Fields

Fields#

The pyathena.fields module provides a registry of derived fields and their visualization metadata. A derived field is any quantity that can be computed from the primitive fields stored in the simulation output (density, pressure, velocity, magnetic field, etc.).

DerivedFields#

class pyathena.fields.fields.DerivedFields(par, x0=array([0., 0., 0.]))[source]#

Registry of derived fields for an Athena/Athena++ simulation.

Reads simulation parameters and builds dictionaries of derived field metadata (compute function, primitive field dependencies, plot label, colormap, value range, and log-scale flag). The active set of fields is determined automatically from the par configuration (e.g. MHD, cooling, radiation, cosmic rays).

Parameters

par (dict) – Simulation parameter dictionary as returned by pyathena.read_athinput().
x0 (array-like of float, optional) – Reference position [x, y, z] used for distance-based fields such as radial velocity. Default is [0.0, 0.0, 0.0].

func#

Maps field name → callable f(d, u) that computes the field.

Type: dict

field_dep#

Maps field name → set of required primitive field names.

Type: dict

label#

Maps field name → LaTeX label string for colorbars/axes.

Type: dict

cmap#

Maps field name → colormap.

Type: dict

vminmax#

Maps field name → (vmin, vmax) defaults for visualization.

Type: dict

take_log#

Maps field name → bool; if True use log normalization.

Type: dict

norm#

Maps field name → matplotlib.colors.Normalize instance.

Type: dict

imshow_args#

Maps field name → dict of kwargs suitable for imshow/colorbar calls.

Type: dict

dfi#

Combined per-field metadata dict (union of all the above).

Type: dict

Examples

>>> from pyathena import read_athinput
>>> from pyathena.fields.fields import DerivedFields
>>> par = read_athinput("/path/to/athinput")
>>> df = DerivedFields(par)
>>> print(list(df.func.keys())[:5])

Derived Field Builders#

Each set_derived_fields_* function populates the registry for a specific physics category. They are called automatically by DerivedFields based on the simulation configuration.

pyathena.fields.fields.set_derived_fields_def(par, x0)[source]#

Function to define derived fields info, for example, functions to calculate derived fields, dependency, label, colormap, etc.

May not work correctly for problems using different unit system. Assume that density = nH, length unit = pc, etc.

This includes: - density (rho, nH) - pressure (pok, pok_trbz) - distance (r) - velocity (vmag, vr, vx/vy/vz) - sound speeds (cs, csound) - momentum density, ram pressure (Mr, Mr_abs, rhovr2ok)

Parameters

par (dict) – Dictionary containing simulation parameter information
x0 (sequence of floats) – Coordinate of the center with respect to which distance is measured

Return type

Tuple of dictionaries containing derived fields info

pyathena.fields.fields.set_derived_fields_cooling(par, newcool)[source]#

Function to define derived fields info, for example, functions to calculate derived fields, dependency, label, colormap, etc.

May not work correctly for problems using different unit system. Assume that density = nH, length unit = pc, etc.

Parameters

par (dict) – Dictionary containing simulation parameter information
newcool (bool) – Is new cooling turned on?

Return type

Tuple of dictionaries containing derived fields info

pyathena.fields.fields.set_derived_fields_mag(par, x0)[source]#: Magnetic-field / MHD derived fields.

pyathena.fields.fields.set_derived_fields_rad(par, x0)[source]#

Register radiation field derived fields.

Includes normalized FUV (PE and LW band), C ionizing, and H2 dissociating radiation field strengths in Draine ISRF units (chi_PE, chi_LW, chi_FUV, chi_CI, chi_H2).

Parameters

par (dict) – Dictionary containing simulation parameter information.
x0 (sequence of floats) – Reference coordinate (unused here, kept for interface consistency).

Returns

Six dictionaries: (func, field_dep, label, cmap, vminmax, take_log).

Return type

tuple

pyathena.fields.fields.set_derived_fields_newcool(par, x0)[source]#

Register new-cooling (NCR) chemistry derived fields.

Includes temperature, molecular/atomic hydrogen fractions and densities (T, xH2, nH2, xHI, nHI, xe), carbon/oxygen species (xCII, nCII, xCI, nCI, xCO, nCO, xOI), cosmic-ray ionization rate, and cooling/heating rates.

Parameters

par (dict) – Dictionary containing simulation parameter information.
x0 (sequence of floats) – Reference coordinate (unused here, kept for interface consistency).

Returns

Six dictionaries: (func, field_dep, label, cmap, vminmax, take_log).

Return type

tuple

pyathena.fields.fields.set_derived_fields_sixray(par, x0)[source]#

Register six-ray external radiation field derived fields.

Includes external (attenuated) PE and LW radiation field strengths in Draine ISRF units (chi_PE_ext, chi_LW_ext, chi_H2_ext).

Parameters

par (dict) – Dictionary containing simulation parameter information.
x0 (sequence of floats) – Reference coordinate (unused here, kept for interface consistency).

Returns

Six dictionaries: (func, field_dep, label, cmap, vminmax, take_log).

Return type

tuple

pyathena.fields.fields.set_derived_fields_xray(par, x0, newcool)[source]#

Register X-ray emissivity derived fields.

Registers the X-ray emissivity field (j_X) in the 0.5–7 keV band, computed using APEC emissivity tables via the yt library.

Note

Requires the optional dependency yt. Raises ModuleNotFoundError if yt is not installed.

Parameters

par (dict) – Dictionary containing simulation parameter information.
x0 (sequence of floats) – Reference coordinate (unused here, kept for interface consistency).
newcool (bool) – If True, use new-cooling chemistry fields for the emissivity calculation; otherwise use classic fields.

Returns

Six dictionaries: (func, field_dep, label, cmap, vminmax, take_log).

Return type

tuple

pyathena.fields.fields.set_derived_fields_cosmic_ray(par)[source]#

Register cosmic-ray derived fields.

Includes CR parallel diffusion coefficient (sigma_para), CR pressure (pok_cr), CR energy density (Ec), and CR-related velocity fields.

Parameters: par (dict) – Dictionary containing simulation parameter information. Must include a cr block with at least vmax (maximum CR streaming speed in cm/s).
Returns: Six dictionaries: (func, field_dep, label, cmap, vminmax, take_log).
Return type: tuple

pyathena.fields.fields.set_derived_fields_feedback_scalars(par)[source]#

Register feedback scalar derived fields.

Includes gas metallicity (Zgas) and SN ejecta mass fraction (rSN) derived from passive scalar fields tracked during stellar feedback.

Parameters: par (dict) – Dictionary containing simulation parameter information.
Returns: Six dictionaries: (func, field_dep, label, cmap, vminmax, take_log).
Return type: tuple

X-ray Emissivity#

Note

This module requires yt as an optional dependency. It is imported lazily; if yt is not installed, X-ray derived fields will be unavailable.

class pyathena.fields.xray_emissivity.XrayEmissivityIntegrator(table_type, redshift=0.0, data_dir=None, use_metals=True)[source]#

Class for making X-ray emissivity fields. Uses hdf5 data tables generated from Cloudy and AtomDB/APEC.

Initialize an XrayEmissivityIntegrator object.

Parameters

table_type (string) – The type of data to use when computing the emissivity values. If “cloudy”, a file called “cloudy_emissivity.h5” is used, for photoionized plasmas. If, “apec”, a file called “apec_emissivity.h5” is used for collisionally ionized plasmas. These files contain emissivity tables for primordial elements and for metals at solar metallicity for the energy range 0.1 to 100 keV.
redshift (float, optional) – The cosmological redshift of the source of the field. Default: 0.0.
data_dir (string, optional) – The location to look for the data table in. If not supplied, the file will be looked for in the location of the YT_DEST environment variable or in the current working directory.
use_metals (boolean, optional) – If set to True, the emissivity will include contributions from metals. Default: True

pyathena.fields.xray_emissivity.get_xray_emissivity(T, Z=1.0, emin=0.5, emax=7.0, table_type='apec', energy=True)[source]#

Fields

Contents

Fields#

DerivedFields#

Derived Field Builders#

X-ray Emissivity#