Index

_

__init__() (narupatools.core.dynamics.OnPostStepCallback method) (narupatools.core.dynamics.OnPreStepCallback method) (narupatools.core.dynamics.OnResetCallback method) (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.event.Event method) (narupatools.core.event.EventListener method) (narupatools.core.health_check.HealthCheck method) (narupatools.flake8.NarupatoolsFlake8Plugin method) (narupatools.frame.fields.FrameKey method) (narupatools.lammps.atom_properties.AtomProperty method) (narupatools.lammps.computes.ComputeAtomReference method) (narupatools.lammps.computes.ComputeGlobalReference method) (narupatools.lammps.computes.ComputeGlobalStyle method) (narupatools.lammps.computes.ComputeLocalReference method) (narupatools.lammps.computes.ComputeReference method) (narupatools.lammps.globals.Global method) (narupatools.lammps.regions.Box method) (narupatools.lammps.regions.Region method) (narupatools.lammps.regions.RegionSpecification method) (narupatools.lammps.settings.BooleanSetting method) (narupatools.lammps.settings.Setting method) (narupatools.lammps.thermo.FloatThermoKeyword method) (narupatools.lammps.thermo.IntegerThermoKeyword method) (narupatools.physics.transformation.Rotation method) (narupatools.physics.transformation.Translation method) (narupatools.physics.units.Prefix method) (narupatools.physics.units.UnfinishedUnitOrQuantity method) (narupatools.physics.units.Unit method) (narupatools.physics.units.UnitConversion method) (narupatools.physics.units.UnitSystem method) (narupatools.state.typing.SerializableIterable method) (narupatools.state.typing.SerializableMapping method) (narupatools.state.typing.SerializableObject method) (narupatools.util.collections.infinite_seq method)

A

add_callback() (narupatools.core.event.Event method) (narupatools.core.event.EventListener method) angle() (in module narupatools.physics.vector) angular_momenta (narupatools.core.dynamics.SimulationDynamics attribute) angular_velocities (narupatools.core.dynamics.SimulationDynamics attribute) angular_velocity() (in module narupatools.physics.rigidbody) args (narupatools.lammps.regions.Box attribute) (narupatools.lammps.regions.RegionSpecification attribute)

around_x_axis() (narupatools.physics.transformation.Rotation class method) around_y_axis() (narupatools.physics.transformation.Rotation class method) around_z_axis() (narupatools.physics.transformation.Rotation class method) atomic_radius() (in module narupatools.physics.atomic) AtomProperty (class in narupatools.lammps.atom_properties) AtomProperty() (in module narupatools.lammps.computes) atoms_from_lammps_simulation() (in module narupatools.ase.lammps) auto() (in module narupatools.util.properties)

B

BondLocal() (in module narupatools.lammps.computes) boolean() (in module narupatools.util.properties)

BooleanSetting (class in narupatools.lammps.settings) bounds() (narupatools.lammps.regions.Box class method) Box (class in narupatools.lammps.regions)

C

calculate_residue_entities() (in module narupatools.frame.util) capitalize() (narupatools.frame.fields.FrameKey method) casefold() (narupatools.frame.fields.FrameKey method) center() (narupatools.frame.fields.FrameKey method) center_of_mass() (in module narupatools.physics.rigidbody) center_of_mass_acceleration() (in module narupatools.physics.rigidbody) center_of_mass_velocity() (in module narupatools.physics.rigidbody) centripetal_force() (in module narupatools.physics.force) check_task() (narupatools.core.dynamics.SimulationDynamics class method) (narupatools.core.health_check.HealthCheck class method) ComputeAtomReference (class in narupatools.lammps.computes) ComputeGlobalReference (class in narupatools.lammps.computes) ComputeGlobalStyle (class in narupatools.lammps.computes)

ComputeLocalReference (class in narupatools.lammps.computes) ComputeReference (class in narupatools.lammps.computes) convert() (narupatools.frame.fields.FrameKey method) count() (narupatools.frame.fields.FrameKey method) covalent_radius() (in module narupatools.physics.atomic) create() (narupatools.lammps.computes.ComputeGlobalReference class method) (narupatools.lammps.computes.ComputeGlobalStyle method) create_from_object() (narupatools.core.dynamics.SimulationDynamics static method) critically_damped_rotational_spring_forces() (in module narupatools.physics.force) critically_damped_spring_force() (in module narupatools.physics.force) cross_product() (in module narupatools.physics.vector) cross_product_matrix() (in module narupatools.physics.vector) cumulative_work() (in module narupatools.physics.energy)

D

damped_rotational_spring_forces() (in module narupatools.physics.force) damped_spring_force() (in module narupatools.physics.force) define() (narupatools.lammps.atom_properties.AtomProperty class method) (narupatools.lammps.computes.ComputeGlobalStyle class method) (narupatools.lammps.globals.Global class method)

deserialize() (narupatools.state.typing.SerializableObject class method) dictionary_to_protobuf() (in module narupatools.core.protobuf) distance() (in module narupatools.physics.vector) distribute_angular_velocity() (in module narupatools.physics.rigidbody) dot_product() (in module narupatools.physics.vector) dynamic_fields (narupatools.core.dynamics.SimulationDynamics attribute)

E

elapsed_steps (narupatools.core.dynamics.SimulationDynamics attribute) elapsed_time (narupatools.core.dynamics.SimulationDynamics attribute) encode() (narupatools.frame.fields.FrameKey method) endswith() (narupatools.frame.fields.FrameKey method) Event (class in narupatools.core.event) EventListener (class in narupatools.core.event) expandtabs() (narupatools.frame.fields.FrameKey method) extract() (narupatools.lammps.atom_properties.AtomProperty method) (narupatools.lammps.computes.ComputeAtomReference method) (narupatools.lammps.computes.ComputeGlobalReference method) (narupatools.lammps.computes.ComputeLocalReference method) (narupatools.lammps.computes.ComputeReference method) (narupatools.lammps.globals.Global method) (narupatools.lammps.settings.BooleanSetting method) (narupatools.lammps.settings.Setting method) (narupatools.lammps.thermo.FloatThermoKeyword method) (narupatools.lammps.thermo.IntegerThermoKeyword method)

F

find() (narupatools.frame.fields.FrameKey method) FloatThermoKeyword (class in narupatools.lammps.thermo) forces (narupatools.core.dynamics.SimulationDynamics attribute) format() (narupatools.frame.fields.FrameKey method)

format_map() (narupatools.frame.fields.FrameKey method) FrameKey (class in narupatools.frame.fields) from_rotation_vector() (narupatools.physics.transformation.Rotation class method) from_size() (narupatools.lammps.regions.Box class method)

G

gather() (narupatools.lammps.computes.ComputeAtomReference method) gaussian_force_and_energy() (in module narupatools.physics.force) get() (narupatools.frame.fields.FrameKey method) get_converter() (in module narupatools.util.properties)

get_frame() (narupatools.core.dynamics.SimulationDynamics method) get_frame_key() (in module narupatools.frame.fields) get_with_default() (narupatools.frame.fields.FrameKey method) Global (class in narupatools.lammps.globals)

H

health_check() (narupatools.core.dynamics.SimulationDynamics method) (narupatools.core.health_check.HealthCheck method)

HealthCheck (class in narupatools.core.health_check)

I

identity (narupatools.physics.transformation.Rotation attribute) (narupatools.physics.transformation.Translation attribute) identity_matrix() (in module narupatools.physics.matrix) index() (narupatools.frame.fields.FrameKey method) infinite_seq (class in narupatools.util.collections) integer() (in module narupatools.util.properties) IntegerThermoKeyword (class in narupatools.lammps.thermo) inverse (narupatools.physics.transformation.Rotation attribute) invoke (narupatools.core.event.Event attribute) is_paused (narupatools.core.dynamics.SimulationDynamics attribute) is_playing (narupatools.core.dynamics.SimulationDynamics attribute) is_running (narupatools.core.dynamics.SimulationDynamics attribute)

isalnum() (narupatools.frame.fields.FrameKey method) isalpha() (narupatools.frame.fields.FrameKey method) isascii() (narupatools.frame.fields.FrameKey method) isdecimal() (narupatools.frame.fields.FrameKey method) isdigit() (narupatools.frame.fields.FrameKey method) isidentifier() (narupatools.frame.fields.FrameKey method) islower() (narupatools.frame.fields.FrameKey method) isnumeric() (narupatools.frame.fields.FrameKey method) isprintable() (narupatools.frame.fields.FrameKey method) isspace() (narupatools.frame.fields.FrameKey method) istitle() (narupatools.frame.fields.FrameKey method) isupper() (narupatools.frame.fields.FrameKey method)

J

join() (narupatools.frame.fields.FrameKey method)

K

kinetic_energy (narupatools.core.dynamics.SimulationDynamics attribute) kinetic_energy() (in module narupatools.physics.energy) (in module narupatools.physics.rigidbody)

kronecker_delta() (in module narupatools.physics.matrix)

L

left_vector_triple_product_matrix() (in module narupatools.physics.vector) linear_drag_force() (in module narupatools.physics.force) ljust() (narupatools.frame.fields.FrameKey method) load_ipython_extension() (in module narupatools) (in module narupatools.nglview)

LocalProperty() (in module narupatools.lammps.computes) lower() (narupatools.frame.fields.FrameKey method) lstrip() (narupatools.frame.fields.FrameKey method)

M

magnitude() (in module narupatools.physics.vector) maketrans() (narupatools.frame.fields.FrameKey static method) marked_as_override() (in module narupatools.override) mass_weighted_forces() (in module narupatools.physics.force) masses (narupatools.core.dynamics.SimulationDynamics attribute) matrix_inverse() (in module narupatools.physics.matrix) maxwell_boltzmann_velocities() (in module narupatools.physics.thermodynamics) module narupatools narupatools.app narupatools.app.scivana narupatools.ase narupatools.ase.calculators narupatools.ase.constraints narupatools.ase.lammps narupatools.ase.openmm narupatools.core narupatools.core.dynamics narupatools.core.event narupatools.core.health_check narupatools.core.protobuf narupatools.flake8 narupatools.frame narupatools.frame.fields narupatools.frame.hdf5 narupatools.frame.util narupatools.imd narupatools.imd.interactions narupatools.lammps narupatools.lammps.atom_properties narupatools.lammps.computes narupatools.lammps.exceptions narupatools.lammps.globals narupatools.lammps.regions narupatools.lammps.settings narupatools.lammps.thermo narupatools.mdanalysis narupatools.mdtraj narupatools.nglview narupatools.openmm narupatools.override narupatools.physics narupatools.physics.atomic narupatools.physics.constants narupatools.physics.energy narupatools.physics.force narupatools.physics.matrix narupatools.physics.random narupatools.physics.rigidbody narupatools.physics.thermodynamics narupatools.physics.transformation narupatools.physics.typing narupatools.physics.units narupatools.physics.vector narupatools.state narupatools.state.typing narupatools.state.view narupatools.util narupatools.util.collections narupatools.util.partial narupatools.util.properties narupatools.util.random narupatools.util.timing

moment_of_inertia() (in module narupatools.physics.rigidbody) moment_of_inertia_tensor() (in module narupatools.physics.rigidbody) momenta (narupatools.core.dynamics.SimulationDynamics attribute) moments_of_inertia (narupatools.core.dynamics.SimulationDynamics attribute)

N

name (narupatools.flake8.NarupatoolsFlake8Plugin attribute) narupatools module narupatools.app module narupatools.app.scivana module narupatools.ase module narupatools.ase.calculators module narupatools.ase.constraints module narupatools.ase.lammps module narupatools.ase.openmm module narupatools.core module narupatools.core.dynamics module narupatools.core.event module narupatools.core.health_check module narupatools.core.protobuf module narupatools.flake8 module narupatools.frame module narupatools.frame.fields module narupatools.frame.hdf5 module narupatools.frame.util module narupatools.imd module narupatools.imd.interactions module narupatools.lammps module narupatools.lammps.atom_properties module narupatools.lammps.computes module narupatools.lammps.exceptions module narupatools.lammps.globals module narupatools.lammps.regions module narupatools.lammps.settings module narupatools.lammps.thermo module

narupatools.mdanalysis module narupatools.mdtraj module narupatools.nglview module narupatools.openmm module narupatools.override module narupatools.physics module narupatools.physics.atomic module narupatools.physics.constants module narupatools.physics.energy module narupatools.physics.force module narupatools.physics.matrix module narupatools.physics.random module narupatools.physics.rigidbody module narupatools.physics.thermodynamics module narupatools.physics.transformation module narupatools.physics.typing module narupatools.physics.units module narupatools.physics.vector module narupatools.state module narupatools.state.typing module narupatools.state.view module narupatools.util module narupatools.util.collections module narupatools.util.partial module narupatools.util.properties module narupatools.util.random module narupatools.util.timing module NarupatoolsFlake8Plugin (class in narupatools.flake8) normalized() (in module narupatools.physics.vector) number() (in module narupatools.util.properties) numpy() (in module narupatools.util.properties)

O

on_fields_changed (narupatools.core.dynamics.SimulationDynamics attribute) on_post_step (narupatools.core.dynamics.SimulationDynamics attribute) on_pre_step (narupatools.core.dynamics.SimulationDynamics attribute) on_reset (narupatools.core.dynamics.SimulationDynamics attribute) OnPostStepCallback (class in narupatools.core.dynamics)

OnPreStepCallback (class in narupatools.core.dynamics) OnResetCallback (class in narupatools.core.dynamics) orbital_angular_momentum() (in module narupatools.physics.rigidbody) orientations (narupatools.core.dynamics.SimulationDynamics attribute) outer_product() (in module narupatools.physics.vector) override() (in module narupatools.override)

P

partialclass() (in module narupatools.util.partial) partition() (narupatools.frame.fields.FrameKey method) pause() (narupatools.core.dynamics.SimulationDynamics method) play() (narupatools.core.dynamics.SimulationDynamics method) playback_interval (narupatools.core.dynamics.SimulationDynamics attribute)

playback_rate (narupatools.core.dynamics.SimulationDynamics attribute) positions (narupatools.core.dynamics.SimulationDynamics attribute) potential_energy (narupatools.core.dynamics.SimulationDynamics attribute) Prefix (class in narupatools.physics.units) principal_axes() (in module narupatools.physics.rigidbody) principal_moments_and_axes() (in module narupatools.physics.rigidbody)

R

radius_of_gyration() (in module narupatools.physics.rigidbody) random_float() (in module narupatools.util.random) random_integer() (in module narupatools.util.random) random_letter() (in module narupatools.util.random) random_quaternion() (in module narupatools.physics.random) random_sphere() (in module narupatools.physics.random) random_unit_quaternion() (in module narupatools.physics.random) random_vector() (in module narupatools.physics.random) random_word() (in module narupatools.util.random) Region (class in narupatools.lammps.regions) region_id (narupatools.lammps.regions.Region attribute) RegionSpecification (class in narupatools.lammps.regions) remove_callback() (narupatools.core.event.Event method) (narupatools.core.event.EventListener method) removeprefix() (narupatools.frame.fields.FrameKey method) removesuffix() (narupatools.frame.fields.FrameKey method) replace() (narupatools.frame.fields.FrameKey method)

reset() (narupatools.core.dynamics.SimulationDynamics method) reset_time() (narupatools.core.dynamics.SimulationDynamics method) restart() (narupatools.core.dynamics.SimulationDynamics method) rfind() (narupatools.frame.fields.FrameKey method) right_cross_product_matrix() (in module narupatools.physics.vector) rindex() (narupatools.frame.fields.FrameKey method) rjust() (narupatools.frame.fields.FrameKey method) rotate_around_center_of_mass() (narupatools.physics.transformation.Rotation method) rotate_around_point() (narupatools.physics.transformation.Rotation method) Rotation (class in narupatools.physics.transformation) rotation_matrix (narupatools.physics.transformation.Rotation attribute) rotation_vector (narupatools.physics.transformation.Rotation attribute) rpartition() (narupatools.frame.fields.FrameKey method) rsplit() (narupatools.frame.fields.FrameKey method) rstrip() (narupatools.frame.fields.FrameKey method) run() (narupatools.core.dynamics.SimulationDynamics method) (narupatools.flake8.NarupatoolsFlake8Plugin method)

S

SerializableIterable (class in narupatools.state.typing) SerializableMapping (class in narupatools.state.typing) SerializableObject (class in narupatools.state.typing) serialize() (narupatools.state.typing.SerializableObject method) set() (narupatools.frame.fields.FrameKey method) Setting (class in narupatools.lammps.settings) SimulationDynamics (class in narupatools.core.dynamics) specification (narupatools.lammps.regions.Region attribute) spin_angular_momentum() (in module narupatools.physics.rigidbody) split() (narupatools.frame.fields.FrameKey method) splitlines() (narupatools.frame.fields.FrameKey method) spring_force() (in module narupatools.physics.force)

spring_force_and_energy() (in module narupatools.physics.force) sqr_distance() (in module narupatools.physics.vector) sqr_magnitude() (in module narupatools.physics.vector) start() (narupatools.core.dynamics.SimulationDynamics method) startswith() (narupatools.frame.fields.FrameKey method) step() (narupatools.core.dynamics.SimulationDynamics method) stop() (narupatools.core.dynamics.SimulationDynamics method) string() (in module narupatools.util.properties) strip() (narupatools.frame.fields.FrameKey method) style (narupatools.lammps.regions.Box attribute) (narupatools.lammps.regions.RegionSpecification attribute) swapcase() (narupatools.frame.fields.FrameKey method)

T

temperature (narupatools.core.dynamics.SimulationDynamics attribute) throttle() (in module narupatools.util.timing) timestep (narupatools.core.dynamics.SimulationDynamics attribute) title() (narupatools.frame.fields.FrameKey method) to_bool() (in module narupatools.util.properties) to_float() (in module narupatools.util.properties) to_int() (in module narupatools.util.properties) to_list() (in module narupatools.util.properties) to_property() (in module narupatools.util.properties) to_serializable() (in module narupatools.util.properties)

to_str() (in module narupatools.util.properties) to_unit_quaternion() (in module narupatools.util.properties) torques (narupatools.core.dynamics.SimulationDynamics attribute) total_steps (narupatools.core.dynamics.SimulationDynamics attribute) total_time (narupatools.core.dynamics.SimulationDynamics attribute) total_work() (in module narupatools.physics.energy) translate() (narupatools.frame.fields.FrameKey method) Translation (class in narupatools.physics.transformation) translation (narupatools.physics.transformation.Translation attribute) transpose() (in module narupatools.physics.matrix)

U

UnfinishedUnitOrQuantity (class in narupatools.physics.units) Unit (class in narupatools.physics.units) unit_quaternion() (in module narupatools.util.properties)

UnitConversion (class in narupatools.physics.units) UnitSystem (class in narupatools.physics.units) update_struct() (in module narupatools.core.protobuf) upper() (narupatools.frame.fields.FrameKey method)

V

vdw_radius() (in module narupatools.physics.atomic) vector() (in module narupatools.physics.vector) vector_projection() (in module narupatools.physics.vector)

vector_rejection() (in module narupatools.physics.vector) velocities (narupatools.core.dynamics.SimulationDynamics attribute) version (narupatools.flake8.NarupatoolsFlake8Plugin attribute) versor (narupatools.physics.transformation.Rotation attribute)

W

wait_for() (in module narupatools.util.timing)

work_per_step() (in module narupatools.physics.energy)

Z

zero_matrix() (in module narupatools.physics.matrix)

zero_vector() (in module narupatools.physics.vector) zfill() (narupatools.frame.fields.FrameKey method)