Damped sound wave

.github/actions/compile/action.yml

@@ -24,4 +24,5 @@ runs:
           echo "No env specified, installing outside of any env"
         fi
         pyccel --version
+        struphy compile -d
         struphy compile -y --language ${{ inputs.language }}

.github/workflows/test-PR-pure-python.yml

@@ -97,11 +97,11 @@ jobs:
             mpirun --version
             mpirun --oversubscribe -n 1 python -c "from mpi4py import MPI; print('rank:', MPI.COMM_WORLD.rank); print('size:', MPI.COMM_WORLD.size)"
 
-      - name: Pytest-MPI plugin check
-        shell: bash
-        run: |
-          source env/bin/activate
-          pytest --trace-config | grep mpi || true
+      # - name: Pytest-MPI plugin check
+      #   shell: bash
+      #   run: |
+      #     source env/bin/activate
+      #     pytest --trace-config | grep mpi || true
 
       - name: Pytest with collect-only
         shell: bash

doc/sections/dev_guide.rst

@@ -6,10 +6,6 @@ Developer's guide
 This is a collection of tutorials for developers. They are meant to be a practical guide to how to use Struphy 
 for development purposes, such as implementing new features, propagators or models.
 
-**Getting started with FEEC**: Begin with the :ref:`FEEC basics tutorial <dev_tutorial_feec_basics>` for an introduction to setting up the discrete de Rham complex, creating callable spline functions, and working with differential operators.
-
-**Next FEEC steps**: Continue with the :ref:`FEEC boundary-conditions tutorial <dev_tutorial_feec_bcs>` and then the :ref:`FEEC data-structures tutorial <dev_tutorial_data_structs>` to understand how ``StencilVector`` and ``StencilMatrix`` are used in practice.
-
 The tutorials give an overview of the most important classes used in writing new Propagators.
 These include classes for FEEC (finite element exterior calculus), particles and the coupling between them.
 
@@ -21,8 +17,15 @@ It is recommended to use the same Python environment as for Struphy, e.g., by in
 
 .. toctree::
    :maxdepth: 1
-   :caption: Notebook tutorials:
+   :caption: FEEC tutorials:
 
    ../_collections/tutorials/dev_tutorial_feec_basics
    ../_collections/tutorials/dev_tutorial_feec_bcs
-   ../_collections/tutorials/dev_tutorial_data_structs
+   ../_collections/tutorials/dev_tutorial_data_structs
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: SPH tutorials:
+
+   ../_collections/tutorials/dev_tutorial_sph_eval_kernels

doc/sections/dev_reference.rst

@@ -3,42 +3,11 @@
 Developer reference
 ===================
 
-FEEC
-----
+.. toctree::
+    :maxdepth: 2
+    :caption: Contents:
 
-Derham complex
-^^^^^^^^^^^^^^
+    subsections/dev-feec
+    subsections/dev-pic
+    subsections/dev-sph
 
-.. automodule:: struphy.feec.psydac_derham
-    :members:
-    :special-members:
-    :show-inheritance:
-    :exclude-members: __init__
-
-Grids
-^^^^^
-
-.. automodule:: struphy.topology.grids
-    :members:
-    :special-members:
-    :show-inheritance:
-    :exclude-members: __init__
-
-Mass Operators (bilinear forms)
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: struphy.feec.mass
-    :members:
-    :special-members:
-    :show-inheritance:
-    :exclude-members: __init__
-
-
-Projection of spline functions
-^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
-
-.. automodule:: struphy.feec.basis_projection_ops
-    :members:
-    :special-members:
-    :show-inheritance:
-    :exclude-members: __init__

doc/sections/subsections/dev-feec.rst

@@ -0,0 +1,39 @@
+FEEC
+----
+
+Derham complex
+^^^^^^^^^^^^^^
+
+.. automodule:: struphy.feec.psydac_derham
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__
+
+Grids
+^^^^^
+
+.. automodule:: struphy.topology.grids
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__
+
+Mass Operators (bilinear forms)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: struphy.feec.mass
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__
+
+
+Projection of spline functions
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: struphy.feec.basis_projection_ops
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__

doc/sections/subsections/dev-pic.rst

@@ -0,0 +1,44 @@
+PIC
+---
+
+Particle base class
+^^^^^^^^^^^^^^^^^^^
+
+.. autoclass:: struphy.pic.base.Particles
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__
+
+
+Particel-to-grid accumulation
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: struphy.pic.accumulation.particles_to_grid
+    :members:
+    :special-members:
+    :show-inheritance:
+
+
+Accumulation kernels
+^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: struphy.pic.accumulation.accum_kernels
+    :members:
+    :special-members:
+    :show-inheritance:
+
+.. automodule:: struphy.pic.accumulation.accum_kernels_gc
+    :members:
+    :special-members:
+    :show-inheritance:
+
+
+Pusher class
+^^^^^^^^^^^^
+
+.. autoclass:: struphy.pic.pushing.pusher.Pusher
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__

doc/sections/subsections/dev-sph.rst

@@ -0,0 +1,50 @@
+SPH
+---
+
+
+.. _pusher_kernels_sph:
+
+Pusher kernels
+^^^^^^^^^^^^^^
+
+.. automodule:: struphy.pic.pushing.pusher_kernels_sph
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __in
+
+
+.. _coeff_kernels_sph:
+
+Coefficient kernels
+^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: struphy.pic.pushing.eval_kernels_sph
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__
+
+
+.. _eval_kernels_sph:
+
+Evaluation kernels
+^^^^^^^^^^^^^^^^^^
+
+.. automodule:: struphy.pic.sph_eval_kernels
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__
+
+
+.. _smoothing_kernels:
+
+Smoothing kernels
+^^^^^^^^^^^^^^^^^^
+
+.. automodule:: struphy.pic.sph_smoothing_kernels
+    :members:
+    :special-members:
+    :show-inheritance:
+    :exclude-members: __init__

doc/sections/tutorials.rst

@@ -11,15 +11,36 @@ It is recommended to use the same Python environment as for Struphy, e.g., by in
 
 .. toctree::
    :maxdepth: 1
-   :caption: Notebook tutorials:
+   :caption: Pure FEEC models:
 
    ../_collections/tutorials/tutorial_poisson
    ../_collections/tutorials/tutorial_maxwell
    ../_collections/tutorials/tutorial_linear_mhd_slab_waves_1d
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: PIC models:
+
    ../_collections/tutorials/tutorial_vlasov_ampere_one_species_weak_landau
    ../_collections/tutorials/tutorial_particle_tracing
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: SPH models:
+
+   ../_collections/tutorials/tutorial_beltrami_sph
+   ../_collections/tutorials/tutorial_gas_expansion_sph
+   ../_collections/tutorials/tutorial_viscous_euler_sph
+   ../_collections/tutorials/tutorial_velocity_diffsusion_sph
+   ../_collections/tutorials/tutorial_hagen_poiseuille_sph
+   ../_collections/tutorials/tutorial_dam_break_sph
+
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Geometry and equilibria:
+
    ../_collections/tutorials/tutorial_domains
    ../_collections/tutorials/tutorial_mhd_equilibria
-   ../_collections/tutorials/tutorial_viscous_euler_sph
-   ../_collections/tutorials/tutorial_beltrami_sph
-   ../_collections/tutorials/tutorial_gas_expansion_sph

pyproject.toml

@@ -42,7 +42,7 @@ dependencies = [
     "trame-vuetify<=3.2.2",
     "nest_asyncio2<=1.7.2",
     "vtk<=9.6.1",
-    "pytest<=9.0.3",
+    "pytest<=9.1.0",
     "pytest-mpi<=0.6",
     "pytest-testmon<=2.2.0",
     "ruff>=0.15.0, <=0.15.12",

src/struphy/console/compile.py

@@ -92,6 +92,7 @@ def struphy_compile(
                     and "_tmp.py" not in file
                     and "test" not in file
                     and "__pycache__" not in subdir
+                    and "__pyccel__" not in subdir
                 ):
                     state["kernels"] += [os.path.join(subdir, file)]
 

src/struphy/fields_background/equils.py

@@ -2978,7 +2978,9 @@ def n_xyz(self, x, y, z):
         elif self.params["density_profile"] == "gaussian_xy":
             return self.params["n"] * xp.exp(-(x**2 + y**2) / self.params["p0"])
         elif self.params["density_profile"] == "step_function_xy":
-            assert isinstance(self.domain, domains.Cuboid)
+            from struphy.geometry.domains import Cuboid
+
+            assert isinstance(self.domain, Cuboid)
             l1 = self.domain.params["l1"]
             r1 = self.domain.params["r1"]
             l2 = self.domain.params["l2"]