Merge pull request #172 from Pressio/release-candidate-0.16.0

Release candidate 0.16.0

Author: Francesco Rizzi

.github/workflows/test-all.yml

@@ -46,8 +46,11 @@ jobs:
 
       - name: Install packages
         run: |
+          echo "deb http://security.ubuntu.com/ubuntu focal-security main" | sudo tee /etc/apt/sources.list.d/focal-security.list
           sudo apt-get update
+          sudo apt-get install libssl1.1
           sudo apt-get install -y --install-suggests $APT_PACKAGES
+          sudo rm /etc/apt/sources.list.d/focal-security.list
 
       - name: Install CMake
         run: |
@@ -93,6 +96,7 @@ jobs:
             -DCMAKE_BUILD_TYPE:STRING=${{ matrix.config.mode }} \
             -DPRESSIODEMOAPPS_ENABLE_TESTS:BOOL=ON \
             -DPRESSIODEMOAPPS_ENABLE_BINDINGS:BOOL=OFF \
+            -DCMAKE_CXX_FLAGS="-Wall -Wno-unused-but-set-variable -Werror" \
             -B $BUILD_DIR -S $DEMOAPPS_HOME
 
       # NOTE: -j2 caused g++ crash (out of memory)

.gitmodules

@@ -1,3 +0,0 @@
-[submodule "tpls/pybind11"]
-	path = tpls/pybind11
-	url = https://github.com/Pressio/pybind11.git

CMakeLists.txt

@@ -57,8 +57,8 @@ if(PRESSIODEMOAPPS_ENABLE_BINDINGS)
 
   include_directories(
     ${CMAKE_CURRENT_SOURCE_DIR}/include
-    ${CMAKE_CURRENT_SOURCE_DIR}/tpls/eigen/eigen3)
-  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/tpls/pybind11)
+    ${CMAKE_CURRENT_SOURCE_DIR}/tpls/eigen3)
+  add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/tpls/pybind11-2.10.4)
 
   if(PRESSIODEMOAPPS_ENABLE_OPENMP)
     link_libraries(OpenMP::OpenMP_CXX)

docs/source/advection_diffusion_reaction_2d.rst

@@ -0,0 +1,114 @@
+2D single-species advection-reaction-diffusion
+==============================================
+
+This problem focuses on the following 2D PDE:
+
+.. math::
+
+   \frac{\partial \phi}{\partial t} + u \frac{\partial \phi}{\partial x} + v \frac{\partial \phi}{\partial y} = D \left(\frac{\partial^2 \phi}{\partial x^2} + \frac{\partial^2 \phi}{\partial y^2} \right) - \sigma \phi + f(x, y, t)
+
+
+* Initial conditions: :math:`\phi(x, y, 0) = 0`
+
+* Default settings:
+
+  - :math:`u = 0.5 \cos(\pi/3), v = 0.5 \sin(\pi/3)`
+
+  - :math:`D = 0.001`, :math:`\sigma = 1`
+
+  - :math:`f(x, y, t) = 1`
+
+* Domain is unit square :math:`[0,1]^2` with homogeneous Dirichlet BC
+
+* :math:`u, v, D, \sigma` can be customized via the problem constructor (more below)
+
+Mesh
+----
+
+.. code-block:: shell
+
+   python3 pressio-demoapps/meshing_scripts/create_full_mesh_for.py \
+           --problem advdiffreac2d_s<stencilSize> -n Nx Ny --outDir <destination-path>
+
+where
+
+- ``Nx, Ny`` is the number of cells you want along :math:`x` and :math:`y` respectively
+
+- ``<stencilSize> = 3 or 5 or 7``: defines the neighboring connectivity of each cell
+
+- ``<destination-path>`` is where you want the mesh files to be generated
+
+
+C++ synopsis
+------------
+
+.. code-block:: c++
+
+   #include "pressiodemoapps/advection_diffusion_reaction2d.hpp"
+
+   int main(){
+     namespace pda = pressiodemoapps;
+
+     const auto meshObj = pda::load_cellcentered_uniform_mesh_eigen("path-to-mesh");
+
+     const auto inviscidScheme = pda::InviscidFluxReconstruction::FirstOder; //or Weno3, Weno5
+
+     // A. constructor for problem using default values
+     {
+       const auto probId  = pda::AdvectionDiffusionReaction2d::ProblemA;
+       auto problem = pda::create_problem_eigen(meshObj, probId, inviscidScheme);
+     }
+
+     // B. setting custom coefficients
+     {
+       using scalar_type = typename decltype(meshObj)::scalar_t;
+       const scalar_type ux = 0.2;
+       const scalar_type uy = 0.8;
+       const scalar_type diff  = 0.01;
+       const scalar_type sigma = 1.5;
+       auto problem = pda::create_advdiffreac_2d_problem_A_eigen(meshObj, inviscidScheme,
+                                                                 ux, uy, diff, sigma);
+     }
+   }
+
+
+Python synopsis
+---------------
+
+.. code-block:: py
+
+   import pressiodemoapps as pda
+
+   meshObj = pda.load_cellcentered_uniform_mesh("path-to-mesh")
+
+   scheme  = pda.InviscidFluxReconstruction.FirstOrder # or Weno3, Weno5
+
+   # A. constructor for problem using default values
+   probId  = pda.AdvectionDiffusionReaction2d.ProblemA
+   problem = pda.create_problem(meshObj, probId, scheme)
+
+   # B. setting custom coefficients
+   ux, uy, myD, sigma = 0.1, 0.5, 0.001, 1.5
+   problem = pda.create_adv_diff_reac_2d_problem_A(meshObj, scheme, ux, uy, myD, sigma)
+
+Notes:
+------
+
+.. important::
+
+   Currently, for this problem the viscous schemes is fixed
+   such that it yields a second-order viscuous scheme.
+
+
+Sample Solution
+---------------
+
+Representative plot at :math:`t=0` (left) and :math:`t=3`,
+using a ``50x50`` mesh with Weno5 and RK4 time integration with :math:`dt = 0.01`,
+and default values for the physical coefficients:
+
+.. image:: ../../figures/wiki_2d_advdiffreac_probA_solution0.png
+    :width: 44 %
+
+.. image:: ../../figures/wiki_2d_advdiffreac_probA_solution1.png
+    :width: 44 %

docs/source/burgers_2d_periodic.rst

@@ -59,12 +59,12 @@ C++ synopsis
 
      const auto meshObj = pda::load_cellcentered_uniform_mesh_eigen("path-to-mesh");
 
+     const auto probId  = pda::AdvectionDiffusion2d::BurgersPeriodic;
      const auto inviscidScheme = pda::InviscidFluxReconstruction::FirstOrder; // or Weno3, Weno5
      const auto viscousScheme  = pda::ViscousFluxReconstruction::FirstOrder;  // must be FirstOrder
 
      // A. constructor for problem using default values
      {
-       const auto probId = pda::AdvectionDiffusion2d::BurgersPeriodic;
        auto problem = pda::create_problem_eigen(meshObj, probId, inviscidScheme, viscousScheme);
      }
 
@@ -76,9 +76,9 @@ C++ synopsis
        const auto D      = /* something */;
        const auto x0     = /* something */;
        const auto y0     = /* something */;
-       auto problem = pda::create_periodic_burgers_2d_problem_eigen(meshObj, inviscidScheme,
-								    viscousScheme, alpha,
-								    delta, D, x0, y0)
+       auto problem = pda::create_problem_eigen(meshObj, probId, inviscidScheme,
+						viscousScheme, alpha,
+						delta, D, x0, y0)
      }
    }
 
@@ -91,11 +91,11 @@ Python synopsis
 
    meshObj = pda.load_cellcentered_uniform_mesh("path-to-mesh")
 
+   probId  = pda.AdvectionDiffusion2d.BurgersPeriodic
    inviscidScheme = pda.InviscidFluxReconstruction.FirstOrder; # or Weno3, Weno5
    viscousScheme  = pda.ViscousFluxReconstruction.FirstOrder;  # must be FirstOrder
 
    # A. constructor for problem using default values
-   probId  = pda.AdvectionDiffusion2d.BurgersPeriodic
    problem = pda.create_problem(meshObj, probId, inviscidScheme, viscousScheme)
 
    # B. setting custom coefficients
@@ -104,9 +104,9 @@ Python synopsis
    D      = # something
    x0     = # something
    y0     = # something
-   problem = pda.create_periodic_burgers_2d_problem(meshObj, inviscidScheme,
-                                                    viscousScheme, alpha,
-                                                    delta, D, x0, y0)
+   problem = pda.create_burgers_2d_problem(meshObj, probId, inviscidScheme,
+					   viscousScheme, alpha,
+					   delta, D, x0, y0)
 
 
 Sample Plot

docs/source/conf.py

@@ -63,10 +63,8 @@ def get_version():
   with open("../../version.txt") as version_file:
     return version_file.read().strip()
 
-version = get_version()
-
 # The full version, including alpha/beta/rc tags.
-release = version
+release = get_version()
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used: