Merge branch 'main' of https://github.com/ipc-sim/ipc-toolkit into dynamic

Author: Huangzizhou

docs/source/changelog.rst

@@ -307,7 +307,7 @@ Added
 Changed
 ^^^^^^^
 
-* Changed CMake target name to :cmake:`ipc::toolkit`
+* Changed CMake target name to ``ipc::toolkit``
 
 2021-07-26 (`1479aae <https://github.com/ipc-sim/ipc-toolkit/commit/1479aaea958daaa4e963529493e4169dc7757913>`__)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -317,7 +317,7 @@ Changed
 Changed
 ^^^^^^^
 
-* Updated the CMake system to use modern :cpp:`FetchContent` to download externals
+* Updated the CMake system to use modern ``FetchContent`` to download externals
 
 2021-07-22 (`e24c76d <https://github.com/ipc-sim/ipc-toolkit/commit/e24c76ddc818fb9efc4d522ef72a581a15abf751>`__)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -414,7 +414,7 @@ Changed
 ^^^^^^^
 
 * :cpp:`ignore_codimensional_vertices` to :cpp:`false` by default
-* CMake option :cmake:`TIGHT_INCLUSION_WITH_NO_ZERO_TOI=ON` as default
+* CMake option ``TIGHT_INCLUSION_WITH_NO_ZERO_TOI=ON`` as default
 
 2021-06-18 (`aa59aeb <https://github.com/ipc-sim/ipc-toolkit/commit/aa59aeb0634af981a8f1cfbb6d2ff2b76a04d610>`__)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

docs/source/conf.py

@@ -21,7 +21,10 @@
 # -- Project information -----------------------------------------------------
 
 from datetime import datetime
-import ipctk
+
+import sys
+sys.path.append(str(pathlib.Path(__file__).parents[2] / "python"))
+from _find_ipctk import ipctk  # noqa
 
 project = "IPC Toolkit"
 copyright = f'2020-{datetime.now().year}, IPC-Sim Organization; MIT License'

docs/source/cpp-api/barrier.rst

@@ -20,7 +20,7 @@ Adaptive Barrier Stiffness
 Semi-Implicit Stiffness
 ~~~~~~~~~~~~~~~~~~~~~~~
 
-.. doxygenfunction:: ipc::semi_implicit_stiffness(const CollisionMesh&, const Eigen::MatrixXd&, const StencilsT&, const Eigen::VectorXd&, const Eigen::SparseMatrix<double>&, const double)
+.. doxygenfunction:: ipc::semi_implicit_stiffness(const CollisionMesh&, Eigen::ConstRef<Eigen::MatrixXd>, const StencilsT&, Eigen::ConstRef<Eigen::VectorXd>, const Eigen::SparseMatrix<double>&, const double)
 
 Barrier Class
 -------------
@@ -34,10 +34,10 @@ Clamped Log Barrier
 .. doxygenclass:: ipc::ClampedLogBarrier
     :allow-dot-graphs:
 
-Normalized Clamped Log Barrier
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+Normalized Barrier
+~~~~~~~~~~~~~~~~~~
 
-.. doxygenclass:: ipc::NormalizedClampedLogBarrier
+.. doxygenclass:: ipc::NormalizedBarrier
     :allow-dot-graphs:
 
 Clamped Log Squared Barrier

docs/source/cpp-api/distance.rst

@@ -19,11 +19,11 @@ Edge-Edge Mollifier
 .. doxygenfunction:: edge_edge_cross_squarednorm
 .. doxygenfunction:: ipc::edge_edge_cross_squarednorm_gradient
 .. doxygenfunction:: ipc::edge_edge_cross_squarednorm_hessian
-.. doxygenfunction:: edge_edge_mollifier(const Eigen::Ref<const Eigen::Vector3d>& ea0, const Eigen::Ref<const Eigen::Vector3d>& ea1, const Eigen::Ref<const Eigen::Vector3d>& eb0, const Eigen::Ref<const Eigen::Vector3d>& eb1, const double eps_x)
+.. doxygenfunction:: edge_edge_mollifier(Eigen::ConstRef<Eigen::Vector3d> ea0, Eigen::ConstRef<Eigen::Vector3d> ea1, Eigen::ConstRef<Eigen::Vector3d> eb0, Eigen::ConstRef<Eigen::Vector3d> eb1, const double eps_x)
 .. doxygenfunction:: edge_edge_mollifier(const double x, const double eps_x)
-.. doxygenfunction:: edge_edge_mollifier_gradient(const Eigen::Ref<const Eigen::Vector3d>& ea0, const Eigen::Ref<const Eigen::Vector3d>& ea1, const Eigen::Ref<const Eigen::Vector3d>& eb0, const Eigen::Ref<const Eigen::Vector3d>& eb1, const double eps_x)
+.. doxygenfunction:: edge_edge_mollifier_gradient(Eigen::ConstRef<Eigen::Vector3d> ea0, Eigen::ConstRef<Eigen::Vector3d> ea1, Eigen::ConstRef<Eigen::Vector3d> eb0, Eigen::ConstRef<Eigen::Vector3d> eb1, const double eps_x)
 .. doxygenfunction:: edge_edge_mollifier_gradient(const double x, const double eps_x)
-.. doxygenfunction:: edge_edge_mollifier_hessian(const Eigen::Ref<const Eigen::Vector3d>& ea0, const Eigen::Ref<const Eigen::Vector3d>& ea1, const Eigen::Ref<const Eigen::Vector3d>& eb0, const Eigen::Ref<const Eigen::Vector3d>& eb1, const double eps_x)
+.. doxygenfunction:: edge_edge_mollifier_hessian(Eigen::ConstRef<Eigen::Vector3d> ea0, Eigen::ConstRef<Eigen::Vector3d> ea1, Eigen::ConstRef<Eigen::Vector3d> eb0, Eigen::ConstRef<Eigen::Vector3d> eb1, const double eps_x)
 .. doxygenfunction:: edge_edge_mollifier_hessian(const double x, const double eps_x)
 
 Edge-Edge
@@ -57,12 +57,12 @@ Point-Line
 Point-Plane
 -----------
 
-.. doxygenfunction:: point_plane_distance(const Eigen::Ref<const Eigen::Vector3d>& p, const Eigen::Ref<const Eigen::Vector3d>& origin, const Eigen::Ref<const Eigen::Vector3d>& normal)
-.. doxygenfunction:: point_plane_distance(const Eigen::Ref<const Eigen::Vector3d>& p, const Eigen::Ref<const Eigen::Vector3d>& t0, const Eigen::Ref<const Eigen::Vector3d>& t1, const Eigen::Ref<const Eigen::Vector3d>& t2)
-.. doxygenfunction:: point_plane_distance_gradient(const Eigen::Ref<const Eigen::Vector3d>& p, const Eigen::Ref<const Eigen::Vector3d>& origin, const Eigen::Ref<const Eigen::Vector3d>& normal)
-.. doxygenfunction:: point_plane_distance_gradient(const Eigen::Ref<const Eigen::Vector3d>& p, const Eigen::Ref<const Eigen::Vector3d>& t0, const Eigen::Ref<const Eigen::Vector3d>& t1, const Eigen::Ref<const Eigen::Vector3d>& t2)
-.. doxygenfunction:: point_plane_distance_hessian(const Eigen::Ref<const Eigen::Vector3d>& p, const Eigen::Ref<const Eigen::Vector3d>& origin, const Eigen::Ref<const Eigen::Vector3d>& normal)
-.. doxygenfunction:: point_plane_distance_hessian(const Eigen::Ref<const Eigen::Vector3d>& p, const Eigen::Ref<const Eigen::Vector3d>& t0, const Eigen::Ref<const Eigen::Vector3d>& t1, const Eigen::Ref<const Eigen::Vector3d>& t2)
+.. doxygenfunction:: point_plane_distance(Eigen::ConstRef<Eigen::Vector3d> p, Eigen::ConstRef<Eigen::Vector3d> origin, Eigen::ConstRef<Eigen::Vector3d> normal)
+.. doxygenfunction:: point_plane_distance(Eigen::ConstRef<Eigen::Vector3d> p, Eigen::ConstRef<Eigen::Vector3d> t0, Eigen::ConstRef<Eigen::Vector3d> t1, Eigen::ConstRef<Eigen::Vector3d> t2)
+.. doxygenfunction:: point_plane_distance_gradient(Eigen::ConstRef<Eigen::Vector3d> p, Eigen::ConstRef<Eigen::Vector3d> origin, Eigen::ConstRef<Eigen::Vector3d> normal)
+.. doxygenfunction:: point_plane_distance_gradient(Eigen::ConstRef<Eigen::Vector3d> p, Eigen::ConstRef<Eigen::Vector3d> t0, Eigen::ConstRef<Eigen::Vector3d> t1, Eigen::ConstRef<Eigen::Vector3d> t2)
+.. doxygenfunction:: point_plane_distance_hessian(Eigen::ConstRef<Eigen::Vector3d> p, Eigen::ConstRef<Eigen::Vector3d> origin, Eigen::ConstRef<Eigen::Vector3d> normal)
+.. doxygenfunction:: point_plane_distance_hessian(Eigen::ConstRef<Eigen::Vector3d> p, Eigen::ConstRef<Eigen::Vector3d> t0, Eigen::ConstRef<Eigen::Vector3d> t1, Eigen::ConstRef<Eigen::Vector3d> t2)
 
 Point-Point
 -----------

docs/source/cpp.rst

@@ -24,7 +24,7 @@ C++
     :end-before: <!--- BEGIN C++ README 2 --->
 
 .. tip::
-   If your :cmake:`IPC_TOOLKIT_GIT_TAG` is a tag (e.g. ``v1.3.1``), then you can use the :cmake:`FetchContent_Declare` argument :cmake:`GIT_SHALLOW TRUE` to download only a single commit. Otherwise, you should use the default :cmake:`GIT_SHALLOW FALSE`.
+   If your ``IPC_TOOLKIT_GIT_TAG`` is a tag (e.g. ``v1.3.1``), then you can use the ``FetchContent_Declare`` argument ``GIT_SHALLOW TRUE`` to download only a single commit. Otherwise, you should use the default ``GIT_SHALLOW FALSE``.
 
 .. include:: ../../README.md
     :parser: myst_parser.sphinx_
@@ -34,7 +34,7 @@ C++
 .. _filib_dependency_note:
 
 .. warning::
-    ``filib`` is licensed under `LGPL-2.1 <https://github.com/zfergus/filib/blob/main/LICENSE>`_ and as such it is required to be dynamically linked. Doing so automatically is a challenge, so by default we use static linkage. Enabling dynaic linkage requires copying the ``.so``/``.dylib``/``.dll`` file to the binary directory or system path. To enable this, set the CMake option :cmake:`FILIB_BUILD_SHARED_LIBS` to :cmake:`ON` and add this CMake code to copy the shared libaray object to the binary directory:
+    ``filib`` is licensed under `LGPL-2.1 <https://github.com/zfergus/filib/blob/main/LICENSE>`_ and as such it is required to be dynamically linked. Doing so automatically is a challenge, so by default we use static linkage. Enabling dynaic linkage requires copying the ``.so``/``.dylib``/``.dll`` file to the binary directory or system path. To enable this, set the CMake option ``FILIB_BUILD_SHARED_LIBS`` to ``ON`` and add this CMake code to copy the shared libaray object to the binary directory:
 
     .. code-block:: cmake
 
@@ -47,7 +47,7 @@ C++
 
     where ``${MY_EXE_TARGET}`` is the name of your executable target. If you know a better way to handle this, please `let us know <https://github.com/ipc-sim/ipc-toolkit/discussions>`_!
 
-    If you would rather avoid LGPL code entirely, you can disable filib by setting :cmake:`IPC_TOOLKIT_WITH_FILIB` to :cmake:`OFF`. With this option disabled, CMake will not download or use any of filib's code.
+    If you would rather avoid LGPL code entirely, you can disable filib by setting ``IPC_TOOLKIT_WITH_FILIB`` to ``OFF``. With this option disabled, CMake will not download or use any of filib's code.
 
 .. include:: ../../README.md
     :parser: myst_parser.sphinx_

docs/source/tutorial/faq.rst

@@ -13,7 +13,7 @@ Frequently Asked Questions
 How do I include IPC Toolkit in my project?
 -------------------------------------------
 
-If you are using CMake, the public include directory is added to the :cmake:`ipc::toolkit` cmake target which means that any lib/bin that includes :cmake:`ipc::toolkit` as a dependency also adds those include directories too.
+If you are using CMake, the public include directory is added to the `ipc::toolkit` cmake target which means that any lib/bin that includes `ipc::toolkit` as a dependency also adds those include directories too.
 
 If you are not using CMake, the include path is ``src``.
 

docs/source/tutorial/nonlinear_ccd.rst

@@ -57,15 +57,17 @@ Let's dive deeper by breaking down the implementation of ``Rigid2DTrajectory``.
 
         .. literalinclude:: ../../../tests/src/tests/ccd/test_nonlinear_ccd.cpp
             :language: c++
-            :lines: 127-134
+            :start-after: // BEGIN_RIGID_2D_CALL
+            :end-before: // END_RIGID_2D_CALL
             :dedent: 4
 
 
     .. md-tab-item:: Python
 
         .. literalinclude:: ../../../python/tests/test_ccd.py
             :language: python
-            :lines: 90-94
+            :start-after: # BEGIN_RIGID_2D_CALL
+            :end-before: # END_RIGID_2D_CALL
             :dedent: 8
 
 This function computes the position of the point at a time :math:`t \in [0, 1]`. This defines the trajectory of the point. In this case, we have a rigid body with a center of mass (COM) at the origin. The trajectory of the point is given by:
@@ -87,14 +89,16 @@ The second function we need to implement is ``max_distance_from_linear``.
 
         .. literalinclude:: ../../../tests/src/tests/ccd/test_nonlinear_ccd.cpp
             :language: c++
-            :lines: 136-147
+            :start-after: // BEGIN_RIGID_2D_MAX_DISTANCE_FROM_LINEAR
+            :end-before: // END_RIGID_2D_MAX_DISTANCE_FROM_LINEAR
             :dedent: 4
 
     .. md-tab-item:: Python
 
         .. literalinclude:: ../../../python/tests/test_ccd.py
             :language: python
-            :lines: 96-102
+            :start-after: # BEGIN_RIGID_2D_MAX_DISTANCE_FROM_LINEAR
+            :end-before: # END_RIGID_2D_MAX_DISTANCE_FROM_LINEAR
             :dedent: 8
 
 This function computes the maximum distance over a time interval :math:`[t_0, t_1]` between the nonlinear trajectory and a line segment from :math:`x(t_0)` to :math:`x(t_1)`. Mathematically this function computes

notebooks/find_ipctk.py

@@ -1,20 +1,4 @@
-try:
-    import ipctk  # Try to import the built module
-except ImportError:
-    import sys
-    import pathlib
-    repo_root = pathlib.Path(__file__).parents[1]
-    possible_paths = [
-        pathlib.Path("python").resolve(),
-        repo_root / "build" / "python",
-        repo_root / "build" / "release" / "python",
-        repo_root / "build" / "debug" / "python",
-    ]
-    for path in possible_paths:
-        if path.exists() and len(list(path.glob("ipctk.*"))) > 0:
-            sys.path.append(str(path))
-            break
-    else:
-        raise ImportError("Could not find the ipctk module")
-    print(f"Using found ipctk module at {path}")
-    import ipctk  # Try again
+import sys
+import pathlib
+sys.path.append(str(pathlib.Path(__file__).parents[1] / "python"))
+from _find_ipctk import ipctk  # noqa

python/_find_ipctk.py

@@ -0,0 +1,20 @@
+try:
+    import ipctk  # Try to import the built module
+except ImportError:
+    import sys
+    import pathlib
+    repo_root = pathlib.Path(__file__).parents[1]
+    possible_paths = [
+        pathlib.Path("python").resolve(),
+        repo_root / "build" / "python",
+        repo_root / "build" / "release" / "python",
+        repo_root / "build" / "debug" / "python",
+    ]
+    for path in possible_paths:
+        if path.exists() and len(list(path.glob("ipctk.*"))) > 0:
+            sys.path.append(str(path))
+            break
+    else:
+        raise ImportError("Could not find the ipctk module")
+    print(f"Using found ipctk module at {path}")
+    import ipctk  # Try again

python/src/adhesion/adhesion.cpp

@@ -2,7 +2,6 @@
 
 #include <ipc/adhesion/adhesion.hpp>
 
-namespace py = pybind11;
 using namespace ipc;
 
 void define_adhesion(py::module_& m)
@@ -21,7 +20,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The normal adhesion potential.
         )ipc_Qu8mg5v7",
-        py::arg("d"), py::arg("dhat_p"), py::arg("dhat_a"), py::arg("a2"));
+        "d"_a, "dhat_p"_a, "dhat_a"_a, "a2"_a);
 
     m.def(
         "normal_adhesion_potential_first_derivative",
@@ -38,7 +37,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The first derivative of the normal adhesion potential wrt d.
         )ipc_Qu8mg5v7",
-        py::arg("d"), py::arg("dhat_p"), py::arg("dhat_a"), py::arg("a2"));
+        "d"_a, "dhat_p"_a, "dhat_a"_a, "a2"_a);
 
     m.def(
         "normal_adhesion_potential_second_derivative",
@@ -55,7 +54,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The second derivative of the normal adhesion potential wrt d.
         )ipc_Qu8mg5v7",
-        py::arg("d"), py::arg("dhat_p"), py::arg("dhat_a"), py::arg("a2"));
+        "d"_a, "dhat_p"_a, "dhat_a"_a, "a2"_a);
 
     m.def(
         "max_normal_adhesion_force_magnitude",
@@ -71,7 +70,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The maximum normal adhesion force magnitude.
         )ipc_Qu8mg5v7",
-        py::arg("dhat_p"), py::arg("dhat_a"), py::arg("a2"));
+        "dhat_p"_a, "dhat_a"_a, "a2"_a);
 
     m.def(
         "tangential_adhesion_f0", &tangential_adhesion_f0,
@@ -85,7 +84,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The tangential adhesion mollifier function at y.
         )ipc_Qu8mg5v7",
-        py::arg("y"), py::arg("eps_a"));
+        "y"_a, "eps_a"_a);
 
     m.def(
         "tangential_adhesion_f1", &tangential_adhesion_f1,
@@ -99,7 +98,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The first derivative of the tangential adhesion mollifier function at y.
         )ipc_Qu8mg5v7",
-        py::arg("y"), py::arg("eps_a"));
+        "y"_a, "eps_a"_a);
 
     m.def(
         "tangential_adhesion_f2", &tangential_adhesion_f2,
@@ -113,7 +112,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The second derivative of the tangential adhesion mollifier function at y.
         )ipc_Qu8mg5v7",
-        py::arg("y"), py::arg("eps_a"));
+        "y"_a, "eps_a"_a);
 
     m.def(
         "tangential_adhesion_f1_over_x", &tangential_adhesion_f1_over_x,
@@ -127,7 +126,7 @@ void define_adhesion(py::module_& m)
         Returns:
             The first derivative of the tangential adhesion mollifier function divided by y.
         )ipc_Qu8mg5v7",
-        py::arg("y"), py::arg("eps_a"));
+        "y"_a, "eps_a"_a);
 
     m.def(
         "tangential_adhesion_f2_x_minus_f1_over_x3",
@@ -142,5 +141,5 @@ void define_adhesion(py::module_& m)
         Returns:
             The second derivative of the tangential adhesion mollifier function times y minus the first derivative all divided by y cubed.
         )ipc_Qu8mg5v7",
-        py::arg("y"), py::arg("eps_a"));
+        "y"_a, "eps_a"_a);
 }