plasma-bgkmd

Dependencies

Python:

1. numpy

2. scipy

3. f2py

Other stuff:

1. gfortran compiler

2. Vlasov-BGK code (being open-sourced separately) Note: the molecular dynamics and collision rate computation components will work independently of the VBGK, but running a heterogeneous multiscale method simulation requires the separate code.

Setup and compiling

1. cd into the bgk-md repository

   cd bgk-md

2. add the bgk-md folder to your $PYTHONPATH

   export PYTHONPATH=pwd (or add to .bashrc file)

3. cd into the hmm folder

   cd hmm

4. compile the MD fortran code using f2py

   f2py -m md --fcompiler=gfortran --f90flags='-fopenmp' -lgomp -c ../md/md.f90

HMM input file

Note: the list of inputs below is somewhat outdated. See hmm.py for a more complete list.

Syntax

The HMM code takes in an input file with all the parameters. The format is

paramter_name : parameter_value

Comment lines start with a # symbol, for example

# this is a comment    

Parameters that take a list or array input should have comma-separated values, in row-major format. Whitespace is ignored. These can be broken up over multiple lines as long as each line ends with a comma. Comments in the middle of a parameter specification are not allowed.

For example, these are valid:

parameter : 1, 2, 3, 4, 5, 6, 7, 8, 9
parameter : 1, 2,
3,4,5,6,7,8,9
parameter : 1, 2, 3,
            4, 5, 6,
            7, 8, 9

But these are not:

parameter : 1, 2,  3
, 4, 5, 6, 7, 8, 9
parameter : 1, 2, 3,
# some comment
4, 5, 6, 7, 8, 9

Parameters

The following parameters are mostly required, with the exception of the cell a few, which have defaults noted. Order does not matter. See the hmm_basic_test for an example input file.

Testcase information

• testcase : name of test case
• only_md : flag to only do an MD simulation instead of a full HMM, alleviates the need to set any of the BGK parameters except n_vel, although one can set the distribution refresh rate via tau_update_rate

Species information

• n_species : number of species
• mass : mass of a particle in each species (in grams)
• charge : charge of a particle in each species (multiple of electron charge)
• initial_density : the initial density of each species in each cell (per cc)
• initial_temperature : the initial temperature of each species in each cell (in eV)
• initial_velocity : the initial drift velocity (x-direction) of each species in each cell (in cm/s)

Note: initial values should have a value for each species in each BGK cell. One value per species if only_md is set.

Macroscale (BGK) parameters

• n_dim : number of spatial dimensions (0 or 1) (only 0D is supported currently)
• n_cells_bgk : number of BGK cells in space (will be ignored and automatically set to 1 if 0D)
• n_vel : number of velocity gridpoints in each direction (uniform grid)
• cell_length_bgk : length of each BGK cell (ignored in 0D)
• order : whether to use first or second order (1 or 2) (2 not tested), default is 1
• implicit : whether to use implicit time stepping (not tested)
• timestep_bgk : time step to use in the bgk simulations (in seconds)
• final_time : end simulation time (in seconds)
• tau_update_rate : how many timesteps to take between each update of the relaxation rates
• data_rate_bgk : how many timesteps between writing the BGK simulation outputs to file, default is 1
• bgk_path : path the the root directory of the BGK code

Microscale (MD) inputs

• n_simulations_md : number of MD simulation trials for ensemble averaging when gathering data to compute relaxation times
• timestep_md : timestep to take in each MD simulation as proportion of shortest plasma period (timestep is timestep_md / f_p)
• friction : how powerful the thermostat is, as fraction of plasma frequency
• n_timesteps_md : number of timesteps to take in the MD simulations
• max_timesteps_md : max number of timesteps for MD simulation if the statistics are bad (default is only take n_timesteps_md steps). Note: need save_rate % n_timesteps_md = 0 and save_rate % max_timesteps_md = 0.
• equilibration_time : equlibration times in terms of slowest plasma period for the strong and weak thermostat phases
• small_box_equilibration : equilibration time in terms of slowest plasma period on a box half the size in each direction (1/8 the particles) for speeding up equilibration. Step is skipped if set to zero.
• cell_length_md : length of an MD simulation cell as proportion of the electron screening length, must be greater than double cutoff_md
• cutoff_md : cutoff radius for computing forces as proportion of the electron screening length
• mts_threshold_md : threshold relative jump in total energy to trigger redoing a time step using small time steps on the particles that are causing conservation problems, default is to turn MTS off by setting to 100
• mts_cutoff_md : cutoff radius around the particles exerting most force on each other over which to apply small time step, default is 0.0
• mts_timesteps_md : number of time steps to take over the course of one regular time step for the labeled particles, default is 100
• movie_rate : how often to save data for an ovito movie (I think this is somewhat broken right now and the movies will overwrite themselves if doing multiple simulations)
• md_save_rate : how often to save MD phasespace and data for future resume
• md_resume : whether resuming from previous simulation, default is false
• md_last_step : last step taken to resume from, default is 0
• md_resample : whether or not to resample velocity distribution after equilibrating the MD simulation
• md_nprocs : how mnay processors to use for the MD simulation (openMP parallelized). The default is to use all available cores.