.cvsignore

-Makefile
-Makefile.in
-config.*
-configure
-aclocal.m4
-autom4te.cache
-depcomp
-install-sh
-missing
-mkinstalldirs
-libtool
-dune.pc
-semantic.cache
-stamp-h1
-html
-.deps
-.libs

.git-blame-ignore-revs

+# First use of uncrustify, with the vanilla config from dune-project.org
+d13f34469065230dd86e63733e4dc8d1f775acfb
+
+# Cleanup after having moved everything into the Dune::GFE namespace
+c2eb8dacb5885363c30c2b7373c479ed9c66ac12

.gitignore

+# ignore all build folders
+/build*/
+# ignore backup files
+*~
+# ignore Python files
+*.pyc

.gitlab-ci.yml

+---
+variables:
+  DUNECI_CMAKE_FLAGS: "-DDUNE_PYTHON_FORCE_PYTHON3=TRUE"
+
+before_script: &before
+  - duneci-install-module https://gitlab.dune-project.org/fufem/dune-matrix-vector.git
+  - duneci-install-module https://git.imp.fu-berlin.de/agnumpde/dune-solvers.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-vtk.git
+  - duneci-install-module https://gitlab.dune-project.org/fufem/dune-fufem.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-gmsh4
+
+#  Tests with the 2.9 release.  That's the one in Debian bookworm
+#--------------------------------------------------------------------
+dune:2.9 gcc:
+  variables:
+    DUNECI_BRANCH: releases/2.9
+  image: registry.dune-project.org/docker/ci/dune:2.9-debian-11-gcc-10-20
+  before_script:
+  - *before
+  script: duneci-standard-test
+
+dune:2.9 dune-elasticity gcc:
+  variables:
+    DUNECI_BRANCH: releases/2.9
+  image: registry.dune-project.org/docker/ci/dune:2.9-debian-11-gcc-10-20
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab.mn.tu-dresden.de/ag-sander/dune/dune-elasticity.git
+  script: duneci-standard-test
+
+#  Tests with the 2.10 release.  That's the one in Debian trixie
+#--------------------------------------------------------------------
+dune:2.10 gcc-10:
+  image: registry.dune-project.org/docker/ci/dune:2.10-debian-11-gcc-10-20
+  variables:
+    DUNECI_BRANCH: releases/2.10
+  before_script:
+  - *before
+  script: duneci-standard-test
+
+dune:2.10 dune-elasticity gcc-10:
+  image: registry.dune-project.org/docker/ci/dune:2.10-debian-11-gcc-10-20
+  variables:
+    DUNECI_BRANCH: releases/2.10
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab.mn.tu-dresden.de/ag-sander/dune/dune-elasticity.git
+  script: duneci-standard-test
+
+dune:2.10 dune-curvedgrid dune-foamgrid gcc-10 C++20:
+  image: registry.dune-project.org/docker/ci/dune:2.10-debian-11-gcc-10-20
+  variables:
+    DUNECI_BRANCH: releases/2.10
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgeometry.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgrid.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-foamgrid.git
+  script: duneci-standard-test
+
+dune:2.10 dune-parmg dune-curvedgrid dune-foamgrid dune-elasticity gcc-10 C++20:
+  image: registry.dune-project.org/docker/ci/dune:2.10-debian-11-gcc-10-20
+  variables:
+    DUNECI_BRANCH: releases/2.10
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.mn.tu-dresden.de/paraphase/dune-parmg.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgeometry.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgrid.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-foamgrid.git
+  - duneci-install-module https://gitlab.mn.tu-dresden.de/ag-sander/dune/dune-elasticity.git
+  script: duneci-standard-test
+
+# Full tests again, but this time with clang.
+dune:2.10 dune-parmg dune-curvedgrid dune-foamgrid dune-elasticity clang-11 C++20:
+  image: registry.dune-project.org/docker/ci/dune:2.10-debian-11-clang-11-20
+  variables:
+    DUNECI_BRANCH: releases/2.10
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.mn.tu-dresden.de/paraphase/dune-parmg.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgeometry.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgrid.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-foamgrid.git
+  - duneci-install-module https://gitlab.mn.tu-dresden.de/ag-sander/dune/dune-elasticity.git
+  script: duneci-standard-test
+
+
+#  Tests with the git master branch
+#  Some, but not all optional dependencies are made available.
+#------------------------------------------------------------------
+dune:git gcc-10 C++20:
+  image: registry.dune-project.org/docker/ci/dune:git-debian-11-gcc-10-20
+  before_script:
+  - *before
+  script: duneci-standard-test
+
+dune:git clang-11 C++20:
+  image: registry.dune-project.org/docker/ci/dune:git-debian-11-clang-11-20
+  before_script:
+  - *before
+  script: duneci-standard-test
+
+dune:git dune-elasticity gcc-10 C++20:
+  image: registry.dune-project.org/docker/ci/dune:git-debian-11-gcc-10-20
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab.mn.tu-dresden.de/ag-sander/dune/dune-elasticity.git
+  script: duneci-standard-test
+
+dune:git dune-curvedgrid dune-foamgrid gcc-10 C++20:
+  image: registry.dune-project.org/docker/ci/dune:git-debian-11-gcc-10-20
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgeometry.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgrid.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-foamgrid.git
+  script: duneci-standard-test
+
+#  Tests with all optional dependencies
+#-------------------------------------------
+dune:git dune-parmg dune-curvedgrid dune-foamgrid dune-elasticity gcc-10 C++20:
+  image: registry.dune-project.org/docker/ci/dune:git-debian-11-gcc-10-20
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.mn.tu-dresden.de/paraphase/dune-parmg.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgeometry.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgrid.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-foamgrid.git
+  - duneci-install-module https://gitlab.mn.tu-dresden.de/ag-sander/dune/dune-elasticity.git
+  script: duneci-standard-test
+
+dune:git dune-parmg dune-curvedgrid dune-foamgrid dune-elasticity clang-11 C++20:
+  image: registry.dune-project.org/docker/ci/dune:git-debian-11-clang-11-20
+  before_script:
+  - *before
+  - duneci-install-module https://gitlab-ci-token:${CI_JOB_TOKEN}@gitlab.mn.tu-dresden.de/paraphase/dune-parmg.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgeometry.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-curvedgrid.git
+  - duneci-install-module https://gitlab.dune-project.org/extensions/dune-foamgrid.git
+  - duneci-install-module https://gitlab.mn.tu-dresden.de/ag-sander/dune/dune-elasticity.git
+  script: duneci-standard-test
+
+# Check for spelling mistakes in text
+code-spelling-check:
+  stage: .pre
+  # Avoid the global 'before_script'
+  before_script: ""
+  image: registry.dune-project.org/docker/ci/debian:11
+  script:
+  - codespell
+    --ignore-words-list numer
+
+# Verify code-formatting rules
+code-formatting-check:
+  stage: .pre
+  # Avoid the global 'before_script'
+  before_script: ""
+  image: registry.dune-project.org/docker/ci/debian:11
+  script:
+    # Format all *.cc and *.hh files using the uncrustify tool
+    # We ignore the return value of 'uncrustify', because it is
+    # apparently unreliable, and returns 'failure' without a reason.
+    - uncrustify -l CPP -c dune-uncrustify.cfg --no-backup `find -name "*.cc" -o -name "*.hh"` || true
+
+    # Did anything change?  That would indicate a violation of the formatting rules
+    # But before, work around an issue where git doesn't recognize the source tree as a git directory.
+    # See https://forum.gitlab.com/t/ci-cd-job-git-diff/76666
+    - git config --global --add safe.directory "$(pwd)"
+    - git diff --exit-code

CHANGELOG.md

+# Master
+
+- The `SimoFoxEnergy` class (formerly known as `SimoFoxEnergyLocalStiffness`)
+  does not accept a surface load density anymore. Use the
+  `NeumannEnergy` class for assembling surface loads.
+
+- The class `LocalIntegralEnergy` now does not construct the local interpolation
+  rule itself anymore.  Rather, it expects to be given one in its constructor.
+  This will allow interpolation rules with state.
+  
+- The same holds for `CosseratRodEnergy`.  Unfortunately, that move
+  implies that `CosseratRodEnergy` gains an extra template argument
+  which specifies the GFE function used to implement the reference
+  configuration.
+
+- The classes `LocalGeodesicFEFunction` and `LocalProjectedFEFunction`
+  now take a `dune-functions` basis as their first arguments, instead
+  of a `LocalFiniteElement`. In addition, they need to be given an object
+  of this type in the constructor.  This is the basis to be used for
+  interpolation weights (for `LocalGeodesicFEFunction`) and for
+  interpolating in the embedding space (for `LocalProjectedFEFunction`).
+
+- The entire code is now in the `Dune::GFE` namespace.
+
+- Remove the files `localgfetestfunctionbasis.hh` and `localtangentfefunction.hh`.
+  They were never used for anything at all, I and currently wouldn't know
+  what to use them for, either.
+
+- All implementations of functions have been move to a `functions` subdirectory.
+
+- The `LocalDensity` class now has a template parameter `ElementOrIntersection`,
+  which replaces the parameter `Position`.  As the name says, this parameter
+  has to be a grid element, or a grid intersection.  As it turned out,
+  just depending on the position type of the integration domain was not enough.
+
+- The `LocalDensity` class now has a `bind` method, which binds the density
+  to a given element or intersection. This is necessary, for example, to in turn
+  bind coefficient functions that the density may own.
+
+# Release 2.10 (2024-12-29)
+
+- The module `dune-elasticity` has been downgraded from a required
+  dependency to an optional dependency.  It is currently only needed
+  by the `film-on-substrate.cc` program.
+
+- `cosserat-rod.cc` (formerly `rod3d.cc`) now reads the reference configuration
+  and the initial iterate from the Python file.
+
+- The file `rod3d.cc` has been renamed to `cosserat-rod.cc`,
+  to better reflect what it does.
+
+- In the `BulkCosseratDensity` class: Make the type of curvature
+  tensor controllable at run-time (previously, ugly preprocessor switches
+  where used).  Among its parameters `BulkCosseratDensity` now expects
+  a string `curvatureType`, which has to take one of the values `norm`,
+  `curl`, or `wryness`.
+
+- Building `dune-gfe` now requires Dune 2.9 or newer. Older configurations
+  have not gotten CI-tested for quite a while, anyway.
+
+- The `RigidBodyMotion` class has been removed.  Please use
+  `ProductManifold<RealTuple,Rotation>` from now on.
+
+- You can use `std::tuple_element` and `std::tuple_size` with
+  `ProductManifold`s now.
+
+- Building the module requires CMake version 3.16 now, to be in line
+  with the current core modules.
+
+- All files that implement densities have been put into the
+  `densities` subdirectory.
+
+- All files that implement assemblers have been moved to the
+  `assemblers` subdirectory.
+  
+- All files that implement target spaces have been moved to the
+  `spaces` subdirectory.
+
+- The file `periodic1dpq1nodalbasis.hh` has been removed.  Use `periodicbasis.hh`
+  from the `dune-functions` module in the future.
+
+- Replaced the class `GlobalGeodesicFEFunction` by a new one called
+  `GlobalGFEFunction`.  There are two important changes:  First of all,
+  the new class implements the `dune-functions` interface rather than
+  the deprecated one based on inheritance from `VirtualGridViewFunction`.
+  Secondly, the new class does not hard-wire geodesic interpolation
+  anymore.  Rather, you can give it interpolation classes which then
+  govern how interpolation is done.
+
+- Added dune-gmsh4 as a dependency
+- Build cosserat-continuum for different combinations of LFE-orders and
+  GFE-orders, the respective program is called
+  cosserat-continuum-Xd-in-Xd-LFE_ORDER-GFE_ORDER
+  TODO: This is now set during compile time, but shall be changed to be
+  set during runtime.
+
+- Do not scale the density functions  with the thickness to avoid confusion
+  since some densities need to be scaled and some do not need to be scaled
+  with the thickness depending on the dimension of the grid, their direction
+  and their kind (Neumann or volume load).
+
+- Fix bug in the `RealTuple::log` method: Calling `log(a,b)`returned `a-b`
+  instead of `b-a`.
+
+- Fix the return value of `ProductManifold::log`: It was `TangentVector`,
+  but now it is `EmbeddedTangentVector`.
+
+- The `RigidBodyMotion` class has a `log` method now.
+
+- The method `Rotation<3>::log` now returns an `EmbeddedTangentVector`
+  instead of a `SkewMatrix`.  This is consistent with the other manifold
+  implementations.
+
+- Deprecate the method `RigidBodyMotion::difference`; the method
+  `RigidBodyMotion::log`.  Watch out: The `difference` method was buggy!
+  See https://gitlab.mn.tu-dresden.de/osander/dune-gfe/-/merge_requests/2
+  for details.

CMakeLists.txt

+cmake_minimum_required(VERSION 3.16)
+project(dune-gfe CXX)
+
+if(NOT (dune-common_DIR OR dune-common_ROOT OR
+      "${CMAKE_PREFIX_PATH}" MATCHES ".*dune-common.*"))
+    string(REPLACE  ${CMAKE_PROJECT_NAME} dune-common dune-common_DIR
+      ${PROJECT_BINARY_DIR})
+endif()
+
+#find dune-common and set the module path
+find_package(dune-common REQUIRED)
+list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/cmake/modules"
+  ${dune-common_MODULE_PATH})
+
+#include the dune macros
+include(DuneMacros)
+
+# start a dune project with information from dune.module
+dune_project()
+
+# Create a module library
+if(dune-common_VERSION VERSION_GREATER_EQUAL 2.9.0)
+  dune_add_library(dunegfe INTERFACE EXPORT_NAME GFE NAMESPACE Dune::
+    LINK_LIBRARIES ${DUNE_LIBS})
+endif()
+
+dune_enable_all_packages()
+add_subdirectory("src")
+add_subdirectory("dune")
+add_subdirectory("doc")
+add_subdirectory("cmake/modules")
+add_subdirectory("test")
+
+# finalize the dune project, e.g. generating config.h etc.
+if(dune-common_VERSION VERSION_GREATER_EQUAL 2.10.0)
+    finalize_dune_project()
+else()
+    finalize_dune_project(GENERATE_CONFIG_H_CMAKE)
+endif()

Makefile.am

-# $Id$
-
-# we need the module file to be able to build via dunecontrol
-EXTRA_DIST=dune.module
-
-SUBDIRS = m4 src test
-
-# possible options
-LDADD = $(IPOPT_LDFLAGS) $(IPOPT_LIBS)
-AM_CPPFLAGS += $(IPOPT_CPPFLAGS)
-
-noinst_PROGRAMS = rodobstacle rod3d harmonicmaps harmonicmaps-eoc dirneucoupling rod-eoc 
-
-rodobstacle_SOURCES = rodobstacle.cc
-rod3d_SOURCES = rod3d.cc
-
-rod_eoc_SOURCES = rod-eoc.cc
-
-harmonicmaps_SOURCES = harmonicmaps.cc
-harmonicmaps_CXXFLAGS = $(UG_CPPFLAGS) $(AMIRAMESH_CPPFLAGS) $(IPOPT_CPPFLAGS) $(PSURFACE_CPPFLAGS)
-harmonicmaps_LDADD    = $(UG_LDFLAGS) $(AMIRAMESH_LDFLAGS) $(UG_LIBS) $(AMIRAMESH_LIBS) \
-                          $(IPOPT_LDFLAGS) $(IPOPT_LIBS) $(PSURFACE_LDFLAGS) $(PSURFACE_LIBS)
-
-harmonicmaps_eoc_SOURCES = harmonicmaps-eoc.cc
-harmonicmaps_eoc_CXXFLAGS = $(UG_CPPFLAGS) $(AMIRAMESH_CPPFLAGS) $(IPOPT_CPPFLAGS) $(PSURFACE_CPPFLAGS)
-harmonicmaps_eoc_LDADD    = $(UG_LDFLAGS) $(AMIRAMESH_LDFLAGS) $(UG_LIBS) $(AMIRAMESH_LIBS) \
-                          $(IPOPT_LDFLAGS) $(IPOPT_LIBS) $(PSURFACE_LDFLAGS) $(PSURFACE_LIBS)
-
-dirneucoupling_SOURCES  = dirneucoupling.cc
-dirneucoupling_CXXFLAGS = $(UG_CPPFLAGS) $(AMIRAMESH_CPPFLAGS) $(IPOPT_CPPFLAGS) $(PSURFACE_CPPFLAGS)
-dirneucoupling_LDADD    = $(UG_LDFLAGS) $(AMIRAMESH_LDFLAGS) $(UG_LIBS) $(AMIRAMESH_LIBS) \
-                          $(IPOPT_LDFLAGS) $(IPOPT_LIBS) $(PSURFACE_LDFLAGS) $(PSURFACE_LIBS)
-
-# don't follow the full GNU-standard
-# we need automake 1.5
-AUTOMAKE_OPTIONS = foreign 1.5
-
-include $(top_srcdir)/am/global-rules
-include $(top_srcdir)/am/top-rules

README

-Preparing the Sources
-=========================
-
-Additional to the software mentioned in README you'll need the
-following programs installed on your system:
-
-  automake >= 1.5
-
-  autoconf >= 2.50
-
-  libtool
-
-Getting started
----------------
-
-If these preliminaries are met, you should run the script
-
-  ./autogen.sh
-
-which calls the GNU autoconf/automake to create a ./configure-script
-and the Makefiles. Most probably you'll have to provide where to find
-the DUNE-files by
-
-   ./autogen.sh --with-dune=PATH
-
-where PATH is a directory with a dune/-subdirectory inside (this
-convention is needed to keep the #include-syntax consistent even when
-the headers are installed into /usr/include/dune later).
-
-
-Passing options to ./configure
-------------------------------
-
-autogen.sh also calls the newly created configure-script to
-conveniently pass on options about the used compiler. Thus you'll have
-to provide autogen.sh any options you want configure to get, e.g.
-
-  ./autogen.sh --with-dune=... --with-albert=... --without-x
-
-
-Choosing the compiler and the options
--------------------------------------
-
-The selection of the compiler works as follows: if --gnu or --intel is
-passed to autogen it reads the content of gcc.opts or icc.opts to get
-the default compiler flags. With the option --optim you can switch the
-compiler-specific optimization parameters on.
-
-If you want to change the compiler options to your favourites you can
-either
-
- - adapt the appropriate .opts-file and rerun autogen.sh. Please don't
-   commit this changed file to CVS if you're not sure if the options
-   work for everybody.
-
- - copy an existing .opts-file to a new name, change the options and
-   use
-
-      ./autogen.sh --opts=my.opts
-
-
-More info
----------
-
-See
-
-     ./autogen.sh --help
-   
-and (if it exists)
- 
-     ./configure --help
-
-for further options.
-
-
-The full build-system is described in the dune/doc/Buildsystem (not in
-duneapps/doc!)
-
-$Id$
-

README.md

+# dune-gfe
+
+This module contains implementations of various geometric finite element methods (GFE).
+
+
+## Automatic code formatting
+
+The GitLab CI system of this module (in the file `.gitlab-ci.yml`) includes a job
+that checks for proper code formatting.   The CI system
+uses the tool [uncrustify](https://github.com/uncrustify/uncrustify) to enforce the rules, guided by
+the configuration file `dune-uncrustify.cfg` in the `dune-gfe` module source directory.
+
+CI testing of the code formatting means that any merge request will fail CI
+testing if it introduces code changes that violate the formatting rules.
+To check locally whether code changes that you have made comply with the rules,
+run
+```
+uncrustify -l CPP -c dune-uncrustify.cfg --no-backup `find -name "*.cc" -o -name "*.hh"`
+```
+in your source directory.  If this does not modify the code, then your formatting
+is correct.
+
+When starting to use `uncrustify` to enforce proper code formatting, one large commit
+had to be made that applied large amounts of white-space changes to pretty much
+every source file.  If you are bothered by this when using `git blame`, you can
+tell `git` to ignore this particular commit by saying
+```
+git blame --ignore-revs-file=.git-blame-ignore-revs <file>
+```

cmake/modules/CMakeLists.txt

+set(modules "DuneGfeMacros.cmake")
+
+install(FILES ${modules} DESTINATION ${DUNE_INSTALL_MODULEDIR})

cmake/modules/DuneGfeMacros.cmake

+# File for module specific CMake tests.

config.h.cmake

+/* begin dune-gfe
+   put the definitions for config.h specific to
+   your project here. Everything above will be
+   overwritten
+*/
+
+/* begin private */
+/* Name of package */
+#define PACKAGE "@DUNE_MOD_NAME@"
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT "@DUNE_MAINTAINER@"
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME "@DUNE_MOD_NAME@"
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING "@DUNE_MOD_NAME@ @DUNE_MOD_VERSION@"
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME "@DUNE_MOD_NAME@"
+
+/* Define to the home page for this package. */
+#define PACKAGE_URL "@DUNE_MOD_URL@"
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION "@DUNE_MOD_VERSION@"
+
+/* end private */
+
+/* Define to the version of dune-gfe */
+#define DUNE_GFE_VERSION "@DUNE_GFE_VERSION@"
+
+/* Define to the major version of dune-gfe */
+#define DUNE_GFE_VERSION_MAJOR @DUNE_GFE_VERSION_MAJOR@
+
+/* Define to the minor version of dune-gfe */
+#define DUNE_GFE_VERSION_MINOR @DUNE_GFE_VERSION_MINOR@
+
+/* Define to the revision of dune-gfe */
+#define DUNE_GFE_VERSION_REVISION @DUNE_GFE_VERSION_REVISION@
+
+/* end dune-gfe
+   Everything below here will be overwritten
+*/

configure.ac

-#                                               -*- Autoconf -*-
-# Process this file with autoconf to produce a configure script.
-
-AC_PREREQ(2.50)
-DUNE_AC_INIT
-AM_INIT_AUTOMAKE
-AC_CONFIG_SRCDIR([rod3d.cc])
-AM_CONFIG_HEADER([config.h])
-
-DUNE_SYMLINK
-# we need no more than the standard DUNE-stuff
-DUNE_CHECK_ALL
-
-# implicitly set the Dune-flags everywhere
-AC_SUBST(AM_CPPFLAGS, $DUNE_CPPFLAGS)
-AC_SUBST(AM_LDFLAGS, $DUNE_LDFLAGS)
-LIBS="$DUNE_LIBS"
-
-AC_CONFIG_FILES([Makefile
-                 src/Makefile
-                 test/Makefile
-                 m4/Makefile
-                 rods.pc
-                ])
-AC_OUTPUT
-
-# finally print the summary information
-DUNE_SUMMARY_ALL

dirneu_testsuite/testsuite.sh

@@ -21,11 +21,29 @@ cat > "${PARAMETERFILE}" <<EOF
 # Number of grid levels
 numLevels = $2
 
+# Type of the domain decomposition algorithm
+# Currently supported:
+#  - FixedPointIteration
+#  - RichardsonIteration
+ddType = RichardsonIteration
+#ddType = FixedPointIteration
+
+# What is the preconditioner, if we are doing a Richardson iteration?
+# Possible values:
+#  - DirichletNeumann
+#  - NeumannDirichlet
+#  - NeumannNeumann
+#  - RobinRobin
+preconditioner = $4
+
+#
+NeumannNeumannDamping = 0.5 0.5
+
 # Tolerance of the Dirichlet-Neumann solver
 ddTolerance = 1e-9
 
 # Max number of Dirichlet-Neumann steps
-maxDirichletNeumannSteps = 30
+maxDirichletNeumannSteps = 100
 
 # Tolerance of the trust-region solver for the rod problem
 trTolerance = 1e-12
@@ -70,7 +88,7 @@ instrumented = 0
 #   Problem specifications
 ############################
 
-#path = /home/haile/sander/data/multicoupling/simplecoupling/
+#path = /home/sander/data/multicoupling/simplecoupling/
 #gridFile = hexarod.grid
 #dirichletNodes = hexarod.dn
 #dirichletValues = hexarod.nodv
@@ -92,26 +110,18 @@ instrumented = 0
 #E     = 1e6
 #nu    = 0.3
 
-#rodRestEndPoint0X = 0.125
-#rodRestEndPoint0Y = 0.125
-#rodRestEndPoint0Z = 1
-#rodRestEndPoint1X = 0.125
-#rodRestEndPoint1Y = 0.125
-#rodRestEndPoint1Z = 2
+#rodRestEndPoint0 = 0.125 0.125 1
+#rodRestEndPoint1 = 0.125 0.125 2
 
 ## Dirichlet values
-#dirichletValueX = 0.125
-#dirichletValueY = 0.125
-#dirichletValueZ = 2.5
+#dirichletValue = 0.125 0.125 2.5
 
-#dirichletAxisX = 0
-#dirichletAxisY = 0
-#dirichletAxisZ = 1
+#dirichletAxis = 0 0 1
 #dirichletAngle = 0
 
 
 ########################################################
-#path = /home/haile/sander/data/multicoupling/simplecoupling/
+#path = /home/sander/data/multicoupling/simplecoupling/
 #gridFile = cube_5x5x5.grid
 #dirichletNodes = cube_5x5x5.dn
 #dirichletValues = cube_5x5x5.nodv
@@ -123,25 +133,23 @@ instrumented = 0
 #rodA = 1
 
 # Geometric moments (here: square of edge length one)
-#rod J1 = 0.0833333
-#rod J2 = 0.0833333
+#rodJ1 = 0.0833333
+#rodJ2 = 0.0833333
 
 # Material parameters
 #rodE  = 2.5e5
 #rodNu = 0.3
+#E     = 1e6
+#nu    = 0.3
 
 ## Dirichlet values
-#dirichletValueX = 0.5
-#dirichletValueY = 1.5
-#dirichletValueZ = 10
+#dirichletValue = 0.5 1.5 10
 
-#dirichletAxisX = 0
-#dirichletAxisY = 0
-#dirichletAxisZ = 1
+#dirichletAxis = 0 0 1
 #dirichletAngle = 90
 
 ########################################################
-path = /home/haile/sander/data/multicoupling/simplecoupling/
+path = /home/sander/data/multicoupling/simplecoupling/
 gridFile = cube_4x4x4.grid
 dirichletNodes = cube_4x4x4.dn
 dirichletValues = cube_4x4x4.nodv
@@ -153,8 +161,10 @@ numRodBaseElements = 4
 rodA = 0.0625
 
 # Geometric moments (here: square of edge length 0.25)
-rodJ1 = 0.0013021
-rodJ2 = 0.0013021
+#rodJ1 = 0.0013021
+#rodJ2 = 0.0013021
+rodJ1 = 0.00032552
+rodJ2 = 0.00032552
 
 # Material parameters
 rodE  = 1e6
@@ -162,61 +172,106 @@ rodNu = 0.3
 E     = 1e6
 nu    = 0.3
 
-rodRestEndPoint0X = 0.625
-rodRestEndPoint0Y = 0.625
-rodRestEndPoint0Z = 1
-#rodRestEndPoint1X = 0.625
-#rodRestEndPoint1Y = 0.625
-#rodRestEndPoint1Z = 2
-rodRestEndPoint1X = 0.625
-rodRestEndPoint1Y = -0.082
-rodRestEndPoint1Z = 1.707
+rodRestEndPoint0 = 0.625 0.625 1
+rodRestEndPoint1 = 0.625 0.625 2
+#rodRestEndPoint1 = 0.625 -0.082 1.707
 
 # Dirichlet values
-dirichletValueX = 0.625
-dirichletValueY = 0.875
-dirichletValueZ = 2
+dirichletValue1 = 0.625 0.875 2.0
 
-dirichletAxisX = 0
-dirichletAxisY = 0
-dirichletAxisZ = 1
-dirichletAngle = 90
+dirichletAxis1 = 0 0 1
+dirichletAngle1 = 90
 
 # Where to write the results
 resultPath = $RESULTPATH
 
 EOF
 
+mkdir -p ${RESULTPATH}"/tmp_"$3
+
 # run simulation
 ../dirneucoupling ${PARAMETERFILE} | tee ${LOGFILE}
+
+rm -rf ${RESULTPATH}"/tmp_"$3
 }
 
 # Parameters:
 # 1: result directory
 # 2: number of levels
 # 3: damping factor
+# 4: preconditioner
 
 # run problems
 
+MAXPROCS=4
 
-for level in 4; do
+for level in 1; do
 #for level in 1 2 3 4; do
 
-    LEVELDIR=${level}"levels_rot"
     
-    if test -e ${LEVELDIR}/convrates; then
-        rm ${LEVELDIR}/convrates
-    fi
+#     if test -e ${LEVELDIR}/convrates; then
+#         rm ${LEVELDIR}/convrates
+#     fi
+    preconditioner=NeumannNeumann
+    LEVELDIR=${preconditioner}"_"${level}"levels"
+#  for damping in 0.1; do
+#    for damping in 0.1 0.6 0.9; do
+    for damping in 0.001 0.0025 0.005 0.0075 0.01 0.025 0.05 0.075 0.1 0.2 0.225 0.25 0.275 0.3 0.35 0.4 0.45; do
 
-    for damping in 0.6; do
-#    for damping in 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3; do
+        echo "Computing on "${level}" levels with damping factor "${damping}
+        runComputation $LEVELDIR $level $damping $preconditioner &
+
+        # Append convergence rate of this run to overall list for this level
+        #cat convrate >> ${LEVELDIR}/convrates
+
+        # Never have more than MAXPROCS processes
+        NPROC=$(($NPROC+1))  
+        if [ "$NPROC" -ge "$MAXPROCS" ]; then  
+          wait  
+          NPROC=0  
+        fi  
+
+    done
+
+
+
+    preconditioner=DirichletNeumann
+    LEVELDIR=${preconditioner}"_"${level}"levels"
+    for damping in 0.001 0.005 0.01 0.05 0.1 0.2 0.3 0.4 0.5 0.6 0.7 0.8 0.9 1.0 1.1 1.2 1.3 1.4 1.5; do
 
         echo "Computing on "${level}" levels with damping factor "${damping}
-        runComputation $LEVELDIR $level $damping
+        runComputation $LEVELDIR $level $damping $preconditioner &
 
         # Append convergence rate of this run to overall list for this level
         #cat convrate >> ${LEVELDIR}/convrates
 
+        # Never have more than MAXPROCS processes
+        NPROC=$(($NPROC+1))  
+        if [ "$NPROC" -ge "$MAXPROCS" ]; then  
+          wait  
+          NPROC=0  
+        fi  
+
+    done
+
+    preconditioner=NeumannDirichlet
+    LEVELDIR=${preconditioner}"_"${level}"levels"
+    #for damping in 0.115; do
+    for damping in 0.001 0.0025 0.005 0.0075 0.01 0.025 0.05 0.075 0.1 0.2 0.225 0.25 0.275 0.3 0.35 0.4 0.45; do
+
+        echo "Computing on "${level}" levels with damping factor "${damping}
+        runComputation $LEVELDIR $level $damping $preconditioner &
+
+        # Append convergence rate of this run to overall list for this level
+        #cat convrate >> ${LEVELDIR}/convrates
+
+        # Never have more than MAXPROCS processes
+        NPROC=$(($NPROC+1))  
+        if [ "$NPROC" -ge "$MAXPROCS" ]; then  
+          wait  
+          NPROC=0  
+        fi  
+
     done
 
 done
\ No newline at end of file

doc/CMakeLists.txt

+add_subdirectory("doxygen")
+add_subdirectory("manual")

doc/doxygen/CMakeLists.txt

+# shortcut for creating the Doxyfile.in and Doxyfile
+add_doxygen_target()

doc/doxygen/Doxylocal

+INPUT                  += @top_srcdir@/dune/gfe
+EXCLUDE                += 
+EXAMPLE_PATH           +=
+EXAMPLE_PATTERNS       +=
+IMAGE_PATH             +=
+PREDEFINED             += DOXYGEN 

doc/manual/.gitignore

+*.aux
+*.log
+*.gz
+*.toc
+*.out
+*.upa
+*.bcf
+*.run.xml
+*.bbl
+*.blg
+*.sublime-*
+*.tdo
+*.upb
+*.fdb_latexmk
+*.fls
+*.loc
+*.soc
+
+# Final documents
+dune-gfe-manual.pdf

doc/manual/CMakeLists.txt

+dune_add_latex_document(
+  SOURCE dune-gfe-manual.tex
+  FATHER_TARGET doc
+  BUILD_ON_INSTALL
+  INSTALL ${CMAKE_INSTALL_DOCDIR}/manual)