTransNN attribute) (IMLCV.base.CV.NormalizingFlow attribute) (IMLCV.implementations.CV.DistraxRealNVP attribute) (IMLCV.implementations.CV.RealNVP attribute) (IMLCV.implementations.CvDiscovery.Decoder attribute) (IMLCV.implementations.CvDiscovery.Encoder attribute) (IMLCV.implementations.CvDiscovery.VAE attribute) parser (in module IMLCV.configs.bash_app_python) (in module IMLCV.examples.replot) (in module IMLCV.examples.simul)

path() (IMLCV.base.rounds.Rounds method), [1] periodic_wrap() (IMLCV.base.CV.CvMetric method), [1] PeriodicLayer (class in IMLCV.implementations.tensorflow.CV), [1] plot() (IMLCV.base.bias.Bias method), [1] plot_app() (IMLCV.base.CVDiscovery.CVDiscovery static method), [1] (in module IMLCV.base.bias) plumed_dat (IMLCV.implementations.MdEngine.PlumedEngine attribute), [1] PlumedBias (class in IMLCV.implementations.bias), [1] PlumedEnerg (class in IMLCV.base.bias), [1] PlumedEngine (class in IMLCV.implementations.MdEngine), [1] polynomial_matrix() (in module IMLCV.tools._rbfinterp_pythran) polynomial_vector() (in module IMLCV.tools._rbfinterp_pythran) pos (IMLCV.base.MdEngine.MDEngine.YaffSys property), [1] positions (IMLCV.base.MdEngine.TrajectoryInfo property), [1] post_fit() (IMLCV.base.CVDiscovery.Transformer method), [1] pre_fit() (IMLCV.base.CVDiscovery.Transformer method), [1] project_distances() (in module IMLCV.implementations.CV), [1] py_env (in module IMLCV.configs.config_general)

Q

quintic() (in module IMLCV.tools._rbfinterp_pythran)

R

r_cut (IMLCV.base.CV.NeighbourList attribute), [1] (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] r_skin (IMLCV.base.CV.NeighbourList attribute), [1] RbfBias (class in IMLCV.implementations.bias), [1] RBFInterpolator (class in IMLCV.tools._rbf_interp) RealNVP (class in IMLCV.implementations.CV), [1] recover() (IMLCV.base.rounds.Rounds method), [1] rel_path() (IMLCV.base.rounds.Rounds method), [1] reparameterize() (IMLCV.implementations.CvDiscovery.VAE class method), [1] ROOT_DIR (in module IMLCV.configs.config_general) (in module IMLCV.configs.hpc_ugent)

rotate_2d() (in module IMLCV.implementations.CV), [1] round (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.Rounds property), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] round_information() (IMLCV.base.rounds.Rounds method), [1] RoundInformation (class in IMLCV.base.rounds), [1] Rounds (class in IMLCV.base.rounds), [1] run() (IMLCV.base.MdEngine.MDEngine method), [1] (IMLCV.base.rounds.Rounds method), [1] run_par() (IMLCV.base.rounds.Rounds method), [1] rvecs (IMLCV.base.MdEngine.MDEngine.YaffSys.YaffCell property), [1]

S

save() (IMLCV.base.bias.BC method), [1] (IMLCV.base.MdEngine.MDEngine method), [1] (IMLCV.base.MdEngine.StaticTrajectoryInfo method), [1] (IMLCV.base.MdEngine.TrajectoryInfo method), [1] (IMLCV.scheme.Scheme method), [1] save_step() (IMLCV.base.MdEngine.MDEngine method), [1] sb_descriptor() (in module IMLCV.implementations.CV), [1] scale() (in module IMLCV.tools._rbfinterp_pythran) scale_cv_trans() (in module IMLCV.implementations.CV), [1] Scheme (class in IMLCV.scheme), [1] scope (IMLCV.base.CV.CvFunDistrax attribute) (IMLCV.base.CV.CvFunNn attribute) (IMLCV.base.CV.CvTransNN attribute) (IMLCV.base.CV.NormalizingFlow attribute) (IMLCV.implementations.CV.DistraxRealNVP attribute) (IMLCV.implementations.CV.RealNVP attribute) (IMLCV.implementations.CvDiscovery.Decoder attribute) (IMLCV.implementations.CvDiscovery.Encoder attribute) (IMLCV.implementations.CvDiscovery.VAE attribute) screen_log (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] setup() (IMLCV.base.CV.CvFunDistrax method), [1] (IMLCV.base.CV.CvFunNn method), [1] (IMLCV.base.CV.CvTransNN method), [1] (IMLCV.base.CV.NormalizingFlow method), [1] (IMLCV.implementations.CV.DistraxRealNVP method), [1] (IMLCV.implementations.CV.RealNVP method), [1] (IMLCV.implementations.CvDiscovery.VAE method), [1]

setup_plumed() (IMLCV.implementations.bias.PlumedBias 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] shift_and_scale() (IMLCV.implementations.CV.DistraxRealNVP method), [1] size (IMLCV.base.CV.CV property), [1] SlurmProviderVSC (class in IMLCV.configs.hpc_ugent), [1] sp (IMLCV.base.bias.Energy property), [1] (IMLCV.base.MdEngine.MDEngine property), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] (IMLCV.implementations.MdEngine.YaffEngine.YaffFF property), [1] sp_orig (IMLCV.base.CV.NeighbourList attribute), [1] spherical_jn (in module IMLCV.tools.bessel_callback) spherical_yn (in module IMLCV.tools.bessel_callback) split() (IMLCV.base.CV.CV method), [1] (IMLCV.base.CV.CvFunInput method), [1] stack() (IMLCV.base.CV.CV static method), [1] (IMLCV.base.CV.CvTrans static method), [1] (IMLCV.base.CV.NeighbourList static method), [1] stack_dims (IMLCV.base.CV.CV property), [1] StaticTrajectoryInfo (class in IMLCV.base.MdEngine), [1] submit() (IMLCV.configs.hpc_ugent.SlurmProviderVSC method), [1] system (IMLCV.implementations.MdEngine.YaffEngine.YaffFF property), [1] SystemParams (class in IMLCV.base.CV), [1]

T

T (IMLCV.base.MdEngine.StaticTrajectoryInfo 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.tools.tools) tfl (IMLCV.implementations.tensorflow.CV.PeriodicLayer attribute) ThermoLIB (class in IMLCV.base.Observable), [1] thermostat (IMLCV.base.MdEngine.StaticTrajectoryInfo property), [1] thin_plate_spline() (in module IMLCV.tools._rbfinterp_pythran) ti (IMLCV.base.rounds.TrajectoryInformation attribute), [1] tic (IMLCV.base.rounds.RoundInformation attribute), [1] time_per_bin (IMLCV.base.Observable.ThermoLIB attribute), [1]

timecon_baro (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] timecon_thermo (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] timestep (IMLCV.base.MdEngine.StaticTrajectoryInfo 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.CvTrans attribute), [1] (IMLCV.base.CV.CvTransNN attribute), [1] Transformer (class in IMLCV.base.CVDiscovery), [1] translate_table (in module IMLCV.configs.hpc_ugent) TransoformerLDA (class in IMLCV.implementations.CvDiscovery), [1] trunc_svd() (in module IMLCV.implementations.CV), [1]

U

un_atomize() (in module IMLCV.implementations.CV) unbatch() (IMLCV.base.CV.CV method), [1] (IMLCV.base.CV.SystemParams method), [1] unmap() (IMLCV.base.CV.CvMetric method), [1] unstack() (IMLCV.base.CV.CV method), [1] update() (IMLCV.base.CV.NeighbourList method), [1] update_bias() (IMLCV.base.bias.Bias method), [1] (IMLCV.base.bias.CompositeBias method), [1] (IMLCV.implementations.bias.BiasMTD method), [1] (IMLCV.implementations.bias.PlumedBias method), [1]

update_CV() (IMLCV.scheme.Scheme method), [1] update_pos() (IMLCV.implementations.MdEngine.YaffEngine.YaffFF method), [1] update_rvecs() (IMLCV.base.MdEngine.MDEngine.YaffSys.YaffCell method), [1] (IMLCV.implementations.MdEngine.YaffEngine.YaffFF method), [1]

V

VAE (class in IMLCV.implementations.CvDiscovery), [1] valid (IMLCV.base.rounds.RoundInformation attribute), [1] (IMLCV.base.rounds.TrajectoryInformation attribute), [1] visible_devices (in module IMLCV.implementations.tensorflow)

volume (IMLCV.base.MdEngine.MDEngine.YaffSys.YaffCell property), [1] (IMLCV.base.MdEngine.TrajectoryInfo property), [1] Volume() (in module IMLCV.implementations.CV) vtens (IMLCV.base.bias.EnergyResult attribute), [1]

W

wrap_positions() (IMLCV.base.CV.SystemParams method), [1]

write_step (IMLCV.base.MdEngine.StaticTrajectoryInfo attribute), [1] write_xyz() (IMLCV.base.rounds.Rounds method), [1]

Y

yaff_system (IMLCV.base.MdEngine.MDEngine property), [1] YaffEnergy (class in IMLCV.implementations.energy), [1]

YaffEngine (class in IMLCV.implementations.MdEngine), [1] YaffEngine.YaffFF (class in IMLCV.implementations.MdEngine), [1] yv (in module IMLCV.tools.bessel_callback)

Z

z_array (IMLCV.base.CV.NeighbourList attribute), [1]

z_unique (IMLCV.base.CV.NeighbourList attribute), [1]