nonos 0.1.1

A tool to analyze results from idefix/pluto simulations (for protoplanetary disks more specifically)

nonos

nonos is a 2D visualization command line application for planet-disk hydro simulations, as well as a Python library. It works seamlessly with vtu-formatted data from Pluto, Fargo3D and Idefix.

:construction: This project and documentation are under construction :construction:

Ongoing progress

• spherical coordinates
• error: streamlines & midplane=False -> not yet implemented
• warning: isPlanet=False & corotate=True -> we don't rotate the grid if there is no planet for now. omegagrid = 0.
• warning: cartesian=False & midplane=False -> plot not optimized for now in the (R,z) plane in polar.

Installation

:warning: Nonos requires Python 3.8 or newer. The easiest installation method is

pip install nonos

Usage

There are three ways to use nonos:

1. use the command line tool
2. use the local mode with the config.toml file
3. write a Python script using the nonos library

1. On the command line

To get help, run

$ nonos --help

nonos -mod d/f [options]
-info: give the default parameters in the config.toml file.
-dir: where .vtk files and the inifile are stored ("." by default).
-mod [d/f]: display/film ("" home page by default).
-f [str]: field (for now RHO, VX1 and VX2 in 2D, + VX3 in 3D, RHO by default).
-on [int]: if -mod d -> we plot the field of the data.on.vtk file (1 by default).
-onend [int]: if -mod f and -partial (15 by default).
-partial: if -mod f -> partial movie between -on and -onend (false by default).
-vmin [float]: minimum value for the data (-0.5 by default).
-vmax [float]: maximum value for the data (0.5 by default).
-diff: plot the relative perturbation of the field f, i.e. (f-f0)/f0 (false by default).
-log: plot the log of the field f, i.e. log(f) (false by default).
-cor: does the grid corotate? For now, works in pair with -isp (false by default).
-isp: is there a planet in the grid ? (false by default)
-p [1d/2d]: 1D axisymmetric radial profile or 2D field (2d by default).
-mid/-rz: 2D plot in the (R-phi) plane or in the (R-z) plane (-mid by default).
-cart/-pol: 2D plot in cartesian or polar coordinates (-cart by default).
-avr/-noavr: do we average is the 3rd dimension, i.e. vertically when -mid and azimuthally when -rz (-avr by default).
-s: do we compute streamlines? (false by default)
-stype [random/fixed/lic]: do we compute random, fixed streams, or do we use line integral convolution? (random by default)
-srmin [float]: minimum radius for streamlines computation (0.7 by default).
-srmax [float]: maximum radius for streamlines computation (1.3 by default).
-sn [int]: number of streamlines (50 by default).
-ft [float]: fontsize in the graph (11 by default).
-cmap [str]: choice of colormap for the -p 2d maps (RdYlBu_r by default).
-pbar: do we display the progress bar when -mod f? (false by default)
-multi: load and save figures in parallel when -mod f (false by default).
-cpu [int]: number of cpus if -multi (4 by default).
-l: local mode.

2. Use of the local mode

Run the following command to copy the default config.toml file to the current working directory.

$ nonos -l

You can then edit it directly, and change the parameters. Then run again:

$ nonos -l

3. Programmatic usage

Here are some example Python scripts using nonos' api.

Example of field

from nonos import InitParamNonos, FieldNonos

init = InitParamNonos(info=True) #info=True gives the default parameters in the param file config.toml
fieldon = FieldNonos(init, field='RHO', on=25, diff=True)

Example of plot without streamlines

import matplotlib.pyplot as plt
from nonos import InitParamNonos, PlotNonos

init = InitParamNonos()
ploton = PlotNonos(init, field='RHO', on=25, diff=True)

fig, ax = plt.subplots()
ploton.plot(ax, cartesian=True)
plt.show()

Example of (R,z) plot with quiver

import matplotlib.pyplot as plt
import numpy as np
from nonos import InitParamNonos, FieldNonos, PlotNonos, StreamNonos


init = InitParamNonos(isPlanet=True, corotate=True)

ploton = PlotNonos(init, field='RHO', on=25, diff=True)
streamon = StreamNonos(init, on=25)
vx1on = FieldNonos(init, field='VX1', on=25)
vr = vx1on.data
vx2on = FieldNonos(init, field='VX3', on=25)
vz = vx2on.data

fig, ax = plt.subplots()
ploton.plot(ax, vmin=-0.15, vmax=0.15, midplane=False, cartesian=True, fontsize=8)
Z,R = np.meshgrid(ploton.zmed, ploton.xmed)
ax.quiver(R[:,::2], Z[:,::2], vr[:,ploton.ny//2,::2], vz[:,ploton.ny//2,::2])
plt.show()

Example of plot with streamlines with a planet

import matplotlib.pyplot as plt
from nonos import InitParamNonos, FieldNonos, PlotNonos, StreamNonos

init = InitParamNonos(isPlanet=True, corotate=True)

ploton = PlotNonos(init, field='RHO', on=25, diff=True)
streamon = StreamNonos(init, on=25)
vx1on = FieldNonos(init, field='VX1', on=25, diff=False, log=False)
vr = vx1on.data
vx2on = FieldNonos(init, field='VX2', on=25, diff=False, log=False)
vphi = vx2on.data
vphi -= vx2on.omegaplanet[25]*vx2on.xmed[:,None,None]
streams = streamon.get_random_streams(vr,vphi,xmin=0.7,xmax=1.3, n=30)

fig, ax = plt.subplots()
ploton.plot(ax, cartesian=True, fontsize=8)
streamon.plot_streams(ax,streams, cartesian=True, color='k', linewidth=2, alpha=0.5)
plt.show()

Example of plot with a comparison between several simulations

import matplotlib.pyplot as plt
from nonos import InitParamNonos, PlotNonos

dirpath = ['path_to_dir1', 'path_to_dir2', 'path_to_dir3']

fig, axes = plt.subplots(figsize=(9,2.5), ncols=len(dirpath))
plt.subplots_adjust(left=0.05, right=0.94, top=0.95, bottom=0.1, wspace=0.4)

for dirp, ax in zip(dirpath, axes):
    init = InitParamNonos(directory=dirp)
    ploton = PlotNonos(init, field='RHO', on=10, diff=True, directory=dirp)
    ploton.plot(ax, cartesian=True, fontsize=6)

plt.show()