Merge pull request #120 from Pressio/version_0130

version 0.13.0

CMakeLists.txt

@@ -73,19 +73,11 @@ else()
 
   if(PRESSIODEMOAPPS_ENABLE_TESTS)
     enable_testing()
-    include_directories(
-      ${CMAKE_CURRENT_SOURCE_DIR}/include
-      ${CMAKE_CURRENT_SOURCE_DIR}/tpls/eigen/eigen3
-      ${CMAKE_CURRENT_SOURCE_DIR}/tpls/pressio/include)
     add_subdirectory(tests_mesh)
     add_subdirectory(tests_cpp)
   endif()
 
   if(PRESSIODEMOAPPS_ENABLE_PERF)
-    include_directories(
-      ${CMAKE_CURRENT_SOURCE_DIR}/include
-      ${CMAKE_CURRENT_SOURCE_DIR}/tpls/eigen/eigen3
-      ${CMAKE_CURRENT_SOURCE_DIR}/tpls/pressio/include)
     add_subdirectory(tests_perf)
   endif()
 

docs/source/apicpp.rst

@@ -20,19 +20,23 @@ A *pressio-demoapps* C++ problem class meets the following API
 
       The scalar type: this is by default ``double``.
 
+   .. cpp:type:: independent_variable_type
+
+      This represents "time" and is the same as the ``scalar_type``.
+
    .. cpp:type:: state_type
 
       Data structure type storing the state: this depends on which specific implementation
       you use when you instantiate the problem using the ``create_problem_<>`` API
       (see `Supported Backends And Types`_ for more details about backends and corresponding types).
       For example, if you use ``create_problem_eigen``, the ``state_type`` will be an Eigen vector.
 
-   .. cpp:type:: velocity_type
+   .. cpp:type:: right_hand_side_type
 
-      Data structure type to store the velocity (or RHS): this depends on which specific implementation
+      Data structure type to store the RHS: this depends on which specific implementation
       you use when you instantiate the problem using the ``create_problem_<>`` API
       (see `Supported Backends And Types`_ for more details about backends and corresponding types).
-      For example, if you use ``create_problem_eigen``, the ``velocity_type`` will be an Eigen vector.
+      For example, if you use ``create_problem_eigen``, the ``right_hand_side_type`` will be an Eigen vector.
 
    .. cpp:type:: jacobian_type
 
@@ -45,31 +49,25 @@ A *pressio-demoapps* C++ problem class meets the following API
 
       Constructs and returns an instance of the initial condition for the target problem.
 
-   .. cpp:function:: velocity_type createVelocity()
+   .. cpp:function:: right_hand_side_type createRightHandSide()
 
-      Constructs and returns an instance of the velocity.
+      Constructs and returns an instance of the right hand side.
 
    .. cpp:function:: jacobian_type createJacobian()
 
       Constructs and returns an instance of the jacobian.
 
-   .. cpp:function:: void velocity(const state_type & y, scalar_type time, velocity_type & v)
-
-      Given a state :math:`y` and time :math:`time`,
-      evaluates the RHS of the system and overwrites :math:`v`.
-
-   .. cpp:function:: void jacobian(const state_type & y, scalar_type time, jacobian_type & J)
+   .. cpp:function:: void operator()(const state_type & y, scalar_type time, right_hand_side_type & v)
 
       Given a state :math:`y` and time :math:`time`,
-      evaluates the Jacobian of the RHS and stores it into :math:`J`.
+      evaluates the RHS of the system overwriting :math:`v`.
 
-   .. cpp:function:: void velocityAndJacobian(const state_type & y, \
-		                              scalar_type time, \
-					      velocity_type & v, \
-					      jacobian_type & J)
+   .. cpp:function:: void operator()(const state_type & y, scalar_type time,\
+		     right_hand_side_type & v, jacobian_type & J, bool computeJac)
 
       Given a state :math:`y` and time :math:`time`,
-      evaluates the RHS and its Jacobian.
+      evaluates the RHS of the system overwriting :math:`v` and  if ``computeJac == true``,
+      its Jacobian and stores it into :math:`J`.
 
    .. cpp:function:: auto totalDofSampleMesh()
 
@@ -100,7 +98,7 @@ C++ Backends and Corresponding Types
      - Type alias
 
    * - Eigen
-     - ``using state_type = Eigen::Matrix<scalar_type, Eigen::Dynamic, 1>`` :raw-html-m2r:`<br/>` :raw-html-m2r:`<br/>` ``using velocity_type = Eigen::Matrix<scalar_type, Eigen::Dynamic, 1>`` :raw-html-m2r:`<br/>` :raw-html-m2r:`<br/>` ``using jacobian_type = Eigen::SparseMatrix<scalar_type, Eigen::RowMajor, int32_t>;``
+     - ``using state_type = Eigen::Matrix<scalar_type, Eigen::Dynamic, 1>`` :raw-html-m2r:`<br/>` :raw-html-m2r:`<br/>` ``using right_hand_side_type = Eigen::Matrix<scalar_type, Eigen::Dynamic, 1>`` :raw-html-m2r:`<br/>` :raw-html-m2r:`<br/>` ``using jacobian_type = Eigen::SparseMatrix<scalar_type, Eigen::RowMajor, int32_t>;``
 
 
 .. _cpp-mesh-api:
@@ -137,7 +135,7 @@ A *pressio-demoapps* C++ cell-centered mesh class meets the following API
    .. cpp:function:: index_type sampleMeshSize() const
 
       Returns the number of *sample* cells in the mesh.
-      This corresponds to all cells where the velocity (or RHS) is defined.
+      This corresponds to all cells where the RHS is defined.
 
    .. cpp:function:: scalar_type dx() const
 

docs/source/apipy.rst

@@ -18,9 +18,9 @@ Problem Class
 
       :rtype: numpy array
 
-   .. py:method:: createVelocity()
+   .. py:method:: createRightHandSide()
 
-      Constructs and returns an instance of the velocity.
+      Constructs and returns an instance of the rhs.
 
       :rtype: numpy array
 
@@ -33,14 +33,14 @@ Problem Class
       :rtype: numpy array
 
 
-   .. py:method:: velocity(y, time, v)
+   .. py:method:: rightHandSide(y, time, rhs)
 
       Given a state :math:`y` and time :math:`time`,
       evaluates the RHS of the system and stores it into :math:`v`.
 
       :param numpy array y: state vector
       :param float time: evaluation time
-      :param numpy array v: velocity to overwrite
+      :param numpy array rhs: rhs to overwrite
 
    .. py:method:: applyJacobian(y, operand, time, result)
 
@@ -107,7 +107,7 @@ A *pressio-demoapps* Python cell-centered mesh class meets the following API
    .. py:method:: sampleMeshSize()
 
       Returns the number of *sample* cells in the mesh.
-      This corresponds to all cells where the velocity (or RHS) is defined.
+      This corresponds to all cells where the RHS is defined.
 
       :rtype: int
 

docs/source/howtouse.rst

@@ -109,14 +109,14 @@ Here we show some things you can do using the C++ as an example:
    auto state = problem.initialCondition();
 
    // having the problem and initial condition, create instance of the RHS
-   auto rhs = problem.createVelocity()
+   auto rhs = problem.createRightHandSide()
    // compute the rhs of the discrete system at time=0.0
-   problem.velocity(state, 0.0, rhs);
+   problem.rightHandSide(state, 0.0, rhs);
 
    // create the Jacobian
    auto J = problem.createJacobian()
    // compute J at time=0.0
-   problem.velocityAndJacobian(state, 0.0, rhs, J);
+   problem.rightHandSideAndJacobian(state, 0.0, rhs, J);
    // or we can compute just the Jacobian
    problem.jacobian(state, 0.0, J);
 

docs/source/installation.rst

@@ -15,8 +15,6 @@ To use it, you need a C++14 compiler and you have to:
 
 2. include the Eigen library (whose headers you can find inside ``pressiodemoapps/tpls``).
 
-3. specify the CMake option ``-DPRESSIODEMOAPPS_ENABLE_TPL_EIGEN=ON`` while building your code.
-
 Building the test suite
 ~~~~~~~~~~~~~~~~~~~~~~~
 
@@ -25,7 +23,7 @@ If you want to build the C++ tests, you need CMake > 3.18.0 and then do::
   git clone --recursive [email protected]:Pressio/pressio-demoapps.git
   export CXX=<path-to-your-CXX-compiler> #must support C++14
   cd pressio-demoapps && mkdir build && cd build
-  cmake -DPRESSIODEMOAPPS_ENABLE_TESTS=On -DPRESSIODEMOAPPS_ENABLE_TPL_EIGEN=ON ..
+  cmake -DPRESSIODEMOAPPS_ENABLE_TESTS=On ..
   make -j4
   ctest -j4
 
@@ -54,18 +52,6 @@ Then, you can do:
 
 This builds/installs pressiodemoapps with default options (build_mode=Release).
 
-
-
-..
-   To build/install pressiodemoapps with OpenMP and Release mode:
-   git clone --recursive [email protected]:Pressio/pressio-demoapps.git
-   export CXX=<path-to-your-CXX-compiler> #must support C++14
-   python3 cmake_build.py --openmp
-   pip3 install .
-   # to just build do
-   python -m build
-
-
 You can run the tests to verify things::
 
   cd pressio-demoapps

docs/source/meshsample.rst

@@ -8,7 +8,7 @@ What is a sample mesh and why?
 
 .. Important::
    In practice, a sample mesh is a disjoint collection
-   of cells where one computes the velocity (or RHS or residual) vector
+   of cells where one computes the RHS (or residual) vector
    and Jacobian matrix of the target system.
 
 The sample mesh is critical, for example, for projection-based ROMs of nonlinear systems.
@@ -26,9 +26,9 @@ and the `discrete empirical interpolation method (DEIM) <https://doi.org/10.1137
 While the sample mesh strictly speaking refers to the collection of cells
 where we compute the residual and Jacobian, a related concept is what we refer to as **stencil mesh**.
 We refer to **stencil mesh** the collection of cells that are needed to compute
-the velocity or residual vector on the *sample mesh*.
+the RHS or residual vector on the *sample mesh*.
 Note that, in general, the sample mesh is a subset of the stencil mesh,
-because to compute the velocity or residual at a given cell, one also needs
+because to compute the RHS or residual at a given cell, one also needs
 the cell-centered values at that target cell.
 
 For more discussion on this, see `this page <https://pressio.github.io/proms/hyper/>`_.