yt-idefix 2.3.0

An extension module for yt, adding a frontend for Idefix and Pluto

yt_idefix

A maturing yt frontend for Idefix and Pluto, packaged as an extension for yt.

Installation

python -m pip install yt_idefix

Supported formats

Code	format	supported since	additional dependencies
Idefix	.dmp	v0.1.0
Idefix	.vtk	v0.3.0
Pluto	.vtk	v0.9.0
Pluto	XDMF	v1.1.0	h5py

Usage

Integration with yt is seamless. Installing this plugin is all that's required to make yt compatible with data formats supported by yt_idefix !

Additional arguments to yt.load

The metadata are parsed from data file, definitions header file and inifile when loading dataset.

Definitions header file (definitions.h for Pluto, or definitions.hpp for Idefix) and inifile (pluto.ini and idefix.ini respectively) are discovered automatically if they match default names, are located along with data files, and unique. Otherwise, they can be specified explicitly as paths (either relative to data files or absolute paths) with parameters definitions_header and inifile respectively.

Geometry is parsed automatically whenever possible, but as a last resort, it can also be specified as a keyword argument (possible values are "cartesian", "spherical", "cylindrical" and "polar").

# Examples
ds = yt.load(
    "data.0010.vtk", definitions_header="../definitions.h", inifile="example.ini"
)
ds = yt.load("data.0010.vtk", geometry="spherical")

The data are loaded as physical quantities with units. The default unit system is cgs in yt. This frontend can convert data from code units into cgs properly, based on the unit definitions from metadata.

Users are able to choose the unit displayed in two ways, through unit_system ("code", "mks" and "cgs") and units_override(only valid for Pluto).

# Examples on units
ds = yt.load("data.0010.vtk", unit_system="mks")

units_override = dict(length_unit=(100.0, "au"), mass_unit=yt.units.mass_sun)

# Caution that other units will also be changed for consistency!
ds = yt.load("data.0010.vtk", unit_override=unit_override)

With Pluto data, the rest of the system will be derived consistently with given units, within the following rules:

1. Temperature unit cannot be overridden (always set to Kelvin)
2. No more than three units can be overridden at once (overconstrained systems are never validated for simplicity)
3. When given less than three overrides, base units in Pluto (ordered: velocity_unit, density_unit, length_unit) are assumed
4. The following combinations are not allowed

{"magnetic_unit", "velocity_unit", "density_unit"},
{"velocity_unit", "time_unit", "length_unit"},
{"density_unit", "length_unit", "mass_unit"},

yt is able to provide some derived fields from existed fields, e.g., "cell_volume". Fields related to element species can be created according to primordial abundances of H and He, through default_species_fields ("neutral" and "ionized") parameters.

# Example
ds = yt.load("data.0010.vtk", default_species_fields="ionized")

Convention of field names

The outputs are loaded from disk with field names in uppercase. This normalization is only applied to the standard outputs but user-defined outputs and Pluto's ion fraction outputs.

# Example
ds.field_list
# Output:
# [('pluto-vtk', 'PRS'),   # standard output
#  ('pluto-vtk', 'RHO'),   # standard output
#  ('pluto-vtk', 'VX1'),   # standard output
#  ('pluto-vtk', 'VX2'),   # standard output
#  ('pluto-vtk', 'VX3'),   # standard output
#  ('pluto-vtk', 'temp')]  # This is a user-defined output