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SARKAS: Python MD code for plasma physics
Documentation:
Why Sarkas
Get Started
Quickstart
Tutorial
Input File
Pre Simulation Testing
Running a Simulation
Data Analysis
Available Features
Integrators
Thermostats
Potentials
Theory:
Theoretical Background
Particle-Particle Particle-Mesh Algorithm
Force Error
Coupling Constant
Electron Properties
References
Contributing:
Contributing to Sarkas
Setup
Reporting Issues
Documentation
Example of a contribution
Simulations:
Examples
One Component Plasma (OCP)
H-He Mixture
Quantum Statistical Potential
Magnetized Plasma
Yukawa vs Egs potential
Viscosity Coefficients
Moliere Potential
MD for Experiment Validation
Ultrafast electron cooling in an expanding ultracold plasma
Binary Ultracold Neutral Plasma Mixture
API:
API reference
sarkas.core
sarkas.core.Parameters
sarkas.core.Parameters.__init__
sarkas.core.Parameters.calc_coupling_constant
sarkas.core.Parameters.calc_electron_properties
sarkas.core.Parameters.calc_magnetic_parameters
sarkas.core.Parameters.calc_parameters
sarkas.core.Parameters.check_units
sarkas.core.Parameters.copy_io_attrs
sarkas.core.Parameters.create_species_arrays
sarkas.core.Parameters.create_unit_dict
sarkas.core.Parameters.from_dict
sarkas.core.Parameters.pretty_print
sarkas.core.Parameters.set_species_attributes
sarkas.core.Parameters.setup
sarkas.core.Parameters.sim_box_setup
sarkas.particles
sarkas.particles.calc_pressure_tensor
sarkas.particles.remove_drift_nb
sarkas.particles.scalar_species_loop
sarkas.particles.tensor_cross_species_loop
sarkas.particles.tensor_species_loop
sarkas.particles.vector_cross_species_loop
sarkas.particles.vector_species_loop
sarkas.particles.Particles
sarkas.particles.Particles.__init__
sarkas.particles.Particles.calculate_electric_current
sarkas.particles.Particles.calculate_kinetic_energy
sarkas.particles.Particles.calculate_observables
sarkas.particles.Particles.calculate_species_electric_current
sarkas.particles.Particles.calculate_species_enthalpy
sarkas.particles.Particles.calculate_species_heat_flux
sarkas.particles.Particles.calculate_species_kinetic_temperature
sarkas.particles.Particles.calculate_species_momentum
sarkas.particles.Particles.calculate_species_potential_energy
sarkas.particles.Particles.calculate_species_pressure_tensor
sarkas.particles.Particles.calculate_thermodynamic_quantities_full
sarkas.particles.Particles.calculate_thermodynamic_quantities_partial
sarkas.particles.Particles.calculate_total_electric_current
sarkas.particles.Particles.calculate_total_enthalpy
sarkas.particles.Particles.calculate_total_kinetic_energy
sarkas.particles.Particles.calculate_total_momentum
sarkas.particles.Particles.calculate_total_potential_energy
sarkas.particles.Particles.calculate_total_pressure
sarkas.particles.Particles.copy_params
sarkas.particles.Particles.dump_arrays
sarkas.particles.Particles.dump_pva_h5
sarkas.particles.Particles.gaussian
sarkas.particles.Particles.halton_reject
sarkas.particles.Particles.initialize_accelerations
sarkas.particles.Particles.initialize_arrays
sarkas.particles.Particles.initialize_positions
sarkas.particles.Particles.initialize_velocities
sarkas.particles.Particles.kinetic_temperature
sarkas.particles.Particles.lattice
sarkas.particles.Particles.load
sarkas.particles.Particles.load_from_checkpoint
sarkas.particles.Particles.load_from_file
sarkas.particles.Particles.load_from_npz
sarkas.particles.Particles.load_from_restart
sarkas.particles.Particles.make_thermodynamics_dictionary_full
sarkas.particles.Particles.make_thermodynamics_dictionary_partial
sarkas.particles.Particles.random_reject
sarkas.particles.Particles.random_unit_vectors
sarkas.particles.Particles.remove_drift
sarkas.particles.Particles.setup
sarkas.particles.Particles.uniform_no_reject
sarkas.particles.Particles.update_attributes
sarkas.plasma
sarkas.plasma.Species
sarkas.plasma.Species.__init__
sarkas.plasma.Species.calc_coupling
sarkas.plasma.Species.calc_cyclotron_frequency
sarkas.plasma.Species.calc_debroglie_wavelength
sarkas.plasma.Species.calc_debye_length
sarkas.plasma.Species.calc_landau_length
sarkas.plasma.Species.calc_plasma_frequency
sarkas.plasma.Species.calc_quantum_attributes
sarkas.plasma.Species.calc_ws_radius
sarkas.plasma.Species.copy_params
sarkas.plasma.Species.from_dict
sarkas.plasma.Species.pretty_print
sarkas.processes
sarkas.processes.PostProcess
sarkas.processes.PostProcess.__init__
sarkas.processes.PostProcess.common_parser
sarkas.processes.PostProcess.directory_sizes
sarkas.processes.PostProcess.evolve
sarkas.processes.PostProcess.evolve_loop_threading
sarkas.processes.PostProcess.initialization
sarkas.processes.PostProcess.instantiate_subclasses_from_dict
sarkas.processes.PostProcess.print_initial_state
sarkas.processes.PostProcess.run
sarkas.processes.PostProcess.setup
sarkas.processes.PostProcess.setup_from_dict
sarkas.processes.PostProcess.setup_from_simulation
sarkas.processes.PostProcess.update_subclasses_from_dict
sarkas.processes.PreProcess
sarkas.processes.PreProcess.__init__
sarkas.processes.PreProcess.analytical_approx_pppm
sarkas.processes.PreProcess.common_parser
sarkas.processes.PreProcess.directory_sizes
sarkas.processes.PreProcess.evolve
sarkas.processes.PreProcess.evolve_loop_threading
sarkas.processes.PreProcess.green_function_timer
sarkas.processes.PreProcess.initialization
sarkas.processes.PreProcess.instantiate_subclasses_from_dict
sarkas.processes.PreProcess.make_color_map
sarkas.processes.PreProcess.make_fit_plot
sarkas.processes.PreProcess.make_force_v_timing_plot
sarkas.processes.PreProcess.make_lagrangian_plot
sarkas.processes.PreProcess.make_line_plot
sarkas.processes.PreProcess.make_pppm_color_map
sarkas.processes.PreProcess.make_pppm_line_plot
sarkas.processes.PreProcess.make_pppm_plots_dir
sarkas.processes.PreProcess.make_timing_plots
sarkas.processes.PreProcess.postproc_estimates
sarkas.processes.PreProcess.pppm_approximation
sarkas.processes.PreProcess.print_initial_state
sarkas.processes.PreProcess.remove_preproc_dumps
sarkas.processes.PreProcess.run
sarkas.processes.PreProcess.setup
sarkas.processes.PreProcess.setup_from_dict
sarkas.processes.PreProcess.time_acceleration
sarkas.processes.PreProcess.time_evolution_loop
sarkas.processes.PreProcess.time_n_space_estimates
sarkas.processes.PreProcess.timing_study_calculation
sarkas.processes.PreProcess.update_subclasses_from_dict
sarkas.processes.Process
sarkas.processes.Process.__init__
sarkas.processes.Process.common_parser
sarkas.processes.Process.directory_sizes
sarkas.processes.Process.evolve
sarkas.processes.Process.evolve_loop_threading
sarkas.processes.Process.initialization
sarkas.processes.Process.instantiate_subclasses_from_dict
sarkas.processes.Process.print_initial_state
sarkas.processes.Process.setup
sarkas.processes.Process.setup_from_dict
sarkas.processes.Process.update_subclasses_from_dict
sarkas.processes.Simulation
sarkas.processes.Simulation.__init__
sarkas.processes.Simulation.check_restart
sarkas.processes.Simulation.common_parser
sarkas.processes.Simulation.directory_sizes
sarkas.processes.Simulation.equilibrate
sarkas.processes.Simulation.evolve
sarkas.processes.Simulation.evolve_loop_threading
sarkas.processes.Simulation.initialization
sarkas.processes.Simulation.instantiate_subclasses_from_dict
sarkas.processes.Simulation.magnetize
sarkas.processes.Simulation.print_initial_state
sarkas.processes.Simulation.produce
sarkas.processes.Simulation.run
sarkas.processes.Simulation.setup
sarkas.processes.Simulation.setup_from_dict
sarkas.processes.Simulation.update_subclasses_from_dict
sarkas.potentials
sarkas.potentials.core
sarkas.potentials.core.Potential
sarkas.potentials.coulomb
sarkas.potentials.coulomb.coulomb_force
sarkas.potentials.coulomb.coulomb_force_pppm
sarkas.potentials.coulomb.potential_derivatives
sarkas.potentials.coulomb.pretty_print_info
sarkas.potentials.coulomb.update_params
sarkas.potentials.egs
sarkas.potentials.egs.calc_force_error_quad
sarkas.potentials.egs.egs_force
sarkas.potentials.egs.force_error_integrand
sarkas.potentials.egs.potential_derivatives
sarkas.potentials.egs.pretty_print_info
sarkas.potentials.egs.update_params
sarkas.potentials.fitted_pot
sarkas.potentials.fitted_pot.calc_force_error_quad
sarkas.potentials.fitted_pot.fit_force
sarkas.potentials.fitted_pot.force_error_integrand
sarkas.potentials.fitted_pot.potential_derivatives
sarkas.potentials.fitted_pot.pretty_print_info
sarkas.potentials.fitted_pot.update_params
sarkas.potentials.force_pm
sarkas.potentials.force_pm.assgnmnt_func
sarkas.potentials.force_pm.calc_acc_pm
sarkas.potentials.force_pm.calc_charge_dens
sarkas.potentials.force_pm.calc_field
sarkas.potentials.force_pm.calc_mesh_coord
sarkas.potentials.force_pm.calc_pot_pm
sarkas.potentials.force_pm.create_k_aliases
sarkas.potentials.force_pm.create_k_arrays
sarkas.potentials.force_pm.force_optimized_green_function
sarkas.potentials.force_pm.mesh_point_shift
sarkas.potentials.force_pm.sum_over_aliases
sarkas.potentials.force_pm.update
sarkas.potentials.force_pp
sarkas.potentials.force_pp.calculate_heat_flux
sarkas.potentials.force_pp.calculate_virial
sarkas.potentials.force_pp.create_cells_array
sarkas.potentials.force_pp.create_head_list_arrays
sarkas.potentials.force_pp.particles_interaction_loop
sarkas.potentials.force_pp.update
sarkas.potentials.force_pp.update_0D
sarkas.potentials.hs_yukawa
sarkas.potentials.hs_yukawa.force_deriv
sarkas.potentials.hs_yukawa.hs_yukawa_force
sarkas.potentials.hs_yukawa.pretty_print_info
sarkas.potentials.hs_yukawa.update_params
sarkas.potentials.lennardjones
sarkas.potentials.lennardjones.lj_force
sarkas.potentials.lennardjones.potential_derivatives
sarkas.potentials.lennardjones.pretty_print_info
sarkas.potentials.lennardjones.update_params
sarkas.potentials.moliere
sarkas.potentials.moliere.calc_force_error_quad
sarkas.potentials.moliere.force_error_integrand
sarkas.potentials.moliere.moliere_force
sarkas.potentials.moliere.potential_derivatives
sarkas.potentials.moliere.update_params
sarkas.potentials.qsp
sarkas.potentials.qsp.deutsch_force
sarkas.potentials.qsp.deutsch_potential_derivatives
sarkas.potentials.qsp.hansen_force
sarkas.potentials.qsp.hansen_potential_derivatives
sarkas.potentials.qsp.kelbg_force
sarkas.potentials.qsp.kelbg_potential_derivatives
sarkas.potentials.qsp.pauli_force
sarkas.potentials.qsp.pretty_print_info
sarkas.potentials.qsp.update_params
sarkas.potentials.tabulated
sarkas.potentials.tabulated.calc_force_error_quad
sarkas.potentials.tabulated.force_error_integrand
sarkas.potentials.tabulated.potential_derivatives
sarkas.potentials.tabulated.pretty_print_info
sarkas.potentials.tabulated.tab_force
sarkas.potentials.tabulated.update_params
sarkas.potentials.yukawa
sarkas.potentials.yukawa.calc_force_error_quad
sarkas.potentials.yukawa.force_deriv
sarkas.potentials.yukawa.force_error_integrand
sarkas.potentials.yukawa.potential_derivatives
sarkas.potentials.yukawa.pretty_print_info
sarkas.potentials.yukawa.update_params
sarkas.potentials.yukawa.yukawa_force
sarkas.potentials.yukawa.yukawa_force_pppm
sarkas.time_evolution
sarkas.time_evolution.integrators
sarkas.time_evolution.integrators.berendsen
sarkas.time_evolution.integrators.enforce_abc
sarkas.time_evolution.integrators.enforce_pbc
sarkas.time_evolution.integrators.enforce_rbc
sarkas.time_evolution.integrators.Integrator
sarkas.time_evolution.thermostats
sarkas.time_evolution.thermostats.berendsen
sarkas.time_evolution.thermostats.Thermostat
sarkas.tools
sarkas.tools.fit_functions
sarkas.tools.fit_functions.acf_fit_p11
sarkas.tools.fit_functions.acf_fit_p5
sarkas.tools.fit_functions.cf_second
sarkas.tools.fit_functions.cf_third
sarkas.tools.fit_functions.const_exp
sarkas.tools.fit_functions.exponential
sarkas.tools.fit_functions.gaussian
sarkas.tools.fit_functions.rse
sarkas.tools.observables
sarkas.tools.observables.arg_update_doc
sarkas.tools.observables.avg_acf_slices_doc
sarkas.tools.observables.avg_slices_doc
sarkas.tools.observables.calc_Sk
sarkas.tools.observables.calc_Skw
sarkas.tools.observables.calc_acf_slices_doc
sarkas.tools.observables.calc_diff_flux_acf
sarkas.tools.observables.calc_elec_current
sarkas.tools.observables.calc_moments
sarkas.tools.observables.calc_nk
sarkas.tools.observables.calc_nkt
sarkas.tools.observables.calc_slices_doc
sarkas.tools.observables.calc_statistical_efficiency
sarkas.tools.observables.calc_vk
sarkas.tools.observables.calc_vkt
sarkas.tools.observables.calculate_herm_coeff
sarkas.tools.observables.col_mapper
sarkas.tools.observables.compute_acf_doc
sarkas.tools.observables.compute_doc
sarkas.tools.observables.grad_expansion
sarkas.tools.observables.kspace_setup
sarkas.tools.observables.load_from_restart
sarkas.tools.observables.make_gaussian_plot
sarkas.tools.observables.plot_labels
sarkas.tools.observables.setup_doc
sarkas.tools.observables.CurrentCorrelationFunction
sarkas.tools.observables.DiffusionFlux
sarkas.tools.observables.DynamicStructureFactor
sarkas.tools.observables.ElectricCurrent
sarkas.tools.observables.HeatFlux
sarkas.tools.observables.Observable
sarkas.tools.observables.PressureTensor
sarkas.tools.observables.RadialDistributionFunction
sarkas.tools.observables.StaticStructureFactor
sarkas.tools.observables.Thermodynamics
sarkas.tools.observables.VelocityAutoCorrelationFunction
sarkas.tools.observables.VelocityDistribution
sarkas.tools.transport
sarkas.tools.transport.Diffusion
sarkas.tools.transport.ElectricalConductivity
sarkas.tools.transport.InterDiffusion
sarkas.tools.transport.ThermalConductivity
sarkas.tools.transport.TransportCoefficients
sarkas.tools.transport.Viscosity
sarkas.utilities
sarkas.utilities.exceptions
sarkas.utilities.exceptions.AlgorithmError
sarkas.utilities.exceptions.AlgorithmWarning
sarkas.utilities.exceptions.ParticlesError
sarkas.utilities.exceptions.ParticlesWarning
sarkas.utilities.exceptions.PhysicsWarning
sarkas.utilities.exceptions.SarkasError
sarkas.utilities.exceptions.SarkasWarning
sarkas.utilities.exceptions.TimerError
sarkas.utilities.fdints
sarkas.utilities.fdints.fd0h
sarkas.utilities.fdints.fd10h
sarkas.utilities.fdints.fd11h
sarkas.utilities.fdints.fd12h
sarkas.utilities.fdints.fd13h
sarkas.utilities.fdints.fd14h
sarkas.utilities.fdints.fd15h
sarkas.utilities.fdints.fd16h
sarkas.utilities.fdints.fd17h
sarkas.utilities.fdints.fd18h
sarkas.utilities.fdints.fd19h
sarkas.utilities.fdints.fd1h
sarkas.utilities.fdints.fd20h
sarkas.utilities.fdints.fd21h
sarkas.utilities.fdints.fd2h
sarkas.utilities.fdints.fd3h
sarkas.utilities.fdints.fd4h
sarkas.utilities.fdints.fd5h
sarkas.utilities.fdints.fd6h
sarkas.utilities.fdints.fd7h
sarkas.utilities.fdints.fd8h
sarkas.utilities.fdints.fd9h
sarkas.utilities.fdints.fd_doc_hparams
sarkas.utilities.fdints.fd_doc_iparams
sarkas.utilities.fdints.fdm1h
sarkas.utilities.fdints.fdm3h
sarkas.utilities.fdints.fdm5h
sarkas.utilities.fdints.fdm7h
sarkas.utilities.fdints.fdm9h
sarkas.utilities.fdints.fermidirac_integral
sarkas.utilities.fdints.invfd1h
sarkas.utilities.io
sarkas.utilities.io.alpha_to_int
sarkas.utilities.io.convert_bytes
sarkas.utilities.io.num_sort
sarkas.utilities.io.print_to_logger
sarkas.utilities.io.InputOutput
sarkas.utilities.maths
sarkas.utilities.maths.betamp
sarkas.utilities.maths.correlationfunction
sarkas.utilities.maths.fast_integral_loop
sarkas.utilities.maths.force_error_analytic_lcl
sarkas.utilities.maths.force_error_analytic_pp
sarkas.utilities.maths.force_error_approx_pm
sarkas.utilities.maths.force_error_approx_pppm
sarkas.utilities.maths.yukawa_green_function
sarkas.utilities.misc
sarkas.utilities.misc.add_col_to_df
sarkas.utilities.timing
sarkas.utilities.timing.datetime_stamp
sarkas.utilities.timing.time_stamp
sarkas.utilities.timing.SarkasTimer
Credits:
Credits
Publications
Dev Team
.rst
.pdf
sarkas.tools.observables.DynamicStructureFactor.initialize_hdf
sarkas.tools.observables.DynamicStructureFactor.initialize_hdf
#
DynamicStructureFactor.
initialize_hdf
(
)
#
