Merge pull request #22 from PlasmaFAIR/fix-arrays-without-grids

Fix reading arrays without grids

src/sdf_xarray/__init__.py

@@ -275,12 +275,18 @@ def _grid_species_name(grid_name: str) -> str:
                 continue
 
             if isinstance(value, Constant) or value.grid is None:
-                # No grid, so just a scalar
                 data_attrs = {}
                 if value.units is not None:
                     data_attrs["units"] = value.units
 
-                data_vars[key] = Variable((), value.data, data_attrs)
+                # We don't have a grid, either because it's just a
+                # scalar, or because it's an array over something
+                # else. We have no more information, so just make up
+                # some (hopefully) unique dimension names
+                shape = getattr(value.data, "shape", ())
+                dims = [f"dim_{key}_{n}" for n, _ in enumerate(shape)]
+
+                data_vars[key] = Variable(dims, value.data, attrs=data_attrs)
                 continue
 
             if value.is_point_data:

tests/example_array_no_grids/README.md

@@ -0,0 +1,9 @@
+# Test files
+
+These files were generated using EPOCH commit aafed39 and the
+`input.deck` here, which is modified from a run by Joel Adams. It is
+not intended to be physical. Run with:
+
+    echo "." | mpirun -np 2 $EPOCH1D
+
+where `$EPOCH1D` is the path to the `epoch1d` executable

tests/example_array_no_grids/input.deck

@@ -0,0 +1,119 @@
+begin:constant
+  nel = 1e+23
+  intens = 2e+22
+  omega = 2.0 * pi * c / (1.0e-6)
+  den_crit = critical(omega)
+  scale = 1e-06
+  den_max = 5.0 * den_crit
+  den_maxpoint = 4e-05
+  den_contrast = 1.0
+  amax = 1.0
+end:constant
+
+begin:control
+  nx = 8
+  nparticles = nx * 2
+  nsteps = 1
+  t_end = 2e-15
+  x_min = -1e-05
+  x_max = 1e-05
+  dt_multiplier = 0.8
+end:control
+
+begin:qed
+  use_qed = F
+  qed_start_time = 0
+  produce_photons = F
+  photon_energy_min = 50 * kev
+  produce_pairs = F
+  photon_dynamics = F
+end:qed
+
+begin:collisions
+  use_collisions = T
+  coulomb_log = auto
+  collide = all
+end:collisions
+
+begin:boundaries
+  bc_x_min = simple_laser
+  bc_x_max = simple_laser
+end:boundaries
+
+begin:species
+  name = Electron
+  fraction = 0.5
+  dump = F
+  temperature = 0
+  number_density = if (x gt 0e-6, nel * 1.0e6, 0)
+  number_density_min = 1
+  identify:electron
+end:species
+
+begin:species
+  name = Ion
+  fraction = 0.5
+  dump = F
+  number_density = number_density(Electron)
+  temperature = temperature_x(Electron)
+  number_density_min = 1
+  identify:proton
+end:species
+
+begin:species
+  name = Photon
+  nparticles = 0
+  dump = F
+  identify:photon
+end:species
+
+begin:output_global
+  force_final_to_be_restartable = T
+end:output_global
+
+begin:output
+  name = normal
+  use_offset_grid = F
+  dt_snapshot = 5e-15
+  particles = never
+  px = never
+  py = never
+  pz = never
+  vx = never
+  vy = never
+  vz = never
+  charge = never
+  mass = never
+  particle_weight = never
+  species_id = never
+  grid = always
+  ex = never
+  ey = never
+  ez = never
+  bx = never
+  by = never
+  bz = never
+  jx = never
+  jy = never
+  jz = never
+  average_particle_energy = always + species
+  mass_density = never + species
+  charge_density = never
+  number_density = never + species
+  temperature = never + species
+  distribution_functions = always
+  particle_probes = never
+  absorption = always
+  total_energy_sum = always + species
+end:output
+
+begin:laser
+  boundary = x_min
+  intensity = intens * 1.0e4
+  omega = omega
+  polarisation = 0.0
+  phase = 0.0
+  t_profile = gauss(time, 40.0e-15, 30.0e-15)
+  t_start = 0.0
+  t_end = end
+end:laser

tests/test_basic.py

@@ -8,6 +8,7 @@
 EXAMPLE_MISMATCHED_FILES_DIR = (
     pathlib.Path(__file__).parent / "example_mismatched_files"
 )
+EXAMPLE_ARRAYS_DIR = pathlib.Path(__file__).parent / "example_array_no_grids"
 
 
 def test_basic():
@@ -101,3 +102,25 @@ def test_erroring_on_mismatched_jobid_files():
             compat="override",
             preprocess=SDFPreprocess(),
         )
+
+
+def test_arrays_with_no_grids():
+    with xr.open_dataset(EXAMPLE_ARRAYS_DIR / "0001.sdf") as df:
+        laser_phase = "laser_x_min_phase"
+        assert laser_phase in df
+        assert df[laser_phase].shape == (1,)
+
+        random_states = "Random States"
+        assert random_states in df
+        assert df[random_states].shape == (8,)
+
+
+def test_arrays_with_no_grids_multifile():
+    df = xr.open_mfdataset(EXAMPLE_ARRAYS_DIR.glob("*.sdf"), preprocess=SDFPreprocess())
+    laser_phase = "laser_x_min_phase"
+    assert laser_phase in df
+    assert df[laser_phase].shape == (2, 1)
+
+    random_states = "Random States"
+    assert random_states in df
+    assert df[random_states].shape == (2, 8)