pdspy.modeling

Model

class pdspy.modeling.Model

A class that can be used to set up a generic model with arbitrary coordinates and densities.

Base Attributes:

grid (Grid):

The Grid object that contains information about the 3D spatial distribution of the material in the system.

images (dict):

A dictionary containing the radiative transfer model images that have been generated for the model.

spectra (dict):

A dictionary containing the radiative transfer model spectra that have been generated for the model.

visibilities (dict):

A dictionary containing the radiative transfer model visibilities that have been generated for the model.

read(filename=None, usefile=None)

Read a model in from an HDF5 model file.

Args:

filename (str, optional):

The filename of the file storing the model to read in. Default: None

usefile (h5py.File, optional):

If filename = None, then use this keyword to provide an instance of an h5py.File that has already be opened that the model can be read from.

run_image(name=None, nphot=1000000.0, code='radmc3d', **keywords)

Run an image of the model.

Args:

name (str, optional):

The name of the image, to use as a key in the Model.images dictionary. Default: None

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

code (str, optional):

Which underlying radiative transfer modeling code to use for the radiative equilibrium calculation. radmc3d or hyperion. Default: radmc3d

kwargs (optional):

Can be used to pass arguments to either Model.run_scattering_hyperion or Model.run_scattering_radmc3d, depending on the value of code.

run_image_hyperion(nphot=1000000.0, mrw=False, pda=False, niterations=20, percentile=99.0, absolute=2.0, relative=1.02, max_interactions=100000000.0, mpi=False, nprocesses=None, sublimation_temperature=None, verbose=True, incl=45, pa=45, dpc=1, lam=1300.0, track_origin='basic', nphot_imaging=1000000.0, name=None, npix=256, pixelsize=1.0)

Run the radiative equilibrium calculation using the Hyperion radiative transfer code. As a result, the Model.grid.temperature list will be populated with the temperatures calculated.

Args:

name (str, optional):

The name of the spectrum, to use as a key in the Model.spectra dictionary. Default: None

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

mrw (bool, optional):

If using hyperion, whether or not to use the Modified Random Walk Algorithm. Default: False

pda (bool, optional):

If using hyperion, whether or not to use the Partial Diffusion Approximation algorithm. Default: False

niterations (int, optional):

The maximum number of iterations to perform, if convergence is not reached, before giving up. Default: 20

percentile (float, optional):

Which percentile of cells to use when calculating the convergence criteria. Default: 99.

absolute (float, optional):

Maximum absolute difference of the ratio between cells for convergence to be reached. Default: 2.0

relative (float, optional):

Relative difference between cells for convergence to be reached. Default: 1.02

max_interactions (int, optional):

Maximum number of interactions a photon can have before it is killed. Default: 1e8

mpi (bool, optional):

If using hyperion, whether or not to run the model in parallel with MPI. Default: False

nprocesses (bool, optional):

If mpi=True, the number of MPI threads to use. Default: None

sublimation_temperature (float, optional):

If you would like to sublimate dust above a certain temperature, set that here. Default: None

verbose (bool, False):

Should output be printed to the screen, or hidden. Default: False

incl (float, optional):

The inclination of the model to use for the image. Default: 0.

pa (float, optional):

The position angle to use for the image. Default: 0.

dpc (float, optional):

The distance to the model in units of parsecs. Default: 1.

lam (float, optional):

The wavelength, in microns, to make the image at. Default: 1300.

nphot_imaging (float, optional):

The number of photons to use in making the image. Default: 1e6

npix (int, optional):

The number of pixels (squared) that the image should have. Default: 256

pixelsize (float, optional):

The size of the pixels, in arcseconds. Default: 1.

run_scattering(nphot=1000000.0, code='radmc3d', **keywords)

Run a scattering phase function calculation for the model.

Args:

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

code (str, optional):

Which underlying radiative transfer modeling code to use for the radiative equilibrium calculation. radmc3d or hyperion. Default: radmc3d

kwargs (optional):

Can be used to pass arguments to either Model.run_scattering_hyperion or Model.run_scattering_radmc3d, depending on the value of code.

run_scattering_radmc3d(nphot=1000000.0, verbose=True, nice=None, loadlambda=None, **keywords)

Run a scattering phase function calculation using the RADMC-3D radiative transfer code. As a result, the Model.grid.scattering_phase list will be populated with the scattering phase functions calculated.

Args:

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

verbose (bool, False):

Should output be printed to the screen, or hidden. Default: False

loadlambda (bool, optional):

If True, use the Model.camera_wavelength array as the list of wavelengths for the scattering phase function calculation. If None, use the Model.grid.lam array. Default: None

**keywords (optional):

This can be used to pass any options to RADMC-3D. For a list of all possibilities for the scattering phase function code, check the RADMC-3D documentation. Two commonly used ones are described below.

setthreads (int, optional):

The number of OpenMP threads to use. Default: 1

run_sed(name=None, nphot=1000000.0, code='radmc3d', **keywords)

Run a spectrum of the model.

Args:

name (str, optional):

The name of the spectrum, to use as a key in the Model.spectra dictionary. Default: None

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

code (str, optional):

Which underlying radiative transfer modeling code to use for the radiative equilibrium calculation. radmc3d or hyperion. Default: radmc3d

kwargs (optional):

Can be used to pass arguments to either Model.run_sed_hyperion or Model.run_sed_radmc3d, depending on the value of code.

run_sed_radmc3d(name=None, nphot=1000000.0, incl=0, pa=0, phi=0, dpc=1, loadlambda=False, verbose=True, nice=None, **keywords)

Run a spectrum of the model with RADMC-3D. As a result, the Model.spectra dictionary will have a pdspy.spectroscopy.Spectrum added with key name.

Args:

name (str, optional):

The name of the spectrum, to use as a key in the Model.spectra dictionary. Default: None

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

incl (float, optional):

The inclination of the model to use for the image. Default: 0.

loadlambda (bool, optional):

If True, use the Model.camera_wavelength array as the list of wavelengths for the scattering phase function calculation. If False, use the Model.grid.lam array. Default: False

code (str, optional):

Which underlying radiative transfer modeling code to use for the radiative equilibrium calculation. radmc3d or hyperion. Default: radmc3d

kwargs (optional):

Can be used to pass arguments to RADMC-3D. This can be used to pass any options to RADMC-3D. For a list of all possibilities for spectra, check the RADMC-3D documentation.

run_thermal(nphot=1000000.0, code='radmc3d', **keywords)

Run the radiative equilibrium calculation for the model.

Args:

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

code (str, optional):

Which underlying radiative transfer modeling code to use for the radiative equilibrium calculation. radmc3d or hyperion. Default: radmc3d

kwargs (optional):

Can be used to pass arguments to either Model.run_thermal_hyperion or Model.run_thermal_radmc3d, depending on the value of code.

run_thermal_hyperion(nphot=1000000.0, mrw=False, pda=False, niterations=20, percentile=99.0, absolute=2.0, relative=1.02, max_interactions=100000000.0, mpi=False, nprocesses=None, sublimation_temperature=None, verbose=True, timeout=3600, increase_photons_until_convergence=False)

Run the radiative equilibrium calculation using the Hyperion radiative transfer code. As a result, the Model.grid.temperature list will be populated with the temperatures calculated.

Args:

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

mrw (bool, optional):

If using hyperion, whether or not to use the Modified Random Walk Algorithm. Default: False

pda (bool, optional):

If using hyperion, whether or not to use the Partial Diffusion Approximation algorithm. Default: False

niterations (int, optional):

The maximum number of iterations to perform, if convergence is not reached, before giving up. Default: 20

percentile (float, optional):

Which percentile of cells to use when calculating the convergence criteria. Default: 99.

absolute (float, optional):

Maximum absolute difference of the ratio between cells for convergence to be reached. Default: 2.0

relative (float, optional):

Relative difference between cells for convergence to be reached. Default: 1.02

max_interactions (int, optional):

Maximum number of interactions a photon can have before it is killed. Default: 1e8

mpi (bool, optional):

If using hyperion, whether or not to run the model in parallel with MPI. Default: False

nprocesses (bool, optional):

If mpi=True, the number of MPI threads to use. Default: None

sublimation_temperature (float, optional):

If you would like to sublimate dust above a certain temperature, set that here. Default: None

verbose (bool, False):

Should output be printed to the screen, or hidden. Default: False

run_thermal_radmc3d(nphot=1000000.0, verbose=True, timelimit=7200, nice=None, **keywords)

Run the radiative equilibrium calculation using the RADMC-3D radiative transfer code. As a result, the Model.grid.temperature list will be populated with the temperatures calculated.

Args:

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

verbose (bool, False):

Should output be printed to the screen, or hidden. Default: False

**keywords (optional):

This can be used to pass any options to RADMC-3D. For a list of all possibilities for the thermal code, check the RADMC-3D documentation. Two commonly used ones are described below.

modified_random_walk (bool, optional):

If using radmc3d, whether or not to use the Modified Random Walk Algorithm. Default: False

setthreads (int, optional):

The number of OpenMP threads to use. Default: 1

run_visibilities(name=None, nphot=1000000.0, code='radmc3d', **keywords)

Run visibilities for the model.

Args:

name (str, optional):

The name of the visibilities, to use as a key in the Model.visibilities dictionary. Default: None

nphot (int, optional):

The number of photons to use for the calculation. Default: 1e6

code (str, optional):

Which underlying radiative transfer modeling code to use for the radiative equilibrium calculation. radmc3d or hyperion. Default: radmc3d

kwargs (optional):

Can be used to pass arguments to either Model.run_scattering_hyperion or Model.run_scattering_radmc3d, depending on the value of code.

set_camera_wavelength(lam)

Set the wavelengths that the camera should use for generating images, visibilities, and spectra.

Args:

lam (numpy.ndarray n):

The array of wavelengths, in microns.

write(filename=None, usefile=None)

Write a model to an HDF5 model file.

Args:

filename (str, optional):

The filename of the file that will be written out with the model. Default: None

usefile (h5py.File, optional):

If filename = None, then use this keyword to provide an instance of an h5py.File that has already be opened that the model can be written to.

YSOModel

class pdspy.modeling.YSOModel

A Model that specifically represents a young star, including a star, disk, and envelope.