sdf-xarray 0.2.2__tar.gz → 0.2.3__tar.gz

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.2
 Name: sdf-xarray
-Version: 0.2.2
+Version: 0.2.3
 Summary: Provides a backend for xarray to read SDF files as created by the EPOCH plasma PIC code.
 Author-Email: Peter Hill <peter.hill@york.ac.uk>, Joel Adams <joel.adams@york.ac.uk>, Shaun Doherty <shaun.doherty@york.ac.uk>
 License: Copyright 2024, Peter Hill, Joel Adams, epochpic team
@@ -32,6 +32,15 @@ License: Copyright 2024, Peter Hill, Joel Adams, epochpic team
          (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
          OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
          
+Classifier: Programming Language :: Python
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Operating System :: OS Independent
 Requires-Python: >=3.10
 Requires-Dist: numpy>=2.0.0
 Requires-Dist: xarray>=2024.1.0
@@ -67,9 +76,13 @@ Description-Content-Type: text/markdown
 
 # sdf-xarray
 
-![PyPI](https://img.shields.io/pypi/v/sdf-xarray?color=blue)
+![Dynamic TOML Badge](https://img.shields.io/badge/dynamic/toml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fepochpic%2Fsdf-xarray%2Frefs%2Fheads%2Fmain%2Fpyproject.toml&query=%24.project.requires-python&label=python&logo=python)
+[![Available on PyPI](https://img.shields.io/pypi/v/sdf-xarray?color=blue&logo=pypi)](https://pypi.org/project/sdf-xarray/)
 ![Build/Publish](https://github.com/epochpic/sdf-xarray/actions/workflows/build_publish.yml/badge.svg)
 ![Tests](https://github.com/epochpic/sdf-xarray/actions/workflows/tests.yml/badge.svg)
+[![Read the Docs](https://img.shields.io/readthedocs/sdf-xarray?logo=readthedocs&link=https%3A%2F%2Fsdf-xarray.readthedocs.io%2F)](https://sdf-xarray.readthedocs.io)
+[![Formatted with black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+
 
 sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files as created by
 [EPOCH](https://epochpic.github.io) using the [SDF-C](https://github.com/epochpic/SDF_C) library.

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/README.md

@@ -1,8 +1,12 @@
 # sdf-xarray
 
-![PyPI](https://img.shields.io/pypi/v/sdf-xarray?color=blue)
+![Dynamic TOML Badge](https://img.shields.io/badge/dynamic/toml?url=https%3A%2F%2Fraw.githubusercontent.com%2Fepochpic%2Fsdf-xarray%2Frefs%2Fheads%2Fmain%2Fpyproject.toml&query=%24.project.requires-python&label=python&logo=python)
+[![Available on PyPI](https://img.shields.io/pypi/v/sdf-xarray?color=blue&logo=pypi)](https://pypi.org/project/sdf-xarray/)
 ![Build/Publish](https://github.com/epochpic/sdf-xarray/actions/workflows/build_publish.yml/badge.svg)
 ![Tests](https://github.com/epochpic/sdf-xarray/actions/workflows/tests.yml/badge.svg)
+[![Read the Docs](https://img.shields.io/readthedocs/sdf-xarray?logo=readthedocs&link=https%3A%2F%2Fsdf-xarray.readthedocs.io%2F)](https://sdf-xarray.readthedocs.io)
+[![Formatted with black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/python/black)
+
 
 sdf-xarray provides a backend for [xarray](https://xarray.dev) to read SDF files as created by
 [EPOCH](https://epochpic.github.io) using the [SDF-C](https://github.com/epochpic/SDF_C) library.

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/docs/getting_started.rst

@@ -25,7 +25,14 @@ Usage
 -----
 
 ``sdf-xarray`` is a backend for xarray, and so is usable directly from
-`xarray`.
+`xarray`. There are several ways to load SDF files:
+
+- To load a single file, use :func:`xarray.open_dataset`.
+- To load multiple files, use :func:`xarray.open_mfdataset` or :func:`sdf_xarray.open_mfdataset`.
+- To access the raw contents of a single SDF file, use :func:`sdf_xarray.sdf_interface.SDFFile`.
+
+.. note::
+   When loading ``*.sdf`` files, variables related to ``boundaries``, ``cpu`` and ``output file`` are excluded as they are problematic.
 
 Single file loading
 ~~~~~~~~~~~~~~~~~~~

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/docs/key_functionality.rst

@@ -13,11 +13,14 @@ Key Functionality
 
 Loading SDF Files
 -----------------
-There are several ways to load in SDF files using ``sdf-xarray``.
-You can load in a single file using :func:`xarray.open_dataset`,
-load in multiple files using :func:`xarray.open_mfdataset` or
-:func:`sdf_xarray.open_mfdataset`, or load in a single raw SDF file
-using :func:`sdf_xarray.sdf_interface.SDFFile`.
+There are several ways to load SDF files:
+
+- To load a single file, use :func:`xarray.open_dataset`.
+- To load multiple files, use :func:`xarray.open_mfdataset` or :func:`sdf_xarray.open_mfdataset`.
+- To access the raw contents of a single SDF file, use :func:`sdf_xarray.sdf_interface.SDFFile`.
+
+.. note::
+   When loading ``*.sdf`` files, variables related to ``boundaries``, ``cpu`` and ``output file`` are excluded as they are problematic.
 
 Loading a Single SDF File
 ~~~~~~~~~~~~~~~~~~~~~~~~~

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/pyproject.toml

@@ -25,6 +25,17 @@ dependencies = [
   "cython>=3.0",
 ]
 description = "Provides a backend for xarray to read SDF files as created by the EPOCH plasma PIC code."
+classifiers = [
+  "Programming Language :: Python",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3.10",
+  "Programming Language :: Python :: 3.11",
+  "Programming Language :: Python :: 3.12",
+  "Programming Language :: Python :: 3.13",
+  "Intended Audience :: Science/Research",
+  "Topic :: Scientific/Engineering",
+  "Operating System :: OS Independent",
+]
 
 [project.optional-dependencies]
 docs = [

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/src/sdf_xarray/__init__.py

@@ -310,6 +310,8 @@ class SDFDataStore(AbstractDataStore):
             # Had some problems with these variables, so just ignore them for now
             if "cpu" in key.lower():
                 continue
+            if "boundary" in key.lower():
+                continue
             if "output file" in key.lower():
                 continue
 

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/src/sdf_xarray/_version.py

@@ -17,5 +17,5 @@ __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
 
-__version__ = version = '0.2.2'
-__version_tuple__ = version_tuple = (0, 2, 2)
+__version__ = version = '0.2.3'
+__version_tuple__ = version_tuple = (0, 2, 3)

sdf_xarray-0.2.3/tests/example_dist_fn/input.deck

@@ -0,0 +1,154 @@
+begin:control
+
+  # global number of gridpoints
+  # Divide nx and ny by 2 from 40 to 20  
+  nx = 16 # in x
+  ny = 8
+  nparticles = nx * ny * 4
+
+  # maximum number of iterations
+  # set to -1 to run until finished
+  nsteps = -1
+
+  # final time of simulation
+  t_end = 200e-15
+
+  # size of domain
+  x_min = 0e-6
+  x_max =  40e-6
+  y_min = -10e-6
+  y_max = -y_min
+
+  dt_multiplier = 0.8
+  dlb_threshold = 0.8
+
+end:control
+
+begin:laser
+
+  boundary = x_min
+  intensity_w_cm2 = 1.0e23
+  lambda = 1e-6
+  phase = 0.0
+  t_profile = gauss(time, 40.0e-15, 30.0e-15)  # This profile means your laser pulse has a maximum intensity at t=40 fs, and the intensity will smoothly decrease as time moves away from this point, with a width parameter of 30 fs.
+  t_start = 0.0
+  t_end = end
+end:laser
+
+begin:collisions
+
+  use_collisions = T
+  coulomb_log = auto
+  collide = all
+
+end:collisions
+
+
+begin:boundaries
+
+  bc_x_min = simple_laser
+  bc_x_max = open
+  bc_y_min = periodic
+  bc_y_max = periodic
+
+end:boundaries
+
+
+begin:species
+
+  # electrons
+  name = Electron
+  fraction = 0.5
+  dump = T
+
+  temperature = 0
+  number_density = if ((x gt 10e-6) and (x lt 30e-6), 1e22, 0)
+  number_density_min = 1
+
+  identify:electron
+
+end:species
+
+
+begin:output_global
+
+  force_final_to_be_restartable = F
+
+end:output_global
+
+
+begin:output
+
+  name = normal
+
+  # If use_offset_grid is true then the code dumps a grid which displays
+  # positions relative to the left hand edge of the window
+  use_offset_grid = F
+
+  # number of timesteps between output dumps
+  dt_snapshot = 100.0e-15 # 100.0e-15 / 100.0
+
+  # Properties at particle positions
+  particles = never
+  px = never
+  py = never
+  pz = never
+  vx = never
+  vy = never
+  vz = never
+  charge = never
+  mass = never
+  particle_weight = never
+  species_id = never
+
+  # Properties on grid
+  grid = always
+  ex = never
+  ey = always
+  ez = never
+  bx = never
+  by = never
+  bz = never
+  jx = never
+  jy = never
+  jz = never
+  poynt_flux = always
+  average_particle_energy = never
+  mass_density = never
+  charge_density = never
+  number_density = never
+  temperature = never
+
+  # extended io
+  distribution_functions = always
+  particle_probes = never
+  absorption = never
+  total_energy_sum = never
+
+end:output
+
+
+begin:dist_fn
+
+  name = x_px_py
+  ndims = 3
+  dumpmask = always
+
+  direction1 = dir_x
+  direction2 = dir_px
+  direction3 = dir_py
+
+  # range is ignored for spatial coordinates
+  range1 = (1, 1)
+  range2 = (1.6e-20, 1.6e-19)
+  range3 = (1.6e-20, 1.6e-19)
+
+  # resolution is ignored for spatial coordinates
+  resolution1 = 1
+  resolution2 = 20
+  resolution3 = 20
+
+  #include_species:Photon
+  include_species:Electron
+
+end:dist_fn

{sdf_xarray-0.2.2 → sdf_xarray-0.2.3}/tests/test_basic.py

@@ -10,6 +10,7 @@ EXAMPLE_MISMATCHED_FILES_DIR = (
     pathlib.Path(__file__).parent / "example_mismatched_files"
 )
 EXAMPLE_ARRAYS_DIR = pathlib.Path(__file__).parent / "example_array_no_grids"
+EXAMPLE_3D_DIST_FN = pathlib.Path(__file__).parent / "example_dist_fn"
 
 
 def test_basic():
@@ -178,3 +179,9 @@ def test_arrays_with_no_grids_multifile():
         random_states = "Random_States"
         assert random_states in df
         assert df[random_states].shape == (2, 8)
+
+
+def test_3d_distribution_function():
+    with xr.open_dataset(EXAMPLE_3D_DIST_FN / "0000.sdf") as df:
+        distribution_function = "dist_fn_x_px_py_Electron"
+        assert df[distribution_function].shape == (16, 20, 20)