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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 Simulation
Magnetized Plasma
Yukawa vs Egs potential
Viscosity Coefficients
Moliere Potential
MD for Experiment Validation
Ultrafast electron cooling in an expanding ultracold plasma
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.create_species_arrays
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.processes
sarkas.processes.PostProcess
sarkas.processes.PostProcess.__init__
sarkas.processes.PostProcess.common_parser
sarkas.processes.PostProcess.evolve_loop
sarkas.processes.PostProcess.initialization
sarkas.processes.PostProcess.run
sarkas.processes.PostProcess.setup
sarkas.processes.PostProcess.setup_from_simulation
sarkas.processes.PreProcess
sarkas.processes.PreProcess.__init__
sarkas.processes.PreProcess.analytical_approx_pppm
sarkas.processes.PreProcess.common_parser
sarkas.processes.PreProcess.evolve_loop
sarkas.processes.PreProcess.green_function_timer
sarkas.processes.PreProcess.initialization
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_timing_plots
sarkas.processes.PreProcess.postproc_estimates
sarkas.processes.PreProcess.pppm_approximation
sarkas.processes.PreProcess.remove_preproc_dumps
sarkas.processes.PreProcess.run
sarkas.processes.PreProcess.setup
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.Process
sarkas.processes.Process.__init__
sarkas.processes.Process.common_parser
sarkas.processes.Process.evolve_loop
sarkas.processes.Process.initialization
sarkas.processes.Process.setup
sarkas.processes.Simulation
sarkas.processes.Simulation.__init__
sarkas.processes.Simulation.check_restart
sarkas.processes.Simulation.common_parser
sarkas.processes.Simulation.equilibrate
sarkas.processes.Simulation.evolve_loop
sarkas.processes.Simulation.initialization
sarkas.processes.Simulation.magnetize
sarkas.processes.Simulation.produce
sarkas.processes.Simulation.run
sarkas.processes.Simulation.setup
sarkas.potentials
sarkas.potentials.core
sarkas.potentials.core.Potential
sarkas.potentials.coulomb
sarkas.potentials.coulomb.pretty_print_info
sarkas.potentials.coulomb.update_params
sarkas.potentials.egs
sarkas.potentials.egs.pretty_print_info
sarkas.potentials.egs.update_params
sarkas.potentials.force_pm
sarkas.potentials.force_pp
sarkas.potentials.hs_yukawa
sarkas.potentials.hs_yukawa.pretty_print_info
sarkas.potentials.hs_yukawa.update_params
sarkas.potentials.lennardjones
sarkas.potentials.lennardjones.pretty_print_info
sarkas.potentials.lennardjones.update_params
sarkas.potentials.moliere
sarkas.potentials.moliere.update_params
sarkas.potentials.qsp
sarkas.potentials.qsp.pretty_print_info
sarkas.potentials.qsp.update_params
sarkas.potentials.tests
sarkas.potentials.tests.test_coulomb
sarkas.potentials.tests.test_egs
sarkas.potentials.tests.test_force_pm
sarkas.potentials.tests.test_force_pp
sarkas.potentials.tests.test_lennardjones
sarkas.potentials.tests.test_moliere
sarkas.potentials.tests.test_qsp
sarkas.potentials.tests.test_yukawa
sarkas.potentials.yukawa
sarkas.potentials.yukawa.pretty_print_info
sarkas.potentials.yukawa.update_params
sarkas.time_evolution
sarkas.time_evolution.integrators
sarkas.time_evolution.integrators.Integrator
sarkas.time_evolution.thermostats
sarkas.time_evolution.thermostats.Thermostat
sarkas.tools
sarkas.tools.observables
sarkas.tools.observables.arg_update_doc
sarkas.tools.observables.calc_Skw
sarkas.tools.observables.calc_diff_flux_acf
sarkas.tools.observables.calc_moments
sarkas.tools.observables.calc_nkt
sarkas.tools.observables.calc_pressure_tensor
sarkas.tools.observables.calc_vacf
sarkas.tools.observables.calc_vkt
sarkas.tools.observables.calculate_herm_coeff
sarkas.tools.observables.col_mapper
sarkas.tools.observables.compute_doc
sarkas.tools.observables.grad_expansion
sarkas.tools.observables.kspace_setup
sarkas.tools.observables.load_from_restart
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.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.TransportCoefficients
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.fd_doc_hparams
sarkas.utilities.fdints.fd_doc_iparams
sarkas.utilities.fdints.fermidirac_integral
sarkas.utilities.io
sarkas.utilities.io.alpha_to_int
sarkas.utilities.io.convert_bytes
sarkas.utilities.io.num_sort
sarkas.utilities.io.InputOutput
sarkas.utilities.maths
sarkas.utilities.maths.betamp
sarkas.utilities.maths.correlationfunction
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.tests
sarkas.utilities.tests.test_fdints
sarkas.utilities.tests.test_maths
sarkas.utilities.timing
sarkas.utilities.timing.SarkasTimer
Credits:
Credits
Publications
Dev Team
.rst
.pdf
sarkas.tools.observables.DynamicStructureFactor.grab_sim_data
sarkas.tools.observables.DynamicStructureFactor.grab_sim_data
#
DynamicStructureFactor.
grab_sim_data
(
pva
=
None
)
#
Read in particles data
