Merge branch 'master' into piola_matrix_free

.github/workflows/linux.yml

@@ -65,6 +65,7 @@ jobs:
             libp4est-dev \
             trilinos-all-dev \
             petsc-dev \
+            libcgal-dev \
             libmetis-dev \
             libhdf5-mpi-dev
     - name: info

cmake/configure/configure_cgal.cmake

@@ -0,0 +1,20 @@
+## ---------------------------------------------------------------------
+##
+## Copyright (C) 2022 by the deal.II authors
+##
+## This file is part of the deal.II library.
+##
+## The deal.II library is free software; you can use it, redistribute
+## it, and/or modify it under the terms of the GNU Lesser General
+## Public License as published by the Free Software Foundation; either
+## version 2.1 of the License, or (at your option) any later version.
+## The full text of the license can be found in the file LICENSE.md at
+## the top level directory of deal.II.
+##
+## ---------------------------------------------------------------------
+
+#
+# Configuration for the CGAL library:
+#
+
+CONFIGURE_FEATURE(CGAL)

cmake/modules/FindCGAL.cmake

@@ -0,0 +1,46 @@
+## ---------------------------------------------------------------------
+##
+## Copyright (C) 2022 by the deal.II authors
+##
+## This file is part of the deal.II library.
+##
+## The deal.II library is free software; you can use it, redistribute
+## it, and/or modify it under the terms of the GNU Lesser General
+## Public License as published by the Free Software Foundation; either
+## version 2.1 of the License, or (at your option) any later version.
+## The full text of the license can be found in the file LICENSE.md at
+## the top level directory of deal.II.
+##
+## ---------------------------------------------------------------------
+
+#
+# Try to find the CGAL libraries
+#
+# This module exports
+#   
+#   CGAL_INCLUDE_DIRS
+#
+
+SET(CGAL_DIR "" CACHE PATH "An optional hint to a CGAL installation")
+SET_IF_EMPTY(CGAL_DIR "$ENV{CGAL_DIR}")
+
+IF(NOT "${CGAL_DIR}" STREQUAL "")
+  SET(CGAL_DIR ${CGAL_DIR})
+ENDIF()
+
+IF(DEAL_II_HAVE_CXX17)
+  # temporarily disable ${CMAKE_SOURCE_DIR}/cmake/modules for module lookup
+  LIST(REMOVE_ITEM CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules/)
+  FIND_PACKAGE(CGAL)
+  LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules/)
+ELSE(DEAL_II_HAVE_CXX17)
+  SET(CGAL_FOUND FALSE)
+  SET(CGAL_INCLUDE_DIRS "-NOTFOUND")
+  MESSAGE(WARNING "CGAL wrappers require C++17. Disabling CGAL Support.")
+ENDIF(DEAL_II_HAVE_CXX17)
+
+DEAL_II_PACKAGE_HANDLE(CGAL
+  INCLUDE_DIRS REQUIRED CGAL_INCLUDE_DIRS
+  USER_INCLUDE_DIRS REQUIRED CGAL_INCLUDE_DIRS
+  CLEAR CGAL_INCLUDE_DIRS
+  )

doc/doxygen/options.dox.in

@@ -194,6 +194,7 @@ PREDEFINED             = DOXYGEN=1 \
                          DEAL_II_ARPACK_WITH_PARPACK=1 \
                          DEAL_II_WITH_ASSIMP=1 \
                          DEAL_II_WITH_BOOST=1 \
+                         DEAL_II_WITH_CGAL=1 \
                          DEAL_II_WITH_TASKFLOW=1 \
                          DEAL_II_WITH_COMPLEX_VALUES=1 \
                          DEAL_II_WITH_CUDA=1 \

doc/news/changes/major/20220426FederHeltai

@@ -0,0 +1,3 @@
+New: Added support for the CGAL library (www.cgal.org).
+<br>
+(Marco Feder, Luca Heltai, 2022/04/26)

doc/news/changes/minor/20220420PasqualeAfrica

@@ -0,0 +1,3 @@
+Added: New function enable_abort_on_exception.
+<br>
+(Pasquale Claudio Africa, 2022/04/20)

doc/news/changes/minor/20220426DanielSun

@@ -0,0 +1,5 @@
+Fixed: The building process now works well with MPI option on Windows system.
+If configured properly, we can explore the capability of distributed computing
+on Windows system within Deal.II framework.
+<br>
+(Daniel Sun, 2022/04/26)

doc/news/changes/minor/20220426Jean-PaulPelteret

@@ -0,0 +1,6 @@
+Improved: The step-44 tutorial now uses FE_DGP elements to discretize the
+pressure and dilatation fields, rather than FE_DGPMonomial. This improves
+the condition number of the linear system, necessitating fewer iterations
+to compute its iterative inverse.
+<br>
+(Jean-Paul Pelteret, 2022/04/26)

doc/readme.html

@@ -455,6 +455,32 @@ <h4>Optional interfaces to other software packages</h4>
             </p>
         </dd>
 
+        <dt><a name="CGAL" />
+            <a href="https://www.cgal.org/" target="_top">CGAL</a>
+        </dt>
+        <dd>
+            <p>
+                <a href="https://www.cgal.org/" target="_top">CGAL</a>
+                is a software project that provides easy access to
+                efficient and reliable geometric algorithms in the form of a C++
+                library. CGAL is used in various areas needing geometric
+                computation, such as geographic information systems, computer
+                aided design, molecular biology, medical imaging, computer
+                graphics, and robotics.
+
+                The library offers data structures and algorithms like
+                triangulations, Voronoi diagrams, Boolean operations on polygons
+                and polyhedra, point set processing, arrangements of curves,
+                surface and volume mesh generation, geometry processing, alpha
+                shapes, convex hull algorithms, shape reconstruction, AABB and
+                KD trees.
+
+                The CGAL Wrappers use c++17 features. In order to use CGAL, add
+                <code>-DCGAL_DIR=/path/to/cgal</code> to the deal.II CMake call,
+                and make sure that <code>DEAL_II_HAVE_CXX17</code> is enabled.
+            </p>
+        </dd>
+
 
         <dt><a name="CUDA"></a><a href="https://developer.nvidia.com/cuda-zone">CUDA</a></dt>
         <dd>

doc/users/cmake_dealii.html

@@ -456,6 +456,7 @@ <h3>Feature configuration</h3>
 DEAL_II_WITH_ARPACK
 DEAL_II_WITH_ASSIMP
 DEAL_II_WITH_BOOST
+DEAL_II_WITH_CGAL
 DEAL_II_WITH_COMPLEX_VALUES
 DEAL_II_WITH_CUDA
 DEAL_II_WITH_GINKGO

examples/step-44/step-44.cc

@@ -43,7 +43,7 @@
 #include <deal.II/grid/grid_in.h>
 #include <deal.II/grid/tria.h>
 
-#include <deal.II/fe/fe_dgp_monomial.h>
+#include <deal.II/fe/fe_dgp.h>
 #include <deal.II/fe/fe_q.h>
 #include <deal.II/fe/fe_system.h>
 #include <deal.II/fe/fe_tools.h>
@@ -1037,19 +1037,18 @@ namespace Step44
     // The Finite Element System is composed of dim continuous displacement
     // DOFs, and discontinuous pressure and dilatation DOFs. In an attempt to
     // satisfy the Babuska-Brezzi or LBB stability conditions (see Hughes
-    // (2000)), we setup a $Q_n \times DGPM_{n-1} \times DGPM_{n-1}$
-    // system. $Q_2 \times DGPM_1 \times DGPM_1$ elements satisfy this
-    // condition, while $Q_1 \times DGPM_0 \times DGPM_0$ elements do
+    // (2000)), we setup a $Q_n \times DGP_{n-1} \times DGP_{n-1}$
+    // system. $Q_2 \times DGP_1 \times DGP_1$ elements satisfy this
+    // condition, while $Q_1 \times DGP_0 \times DGP_0$ elements do
     // not. However, it has been shown that the latter demonstrate good
     // convergence characteristics nonetheless.
     fe(FE_Q<dim>(parameters.poly_degree),
        dim, // displacement
-       FE_DGPMonomial<dim>(parameters.poly_degree - 1),
+       FE_DGP<dim>(parameters.poly_degree - 1),
        1, // pressure
-       FE_DGPMonomial<dim>(parameters.poly_degree - 1),
-       1)
-    , // dilatation
-    dof_handler(triangulation)
+       FE_DGP<dim>(parameters.poly_degree - 1),
+       1) // dilatation
+    , dof_handler(triangulation)
     , dofs_per_cell(fe.n_dofs_per_cell())
     , u_fe(first_u_component)
     , p_fe(p_component)
@@ -1080,10 +1079,11 @@ namespace Step44
   // constraint $\widetilde{J}=1$ on the initial solution field. The constraint
   // corresponds to the determinant of the deformation gradient in the
   // undeformed configuration, which is the identity tensor. We use
-  // FE_DGPMonomial bases to interpolate the dilatation field, thus we can't
+  // FE_DGP bases to interpolate the dilatation field, thus we can't
   // simply set the corresponding dof to unity as they correspond to the
-  // monomial coefficients. Thus we use the VectorTools::project function to do
-  // the work for us. The VectorTools::project function requires an argument
+  // coefficients of a truncated Legendre polynomial.
+  // Thus we use the VectorTools::project function to do the work for us.
+  // The VectorTools::project function requires an argument
   // indicating the hanging node constraints. We have none in this program
   // So we have to create a constraint object. In its original state, constraint
   // objects are unsorted, and have to be sorted (using the

include/deal.II/base/config.h.in

@@ -39,6 +39,7 @@
 #cmakedefine DEAL_II_WITH_ARPACK
 #cmakedefine DEAL_II_WITH_ARBORX
 #cmakedefine DEAL_II_WITH_ASSIMP
+#cmakedefine DEAL_II_WITH_CGAL
 #cmakedefine DEAL_II_WITH_COMPLEX_VALUES
 #cmakedefine DEAL_II_WITH_CUDA
 #cmakedefine DEAL_II_WITH_GINKGO

include/deal.II/base/exceptions.h

@@ -1286,11 +1286,23 @@ namespace deal_II_exceptions
    * still call abort(), e.g. when an exception is caught during exception
    * handling.
    *
+   * @see enable_abort_on_exception
    * @see Exceptions
    */
   void
   disable_abort_on_exception();
 
+  /**
+   * Calling this function switches on the use of <tt>std::abort()</tt> when
+   * an exception is created using the Assert() macro, instead of throwing it.
+   * This restores the standard behavior.
+   *
+   * @see disable_abort_on_exception
+   * @see Exceptions
+   */
+  void
+  enable_abort_on_exception();
+
   /**
    * The functions in this namespace are in connection with the Assert and
    * AssertThrow mechanism but are solely for internal purposes and are not

include/deal.II/base/numbers.h

@@ -142,7 +142,9 @@ DEAL_II_NAMESPACE_CLOSE
 // import the whole Sacado header at this point to get the math
 // functions imported into the standard namespace.
 #ifdef DEAL_II_TRILINOS_WITH_SACADO
+DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
 #  include <Sacado.hpp>
+DEAL_II_ENABLE_EXTRA_DIAGNOSTICS
 #endif
 
 namespace std

include/deal.II/base/time_stepping.h

@@ -767,6 +767,10 @@ namespace TimeStepping
      */
     struct Status : public TimeStepping<VectorType>::Status
     {
+      Status()
+        : method(invalid)
+      {}
+
       runge_kutta_method             method;
       embedded_runge_kutta_time_step exit_delta_t;
       unsigned int                   n_iterations;

include/deal.II/base/time_stepping.templates.h

@@ -27,6 +27,10 @@ DEAL_II_NAMESPACE_OPEN
 
 namespace TimeStepping
 {
+  DeclExceptionMsg(ExcNoMethodSelected,
+                   "No method selected. You need to call initialize or pass a "
+                   "runge_kutta_method to the constructor.");
+
   // ----------------------------------------------------------------------
   // RungeKutta
   // ----------------------------------------------------------------------
@@ -198,6 +202,8 @@ namespace TimeStepping
     double                                                             delta_t,
     VectorType &                                                       y)
   {
+    Assert(status.method != runge_kutta_method::invalid, ExcNoMethodSelected());
+
     std::vector<VectorType> f_stages(this->n_stages, y);
     // Compute the different stages needed.
     compute_stages(f, t, delta_t, y, f_stages);
@@ -390,6 +396,8 @@ namespace TimeStepping
     VectorType &                                                       vec_ri,
     VectorType &                                                       vec_ki)
   {
+    Assert(status.method != runge_kutta_method::invalid, ExcNoMethodSelected());
+
     compute_one_stage(f,
                       t,
                       this->b[0] * delta_t,
@@ -566,6 +574,8 @@ namespace TimeStepping
     double                                               delta_t,
     VectorType &                                         y)
   {
+    Assert(status.method != runge_kutta_method::invalid, ExcNoMethodSelected());
+
     VectorType              old_y(y);
     std::vector<VectorType> f_stages(this->n_stages, y);
     // Compute the different stages needed.
@@ -996,6 +1006,8 @@ namespace TimeStepping
     double                                                             delta_t,
     VectorType &                                                       y)
   {
+    Assert(status.method != runge_kutta_method::invalid, ExcNoMethodSelected());
+
     bool                    done       = false;
     unsigned int            count      = 0;
     double                  error_norm = 0.;

include/deal.II/base/utilities.h

@@ -28,6 +28,8 @@
 #include <utility>
 #include <vector>
 
+DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
+
 #ifdef DEAL_II_WITH_TRILINOS
 #  include <Epetra_Comm.h>
 #  include <Epetra_Map.h>
@@ -40,8 +42,6 @@
 #  endif
 #endif
 
-DEAL_II_DISABLE_EXTRA_DIAGNOSTICS
-
 #include <boost/archive/binary_iarchive.hpp>
 #include <boost/archive/binary_oarchive.hpp>
 #include <boost/core/demangle.hpp>