Index

A

add_property() (torch_sim.properties.correlations.CorrelationCalculator method) append() (torch_sim.properties.correlations.CircularBuffer method) array_registry (torch_sim.trajectory.TrajectoryReporter property) ase_fire_key (in module torch_sim.optimizers)

asymmetric_particle_pair_force() (in module torch_sim.models.particle_life) asymmetric_particle_pair_force_jit() (in module torch_sim.models.particle_life) atoms_to_state() (in module torch_sim.io) attributes (torch_sim.state.SimState property)

B

backward() (torch_sim.math.expm static method) BaseConstant (class in torch_sim.units) batched_vdot() (in module torch_sim.math)

bc (in module torch_sim.units) BinningAutoBatcher (class in torch_sim.autobatching) build_linked_cell_neighborhood() (in module torch_sim.transforms) build_naive_neighborhood() (in module torch_sim.transforms)

C

calc_heat_flux() (in module torch_sim.quantities) calc_kinetic_energy() (in module torch_sim.quantities) calc_kT() (in module torch_sim.quantities) calc_temperature() (in module torch_sim.quantities) (torch_sim.integrators.md.MDState method) calculate_elastic_moduli() (in module torch_sim.elastic) calculate_elastic_tensor() (in module torch_sim.elastic) calculate_memory_scaler() (in module torch_sim.autobatching) calculate_momenta() (in module torch_sim.integrators.md) CELL_FILTER_REGISTRY (in module torch_sim.optimizers.cell_filters) CellFilter (class in torch_sim.optimizers.cell_filters) CellFireState (class in torch_sim.optimizers.cell_filters) CellOptimState (class in torch_sim.optimizers.cell_filters) ChemicalSpeciesToAtomTypeMapper (class in torch_sim.models.nequip_framework)

CircularBuffer (class in torch_sim.properties.correlations) clone() (torch_sim.state.SimState method) close() (torch_sim.trajectory.TorchSimTrajectory method) (torch_sim.trajectory.TrajectoryReporter method) column_vector_cell (torch_sim.state.SimState property) compute_cell_forces() (in module torch_sim.optimizers.cell_filters) compute_cell_shifts() (in module torch_sim.transforms) compute_distances_with_cell_shifts() (in module torch_sim.transforms) compute_forces (torch_sim.models.interface.ModelInterface property) compute_stress (torch_sim.models.interface.ModelInterface property) concatenate_states() (in module torch_sim.state) construct_nose_hoover_chain() (in module torch_sim.integrators.md) CorrelationCalculator (class in torch_sim.properties.correlations) current_cell (torch_sim.integrators.npt.NPTNoseHooverState property)

D

DEFAULT_ALPHA (in module torch_sim.models.morse) DEFAULT_EPSILON (in module torch_sim.models.lennard_jones) (in module torch_sim.models.morse) DEFAULT_SIGMA (in module torch_sim.models.lennard_jones) (in module torch_sim.models.morse) deform_grad() (in module torch_sim.optimizers.cell_filters) (torch_sim.state.DeformGradMixin method) DeformationRule (class in torch_sim.elastic)

DeformGradMixin (class in torch_sim.state) determine_max_batch_size() (in module torch_sim.autobatching) device (torch_sim.models.fairchem.FairChemModel property) (torch_sim.models.interface.ModelInterface property) (torch_sim.state.SimState property) dtype (torch_sim.models.fairchem.FairChemModel property) (torch_sim.models.interface.ModelInterface property) (torch_sim.state.SimState property)

E

ell_table_61 (in module torch_sim.math) estimate_max_memory_scaler() (in module torch_sim.autobatching) expm (class in torch_sim.math) expm_cond() (in module torch_sim.math)

expm_frechet() (in module torch_sim.math) expm_frechet_algo_64() (in module torch_sim.math) expm_frechet_block_enlarge() (in module torch_sim.math) expm_frechet_kronform() (in module torch_sim.math)

F

FairChemModel (class in torch_sim.models.fairchem) FairChemV1Model (class in torch_sim.models.fairchem_legacy) finish() (torch_sim.trajectory.TrajectoryReporter method) fire_init() (in module torch_sim.optimizers.fire) fire_step() (in module torch_sim.optimizers.fire) FireState (class in torch_sim.optimizers.state) flush() (torch_sim.trajectory.TorchSimTrajectory method) forward() (torch_sim.math.expm static method) (torch_sim.models.fairchem.FairChemModel method) (torch_sim.models.fairchem_legacy.FairChemV1Model method) (torch_sim.models.graphpes.GraphPESWrapper method) (torch_sim.models.interface.ModelInterface method) (torch_sim.models.lennard_jones.LennardJonesModel method) (torch_sim.models.mace.MaceModel method) (torch_sim.models.mattersim.MatterSimModel method) (torch_sim.models.morse.MorseModel method) (torch_sim.models.nequip_framework.NequIPFrameworkModel method) (torch_sim.models.orb.OrbModel method) (torch_sim.models.particle_life.ParticleLifeModel method) (torch_sim.models.sevennet.SevenNetModel method) (torch_sim.models.soft_sphere.SoftSphereModel method) (torch_sim.models.soft_sphere.SoftSphereMultiModel method)

frechet_cell_filter_init() (in module torch_sim.optimizers.cell_filters) frechet_cell_step() (in module torch_sim.optimizers.cell_filters) from_compiled_model() (in module torch_sim.models.nequip_framework) from_state() (torch_sim.state.SimState class method) full_3x3_to_voigt_6_stress() (in module torch_sim.elastic)

G

generate_energy_convergence_fn() (in module torch_sim.runners) generate_force_convergence_fn() (in module torch_sim.runners) generate_swaps() (in module torch_sim.monte_carlo) get_array() (torch_sim.properties.correlations.CircularBuffer method) (torch_sim.trajectory.TorchSimTrajectory method) get_atoms() (torch_sim.trajectory.TorchSimTrajectory method) get_attrs_for_scope() (in module torch_sim.state) get_auto_correlations() (torch_sim.properties.correlations.CorrelationCalculator method) get_bravais_type() (in module torch_sim.elastic) get_cart_deformed_cell() (in module torch_sim.elastic) get_cell_filter() (in module torch_sim.optimizers.cell_filters) get_cell_shift_idx() (in module torch_sim.transforms) get_cross_correlations() (torch_sim.properties.correlations.CorrelationCalculator method) get_elastic_coeffs() (in module torch_sim.elastic) get_elastic_tensor_from_coeffs() (in module torch_sim.elastic) get_elementary_deformations() (in module torch_sim.elastic)

get_fractional_coordinates() (in module torch_sim.transforms) get_fully_connected_mapping() (in module torch_sim.transforms) get_linear_bin_idx() (in module torch_sim.transforms) get_number_of_cell_repeats() (in module torch_sim.transforms) get_number_of_degrees_of_freedom() (torch_sim.integrators.npt.NPTNoseHooverState method) (torch_sim.integrators.nvt.NVTNoseHooverState method) (torch_sim.state.SimState method) get_pair_displacements() (in module torch_sim.transforms) get_pressure() (in module torch_sim.quantities) get_state() (torch_sim.trajectory.TorchSimTrajectory method) get_steps() (torch_sim.trajectory.TorchSimTrajectory method) get_strain() (in module torch_sim.elastic) get_structure() (torch_sim.trajectory.TorchSimTrajectory method) gradient_descent_init() (in module torch_sim.optimizers.gradient_descent) gradient_descent_step() (in module torch_sim.optimizers.gradient_descent) GraphPESWrapper (class in torch_sim.models.graphpes)

H

HeatFluxAutoCorrelation (class in torch_sim.properties.correlations) hexagonal_symmetry() (in module torch_sim.elastic)

hfacf (torch_sim.properties.correlations.HeatFluxAutoCorrelation property) high_precision_sum() (in module torch_sim.transforms)

I

InFlightAutoBatcher (class in torch_sim.autobatching) initialize_state() (in module torch_sim.state) integrate() (in module torch_sim.runners) Integrator (class in torch_sim.integrators)

INTEGRATOR_REGISTRY (in module torch_sim.integrators) (in module torch_sim.runners) inverse_box() (in module torch_sim.transforms) is_full (torch_sim.properties.correlations.CircularBuffer property)

L

lennard_jones_pair() (in module torch_sim.models.lennard_jones) lennard_jones_pair_force() (in module torch_sim.models.lennard_jones) LennardJonesModel (class in torch_sim.models.lennard_jones) linked_cell() (in module torch_sim.transforms)

load_checkpoint() (torch_sim.models.fairchem_legacy.FairChemV1Model method) load_new_trajectories() (torch_sim.trajectory.TrajectoryReporter method) load_states() (torch_sim.autobatching.BinningAutoBatcher method) (torch_sim.autobatching.InFlightAutoBatcher method)

M

MaceModel (class in torch_sim.models.mace) MaceUrls (class in torch_sim.models.mace) matrix_exp() (in module torch_sim.math) matrix_log_33() (in module torch_sim.math) matrix_log_scipy() (in module torch_sim.math) MatterSimModel (class in torch_sim.models.mattersim) MDState (class in torch_sim.integrators.md) measure_model_memory_forward() (in module torch_sim.autobatching) memory_scales_with (torch_sim.models.interface.ModelInterface property) metadata (torch_sim.trajectory.TorchSimTrajectory property) metal (torch_sim.units.UnitSystem attribute) MetalUnits (class in torch_sim.units) metropolis_criterion() (in module torch_sim.monte_carlo) minimum_image_displacement() (in module torch_sim.transforms) ModelInterface (class in torch_sim.models.interface) module torch_sim.autobatching torch_sim.elastic torch_sim.integrators torch_sim.integrators.md torch_sim.integrators.npt torch_sim.integrators.nve torch_sim.integrators.nvt torch_sim.io torch_sim.math torch_sim.models torch_sim.models.fairchem torch_sim.models.fairchem_legacy torch_sim.models.graphpes torch_sim.models.interface torch_sim.models.lennard_jones torch_sim.models.mace torch_sim.models.mattersim torch_sim.models.morse torch_sim.models.nequip_framework torch_sim.models.orb torch_sim.models.particle_life torch_sim.models.sevennet torch_sim.models.soft_sphere torch_sim.monte_carlo torch_sim.neighbors torch_sim.optimizers torch_sim.optimizers.cell_filters torch_sim.optimizers.fire torch_sim.optimizers.gradient_descent torch_sim.optimizers.state torch_sim.properties.correlations torch_sim.quantities torch_sim.runners torch_sim.state torch_sim.trajectory torch_sim.transforms torch_sim.units

momentum_step() (in module torch_sim.integrators.md) monoclinic_symmetry() (in module torch_sim.elastic) morse_pair() (in module torch_sim.models.morse) morse_pair_force() (in module torch_sim.models.morse) MorseModel (class in torch_sim.models.morse) multiplicative_isotropic_cutoff() (in module torch_sim.transforms)

N

n_atoms (torch_sim.state.SimState property) n_atoms_per_system (torch_sim.state.SimState property) n_systems (torch_sim.state.SimState property) NequIPFrameworkModel (class in torch_sim.models.nequip_framework) next_batch() (torch_sim.autobatching.BinningAutoBatcher method) (torch_sim.autobatching.InFlightAutoBatcher method) NoseHooverChain (class in torch_sim.integrators.md) NoseHooverChainFns (class in torch_sim.integrators.md) npt_langevin_init() (in module torch_sim.integrators.npt) npt_langevin_step() (in module torch_sim.integrators.npt) npt_nose_hoover_init() (in module torch_sim.integrators.npt)

npt_nose_hoover_invariant() (in module torch_sim.integrators.npt) npt_nose_hoover_step() (in module torch_sim.integrators.npt) NPTLangevinState (class in torch_sim.integrators.npt) NPTNoseHooverState (class in torch_sim.integrators.npt) nve_init() (in module torch_sim.integrators.nve) nve_step() (in module torch_sim.integrators.nve) nvt_langevin_init() (in module torch_sim.integrators.nvt) nvt_langevin_step() (in module torch_sim.integrators.nvt) nvt_nose_hoover_init() (in module torch_sim.integrators.nvt) nvt_nose_hoover_invariant() (in module torch_sim.integrators.nvt) nvt_nose_hoover_step() (in module torch_sim.integrators.nvt) NVTNoseHooverState (class in torch_sim.integrators.nvt)

O

OPTIM_REGISTRY (in module torch_sim.optimizers) (in module torch_sim.runners) optimize() (in module torch_sim.runners)

Optimizer (class in torch_sim.optimizers) OptimState (class in torch_sim.optimizers.state) OrbModel (class in torch_sim.models.orb) orthorhombic_symmetry() (in module torch_sim.elastic)

P

ParticleLifeModel (class in torch_sim.models.particle_life) pbc_wrap_batched() (in module torch_sim.transforms) pbc_wrap_general() (in module torch_sim.transforms)

phonopy_to_state() (in module torch_sim.io) pi (in module torch_sim.units) pop() (torch_sim.state.SimState method) position_step() (in module torch_sim.integrators.md)

R

ravel_3d() (in module torch_sim.transforms) real (torch_sim.units.UnitSystem attribute) RealUnits (class in torch_sim.units) reference_row_vector_cell (torch_sim.state.DeformGradMixin property) regular_symmetry() (in module torch_sim.elastic)

report() (torch_sim.trajectory.TrajectoryReporter method) reset() (torch_sim.properties.correlations.CorrelationCalculator method) restore_original_order() (torch_sim.autobatching.BinningAutoBatcher method) (torch_sim.autobatching.InFlightAutoBatcher method) row_vector_cell (torch_sim.state.SimState property)

S

safe_mask() (in module torch_sim.transforms) scatter_bin_index() (in module torch_sim.transforms) setup_from_system_idx() (torch_sim.models.mace.MaceModel method) (torch_sim.models.nequip_framework.NequIPFrameworkModel method) SevenNetModel (class in torch_sim.models.sevennet) SimState (class in torch_sim.state) soft_sphere_pair() (in module torch_sim.models.soft_sphere) soft_sphere_pair_force() (in module torch_sim.models.soft_sphere) SoftSphereModel (class in torch_sim.models.soft_sphere) SoftSphereMultiModel (class in torch_sim.models.soft_sphere) split() (torch_sim.state.SimState method) state_to_atom_graphs() (in module torch_sim.models.orb) state_to_atomic_graph() (in module torch_sim.models.graphpes)

state_to_atoms() (in module torch_sim.io) state_to_phonopy() (in module torch_sim.io) state_to_structures() (in module torch_sim.io) static() (in module torch_sim.runners) strict_nl() (in module torch_sim.neighbors) strides_of() (in module torch_sim.transforms) structures_to_state() (in module torch_sim.io) SUZUKI_YOSHIDA_WEIGHTS (in module torch_sim.integrators.md) swap_mc_init() (in module torch_sim.monte_carlo) swap_mc_step() (in module torch_sim.monte_carlo) SwapMCState (class in torch_sim.monte_carlo) swaps_to_permutation() (in module torch_sim.monte_carlo) system_wise_max_force() (in module torch_sim.quantities)

T

tetragonal_symmetry() (in module torch_sim.elastic) to() (torch_sim.properties.correlations.CorrelationCalculator method) (torch_sim.state.SimState method) to_atoms() (torch_sim.state.SimState method) to_constant_volume_bins() (in module torch_sim.autobatching) to_one_hot() (in module torch_sim.models.mace) to_phonopy() (torch_sim.state.SimState method) to_structures() (torch_sim.state.SimState method) torch_sim.autobatching module torch_sim.elastic module torch_sim.integrators module torch_sim.integrators.md module torch_sim.integrators.npt module torch_sim.integrators.nve module torch_sim.integrators.nvt module torch_sim.io module torch_sim.math module torch_sim.models module torch_sim.models.fairchem module torch_sim.models.fairchem_legacy module torch_sim.models.graphpes module torch_sim.models.interface module torch_sim.models.lennard_jones module torch_sim.models.mace module torch_sim.models.mattersim module torch_sim.models.morse module torch_sim.models.nequip_framework module torch_sim.models.orb module

torch_sim.models.particle_life module torch_sim.models.sevennet module torch_sim.models.soft_sphere module torch_sim.monte_carlo module torch_sim.neighbors module torch_sim.optimizers module torch_sim.optimizers.cell_filters module torch_sim.optimizers.fire module torch_sim.optimizers.gradient_descent module torch_sim.optimizers.state module torch_sim.properties.correlations module torch_sim.quantities module torch_sim.runners module torch_sim.state module torch_sim.trajectory module torch_sim.transforms module torch_sim.units module TorchSimTrajectory (class in torch_sim.trajectory) TrajectoryReporter (class in torch_sim.trajectory) translate_pretty() (in module torch_sim.transforms) triclinic_symmetry() (in module torch_sim.elastic) trigonal_symmetry() (in module torch_sim.elastic) TYPE_CHECKING (in module torch_sim.io) (in module torch_sim.models.mattersim) (in module torch_sim.models.sevennet) (in module torch_sim.optimizers.fire) (in module torch_sim.optimizers.gradient_descent) (in module torch_sim.quantities) (in module torch_sim.state) (in module torch_sim.trajectory)

U

uc (in module torch_sim.units) unbatched_forward() (torch_sim.models.lennard_jones.LennardJonesModel method) (torch_sim.models.morse.MorseModel method) (torch_sim.models.particle_life.ParticleLifeModel method) (torch_sim.models.soft_sphere.SoftSphereModel method) (torch_sim.models.soft_sphere.SoftSphereMultiModel method)

unit_cell_filter_init() (in module torch_sim.optimizers.cell_filters) unit_cell_step() (in module torch_sim.optimizers.cell_filters) UnitConversion (class in torch_sim.units) UnitSystem (class in torch_sim.units) unravel_3d() (in module torch_sim.transforms) update() (torch_sim.properties.correlations.CorrelationCalculator method)

V

vacf (torch_sim.properties.correlations.VelocityAutoCorrelation property) validate_model_outputs() (in module torch_sim.models.interface) vec() (in module torch_sim.math) velocities (torch_sim.integrators.md.MDState property) (torch_sim.integrators.npt.NPTNoseHooverState property) (torch_sim.integrators.nvt.NVTNoseHooverState property)

velocity_verlet() (in module torch_sim.integrators.md) VelocityAutoCorrelation (class in torch_sim.properties.correlations) vesin_nl() (in module torch_sim.neighbors) voigt_6_to_full_3x3_stress() (in module torch_sim.elastic) volume (torch_sim.state.SimState property) vv_fire_key (in module torch_sim.optimizers)

W

wrap_positions (torch_sim.state.SimState property) wrap_positions() (in module torch_sim.transforms)

write_arrays() (torch_sim.trajectory.TorchSimTrajectory method) write_ase_trajectory() (torch_sim.trajectory.TorchSimTrajectory method) write_state() (torch_sim.trajectory.TorchSimTrajectory method)