Index

A

ACSF (in module pantea.descriptors) (in module pantea.descriptors.acsf) (in module pantea.descriptors.acsf.acsf) add_energy_offset() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) angular_symmetry_functions (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction attribute) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction attribute) (pantea.descriptors.AtomCenteredSymmetryFunction attribute) AngularSymmetryFunction (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.angular) apply_pbc() (pantea.atoms.Box method) (pantea.atoms.box.Box method)

as_kernel_args() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) asarray() (in module pantea.utils.attribute) atom_type_to_element (pantea.atoms.element.ElementMap attribute) (pantea.atoms.ElementMap attribute) atom_types (pantea.atoms.element.StructureInterface attribute) (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) (pantea.atoms.structure.StructureAsKernelArgs attribute) AtomCenteredSymmetryFunction (class in pantea.descriptors) (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.acsf)

B

BaseJaxPytreeDataClass (class in pantea.pytree) BaseSymmetryFunction (class in pantea.descriptors.acsf.symmetry) BOLTZMANN_CONSTANT (pantea.units.PhysicalUnits attribute) Box (class in pantea.atoms) (class in pantea.atoms.box) box (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) (pantea.simulation.System property) (pantea.simulation.system.System property)

BrendsenThermostat (class in pantea.simulation) (class in pantea.simulation.thermostat) BrendsenThermostatParams (class in pantea.simulation.thermostat)

C

cache (pantea.datasets.Dataset attribute) (pantea.datasets.dataset.Dataset attribute) calculate_distances() (in module pantea.atoms) (in module pantea.atoms.distance) central_element (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction attribute) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction attribute) (pantea.descriptors.AtomCenteredSymmetryFunction attribute) cfn (pantea.descriptors.acsf.angular.G3 attribute) (pantea.descriptors.acsf.angular.G9 attribute) (pantea.descriptors.acsf.G1 attribute) (pantea.descriptors.acsf.G2 attribute) (pantea.descriptors.acsf.G3 attribute) (pantea.descriptors.acsf.G9 attribute) (pantea.descriptors.acsf.radial.G1 attribute) (pantea.descriptors.acsf.radial.G2 attribute) charges (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute)

check_warnings() (pantea.descriptors.DescriptorScaler class method) (pantea.descriptors.scaler.DescriptorScaler class method) compare() (in module pantea.utils.compare) compute_forces() (pantea.simulation.lennard_jones.LJPotential method) (pantea.simulation.LJPotential method) (pantea.simulation.monte_carlo.PotentialInterface method) (pantea.simulation.simulate.PotentialInterface method) (pantea.simulation.System class method) (pantea.simulation.system.PotentialInterface method) (pantea.simulation.system.System class method) cos() (in module pantea.models.nn.activation) create_batch() (in module pantea.utils.batch) current_temperature (pantea.simulation.thermostat.BrendsenThermostatParams attribute) cutoff_function (pantea.descriptors.acsf.cutoff.CutoffFunction attribute) (pantea.descriptors.acsf.CutoffFunction attribute) CutoffFunction (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.cutoff)

D

Dataset (class in pantea.datasets) (class in pantea.datasets.dataset) datasource (pantea.datasets.Dataset attribute) (pantea.datasets.dataset.Dataset attribute) DataSourceInterface (class in pantea.datasets.dataset) DataType (class in pantea.types) debug() (pantea.logger.Logger method)

DescriptorScaler (class in pantea.descriptors) (class in pantea.descriptors.scaler) dimension (pantea.descriptors.scaler.ScalerParams attribute) (pantea.descriptors.ScalerParams attribute) dtype (pantea.atoms.Box property) (pantea.atoms.box.Box property) (pantea.atoms.Structure property) (pantea.atoms.structure.Structure property)

E

element_map (pantea.atoms.element.StructureInterface attribute) (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) (pantea.atoms.structure.StructureAsKernelArgs attribute) element_to_atom_type (pantea.atoms.element.ElementMap attribute) (pantea.atoms.ElementMap attribute) element_to_atomic_number (pantea.atoms.element.ElementMap attribute) (pantea.atoms.ElementMap attribute) ElementMap (class in pantea.atoms) (class in pantea.atoms.element)

energies (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) epsilon (pantea.simulation.lennard_jones.LJPotentialParams attribute) error() (pantea.logger.Logger method) eta (pantea.descriptors.acsf.angular.G3 attribute) (pantea.descriptors.acsf.angular.G9 attribute) (pantea.descriptors.acsf.G2 attribute) (pantea.descriptors.acsf.G3 attribute) (pantea.descriptors.acsf.G9 attribute) (pantea.descriptors.acsf.radial.G2 attribute) exp() (in module pantea.models.nn.activation)

F

fit() (pantea.descriptors.DescriptorScaler class method) (pantea.descriptors.scaler.DescriptorScaler class method) FLOATX (pantea.types.DataType attribute) forces (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) (pantea.simulation.System property) (pantea.simulation.system.System property) FROM_ANGSTROM (pantea.units.PhysicalUnits attribute) from_ase() (pantea.atoms.Structure class method) (pantea.atoms.structure.Structure class method) FROM_ATOMIC_MASS (pantea.units.PhysicalUnits attribute) FROM_BAR (pantea.units.PhysicalUnits attribute) from_dict() (pantea.atoms.Structure class method) (pantea.atoms.structure.Structure class method) FROM_ELECTRON_VOLT (pantea.units.PhysicalUnits attribute) FROM_FEMTO_SECOND (pantea.units.PhysicalUnits attribute) FROM_GIGA_PASCAL (pantea.units.PhysicalUnits attribute) FROM_KCAL_PER_MOL (pantea.units.PhysicalUnits attribute)

FROM_KILO_BAR (pantea.units.PhysicalUnits attribute) from_list() (pantea.atoms.Box class method) (pantea.atoms.box.Box class method) (pantea.atoms.element.ElementMap class method) (pantea.atoms.ElementMap class method) FROM_NANO_METER (pantea.units.PhysicalUnits attribute) FROM_NANO_SECOND (pantea.units.PhysicalUnits attribute) FROM_PICO_SECOND (pantea.units.PhysicalUnits attribute) from_runner() (pantea.datasets.Dataset class method) (pantea.datasets.dataset.Dataset class method) from_structure() (pantea.atoms.Neighbor class method) (pantea.atoms.neighbor.Neighbor class method) (pantea.simulation.System class method) (pantea.simulation.system.System class method) from_type() (pantea.descriptors.acsf.cutoff.CutoffFunction class method) (pantea.descriptors.acsf.CutoffFunction class method) (pantea.descriptors.DescriptorScaler class method) (pantea.descriptors.scaler.DescriptorScaler class method)

G

G1 (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.radial) G2 (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.radial) G3 (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.angular) G9 (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.angular) gaussian() (in module pantea.models.nn.activation) generate_random_velocities() (pantea.simulation.System class method) (pantea.simulation.system.System class method) get_atom_type_from_element() (pantea.atoms.element.ElementMap method) (pantea.atoms.ElementMap method) get_atomic_mass_from_element() (pantea.atoms.element.ElementMap class method) (pantea.atoms.ElementMap class method) get_atomic_number_from_element() (pantea.atoms.element.ElementMap class method) (pantea.atoms.ElementMap class method) get_center_of_mass_position() (pantea.simulation.System method) (pantea.simulation.system.System method) get_center_of_mass_velocity() (pantea.simulation.System method) (pantea.simulation.system.System method) get_dataframe() (pantea.utils.Profiler method) (pantea.utils.profiler.Profiler method) get_element_from_atom_type() (pantea.atoms.element.ElementMap method) (pantea.atoms.ElementMap method) get_element_from_atomic_number() (pantea.atoms.element.ElementMap class method) (pantea.atoms.ElementMap class method)

get_elements() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) (pantea.simulation.System method) (pantea.simulation.system.System method) get_forces_per_element() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) get_kinetic_energy() (pantea.simulation.System method) (pantea.simulation.system.System method) get_masses_from_structure() (pantea.atoms.element.ElementMap class method) (pantea.atoms.ElementMap class method) get_positions_per_element() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) get_potential_energy() (pantea.simulation.System method) (pantea.simulation.system.System method) get_pressure() (pantea.simulation.System method) (pantea.simulation.system.System method) get_rescaled_velocities() (pantea.simulation.BrendsenThermostat method) (pantea.simulation.thermostat.BrendsenThermostat method) get_temperature() (pantea.simulation.System method) (pantea.simulation.system.System method) (pantea.simulation.thermostat.SystemInterface method) get_total_energy() (pantea.simulation.System method) (pantea.simulation.system.System method) get_unique_elements() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) grad() (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction method) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction method) (pantea.descriptors.AtomCenteredSymmetryFunction method)

H

harmonic() (in module pantea.models.nn.activation)

I

identity() (in module pantea.models.nn.activation) INDEX (pantea.types.DataType attribute) info() (pantea.logger.Logger method)

initialize_warnings() (pantea.descriptors.DescriptorScaler class method) (pantea.descriptors.scaler.DescriptorScaler class method) INT (pantea.types.DataType attribute)

L

lambda0 (pantea.descriptors.acsf.angular.G3 attribute) (pantea.descriptors.acsf.angular.G9 attribute) (pantea.descriptors.acsf.G3 attribute) (pantea.descriptors.acsf.G9 attribute) lattice (pantea.atoms.Box attribute) (pantea.atoms.box.Box attribute) (pantea.atoms.distance.StructureInterface attribute) (pantea.atoms.neighbor.StructureInterface attribute) (pantea.atoms.Structure property) (pantea.atoms.structure.Structure property) (pantea.atoms.structure.StructureAsKernelArgs attribute) length (pantea.atoms.Box property) (pantea.atoms.box.Box property)

LJPotential (class in pantea.simulation) (class in pantea.simulation.lennard_jones) LJPotentialParams (class in pantea.simulation.lennard_jones) load() (pantea.descriptors.DescriptorScaler class method) (pantea.descriptors.scaler.DescriptorScaler class method) Logger (class in pantea.logger) LoggingContextManager (class in pantea.logger) logistic() (in module pantea.models.nn.activation) lx (pantea.atoms.Box property) (pantea.atoms.box.Box property) ly (pantea.atoms.Box property) (pantea.atoms.box.Box property) lz (pantea.atoms.Box property) (pantea.atoms.box.Box property)

M

masks (pantea.atoms.Neighbor attribute) (pantea.atoms.neighbor.Neighbor attribute) masses (pantea.simulation.System attribute) (pantea.simulation.system.System attribute) max_number_of_warnings (pantea.descriptors.scaler.ScalerWarnings attribute) max_value (pantea.descriptors.scaler.ScaleRange attribute) maxval (pantea.descriptors.scaler.ScalerParams attribute) (pantea.descriptors.ScalerParams attribute) MCSimulator (class in pantea.simulation) (class in pantea.simulation.monte_carlo) MDSimulator (class in pantea.simulation) (class in pantea.simulation.molecular_dynamics) MDSimulatorInterface (class in pantea.simulation.thermostat) MDSystemInterface (class in pantea.simulation.simulate) mean (pantea.descriptors.scaler.ScalerParams attribute) (pantea.descriptors.ScalerParams attribute) metropolis_algorithm() (pantea.simulation.MCSimulator method) (pantea.simulation.monte_carlo.MCSimulator method) min_value (pantea.descriptors.scaler.ScaleRange attribute) minval (pantea.descriptors.scaler.ScalerParams attribute) (pantea.descriptors.ScalerParams attribute) module pantea pantea.atoms pantea.atoms.box pantea.atoms.distance pantea.atoms.element pantea.atoms.neighbor pantea.atoms.structure pantea.config pantea.datasets pantea.datasets.dataset pantea.datasets.runner pantea.descriptors pantea.descriptors.acsf pantea.descriptors.acsf.acsf pantea.descriptors.acsf.angular pantea.descriptors.acsf.cutoff pantea.descriptors.acsf.radial pantea.descriptors.acsf.symmetry pantea.descriptors.scaler pantea.logger pantea.models.nn.activation pantea.models.nn.initializer pantea.pytree pantea.simulation pantea.simulation.lennard_jones pantea.simulation.molecular_dynamics pantea.simulation.monte_carlo pantea.simulation.simulate pantea.simulation.system pantea.simulation.thermostat pantea.types pantea.units pantea.utils pantea.utils.attribute pantea.utils.batch pantea.utils.compare pantea.utils.profiler pantea.utils.tokenize

N

natoms (pantea.atoms.Structure property) (pantea.atoms.structure.Structure property) (pantea.simulation.System property) (pantea.simulation.system.System property) Neighbor (class in pantea.atoms) (class in pantea.atoms.neighbor) neighbor_j (pantea.descriptors.acsf.NeighborElements attribute) (pantea.descriptors.acsf.symmetry.NeighborElements attribute) neighbor_k (pantea.descriptors.acsf.NeighborElements attribute) (pantea.descriptors.acsf.symmetry.NeighborElements attribute) NeighborElements (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.symmetry)

nsamples (pantea.descriptors.scaler.ScalerParams attribute) (pantea.descriptors.ScalerParams attribute) num_angular_symmetry_functions (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.AtomCenteredSymmetryFunction property) num_radial_symmetry_functions (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.AtomCenteredSymmetryFunction property) num_symmetry_functions (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.AtomCenteredSymmetryFunction property) number_of_warnings (pantea.descriptors.scaler.ScalerWarnings attribute)

P

pantea module pantea.atoms module pantea.atoms.box module pantea.atoms.distance module pantea.atoms.element module pantea.atoms.neighbor module pantea.atoms.structure module pantea.config module pantea.datasets module pantea.datasets.dataset module pantea.datasets.runner module pantea.descriptors module pantea.descriptors.acsf module pantea.descriptors.acsf.acsf module pantea.descriptors.acsf.angular module pantea.descriptors.acsf.cutoff module pantea.descriptors.acsf.radial module pantea.descriptors.acsf.symmetry module pantea.descriptors.scaler module pantea.logger module pantea.models.nn.activation module pantea.models.nn.initializer module pantea.pytree module pantea.simulation module pantea.simulation.lennard_jones module

pantea.simulation.molecular_dynamics module pantea.simulation.monte_carlo module pantea.simulation.simulate module pantea.simulation.system module pantea.simulation.thermostat module pantea.types module pantea.units module pantea.utils module pantea.utils.attribute module pantea.utils.batch module pantea.utils.compare module pantea.utils.profiler module pantea.utils.tokenize module partial_fit() (pantea.descriptors.DescriptorScaler class method) (pantea.descriptors.scaler.DescriptorScaler class method) persist (pantea.datasets.Dataset attribute) (pantea.datasets.dataset.Dataset attribute) PhysicalUnits (class in pantea.units) positions (pantea.atoms.distance.StructureInterface attribute) (pantea.atoms.neighbor.StructureInterface attribute) (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) (pantea.atoms.structure.StructureAsKernelArgs attribute) (pantea.simulation.System property) (pantea.simulation.system.System property) potential (pantea.simulation.simulate.MDSystemInterface attribute) (pantea.simulation.System attribute) (pantea.simulation.system.System attribute) PotentialInterface (class in pantea.simulation.monte_carlo) (class in pantea.simulation.simulate) (class in pantea.simulation.system) preload() (pantea.datasets.Dataset method) (pantea.datasets.dataset.Dataset method) profile() (pantea.utils.Profiler static method) (pantea.utils.profiler.Profiler static method) Profiler (class in pantea.utils) (class in pantea.utils.profiler)

R

r_cutoff (pantea.atoms.Neighbor attribute) (pantea.atoms.neighbor.Neighbor attribute) (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction property) (pantea.descriptors.acsf.cutoff.CutoffFunction attribute) (pantea.descriptors.acsf.CutoffFunction attribute) (pantea.descriptors.acsf.symmetry.BaseSymmetryFunction property) (pantea.descriptors.AtomCenteredSymmetryFunction property) r_shift (pantea.descriptors.acsf.angular.G3 attribute) (pantea.descriptors.acsf.angular.G9 attribute) (pantea.descriptors.acsf.G2 attribute) (pantea.descriptors.acsf.G3 attribute) (pantea.descriptors.acsf.G9 attribute) (pantea.descriptors.acsf.radial.G2 attribute) radial_symmetry_functions (pantea.descriptors.acsf.acsf.AtomCenteredSymmetryFunction attribute) (pantea.descriptors.acsf.AtomCenteredSymmetryFunction attribute) (pantea.descriptors.AtomCenteredSymmetryFunction attribute)

RadialSymmetryFunction (class in pantea.descriptors.acsf) (class in pantea.descriptors.acsf.radial) read_structures() (pantea.datasets.dataset.DataSourceInterface method) (pantea.datasets.runner.RunnerDataSource method) (pantea.datasets.RunnerDataSource method) register_jax_pytree_node() (in module pantea.pytree) relu() (in module pantea.models.nn.activation) remove_energy_offset() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) repr_physical_params() (pantea.simulation.MCSimulator method) (pantea.simulation.MDSimulator method) (pantea.simulation.molecular_dynamics.MDSimulator method) (pantea.simulation.monte_carlo.MCSimulator method) (pantea.simulation.simulate.SimulatorInterface method) revlogistic() (in module pantea.models.nn.activation) RunnerDataSource (class in pantea.datasets) (class in pantea.datasets.runner)

S

save() (pantea.descriptors.DescriptorScaler class method) (pantea.descriptors.scaler.DescriptorScaler class method) scale_max (pantea.descriptors.DescriptorScaler property) (pantea.descriptors.scaler.DescriptorScaler property) scale_min (pantea.descriptors.DescriptorScaler property) (pantea.descriptors.scaler.DescriptorScaler property) ScaleRange (class in pantea.descriptors.scaler) ScalerParams (class in pantea.descriptors) (class in pantea.descriptors.scaler) ScalerWarnings (class in pantea.descriptors.scaler) select() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) set_as_attribute() (in module pantea.utils.attribute) set_level() (pantea.logger.Logger method) set_logging_level() (in module pantea.logger) sigma (pantea.descriptors.scaler.ScalerParams attribute) (pantea.descriptors.ScalerParams attribute) (pantea.simulation.lennard_jones.LJPotentialParams attribute) simulate() (in module pantea.simulation) (in module pantea.simulation.simulate)

simulate_one_step() (pantea.simulation.MCSimulator method) (pantea.simulation.MDSimulator method) (pantea.simulation.molecular_dynamics.MDSimulator method) (pantea.simulation.monte_carlo.MCSimulator method) (pantea.simulation.simulate.SimulatorInterface method) SimulatorInterface (class in pantea.simulation.simulate) softplus() (in module pantea.models.nn.activation) step (pantea.simulation.simulate.SimulatorInterface attribute) Structure (class in pantea.atoms) (class in pantea.atoms.structure) structure (pantea.simulation.simulate.MDSystemInterface attribute) (pantea.simulation.System attribute) (pantea.simulation.system.System attribute) StructureAsKernelArgs (class in pantea.atoms.structure) StructureInterface (class in pantea.atoms.distance) (class in pantea.atoms.element) (class in pantea.atoms.neighbor) System (class in pantea.simulation) (class in pantea.simulation.system) SystemInterface (class in pantea.simulation.thermostat)

T

tanh() (in module pantea.models.nn.activation) target_temperature (pantea.simulation.thermostat.BrendsenThermostatParams attribute) time_constant (pantea.simulation.thermostat.BrendsenThermostatParams attribute) time_step (pantea.simulation.thermostat.BrendsenThermostatParams attribute) (pantea.simulation.thermostat.MDSimulatorInterface attribute) Timer (class in pantea.utils.profiler) timer() (in module pantea.utils.profiler) TO_ANGSTROM (pantea.units.PhysicalUnits attribute) to_ase() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method) TO_ATMOSPHERE (pantea.units.PhysicalUnits attribute) TO_ATOMIC_MASS (pantea.units.PhysicalUnits attribute) TO_BAR (pantea.units.PhysicalUnits attribute) to_dict() (pantea.atoms.Structure method) (pantea.atoms.structure.Structure method)

TO_ELECTRON_VOLT (pantea.units.PhysicalUnits attribute) TO_FEMTO_SECOND (pantea.units.PhysicalUnits attribute) TO_GIGA_PASCAL (pantea.units.PhysicalUnits attribute) TO_KCAL_PER_MOL (pantea.units.PhysicalUnits attribute) TO_KILO_BAR (pantea.units.PhysicalUnits attribute) TO_NANO_METER (pantea.units.PhysicalUnits attribute) TO_NANO_SECOND (pantea.units.PhysicalUnits attribute) TO_PASCAL (pantea.units.PhysicalUnits attribute) TO_PICO_SECOND (pantea.units.PhysicalUnits attribute) tokenize() (in module pantea.utils.tokenize) total_charge (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) total_energy (pantea.atoms.Structure attribute) (pantea.atoms.structure.Structure attribute) (pantea.atoms.structure.StructureAsKernelArgs attribute)

U

UINT (pantea.types.DataType attribute) UniformInitializer (class in pantea.models.nn.initializer) unique_elements (pantea.atoms.element.ElementMap attribute) (pantea.atoms.ElementMap attribute)

update_forces_from_positions() (pantea.simulation.System method) (pantea.simulation.system.System method) update_total_potential_energy_from_positions() (pantea.simulation.System method) (pantea.simulation.system.System method)

V

velocities (pantea.simulation.System attribute) (pantea.simulation.system.System attribute) (pantea.simulation.thermostat.SystemInterface attribute)

verlet_integration() (pantea.simulation.MDSimulator method) (pantea.simulation.molecular_dynamics.MDSimulator method) volume (pantea.atoms.Box property) (pantea.atoms.box.Box property)

W

warn() (pantea.logger.Logger method) warning() (pantea.logger.Logger method)

wrap_into_box() (pantea.atoms.Box method) (pantea.atoms.box.Box method)

Z

zeta (pantea.descriptors.acsf.angular.G3 attribute) (pantea.descriptors.acsf.angular.G9 attribute) (pantea.descriptors.acsf.G3 attribute) (pantea.descriptors.acsf.G9 attribute)