Merge pull request #54 from epochpic/drop-boundaries

ignore boundary variables when loading

Author: JoelLucaAdams

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
 ~~~~~~~~~~~~~~~~~~~

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
 ~~~~~~~~~~~~~~~~~~~~~~~~~

src/sdf_xarray/__init__.py

@@ -310,6 +310,8 @@ def _process_grid_name(grid_name: str, transform_func) -> str:
             # 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
 

tests/example_dist_fn/0000.sdf

@@ -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

tests/example_dist_fn/0001.sdf

@@ -10,6 +10,7 @@
     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)