nonos is a 2D visualization command line application for planet-disk numerical simulations, as well as a Python library. It works with vtk-formatted data from Pluto and Idefix, and dat-formatted data for Fargo-adsg and Fargo3D.
For more, read the documentation !
We list here the accepted formats for the data: Pluto and Idefix: data.****.vtk Fargo-adsg: gasdens.dat, gasvy*.dat, gasvx*.dat Fargo3D: same as Fargo-adsg + gasvz*.dat
🚧 This project and documentation are under construction 🚧
- spherical coordinates
- nonos' api
$ pip install nonosThe nonos CLI gets its parameters from three sources:
- command line parameters
- a configuration file
- default values
Command line parameters take priority over the configuration file, which itself takes priority over default values.
To get help, run
$ nonos --helpusage: nonos [-h] [-dir DATADIR] [-field FIELD]
[-geometry {polar,cylindrical,spherical,cartesian}]
[-operation {vm,vp,vz,lt,lp,aa,ap,apl,rr} [{vm,vp,vz,lt,lp,aa,ap,apl,rr} ...]]
[-plane PLANE [PLANE ...]] [-corotate COROTATE] [-range RANGE [RANGE ...]]
[-vmin VMIN] [-vmax VMAX] [-theta THETA] [-z Z] [-phi PHI]
[-distance DISTANCE] [-cpu NCPU] [-on ON [ON ...] | -all] [-diff] [-log]
[-pbar] [-scaling SCALING] [-cmap CMAP] [-title TITLE]
[-uc UNIT_CONVERSION] [-fmt FORMAT] [-dpi DPI] [-input INPUT | -isolated]
[-d | -version | -logo | -config] [-v]
Analysis tool for idefix/pluto/fargo3d simulations (in polar coordinates).
options:
-h, --help show this help message and exit
-dir DATADIR location of output files and param files (default: '.').
-field FIELD name of field to plot (default: 'RHO').
-geometry {polar,cylindrical,spherical,cartesian}
if the geometry of idefix outputs is not recognized (default:
'unset').
-operation {vm,vp,vz,lt,lp,aa,ap,apl,rr} [{vm,vp,vz,lt,lp,aa,ap,apl,rr} ...]
operation to apply to the fild (default: 'unset').
-plane PLANE [PLANE ...]
abscissa and ordinate of the plane of projection (default:
'unset'), example: r phi
-corotate COROTATE planet number that defines with which planet the grid corotates.
-range RANGE [RANGE ...]
range of matplotlib window (default: unset), example: x x -2 2
-vmin VMIN min value (default: unset)
-vmax VMAX max value (default: unset)
-theta THETA if latitudinal operation (default: unset)
-z Z if vertical operation (default: unset)
-phi PHI if azimuthal operation (default: unset)
-distance DISTANCE if radial operation (default: unset)
-cpu NCPU, -ncpu NCPU
number of parallel processes (default: 1).
-on ON [ON ...] output number(s) (on) to plot. This can be a single value or a
range (start, end, [step]) where both ends are inclusive.
(default: last output available).
-all save an image for every available snapshot (this will force
show=False).
-scaling SCALING scale the overall sizes of features in the graph (fonts,
linewidth...) (default: 1).
-cmap CMAP choice of colormap for the 2D maps (default: 'RdYlBu_r').
-title TITLE name of the field in the colorbar for the 2D maps (default:
'unset').
-uc UNIT_CONVERSION, -unit_conversion UNIT_CONVERSION
conversion factor for the considered quantity (default: '1').
-fmt FORMAT, -format FORMAT
select output image file format (default: unset)
-dpi DPI image file resolution (default: 200)
boolean flags:
-diff plot the relative perturbation of the field f, i.e. (f-f0)/f0.
-log plot the log10 of the field f, i.e. log(f).
-pbar display a progress bar
CLI-only options:
-input INPUT, -i INPUT
specify a configuration file.
-isolated ignore any existing 'nonos.ini' file.
-d, -display open a graphic window with the plot (only works with a single
image)
-version, --version show raw version number and exit
-logo show Nonos logo with version number, and exit.
-config show configuration and exit.
-v, -verbose, --verbose
increase output verbosity (-v: info, -vv: debug).
The -operation command allows you to choose what operation is applied to the data, and can be paired with -z, -theta, -phi, or -distance depending on the operation.
-
vm: vertical_at_midplane -
vz: vertical_at_z, can be paired with-zto give the altitude at which the vertical slice is performed. -
vp: vertical_projection, can be paired with-zto give the interval of the vertical integral. -
lt: latitudinal_at_theta, can be paired with-thetato give the latitude at which the latitudinal slice is performed. -
lp: latitudinal_projection, can be paired with-thetato give the interval of the latitudinal integral. -
ap: azimuthal_at_phi, can be paired with-phito give the azimuth at which the azimuthal slice is performed. -
apl: azimuthal_at_planet, has to be paired with-corotateto perform a slice at the planet azimuth. -
aa: azimuthal_average -
rr: radial_at_r, can be paired with-distanceto give the distance at which the radial slice is performed. You can cumulate some operations, likelpandaawhich will given for example for-field=RHOthe gas surface density.
Note that for old idefix outputs, you will need to add the -geometry command to process the data.
The CLI will read parameters from a local file named nonos.ini if it exists,
or any other name specified using the -i/-input parameter.
To ignore any existing nonos.ini file, use the -isolated flag.
One way to configure nonos is to use
$ nonos -configwhich prints the current configuration to stdout. You can then redirect it to get a working configuration file as
$ nonos -config > nonos.iniThis method can also be used to store a complete configuration file from command line arguments:
$ nonos -ncpu 8 -cmap viridis -operation vm -diff -vmin=-10 -vmax=+100 -configAs of nonos 0.7.0, this will print
# Generated with nonos 0.7.0
datadir .
field RHO
operation vm
theta unset
z unset
phi unset
distance unset
geometry unset
on unset
diff True
log False
range unset
vmin -1e1
vmax 1e2
plane unset
progressBar False
corotate unset
ncpu 8
scaling 1
cmap viridis
title unset
unit_conversion 1
format unset
dpi 200
from nonos.api import GasDataSet
import matplotlib.pyplot as plt
plt.close("all")
# We use GasDataSet which takes as argument the output number of the output file given by idefix/pluto/fargo
# contains in particular a dictionary with the different fields.
ds = GasDataSet(43, geometry="polar", directory="nonos/tests/data/idefix_planet3d")
# We select the GasField "RHO", then
# we perform a vertical slice in the midplane,
# and make the result plotable in the xy plane,
# rotating the grid given the planet number 0
# (which orbit is described in the planet0.dat file).
dsop = ds["RHO"].vertical_at_midplane().map("x", "y", planet_corotation=0)
fig, ax = plt.subplots()
# dsop is now a Plotable object.
# We represent its log10, with a given colormap,
# and we display the colorbar by adding the argument title.
dsop.plot(fig, ax, log=True, cmap="inferno", title=r"$\rho_{\rm mid}$")
ax.set_aspect("equal")
# This time, we perform a latitudinal projection,
# i.e. the integral of "RHO" between -theta and theta,
# and then an azimuthal average,
# before mapping it in the radial ("R") direction.
dsop = ds["RHO"].latitudinal_projection(theta=3*0.05).azimuthal_average().map("R")
fig, ax = plt.subplots()
# We display the y-axis by adding the argument title.
dsop.plot(fig, ax, c="k", title=r"$\Sigma$")
plt.show()requires matplotlib >= 3.7
nonos CLI uses a custom style that can be reused programmatically, without
importing the package, using matplotlib API
import matplotlib.pyplot as plt
plt.style.use("nonos.default")See matplotlib.style's documentation for more.
![pre-commit-ci[bot]](https://avatars.githubusercontent.com/u/66853113?size=120)
![dependabot[bot]](https://avatars.githubusercontent.com/u/49699333?size=120)