Index _ | A | B | C | D | E | F | G | I | L | M | N | P | Q | R | S | T | U | V | W | Z _ _dftd3_matrix_op() (in module nvalchemiops.torch.interactions.dispersion._dftd3) _dftd3_matrix_pbc_op() (in module nvalchemiops.torch.interactions.dispersion._dftd3) _dftd3_nl_impl() (in module nvalchemiops.jax.interactions.dispersion._dftd3) _dftd3_nm_impl() (in module nvalchemiops.jax.interactions.dispersion._dftd3) _dftd3_op() (in module nvalchemiops.torch.interactions.dispersion._dftd3) _dftd3_pbc_op() (in module nvalchemiops.torch.interactions.dispersion._dftd3) A align_cell() (in module nvalchemiops.dynamics.utils.cell_filter) allocate_cell_list() (in module nvalchemiops.jax.neighbors.neighbor_utils) (in module nvalchemiops.torch.neighbors.neighbor_utils) alpha (nvalchemiops.jax.interactions.electrostatics.EwaldParameters attribute) (nvalchemiops.jax.interactions.electrostatics.PMEParameters attribute) (nvalchemiops.torch.interactions.electrostatics.EwaldParameters attribute) (nvalchemiops.torch.interactions.electrostatics.PMEParameters attribute) apply_strain_to_cell() (in module nvalchemiops.dynamics.utils.cell_utils) B batch_build_cell_list() (in module nvalchemiops.jax.neighbors.batch_cell_list) (in module nvalchemiops.neighbors.batch_cell_list) (in module nvalchemiops.torch.neighbors.batch_cell_list) batch_cell_list() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) batch_coulomb_energy() (in module nvalchemiops.interactions.electrostatics) batch_coulomb_energy_forces() (in module nvalchemiops.interactions.electrostatics) batch_coulomb_energy_forces_matrix() (in module nvalchemiops.interactions.electrostatics) batch_coulomb_energy_matrix() (in module nvalchemiops.interactions.electrostatics) batch_ewald_real_space_energy() (in module nvalchemiops.interactions.electrostatics) batch_ewald_real_space_energy_forces() (in module nvalchemiops.interactions.electrostatics) batch_ewald_real_space_energy_forces_matrix() (in module nvalchemiops.interactions.electrostatics) batch_ewald_real_space_energy_matrix() (in module nvalchemiops.interactions.electrostatics) batch_ewald_reciprocal_space_compute_energy() (in module nvalchemiops.interactions.electrostatics) batch_ewald_reciprocal_space_energy_forces() (in module nvalchemiops.interactions.electrostatics) batch_ewald_reciprocal_space_fill_structure_factors() (in module nvalchemiops.interactions.electrostatics) batch_ewald_subtract_self_energy() (in module nvalchemiops.interactions.electrostatics) batch_naive_neighbor_list() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) batch_naive_neighbor_list_dual_cutoff() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) batch_naive_neighbor_matrix() (in module nvalchemiops.neighbors.batch_naive) batch_naive_neighbor_matrix_dual_cutoff() (in module nvalchemiops.neighbors.batch_naive_dual_cutoff) batch_naive_neighbor_matrix_pbc() (in module nvalchemiops.neighbors.batch_naive) batch_naive_neighbor_matrix_pbc_dual_cutoff() (in module nvalchemiops.neighbors.batch_naive_dual_cutoff) batch_pme_energy_corrections() (in module nvalchemiops.interactions.electrostatics) batch_pme_energy_corrections_with_charge_grad() (in module nvalchemiops.interactions.electrostatics) batch_pme_green_structure_factor() (in module nvalchemiops.interactions.electrostatics) batch_query_cell_list() (in module nvalchemiops.jax.neighbors.batch_cell_list) (in module nvalchemiops.neighbors.batch_cell_list) (in module nvalchemiops.torch.neighbors.batch_cell_list) batch_spline_gather() (in module nvalchemiops.math) batch_spline_gather_gradient() (in module nvalchemiops.math) batch_spline_gather_vec3() (in module nvalchemiops.math) batch_spline_spread() (in module nvalchemiops.math) build_cell_list() (in module nvalchemiops.jax.neighbors.cell_list) (in module nvalchemiops.neighbors.cell_list) (in module nvalchemiops.torch.neighbors.cell_list) C c6ab (nvalchemiops.jax.interactions.dispersion.D3Parameters attribute) (nvalchemiops.torch.interactions.dispersion.D3Parameters attribute) cartesian_to_fractional() (in module nvalchemiops.dynamics.utils.cell_utils) cell_list() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) cell_list_needs_rebuild() (in module nvalchemiops.jax.neighbors.rebuild_detection) (in module nvalchemiops.torch.neighbors.rebuild_detection) check_cell_list_rebuild() (in module nvalchemiops.neighbors.rebuild_detection) check_cell_list_rebuild_needed() (in module nvalchemiops.jax.neighbors.rebuild_detection) (in module nvalchemiops.torch.neighbors.rebuild_detection) check_neighbor_list_rebuild() (in module nvalchemiops.neighbors.rebuild_detection) check_neighbor_list_rebuild_needed() (in module nvalchemiops.jax.neighbors.rebuild_detection) (in module nvalchemiops.torch.neighbors.rebuild_detection) cn_ref (nvalchemiops.jax.interactions.dispersion.D3Parameters attribute) (nvalchemiops.torch.interactions.dispersion.D3Parameters attribute) compute_barostat_mass() (in module nvalchemiops.dynamics.integrators.npt) compute_barostat_potential_energy() (in module nvalchemiops.dynamics.integrators.npt) compute_cell_inverse() (in module nvalchemiops.dynamics.utils.cell_utils) compute_cell_kinetic_energy() (in module nvalchemiops.dynamics.integrators.npt) compute_cell_volume() (in module nvalchemiops.dynamics.utils.cell_utils) compute_kinetic_energy() (in module nvalchemiops.dynamics.utils.thermostat_utils) compute_naive_num_shifts() (in module nvalchemiops.jax.neighbors.neighbor_utils) compute_pressure_tensor() (in module nvalchemiops.dynamics.integrators.npt) compute_scalar_pressure() (in module nvalchemiops.dynamics.integrators.npt) compute_strain_tensor() (in module nvalchemiops.dynamics.utils.cell_utils) compute_temperature() (in module nvalchemiops.dynamics.utils.thermostat_utils) coulomb_energy() (in module nvalchemiops.interactions.electrostatics) (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) coulomb_energy_forces() (in module nvalchemiops.interactions.electrostatics) (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) coulomb_energy_forces_matrix() (in module nvalchemiops.interactions.electrostatics) coulomb_energy_matrix() (in module nvalchemiops.interactions.electrostatics) coulomb_forces() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) D D3Parameters (class in nvalchemiops.jax.interactions.dispersion) (class in nvalchemiops.torch.interactions.dispersion) device (nvalchemiops.torch.interactions.dispersion.D3Parameters property) dftd3() (in module nvalchemiops.interactions.dispersion._dftd3) (in module nvalchemiops.jax.interactions.dispersion) (in module nvalchemiops.torch.interactions.dispersion) dftd3_matrix() (in module nvalchemiops.interactions.dispersion._dftd3) dftd3_matrix_pbc() (in module nvalchemiops.interactions.dispersion._dftd3) dftd3_pbc() (in module nvalchemiops.interactions.dispersion._dftd3) dsf_coulomb() (in module nvalchemiops.torch.interactions.electrostatics) dsf_csr() (in module nvalchemiops.interactions.electrostatics) dsf_matrix() (in module nvalchemiops.interactions.electrostatics) E estimate_batch_cell_list_sizes() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) estimate_cell_list_sizes() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) estimate_ewald_parameters() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) estimate_max_neighbors() (in module nvalchemiops.jax.neighbors.neighbor_utils) (in module nvalchemiops.neighbors.neighbor_utils) estimate_pme_mesh_dimensions() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) estimate_pme_parameters() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) eval_gto_density_pytorch() (in module nvalchemiops.math) eval_gto_fourier_pytorch() (in module nvalchemiops.math) ewald_real_space() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) ewald_real_space_energy() (in module nvalchemiops.interactions.electrostatics) ewald_real_space_energy_forces() (in module nvalchemiops.interactions.electrostatics) ewald_real_space_energy_forces_matrix() (in module nvalchemiops.interactions.electrostatics) ewald_real_space_energy_matrix() (in module nvalchemiops.interactions.electrostatics) ewald_reciprocal_space() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) ewald_reciprocal_space_compute_energy() (in module nvalchemiops.interactions.electrostatics) ewald_reciprocal_space_energy_forces() (in module nvalchemiops.interactions.electrostatics) ewald_reciprocal_space_fill_structure_factors() (in module nvalchemiops.interactions.electrostatics) ewald_subtract_self_energy() (in module nvalchemiops.interactions.electrostatics) ewald_summation() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) EwaldParameters (class in nvalchemiops.jax.interactions.electrostatics) (class in nvalchemiops.torch.interactions.electrostatics) extend_atom_ptr() (in module nvalchemiops.dynamics.utils.cell_filter) extend_batch_idx() (in module nvalchemiops.dynamics.utils.cell_filter) F fire2_step() (in module nvalchemiops.dynamics.optimizers.fire2) fire2_step_coord() (in module nvalchemiops.torch.fire2) fire2_step_coord_cell() (in module nvalchemiops.torch.fire2) fire2_step_extended() (in module nvalchemiops.torch.fire2) fire_step() (in module nvalchemiops.dynamics.optimizers.fire) fire_update() (in module nvalchemiops.dynamics.optimizers.fire) fractional_to_cartesian() (in module nvalchemiops.dynamics.utils.cell_utils) G generate_k_vectors_ewald_summation() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) generate_k_vectors_pme() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) generate_miller_indices() (in module nvalchemiops.jax.interactions.electrostatics) get_neighbor_list_from_neighbor_matrix() (in module nvalchemiops.jax.neighbors.neighbor_utils) get_wp_dtype() (in module nvalchemiops.torch.types) get_wp_mat_dtype() (in module nvalchemiops.torch.types) get_wp_vec_dtype() (in module nvalchemiops.torch.types) I initialize_velocities() (in module nvalchemiops.dynamics.utils.thermostat_utils) initialize_velocities_out() (in module nvalchemiops.dynamics.utils.thermostat_utils) interp_mesh (nvalchemiops.jax.interactions.dispersion.D3Parameters attribute) (nvalchemiops.torch.interactions.dispersion.D3Parameters attribute) L langevin_baoab_finalize() (in module nvalchemiops.dynamics.integrators.langevin) langevin_baoab_finalize_out() (in module nvalchemiops.dynamics.integrators.langevin) langevin_baoab_half_step() (in module nvalchemiops.dynamics.integrators.langevin) langevin_baoab_half_step_out() (in module nvalchemiops.dynamics.integrators.langevin) M max_z (nvalchemiops.jax.interactions.dispersion.D3Parameters property) (nvalchemiops.torch.interactions.dispersion.D3Parameters property) mesh_dimensions (nvalchemiops.jax.interactions.electrostatics.PMEParameters attribute) (nvalchemiops.torch.interactions.electrostatics.PMEParameters attribute) mesh_spacing (nvalchemiops.jax.interactions.electrostatics.PMEParameters attribute) (nvalchemiops.torch.interactions.electrostatics.PMEParameters attribute) mesh_spacing_to_dimensions() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) module nvalchemiops.dynamics nvalchemiops.interactions.dispersion nvalchemiops.interactions.electrostatics nvalchemiops.jax.interactions.dispersion nvalchemiops.jax.neighbors nvalchemiops.math nvalchemiops.neighbors nvalchemiops.torch nvalchemiops.torch.interactions.dispersion nvalchemiops.torch.neighbors nvalchemiops.torch.types N naive_neighbor_list() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) naive_neighbor_list_dual_cutoff() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) naive_neighbor_matrix() (in module nvalchemiops.neighbors.naive) naive_neighbor_matrix_dual_cutoff() (in module nvalchemiops.neighbors.naive_dual_cutoff) naive_neighbor_matrix_pbc() (in module nvalchemiops.neighbors.naive) naive_neighbor_matrix_pbc_dual_cutoff() (in module nvalchemiops.neighbors.naive_dual_cutoff) neighbor_list() (in module nvalchemiops.jax.neighbors) (in module nvalchemiops.torch.neighbors) neighbor_list_needs_rebuild() (in module nvalchemiops.jax.neighbors.rebuild_detection) (in module nvalchemiops.torch.neighbors.rebuild_detection) NeighborOverflowError nhc_compute_chain_energy() (in module nvalchemiops.dynamics.integrators.nose_hoover) nhc_compute_masses() (in module nvalchemiops.dynamics.integrators.nose_hoover) nhc_position_update() (in module nvalchemiops.dynamics.integrators.nose_hoover) nhc_position_update_out() (in module nvalchemiops.dynamics.integrators.nose_hoover) nhc_thermostat_chain_update() (in module nvalchemiops.dynamics.integrators.nose_hoover) nhc_thermostat_chain_update_out() (in module nvalchemiops.dynamics.integrators.nose_hoover) nhc_velocity_half_step() (in module nvalchemiops.dynamics.integrators.nose_hoover) nhc_velocity_half_step_out() (in module nvalchemiops.dynamics.integrators.nose_hoover) nph_barostat_half_step() (in module nvalchemiops.dynamics.integrators.npt) nph_cell_update() (in module nvalchemiops.dynamics.integrators.npt) nph_position_update() (in module nvalchemiops.dynamics.integrators.npt) nph_position_update_out() (in module nvalchemiops.dynamics.integrators.npt) nph_velocity_half_step() (in module nvalchemiops.dynamics.integrators.npt) nph_velocity_half_step_out() (in module nvalchemiops.dynamics.integrators.npt) npt_barostat_half_step() (in module nvalchemiops.dynamics.integrators.npt) npt_cell_update() (in module nvalchemiops.dynamics.integrators.npt) npt_cell_update_out() (in module nvalchemiops.dynamics.integrators.npt) npt_position_update() (in module nvalchemiops.dynamics.integrators.npt) npt_position_update_out() (in module nvalchemiops.dynamics.integrators.npt) npt_thermostat_half_step() (in module nvalchemiops.dynamics.integrators.npt) npt_velocity_half_step() (in module nvalchemiops.dynamics.integrators.npt) npt_velocity_half_step_out() (in module nvalchemiops.dynamics.integrators.npt) nvalchemiops.dynamics module nvalchemiops.interactions.dispersion module nvalchemiops.interactions.electrostatics module nvalchemiops.jax.interactions.dispersion module nvalchemiops.jax.neighbors module nvalchemiops.math module nvalchemiops.neighbors module nvalchemiops.torch module nvalchemiops.torch.interactions.dispersion module nvalchemiops.torch.neighbors module nvalchemiops.torch.types module P pack_forces_with_cell() (in module nvalchemiops.dynamics.utils.cell_filter) pack_masses_with_cell() (in module nvalchemiops.dynamics.utils.cell_filter) pack_positions_with_cell() (in module nvalchemiops.dynamics.utils.cell_filter) pack_velocities_with_cell() (in module nvalchemiops.dynamics.utils.cell_filter) particle_mesh_ewald() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) pme_energy_corrections() (in module nvalchemiops.interactions.electrostatics) (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) pme_energy_corrections_with_charge_grad() (in module nvalchemiops.interactions.electrostatics) (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) pme_green_structure_factor() (in module nvalchemiops.interactions.electrostatics) (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) pme_reciprocal_space() (in module nvalchemiops.jax.interactions.electrostatics) (in module nvalchemiops.torch.interactions.electrostatics) PMEParameters (class in nvalchemiops.jax.interactions.electrostatics) (class in nvalchemiops.torch.interactions.electrostatics) prepare_batch_idx_ptr() (in module nvalchemiops.jax.neighbors.neighbor_utils) (in module nvalchemiops.torch.neighbors.neighbor_utils) Q query_cell_list() (in module nvalchemiops.jax.neighbors.cell_list) (in module nvalchemiops.neighbors.cell_list) (in module nvalchemiops.torch.neighbors.cell_list) R r4r2 (nvalchemiops.jax.interactions.dispersion.D3Parameters attribute) (nvalchemiops.torch.interactions.dispersion.D3Parameters attribute) rattle_constraints() (in module nvalchemiops.dynamics.utils.constraints) rattle_constraints_out() (in module nvalchemiops.dynamics.utils.constraints) rattle_iteration() (in module nvalchemiops.dynamics.utils.constraints) rattle_iteration_out() (in module nvalchemiops.dynamics.utils.constraints) rcov (nvalchemiops.jax.interactions.dispersion.D3Parameters attribute) (nvalchemiops.torch.interactions.dispersion.D3Parameters attribute) real_space_cutoff (nvalchemiops.jax.interactions.electrostatics.EwaldParameters attribute) (nvalchemiops.jax.interactions.electrostatics.PMEParameters attribute) (nvalchemiops.torch.interactions.electrostatics.EwaldParameters attribute) (nvalchemiops.torch.interactions.electrostatics.PMEParameters attribute) reciprocal_space_cutoff (nvalchemiops.jax.interactions.electrostatics.EwaldParameters attribute) (nvalchemiops.torch.interactions.electrostatics.EwaldParameters attribute) remove_com_motion() (in module nvalchemiops.dynamics.utils.thermostat_utils) remove_com_motion_out() (in module nvalchemiops.dynamics.utils.thermostat_utils) run_nph_step() (in module nvalchemiops.dynamics.integrators.npt) run_npt_step() (in module nvalchemiops.dynamics.integrators.npt) S scale_positions_with_cell() (in module nvalchemiops.dynamics.utils.cell_utils) scale_positions_with_cell_out() (in module nvalchemiops.dynamics.utils.cell_utils) shake_constraints() (in module nvalchemiops.dynamics.utils.constraints) shake_constraints_out() (in module nvalchemiops.dynamics.utils.constraints) shake_iteration() (in module nvalchemiops.dynamics.utils.constraints) shake_iteration_out() (in module nvalchemiops.dynamics.utils.constraints) spline_gather() (in module nvalchemiops.math) spline_gather_gradient() (in module nvalchemiops.math) spline_gather_vec3() (in module nvalchemiops.math) spline_spread() (in module nvalchemiops.math) stress_to_cell_force() (in module nvalchemiops.dynamics.utils.cell_filter) T to() (nvalchemiops.torch.interactions.dispersion.D3Parameters method) U unpack_positions_with_cell() (in module nvalchemiops.dynamics.utils.cell_filter) unpack_velocities_with_cell() (in module nvalchemiops.dynamics.utils.cell_filter) V velocity_rescale() (in module nvalchemiops.dynamics.integrators.velocity_rescaling) velocity_rescale_out() (in module nvalchemiops.dynamics.integrators.velocity_rescaling) velocity_verlet_position_update() (in module nvalchemiops.dynamics.integrators.velocity_verlet) velocity_verlet_position_update_out() (in module nvalchemiops.dynamics.integrators.velocity_verlet) velocity_verlet_velocity_finalize() (in module nvalchemiops.dynamics.integrators.velocity_verlet) velocity_verlet_velocity_finalize_out() (in module nvalchemiops.dynamics.integrators.velocity_verlet) W wpdivmod() (in module nvalchemiops.math) wrap_positions_to_cell() (in module nvalchemiops.dynamics.utils.cell_utils) wrap_positions_to_cell_out() (in module nvalchemiops.dynamics.utils.cell_utils) Z zero_array() (in module nvalchemiops.neighbors.neighbor_utils)
