nt2py 0.5.0

Post-processing & visualization toolkit for the Entity PIC code

nt2.py

Python package for visualization and post-processing of the Entity simulation data. For usage, please refer to the documentation. The package is distributed via PyPI:

pip install nt2py

Usage

The Library works both with single-file output as well as with separate files. In either case, the location of the data is passed via path keyword argument.

import nt2

data = nt2.Data(path="path/to/data")
# example: 
#   data = nt2.Data(path="path/to/shock.h5") : for single-file
#   data = nt2.Data(path="path/to/shock") : for multi-file

The data is stored in specialized containers which can be accessed via corresponding attributes:

data.fields     # < xr.Dataset
data.particles  # < dict[int : xr.Dataset]
data.spectra    # < xr.Dataset

Examples

Plot a field (in cartesian space) at a specific time (or output step):

data.fields.Ex.sel(t=10.0, method="nearest").plot() # time ~ 10
data.fields.Ex.isel(t=5).plot()                     # output step = 5

Plot a slice or time-averaged field quantities:

data.fields.Bz.mean("t").plot()
data.fields.Bz.sel(t=10.0, x=0.5, method="nearest").plot()

Plot in spherical coordinates (+ combine several fields):

e_dot_b = (data.fields.Er * data.fields.Br +\
           data.fields.Eth * data.fields.Bth +\
           data.fields.Eph * data.fields.Bph)
bsqr = data.fields.Br**2 + data.fields.Bth**2 + data.fields.Bph**2
# only plot radial extent of up to 10
(e_dot_b / bsqr).sel(t=50.0, method="nearest").sel(r=slice(None, 10)).polar.pcolor()

You can also quickly plot the fields at a specific time using the handy .inspect accessor:

data.fields\
    .sel(t=3.0, method="nearest")\
    .sel(x=slice(-0.2, 0.2))\
    .inspect.plot(only_fields=["E", "B"])
# Hint: use `<...>.plot?` to see all options

Or if no time is specified, it will create a quick movie (need to also provide a name in that case):

data.fields\
    .sel(x=slice(-0.2, 0.2))\
    .inspect.plot(name="inspect", only_fields=["E", "B", "N"])

You can also create a movie of a single field quantity (can be custom):

(data.fields.Ex * data.fields.Bx).sel(x=slice(None, 0.2)).movie.plot(name="ExBx", vmin=-0.01, vmax=0.01, cmap="BrBG")

You may also combine different quantities and plots (e.g., fields & particles) to produce a more customized movie:

def plot(t, data):
    fig, ax = mpl.pyplot.subplots()
    data.fields.Ex.sel(t=t, method="nearest").sel(x=slice(None, 0.2)).plot(
        ax=ax, vmin=-0.001, vmax=0.001, cmap="BrBG"
    )
    for sp in range(1, 3):
        ax.scatter(
            data.particles[sp].sel(t=t, method="nearest").x,
            data.particles[sp].sel(t=t, method="nearest").y,
            c="r" if sp == 1 else "b",
        )
    ax.set_aspect(1)
data.makeMovie(plot)

If using Jupyter notebook, you can quickly preview the loaded metadata by simply running a cell with just data in it (or in regular python, by doing print(data)).

Dashboard

Support for the dask dashboard is still in beta, but you can access it by first launching the dashboard client:

import nt2 
nt2.Dashboard()

This will output the port where the dashboard server is running, e.g., Dashboard: http://127.0.0.1:8787/status. Click on it (or enter in your browser) to open the dashboard.

Features

1. Lazy loading and parallel processing of the simulation data with dask.
2. Context-aware data manipulation with xarray.
3. Parellel plotting and movie generation with multiprocessing and ffmpeg.

TODO

• Unit tests
• Plugins for other simulation data formats
• Usage examples