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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
Theme by the Executable Book Project
  • .rst

Examples

Examples#

To add your example notebook to this gallery see the related section in the Contributing page.

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

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Example of a contribution

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One Component Plasma (OCP)

By MurilloGroup
© Copyright 2019-2023, MurilloGroup.
Last updated on Mar 01, 2024.