Address minor issues in NOX wrapper

dealii · Jan 1, 2023 · 2ae3f56 · 2ae3f56
1 parent e612296
commit 2ae3f56
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Showing 6 changed files with 83 additions and 59 deletions.
diff --git a/.clang-format b/.clang-format
@@ -117,6 +117,8 @@ IncludeCategories:
     Priority: 300
   - Regex:    "deal.II/sundials/.*\\.h"
     Priority: 310
+  - Regex:    "deal.II/trilinos/.*\\.h"
+    Priority: 320
 # put boost right after deal:
   - Regex: "<boost.*>"
     Priority: 500

diff --git a/doc/doxygen/options.dox.in b/doc/doxygen/options.dox.in
@@ -240,6 +240,7 @@ PREDEFINED             = DOXYGEN=1 \
                          DEAL_II_WITH_TRILINOS=1 \
                          DEAL_II_TRILINOS_WITH_EPETRAEXT=1 \
                          DEAL_II_TRILINOS_WITH_MUELU=1 \
+                         DEAL_II_TRILINOS_WITH_NOX=1 \
                          DEAL_II_TRILINOS_WITH_ROL=1 \
                          DEAL_II_TRILINOS_WITH_SACADO=1 \
                          DEAL_II_TRILINOS_WITH_TPETRA=1 \

diff --git a/include/deal.II/trilinos/nox.h b/include/deal.II/trilinos/nox.h
@@ -36,7 +36,7 @@ namespace TrilinosWrappers
 
   /**
    * Wrapper around the nonlinear solver from the NOX
-   * packge (https://docs.trilinos.org/dev/packages/nox/doc/html/index.html),
+   * package (https://docs.trilinos.org/dev/packages/nox/doc/html/index.html),
    * targeting deal.II data structures.
    *
    * The following code shows the steps how to use this class:
@@ -47,16 +47,16 @@ namespace TrilinosWrappers
    * // create nonlinear solver
    * TrilinosWrappers::NOXSolver<VectorType> solver(additional_data);
    *
-   * // set user functions to compute residual,
-   * // set up Jacobian, and to apply the inverse of
-   * // Jacobian; note that there are more functions that
-   * // can be set
+   * // Set user functions to compute residual,
+   * // set up the Jacobian, and to apply the inverse of
+   * // Jacobian.
+   * // Note that there are more functions that can be set.
    * solver.residual = [](const auto &src, auto &dst) {...};
    * solver.setup_jacobian = [](const auto &src) {...};
    * solver.solve_with_jacobian =
    *   [](const auto &src, auto &dst, const auto) {...};
    *
-   * // solver nonlinear system with solution containing the intial guess and
+   * // solver nonlinear system with solution containing the initial guess and
    * // the final solution
    * solver.solve(solution);
    * @endcode
@@ -91,15 +91,15 @@ namespace TrilinosWrappers
       /**
        * Absolute l2 tolerance of the residual to be reached.
        *
-       * @note Solver terminates successfully if either the absolut or
+       * @note Solver terminates successfully if either the absolute or
        * the relative tolerance has been reached.
        */
       double abs_tol;
 
       /**
        * Relative l2 tolerance of the residual to be reached.
        *
-       * @note Solver terminates successfully if either the absolut or
+       * @note Solver terminates successfully if either the absolute or
        * the relative tolerance has been reached.
        */
       double rel_tol;
@@ -112,8 +112,9 @@ namespace TrilinosWrappers
 
       /**
        * Max number of linear iterations after which the preconditioner
-       * should be updated. This is only used if a lambda is attached to
-       * solve_with_jacobian_and_track_n_linear_iterations.
+       * should be updated. This is only used if
+       * solve_with_jacobian_and_track_n_linear_iterations has been given
+       * a target (i.e., it is not empty).
        */
       unsigned int threshold_n_linear_iterations;
 
@@ -185,8 +186,8 @@ namespace TrilinosWrappers
      *
      * @note This function is optional and is used in the case of certain
      * configurations. For instance, this function is required if the
-     * polynomial line search (@p NOX::LineSearch::Polynomial) is
-     * chosen, whereas for the full step case (@p NOX::LineSearch::FullStep)
+     * polynomial line search (`NOX::LineSearch::Polynomial`) is
+     * chosen, whereas for the full step case (`NOX::LineSearch::FullStep`)
      * it won't be called.
      *
      * @note This function should return 0 in the case of success.
@@ -196,7 +197,7 @@ namespace TrilinosWrappers
     /**
      * A user function that applies the inverse of the Jacobian to
      * @p x and writes the result in @p x. The parameter @p tolerance
-     * species the error reduction if a interative solver is used.
+     * specifies the error reduction if an iterative solver is used.
      *
      * @note This function is optional and is used in the case of certain
      * configurations.
@@ -246,7 +247,7 @@ namespace TrilinosWrappers
      * of linear iterations is exceeded.
      *
      * @note This function is optional. If no function is attached, this
-     * means implicitly a return value of false.
+     * means implicitly a return value of `false`.
      */
     std::function<bool()> update_preconditioner_predicate;
 

diff --git a/include/deal.II/trilinos/nox.templates.h b/include/deal.II/trilinos/nox.templates.h
@@ -18,10 +18,10 @@
 
 #include <deal.II/base/config.h>
 
-#include <deal.II/trilinos/nox.h>
-
 #ifdef DEAL_II_TRILINOS_WITH_NOX
 
+#  include <deal.II/trilinos/nox.h>
+
 #  include <NOX_Abstract_Group.H>
 #  include <NOX_Abstract_Vector.H>
 #  include <NOX_Solver_Factory.H>
@@ -68,7 +68,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Initialize every element of this vector with gamma.
+         * Initialize every element of this vector with @p gamma.
          */
         NOX::Abstract::Vector &
         init(double gamma) override
@@ -92,7 +92,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Put element-wise absolute values of source vector y into this vector.
+         * Put element-wise absolute values of source vector @p y into this vector.
          */
         NOX::Abstract::Vector &
         abs(const NOX::Abstract::Vector &y) override
@@ -105,7 +105,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Copy source vector y into this vector.
+         * Copy source vector @p y into this vector.
          */
         NOX::Abstract::Vector &
         operator=(const NOX::Abstract::Vector &y) override
@@ -125,7 +125,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Put element-wise reciprocal of source vector y into this vector.
+         * Put element-wise reciprocal of source vector @p y into this vector.
          */
         NOX::Abstract::Vector &
         reciprocal(const NOX::Abstract::Vector &y) override
@@ -138,7 +138,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Scale each element of this vector by gamma.
+         * Scale each element of this vector by @p gamma.
          */
         NOX::Abstract::Vector &
         scale(double gamma) override
@@ -149,7 +149,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Scale this vector element-by-element by the vector a.
+         * Scale this vector element-by-element by the vector @p a.
          */
         NOX::Abstract::Vector &
         scale(const NOX::Abstract::Vector &a) override
@@ -164,7 +164,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Compute x = (alpha * a) + (gamma * x) where x is this vector.
+         * Compute `x = (alpha * a) + (gamma * x)` where `x` is this vector.
          */
         NOX::Abstract::Vector &
         update(double                       alpha,
@@ -183,8 +183,8 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Compute x = (alpha * a) + (beta * b) + (gamma * x) where x is this
-         * vector.
+         * Compute `x = (alpha * a) + (beta * b) + (gamma * x)` where `x` is
+         * this vector.
          */
         NOX::Abstract::Vector &
         update(double                       alpha,
@@ -248,7 +248,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Return the vector's weighted 2-Norm.
+         * Return the vector's weighted 2-norm.
          */
         double
         norm(const NOX::Abstract::Vector &weights) const override
@@ -408,7 +408,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Set the solution vector `x` to @y.
+         * Set the solution vector `x` to @p y.
          */
         void
         setX(const NOX::Abstract::Vector &y) override
@@ -456,7 +456,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Return true if the residual vector `F` is valid.
+         * Return `true` if the residual vector `F` is valid.
          */
         bool
         isF() const override
@@ -482,7 +482,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Return true if the Jacobian is valid.
+         * Return `true` if the Jacobian is valid.
          */
         bool
         isJacobian() const override
@@ -536,7 +536,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Return an `RCP` to solution vector.
+         * Return a reference counting pointer to solution vector.
          */
         Teuchos::RCP<const NOX::Abstract::Vector>
         getXPtr() const override
@@ -546,7 +546,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Return an RCP to the residual `F(x)`.
+         * Return a reference counting pointer to the residual `F(x)`.
          */
         Teuchos::RCP<const NOX::Abstract::Vector>
         getFPtr() const override
@@ -556,7 +556,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Return an `RCP` to gradient.
+         * Return a reference counting pointer to gradient.
          */
         Teuchos::RCP<const NOX::Abstract::Vector>
         getGradientPtr() const override
@@ -566,7 +566,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Return an `RCP` to the Newton descent direction.
+         * Return a reference counting pointer to the Newton descent direction.
          */
         Teuchos::RCP<const NOX::Abstract::Vector>
         getNewtonPtr() const override
@@ -577,8 +577,8 @@ namespace TrilinosWrappers
 
         /**
          * Create a new Group of the same derived type as this one by
-         * cloning this one, and return a reference counting
-         * pointer to the new group.
+         * cloning this one, and return a reference counting pointer to
+         * the new group.
          */
         Teuchos::RCP<NOX::Abstract::Group>
         clone(NOX::CopyType copy_type) const override
@@ -666,7 +666,7 @@ namespace TrilinosWrappers
         }
 
         /**
-         * Applies the Jacobian to the given input vector and assigns
+         * Applies the Jacobian to the given @p input vector and assigns
          * the output to the @p result.
          */
         NOX::Abstract::Group::ReturnType
@@ -691,7 +691,7 @@ namespace TrilinosWrappers
 
       private:
         /**
-         * Reset state.
+         * Reset the state of this object.
          */
         void
         reset()
@@ -700,36 +700,56 @@ namespace TrilinosWrappers
           is_valid_j = false;
         }
 
-        // internal vector for the current solution
+        /**
+         * An internal vector for the current solution.
+         */
         Vector<VectorType> x;
 
-        // internal vector for the residual
+        /**
+         * An internal vector for the residual.
+         */
         Vector<VectorType> f;
 
-        // internal vector for the solution gradient
+        /**
+         * An internal vector for the solution gradient.
+         */
         Vector<VectorType> gradient;
 
-        // internal vector for the newton step
+        /**
+         * An internal vector for the newton step.
+         */
         Vector<VectorType> newton;
 
-        // helper function to compute residual
+        /**
+         * A helper function to compute residual.
+         */
         std::function<int(const VectorType &x, VectorType &f)> residual;
 
-        // helper function to setup Jacobian
+        /**
+         * A helper function to setup Jacobian.
+         */
         std::function<int(const VectorType &x)> setup_jacobian;
 
-        // helper function to apply Jacobian
+        /**
+         * A helper function to apply Jacobian.
+         */
         std::function<int(const VectorType &x, VectorType &v)> apply_jacobian;
 
-        // helper function to solve jacobian
+        /**
+         * A helper function to solve Jacobian.
+         */
         std::function<
           int(const VectorType &f, VectorType &x, const double tolerance)>
           solve_with_jacobian;
 
-        // internal state (is residual computed?)
+        /**
+         * A flag that indicates if the has residual been computed.
+         */
         bool is_valid_f;
 
-        // internal state (is Jacobian computed?)
+        /**
+         * A flag that indicates if the Jacobian has been computed.
+         */
         bool is_valid_j;
       };
 

diff --git a/source/trilinos/nox.cc b/source/trilinos/nox.cc
@@ -17,20 +17,20 @@
 
 #include <deal.II/base/config.h>
 
-#include <deal.II/lac/block_vector.h>
-#include <deal.II/lac/la_parallel_block_vector.h>
-#include <deal.II/lac/la_parallel_vector.h>
-#include <deal.II/lac/la_vector.h>
-#include <deal.II/lac/petsc_block_vector.h>
-#include <deal.II/lac/petsc_vector.h>
-#include <deal.II/lac/trilinos_parallel_block_vector.h>
-#include <deal.II/lac/trilinos_vector.h>
-#include <deal.II/lac/vector_memory.h>
-
-#include <deal.II/trilinos/nox.templates.h>
-
 #ifdef DEAL_II_TRILINOS_WITH_NOX
 
+#  include <deal.II/lac/block_vector.h>
+#  include <deal.II/lac/la_parallel_block_vector.h>
+#  include <deal.II/lac/la_parallel_vector.h>
+#  include <deal.II/lac/la_vector.h>
+#  include <deal.II/lac/petsc_block_vector.h>
+#  include <deal.II/lac/petsc_vector.h>
+#  include <deal.II/lac/trilinos_parallel_block_vector.h>
+#  include <deal.II/lac/trilinos_vector.h>
+#  include <deal.II/lac/vector_memory.h>
+
+#  include <deal.II/trilinos/nox.templates.h>
+
 DEAL_II_NAMESPACE_OPEN
 
 namespace TrilinosWrappers

diff --git a/...s/nox_solver_01.with_trilinos=true.output → ...ver_01.with_trilinos_with_nox=true.output b/...s/nox_solver_01.with_trilinos=true.output → ...ver_01.with_trilinos_with_nox=true.output