nt2py 1.5.0

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

Simply pass the location to the data when initializing the main Data object:

import nt2

data = nt2.Data("path/to/data")

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

data.fields     # < xr.Dataset
data.particles  # < special object which returns a pd.DataFrame when .load() is called
data.spectra    # < xr.Dataset

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)).

Note, that by default, the hdf5 support is disabled in nt2py (i.e., only ADIOS2 format is supported). To enable it, install the package as pip install "nt2py[hdf5]" instead of simply pip install nt2py.

Accessing the data

Fields and spectra are stored as lazily loaded xarray datasets (a collection of equal-sized arrays with shared axis coordinates). You may access the coordinates in each dimension using .coords:

data.fields.coords
data.spectra.coords

Individual arrays can be requested by simply using, e.g., data.fields.Ex etc. One can also use slicing/selecting via the coordinates, i.e.,

data.fields.sel(t=5, method="nearest")

accesses all the fields at time t=5 (using method="nearest" means it will take the closest time to value 5). You may also access by index in each coordinate:

data.fields.isel(x=-1)

accesses all the fields in the last position along the x coordinate.

Note that all these operations do not load the actual data into memory; instead, the data is only loaded when explicitly requested (i.e., when plotting or explicitly calling .values or .load().

Particles are stored in a special lazy container which acts very similar to xarray; you can still make selections using specific queries. For instance,

data.particles.sel(sp=[1, 2, 4]).isel(t=-1)

selects all the particles of species 1, 2, and 4 on the last timestep. The loading of the data itself is done by calling: .load() method, which returns a simple pandas dataframe.

Plotting

Plot a field (in Cartesian coordinates) 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")

For particles, one can also make 2D phase-space plots:

data.particles.sel(sp=1).sel(t=1.0, method="nearest").phase_plot(
    x_quantity=lambda f: f.x,
    y_quantity=lambda f: f.ux,
    xy_bins=(np.linspace(0, 60, 100), np.linspace(-2, 2, 100)),
)

or a spectrum plot:

data.particles.sel(sp=[1, 2]).sel(t=1.0, method="nearest").spectrum_plot()

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

def plot(t, data):
    fig, ax = plt.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"
    )
    prtls = data.particles.sel(t=t, method="nearest").load()
    ax.scatter(prtls.x, prtls.y, c="r" if prtls.sp == 1 else "b")
    ax.set_aspect(1)
data.makeMovie(plot)

You may also access the movie-making functionality directly in case you want to use it for other things:

import nt2.plotters.export as nt2e

def plot(t):
  ...

#             this will be the array of `t`-s passed to `plot`
#                           |
#                           V
nt2e.makeFrames(plot, np.arange(100), "myAnim")
nt2e.makeMovie(
    input="myAnim/", output="myAnim.mp4", number=5, overwrite=True
)

# or combined together
nt2e.makeFramesAndMovie(
    name="myAnim", plot=plot, times=np.arange(100)
)

Raw readers

In case you want to access the raw data without using nt2py's xarray/dask lazy-loading, you may do so by using the readers. For example, for ADIOS2 output data format:

import nt2.readers.adios2 as nt2a

# define a reader
reader = nt2a.Reader()

# get all the valid steps for particles
valid_steps = reader.GetValidSteps("path/to/sim", "particles")

# get all variable names which have prefix "p" at the first valid step
variable_names = reader.ReadCategoryNamesAtTimestep(
    "path/to/sim", "particles", "p", valid_steps[0]
)

# convert the variable set into a list and take the first element
variable = list(variable_names)[0]

# read the actual array from the file
reader.ReadArrayAtTimestep(
    "path/to/sim", "particles", variable, valid_steps[0]
)

There are many more functions available within the reader. For hdf5, you can simply change the import to nt2.readers.hdf5, and the rest should remain the same.

CLI

Since version 1.0.0, nt2py also offers a command-line interface, accessed via nt2 command. To view all the options, simply run:

nt2 --help

The plotting routine is pretty customizable. For instance, if the data is located in myrun/mysimulation, you can inspect the content of the data structure using:

nt2 show myrun/mysimulation

Or if you want to make a quick plot (a-la inspect discussed above) of the specific quantities, you may simply run:

nt2 plot myrun/mysimulation --fields "E.*;B.*" --isel "t=5" --sel "x=slice(-5, None); z=0.5"

This plots the 6-th snapshot (t=5) of all the E and B field components, sliced for x > -5, and at z = 0.5 (notice, that you can use both --isel and --sel). If instead, you prefer to make a movie, simply do not specify the time:

nt2 plot myrun/mysimulation --fields "E.*;B.*" --sel "x=slice(-5, None); z=0.5"

If you want to only install the CLI, without the library itself, you may do that via pipx: pipx install nt2py.

Features

1. Lazy loading and parallel processing of the simulation data with dask.
2. Context-aware data manipulation with xarray.
3. Parallel plotting and movie generation with loky and ffmpeg.
4. Command-line interface, the nt2 command, for quick plotting (both movies and snapshots).

Testing

There are unit tests included with the code which also require downloading test data with git lfs (installed separately from git). You may download the data simply by running git lfs pull.

TODO

• Unit tests
• Plugins for other simulation data formats
• Support for sparse arrays for particles via Sparse library
• Command-line interface
• Support for multiple runs
• Interactive regime (hvplot, bokeh, panel)
• Ghost cells support
• Usage examples
• Parse the log file with timings
• Raw reader
• 3.14-compatible parallel output