add license and cleanup

Author: Francesco Rizzi

docs/source/endtoend/swe_galerkin_default.rst

@@ -29,8 +29,8 @@ Workflow File
 -------------
 
 The `workflow file <../../../end-to-end-roms/2d_swe_galerkin_default/wf.yaml>`_
-is shown below for exposition purposes, but it is automatically copied to the
-build directory, so you don't need to do anything:
+for this demo is shown below for exposition purposes, but it is automatically
+copied to the build directory, so you don't need to do anything:
 
 .. literalinclude:: ../../../end-to-end-roms/2d_swe_galerkin_default/wf.yaml
    :language: yaml
@@ -49,7 +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: 15-35
+   :lines: 56-76
 
 At the end, doing ``tree -L 1 .`` should produce:
 
@@ -101,7 +101,7 @@ The following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_default_galerkin.hpp
    :language: cpp
-   :lines: 26-58, 18-18, 60-62
+   :lines: 57-79, 82-87, 92
 
 At the end, you should have the following directory structure:
 

docs/source/endtoend/swe_galerkin_hypred_1.rst

@@ -29,8 +29,8 @@ Workflow File
 -------------
 
 The `workflow file <../../../end-to-end-roms/2d_swe_galerkin_hypred_1/wf.yaml>`_
-is shown below for exposition purposes, but it is automatically copied to the
-build directory, so you don't need to do anything:
+for this demo is shown below for exposition purposes, but it is automatically
+copied to the build directory, so you don't need to do anything:
 
 .. literalinclude:: ../../../end-to-end-roms/2d_swe_galerkin_hypred_1/wf.yaml
    :language: yaml
@@ -104,7 +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: 26-94, 18-18, 96-97
+   :lines: 57-109, 112-121, 126
 
 At the end, you should have the following directory structure:
 

docs/source/endtoend/swe_lspg_default.rst

@@ -29,8 +29,8 @@ Workflow File
 -------------
 
 The `workflow file <../../../end-to-end-roms/2d_swe_lspg_default/wf.yaml>`_
-is shown below for exposition purposes, but it is automatically copied to the
-build directory, so you don't need to do anything:
+for this demo is shown below for exposition purposes, but it is automatically
+copied to the build directory, so you don't need to do anything:
 
 .. literalinclude:: ../../../end-to-end-roms/2d_swe_lspg_default/wf.yaml
    :language: yaml
@@ -53,7 +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: 15-49
+   :lines: 56-90
 
 At the end, doing ``tree -L 1 .`` should produce:
 
@@ -102,11 +102,11 @@ The following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_default_lspg.hpp
    :language: cpp
-   :lines: 22-46
+   :lines: 58-82
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/lspg_pick_solver_and_run.hpp
    :language: cpp
-   :lines: 21-35, 36-51, 18-18, 62-65, 18-18, 79-80
+   :lines: 52-64, 67-78, 111
 
 At the end, you should have the following directory structure:
 

docs/source/endtoend/swe_lspg_hypred_1.rst

@@ -27,8 +27,8 @@ Workflow File
 -------------
 
 The `workflow file <../../../end-to-end-roms/2d_swe_lspg_hypred_1/wf.yaml>`_
-is shown below for exposition purposes, but it is automatically copied to the
-build directory, so you don't need to do anything:
+for this demo is shown below for exposition purposes, but it is automatically
+copied to the build directory, so you don't need to do anything:
 
 .. literalinclude:: ../../../end-to-end-roms/2d_swe_lspg_hypred_1/wf.yaml
    :language: yaml
@@ -106,13 +106,11 @@ The following C++ code is being executed:
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/run_hyperreduced_lspg.hpp
    :language: cpp
-   :lines: 82-111
-   :linenos:
+   :lines: 58-155
 
 .. literalinclude:: ../../../end-to-end-roms/cpp/lspg_pick_solver_and_run.hpp
    :language: cpp
-   :lines: 23-37
-   :linenos:
+   :lines: 52-64, 67-78, 111
 
 At the end, you should have the following directory structure:
 

docs/source/using_eigen/nonlinsolvers1.rst

@@ -1,7 +1,8 @@
 nonlinear solvers: tutorial 1
 =============================
 
+This tutorial shows how to solve via Gauss-Newton one variant of the Rosenbrock problem.
+
 .. literalinclude:: ../../../nonlinearsolvers-using-eigen-types/main1.cc
    :language: cpp
-   :lines: 1-99
-   :linenos:
+   :lines: 48-145

docs/source/using_eigen/ode1.rst

@@ -3,4 +3,4 @@ ode: tutorial 1
 
 .. literalinclude:: ../../../ode-using-eigen-types/main1.cc
    :language: cpp
-   :lines: 1-85
+   :lines: 48-132

docs/source/using_eigen/ode2.rst

@@ -1,9 +1,11 @@
 ode: tutorial 2
 ===============
 
+This tutorial shows how to integrate the `original Lorenz system <https://en.wikipedia.org/wiki/Lorenz_system>`__ using explicit time integration.
+
 .. literalinclude:: ../../../ode-using-eigen-types/tutorial2/main.cc
    :language: cpp
-   :lines: 1-96
+   :lines: 48-143
 
 
 Process results

docs/source/using_eigen/ode3.rst

@@ -1,9 +1,11 @@
 ode: tutorial 3
 ===============
 
+This tutorial shows how to integrate the `original Lorenz system <https://en.wikipedia.org/wiki/Lorenz_system>`__ using implicit time integration.
+
 .. literalinclude:: ../../../ode-using-eigen-types/tutorial3/main.cc
    :language: cpp
-   :lines: 1-157
+   :lines: 48-187
 
 Process results
 ---------------

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

@@ -1,6 +1,8 @@
 
-/* 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
-*/
+- the formatting and line order in all files **matters**
+  because the rst docs use literalinclude to pick up snippets of code,
+  so if you change something in a file, t is likely you impact the documentation,
+  so be careful
+
+- indentation is in some places **intentionally* not set for the a
+  similar reason as above

end-to-end-roms/cpp/lspg_pick_solver_and_run.hpp

@@ -1,23 +1,54 @@
+/*
+//@HEADER
+// ************************************************************************
+//
+// lspg_pick_solver_and_run.hpp
+//                     		  Pressio
+//                             Copyright 2019
+//    National Technology & Engineering Solutions of Sandia, LLC (NTESS)
+//
+// Under the terms of Contract DE-NA0003525 with NTESS, the
+// U.S. Government retains certain rights in this software.
+//
+// Pressio is licensed under BSD-3-Clause terms of use:
+//
+// Redistribution and use in source and binary forms, with or without
+// modification, are permitted provided that the following conditions
+// are met:
+//
+// 1. Redistributions of source code must retain the above copyright
+// notice, this list of conditions and the following disclaimer.
+//
+// 2. Redistributions in binary form must reproduce the above copyright
+// notice, this list of conditions and the following disclaimer in the
+// documentation and/or other materials provided with the distribution.
+//
+// 3. Neither the name of the copyright holder nor the names of its
+// contributors may be used to endorse or promote products derived
+// from this software without specific prior written permission.
+//
+// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
+// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
+// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS
+// FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE
+// COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT,
+// INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+// (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)
+// HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,
+// STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
+// IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+// POSSIBILITY OF SUCH DAMAGE.
+//
+// Questions? Contact Francesco Rizzi ([email protected])
+//
+// ************************************************************************
+//@HEADER
+*/
 
 #ifndef RUN_LSPG_PICK_SOLVER_AND_RUN_HPP_
 #define RUN_LSPG_PICK_SOLVER_AND_RUN_HPP_
 
-/* 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,
@@ -33,49 +64,49 @@ void lspg_pick_solver_and_run(const ParserType & parser,
 
   if (parser.nonlinearSolver() == "GaussNewton")
   {
-    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;
+  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;
 
-    auto solver = pnlins::create_gauss_newton(lspgStepper, linearSolver);
-    solver.setStoppingCriterion(pnlins::Stop::WhenGradientAbsoluteNormBelowTolerance);
-    solver.setTolerance(parser.nonlinearSolverTolerance());
+  auto solver = pnlins::create_gauss_newton(lspgStepper, linearSolver);
+  solver.setStoppingCriterion(pnlins::Stop::WhenGradientAbsoluteNormBelowTolerance);
+  solver.setTolerance(parser.nonlinearSolverTolerance());
 
-    pode::advance_n_steps(lspgStepper, reducedState, startTime,
-			  parser.timeStepSize(), numSteps,
-			  observer, solver);
+  pode::advance_n_steps(lspgStepper, reducedState, startTime,
+			parser.timeStepSize(), numSteps,
+			observer, solver);
   }
 
   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;
-    auto solver = pnlins::create_gauss_newtonQR(lspgStepper, qrSolver);
-    solver.setStoppingCriterion(pnlins::Stop::WhenGradientAbsoluteNormBelowTolerance);
-    solver.setTolerance(parser.nonlinearSolverTolerance());
+  using mat_t = typename LspgStepperType::jacobian_type;
+  using qr_solver_t = pressio::qr::QRSolver<mat_t, pressio::qr::Householder>;
+  qr_solver_t qrSolver;
+  auto solver = pnlins::create_gauss_newtonQR(lspgStepper, qrSolver);
+  solver.setStoppingCriterion(pnlins::Stop::WhenGradientAbsoluteNormBelowTolerance);
+  solver.setTolerance(parser.nonlinearSolverTolerance());
 
-    pode::advance_n_steps(lspgStepper, reducedState, startTime,
-			  parser.timeStepSize(), numSteps,
-			  observer, solver);
+  pode::advance_n_steps(lspgStepper, reducedState, startTime,
+			parser.timeStepSize(), numSteps,
+			observer, solver);
   }
 
   else if (parser.nonlinearSolver() == "LevenbergMarquardt")
   {
-    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;
+  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;
 
-    auto solver = pnlins::create_levenberg_marquardt(lspgStepper, linearSolver);
-    solver.setUpdatingCriterion(pnlins::Update::LMSchedule2);
-    solver.setStoppingCriterion(pnlins::Stop::WhenGradientAbsoluteNormBelowTolerance);
-    solver.setTolerance(parser.nonlinearSolverTolerance());
+  auto solver = pnlins::create_levenberg_marquardt(lspgStepper, linearSolver);
+  solver.setUpdatingCriterion(pnlins::Update::LMSchedule2);
+  solver.setStoppingCriterion(pnlins::Stop::WhenGradientAbsoluteNormBelowTolerance);
+  solver.setTolerance(parser.nonlinearSolverTolerance());
 
-    pode::advance_n_steps(lspgStepper, reducedState, startTime,
-			  parser.timeStepSize(), numSteps,
-			  observer, solver);
+  pode::advance_n_steps(lspgStepper, reducedState, startTime,
+			parser.timeStepSize(), numSteps,
+			observer, solver);
   }
 }
 #endif