wip before adding license

Author: Francesco Rizzi

docs/source/endtoend/swe_galerkin_default.rst

@@ -35,7 +35,6 @@ build directory, so you don't need to do anything:
 .. literalinclude:: ../../../end-to-end-roms/2d_swe_galerkin_default/wf.yaml
    :language: yaml
    :lines: 1-35
-   :linenos:
 
 
 Step 1: execute FOMs
@@ -50,8 +49,7 @@ When we run the FOM driver, the following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_fom_explicit.hpp
    :language: cpp
-   :lines: 9-31
-   :linenos:
+   :lines: 15-35
 
 At the end, doing ``tree -L 1 .`` should produce:
 
@@ -103,9 +101,7 @@ The following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_default_galerkin.hpp
    :language: cpp
-   :lines: 10-43
-   :linenos:
-
+   :lines: 26-58, 18-18, 60-62
 
 At the end, you should have the following directory structure:
 

docs/source/endtoend/swe_galerkin_hypred_1.rst

@@ -104,8 +104,7 @@ Running the Galerkin driver means the following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_hyperreduced_galerkin.hpp
    :language: cpp
-   :lines: 40-77
-   :linenos:
+   :lines: 26-94, 18-18, 96-97
 
 At the end, you should have the following directory structure:
 

docs/source/endtoend/swe_lspg_default.rst

@@ -35,7 +35,6 @@ build directory, so you don't need to do anything:
 .. literalinclude:: ../../../end-to-end-roms/2d_swe_lspg_default/wf.yaml
    :language: yaml
    :lines: 1-35
-   :linenos:
 
 
 Step 1: execute FOMs
@@ -54,8 +53,7 @@ When we run the FOM driver, the following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_fom_implicit.hpp
    :language: cpp
-   :lines: 9-45
-   :linenos:
+   :lines: 15-49
 
 At the end, doing ``tree -L 1 .`` should produce:
 
@@ -93,7 +91,7 @@ and creates all data into an "offline_rom" subdirectory:
 
 
 Step 3: lspg rom
---------------------
+----------------
 
 .. code-block:: bash
 
@@ -104,13 +102,11 @@ The following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_default_lspg.hpp
    :language: cpp
-   :lines: 10-37
-   :linenos:
+   :lines: 22-46
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/lspg_pick_solver_and_run.hpp
    :language: cpp
-   :lines: 23-37
-   :linenos:
+   :lines: 21-35, 36-51, 18-18, 62-65, 18-18, 79-80
 
 At the end, you should have the following directory structure:
 

docs/source/endtoend/templateyaml.rst

@@ -3,8 +3,7 @@ ode: tutorial 3
 
 .. literalinclude:: ../../../ode-using-eigen-types/tutorial3/main.cc
    :language: cpp
-   :lines: 1-158
-
+   :lines: 1-157
 
 Process results
 ---------------

docs/source/using_eigen/ode3.rst

@@ -26,7 +26,7 @@ def assert_valid_and_supported_problem(wfDic, ptutRepoEndToEndFullPath):
   assert('problem' in wfDic)
 
   problemName = find_problem_name_from_wf_dic(wfDic)
-  moduleName  = 'customizations_'+problemName
+  moduleName = problemName+'_customizations'
   modulePath  = os.path.realpath(ptutRepoEndToEndFullPath+'/'+moduleName)
   if not os.path.exists(modulePath):
     print("\n")

…d-roms/customizations_2d_swe/__init__.py …d-roms/2d_swe_customizations/__init__.pyend-to-end-roms/customizations_2d_swe/__init__.py renamed to end-to-end-roms/2d_swe_customizations/__init__.py end-to-end-roms/customizations_2d_swe/__init__.py renamed to end-to-end-roms/2d_swe_customizations/__init__.py

@@ -0,0 +1,6 @@
+
+/* NOTE: the formatting and line order below matters because
+   the rst docs use literalinclude to pick up snippets of code,
+   so if you change something below
+   it is likely you impact the documentation, so be careful
+*/

end-to-end-roms/all.py

@@ -2,28 +2,39 @@
 #ifndef RUN_LSPG_PICK_SOLVER_AND_RUN_HPP_
 #define RUN_LSPG_PICK_SOLVER_AND_RUN_HPP_
 
-template<
-  class LspgStepperType,
-  class ParserType,
-  class RomStateType
-  >
+/* NOTE:
+   1. the formatting here matters because the rst docs
+      use literalincludes so if you change somehting below
+      it is likely you impact the documentation
+
+   2. the comments below are used by the rst documentaion
+      in non contiguous literalinclude statetements so that
+      we can make the documentation more clear
+
+   3. do NOT erase these comments, and do NOT move them
+      or you impact the rst docs
+
+   // branch taken in this demo
+   // branch not used in this demo
+*/
+
+template<class LspgStepperType, class ParserType, class RomStateType>
 void lspg_pick_solver_and_run(const ParserType & parser,
 			      LspgStepperType & lspgStepper,
 			      RomStateType & reducedState)
 {
-  using scalar_t = typename pressio::Traits<RomStateType>::scalar_type;
-  namespace pode = pressio::ode;
+  namespace pode   = pressio::ode;
   namespace pnlins = pressio::nonlinearsolvers;
 
-  StateObserver observer(parser.stateSamplingFreq());
-
-  const pressio::ode::StepCount numSteps(parser.numSteps());
+  using scalar_type = typename pressio::Traits<RomStateType>::scalar_type;
   const auto startTime = static_cast<typename LspgStepperType::independent_variable_type>(0);
+  const pressio::ode::StepCount numSteps(parser.numSteps());
+  StateObserver observer(parser.stateSamplingFreq());
 
   if (parser.nonlinearSolver() == "GaussNewton")
   {
-    using hessian_t = Eigen::Matrix<scalar_t, -1, -1>;
-    using solver_tag = pressio::linearsolvers::direct::HouseholderQR;
+    using hessian_t       = Eigen::Matrix<scalar_type, -1, -1>;
+    using solver_tag      = pressio::linearsolvers::direct::HouseholderQR;
     using linear_solver_t = pressio::linearsolvers::Solver<solver_tag, hessian_t>;
     linear_solver_t linearSolver;
 
@@ -38,7 +49,6 @@ void lspg_pick_solver_and_run(const ParserType & parser,
 
   else if (parser.nonlinearSolver() == "GaussNewtonQR")
   {
-
     using mat_t = typename LspgStepperType::jacobian_type;
     using qr_solver_t = pressio::qr::QRSolver<mat_t, pressio::qr::Householder>;
     qr_solver_t qrSolver;
@@ -53,8 +63,8 @@ void lspg_pick_solver_and_run(const ParserType & parser,
 
   else if (parser.nonlinearSolver() == "LevenbergMarquardt")
   {
-    using hessian_t = Eigen::Matrix<scalar_t, -1, -1>;
-    using solver_tag = pressio::linearsolvers::direct::HouseholderQR;
+    using hessian_t       = Eigen::Matrix<scalar_type, -1, -1>;
+    using solver_tag      = pressio::linearsolvers::direct::HouseholderQR;
     using linear_solver_t = pressio::linearsolvers::Solver<solver_tag, hessian_t>;
     linear_solver_t linearSolver;
 
@@ -68,5 +78,4 @@ void lspg_pick_solver_and_run(const ParserType & parser,
 			  observer, solver);
   }
 }
-
 #endif

end-to-end-roms/cpp/README_BEFORE_DEVELOPING.md

@@ -75,7 +75,7 @@ int main(int argc, char *argv[])
     const auto problemNode = node["problem"];
     if (!problemNode){ throw std::runtime_error("Missing problem in yaml input!"); }
     const auto problemName = problemNode.as<std::string>();
-    std::cout << problemName << std::endl;
+    std::cout << "Running: " << problemName << std::endl;
 
     // start timer
     auto t1 = std::chrono::high_resolution_clock::now();
@@ -86,7 +86,6 @@ int main(int argc, char *argv[])
       using scalar_t = double;
       ParserTwoDimShallowWater<scalar_t> parser(node);
       const auto meshObj = pda::load_cellcentered_uniform_mesh_eigen<scalar_t>(parser.meshDir());
-      const auto probId  = pda::Swe2d::SlipWall;
       const auto invScheme = string_to_inviscid_flux_scheme(parser.inviscidFluxReconstruction());
       const auto gravity   = parser.gravity();
       const auto coriolis  = parser.coriolis();
@@ -104,36 +103,3 @@ int main(int argc, char *argv[])
   pressio::log::finalize();
   return 0;
 }
-
-  // if (problem == "2d_rd")
-  // {
-  //   namespace pda  = pressiodemoapps;
-  //   ParserTwoDimReacDiff<scalar_t> parser(node);
-  //   const auto meshObj   = pda::load_cellcentered_uniform_mesh_eigen<scalar_t>(parser.meshDir());
-  //   const auto diffusion = parser.diffusion();
-  //   const auto reaction  = parser.reaction();
-  //   const auto scheme    = pda::ViscousFluxReconstruction::FirstOrder;
-  //   const auto probId    = pda::DiffusionReaction2d::ProblemA;
-  //   auto fomSystem = pda::create_problem_eigen(meshObj, probId, scheme,
-  // 					    mySource, diffusion, reaction);
-  //   dispatch(fomSystem, parser);
-  // }
-
-
-  // if (problem == "2d_gs")
-  // {
-  //   namespace pda  = pressiodemoapps;
-  //   ParserTwoDimGrayScott<scalar_t> parser(node);
-  //   const auto meshObj = pda::load_cellcentered_uniform_mesh_eigen<scalar_t>(parser.meshDir());
-  //   const auto probId  = pda::DiffusionReaction2d::GrayScott;
-  //   const auto scheme  = pda::ViscousFluxReconstruction::FirstOrder;
-
-  //   const auto diffusionA = parser.diffusionA();
-  //   const auto diffusionB = parser.diffusionB();
-  //   const auto feedRate   = parser.feedRate();
-  //   const auto killRate   = parser.killRate();
-  //   auto fomSystem = pda::create_problem_eigen(meshObj, probId, scheme,
-  // 			    diffusionA, diffusionB,
-  // 			    feedRate, killRate);
-  //   dispatch(fomSystem, parser);
-  // }