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Useful Tools

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Isaac Backus edited this page Nov 4, 2017 · 13 revisions

Highlights of useful tools/features in diskpy. Refer to the docstrings of the functions for more information. These are just a few of the available functions.

utils

Module diskpy.utils containing utilities used by all of diskpy. Here are a few useful ones.

  • configparser: Reads tipsy .param files and ChaNGa .director files and returns them as a dict. Use in conjunction with utils.configsave.
  • configsave: Save a tipsy .param file or ChaNGa .director file
  • logparser: parse a ChaNGa log file and return a dict of the runtime parameters used.
  • deepreload: Can be useful for reloading sub-packages during development. If using IPython, you should use %load_ext autoreload, %autoreload 2 instead.

disk

Module diskpy.disk, containing functions useful for analyzing and dealing with protoplanetary disks. Here are a few useful ones.

Radial profiles

  • height: Disk height
  • kappa: Disk epicyclic frequency
  • sigma: Surface density
  • Q: Toomre Q
  • Qeff: Effective Toomre Q for 3D disks (Backus & Quinn 2016).

pychanga

Module diskpy.pychanga containing functions to interface with and execute ChaNGa from python. Here are a few useful modules.

  • changa_command: Generate a command to run ChaNGa, uses the ChaNGa presets defined in diskpy.global_settings['changa_presets']. Use in conjunction with changa_run
  • changa_run: Run ChaNGa from python, using a command generated by changa_command
  • get_fnames: Get output filenames from a ChaNGa simulation (as of writing, this only works with tipsy formatting).
  • snapshot_time: Get the time of a snapshot
  • units_from_param: Try to infer the simulation units from a .param file or a param dict
  • walltime: Read walltime from a ChaNGa log file. Useful for monitoring a simulation

pdmath

Module diskpy.pdmath containing math utilities

  • binned_mean: for (x, y, z) observations, bin y according to x and take the mean of z in each bin. Respects units.
  • `setupbins': setup bins for binning data. Can handle linear/logarithmic spacing
  • digitize_threshold: Bin data and setup the bins requiring at least N data points per bin.

plot

Module diskpy.plot for some plotting functions

  • colorCodedArray: Plot a pynbody.image for one quantity, color coded by another.

ICgen

Module diskpy.ICgen for generating ICs for protoplanetary disks.

  • ICgen.IC: The class for generating initial conditions for protoplanetary disks. Initialize with IC = diskpy.ICgen.IC()
    • IC.settings: Contains the settings
  • ICgen.load(...): Load an ICgen file. Example: 
    # First cd into simulation directory, then load ICs:
IC = diskpy.ICgen.load('IC.p')
  • ICgen.ICgen_settings.defaults(): Echo default settings with descriptions of the settings

global_settings

Settings used by diskpy

  • global_settings['max_particles']: Maximum number of particles to use in ICgen calculations. Calculating velocities very accurately probably doesn't need more than 10^6 particles, often not more than 10^5.
  • global_settings['changa_presets]`: Presets used for running ChaNGa. Make sure these are set (see (Installing diskpy)[https://github.com/ibackus/diskpy/wiki#3-setup-diskpy].

Automatically derived arrays

pynbody defines an interface to allow users to define automatically derived arrays for SimSnaps (see pynbody automatically derived arrays). diskpy defines a number of automatically derived arrays, useful for PPDs and dusty-gas. They are described below. These arrays are defined in diskpy/utils/_derivedarrays.py. If you add a new array this wiki entry can be updated with the script generate_wiki_stuff.py in the wiki repo.

abs_dust_rho_dot: abs(rho * dustFracDot)

abs_z: Absolute value of z

cs: Sound speed

dust_delta_v: Dust delta v is defined as v_dust - v_gas

dust_delta_v_phi: Cylindrical tangential component of the dust delta v velocity in the x-y plane. Dust delta v is defined as v_dust - v_gas

dust_delta_v_rxy: Radial dust delta v in x-y plane. Dust delta v is defined as v_dust - v_gas

dust_midplane_v: component of delta v (v_dust - v_gas) in the direction of the midplane

dust_rho_dot: dustFracDot * rho

dustmass: dustFrac * mass

dustVel_phi: Cylindrical tangential component of the dust velocity in the x-y plane

dustVel_rxy: Radial dust velocity in the x-y plane

gas_v_phi: Cylindrical tangential component of the gas velocity in the x-y plane

gas_v_rxy: Gas cylindrical radial velocity

gas_vel: Gas velocity

P: Pressure

rho_dust: Dust density

roche_rho: Roche density .. math:: \rho_{roche} \equiv M_{star}/r^3 where :math:r is the distance to the center of mass of the star(s). The total star mass is used.

roche_rho_fac: Gas density divided by roche density

s: An alias for u_dustGrainSize

scaleheight: |z|/r (in cylindrical coords)

stokes: Dust stokes parameter, defined as the dust stopping time times the Keplerian orbital angular velocity R is calculated relative to the origin! NOT THE STARS!

tstop: Dust stopping time

u_dustFrac: Returns the auxilliary array of the same name (excluding the 'u_' prefix) with units inferred from the runtime parameters.

u_dustFracDot: Returns the auxilliary array of the same name (excluding the 'u_' prefix) with units inferred from the runtime parameters.

u_dustGrainSize: Returns the dust grain size with units for onefluid dust. If grain growth is not on, i.e. if there is not a variable dust size, the dust size is found in the snapshot param If grain growth is turned on, i.e. if there is a variable grain size, the 'dustGrainSize' is returned with proper units.

u_dustVel: Returns the auxilliary array of the same name (excluding the 'u_' prefix) with units inferred from the runtime parameters.

u_smoothlength: Returns the auxilliary array of the same name (excluding the 'u_' prefix) with units inferred from the runtime parameters.

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