toprodimo

Interface to interpolate and convert 2D (r, theta) datasets from simulation outputs (readable with nonos) to ProDiMo models. Based on the ProDiMo 2D interface notebook by Christian Rab

Development status

Word of caution: toprodimo has still to be tested, in particular to be sure that everything works smoothly when the ProDiMo model created by toprodimo is used in a ProDiMo computation.

To be implemented :

• For now, toprodimo takes only the upper half of a 2D (r, theta) disk, if theta is symmetric compared to the midplane. Could add some flexibility if the user wants to focus on the lower half of the disk, or to average azimuthally a 3D (r, theta, phi) disk, or even add a prescription to extend vertically a 2D (r, phi) disk (e.g., with vertical hydrostatic equilibrium).

Installation

We recommend to install toprodimo using the package and project manager uv. See the documentation to install uv on your system. After creating an environment (uv venv), run the following:

uv tool install toprodimo

Use the interface

You can use the interface inside the project's virtual environment using a parameter .toml file:

toprodimo toprodimo.toml

See the TOML documentation to know more about this config file format.

Configuration file

Example

You can find an example for the parameter file in toprodimo/toprodimo.toml.

1. Section [simulation]

Mandatory parameters:

• on : simulation output number (int)
• input_dir : directory of the simulated output (str)
• unit_length_au : code unit of length [au] (float)
• unit_mass_msun : code unit of mass [solMass] (float)
• component : which component is included ("dust" and/or "gas") (str|list[str])
• internal_rho : if the "dust" component is included, the internal density used in the simulation [g/cm3] (float)

Optional parameters:

• mask_inside : removes the contribution of the radial and vertical velocities close to the grid's inner edge r_inner, at mask_inside*r_inner, to avoid some spurious effects in ProDiMo (float). By default we do not cancel these velocity components (mask_inside=0.0).
• tgas : compute the gas temperature from the simulations. Implemented: tgas = {eos="ideal", mu_star=1.37}, using an ideal equation of state (tgas = pressure/density) and a user-defined mean molecular weight. For the moment, we recommand to let ProDiMo handle the gas temperature, by not providing any tgas.

2. Section [prodimo]

Mandatory parameters:

• from : directory of the initialized ProDiMo model from which to extract ProDiMo.out and *.in files (str)
• to : directory of the ProDiMo model on which the simulation grid and fields are interpolated (str)

Optional parameters:

• plot : creates 3 .pdf files in the ProDiMo model directory (given by the to parameter), with plots of the fields (bool).
  • simulation.pdf: from the simulation output file, with some post-processing (e.g., removing for all the fields the region inside the cylindrical radius corresponding to the inner edge).
  • prodimo.pdf: from the ProDiMo model, ready to be run with ProDiMo.
  • compare_simulation_prodimo.pdf: look at the 1D density in the midplane and vertically at R=unit_length_au.

Remarks

In order for the procedure to work, you need to keep in mind that:

• toprodimo needs the typical unit_length_au and unit_mass_msun of the simulated model.
• toprodimo works on top of an initialized ProDiMo model that has to be run beforehand with the typical parameters of the simulated model (disk, star, ...). The corresponding (ProDiMo.out, *.in) files are then copied to a new prodimo directory to perform the interpolation of the simulated data to this new ProDiMo model.

See also the ProDiMo documentation.