Index

_

__init__() (sarkas.core.Parameters method) (sarkas.particles.Particles method) (sarkas.plasma.Species method) (sarkas.potentials.core.Potential method) (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) (sarkas.time_evolution.integrators.Integrator method) (sarkas.time_evolution.thermostats.Thermostat method) (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) (sarkas.utilities.io.InputOutput method) (sarkas.utilities.timing.SarkasTimer method)

A

absorbing_bc() (sarkas.time_evolution.integrators.Integrator method) acf_fit_p11() (in module sarkas.tools.fit_functions) acf_fit_p5() (in module sarkas.tools.fit_functions) add_col_to_df() (in module sarkas.utilities.misc) algorithm_info() (sarkas.utilities.io.InputOutput static method) AlgorithmError AlgorithmWarning alpha_to_int() (in module sarkas.utilities.io) analytical_approx_pppm() (sarkas.processes.PreProcess method) arg_update_doc() (in module sarkas.tools.observables) assgnmnt_func() (in module sarkas.potentials.force_pm) average_acf_slices_data() (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method)

average_slices_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) average_slices_date() (sarkas.tools.observables.DiffusionFlux method) avg_acf_slices_doc() (in module sarkas.tools.observables) avg_slices_doc() (in module sarkas.tools.observables)

B

berendsen() (in module sarkas.time_evolution.integrators) (in module sarkas.time_evolution.thermostats)

betamp() (in module sarkas.utilities.maths) boundary_condition_setup() (sarkas.time_evolution.integrators.Integrator method)

C

calc_acc_pm() (in module sarkas.potentials.force_pm) calc_acf_slice_data() (sarkas.tools.observables.Thermodynamics method) calc_acf_slices_data() (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) calc_acf_slices_doc() (in module sarkas.tools.observables) calc_charge_dens() (in module sarkas.potentials.force_pm) calc_coupling() (sarkas.plasma.Species method) calc_coupling_constant() (sarkas.core.Parameters method) calc_cyclotron_frequency() (sarkas.plasma.Species method) calc_debroglie_wavelength() (sarkas.plasma.Species method) calc_debye_length() (sarkas.plasma.Species method) calc_diff_flux_acf() (in module sarkas.tools.observables) calc_elec_current() (in module sarkas.tools.observables) calc_electron_properties() (sarkas.core.Parameters method) (sarkas.potentials.core.Potential static method) calc_field() (in module sarkas.potentials.force_pm) calc_force_error_quad() (in module sarkas.potentials.egs) (in module sarkas.potentials.fitted_pot) (in module sarkas.potentials.moliere) (in module sarkas.potentials.tabulated) (in module sarkas.potentials.yukawa) calc_k_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) calc_landau_length() (sarkas.plasma.Species method) calc_longitudinal_data() (sarkas.tools.observables.CurrentCorrelationFunction method) calc_magnetic_parameters() (sarkas.core.Parameters method) calc_mesh_coord() (in module sarkas.potentials.force_pm) calc_moments() (in module sarkas.tools.observables) calc_nk() (in module sarkas.tools.observables) calc_nkt() (in module sarkas.tools.observables) calc_nkt_slices_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) calc_parameters() (sarkas.core.Parameters method) calc_plasma_frequency() (sarkas.plasma.Species method) calc_pot_pm() (in module sarkas.potentials.force_pm) calc_pressure_tensor() (in module sarkas.particles) calc_quantum_attributes() (sarkas.plasma.Species method) calc_screening_length() (sarkas.potentials.core.Potential method) calc_Sk() (in module sarkas.tools.observables) calc_Skw() (in module sarkas.tools.observables) calc_slices_data() (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) calc_slices_doc() (in module sarkas.tools.observables) calc_statistical_efficiency() (in module sarkas.tools.observables) calc_transverse_data() (sarkas.tools.observables.CurrentCorrelationFunction method) calc_vk() (in module sarkas.tools.observables) calc_vkt() (in module sarkas.tools.observables) calc_vkt_slices_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) calc_ws_radius() (sarkas.plasma.Species method) calculate_average_temperature() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) calculate_beta_simulation() (sarkas.tools.observables.Thermodynamics method) calculate_beta_slices() (sarkas.tools.observables.Thermodynamics method) calculate_corr_times() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) calculate_electric_current() (sarkas.particles.Particles method) calculate_heat_capacity_simulation() (sarkas.tools.observables.Thermodynamics method) calculate_heat_capacity_slices() (sarkas.tools.observables.Thermodynamics method) calculate_heat_flux() (in module sarkas.potentials.force_pp) calculate_herm_coeff() (in module sarkas.tools.observables) calculate_kinetic_energy() (sarkas.particles.Particles method) calculate_observables() (sarkas.particles.Particles method) calculate_species_electric_current() (sarkas.particles.Particles method) calculate_species_enthalpy() (sarkas.particles.Particles method) calculate_species_heat_flux() (sarkas.particles.Particles method) calculate_species_kinetic_temperature() (sarkas.particles.Particles method)

calculate_species_momentum() (sarkas.particles.Particles method) calculate_species_potential_energy() (sarkas.particles.Particles method) calculate_species_pressure_tensor() (sarkas.particles.Particles method) calculate_thermodynamic_quantities_full() (sarkas.particles.Particles method) calculate_thermodynamic_quantities_partial() (sarkas.particles.Particles method) calculate_total_electric_current() (sarkas.particles.Particles method) calculate_total_enthalpy() (sarkas.particles.Particles method) calculate_total_kinetic_energy() (sarkas.particles.Particles method) calculate_total_momentum() (sarkas.particles.Particles method) calculate_total_potential_energy() (sarkas.particles.Particles method) calculate_total_pressure() (sarkas.particles.Particles method) calculate_vacf() (sarkas.tools.observables.VelocityAutoCorrelationFunction method) calculate_virial() (in module sarkas.potentials.force_pp) cf_second() (in module sarkas.tools.fit_functions) cf_third() (in module sarkas.tools.fit_functions) check_restart() (sarkas.processes.Simulation method) check_units() (sarkas.core.Parameters method) col_mapper() (in module sarkas.tools.observables) common_parser() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) compute() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.Viscosity method) compute_acf() (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) compute_acf_doc() (in module sarkas.tools.observables) compute_doc() (in module sarkas.tools.observables) compute_from_rdf() (sarkas.tools.observables.Thermodynamics method) compute_hermite_expansion() (sarkas.tools.observables.VelocityDistribution method) compute_kt_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) compute_moments() (sarkas.tools.observables.VelocityDistribution method) compute_sum_rule_integrals() (sarkas.tools.observables.RadialDistributionFunction method) const_exp() (in module sarkas.tools.fit_functions) convert_bytes() (in module sarkas.utilities.io) copy_io_attrs() (sarkas.core.Parameters method) copy_params() (sarkas.particles.Particles method) (sarkas.plasma.Species method) (sarkas.potentials.core.Potential method) (sarkas.time_evolution.integrators.Integrator method) (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) (sarkas.utilities.io.InputOutput method) correlationfunction() (in module sarkas.utilities.maths) coulomb_force() (in module sarkas.potentials.coulomb) coulomb_force_pppm() (in module sarkas.potentials.coulomb) create_cells_array() (in module sarkas.potentials.force_pp) create_df_filenames() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) create_dirs_filenames() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) create_distribution() (sarkas.tools.observables.VelocityDistribution method) create_file_paths() (sarkas.utilities.io.InputOutput method) create_head_list_arrays() (in module sarkas.potentials.force_pp) create_k_aliases() (in module sarkas.potentials.force_pm) create_k_arrays() (in module sarkas.potentials.force_pm) create_species_arrays() (sarkas.core.Parameters method) create_unit_dict() (sarkas.core.Parameters method) current() (sarkas.utilities.timing.SarkasTimer static method) CurrentCorrelationFunction (class in sarkas.tools.observables) cyclotronic() (sarkas.time_evolution.integrators.Integrator method) cyclotronic_zdir() (sarkas.time_evolution.integrators.Integrator method)

D

datetime_stamp() (in module sarkas.utilities.timing) (sarkas.utilities.io.InputOutput method) deutsch_force() (in module sarkas.potentials.qsp) deutsch_potential_derivatives() (in module sarkas.potentials.qsp) df_column_names() (sarkas.tools.observables.PressureTensor method) Diffusion (class in sarkas.tools.transport) diffusion() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) DiffusionFlux (class in sarkas.tools.observables)

directory_size_report() (sarkas.utilities.io.InputOutput method) directory_sizes() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) dump() (sarkas.utilities.io.InputOutput method) dump_arrays() (sarkas.particles.Particles method) dump_observables() (sarkas.utilities.io.InputOutput method) dump_potfit_config() (sarkas.utilities.io.InputOutput method) dump_pva_h5() (sarkas.particles.Particles method) dump_thermodynamics() (sarkas.utilities.io.InputOutput method) dump_xyz() (sarkas.utilities.io.InputOutput method) DynamicStructureFactor (class in sarkas.tools.observables)

E

egs_force() (in module sarkas.potentials.egs) electrical_conductivity() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) ElectricalConductivity (class in sarkas.tools.transport) ElectricCurrent (class in sarkas.tools.observables) enforce_abc() (in module sarkas.time_evolution.integrators) enforce_pbc() (in module sarkas.time_evolution.integrators)

enforce_rbc() (in module sarkas.time_evolution.integrators) equilibrate() (sarkas.processes.Simulation method) evolve() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) evolve_loop_threading() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) exponential() (in module sarkas.tools.fit_functions)

F

fast_integral_loop() (in module sarkas.utilities.maths) fd0h() (in module sarkas.utilities.fdints) fd10h() (in module sarkas.utilities.fdints) fd11h() (in module sarkas.utilities.fdints) fd12h() (in module sarkas.utilities.fdints) fd13h() (in module sarkas.utilities.fdints) fd14h() (in module sarkas.utilities.fdints) fd15h() (in module sarkas.utilities.fdints) fd16h() (in module sarkas.utilities.fdints) fd17h() (in module sarkas.utilities.fdints) fd18h() (in module sarkas.utilities.fdints) fd19h() (in module sarkas.utilities.fdints) fd1h() (in module sarkas.utilities.fdints) fd20h() (in module sarkas.utilities.fdints) fd21h() (in module sarkas.utilities.fdints) fd2h() (in module sarkas.utilities.fdints) fd3h() (in module sarkas.utilities.fdints) fd4h() (in module sarkas.utilities.fdints) fd5h() (in module sarkas.utilities.fdints) fd6h() (in module sarkas.utilities.fdints) fd7h() (in module sarkas.utilities.fdints) fd8h() (in module sarkas.utilities.fdints) fd9h() (in module sarkas.utilities.fdints) fd_doc_hparams() (in module sarkas.utilities.fdints) fd_doc_iparams() (in module sarkas.utilities.fdints) fdm1h() (in module sarkas.utilities.fdints) fdm3h() (in module sarkas.utilities.fdints) fdm5h() (in module sarkas.utilities.fdints) fdm7h() (in module sarkas.utilities.fdints) fdm9h() (in module sarkas.utilities.fdints) fermidirac_integral() (in module sarkas.utilities.fdints) file_header() (sarkas.utilities.io.InputOutput method) fit_force() (in module sarkas.potentials.fitted_pot) force_deriv() (in module sarkas.potentials.hs_yukawa) (in module sarkas.potentials.yukawa) force_error_analytic_lcl() (in module sarkas.utilities.maths) force_error_analytic_pp() (in module sarkas.utilities.maths) force_error_approx_pm() (in module sarkas.utilities.maths)

force_error_approx_pppm() (in module sarkas.utilities.maths) force_error_integrand() (in module sarkas.potentials.egs) (in module sarkas.potentials.fitted_pot) (in module sarkas.potentials.moliere) (in module sarkas.potentials.tabulated) (in module sarkas.potentials.yukawa) force_optimized_green_function() (in module sarkas.potentials.force_pm) from_dict() (sarkas.core.Parameters method) (sarkas.plasma.Species method) (sarkas.potentials.core.Potential method) (sarkas.time_evolution.integrators.Integrator method) (sarkas.time_evolution.thermostats.Thermostat method) (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.utilities.io.InputOutput method) from_pickle() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) from_yaml() (sarkas.utilities.io.InputOutput method)

G

gaussian() (in module sarkas.tools.fit_functions) (sarkas.particles.Particles method) get_observable_data() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) grab_sim_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method)

grad_expansion() (in module sarkas.tools.observables) green_function_timer() (sarkas.processes.PreProcess method)

H

halton_reject() (sarkas.particles.Particles method) hansen_force() (in module sarkas.potentials.qsp)

hansen_potential_derivatives() (in module sarkas.potentials.qsp) HeatFlux (class in sarkas.tools.observables) hs_yukawa_force() (in module sarkas.potentials.hs_yukawa)

I

initialization() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) initialize_accelerations() (sarkas.particles.Particles method) initialize_arrays() (sarkas.particles.Particles method) initialize_dataframes() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) initialize_hdf() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) initialize_positions() (sarkas.particles.Particles method) initialize_velocities() (sarkas.particles.Particles method)

InputOutput (class in sarkas.utilities.io) instantiate_subclasses_from_dict() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) integrate_normalized_acf_squared() (sarkas.tools.observables.CurrentCorrelationFunction static method) (sarkas.tools.observables.DiffusionFlux static method) (sarkas.tools.observables.DynamicStructureFactor static method) (sarkas.tools.observables.ElectricCurrent static method) (sarkas.tools.observables.HeatFlux static method) (sarkas.tools.observables.Observable static method) (sarkas.tools.observables.PressureTensor static method) (sarkas.tools.observables.RadialDistributionFunction static method) (sarkas.tools.observables.StaticStructureFactor static method) (sarkas.tools.observables.Thermodynamics static method) (sarkas.tools.observables.VelocityAutoCorrelationFunction static method) (sarkas.tools.observables.VelocityDistribution static method) Integrator (class in sarkas.time_evolution.integrators) InterDiffusion (class in sarkas.tools.transport) interdiffusion() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) invfd1h() (in module sarkas.utilities.fdints)

K

kelbg_force() (in module sarkas.potentials.qsp) kelbg_potential_derivatives() (in module sarkas.potentials.qsp)

kinetic_temperature() (sarkas.particles.Particles method) kspace_setup() (in module sarkas.tools.observables)

L

langevin() (sarkas.time_evolution.integrators.Integrator method) lattice() (sarkas.particles.Particles method) lj_force() (in module sarkas.potentials.lennardjones) load() (sarkas.particles.Particles method)

load_from_checkpoint() (sarkas.particles.Particles method) load_from_file() (sarkas.particles.Particles method) load_from_npz() (sarkas.particles.Particles method) load_from_restart() (in module sarkas.tools.observables) (sarkas.particles.Particles method)

M

magnetic_boris() (sarkas.time_evolution.integrators.Integrator method) magnetic_boris_zdir() (sarkas.time_evolution.integrators.Integrator method) magnetic_helpers() (sarkas.time_evolution.integrators.Integrator method) magnetic_pos_verlet() (sarkas.time_evolution.integrators.Integrator method) magnetic_pos_verlet_zdir() (sarkas.time_evolution.integrators.Integrator method) magnetic_setup() (sarkas.time_evolution.integrators.Integrator method) magnetic_verlet() (sarkas.time_evolution.integrators.Integrator method) magnetic_verlet_zdir() (sarkas.time_evolution.integrators.Integrator method) magnetize() (sarkas.processes.Simulation method) make_color_map() (sarkas.processes.PreProcess method) make_directories() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) (sarkas.utilities.io.InputOutput method) make_directory_tree() (sarkas.utilities.io.InputOutput method) make_files_tree() (sarkas.utilities.io.InputOutput method) make_fit_plot() (sarkas.processes.PreProcess static method) make_force_v_timing_plot() (sarkas.processes.PreProcess method) make_gaussian_plot() (in module sarkas.tools.observables) make_lagrangian_plot() (sarkas.processes.PreProcess method) make_line_plot() (sarkas.processes.PreProcess method) make_pppm_color_map() (sarkas.processes.PreProcess method) make_pppm_line_plot() (sarkas.processes.PreProcess method) make_pppm_plots_dir() (sarkas.processes.PreProcess method) make_thermodynamics_dictionary_full() (sarkas.particles.Particles method) make_thermodynamics_dictionary_partial() (sarkas.particles.Particles method) make_timing_plots() (sarkas.processes.PreProcess method) mesh_point_shift() (in module sarkas.potentials.force_pm) method_pretty_print() (sarkas.potentials.core.Potential method) method_setup() (sarkas.potentials.core.Potential method)

module sarkas.core sarkas.particles sarkas.plasma sarkas.potentials sarkas.potentials.core sarkas.potentials.coulomb sarkas.potentials.egs sarkas.potentials.fitted_pot sarkas.potentials.force_pm sarkas.potentials.force_pp sarkas.potentials.hs_yukawa sarkas.potentials.lennardjones sarkas.potentials.moliere sarkas.potentials.qsp sarkas.potentials.tabulated sarkas.potentials.yukawa sarkas.processes sarkas.time_evolution sarkas.time_evolution.integrators sarkas.time_evolution.thermostats sarkas.tools sarkas.tools.fit_functions sarkas.tools.observables sarkas.tools.transport sarkas.utilities sarkas.utilities.exceptions sarkas.utilities.fdints sarkas.utilities.io sarkas.utilities.maths sarkas.utilities.misc sarkas.utilities.timing moliere_force() (in module sarkas.potentials.moliere)

N

normality_tests() (sarkas.tools.observables.VelocityDistribution method)

num_sort() (in module sarkas.utilities.io)

O

Observable (class in sarkas.tools.observables)

open_bc() (sarkas.time_evolution.integrators.Integrator method)

P

Parameters (class in sarkas.core) parse() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) parse_acf() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) parse_k_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) parse_kt_data() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) Particles (class in sarkas.particles) particles_interaction_loop() (in module sarkas.potentials.force_pp) ParticlesError ParticlesWarning pauli_force() (in module sarkas.potentials.qsp) periodic_bc() (sarkas.time_evolution.integrators.Integrator method) PhysicsWarning plot() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.Viscosity method)

plot_labels() (in module sarkas.tools.observables) plot_tc() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) postproc_estimates() (sarkas.processes.PreProcess method) PostProcess (class in sarkas.processes) postprocess_info() (sarkas.utilities.io.InputOutput method) pot_acc_setup() (sarkas.time_evolution.integrators.Integrator method) Potential (class in sarkas.potentials.core) potential_derivatives() (in module sarkas.potentials.coulomb) (in module sarkas.potentials.egs) (in module sarkas.potentials.fitted_pot) (in module sarkas.potentials.lennardjones) (in module sarkas.potentials.moliere) (in module sarkas.potentials.tabulated) (in module sarkas.potentials.yukawa) potential_info() (sarkas.utilities.io.InputOutput static method) pppm_approximation() (sarkas.processes.PreProcess method) pppm_setup() (sarkas.potentials.core.Potential method) prepare_histogram_args() (sarkas.tools.observables.VelocityDistribution method) PreProcess (class in sarkas.processes) preprocess_timing() (sarkas.utilities.io.InputOutput method) PressureTensor (class in sarkas.tools.observables) pretty_print() (sarkas.core.Parameters method) (sarkas.plasma.Species method) (sarkas.potentials.core.Potential method) (sarkas.time_evolution.integrators.Integrator method) (sarkas.time_evolution.thermostats.Thermostat method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) pretty_print_info() (in module sarkas.potentials.coulomb) (in module sarkas.potentials.egs) (in module sarkas.potentials.fitted_pot) (in module sarkas.potentials.hs_yukawa) (in module sarkas.potentials.lennardjones) (in module sarkas.potentials.qsp) (in module sarkas.potentials.tabulated) (in module sarkas.potentials.yukawa) pretty_print_msg() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) print_initial_state() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) print_to_logger() (in module sarkas.utilities.io) Process (class in sarkas.processes) produce() (sarkas.processes.Simulation method)

R

RadialDistributionFunction (class in sarkas.tools.observables) random_reject() (sarkas.particles.Particles method) random_unit_vectors() (sarkas.particles.Particles method) read_npz() (sarkas.utilities.io.InputOutput static method) read_particles_npz() (sarkas.utilities.io.InputOutput static method) read_pickle() (sarkas.utilities.io.InputOutput method) read_pickle_single() (sarkas.utilities.io.InputOutput method)

reflecting_bc() (sarkas.time_evolution.integrators.Integrator method) remove_drift() (sarkas.particles.Particles method) remove_drift_nb() (in module sarkas.particles) remove_preproc_dumps() (sarkas.processes.PreProcess method) rse() (in module sarkas.tools.fit_functions) run() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Simulation method)

S

sarkas.core module sarkas.particles module sarkas.plasma module sarkas.potentials module sarkas.potentials.core module sarkas.potentials.coulomb module sarkas.potentials.egs module sarkas.potentials.fitted_pot module sarkas.potentials.force_pm module sarkas.potentials.force_pp module sarkas.potentials.hs_yukawa module sarkas.potentials.lennardjones module sarkas.potentials.moliere module sarkas.potentials.qsp module sarkas.potentials.tabulated module sarkas.potentials.yukawa module sarkas.processes module sarkas.time_evolution module sarkas.time_evolution.integrators module sarkas.time_evolution.thermostats module sarkas.tools module sarkas.tools.fit_functions module sarkas.tools.observables module sarkas.tools.transport module sarkas.utilities module sarkas.utilities.exceptions module sarkas.utilities.fdints module sarkas.utilities.io module sarkas.utilities.maths module sarkas.utilities.misc module sarkas.utilities.timing module SarkasError SarkasTimer (class in sarkas.utilities.timing) SarkasWarning save_acf_hdf() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) save_acf_slices_data_to_hdf() (sarkas.tools.observables.VelocityAutoCorrelationFunction method) save_hdf() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method)

save_kt_hdf() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) save_pickle() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.utilities.io.InputOutput method) scalar_species_loop() (in module sarkas.particles) screen_figlet() (sarkas.utilities.io.InputOutput static method) select_random_indices() (sarkas.tools.observables.VelocityAutoCorrelationFunction method) set_species_attributes() (sarkas.core.Parameters method) setup() (sarkas.core.Parameters method) (sarkas.particles.Particles method) (sarkas.potentials.core.Potential method) (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) (sarkas.time_evolution.integrators.Integrator method) (sarkas.time_evolution.thermostats.Thermostat method) (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) (sarkas.utilities.io.InputOutput method) setup_checkpoint() (sarkas.utilities.io.InputOutput method) setup_doc() (in module sarkas.tools.observables) setup_from_dict() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method) setup_from_simulation() (sarkas.processes.PostProcess method) setup_init() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) setup_multirun_dirs() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) sim_box_setup() (sarkas.core.Parameters method) Simulation (class in sarkas.processes) simulation_summary() (sarkas.utilities.io.InputOutput method) Species (class in sarkas.plasma) start() (sarkas.utilities.timing.SarkasTimer method) StaticStructureFactor (class in sarkas.tools.observables) stop() (sarkas.utilities.timing.SarkasTimer method) sum_over_aliases() (in module sarkas.potentials.force_pm) sum_rule() (sarkas.tools.observables.PressureTensor method)

T

tab_force() (in module sarkas.potentials.tabulated) temp_energy_plot() (sarkas.tools.observables.Thermodynamics method) tensor_cross_species_loop() (in module sarkas.particles) tensor_species_loop() (in module sarkas.particles) ThermalConductivity (class in sarkas.tools.transport) Thermodynamics (class in sarkas.tools.observables) Thermostat (class in sarkas.time_evolution.thermostats) thermostat_setup() (sarkas.time_evolution.integrators.Integrator method) thermostate() (sarkas.time_evolution.integrators.Integrator method) time_acceleration() (sarkas.processes.PreProcess method) time_division() (sarkas.utilities.timing.SarkasTimer static method) time_evolution_loop() (sarkas.processes.PreProcess method) time_info() (sarkas.utilities.io.InputOutput static method) time_n_space_estimates() (sarkas.processes.PreProcess method)

time_stamp() (in module sarkas.utilities.timing) (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method) (sarkas.utilities.io.InputOutput method) TimerError timing_study() (sarkas.utilities.io.InputOutput method) timing_study_calculation() (sarkas.processes.PreProcess method) TransportCoefficients (class in sarkas.tools.transport) type_setup() (sarkas.potentials.core.Potential method) (sarkas.time_evolution.integrators.Integrator method)

U

uniform_no_reject() (sarkas.particles.Particles method) update() (in module sarkas.potentials.force_pm) (in module sarkas.potentials.force_pp) (sarkas.time_evolution.thermostats.Thermostat method) update_0D() (in module sarkas.potentials.force_pp) update_args() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method) update_attributes() (sarkas.particles.Particles method) update_brute() (sarkas.potentials.core.Potential method) update_finish() (sarkas.tools.observables.CurrentCorrelationFunction method) (sarkas.tools.observables.DiffusionFlux method) (sarkas.tools.observables.DynamicStructureFactor method) (sarkas.tools.observables.ElectricCurrent method) (sarkas.tools.observables.HeatFlux method) (sarkas.tools.observables.Observable method) (sarkas.tools.observables.PressureTensor method) (sarkas.tools.observables.RadialDistributionFunction method) (sarkas.tools.observables.StaticStructureFactor method) (sarkas.tools.observables.Thermodynamics method) (sarkas.tools.observables.VelocityAutoCorrelationFunction method) (sarkas.tools.observables.VelocityDistribution method)

update_fmm_coulomb() (sarkas.potentials.core.Potential method) update_fmm_yukawa() (sarkas.potentials.core.Potential method) update_linked_list() (sarkas.potentials.core.Potential method) update_params() (in module sarkas.potentials.coulomb) (in module sarkas.potentials.egs) (in module sarkas.potentials.fitted_pot) (in module sarkas.potentials.hs_yukawa) (in module sarkas.potentials.lennardjones) (in module sarkas.potentials.moliere) (in module sarkas.potentials.qsp) (in module sarkas.potentials.tabulated) (in module sarkas.potentials.yukawa) update_pm() (sarkas.potentials.core.Potential method) update_pppm() (sarkas.potentials.core.Potential method) update_subclasses_from_dict() (sarkas.processes.PostProcess method) (sarkas.processes.PreProcess method) (sarkas.processes.Process method) (sarkas.processes.Simulation method)

V

vector_cross_species_loop() (in module sarkas.particles) vector_species_loop() (in module sarkas.particles) VelocityAutoCorrelationFunction (class in sarkas.tools.observables) VelocityDistribution (class in sarkas.tools.observables) verlet() (sarkas.time_evolution.integrators.Integrator method) Viscosity (class in sarkas.tools.transport)

viscosity() (sarkas.tools.transport.Diffusion method) (sarkas.tools.transport.ElectricalConductivity method) (sarkas.tools.transport.InterDiffusion method) (sarkas.tools.transport.ThermalConductivity method) (sarkas.tools.transport.TransportCoefficients method) (sarkas.tools.transport.Viscosity method)

W

write_to_logger() (sarkas.utilities.io.InputOutput method)

Y

yukawa_force() (in module sarkas.potentials.yukawa)

yukawa_force_pppm() (in module sarkas.potentials.yukawa) yukawa_green_function() (in module sarkas.utilities.maths)