pylevis 0.216

Python utilities/interface for VENUS-LEVIS fast particle orbit code

pyLEVIS

<<<<<<< HEAD !!! THIS README AND PACKAGE IS STILL INCOMPLETE !!!

Python implementation of the VENUS-LEVIS MATLAB routines. Most of the routines have the same names so the functions should be familiar.

You should be in the direction in which your runs are located to read them in, for instance path/to/levis/runs.

Python implementation of the VENUS-LEVIS matlab routines.

setup

Installation

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Examples

Example: Reading in a simulation and plotting

======= Can be download from PyPI by

setup

    pip3 install pylevis

<<<<<<< HEAD Reading the simulation is similar to the old scripts, except we no longer use Mercury to read data in, also that reading in the simulation will still work if we append "prob" to the name, or we can choose to omit it:

    # Read in some simulation
    sim = pylevis.simulation("probSPEC.0")
    # which is equivalent to
    sim = pylevis.simulation("SPEC.0")

A warning that if you have two runs, one called "probSPEC" and another called "SPEC", this may cause issues reading them in.

Retrieving the particles data is the same as with the matlab routines:

    sim.GetParticle()

although we can now also choose to read in only certain particles (indexed from 1, since that's how the file naming convention is):

    sim.GetParticle(parts=[1,5,6])

note that to access the particles the indexing starts from 0 as per python, so sim.sp[0] is particle 1.

Plotting the energy/momentum conservation is also the same as with the MATLAB routines:

    sim.plot_spconservation()

Note: If a particle number does not exist in sim.sp it will be skipped and the user will be warned that some were not plotted, rather than returning an error like in MATLAB.

Example: Creating a new simulation (experimental)

This is experimental at the moment, but a new simulation can be initialised by calling:

    import pylevis
    f = pylevis.new_simulation('SimulationName',nparts,eqfile="path/to/equilibrium",eqtype="spec",exedir="path/to/mercuryandpostprocessing.x",machine="local")

The equilibrium type can be changed by specifying eqtype="" (default and only supported at the moment is "spec"), the machine you are running the simulation on should be set with machine=,if this is your own computer, it should be "local" (more info below). By default, new_simulation will set up default simulation settings in new_simulation.data, you can check the current config with,

    f.data.properties()

All properties are stored in dictionaries, for instance if we wanted to change the simulation duration we would set f.data["tfin"]=1e-5 (do not change f.data["nparts"] as this isn't actually used except to generate the data file and will be overwritten upon write). A distribution (only uniformly sampled at the moment) of particles with f.nparts number of particles and and by specifying the range or value of input values can be generated, for instance the following:

    f.generate_particles([0.1,1.9],0,0,1,[5e2,2e3],1,1,1)

will generate particles, with $s\in[0.1,1.9]$ and $E\in[5e2,2e3]$ randomly generated, and all other values set as given. The required simulation files can then all be created at the location set by f.simdir by calling,

    f.create_simulation()

If the location already exists you will be prompted to provide the optional input overwrite=True, this will delete existing files and remake them. Finally, we can run the simulation from the python tools as well,

    f.run_simulation()

How the simulation is called depends on the value of f.machine="" (default is "local") (your local machine).

Config

Current machine configs

• local (calls ./mercury.x < data) =======

Usage

You can load the package the usual way (for python packages) by running

    import pylevis

Examples for running the code can be found in ./docs on the github page (see link below).

Developer(s)

• Dean Muir

setup

Github

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---

Progress

TO DO

Function	Purpose
Get_Diffusivity
DecryptEquilibrium	Calls UnfoldEquilibrium?
UnfoldEquilibrium	Reads in equilibrium? Equilibrium reconstruction interface for many equilibrium codes
GetParScenic	Reads in scenic.in file
GetBG	Gets background profiles
GetLostParticles	What a poorly written file
Get_Moments	Gets moments(?) and trapped(?) information

Incomplete

Function	Subfunctions
GetPar	Get_Diffusivity_Params
Get_Dist -> Get_ParticleDist

Completed

Original	New
Get_Particle

======= The source code can be found at https://github.com/Spiffmeister/pyLEVIS

setup