ipc-sim · zfergus · Jul 13, 2025 · Jul 13, 2025 · Jul 13, 2025
diff --git a/docs/Makefile b/docs/Makefile
@@ -23,5 +23,8 @@ clean:
 %: Makefile
 	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
 
+xml:
+	cd "$(SOURCEDIR)" && doxygen Doxyfile
+
 livehtml:
-	sphinx-autobuild --host 0.0.0.0 "$(SOURCEDIR)" "$(BUILDDIR)/html" $(SPHINXOPTS) $(O)
+	sphinx-autobuild --host 0.0.0.0 -j auto -a -q "$(SOURCEDIR)" "$(BUILDDIR)/html" $(SPHINXOPTS) $(O)
diff --git a/docs/source/_static/css/custom.css b/docs/source/_static/css/custom.css
@@ -17,6 +17,10 @@ span.colon {
     margin-left: -1em;
 }
 
+dl.cpp {
+    font-size: 0.64rem;
+}
+
 dl.cpp.objdesc,
 dl.py.objdesc {
     /* border: 0.05rem solid var(--md-primary-fg-color); */
@@ -28,6 +32,7 @@ dl.py.objdesc {
 
 dl.cpp.objdesc>dt,
 dl.py.objdesc>dt {
+    font-size: 0.64rem;
     padding-left: 0.5rem;
     padding-right: 0.5rem;
 }

diff --git a/docs/source/dependencies.rst → docs/source/about/dependencies.rst b/docs/source/dependencies.rst → docs/source/about/dependencies.rst
diff --git a/docs/source/license.rst → docs/source/about/license.rst b/docs/source/license.rst → docs/source/about/license.rst
@@ -4,7 +4,7 @@ License
 
 IPC Toolkit is released under an MIT license, and all of its dependencies are under similar permissive licenses (MIT, Apache, or MPL).
 
-.. literalinclude:: ../../LICENSE
+.. literalinclude:: ../../../LICENSE
     :language: md
 
 Citation

diff --git a/docs/source/release_notes.rst → docs/source/about/release_notes.rst b/docs/source/release_notes.rst → docs/source/about/release_notes.rst
diff --git a/docs/source/building.rst → docs/source/building/building.rst b/docs/source/building.rst → docs/source/building/building.rst
diff --git a/docs/source/python.rst → docs/source/building/python.rst b/docs/source/python.rst → docs/source/building/python.rst
@@ -1,6 +1,6 @@
 Python Bindings
 ===============
 
-.. include:: ../../python/README.md
+.. include:: ../../../python/README.md
     :parser: myst_parser.sphinx_
     :start-line: 10
diff --git a/docs/source/code_of_conduct.rst b/docs/source/code_of_conduct.rst
diff --git a/docs/source/conf.py b/docs/source/conf.py
@@ -101,7 +101,7 @@
     "private-members",
 )
 breathe_show_define_initializer = True
-# breathe_show_include = True
+breathe_show_include = True
 
 autodoc_default_options = {
     "members": True,
@@ -176,14 +176,14 @@
     "icon": {"repo": "fontawesome/brands/github"},
 
     "features": [
-        "navigation.expand",
+        "content.tabs.link",
+        "navigation.footer",
         "navigation.tabs",
         "navigation.top",
         "navigation.tracking",
         "search.highlight",
         "search.share",
         "toc.follow",
-        "content.tabs.link"
     ],
 
     "font": {

diff --git a/docs/source/contributing.rst b/docs/source/contributing.rst
diff --git a/docs/source/cpp-api/adhesion.rst b/docs/source/cpp-api/adhesion.rst
@@ -1,19 +1,42 @@
 Adhesion
 ========
 
+Functions
+---------
+
+.. list-table::
+    :header-rows: 1
+
+    * - Name
+      - Description
+    * - :func:`normal_adhesion_potential`
+      - The normal adhesion potential.
+    * - :func:`normal_adhesion_potential_first_derivative`
+      - The first derivative of the normal adhesion potential wrt d.
+    * - :func:`normal_adhesion_potential_second_derivative`
+      - The second derivative of the normal adhesion potential wrt d.
+    * - :func:`max_normal_adhesion_force_magnitude`
+      - The maximum normal adhesion force magnitude.
+    * - :func:`tangential_adhesion_f0`
+      - The tangential adhesion mollifier function.
+    * - :func:`tangential_adhesion_f1`
+      - The first derivative of the tangential adhesion mollifier function.
+    * - :func:`tangential_adhesion_f2`
+      - The second derivative of the tangential adhesion mollifier function.
+    * - :func:`tangential_adhesion_f1_over_x`
+      - The first derivative of the tangential adhesion mollifier function divided by y.
+    * - :func:`tangential_adhesion_f2_x_minus_f1_over_x3`
+      - The second derivative of the tangential adhesion mollifier function times y minus the first derivative all divided by y cubed.
+
+
 Normal Adhesion Potential
 -------------------------
 
-.. doxygenfunction:: normal_adhesion_potential
-.. doxygenfunction:: normal_adhesion_potential_first_derivative
-.. doxygenfunction:: normal_adhesion_potential_second_derivative
-.. doxygenfunction:: max_normal_adhesion_force_magnitude
+.. doxygengroup:: normal_adhesion
+   :content-only:
 
 Tangential Adhesion Potential
 -----------------------------
 
-.. doxygenfunction:: tangential_adhesion_f0
-.. doxygenfunction:: tangential_adhesion_f1
-.. doxygenfunction:: tangential_adhesion_f2
-.. doxygenfunction:: tangential_adhesion_f1_over_x
-.. doxygenfunction:: tangential_adhesion_f2_x_minus_f1_over_x3
+.. doxygengroup:: tangential_adhesion
+   :content-only:
diff --git a/docs/source/cpp-api/barrier.rst b/docs/source/cpp-api/barrier.rst
diff --git a/docs/source/cpp-api/barrier/Barrier.rst b/docs/source/cpp-api/barrier/Barrier.rst
@@ -0,0 +1,5 @@
+Barrier
+=======
+
+.. doxygenclass:: ipc::Barrier
+    :allow-dot-graphs:
diff --git a/docs/source/cpp-api/barrier/ClampedLogBarrier.rst b/docs/source/cpp-api/barrier/ClampedLogBarrier.rst
@@ -0,0 +1,5 @@
+ClampedLogBarrier
+=================
+
+.. doxygenclass:: ipc::ClampedLogBarrier
+    :allow-dot-graphs:
diff --git a/docs/source/cpp-api/barrier/ClampedLogSqBarrier.rst b/docs/source/cpp-api/barrier/ClampedLogSqBarrier.rst
@@ -0,0 +1,5 @@
+ClampedLogSqBarrier
+===================
+
+.. doxygenclass:: ipc::ClampedLogSqBarrier
+    :allow-dot-graphs:
diff --git a/docs/source/cpp-api/barrier/CubicBarrier.rst b/docs/source/cpp-api/barrier/CubicBarrier.rst
@@ -0,0 +1,5 @@
+CubicBarrier
+============
+
+.. doxygenclass:: ipc::CubicBarrier
+    :allow-dot-graphs:
diff --git a/docs/source/cpp-api/barrier/NormalizedBarrier.rst b/docs/source/cpp-api/barrier/NormalizedBarrier.rst
@@ -0,0 +1,5 @@
+NormalizedBarrier
+============
+
+.. doxygenclass:: ipc::NormalizedBarrier
+    :allow-dot-graphs:
diff --git a/docs/source/cpp-api/barrier/index.rst b/docs/source/cpp-api/barrier/index.rst
@@ -0,0 +1,82 @@
+Barrier
+=======
+
+.. toctree::
+   :caption: Barrier
+   :hidden:
+
+   Barrier.rst
+   ClampedLogBarrier.rst
+   NormalizedBarrier.rst
+   ClampedLogSqBarrier.rst
+   CubicBarrier.rst
+
+Barrier functions and functionals.
+
+Types
+-----
+
+.. list-table::
+    :header-rows: 1
+
+    * - Name
+      - Description
+    * - :doc:`Barrier <Barrier>`
+      - Base class for barrier functions.
+    * - :doc:`ClampedLogBarrier <ClampedLogBarrier>`
+      - Smoothly clamped log barrier functions from [Li et al.].
+    * - :doc:`ClampedLogSqBarrier <ClampedLogSqBarrier>`
+      - Clamped log barrier with a quadratic log term from [Huang et al.].
+    * - :doc:`CubicBarrier <CubicBarrier>`
+      - Cubic barrier function from [Ando 2024].
+    * - :doc:`NormalizedBarrier <NormalizedBarrier>`
+      - Normalized barrier function from [Li et al.].
+
+Functions
+---------
+
+.. list-table::
+    :header-rows: 1
+
+    * - Name
+      - Description
+    * - :func:`ipc::barrier`
+      - Evaluate the barrier function.
+    * - :func:`ipc::barrier_first_derivative`
+      - Derivative of the barrier function.
+    * - :func:`ipc::barrier_second_derivative`
+      - Second derivative of the barrier function.
+    * - :func:`ipc::barrier_force_magnitude`
+      - Compute the barrier force magnitude.
+    * - :func:`ipc::barrier_force_magnitude_gradient`
+      - Compute the gradient of the barrier force magnitude.
+    * - :func:`ipc::initial_barrier_stiffness`
+      - Compute the initial barrier stiffness.
+    * - :func:`ipc::update_barrier_stiffness`
+      - Update the barrier stiffness based on the current state.
+    * - :func:`ipc::semi_implicit_stiffness`
+      - Compute the semi-implicit stiffness for all collisions.
+
+Function Details
+----------------
+
+.. doxygenfunction:: barrier(const double, const double)
+.. doxygenfunction:: barrier_first_derivative
+.. doxygenfunction:: barrier_second_derivative
+
+Barrier Force Magnitude
+~~~~~~~~~~~~~~~~~~~~~~~
+
+.. doxygenfunction:: barrier_force_magnitude
+.. doxygenfunction:: barrier_force_magnitude_gradient
+
+Adaptive Barrier Stiffness
+~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+.. doxygenfunction:: initial_barrier_stiffness
+.. doxygenfunction:: update_barrier_stiffness
+
+Semi-Implicit Stiffness
+^^^^^^^^^^^^^^^^^^^^^^^
+
+.. doxygenfunction:: semi_implicit_stiffness(const CollisionMesh&, Eigen::ConstRef<Eigen::MatrixXd>, const StencilsT&, Eigen::ConstRef<Eigen::VectorXd>, const Eigen::SparseMatrix<double>&, const double)
diff --git a/docs/source/cpp-api/potentials.rst b/docs/source/cpp-api/potentials.rst
diff --git a/docs/source/cpp-api/potentials/BarrierPotential.rst b/docs/source/cpp-api/potentials/BarrierPotential.rst
@@ -0,0 +1,4 @@
+BarrierPotential
+================
+
+.. doxygenclass:: ipc::BarrierPotential
diff --git a/docs/source/cpp-api/potentials/FrictionPotential.rst b/docs/source/cpp-api/potentials/FrictionPotential.rst
@@ -0,0 +1,4 @@
+FrictionPotential
+=================
+
+.. doxygenclass:: ipc::FrictionPotential
diff --git a/docs/source/cpp-api/potentials/NormalAdhesionPotential.rst b/docs/source/cpp-api/potentials/NormalAdhesionPotential.rst
@@ -0,0 +1,4 @@
+NormalAdhesionPotential
+========================
+
+.. doxygenclass:: ipc::NormalAdhesionPotential
diff --git a/docs/source/cpp-api/potentials/NormalPotential.rst b/docs/source/cpp-api/potentials/NormalPotential.rst
@@ -0,0 +1,4 @@
+NormalPotential
+===============
+
+.. doxygenclass:: ipc::NormalPotential
diff --git a/docs/source/cpp-api/potentials/Potential.rst b/docs/source/cpp-api/potentials/Potential.rst
@@ -0,0 +1,4 @@
+Potential
+==========
+
+.. doxygenclass:: ipc::Potential
diff --git a/docs/source/cpp-api/potentials/TangentialAdhesionPotential.rst b/docs/source/cpp-api/potentials/TangentialAdhesionPotential.rst
@@ -0,0 +1,4 @@
+TangentialAdhesionPotential
+============================
+
+.. doxygenclass:: ipc::TangentialAdhesionPotential
diff --git a/docs/source/cpp-api/potentials/TangentialPotential.rst b/docs/source/cpp-api/potentials/TangentialPotential.rst
@@ -0,0 +1,4 @@
+TangentialPotential
+===================
+
+.. doxygenclass:: ipc::TangentialPotential