From 9e5dad4ee6c3d99963a563a165a0598c5897bcdc Mon Sep 17 00:00:00 2001
From: Lars von Wolff <lars.von-wolff@ians.uni-stuttgart.de>
Date: Fri, 28 Feb 2020 11:17:00 +0100
Subject: [PATCH] New Thinstrip code
---
.gitignore | 2 +
CMakeCache.txt | 1974 +++++++++++++++++
CMakeDoxyfile.in | 272 +++
DartConfiguration.tcl | 112 +
FC.h | 16 +
activate | 1 +
compile_commands.json | 317 +++
config.h | 800 +++++++
dune-phasefield.pc | 15 +
dune.module | 2 +-
dune/phasefield/base_parameters.hh | 70 +-
dune/phasefield/base_potentials.hh | 2 +-
dune/phasefield/boundary_fn.hh | 12 +-
dune/phasefield/chns_base.hh | 314 ++-
dune/phasefield/fff_chns.hh | 216 ++
dune/phasefield/ffs_chns_r.hh | 53 +
dune/phasefield/initial_fn.hh | 225 +-
.../localoperator/fem_2p_cahnhilliard.hh | 84 +
.../localoperator/fem_3p_cahnhilliard.hh | 95 +
.../phasefield/localoperator/fem_base_chns.hh | 59 +
.../fem_ffs_chns_navierstokes.hh | 35 +-
.../fem_ffs_chns_r_cahnhilliard.hh | 13 +-
language_tests/Fortran/CMakeCache.txt | 287 +++
language_tests/Fortran/CMakeLists.txt | 6 +
run-in-dune-env | 4 +
src/CMakeLists.txt | 7 +
src/dune-phasefield | Bin 0 -> 20272 bytes
src/example_cahnhilliard/2p_driver.hh | 202 ++
src/example_cahnhilliard/3p_driver.hh | 215 ++
src/example_cahnhilliard/CMakeLists.txt | 3 +
src/example_cahnhilliard/ch2p.ini | 1 +
src/example_cahnhilliard/ch2p_equation.cc | 165 ++
src/example_cahnhilliard/ch3p.ini | 1 +
src/example_cahnhilliard/ch3p_equation.cc | 151 ++
src/example_cahnhilliard/grids/periodic.dgf | 23 +
src/example_cahnhilliard/grids/xperiodic.dgf | 22 +
src/example_nucleus/3p_driver.hh | 224 ++
src/example_nucleus/CMakeLists.txt | 2 +
src/example_nucleus/chns.ini | 1 +
src/example_nucleus/nucleus_equation.cc | 139 ++
src/paper_epsdelta/3p_driver.hh | 222 ++
src/paper_epsdelta/CMakeLists.txt | 2 +
src/paper_epsdelta/chns.ini | 1 +
src/paper_epsdelta/epsdelta_equation.cc | 116 +
src/paper_thinstrip_full/3p_driver.hh | 225 ++
src/paper_thinstrip_full/CMakeLists.txt | 2 +
src/paper_thinstrip_full/chns.ini | 64 +
.../thinstrip_boundary.hh | 211 ++
.../thinstrip_equation.cc | 139 ++
.../thinstrip_full_chns_navierstokes.hh | 148 ++
.../thinstrip_full_chns_r_cahnhilliard.hh | 132 ++
.../thinstrip_parameters.hh | 48 +
src/rectangle_periodic.geo | 2 +-
src/test_contactpointdynamics/3p_driver.hh | 40 +-
src/test_hainesjump/3p_driver.hh | 222 ++
src/test_hainesjump/CMakeLists.txt | 2 +
src/test_hainesjump/chns.ini | 1 +
src/test_hainesjump/h_equation.cc | 116 +
src/test_periodic/3p_driver.hh | 279 +++
src/test_periodic/CMakeLists.txt | 2 +
src/test_periodic/chns.ini | 1 +
src/test_periodic/grids/periodic.dgf | 23 +
src/test_periodic/grids/xperiodic.dgf | 22 +
src/test_periodic/p_equation.cc | 141 ++
src/test_slipvelocity/3p_driver.hh | 222 ++
src/test_slipvelocity/CMakeLists.txt | 2 +
src/test_slipvelocity/chns.ini | 1 +
src/test_slipvelocity/s_equation.cc | 116 +
68 files changed, 8581 insertions(+), 63 deletions(-)
create mode 100644 CMakeCache.txt
create mode 100644 CMakeDoxyfile.in
create mode 100644 DartConfiguration.tcl
create mode 100644 FC.h
create mode 120000 activate
create mode 100644 compile_commands.json
create mode 100644 config.h
create mode 100644 dune-phasefield.pc
create mode 100644 dune/phasefield/fff_chns.hh
create mode 100644 dune/phasefield/localoperator/fem_2p_cahnhilliard.hh
create mode 100644 dune/phasefield/localoperator/fem_3p_cahnhilliard.hh
create mode 100644 language_tests/Fortran/CMakeCache.txt
create mode 100644 language_tests/Fortran/CMakeLists.txt
create mode 100755 run-in-dune-env
create mode 100755 src/dune-phasefield
create mode 100644 src/example_cahnhilliard/2p_driver.hh
create mode 100644 src/example_cahnhilliard/3p_driver.hh
create mode 100644 src/example_cahnhilliard/CMakeLists.txt
create mode 120000 src/example_cahnhilliard/ch2p.ini
create mode 100644 src/example_cahnhilliard/ch2p_equation.cc
create mode 120000 src/example_cahnhilliard/ch3p.ini
create mode 100644 src/example_cahnhilliard/ch3p_equation.cc
create mode 100644 src/example_cahnhilliard/grids/periodic.dgf
create mode 100644 src/example_cahnhilliard/grids/xperiodic.dgf
create mode 100644 src/example_nucleus/3p_driver.hh
create mode 100644 src/example_nucleus/CMakeLists.txt
create mode 120000 src/example_nucleus/chns.ini
create mode 100644 src/example_nucleus/nucleus_equation.cc
create mode 100644 src/paper_epsdelta/3p_driver.hh
create mode 100644 src/paper_epsdelta/CMakeLists.txt
create mode 120000 src/paper_epsdelta/chns.ini
create mode 100644 src/paper_epsdelta/epsdelta_equation.cc
create mode 100644 src/paper_thinstrip_full/3p_driver.hh
create mode 100644 src/paper_thinstrip_full/CMakeLists.txt
create mode 100644 src/paper_thinstrip_full/chns.ini
create mode 100644 src/paper_thinstrip_full/thinstrip_boundary.hh
create mode 100644 src/paper_thinstrip_full/thinstrip_equation.cc
create mode 100644 src/paper_thinstrip_full/thinstrip_full_chns_navierstokes.hh
create mode 100644 src/paper_thinstrip_full/thinstrip_full_chns_r_cahnhilliard.hh
create mode 100644 src/paper_thinstrip_full/thinstrip_parameters.hh
create mode 100644 src/test_hainesjump/3p_driver.hh
create mode 100644 src/test_hainesjump/CMakeLists.txt
create mode 120000 src/test_hainesjump/chns.ini
create mode 100644 src/test_hainesjump/h_equation.cc
create mode 100644 src/test_periodic/3p_driver.hh
create mode 100644 src/test_periodic/CMakeLists.txt
create mode 120000 src/test_periodic/chns.ini
create mode 100644 src/test_periodic/grids/periodic.dgf
create mode 100644 src/test_periodic/grids/xperiodic.dgf
create mode 100644 src/test_periodic/p_equation.cc
create mode 100644 src/test_slipvelocity/3p_driver.hh
create mode 100644 src/test_slipvelocity/CMakeLists.txt
create mode 120000 src/test_slipvelocity/chns.ini
create mode 100644 src/test_slipvelocity/s_equation.cc
diff --git a/.gitignore b/.gitignore
index 359a103..0bfc383 100644
--- a/.gitignore
+++ b/.gitignore
@@ -249,6 +249,8 @@ TSWLatexianTemp*
#cmake files
cmake/
CMakeFiles/
+*.cmake
+*Makefile
# directory files
*.directory
diff --git a/CMakeCache.txt b/CMakeCache.txt
new file mode 100644
index 0000000..78aa25e
--- /dev/null
+++ b/CMakeCache.txt
@@ -0,0 +1,1974 @@
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+# If you do not want to change any of the values, simply exit the editor.
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+
+//Path to a library.
+COLAMD_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libcolamd.so
+
+//Path to convert program
+CONVERT:FILEPATH=/usr/bin/convert
+
+//Path to the coverage program that CTest uses for performing coverage
+// inspection
+COVERAGE_COMMAND:FILEPATH=/usr/bin/gcov
+
+//Extra command line flags to pass to the coverage tool
+COVERAGE_EXTRA_FLAGS:STRING=-l
+
+//Path to a program.
+CP:FILEPATH=/bin/cp
+
+//Enable to build Debian packages
+CPACK_BINARY_DEB:BOOL=OFF
+
+//Enable to build IFW packages
+CPACK_BINARY_IFW:BOOL=OFF
+
+//Enable to build NSIS packages
+CPACK_BINARY_NSIS:BOOL=OFF
+
+//Enable to build RPM packages
+CPACK_BINARY_RPM:BOOL=OFF
+
+//Enable to build STGZ packages
+CPACK_BINARY_STGZ:BOOL=ON
+
+//Enable to build TBZ2 packages
+CPACK_BINARY_TBZ2:BOOL=OFF
+
+//Enable to build TGZ packages
+CPACK_BINARY_TGZ:BOOL=ON
+
+//Enable to build TXZ packages
+CPACK_BINARY_TXZ:BOOL=OFF
+
+//Enable to build TZ packages
+CPACK_BINARY_TZ:BOOL=ON
+
+//Enable to build RPM source packages
+CPACK_SOURCE_RPM:BOOL=OFF
+
+//Enable to build TBZ2 source packages
+CPACK_SOURCE_TBZ2:BOOL=ON
+
+//Enable to build TGZ source packages
+CPACK_SOURCE_TGZ:BOOL=ON
+
+//Enable to build TXZ source packages
+CPACK_SOURCE_TXZ:BOOL=ON
+
+//Enable to build TZ source packages
+CPACK_SOURCE_TZ:BOOL=ON
+
+//Enable to build ZIP source packages
+CPACK_SOURCE_ZIP:BOOL=OFF
+
+//How many times to retry timed-out CTest submissions.
+CTEST_SUBMIT_RETRY_COUNT:STRING=3
+
+//How long to wait between timed-out CTest submissions.
+CTEST_SUBMIT_RETRY_DELAY:STRING=5
+
+//Path to a program.
+CVSCOMMAND:FILEPATH=/usr/bin/cvs
+
+//Options passed to the cvs update command.
+CVS_UPDATE_OPTIONS:STRING=-d -A -P
+
+//highest version of the C++ standard to enable. This version is
+// also used if the version check is disabled
+CXX_MAX_STANDARD:STRING=17
+
+//Path to a program.
+ClangFormat_EXECUTABLE:FILEPATH=/usr/bin/clang-format
+
+//Path to a program.
+ClangTidy_EXECUTABLE:FILEPATH=ClangTidy_EXECUTABLE-NOTFOUND
+
+//Maximum time allowed before CTest will kill the test.
+DART_TESTING_TIMEOUT:STRING=1500
+
+//Path to a file.
+DLMALLOC_INCLUDE_DIR:PATH=DLMALLOC_INCLUDE_DIR-NOTFOUND
+
+//Path list to search for DLMALLOC
+DLMALLOC_ROOT:PATH=
+
+//Dot tool for use with Doxygen
+DOXYGEN_DOT_EXECUTABLE:FILEPATH=/usr/bin/dot
+
+//Doxygen documentation generation tool (http://www.doxygen.org)
+DOXYGEN_EXECUTABLE:FILEPATH=/usr/bin/doxygen
+
+//120
+DS_MAX_MIC_THREADS:STRING=
+
+//If set to ON, shared and static libs will be built
+DUNE_BUILD_BOTH_LIBS:BOOL=OFF
+
+//No help, variable specified on the command line.
+DUNE_BUILD_DIRECTORY_ROOT_PATH:UNINITIALIZED=/home/ians1/vonwolls/ssd_local/dumux/build-release/
+
+//No help, variable specified on the command line.
+DUNE_FORCE_PYTHON3:UNINITIALIZED=TRUE
+
+//Enable compilation and installation of extra utilities from the
+// "src" subdirectory.
+DUNE_GRID_EXTRA_UTILS:BOOL=
+
+//Grid selector definition added to config.h
+DUNE_GRID_GRIDTYPE_SELECTOR:BOOL=OFF
+
+//Installation directory for CMake modules. Default is ${CMAKE_INSTALL_DATAROOTDIR}/dune/cmake/modules
+// when not set explicitely
+DUNE_INSTALL_MODULEDIR:PATH=
+
+//Installation directory for libraries that are not architecture
+// dependent. Default is lib when not set explicitely
+DUNE_INSTALL_NONOBJECTLIBDIR:PATH=
+
+//Enable/Disable the backwards compatibility of the category enum/method
+// in dune-istl solvers, preconditioner, etc. '1'
+DUNE_ISTL_SUPPORT_OLD_CATEGORY_INTERFACE:BOOL=1
+
+//No help, variable specified on the command line.
+DUNE_PYTHON_ALLOW_GET_PIP:UNINITIALIZED=TRUE
+
+//Place Python virtualenv in top-level directory "dune-python-env"
+// when using an absolute build directory
+DUNE_PYTHON_EXTERNAL_VIRTUALENV_FOR_ABSOLUTE_BUILDDIR:BOOL=ON
+
+//No help, variable specified on the command line.
+DUNE_PYTHON_FORCE_PYTHON3:UNINITIALIZED=TRUE
+
+//Location of Python virtualenv created by the Dune build system
+DUNE_PYTHON_VIRTUALENV_PATH:PATH=/home/ians1/vonwolls/ssd_local/dumux/build-release/python_virtualenv
+
+//No help, variable specified on the command line.
+DUNE_PYTHON_VIRTUALENV_SETUP:UNINITIALIZED=TRUE
+
+//If set to ON, we will force static linkage everywhere
+DUNE_USE_ONLY_STATIC_LIBS:BOOL=OFF
+
+//Path to a program.
+DVIPDF_CONVERTER:FILEPATH=/usr/bin/dvipdfm
+
+//Path to a program.
+DVIPS_CONVERTER:FILEPATH=/usr/bin/dvips
+
+//Flags passed to dvips.
+DVIPS_CONVERTER_FLAGS:STRING=-Ppdf -G0 -t letter
+
+//run N tests in parallel
+DXT_TEST_PROCS:STRING=1
+
+//per-test timeout in seconds
+DXT_TEST_TIMEOUT:STRING=180
+
+//Path to a file.
+EIGEN3_INCLUDE_DIR:PATH=/usr/include/eigen3
+
+//enable likwid performance monitoring API usage
+ENABLE_PERFMON:STRING=0
+
+//Path to a program.
+GITCOMMAND:FILEPATH=/usr/bin/git
+
+//Path to a file.
+GMPXX_INCLUDE_DIR:PATH=/usr/include
+
+//GNU GMPXX library
+GMPXX_LIB:FILEPATH=/usr/lib/x86_64-linux-gnu/libgmpxx.so
+
+//GNU GMP library
+GMP_LIB:FILEPATH=/usr/lib/x86_64-linux-gnu/libgmp.so
+
+//Path to a program.
+GZIP:FILEPATH=/bin/gzip
+
+//Path to a program.
+HGCOMMAND:FILEPATH=/usr/bin/hg
+
+//Path to a program.
+HTLATEX_COMPILER:FILEPATH=/usr/bin/htlatex
+
+//Flags passed from htlatex to the LaTeX compiler.
+HTLATEX_COMPILER_LATEX_FLAGS:STRING=-interaction=batchmode -file-line-error
+
+//Options for the t4ht postprocessor.
+HTLATEX_COMPILER_T4HT_POSTPROCESSOR_FLAGS:STRING=
+
+//Options for the tex4ht.sty and *.4ht style files.
+HTLATEX_COMPILER_TEX4HT_FLAGS:STRING=html
+
+//Options for the text4ht postprocessor.
+HTLATEX_COMPILER_TEX4HT_POSTPROCESSOR_FLAGS:STRING=
+
+//Path to a program.
+IMAGEMAGICK_CONVERT:FILEPATH=/usr/bin/convert
+
+//Path to inkscape to generate png files from svg files
+INKSCAPE:FILEPATH=/usr/bin/inkscape
+
+//Path to a library.
+LAPACK_Accelerate_LIBRARY:FILEPATH=LAPACK_Accelerate_LIBRARY-NOTFOUND
+
+//Path to a library.
+LAPACK_goto2_LIBRARY:FILEPATH=LAPACK_goto2_LIBRARY-NOTFOUND
+
+//Path to a library.
+LAPACK_lapack_LIBRARY:FILEPATH=/usr/lib/liblapack.so
+
+//Path to a library.
+LAPACK_openblas_LIBRARY:FILEPATH=LAPACK_openblas_LIBRARY-NOTFOUND
+
+//Path to a library.
+LAPACK_vecLib_LIBRARY:FILEPATH=LAPACK_vecLib_LIBRARY-NOTFOUND
+
+//Path to a program.
+LATEX2HTML_CONVERTER:FILEPATH=LATEX2HTML_CONVERTER-NOTFOUND
+
+//Path to a file.
+LATEXMKRC_TEMPLATE:FILEPATH=/home/ians1/vonwolls/ssd_local/dumux/dune-common/cmake/modules/latexmkrc.cmake
+
+//Path to a program.
+LATEXMK_EXECUTABLE:FILEPATH=/usr/bin/latexmk
+
+//Path to a program.
+LATEX_COMPILER:FILEPATH=/usr/bin/latex
+
+//Flags passed to latex.
+LATEX_COMPILER_FLAGS:STRING=-interaction=batchmode -file-line-error
+
+//Choose the default type of LaTeX build. Valid options are pdf,
+// dvi, ps, safepdf, html
+LATEX_DEFAULT_BUILD:STRING=pdf
+
+//If non empty, specifies the location to place LaTeX output.
+LATEX_OUTPUT_PATH:PATH=
+
+//If on, the raster images will be converted to 1/6 the original
+// size. This is because papers usually require 600 dpi images
+// whereas most monitors only require at most 96 dpi. Thus, smaller
+// images make smaller files for web distribution and can make
+// it faster to read dvi files.
+LATEX_SMALL_IMAGES:BOOL=OFF
+
+//latex/pdflatex flags used to create synctex file.
+LATEX_SYNCTEX_FLAGS:STRING=-synctex=1
+
+//If on, have LaTeX generate a synctex file, which WYSIWYG editors
+// can use to correlate output files like dvi and pdf with the
+// lines of LaTeX source that generates them. In addition to adding
+// the LATEX_SYNCTEX_FLAGS to the command line, this option also
+// adds build commands that "corrects" the resulting synctex file
+// to point to the original LaTeX files rather than those generated
+// by UseLATEX.cmake.
+LATEX_USE_SYNCTEX:BOOL=OFF
+
+//Path to a file.
+LDL_INCLUDE_DIR:PATH=/usr/include/suitesparse
+
+//Path to a library.
+LDL_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libldl.so
+
+//Path to a file.
+LIKWID_INCLUDE_DIR:PATH=LIKWID_INCLUDE_DIR-NOTFOUND
+
+//Path to a library.
+LIKWID_LIBRARY:FILEPATH=LIKWID_LIBRARY-NOTFOUND
+
+//Path to a program.
+LUALATEX_COMPILER:FILEPATH=/usr/bin/lualatex
+
+//Command to build the project
+MAKECOMMAND:STRING=/usr/bin/cmake --build . --config "${CTEST_CONFIGURATION_TYPE}" -- -i
+
+//Flags passed to makeglossaries.
+MAKEGLOSSARIES_COMPILER_FLAGS:STRING=
+
+//Path to a program.
+MAKEINDEX_COMPILER:FILEPATH=/usr/bin/makeindex
+
+//Flags passed to makeindex.
+MAKEINDEX_COMPILER_FLAGS:STRING=
+
+//Flags passed to makenomenclature.
+MAKENOMENCLATURE_COMPILER_FLAGS:STRING=
+
+//Path to a program.
+MAKE_EXECUTABLE:FILEPATH=/usr/bin/make
+
+//Path to the memory checking command, used for memory error detection.
+MEMORYCHECK_COMMAND:FILEPATH=/usr/bin/valgrind
+
+//File that contains suppressions for the memory checker
+MEMORYCHECK_SUPPRESSIONS_FILE:FILEPATH=
+
+//Include directory of metis
+METIS_INCLUDE_DIR:PATH=METIS_INCLUDE_DIR-NOTFOUND
+
+//Full path of the METIS library
+METIS_LIBRARY:FILEPATH=METIS_LIBRARY-NOTFOUND
+
+//Name of the METIS library (default: metis).
+METIS_LIB_NAME:STRING=metis
+
+//set the MINIMAL_DEBUG_LEVEL. Standard debug streams with level
+// below MINIMAL_DEBUG_LEVEL will collapse to doing nothing if
+// output is requested. (default=warn)
+MINIMAL_DEBUG_LEVEL:STRING=ON
+
+//Executable for running MPI programs.
+MPIEXEC:FILEPATH=/usr/bin/mpiexec
+
+//Maximum number of processors available to run MPI applications.
+MPIEXEC_MAX_NUMPROCS:STRING=8
+
+//Flag used by MPI to specify the number of processes for MPIEXEC;
+// the next option will be the number of processes.
+MPIEXEC_NUMPROC_FLAG:STRING=-n
+
+//These flags will come after all flags given to MPIEXEC.
+MPIEXEC_POSTFLAGS:STRING=
+
+//These flags will be directly before the executable that is being
+// run by MPIEXEC.
+MPIEXEC_PREFLAGS:STRING=
+
+//Path to a program.
+MPI_CXX_COMPILER:FILEPATH=/usr/bin/mpicxx
+
+//MPI CXX compilation flags
+MPI_CXX_COMPILE_FLAGS:STRING=
+
+//MPI CXX include path
+MPI_CXX_INCLUDE_PATH:STRING=/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include
+
+//MPI CXX libraries to link against
+MPI_CXX_LIBRARIES:STRING=/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
+
+//MPI CXX linking flags
+MPI_CXX_LINK_FLAGS:STRING=
+
+//Path to a program.
+MPI_C_COMPILER:FILEPATH=/usr/bin/mpicc
+
+//MPI C compilation flags
+MPI_C_COMPILE_FLAGS:STRING=
+
+//MPI C include path
+MPI_C_INCLUDE_PATH:STRING=/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include
+
+//MPI C libraries to link against
+MPI_C_LIBRARIES:STRING=/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
+
+//MPI C linking flags
+MPI_C_LINK_FLAGS:STRING=
+
+//Compile flags used by DUNE when compiling MPI programs
+MPI_DUNE_COMPILE_FLAGS:STRING=
+
+//Include path used by DUNE when compiling MPI programs
+MPI_DUNE_INCLUDE_PATH:STRING=/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent;/usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include;/usr/lib/x86_64-linux-gnu/openmpi/include
+
+//Libraries used by DUNE when linking MPI programs
+MPI_DUNE_LIBRARIES:STRING=-pthread;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
+
+//Linker flags used by DUNE when compiling MPI programs
+MPI_DUNE_LINK_FLAGS:STRING=
+
+//Extra MPI libraries to link against
+MPI_EXTRA_LIBRARY:STRING=/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
+
+//Path to a program.
+MPI_Fortran_COMPILER:FILEPATH=/usr/bin/mpif90
+
+//MPI Fortran compilation flags
+MPI_Fortran_COMPILE_FLAGS:STRING=
+
+//MPI Fortran include path
+MPI_Fortran_INCLUDE_PATH:STRING=/usr/lib/x86_64-linux-gnu/openmpi/include;/usr/lib/x86_64-linux-gnu/openmpi/lib
+
+//MPI Fortran libraries to link against
+MPI_Fortran_LIBRARIES:STRING=/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempif08.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_usempi_ignore_tkr.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_mpifh.so;/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi.so
+
+//MPI Fortran linking flags
+MPI_Fortran_LINK_FLAGS:STRING=
+
+//MPI library to link against
+MPI_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/openmpi/lib/libmpi_cxx.so
+
+//Path to a program.
+MV:FILEPATH=/bin/mv
+
+//Path to a program.
+P4COMMAND:FILEPATH=P4COMMAND-NOTFOUND
+
+//Include directory of ParMETIS
+PARMETIS_INCLUDE_DIR:PATH=PARMETIS_INCLUDE_DIR-NOTFOUND
+
+//Full path of the ParMETIS library
+PARMETIS_LIBRARY:FILEPATH=ParMETIS_LIBRARY-NOTFOUND
+
+//Name of the ParMETIS library (default: parmetis).
+PARMETIS_LIB_NAME:STRING=parmetis
+
+//Path to a file.
+PATH_PKG_PSURFACE:FILEPATH=PATH_PKG_PSURFACE-NOTFOUND
+
+//Path to a program.
+PDFLATEX_COMPILER:FILEPATH=/usr/bin/pdflatex
+
+//Flags passed to pdflatex.
+PDFLATEX_COMPILER_FLAGS:STRING=-interaction=batchmode -file-line-error
+
+//Path to a program.
+PDFTOPS_CONVERTER:FILEPATH=/usr/bin/pdftops
+
+//Flags passed to pdftops.
+PDFTOPS_CONVERTER_FLAGS:STRING=
+
+//Is the configuration for PETSc current? Set to "NO" to reconfigure.
+PETSC_CURRENT:BOOL=YES
+
+//PETSc Directory
+PETSC_DIR:PATH=PETSC_DIR-NOTFOUND
+
+//pkg-config executable
+PKG_CONFIG_EXECUTABLE:FILEPATH=/usr/bin/pkg-config
+
+//Path to a program.
+PS2PDF_CONVERTER:FILEPATH=/usr/bin/ps2pdf14
+
+//Flags passed to ps2pdf.
+PS2PDF_CONVERTER_FLAGS:STRING=-dMaxSubsetPct=100 -dCompatibilityLevel=1.3 -dSubsetFonts=true -dEmbedAllFonts=true -dAutoFilterColorImages=false -dAutoFilterGrayImages=false -dColorImageFilter=/FlateEncode -dGrayImageFilter=/FlateEncode -dMonoImageFilter=/FlateEncode
+
+//Path to a file.
+PSURFACE_INCLUDE_DIR:PATH=PSURFACE_INCLUDE_DIR-NOTFOUND
+
+//Path to a library.
+PSURFACE_LIBRARY:FILEPATH=PSURFACE_LIBRARY-NOTFOUND
+
+//Human readable string containing psurface version information.
+PSURFACE_WITH_VERSION:STRING=psurface 1.3
+
+//The PT-Scotch error library.
+PTSCOTCHERR_LIBRARY:FILEPATH=PTSCOTCHERR_LIBRARY-NOTFOUND
+
+//Include directory of PT-Scotch
+PTSCOTCH_INCLUDE_DIR:PATH=PTSCOTCH_INCLUDE_DIR-NOTFOUND
+
+//The main PT-Scotch library.
+PTSCOTCH_LIBRARY:FILEPATH=PTSCOTCH_LIBRARY-NOTFOUND
+
+//Path to a program.
+PYTHON_EXECUTABLE:FILEPATH=/usr/bin/python3
+
+//Path to a file.
+PYTHON_INCLUDE_DIR:PATH=/usr/include/python3.5m
+
+//Path to a library.
+PYTHON_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libpython3.5m.so
+
+//Path to a library.
+PYTHON_LIBRARY_DEBUG:FILEPATH=PYTHON_LIBRARY_DEBUG-NOTFOUND
+
+//Path to a program.
+ProcessorCount_cmd_getconf:FILEPATH=/usr/bin/getconf
+
+//Path to a program.
+ProcessorCount_cmd_sysctl:FILEPATH=/sbin/sysctl
+
+//Path to a program.
+RM:FILEPATH=/bin/rm
+
+//The Scotch library.
+SCOTCH_LIBRARY:FILEPATH=SCOTCH_LIBRARY-NOTFOUND
+
+//Path to scp command, used by CTest for submitting results to
+// a Dart server
+SCPCOMMAND:FILEPATH=/usr/bin/scp
+
+//directory with SIONLIB headers inside
+SIONLIB_INCLUDEDIR:PATH=
+
+//Path to a file.
+SIONLIB_INCLUDE_DIR:PATH=SIONLIB_INCLUDE_DIR-NOTFOUND
+
+//directory with SIONLIB libraries inside
+SIONLIB_LIBDIR:PATH=
+
+//Path to a library.
+SIONLIB_LIBRARY:FILEPATH=SIONLIB_LIBRARY-NOTFOUND
+
+//Path list to search for SIONLIB
+SIONLIB_ROOT:PATH=
+
+//suffix to the library name , e.g. gcc or something
+SIONLIB_SUFFIX:STRING=_lib64
+
+//Name of the computer/site where compile is being run
+SITE:STRING=am54
+
+//Path to the SLURM sbatch executable
+SLURM_SBATCH_COMMAND:FILEPATH=SLURM_SBATCH_COMMAND-NOTFOUND
+
+//Path to the SLURM srun executable
+SLURM_SRUN_COMMAND:FILEPATH=SLURM_SRUN_COMMAND-NOTFOUND
+
+//Path to a program.
+SPHINX_EXECUTABLE:FILEPATH=/usr/bin/sphinx-build
+
+//Path to a file.
+SPQR_INCLUDE_DIR:PATH=/usr/include/suitesparse
+
+//Path to a library.
+SPQR_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libspqr.so
+
+//Linker flags needed to get working C++11 threads support. On
+// Ubuntu it may be necessary to include -Wl,-no-as-needed (see
+// FS#1650).
+STDTHREAD_LINK_FLAGS:STRING=-pthread
+
+//Whether std::thread works.
+STDTHREAD_WORKS:BOOL=1
+
+//Path to a library.
+SUITESPARSE_CONFIG_LIB:FILEPATH=/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so
+
+//Path to a file.
+SUITESPARSE_INCLUDE_DIR:PATH=/usr/include/suitesparse
+
+//Compile flags used by DUNE when compiling SuperLU programs
+SUPERLU_DUNE_COMPILE_FLAGS:STRING=-I/usr/include/superlu
+
+//Libraries used by DUNE when linking SuperLU programs
+SUPERLU_DUNE_LIBRARIES:STRING=/usr/lib/x86_64-linux-gnu/libsuperlu.so;/usr/lib/libblas.so
+
+//Path to a file.
+SUPERLU_INCLUDE_DIR:PATH=/usr/include/superlu
+
+//The integer version that SuperLU was compiled for (Default is
+// int.
+//\n Should be the same as int_t define in e.g. slu_sdefs.h
+SUPERLU_INT_TYPE:STRING=int
+
+//Path to a library.
+SUPERLU_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libsuperlu.so
+
+//Human readable string containing SuperLU version information.
+SUPERLU_WITH_VERSION:STRING=SuperLU >= 5.0
+
+//Path to a program.
+SVNCOMMAND:FILEPATH=/usr/bin/svn
+
+//Compile Flags used by DUNE when compiling with SuiteSparse programs
+SuiteSparse_DUNE_COMPILE_FLAGS:STRING= -I/usr/include/suitesparse/
+
+//Libraries used by DUNE when linking SuiteSparse programs
+SuiteSparse_DUNE_LIBRARIES:STRING=/usr/lib/libblas.so;/usr/lib/x86_64-linux-gnu/libldl.so;/usr/lib/x86_64-linux-gnu/libspqr.so;/usr/lib/x86_64-linux-gnu/libumfpack.so;/usr/lib/x86_64-linux-gnu/libcholmod.so;/usr/lib/x86_64-linux-gnu/libamd.so;/usr/lib/x86_64-linux-gnu/libcamd.so;/usr/lib/x86_64-linux-gnu/libcolamd.so;/usr/lib/x86_64-linux-gnu/libccolamd.so;/usr/lib/x86_64-linux-gnu/libsuitesparseconfig.so
+
+//Path to a program.
+TAR:FILEPATH=/bin/tar
+
+//Turn on TBB debugging (modifies compiler flags and links against
+// debug version of libraries)
+TBB_DEBUG:BOOL=OFF
+
+//Path to TBB include directory
+TBB_INCLUDE_DIRS:PATH=TBB_INCLUDE_DIRS-NOTFOUND
+
+//Path to TBB library directory
+TBB_LIBRARY_DIR:PATH=TBB_LIBRARY_DIR-NOTFOUND
+
+//Path to TBB library
+TBB_LIBTBB:FILEPATH=TBB_LIBTBB-NOTFOUND
+
+//Path to TBB malloc library
+TBB_LIBTBBMALLOC:FILEPATH=TBB_LIBTBBMALLOC-NOTFOUND
+
+//Path to TBB community preview library
+TBB_LIBTBB_PREVIEW:FILEPATH=TBB_LIBTBB_PREVIEW-NOTFOUND
+
+//Path to tbbvars.sh script
+TBB_VARS_SH:FILEPATH=TBB_VARS_SH-NOTFOUND
+
+//Path to a file.
+UMFPACK_INCLUDE_DIR:PATH=/usr/include/suitesparse
+
+//Path to a library.
+UMFPACK_LIBRARY:FILEPATH=/usr/lib/x86_64-linux-gnu/libumfpack.so
+
+//whether we are using pthreads.
+USE_PTHREADS:BOOL=OFF
+
+//The directory containing a CMake configuration file for Vc.
+Vc_DIR:PATH=Vc_DIR-NOTFOUND
+
+//Path to a program.
+XELATEX_COMPILER:FILEPATH=/usr/bin/xelatex
+
+//Path to a program.
+XINDY_COMPILER:FILEPATH=XINDY_COMPILER-NOTFOUND
+
+//Path to a file.
+ZLIB_INCLUDE_DIR:PATH=/usr/include
+
+//Path to a library.
+ZLIB_LIBRARY_DEBUG:FILEPATH=ZLIB_LIBRARY_DEBUG-NOTFOUND
+
+//Path to a library.
+ZLIB_LIBRARY_RELEASE:FILEPATH=/usr/lib/x86_64-linux-gnu/libz.so
+
+//Path to a file.
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+//ADVANCED property for variable: PYTHON_LIBRARY
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+//ADVANCED property for variable: PYTHON_LIBRARY_DEBUG
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+ProcessorCount_cmd_getconf-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: ProcessorCount_cmd_sysctl
+ProcessorCount_cmd_sysctl-ADVANCED:INTERNAL=1
+//Test QUADMATH_COMPILES
+QUADMATH_COMPILES:INTERNAL=1
+//Have include quadmath.h
+QUADMATH_HEADER:INTERNAL=1
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+RM-ADVANCED:INTERNAL=1
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+//ADVANCED property for variable: SUITESPARSE_MIN_VERSION_4_3
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+SUPERLU_INCLUDE_DIR-ADVANCED:INTERNAL=1
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+SUPERLU_LIBRARY-ADVANCED:INTERNAL=1
+//Test SUPERLU_MIN_VERSION_4
+SUPERLU_MIN_VERSION_4:INTERNAL=1
+//Test SUPERLU_MIN_VERSION_4_3
+SUPERLU_MIN_VERSION_4_3:INTERNAL=1
+//Test SUPERLU_MIN_VERSION_5
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+//ADVANCED property for variable: ZLIB_LIBRARY_RELEASE
+ZLIB_LIBRARY_RELEASE-ADVANCED:INTERNAL=1
+//Components requested for this build tree.
+_Boost_COMPONENTS_SEARCHED:INTERNAL=atomic;chrono;date_time;filesystem;system;thread;timer
+//Last used Boost_INCLUDE_DIR value.
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+__pkg_config_checked_PKG_PSURFACE:INTERNAL=1
+__pkg_config_checked_dune-grid-glue:INTERNAL=1
+//Test compiler_supports_cxx17
+compiler_supports_cxx17:INTERNAL=1
+//Test cxx_std_flag_17
+cxx_std_flag_17:INTERNAL=1
+dune-grid-glue_CFLAGS:INTERNAL=
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diff --git a/CMakeDoxyfile.in b/CMakeDoxyfile.in
new file mode 100644
index 0000000..251de27
--- /dev/null
+++ b/CMakeDoxyfile.in
@@ -0,0 +1,272 @@
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+# DO NOT EDIT! THIS FILE WAS GENERATED BY CMAKE!
+#
+
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+DOT_FONTPATH = @DOXYGEN_DOT_FONTPATH@
+CLASS_GRAPH = @DOXYGEN_CLASS_GRAPH@
+COLLABORATION_GRAPH = @DOXYGEN_COLLABORATION_GRAPH@
+GROUP_GRAPHS = @DOXYGEN_GROUP_GRAPHS@
+UML_LOOK = @DOXYGEN_UML_LOOK@
+UML_LIMIT_NUM_FIELDS = @DOXYGEN_UML_LIMIT_NUM_FIELDS@
+TEMPLATE_RELATIONS = @DOXYGEN_TEMPLATE_RELATIONS@
+INCLUDE_GRAPH = @DOXYGEN_INCLUDE_GRAPH@
+INCLUDED_BY_GRAPH = @DOXYGEN_INCLUDED_BY_GRAPH@
+CALL_GRAPH = @DOXYGEN_CALL_GRAPH@
+CALLER_GRAPH = @DOXYGEN_CALLER_GRAPH@
+GRAPHICAL_HIERARCHY = @DOXYGEN_GRAPHICAL_HIERARCHY@
+DIRECTORY_GRAPH = @DOXYGEN_DIRECTORY_GRAPH@
+DOT_IMAGE_FORMAT = @DOXYGEN_DOT_IMAGE_FORMAT@
+INTERACTIVE_SVG = @DOXYGEN_INTERACTIVE_SVG@
+DOT_PATH = @DOXYGEN_DOT_PATH@
+DOTFILE_DIRS = @DOXYGEN_DOTFILE_DIRS@
+MSCFILE_DIRS = @DOXYGEN_MSCFILE_DIRS@
+DIAFILE_DIRS = @DOXYGEN_DIAFILE_DIRS@
+PLANTUML_JAR_PATH = @DOXYGEN_PLANTUML_JAR_PATH@
+PLANTUML_CFG_FILE = @DOXYGEN_PLANTUML_CFG_FILE@
+PLANTUML_INCLUDE_PATH = @DOXYGEN_PLANTUML_INCLUDE_PATH@
+DOT_GRAPH_MAX_NODES = @DOXYGEN_DOT_GRAPH_MAX_NODES@
+MAX_DOT_GRAPH_DEPTH = @DOXYGEN_MAX_DOT_GRAPH_DEPTH@
+DOT_TRANSPARENT = @DOXYGEN_DOT_TRANSPARENT@
+DOT_MULTI_TARGETS = @DOXYGEN_DOT_MULTI_TARGETS@
+GENERATE_LEGEND = @DOXYGEN_GENERATE_LEGEND@
+DOT_CLEANUP = @DOXYGEN_DOT_CLEANUP@
diff --git a/DartConfiguration.tcl b/DartConfiguration.tcl
new file mode 100644
index 0000000..0461420
--- /dev/null
+++ b/DartConfiguration.tcl
@@ -0,0 +1,112 @@
+# This file is configured by CMake automatically as DartConfiguration.tcl
+# If you choose not to use CMake, this file may be hand configured, by
+# filling in the required variables.
+
+
+# Configuration directories and files
+SourceDirectory: /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield
+BuildDirectory: /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield
+
+# Where to place the cost data store
+CostDataFile:
+
+# Site is something like machine.domain, i.e. pragmatic.crd
+Site: am54
+
+# Build name is osname-revision-compiler, i.e. Linux-2.4.2-2smp-c++
+BuildName: Linux-g++
+
+# Submission information
+IsCDash:
+CDashVersion:
+QueryCDashVersion:
+DropSite:
+DropLocation:
+DropSiteUser:
+DropSitePassword:
+DropSiteMode:
+DropMethod: http
+TriggerSite:
+ScpCommand: /usr/bin/scp
+
+# Dashboard start time
+NightlyStartTime: 00:00:00 EDT
+
+# Commands for the build/test/submit cycle
+ConfigureCommand: "/usr/bin/cmake" "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield"
+MakeCommand: /usr/bin/cmake --build . --config "${CTEST_CONFIGURATION_TYPE}" -- -i
+DefaultCTestConfigurationType: Release
+
+# version control
+UpdateVersionOnly:
+
+# CVS options
+# Default is "-d -P -A"
+CVSCommand: /usr/bin/cvs
+CVSUpdateOptions: -d -A -P
+
+# Subversion options
+SVNCommand: /usr/bin/svn
+SVNOptions:
+SVNUpdateOptions:
+
+# Git options
+GITCommand: /usr/bin/git
+GITInitSubmodules:
+GITUpdateOptions:
+GITUpdateCustom:
+
+# Perforce options
+P4Command: P4COMMAND-NOTFOUND
+P4Client:
+P4Options:
+P4UpdateOptions:
+P4UpdateCustom:
+
+# Generic update command
+UpdateCommand: /usr/bin/git
+UpdateOptions:
+UpdateType: git
+
+# Compiler info
+Compiler: /usr/bin/g++
+CompilerVersion: 6.3.0
+
+# Dynamic analysis (MemCheck)
+PurifyCommand:
+ValgrindCommand:
+ValgrindCommandOptions:
+MemoryCheckType:
+MemoryCheckSanitizerOptions:
+MemoryCheckCommand: /usr/bin/valgrind
+MemoryCheckCommandOptions:
+MemoryCheckSuppressionFile:
+
+# Coverage
+CoverageCommand: /usr/bin/gcov
+CoverageExtraFlags: -l
+
+# Cluster commands
+SlurmBatchCommand: SLURM_SBATCH_COMMAND-NOTFOUND
+SlurmRunCommand: SLURM_SRUN_COMMAND-NOTFOUND
+
+# Testing options
+# TimeOut is the amount of time in seconds to wait for processes
+# to complete during testing. After TimeOut seconds, the
+# process will be summarily terminated.
+# Currently set to 25 minutes
+TimeOut: 1500
+
+# During parallel testing CTest will not start a new test if doing
+# so would cause the system load to exceed this value.
+TestLoad:
+
+UseLaunchers:
+CurlOptions:
+# warning, if you add new options here that have to do with submit,
+# you have to update cmCTestSubmitCommand.cxx
+
+# For CTest submissions that timeout, these options
+# specify behavior for retrying the submission
+CTestSubmitRetryDelay: 5
+CTestSubmitRetryCount: 3
diff --git a/FC.h b/FC.h
new file mode 100644
index 0000000..467bfb6
--- /dev/null
+++ b/FC.h
@@ -0,0 +1,16 @@
+#ifndef FC_HEADER_INCLUDED
+#define FC_HEADER_INCLUDED
+
+/* Mangling for Fortran global symbols without underscores. */
+#define FC_GLOBAL(name,NAME) name##_
+
+/* Mangling for Fortran global symbols with underscores. */
+#define FC_GLOBAL_(name,NAME) name##_
+
+/* Mangling for Fortran module symbols without underscores. */
+#define FC_MODULE(mod_name,name, mod_NAME,NAME) __##mod_name##_MOD_##name
+
+/* Mangling for Fortran module symbols with underscores. */
+#define FC_MODULE_(mod_name,name, mod_NAME,NAME) __##mod_name##_MOD_##name
+
+#endif
diff --git a/activate b/activate
new file mode 120000
index 0000000..cd7e25e
--- /dev/null
+++ b/activate
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/build-release/python_virtualenv/bin/activate
\ No newline at end of file
diff --git a/compile_commands.json b/compile_commands.json
new file mode 100644
index 0000000..7723e0d
--- /dev/null
+++ b/compile_commands.json
@@ -0,0 +1,317 @@
+[
+{
+ "directory": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield",
+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIC -DHEADERCHECK -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/dune/phasefield/archive -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -fext-numeric-literals -o CMakeFiles/headercheck__dune_phasefield_archive_tmp___myincludes.hh.dir/headercheck/dune/phasefield/archive/tmp___myincludes.hh.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/headercheck/dune/phasefield/archive/tmp___myincludes.hh.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/headercheck/dune/phasefield/archive/tmp___myincludes.hh.cc"
+},
+{
+ "directory": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield",
+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIC -DHEADERCHECK -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/dune/phasefield -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -fext-numeric-literals -o CMakeFiles/headercheck__dune_phasefield_ff_chns.hh.dir/headercheck/dune/phasefield/ff_chns.hh.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/headercheck/dune/phasefield/ff_chns.hh.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/headercheck/dune/phasefield/ff_chns.hh.cc"
+},
+{
+ "directory": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield",
+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIC -DHEADERCHECK -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/summerschool -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -fext-numeric-literals -o CMakeFiles/headercheck__src_summerschool_summerschool_timestepmanager.hh.dir/headercheck/src/summerschool/summerschool_timestepmanager.hh.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/headercheck/src/summerschool/summerschool_timestepmanager.hh.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/headercheck/src/summerschool/summerschool_timestepmanager.hh.cc"
+},
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+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIE -fext-numeric-literals -o CMakeFiles/epsdelta_equation.dir/epsdelta_equation.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/paper_epsdelta/epsdelta_equation.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/paper_epsdelta/epsdelta_equation.cc"
+},
+{
+ "directory": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard",
+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIE -fext-numeric-literals -o CMakeFiles/ch3p_equation.dir/ch3p_equation.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard/ch3p_equation.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard/ch3p_equation.cc"
+},
+{
+ "directory": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard",
+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIE -fext-numeric-literals -o CMakeFiles/ch2p_equation.dir/ch2p_equation.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard/ch2p_equation.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard/ch2p_equation.cc"
+},
+{
+ "directory": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_nucleus",
+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIE -fext-numeric-literals -o CMakeFiles/nucleus_equation.dir/nucleus_equation.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_nucleus/nucleus_equation.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_nucleus/nucleus_equation.cc"
+},
+{
+ "directory": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/paper_thinstrip_full",
+ "command": "/usr/bin/g++ -DENABLE_EIGEN=1 -DENABLE_GMP=1 -DENABLE_MPI=1 -DENABLE_QUADMATH=1 -DENABLE_SUITESPARSE=1 -DENABLE_SUPERLU=1 -DENABLE_TBB=1 -DENABLE_UG=1 -DHAVE_CONFIG_H -DMPICH_SKIP_MPICXX -DMPIPP_H -DMPI_NO_CPPBIND -DModelP -DUG_USE_NEW_DIMENSION_DEFINES -D_GLIBCXX_USE_FLOAT128=1 -D_TBB_CPP0X -I/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield -I/usr/local/ssd/home/vonwolls/dumux/dune-phasefield -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent -isystem /usr/lib/x86_64-linux-gnu/openmpi/include/openmpi/opal/mca/event/libevent2022/libevent/include -isystem /usr/lib/x86_64-linux-gnu/openmpi/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-common -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-geometry -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-uggrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/low -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/gm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/dom -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/ui -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/algebra -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/np/udm -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ppif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/dddif -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/util -I/home/ians1/vonwolls/ssd_local/dumux/dune-uggrid/parallel/ddd/include -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-typetree -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-istl -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-grid -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-localfunctions -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-functions -I/usr/include/python3.5m -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-python -isystem /home/ians1/vonwolls/ssd_local/dumux/dune-alugrid -I/home/ians1/vonwolls/ssd_local/dumux/dune-testtools -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-common -I/home/ians1/vonwolls/ssd_local/dumux/dune-xt-grid -I/home/ians1/vonwolls/ssd_local/dumux/dune-pdelab -isystem /usr/include/eigen3 -isystem /usr/include/suitesparse -isystem /usr/include/superlu -std=c++17 -fno-strict-aliasing -fstrict-overflow -fno-finite-math-only -O3 -march=native -funroll-loops -fdiagnostics-color=always -Wall -Wno-deprecated -Wno-deprecated-declarations -Wno-reorder -Wno-sign-compare -fPIE -fext-numeric-literals -o CMakeFiles/thinstrip_equation.dir/thinstrip_equation.cc.o -c /home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/paper_thinstrip_full/thinstrip_equation.cc",
+ "file": "/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/paper_thinstrip_full/thinstrip_equation.cc"
+}
+]
\ No newline at end of file
diff --git a/config.h b/config.h
new file mode 100644
index 0000000..4ab6906
--- /dev/null
+++ b/config.h
@@ -0,0 +1,800 @@
+/* config.h. Generated from config_collected.h.cmake by CMake.
+ It was generated from config_collected.h.cmake which in turn is generated automatically
+ from the config.h.cmake files of modules this module depends on. */
+
+/* Define to 1 if you have module dune-phasefield available */
+#define HAVE_DUNE_PHASEFIELD 1
+
+
+/* Define to 1 if you have module dune-common available */
+#define HAVE_DUNE_COMMON 1
+
+
+/* Define to 1 if you have module dune-geometry available */
+#define HAVE_DUNE_GEOMETRY 1
+
+
+/* Define to 1 if you have module dune-uggrid available */
+#define HAVE_DUNE_UGGRID 1
+
+
+/* Define to 1 if you have module dune-typetree available */
+#define HAVE_DUNE_TYPETREE 1
+
+
+/* Define to 1 if you have module dune-istl available */
+#define HAVE_DUNE_ISTL 1
+
+
+/* Define to 1 if you have module dune-grid available */
+#define HAVE_DUNE_GRID 1
+
+
+/* Define to 1 if you have module dune-localfunctions available */
+#define HAVE_DUNE_LOCALFUNCTIONS 1
+
+
+/* Define to 1 if you have module dune-functions available */
+#define HAVE_DUNE_FUNCTIONS 1
+
+
+/* Define to 1 if you have module dune-python available */
+#define HAVE_DUNE_PYTHON 1
+
+
+/* Define to 1 if you have module dune-alugrid available */
+#define HAVE_DUNE_ALUGRID 1
+
+
+/* Define to 1 if you have module dune-testtools available */
+#define HAVE_DUNE_TESTTOOLS 1
+
+
+/* Define to 1 if you have module dune-grid-glue available */
+#define HAVE_DUNE_GRID_GLUE 0
+
+
+/* Define to 1 if you have module dune-xt-common available */
+#define HAVE_DUNE_XT_COMMON 1
+
+
+/* Define to 1 if you have module dune-xt-grid available */
+#define HAVE_DUNE_XT_GRID 1
+
+
+/* Define to 1 if you have module dune-pdelab available */
+#define HAVE_DUNE_PDELAB 1
+
+
+/* Define to the version of dune-common */
+#define DUNE_COMMON_VERSION "2.7-git"
+
+/* Define to the major version of dune-common */
+#define DUNE_COMMON_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-common */
+#define DUNE_COMMON_VERSION_MINOR 7
+
+/* Define to the revision of dune-common */
+#define DUNE_COMMON_VERSION_REVISION 0
+
+/* Standard debug streams with a level below will collapse to doing nothing */
+#define DUNE_MINIMAL_DEBUG_LEVEL 4
+
+/* does the compiler support __attribute__((deprecated))? */
+#define HAS_ATTRIBUTE_DEPRECATED 1
+
+/* does the compiler support __attribute__((deprecated("message"))? */
+#define HAS_ATTRIBUTE_DEPRECATED_MSG 1
+
+/* does the compiler support __attribute__((unused))? */
+#define HAS_ATTRIBUTE_UNUSED 1
+
+/* does the compiler support C++17's class template argument deduction? */
+/* #undef DUNE_HAVE_CXX_CLASS_TEMPLATE_ARGUMENT_DEDUCTION */
+
+/* does the compiler support C++17's optional? */
+/* #undef DUNE_HAVE_CXX_OPTIONAL */
+
+/* does the compiler support C++17's variant? */
+/* #undef DUNE_HAVE_CXX_VARIANT */
+
+/* does the compiler support conditionally throwing exceptions in constexpr context? */
+#define DUNE_SUPPORTS_CXX_THROW_IN_CONSTEXPR 1
+
+/* does the standard library provide <experimental/type_traits> ? */
+#define DUNE_HAVE_HEADER_EXPERIMENTAL_TYPE_TRAITS 1
+
+/* does the standard library provide make_unique() ? */
+#define DUNE_HAVE_CXX_MAKE_UNIQUE 1
+
+/* does the standard library provide bool_constant ? */
+#define DUNE_HAVE_CXX_BOOL_CONSTANT 1
+
+/* does the standard library provide experimental::bool_constant ? */
+/* #undef DUNE_HAVE_CXX_EXPERIMENTAL_BOOL_CONSTANT */
+
+/* does the standard library provide apply() ? */
+/* #undef DUNE_HAVE_CXX_APPLY */
+
+/* does the standard library provide experimental::apply() ? */
+#define DUNE_HAVE_CXX_EXPERIMENTAL_APPLY 1
+
+/* does the standard library provide experimental::make_array() ? */
+#define DUNE_HAVE_CXX_EXPERIMENTAL_MAKE_ARRAY 1
+
+/* does the standard library provide experimental::is_detected ? */
+#define DUNE_HAVE_CXX_EXPERIMENTAL_IS_DETECTED 1
+
+/* Define if you have a BLAS library. */
+#define HAVE_BLAS 1
+
+/* does the compiler support abi::__cxa_demangle */
+#define HAVE_CXA_DEMANGLE 1
+
+/* Define if you have LAPACK library. */
+#define HAVE_LAPACK 1
+
+/* Define to 1 if you have the <malloc.h> header file. */
+// Not used! #define HAVE_MALLOC_H 1
+
+/* Define if you have the MPI library. */
+#define HAVE_MPI ENABLE_MPI
+
+/* Define if you have the GNU GMP library. The value should be ENABLE_GMP
+ to facilitate activating and deactivating GMP using compile flags. */
+#define HAVE_GMP ENABLE_GMP
+
+/* Define if you have the GCC Quad-Precision library. The value should be ENABLE_QUADMATH
+ to facilitate activating and deactivating QuadMath using compile flags. */
+#define HAVE_QUADMATH ENABLE_QUADMATH
+
+/* Define if you have the Vc library. The value should be ENABLE_VC
+ to facilitate activating and deactivating Vc using compile flags. */
+/* #undef HAVE_VC */
+
+/* Define to 1 if you have the symbol mprotect. */
+#define HAVE_MPROTECT 1
+
+/* Define to 1 if you have the <stdint.h> header file. */
+/* #undef HAVE_STDINT_H */
+
+/* Define to 1 if you have <sys/mman.h>. */
+#define HAVE_SYS_MMAN_H 1
+
+/* Define to 1 if you have the Threading Building Blocks (TBB) library */
+/* #undef HAVE_TBB */
+
+
+
+/* old feature support macros which were tested until 2.4, kept around for one more release */
+/* As these are now always supported due to the new compiler requirements, they are directly */
+/* defined without an explicit test. */
+#define HAVE_NULLPTR 1
+#define HAVE_CONSTEXPR 1
+#define HAVE_RANGE_BASED_FOR 1
+#define HAVE_NOEXCEPT_SPECIFIER 1
+#define HAVE_STD_DECLVAL 1
+#define HAVE_KEYWORD_FINAL 1
+#define MPI_2 1
+
+/* Define to 1 if the compiler properly supports testing for operator[] */
+#define HAVE_IS_INDEXABLE_SUPPORT 1
+
+/* Define to ENABLE_UMFPACK if the UMFPack library is available */
+#define HAVE_UMFPACK ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse library is available */
+#define HAVE_SUITESPARSE ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's AMD library is available */
+#define HAVE_SUITESPARSE_AMD ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's BTF library is available */
+/* #undef HAVE_SUITESPARSE_BTF */
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's CAMD library is available */
+#define HAVE_SUITESPARSE_CAMD ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's CCOLAMD library is available */
+#define HAVE_SUITESPARSE_CCOLAMD ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's CHOLMOD library is available */
+#define HAVE_SUITESPARSE_CHOLMOD ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's COLAMD library is available */
+#define HAVE_SUITESPARSE_COLAMD ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's CXSPARSE library is available */
+/* #undef HAVE_SUITESPARSE_CXSPARSE */
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's KLU library is available */
+/* #undef HAVE_SUITESPARSE_KLU */
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's LDL library is available */
+#define HAVE_SUITESPARSE_LDL ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's RBIO library is available */
+/* #undef HAVE_SUITESPARSE_RBIO */
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's SPQR library is available
+ and if it's version is at least 4.3 */
+#define HAVE_SUITESPARSE_SPQR ENABLE_SUITESPARSE
+
+/* Define to ENABLE_SUITESPARSE if the SuiteSparse's UMFPACK library is available */
+#define HAVE_SUITESPARSE_UMFPACK ENABLE_SUITESPARSE
+
+/* Define to 1 if METIS is available */
+/* #undef HAVE_METIS */
+
+
+/* Define to ENABLE_PARMETIS if you have the Parmetis library.
+ This is only true if MPI was found
+ by configure _and_ if the application uses the PARMETIS_CPPFLAGS */
+/* #undef HAVE_PARMETIS */
+
+/* Define to 1 if PT-Scotch is available */
+/* #undef HAVE_PTSCOTCH */
+
+/* Include always useful headers */
+#include "FC.h"
+#define FC_FUNC FC_GLOBAL_
+
+
+
+
+
+/* Define to the version of dune-geometry */
+#define DUNE_GEOMETRY_VERSION "2.7-git"
+
+/* Define to the major version of dune-geometry */
+#define DUNE_GEOMETRY_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-geometry */
+#define DUNE_GEOMETRY_VERSION_MINOR 7
+
+/* Define to the revision of dune-geometry */
+#define DUNE_GEOMETRY_VERSION_REVISION 0
+
+
+
+/* Define to the version of dune-common */
+#define DUNE_UGGRID_VERSION "2.7-git"
+
+/* Define to the major version of dune-common */
+#define DUNE_UGGRID_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-common */
+#define DUNE_UGGRID_VERSION_MINOR 7
+
+/* Define to the revision of dune-common */
+#define DUNE_UGGRID_VERSION_REVISION 0
+
+/* begin private section */
+
+/* see parallel/ddd/dddi.h */
+/* #undef DDD_MAX_PROCBITS_IN_GID */
+
+/* Define to 1 if you can safely include both <sys/time.h> and <time.h>. */
+/* #undef TIME_WITH_SYS_TIME */
+
+/* Define to 1 if UGGrid should use the complete set of green refinement rules for tetrahedra */
+/* #undef TET_RULESET */
+
+/* Define to 1 if rpc/rpc.h is found (needed for xdr). */
+#ifndef HAVE_RPC_RPC_H
+#define HAVE_RPC_RPC_H 1
+#endif
+
+/* end private section */
+
+
+
+
+
+/* Define to the version of dune-typetree */
+#define DUNE_TYPETREE_VERSION "2.7-git"
+
+/* Define to the major version of dune-typetree */
+#define DUNE_TYPETREE_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-typetree */
+#define DUNE_TYPETREE_VERSION_MINOR 7
+
+/* Define to the revision of dune-typetree */
+#define DUNE_TYPETREE_VERSION_REVISION 0
+
+
+
+
+
+
+/* Define to ENABLE_SUPERLU if the SuperLU library is available */
+#define HAVE_SUPERLU ENABLE_SUPERLU
+
+/* Define to the integer type that SuperLU was compiled for
+ See e.g. what int_t is defined to in slu_sdefs.h */
+#define SUPERLU_INT_TYPE int
+
+/* Define to 1 if header slu_sdefs.h is there. */
+#define HAVE_SLU_SDEFS_H 1
+
+/* Define to 1 if header slu_ddefs.h is there. */
+#define HAVE_SLU_DDEFS_H 1
+
+/* Define to 1 if header slu_cdefs.h is there. */
+#define HAVE_SLU_CDEFS_H 1
+
+/* Define to 1 if header slu_zdefs.h is there. */
+#define HAVE_SLU_ZDEFS_H 1
+
+/* Define to ENABLE_ARPACKPP if the ARPACK++ library is available */
+/* #undef HAVE_ARPACKPP */
+
+/* Define to 0 as all versions since SuperLu 4.0 do no longer provide it that way. */
+#define HAVE_MEM_USAGE_T_EXPANSIONS 1
+
+/* define to 1 if SuperLU header slu_ddefs.h contains SLU_DOUBLE */
+#define SUPERLU_MIN_VERSION_4_3 1
+
+/* define to 1 if SuperLU dgssvx takes a GlobalLU_t parameter */
+#define SUPERLU_MIN_VERSION_5 1
+
+/* Define to the version of dune-istl */
+#define DUNE_ISTL_VERSION "2.7-git"
+
+/* Define to the major version of dune-istl */
+#define DUNE_ISTL_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-istl */
+#define DUNE_ISTL_VERSION_MINOR 7
+
+/* Define to the revision of dune-istl */
+#define DUNE_ISTL_VERSION_REVISION 0
+
+/* Enable/Disable the backwards compatibility of the category enum/method in dune-istl solvers, preconditioner, etc. */
+#define DUNE_ISTL_SUPPORT_OLD_CATEGORY_INTERFACE 1
+
+
+
+
+
+/* Define to the version of dune-grid */
+#define DUNE_GRID_VERSION "2.7-git"
+
+/* Define to the major version of dune-grid */
+#define DUNE_GRID_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-grid */
+#define DUNE_GRID_VERSION_MINOR 7
+
+/* Define to the revision of dune-grid */
+#define DUNE_GRID_VERSION_REVISION 0
+
+/* If this is set, public access to the implementation of facades like Entity, Geometry, etc. is granted. (deprecated) */
+#define DUNE_GRID_EXPERIMENTAL_GRID_EXTENSIONS 1
+
+/* Define to 1 if psurface library is found */
+/* #undef HAVE_PSURFACE */
+
+/* Define to 1 if AmiraMesh library is found */
+/* #undef HAVE_AMIRAMESH */
+
+/* The namespace prefix of the psurface library (deprecated) */
+#define PSURFACE_NAMESPACE psurface::
+
+/* Define to 1 if you have at least psurface version 2.0 */
+/* #undef HAVE_PSURFACE_2_0 */
+
+/* Alberta version found by configure, either 0x200 for 2.0 or 0x300 for 3.0 */
+/* #undef DUNE_ALBERTA_VERSION */
+
+/* This is only true if alberta-library was found by configure _and_ if the
+ application uses the ALBERTA_CPPFLAGS */
+/* #undef HAVE_ALBERTA */
+
+/* This is only true if UG was found by configure _and_ if the application
+ uses the UG_CPPFLAGS */
+#define HAVE_UG ENABLE_UG
+
+/* Define to 1 if you have mkstemp function */
+#define HAVE_MKSTEMP 1
+
+
+
+
+
+
+
+/* Define to the version of dune-localfunctions */
+#define DUNE_LOCALFUNCTIONS_VERSION "2.7-git"
+
+/* Define to the major version of dune-localfunctions */
+#define DUNE_LOCALFUNCTIONS_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-localfunctions */
+#define DUNE_LOCALFUNCTIONS_VERSION_MINOR 7
+
+/* Define to the revision of dune-localfunctions */
+#define DUNE_LOCALFUNCTIONS_VERSION_REVISION 0
+
+
+
+
+
+
+/* Define to the version of dune-functions */
+#define DUNE_FUNCTIONS_VERSION "2.7-git"
+
+/* Define to the major version of dune-functions */
+#define DUNE_FUNCTIONS_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-functions */
+#define DUNE_FUNCTIONS_VERSION_MINOR 7
+
+/* Define to the revision of dune-functions */
+#define DUNE_FUNCTIONS_VERSION_REVISION 0
+
+
+
+
+
+
+/* Define to the version of dune-python */
+#define DUNE_PYTHON_VERSION "2.6"
+
+/* Define to the major version of dune-python */
+#define DUNE_PYTHON_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-python */
+#define DUNE_PYTHON_VERSION_MINOR 6
+
+/* Define to the revision of dune-python */
+#define DUNE_PYTHON_VERSION_REVISION 0
+
+
+
+
+
+
+#define DUNE_ALUGRID_VERSION "2.7"
+
+/* Define to the major version of dune-alugrid */
+#define DUNE_ALUGRID_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-alugrid */
+#define DUNE_ALUGRID_VERSION_MINOR 7
+
+/* Define to the revision of dune-alugrid*/
+#define DUNE_ALUGRID_VERSION_REVISION 0
+
+/* Define to build more .cc into library */
+/* #undef DUNE_ALUGRID_COMPILE_BINDINGS_IN_LIB */
+
+/* Define if we have dlmalloc */
+/* #undef HAVE_DLMALLOC */
+
+/* Define if we have zoltan */
+/* #undef HAVE_ZOLTAN */
+
+/* Define if we have ZLIB */
+#define HAVE_ZLIB 1
+
+/* Include source file for dlmalloc */
+/* #undef DLMALLOC_SOURCE_INCLUDE */
+
+/* Define if we have thread local storage */
+/* #undef HAVE_PTHREAD_TLS */
+
+/* Define if we have pthreads */
+#define HAVE_PTHREAD 1
+
+/* Grid type magic for DGF parser */
+
+/* ALUGRID_CONFORM not available, enable with cmake variable DUNE_GRID_GRIDTYPE_SELECTOR=ON */
+/* ALUGRID_CUBE not available, enable with cmake variable DUNE_GRID_GRIDTYPE_SELECTOR=ON */
+/* ALUGRID_SIMPLEX not available, enable with cmake variable DUNE_GRID_GRIDTYPE_SELECTOR=ON */
+
+
+
+
+
+/* Define to the version of dune-testtools */
+#define DUNE_TESTTOOLS_VERSION "3.0git"
+
+/* Define to the major version of dune-testtools */
+#define DUNE_TESTTOOLS_VERSION_MAJOR 3
+
+/* Define to the minor version of dune-testtools */
+#define DUNE_TESTTOOLS_VERSION_MINOR 0
+
+/* Define to the revision of dune-testtools */
+#define DUNE_TESTTOOLS_VERSION_REVISION 0
+
+
+
+// NEVER delete/alter above comment, dune's cmake relies on it
+
+/* Define to the version of dune-xt-common */
+#define DUNE_XT_COMMON_VERSION 18.11-dev
+
+/* Define to the major version of dune-xt-common */
+#define DUNE_XT_COMMON_VERSION_MAJOR 18
+
+/* Define to the minor version of dune-xt-common */
+#define DUNE_XT_COMMON_VERSION_MINOR 11
+
+/* Define to the revision of dune-xt-common */
+#define DUNE_XT_COMMON_VERSION_REVISION 0
+
+#ifndef HAVE_CBLAS
+#define HAVE_CBLAS 0
+#endif
+
+#ifndef HAVE_EIGEN
+#define HAVE_EIGEN ENABLE_EIGEN
+#endif
+
+#ifndef HAVE_CLP
+#define HAVE_CLP 0
+#endif
+
+#ifndef HAVE_QHULL
+#define HAVE_QHULL 0
+#endif
+
+#ifndef HAVE_LPSOLVE
+#define HAVE_LPSOLVE 0
+#endif
+
+#ifndef HAVE_LAPACKE
+#define HAVE_LAPACKE 0
+#endif
+
+#ifndef HAVE_MKL
+#define HAVE_MKL 0
+#endif
+
+#ifndef HAVE_MATEXP
+#define HAVE_MATEXP 0
+#endif
+
+#ifndef HAVE_FEKETE
+#define HAVE_FEKETE 0
+#endif
+
+#ifndef HAVE_LEBEDEVDATA
+#define HAVE_LEBEDEVDATA 0
+#endif
+
+#ifndef HAVE_TBB
+#define HAVE_TBB 0
+#endif
+
+#ifndef DXT_DISABLE_LARGE_TESTS
+#define DXT_DISABLE_LARGE_TESTS 0
+#endif
+
+#ifndef HAS_WORKING_UNUSED_ATTRIBUTE
+#define HAS_WORKING_UNUSED_ATTRIBUTE 1
+#endif
+
+#ifndef HAVE_LIKWID
+#define HAVE_LIKWID 0
+#endif
+
+#ifndef ENABLE_PERFMON
+#define ENABLE_PERFMON 0
+#endif
+
+#if ENABLE_PERFMON && HAVE_LIKWID
+#define LIKWID_PERFMON 1
+#endif
+
+#ifndef HAVE_MAP_EMPLACE
+#define HAVE_MAP_EMPLACE 1
+#endif
+
+#ifndef DS_MAX_MIC_THREADS
+#define DS_MAX_MIC_THREADS
+#endif
+
+#ifndef HAVE_DUNE_FEM_PARAMETER_REPLACE
+#define HAVE_DUNE_FEM_PARAMETER_REPLACE 0
+#endif
+
+/* needed in dune/xt/common/profiler.hh */
+#ifndef DUNE_XT_COMMON_DO_TIMING
+#define DUNE_XT_COMMON_DO_TIMING 0
+#endif
+
+/*** Silence implicitly False evaluation of undefined macro warnings ****/
+#ifndef HAVE_DUNE_FEM
+#define HAVE_DUNE_FEM 0
+#endif
+
+#ifndef HAVE_DUNE_GRID_MULTISCALE
+#define HAVE_DUNE_GRID_MULTISCALE 0
+#endif
+
+#ifndef HAVE_ALBERTA
+#define HAVE_ALBERTA 0
+#endif
+
+#ifndef ALBERTA_DIM
+#define ALBERTA_DIM 2
+#endif
+
+#ifndef HAVE_DUNE_SPGRID
+#define HAVE_DUNE_SPGRID 0
+#endif
+
+#ifndef HAVE_EMPLACE
+#define HAVE_EMPLACE 0
+#endif
+
+#ifndef HAVE_FASP
+#define HAVE_FASP 0
+#endif
+
+#ifndef ENABLE_SUPERLU
+#define ENABLE_SUPERLU 0
+#endif
+
+#ifndef HAVE_SUPERLU
+#define HAVE_SUPERLU 0
+#endif
+
+#ifndef ENABLE_UMFPACK
+#define ENABLE_UMFPACK 0
+#endif
+
+#ifndef HAVE_UMFPACK
+#define HAVE_UMFPACK 0
+#endif
+
+#ifndef HAVE_UG
+#define HAVE_UG 0
+#endif
+
+#ifndef ENABLE_BOOST
+#define ENABLE_BOOST 0
+#endif
+
+#ifndef ENABLE_PETSC
+#define ENABLE_PETSC 0
+#endif
+
+#ifndef ENABLE_MPI
+#define ENABLE_MPI 0
+#endif
+
+#ifndef HAVE_MPI
+#define HAVE_MPI 0
+#endif
+
+#ifndef HAVE_CONSTEXPR
+#define HAVE_CONSTEXPR 0
+#endif
+
+#ifndef HAVE_PETSC
+#define HAVE_PETSC 0
+#endif
+
+#ifndef DUNE_FEM_COMPATIBILITY
+#define DUNE_FEM_COMPATIBILITY 0
+#endif
+
+#ifndef HAVE_MAP_EMPLACE
+#define HAVE_MAP_EMPLACE 0
+#endif
+
+/*** End: Silence implicitly False evaluation of undefined macro warnings ****/
+
+#include <boost/config.hpp>
+#if HAVE_TBB && defined(BOOST_CLANG)
+ // Hack to fix compilation with clang as tbb does not detect C++11 feature correctly for clang. Recent versions of TBB
+ // allow to set the macro TBB_USE_GLIBCXX_VERSION to the proper version of libstdc++ to fix this issue, see
+ // https://www.threadingbuildingblocks.org/docs/help/reference/appendices/known_issues/linux_os.html. For older versions
+ // we need the hack below.
+ #define TBB_USE_GLIBCXX_VERSION 40902
+ #include "tbb/tbb_stddef.h"
+ #if TBB_INTERFACE_VERSION < 4400
+ #include <tbb/tbb_config.h>
+ #undef __TBB_CPP11_RVALUE_REF_PRESENT
+ #undef __TBB_CPP11_VARIADIC_TEMPLATES_PRESENT
+ #undef __TBB_CPP11_DECLTYPE_PRESENT
+ #undef __TBB_CPP11_LAMBDAS_PRESENT
+ #define __TBB_CPP11_RVALUE_REF_PRESENT 1
+ #define __TBB_CPP11_VARIADIC_TEMPLATES_PRESENT 1
+ #define __TBB_CPP11_DECLTYPE_PRESENT 1
+ #define __TBB_CPP11_LAMBDAS_PRESENT 1
+ #endif // TBB_INTERFACE_VERSION < 4400
+#endif // HAVE_TBB
+
+
+
+// NEVER delete/alter above comment, dune's cmake relies on it
+
+
+
+/* Define to the version of dune-pdelab */
+#define DUNE_PDELAB_VERSION "2.7-git"
+
+/* Define to the major version of dune-pdelab */
+#define DUNE_PDELAB_VERSION_MAJOR 2
+
+/* Define to the minor version of dune-pdelab */
+#define DUNE_PDELAB_VERSION_MINOR 7
+
+/* Define to the revision of dune-pdelab */
+#define DUNE_PDELAB_VERSION_REVISION 0
+
+/* This is only true if PETSc was found by configure _and_ if the application
+ uses the UG_CPPFLAGS */
+#ifndef HAVE_PETSC
+/* #undef HAVE_PETSC */
+#endif
+
+/* This is only true if Eigen3 was found by configure */
+#ifndef HAVE_EIGEN
+#define HAVE_EIGEN ENABLE_EIGEN
+#endif
+
+/* Define to 1 if sequential UG has been found */
+/* #undef PDELAB_SEQUENTIAL_UG */
+
+
+
+/* begin dune-phasefield
+ put the definitions for config.h specific to
+ your project here. Everything above will be
+ overwritten
+*/
+
+/* begin private */
+/* Name of package */
+#define PACKAGE "dune-phasefield"
+
+/* Define to the address where bug reports for this package should be sent. */
+#define PACKAGE_BUGREPORT "lars.von-wolff@mathematik.uni-stuttgart.de"
+
+/* Define to the full name of this package. */
+#define PACKAGE_NAME "dune-phasefield"
+
+/* Define to the full name and version of this package. */
+#define PACKAGE_STRING "dune-phasefield 0.1"
+
+/* Define to the one symbol short name of this package. */
+#define PACKAGE_TARNAME "dune-phasefield"
+
+/* Define to the home page for this package. */
+#define PACKAGE_URL ""
+
+/* Define to the version of this package. */
+#define PACKAGE_VERSION "0.1"
+
+/* end private */
+
+/* Define to the version of dune-phasefield */
+#define DUNE_PHASEFIELD_VERSION "0.1"
+
+/* Define to the major version of dune-phasefield */
+#define DUNE_PHASEFIELD_VERSION_MAJOR 0
+
+/* Define to the minor version of dune-phasefield */
+#define DUNE_PHASEFIELD_VERSION_MINOR 1
+
+/* Define to the revision of dune-phasefield */
+#define DUNE_PHASEFIELD_VERSION_REVISION 0
+
+/* end dune-phasefield
+ Everything below here will be overwritten
+*/
+
+/* Grid type magic for DGF parser */
+
+/* UGGRID not available, enable with cmake variable DUNE_GRID_GRIDTYPE_SELECTOR=ON */
+/* ONEDGRID not available, enable with cmake variable DUNE_GRID_GRIDTYPE_SELECTOR=ON */
+/* YASPGRID not available, enable with cmake variable DUNE_GRID_GRIDTYPE_SELECTOR=ON */
+
diff --git a/dune-phasefield.pc b/dune-phasefield.pc
new file mode 100644
index 0000000..9d3a015
--- /dev/null
+++ b/dune-phasefield.pc
@@ -0,0 +1,15 @@
+prefix=/usr/local
+exec_prefix=${prefix}
+libdir=${exec_prefix}/lib
+includedir=${prefix}/include
+CXX=/usr/bin/g++
+CC=/usr/bin/gcc
+DEPENDENCIES=
+
+Name: dune-phasefield
+Version: 0.1
+Description: dune-phasefield module
+URL: http://dune-project.org/
+Requires: dune-common dune-geometry dune-grid dune-localfunctions dune-typetree dune-istl dune-functions dune-uggrid dune-alugrid dune-pdelab
+Libs: -L${libdir}
+Cflags: -I${includedir}
diff --git a/dune.module b/dune.module
index 84bc85c..44134e0 100644
--- a/dune.module
+++ b/dune.module
@@ -7,4 +7,4 @@ Module: dune-phasefield
Version: 0.1
Maintainer: lars.von-wolff@mathematik.uni-stuttgart.de
#depending on
-Depends: dune-common dune-geometry dune-grid dune-localfunctions dune-typetree dune-istl dune-functions dune-uggrid dune-alugrid dune-pdelab
+Depends: dune-common dune-geometry dune-grid dune-localfunctions dune-typetree dune-istl dune-functions dune-uggrid dune-alugrid dune-pdelab dune-xt-grid
diff --git a/dune/phasefield/base_parameters.hh b/dune/phasefield/base_parameters.hh
index 940f3c8..9cef08f 100644
--- a/dune/phasefield/base_parameters.hh
+++ b/dune/phasefield/base_parameters.hh
@@ -14,7 +14,7 @@ template<typename Number>
class Mobility_Const
{
public:
- const Number mobility;
+ Number mobility;
Mobility_Const(const Dune::ParameterTree & param) :
mobility(param.get("Mobility",(Number)0.1))
{
@@ -125,11 +125,27 @@ public:
//______________________________________________________________________________________________________
+template<typename Number>
+class VelDissipation_Linear
+{
+public:
+ Number velDissipationRate;
+ VelDissipation_Linear(const Dune::ParameterTree & param) :
+ velDissipationRate(param.get("VelDissipationRate",(Number)10))
+ {
+ }
+
+ Number eval( const Number& pf_f) const
+ {
+ return std::max(velDissipationRate*(1-pf_f),0.);
+ }
+};
+
template<typename Number>
class VelDissipation_Quadratic
{
public:
- const Number velDissipationRate;
+ Number velDissipationRate;
VelDissipation_Quadratic(const Dune::ParameterTree & param) :
velDissipationRate(param.get("VelDissipationRate",(Number)10))
{
@@ -141,6 +157,29 @@ public:
}
};
+
+template<typename Number>
+class VelDissipation_Quadratic_Shifted
+{
+public:
+ const Number velDissipationRate;
+ const Number dMax;
+ VelDissipation_Quadratic_Shifted(const Dune::ParameterTree & param) :
+ velDissipationRate(param.get("VelDissipationRate",(Number)10)),
+ dMax(param.get("VelDissipationMax",(Number)0.9))
+ {
+ }
+
+ Number eval( const Number& pf_f) const
+ {
+ if(pf_f>dMax)
+ {
+ return 0;
+ }
+ return velDissipationRate*(dMax-pf_f)*(dMax-pf_f)/(dMax*dMax);
+ }
+};
+
//______________________________________________________________________________________________________
@@ -151,19 +190,23 @@ public:
const Number D;
const Number uAst;
const Number mu;
+ const Number muS;
const Number rho_1;
const Number rho_2;
const Number rho_3;
const Number curvatureAlpha;
+ const Number outerMomentumXForce;
Params_Physical(const Dune::ParameterTree& ptree, const Number eps) :
D(ptree.get("D",(Number)0.1)),
uAst(ptree.get("uAst",(Number)2)),
mu(ptree.get("mu",(Number)0.01)),
+ muS(ptree.get("muS",mu)),
rho_1(ptree.get("rho1",(Number)1)),
rho_2(ptree.get("rho2",(Number)1)),
rho_3(ptree.get("rho1",(Number)1)), //WE ASSUME RHO1 = RHO3 !!!
- curvatureAlpha(ptree.get("CurvatureAlpha", eps))
+ curvatureAlpha(ptree.get("CurvatureAlpha", eps)),
+ outerMomentumXForce(ptree.get("OuterMomentumXForce",(Number)0))
{
}
@@ -172,6 +215,12 @@ public:
return pf1*rho_1+pf2*rho_2;
}
+ Number eval_mu (const Number& pf_f) const
+ {
+ //return pf_f*mu+(1-pf_f)*muS;
+ return 1/(pf_f*1/mu + (1-pf_f)*1/muS); //TODO Evaluate differences
+ }
+
};
//______________________________________________________________________________________________________
@@ -240,6 +289,21 @@ public:
}
};
+template <typename Number, typename TW, typename Mobility>
+class Params_fff : public Params_base<Number, Mobility>
+{
+public:
+
+ TW tw;
+ Number SurfaceTensionScaling;
+
+ Params_fff(const Dune::ParameterTree& ptree) :
+ Params_base<Number, Mobility>(ptree),
+ tw(ptree.sub("Phasefield")),
+ SurfaceTensionScaling(ptree.get("Physics.SurfaceTensionScaling",(Number)1))
+ {
+ }
+};
template <typename Number, typename TW, typename Mobility, typename Reaction, typename VelDissipation>
class Params_ffs_r : public Params_base<Number, Mobility>
diff --git a/dune/phasefield/base_potentials.hh b/dune/phasefield/base_potentials.hh
index f170add..e209cbe 100644
--- a/dune/phasefield/base_potentials.hh
+++ b/dune/phasefield/base_potentials.hh
@@ -123,7 +123,7 @@ public:
Number gammaeval_d;
Limiter_FakeDiverging(const Dune::ParameterTree & ptree) :
delta(ptree.get("DoubleWellDelta",(Number)0.1)),
- gamma(ptree.get("DoubleWellGamma",(Number)delta/20))
+ gamma(ptree.get("DoubleWellGamma",(Number)delta/2))
{
gammaeval=delta*gamma*gamma/(delta-gamma);
gammaeval_d=-delta*gamma*(-gamma+2*delta)/((delta-gamma)*(delta-gamma));
diff --git a/dune/phasefield/boundary_fn.hh b/dune/phasefield/boundary_fn.hh
index 9ad4ac4..b6592c7 100644
--- a/dune/phasefield/boundary_fn.hh
+++ b/dune/phasefield/boundary_fn.hh
@@ -5,10 +5,12 @@
#include <dune/pdelab/constraints/common/constraintsparameters.hh>
#define GRID_EPS 1e-7
-#define GRID_WIDTH 6 // 1.5 for summer school //2 for contactpointtest //6 for full summer school
+#define GRID_WIDTH 2 // 1.5 for summer school //2 for contactpointtest //6 for full summer school
-#define GRID_BOTTOM 0 //0 For summer school //0.35 for contactpointtest
-#define GRID_TOP 0.125 //0.125 for summer school //1 for contactpointtest
+#define GRID_BOTTOM 0 //0 For summer school //0.35 for contactpointtest //0.35 for hainesjump
+#define GRID_TOP 1 //0.125 for summer school //1 for contactpointtest //0.65 for hainesjump
+
+#define GRID_TEST 0.05
class InflowOutflow_v : public Dune::PDELab::DirichletConstraintsParameters
{
@@ -18,7 +20,7 @@ public:
{
Dune::FieldVector<typename I::ctype, I::coorddimension>
xg = intersection.geometry().global( coord );
- if ( (xg[0]> GRID_WIDTH-GRID_EPS /*|| xg[0] < GRID_EPS*/) && xg[1]>GRID_BOTTOM+GRID_EPS && xg[1]<GRID_TOP-GRID_EPS)
+ if ( (xg[0]> GRID_WIDTH-GRID_EPS || xg[0] < GRID_EPS) && xg[1]>GRID_BOTTOM+GRID_EPS+GRID_TEST && xg[1]<GRID_TOP-GRID_EPS - GRID_TEST)
{
return false;
}
@@ -36,7 +38,7 @@ public:
{
Dune::FieldVector<typename I::ctype, I::coorddimension>
xg = intersection.geometry().global( coord );
- if ((xg[0]> GRID_WIDTH-GRID_EPS /*|| xg[0] < GRID_EPS*/) && xg[1]>GRID_BOTTOM+GRID_EPS && xg[1]<GRID_TOP-GRID_EPS)
+ if ((xg[0]> GRID_WIDTH-GRID_EPS || xg[0] < GRID_EPS) && xg[1]>GRID_BOTTOM+GRID_EPS && xg[1]<GRID_TOP-GRID_EPS)
{
return true;
}
diff --git a/dune/phasefield/chns_base.hh b/dune/phasefield/chns_base.hh
index cf3c9b0..abecb54 100644
--- a/dune/phasefield/chns_base.hh
+++ b/dune/phasefield/chns_base.hh
@@ -8,6 +8,7 @@
#include<dune/pdelab/backend/istl.hh>
#include <dune/phasefield/base_parameters.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
//_________________________________________________________________________________________________________________________
@@ -78,22 +79,88 @@ public:
}
catch(...)
{
- if(time.dt <= dtMin)
+ return rejectTimestep();
+ }
+
+ applyTimestep(vtkwriter);
+
+ return 1;
+ }
+
+ // RETURN VALUE: -1 -> ABORT, 0-> REDO TIMESTEP, 1-> OK
+ template<typename NS_NEWTON, typename VTKWRITER>
+ int doOnlyNSTimestep(NS_NEWTON& ns_newton, VTKWRITER& vtkwriter)
+ {
+ try
+ {
+ if (verb > 1) std::cout << "= Begin (only) newtonapply NS:" << std::endl;
+ ns_newton.apply();
+ }
+ catch(...)
+ {
+ return rejectTimestep();
+ }
+ applyTimestep(vtkwriter);
+ return 1;
+ }
+
+ // RETURN VALUE: -1 -> ABORT, 0-> REDO TIMESTEP, 1-> OK
+ template<typename CH_NEWTON, typename VTKWRITER>
+ int doOnlyCHTimestep(CH_NEWTON& ch_newton, VTKWRITER& vtkwriter)
+ {
+ try
+ {
+ if (verb > 1) std::cout << "= Begin (only) newtonapply CH:" << std::endl;
+ ch_newton.apply();
+ }
+ catch(...)
+ {
+ return rejectTimestep();
+ }
+ applyTimestep(vtkwriter);
+ return 1;
+ }
+
+ template<typename NS_NEWTON, typename CH_NEWTON, typename VTKWRITER, typename NS_V, typename CH_V>
+ int doTimestepToConvergence(NS_NEWTON& ns_newton, CH_NEWTON& ch_newton, VTKWRITER& vtkwriter, NS_V& nsV, CH_V& chV)
+ {
+ NS_V nsVLast = nsV;
+ CH_V chVLast = chV;
+ int iter = 0;
+ try
+ {
+ do
{
- std::cout << "===============================" << std::endl;
- if(dtMin==dtMax)
- std::cout << "Problem with Newton Solver, aborting :(" << std::endl;
- else
- std::cout << "Timestep too small, aborting :(" << std::endl;
- std::cout << "===============================" << std::endl;
- return -1;
+ if (verb > 1) std::cout << "= NS/CH Iteration " << iter << std::endl;
+ nsVLast = nsV;
+ chVLast = chV;
+
+ if (verb > 1) std::cout << "= Begin newtonapply NS:" << std::endl;
+ ns_newton.apply();
+
+ if (verb > 1) std::cout << "= Begin newtonapply CH:" << std::endl;
+ ch_newton.apply();
+
+ if (verb > 1) std::cout << "Result: " << ns_newton.result().iterations << " and " << ch_newton.result().iterations << std::endl;
+ iter++;
}
- time.dt = std::max(time.dt*dtDecreaseFactor,dtMin);
- if (verb > 0) std::cout << "Reducing Timestep to "<< time.dt << std::endl;
+ while(iter < 10 && (ns_newton.result().iterations > 0 || ch_newton.result().iterations > 0));
- return 0;
}
+ catch(...)
+ {
+ return rejectTimestep();
+ }
+
+ applyTimestep(vtkwriter);
+ return 1;
+ }
+
+
+ template<typename VTKWRITER>
+ void applyTimestep(VTKWRITER& vtkwriter)
+ {
time.t += time.dt;
if(time.dt < dtMax)
{
@@ -106,7 +173,23 @@ public:
lastsave = time.t;
vtkwriter.write(time.t,Dune::VTK::ascii);
}
- return 1;
+ }
+
+ int rejectTimestep()
+ {
+ if(time.dt <= dtMin)
+ {
+ std::cout << "===============================" << std::endl;
+ if(dtMin==dtMax)
+ std::cout << "Problem with Newton Solver, aborting :(" << std::endl;
+ else
+ std::cout << "Timestep too small, aborting :(" << std::endl;
+ std::cout << "===============================" << std::endl;
+ return -1;
+ }
+ time.dt = std::max(time.dt*dtDecreaseFactor,dtMin);
+ if (verb > 0) std::cout << "Reducing Timestep to "<< time.dt << std::endl;
+ return 0;
}
@@ -131,7 +214,103 @@ void interpolateToBdry(const GFS& gfs, const NS_BDRY_FN& nsBdryFn, const CH_BDRY
//_________________________________________________________________________________________________________________________
-template<typename GV, typename RF, typename EST_LOP, typename CH_GFS>
+template<class Grid, class GV, class GFS1, class GFS2, class X1, class X2>
+void my_adapt_grid (Grid& grid, GV& gv, GFS1& gfs1, X1& x1, GFS2& gfs2, X2& x2, int int_order)
+{
+ typedef Dune::PDELab::L2Projection<GFS1,X1> Projection1;
+ Projection1 projection1(gfs1,int_order);
+ typedef Dune::PDELab::L2Projection<GFS2,X2> Projection2;
+ Projection2 projection2(gfs2,int_order);
+
+ Dune::PDELab::GridAdaptor<Grid,GFS1,X1,Projection1> grid_adaptor1(gfs1);
+ Dune::PDELab::GridAdaptor<Grid,GFS2,X2,Projection2> grid_adaptor2(gfs2);
+
+ // prepare the grid for refinement
+ grid.preAdapt();
+
+ // save solution
+ typename Dune::PDELab::GridAdaptor<Grid,GFS1,X1,Projection1>::MapType transferMap1;
+ grid_adaptor1.backupData(grid,gfs1,projection1,x1,transferMap1);
+ typename Dune::PDELab::GridAdaptor<Grid,GFS2,X2,Projection2>::MapType transferMap2;
+ grid_adaptor2.backupData(grid,gfs2,projection2,x2,transferMap2);
+
+ // adapt the grid
+
+ std::cout << "Grid vor adapt";
+ grid.adapt();
+ std::cout << "Grid nach adapt";
+ gv.update();
+ std::cout << "nach GV adapt";
+
+ // update the function spaces
+ gfs1.update(true);
+ gfs2.update(true);
+
+ // interpolate solution
+ x1 = X1(gfs1,0.0);
+ grid_adaptor1.replayData(grid,gfs1,projection1,x1,transferMap1);
+ x2 = X2(gfs2,0.0);
+ grid_adaptor2.replayData(grid,gfs2,projection2,x2,transferMap2);
+
+ // clean up
+ grid.postAdapt();
+}
+
+
+template<class Grid, class GV, class GFS1, class GFS2, class X1, class X2>
+void my_adapt_grid (Grid& grid, GV& gv, GFS1& gfs1, X1& x1, X1& x1b, GFS2& gfs2, X2& x2, X2& x2b, int int_order)
+{
+ typedef Dune::PDELab::L2Projection<GFS1,X1> Projection1;
+ Projection1 projection1(gfs1,int_order);
+ typedef Dune::PDELab::L2Projection<GFS2,X2> Projection2;
+ Projection2 projection2(gfs2,int_order);
+
+ Dune::PDELab::GridAdaptor<Grid,GFS1,X1,Projection1> grid_adaptor1(gfs1);
+ Dune::PDELab::GridAdaptor<Grid,GFS1,X1,Projection1> grid_adaptor1b(gfs1);
+ Dune::PDELab::GridAdaptor<Grid,GFS2,X2,Projection2> grid_adaptor2(gfs2);
+ Dune::PDELab::GridAdaptor<Grid,GFS2,X2,Projection2> grid_adaptor2b(gfs2);
+
+ // prepare the grid for refinement
+ grid.preAdapt();
+
+ // save solution
+ typename Dune::PDELab::GridAdaptor<Grid,GFS1,X1,Projection1>::MapType transferMap1;
+ grid_adaptor1.backupData(grid,gfs1,projection1,x1,transferMap1);
+ grid_adaptor1b.backupData(grid,gfs1,projection1,x1b,transferMap1);
+ typename Dune::PDELab::GridAdaptor<Grid,GFS2,X2,Projection2>::MapType transferMap2;
+ grid_adaptor2.backupData(grid,gfs2,projection2,x2,transferMap2);
+ grid_adaptor2b.backupData(grid,gfs2,projection2,x2b,transferMap2);
+
+ // adapt the grid
+
+ std::cout << "Grid vor adapt";
+ grid.adapt();
+ std::cout << "Grid nach adapt";
+ gv.update();
+ std::cout << "nach GV adapt";
+
+ // update the function spaces
+ gfs1.update(true);
+ gfs2.update(true);
+
+ // interpolate solution
+ x1 = X1(gfs1,0.0);
+ grid_adaptor1.replayData(grid,gfs1,projection1,x1,transferMap1);
+ x1b = X1(gfs1,0.0);
+ grid_adaptor1b.replayData(grid,gfs1,projection1,x1b,transferMap1);
+ x2 = X2(gfs2,0.0);
+ grid_adaptor2.replayData(grid,gfs2,projection2,x2,transferMap2);
+ x2b = X2(gfs2,0.0);
+ grid_adaptor2b.replayData(grid,gfs2,projection2,x2b,transferMap2);
+ // clean up
+ grid.postAdapt();
+}
+
+
+
+
+//_________________________________________________________________________________________________________________________
+template<typename GV, typename RF, typename EST_LOP, typename EST_GFS>
class RefinementIndicator
{
public:
@@ -152,7 +331,7 @@ public:
EST_LOP estlop;
typedef Dune::PDELab::EmptyTransformation NCC;
typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
- typedef Dune::PDELab::GridOperator<CH_GFS,P0GFS,EST_LOP,MBE,RF,RF,RF,NCC,NCC> ESTGO;
+ typedef Dune::PDELab::GridOperator<EST_GFS,P0GFS,EST_LOP,MBE,RF,RF,RF,NCC,NCC> ESTGO;
ESTGO estgo;
double eta_refine;
@@ -160,7 +339,7 @@ public:
int Rmaxlevel;
int Rminlevel;
- RefinementIndicator(const GV& gv, const CH_GFS chGfs, const Dune::ParameterTree & param) :
+ RefinementIndicator(const GV& gv, const EST_GFS chGfs, const Dune::ParameterTree & param) :
p0fem(Dune::GeometryTypes::simplex(GV::dimension)),
p0Gfs(gv,p0fem),
z0(p0Gfs,0.0),
@@ -190,7 +369,110 @@ public:
template<typename Grid>
void markGrid(Grid &grid, int verbosity=0)
{
- if(verbosity>0) std::cout<<"mark elements"<<std::endl;
+ if(verbosity>0) std::cout<<"mark elements: ";
Dune::PDELab::mark_grid(grid,z0,eta_refine,eta_coarsen, Rminlevel,Rmaxlevel,verbosity,-1);
}
+
+ template<typename Grid, typename CH_V, typename NS_V, typename CH_GFS, typename NS_GFS>
+ void refineGrid(Grid &grid, CH_V &chV, CH_V &chVOld, NS_V &nsV, NS_V &nsVOld, CH_GFS chgfs, NS_GFS nsgfs, int verbosity = 0)
+ {
+ if(verbosity > 1)
+ {
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+
+ // do refinement
+ if(verbosity > 0) std::cout << "adapt grid and solution... ";
+
+ auto chTransfer = transferSolutions(chgfs,4,chV,chVOld);
+ auto nsTransfer = transferSolutions(nsgfs,4,nsV,nsVOld);
+ Dune::PDELab::adaptGrid(grid, chTransfer,nsTransfer);
+
+ if(verbosity > 0) std::cout << " ...adapt ended" << std::endl;
+
+ if(verbosity > 1)
+ {
+
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+ }
+
+ template<typename Grid, typename CH_V, typename NS_V, typename CH_GFS, typename NS_GFS>
+ void refineGrid(Grid &grid, CH_V &chV, NS_V &nsV, CH_GFS chgfs, NS_GFS nsgfs, int verbosity = 0)
+ {
+ if(verbosity > 1)
+ {
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+
+ // do refinement
+ if(verbosity > 0) std::cout << "adapt grid and solution... ";
+ auto chTransfer = transferSolutions(chgfs,4,chV);
+ auto nsTransfer = transferSolutions(nsgfs,4,nsV);
+ Dune::PDELab::adaptGrid(grid, chTransfer,nsTransfer);
+
+ if(verbosity > 0) std::cout << " ...adapt ended" << std::endl;
+
+ if(verbosity > 1)
+ {
+
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+ }
+
+ template<typename Grid, typename CH_V, typename NS_V, typename CH_GFS, typename NS_GFS>
+ void myRefineGrid(Grid &grid, GV& gv, CH_V &chV, NS_V &nsV, CH_GFS chgfs, NS_GFS nsgfs, int verbosity = 0)
+ {
+ if(verbosity > 1)
+ {
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+
+ // do refinement
+ if(verbosity > 0) std::cout << "adapt grid and solution... ";
+ //auto chTransfer = transferSolutions(chgfs,4,chV);
+ //auto nsTransfer = transferSolutions(nsgfs,4,nsV);
+ //Dune::PDELab::adaptGrid(grid, chTransfer,nsTransfer);
+ my_adapt_grid(grid, gv, chgfs, chV, nsgfs, nsV,4);
+
+ if(verbosity > 0) std::cout << " ...adapt ended" << std::endl;
+
+ if(verbosity > 1)
+ {
+
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+ }
+
+ template<typename Grid, typename CH_V, typename NS_V, typename CH_GFS, typename NS_GFS>
+ void myRefineGrid(Grid &grid, GV& gv, CH_V &chV, CH_V &chVOld, NS_V &nsV, NS_V &nsVOld, CH_GFS chgfs, NS_GFS nsgfs, int verbosity = 0)
+ {
+ if(verbosity > 1)
+ {
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+
+ // do refinement
+ if(verbosity > 0) std::cout << "adapt grid and solution... ";
+ //auto chTransfer = transferSolutions(chgfs,4,chV);
+ //auto nsTransfer = transferSolutions(nsgfs,4,nsV);
+ //Dune::PDELab::adaptGrid(grid, chTransfer,nsTransfer);
+ my_adapt_grid(grid, gv, chgfs, chV, chVOld, nsgfs, nsV, nsVOld, 4);
+
+ if(verbosity > 0) std::cout << " ...adapt ended" << std::endl;
+
+ if(verbosity > 1)
+ {
+
+ printVector(chV,verbosity-2,"chV");
+ printVector(nsV,verbosity-2,"nsV");
+ }
+ }
};
diff --git a/dune/phasefield/fff_chns.hh b/dune/phasefield/fff_chns.hh
new file mode 100644
index 0000000..332ff5d
--- /dev/null
+++ b/dune/phasefield/fff_chns.hh
@@ -0,0 +1,216 @@
+#pragma once
+
+#include<dune/pdelab/constraints/common/constraints.hh>
+#include<dune/pdelab/constraints/conforming.hh>
+
+#include<dune/pdelab/gridfunctionspace/gridfunctionspace.hh>
+#include<dune/pdelab/gridfunctionspace/subspace.hh>
+#include<dune/pdelab/gridfunctionspace/vectorgridfunctionspace.hh>
+#include<dune/phasefield/utility/pf_3p_color_dgf.hh>
+
+
+//_________________________________________________________________________________________________________________________
+
+
+template<typename RF, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+class GFS_fff_chns
+{
+public:
+ typedef Dune::PDELab::ConformingDirichletConstraints ConstraintsAssembler;
+ typedef Dune::PDELab::ISTL::VectorBackend<> VectorBackend;
+ typedef Dune::PDELab::ISTL::VectorBackend<Dune::PDELab::ISTL::Blocking::fixed> VB_Block;
+ typedef Dune::PDELab::LexicographicOrderingTag OrderingTagL;
+ typedef Dune::PDELab::EntityBlockedOrderingTag OrderingTagB;
+
+ ConstraintsAssembler conp, conphi, conmu;
+
+ typedef Dune::PDELab::VectorGridFunctionSpace<ES,V_FEM,ES::GridView::dimension,
+ VectorBackend,VectorBackend,ConstraintsAssembler> V_GFS;
+ V_GFS vGfs;
+
+ typedef Dune::PDELab::GridFunctionSpace<ES, P_FEM, ConstraintsAssembler, VectorBackend> P_GFS;
+ P_GFS pGfs;
+
+ typedef Dune::PDELab::GridFunctionSpace<ES, PHI_FEM, ConstraintsAssembler, VectorBackend> PHI_GFS;
+ PHI_GFS phiGfs;
+
+ typedef Dune::PDELab::GridFunctionSpace<ES, PHI_FEM, ConstraintsAssembler, VectorBackend> MU_GFS;
+ MU_GFS muGfs;
+
+ typedef Dune::PDELab::CompositeGridFunctionSpace<VectorBackend, OrderingTagL, V_GFS, P_GFS> NS;
+ NS ns;
+
+ typedef Dune::PDELab::CompositeGridFunctionSpace<VB_Block, OrderingTagB, PHI_GFS, MU_GFS, PHI_GFS, MU_GFS> CH;
+ CH ch;
+
+ typedef typename NS::template ConstraintsContainer<RF>::Type NS_CC;
+ NS_CC nsCC;
+
+ typedef typename CH::template ConstraintsContainer<RF>::Type CH_CC;
+ CH_CC chCC;
+
+ GFS_fff_chns(const ES& es, const V_FEM& vFem, const P_FEM& pFem, const PHI_FEM& phiFem) :
+ conp(),conphi(),conmu(),
+ vGfs(es,vFem),
+ pGfs(es,pFem, conp),
+ phiGfs(es,phiFem, conphi),
+ muGfs(es,phiFem, conmu),
+ ns(vGfs, pGfs),
+ ch(phiGfs, muGfs, phiGfs, muGfs),
+ nsCC(),
+ chCC()
+ {
+ vGfs.name("velocity");
+ pGfs.name("pressure");
+ phiGfs.name("phasefield");
+ muGfs.name("potential");
+ }
+
+ template<typename Bdry>
+ void updateConstraintsContainer(const Bdry& bdry)
+ {
+ Dune::PDELab::constraints(bdry.bdryNS,ns,nsCC, 0);
+ Dune::PDELab::constraints(bdry.bdryCH,ch,chCC, 0);
+ }
+};
+
+//_________________________________________________________________________________________________________________________
+
+
+template<typename GFS, typename NS_V, typename CH_V>
+class DGF_fff_chns
+{
+public:
+
+ typedef Dune::PDELab::GridFunctionSubSpace<typename GFS::NS,Dune::TypeTree::TreePath<0> > VSubGFS;
+ VSubGFS vSubGfs;
+ typedef Dune::PDELab::VectorDiscreteGridFunction<VSubGFS,NS_V> VDGF;
+ VDGF vDgf;
+
+ typedef Dune::PDELab::GridFunctionSubSpace<typename GFS::NS,Dune::TypeTree::TreePath<1> > PSubGFS;
+ PSubGFS pSubGfs;
+ typedef Dune::PDELab::DiscreteGridFunction<PSubGFS,NS_V> PDGF;
+ PDGF pDgf;
+
+ typedef Dune::PDELab::GridFunctionSubSpace<typename GFS::CH,Dune::TypeTree::TreePath<0> > PhiSubGFS;
+ PhiSubGFS phiSubGfs;
+ typedef Dune::PDELab::DiscreteGridFunction<PhiSubGFS,CH_V> PhiDGF;
+ PhiDGF phiDgf;
+
+ typedef Dune::PDELab::GridFunctionSubSpace<typename GFS::CH,Dune::TypeTree::TreePath<1> > MuSubGFS;
+ MuSubGFS muSubGfs;
+ typedef Dune::PDELab::DiscreteGridFunction<MuSubGFS,CH_V> MuDGF;
+ MuDGF muDgf;
+
+ typedef Dune::PDELab::GridFunctionSubSpace<typename GFS::CH,Dune::TypeTree::TreePath<2> > Phi2SubGFS;
+ Phi2SubGFS phi2SubGfs;
+ typedef Dune::PDELab::DiscreteGridFunction<Phi2SubGFS,CH_V> Phi2DGF;
+ Phi2DGF phi2Dgf;
+
+ typedef Dune::PDELab::GridFunctionSubSpace<typename GFS::CH,Dune::TypeTree::TreePath<3> > Mu2SubGFS;
+ Mu2SubGFS mu2SubGfs;
+ typedef Dune::PDELab::DiscreteGridFunction<Mu2SubGFS,CH_V> Mu2DGF;
+ Mu2DGF mu2Dgf;
+
+ typedef PF_3P_Color_DGF<typename GFS::CH,CH_V,3> ColorDGF;
+ ColorDGF colorDgf;
+
+
+ DGF_fff_chns(const GFS& gfs, const NS_V& nsV, const CH_V& chV) :
+ vSubGfs(gfs.ns),
+ vDgf(vSubGfs,nsV),
+ pSubGfs(gfs.ns),
+ pDgf(pSubGfs,nsV),
+
+ phiSubGfs(gfs.ch),
+ phiDgf(phiSubGfs,chV),
+ muSubGfs(gfs.ch),
+ muDgf(muSubGfs,chV),
+ phi2SubGfs(gfs.ch),
+ phi2Dgf(phi2SubGfs,chV),
+ mu2SubGfs(gfs.ch),
+ mu2Dgf(mu2SubGfs,chV),
+
+ colorDgf(gfs.ch,chV)
+ {
+ }
+
+ template<typename VTKWRITER>
+ void addToVTKWriter(VTKWRITER& vtkwriter)
+ {
+ vtkwriter.addVertexData(std::make_shared<Dune::PDELab::VTKGridFunctionAdapter<VDGF> >(vDgf,"v"));
+ vtkwriter.addVertexData(std::make_shared<Dune::PDELab::VTKGridFunctionAdapter<PDGF> >(pDgf,"p"));
+ vtkwriter.addVertexData(std::make_shared<Dune::PDELab::VTKGridFunctionAdapter<PhiDGF> >(phiDgf,"phi"));
+ vtkwriter.addVertexData(std::make_shared<Dune::PDELab::VTKGridFunctionAdapter<MuDGF> >(muDgf,"mu"));
+ vtkwriter.addVertexData(std::make_shared<Dune::PDELab::VTKGridFunctionAdapter<Phi2DGF> >(phi2Dgf,"phi2"));
+ vtkwriter.addVertexData(std::make_shared<Dune::PDELab::VTKGridFunctionAdapter<Mu2DGF> >(mu2Dgf,"mu2"));
+ vtkwriter.addVertexData(std::make_shared<Dune::PDELab::VTKGridFunctionAdapter<ColorDGF> >(colorDgf,"_coloring_"));
+ }
+};
+
+//_________________________________________________________________________________________________________________________
+
+template<typename IniV, typename IniP, typename IniPhi, typename IniMu, typename IniPhi2, typename IniMu2>
+class Ini_fff_chns
+{
+public:
+ IniV iniV;
+ IniP iniP;
+ IniPhi iniPhi;
+ IniMu iniMu;
+ IniPhi2 iniPhi2;
+ IniMu2 iniMu2;
+ typedef Dune::PDELab::CompositeGridFunction<IniV,IniP> IniNS;
+ typedef Dune::PDELab::CompositeGridFunction<IniPhi,IniMu,IniPhi2,IniMu2> IniCH;
+ IniNS iniNS;
+ IniCH iniCH;
+
+ template<typename GV, typename Params>
+ Ini_fff_chns(const GV& gv, const Params& params) :
+ iniV(gv, params),
+ iniP(gv, params),
+ iniPhi(gv, params),
+ iniMu(gv, params),
+ iniPhi2(gv, params),
+ iniMu2(gv, params),
+ iniNS(iniV,iniP),
+ iniCH(iniPhi,iniMu,iniPhi2,iniMu2)
+ {
+ }
+};
+
+//_________________________________________________________________________________________________________________________
+
+template<typename BdryV1, typename BdryV2, typename BdryP,
+ typename BdryPhi, typename BdryMu, typename BdryPhi2, typename BdryMu2>
+class Bdry_fff_chns_compositeV_2d
+{
+public:
+ BdryV1 bdryV1;
+ BdryV2 bdryV2;
+ BdryP bdryP;
+ BdryPhi bdryPhi;
+ BdryMu bdryMu;
+ BdryPhi2 bdryPhi2;
+ BdryMu2 bdryMu2;
+ typedef Dune::PDELab::CompositeConstraintsParameters<BdryV1,BdryV2> BdryV;
+ typedef Dune::PDELab::CompositeConstraintsParameters<BdryV, BdryP> BdryNS;
+ typedef Dune::PDELab::CompositeConstraintsParameters<BdryPhi, BdryMu, BdryPhi2, BdryMu2> BdryCH;
+ BdryV bdryV;
+ BdryNS bdryNS;
+ BdryCH bdryCH;
+
+ Bdry_fff_chns_compositeV_2d() :
+ bdryV1(),
+ bdryV2(),
+ bdryP(),
+ bdryPhi(),
+ bdryMu(),
+ bdryPhi2(),
+ bdryMu2(),
+ bdryV(bdryV1,bdryV2),
+ bdryNS(bdryV,bdryP),
+ bdryCH(bdryPhi,bdryMu,bdryPhi2,bdryMu2)
+ {
+ }
+};
diff --git a/dune/phasefield/ffs_chns_r.hh b/dune/phasefield/ffs_chns_r.hh
index f529752..f3a386a 100644
--- a/dune/phasefield/ffs_chns_r.hh
+++ b/dune/phasefield/ffs_chns_r.hh
@@ -232,3 +232,56 @@ public:
{
}
};
+
+template<typename BdryV1, typename BdryV2, typename BdryP,
+ typename BdryPhi, typename BdryMu, typename BdryPhi2, typename BdryMu2, typename BdryU>
+class Bdry_ffs_chns_r_compositeV_2d_Explicit_Domain
+{
+public:
+ BdryV1 bdryV1;
+ BdryV2 bdryV2;
+ BdryP bdryP;
+ BdryPhi bdryPhi;
+ BdryMu bdryMu;
+ BdryPhi2 bdryPhi2;
+ BdryMu2 bdryMu2;
+ BdryU bdryU;
+ typedef Dune::PDELab::CompositeConstraintsParameters<BdryV1,BdryV2> BdryV;
+ typedef Dune::PDELab::CompositeConstraintsParameters<BdryV, BdryP> BdryNS;
+ typedef Dune::PDELab::CompositeConstraintsParameters<BdryPhi, BdryMu, BdryPhi2, BdryMu2, BdryU> BdryCH;
+ BdryV bdryV;
+ BdryNS bdryNS;
+ BdryCH bdryCH;
+
+ template<typename DomainSize>
+ Bdry_ffs_chns_r_compositeV_2d_Explicit_Domain(DomainSize ds) :
+ bdryV1(ds),
+ bdryV2(ds),
+ bdryP(ds),
+ bdryPhi(ds),
+ bdryMu(ds),
+ bdryPhi2(ds),
+ bdryMu2(ds),
+ bdryU(ds),
+ bdryV(bdryV1,bdryV2),
+ bdryNS(bdryV,bdryP),
+ bdryCH(bdryPhi,bdryMu,bdryPhi2,bdryMu2,bdryU)
+ {
+ }
+};
+
+template<typename RF>
+class DomainSize
+{
+public:
+ const RF bottom;
+ const RF top;
+ const RF left;
+ const RF right;
+ const RF domainEps;
+
+ DomainSize(RF b, RF t, RF l, RF r, RF eps):
+ bottom(b), top(t), left(l), right(r), domainEps(eps)
+ {
+ }
+};
diff --git a/dune/phasefield/initial_fn.hh b/dune/phasefield/initial_fn.hh
index 835b6b5..9fd421a 100644
--- a/dune/phasefield/initial_fn.hh
+++ b/dune/phasefield/initial_fn.hh
@@ -1,6 +1,7 @@
#pragma once
#include <cmath>
+#include <cstdlib>
#include <dune/pdelab/common/function.hh>
#include <dune/phasefield/base_parameters.hh>
@@ -148,6 +149,80 @@ public:
y=0.5*(1+tanh(1/eps/sqrt(2)*d1))*yy;
}
};
+
+//______________________________________________________________________________________________________________________
+
+template<typename GV, typename RF, typename Params, const int Phase>
+class PhiInitial_3pSlipTest :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PhiInitial_3pSlipTest<GV,RF,Params,Phase> >
+{
+ RF eps;
+
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
+
+ PhiInitial_3pSlipTest(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,PhiInitial_3pSlipTest<GV,RF,Params,Phase> > (gv)
+ {
+ eps = params.eps;
+ }
+
+ inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
+ {
+ y = 0.0;
+
+ RF d2 = x[1]-0.25;
+
+ y = 0.5*(1+tanh(1/eps/sqrt(2)*d2));
+ }
+};
+
+
+//______________________________________________________________________________________________________________________
+
+template<typename GV, typename RF, typename Params, const int Phase>
+class PhiInitial_3pSphereAndDroplet :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PhiInitial_3pSphereAndDroplet<GV,RF,Params,Phase> >
+{
+ RF eps;
+ RF radius;
+ RF radius2;
+ RF dx;
+ RF dy;
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
+
+ PhiInitial_3pSphereAndDroplet(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,PhiInitial_3pSphereAndDroplet<GV,RF,Params,Phase> > (gv)
+ {
+ eps = params.eps;
+ radius = params.initial.ptree.get("Radius",0.1);
+ radius2 = params.initial.ptree.get("Radius2",0.15);
+ dx = params.initial.ptree.get("dx",0.0);
+ dy = params.initial.ptree.get("dx",0.15);
+ }
+
+ inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
+ {
+ y = 0.0;
+
+ RF dist = sqrt( (x[0]-1)*(x[0]-1) + (x[1]-0.5)*(x[1]-0.5) );
+ RF dist2 = sqrt( (x[0]-1-dx)*(x[0]-1-dx) + (x[1]-0.5-dy)*(x[1]-0.5-dy) );
+ RF y1 = 0.5*(1+tanh(1/eps/sqrt(2)*(dist-radius)));
+ RF y2 = 0.5*(1+tanh(1/eps/sqrt(2)*(dist2-radius2)));
+
+ if(Phase == 0)
+ {
+ y[0] = y1 * y2;
+ }
+ if(Phase == 1)
+ {
+ y[0] = y1 * (1-y2);
+ }
+ }
+};
//______________________________________________________________________________________________________________________
template<typename GV, typename RF, typename Params>
@@ -310,6 +385,108 @@ public:
}
};
+
+template<typename GV, typename RF, typename Params, const int Phase>
+class PhiInitial_HainesJump :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PhiInitial_HainesJump<GV,RF,Params,Phase> >
+{
+ RF eps;
+ RF period;
+ RF amplitude;
+ RF height;
+ RF offset;
+
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
+
+ PhiInitial_HainesJump(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,PhiInitial_HainesJump<GV,RF,Params,Phase> > (gv)
+ {
+ eps = params.eps;
+ period = params.initial.ptree.get("Period",1);
+ amplitude = params.initial.ptree.get("Amplitude",0.3);
+ height = params.initial.ptree.get("Height",1);
+ offset = params.initial.ptree.get("Offset",0.1);
+
+
+ }
+
+ inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
+ {
+ RF temp = (-std::cos(x[0]*2*3.1415*period) + 1)*amplitude/2 + offset;
+ RF fluid = 0.5*(1+tanh(1/eps/sqrt(2)*(x[1]-temp)));
+ fluid = fluid*0.5*(1+tanh(1/eps/sqrt(2)*(height-x[1]-temp)));
+
+ RF d1 = x[0]-0.25;
+ if(Phase == 0)
+ d1 = -d1;
+ y=0.5*(1+tanh(1/eps/sqrt(2)*d1))*fluid;
+ }
+};
+
+template<typename GV, typename RF, typename Params>
+class PhiInitial_SpinodalDecomposition :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PhiInitial_SpinodalDecomposition<GV,RF,Params> >
+{
+ RF mean;
+ RF deviation;
+ int seed;
+
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
+
+ PhiInitial_SpinodalDecomposition(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,PhiInitial_SpinodalDecomposition<GV,RF,Params> > (gv)
+ {
+ mean = params.initial.ptree.get("Mean",0.5);
+ deviation = params.initial.ptree.get("Deviation",0.1);
+ seed = params.initial.ptree.get("Seed",1);
+ std::srand(seed);
+ }
+
+ inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
+ {
+ y[0] = mean + deviation*(((RF)std::rand())/RAND_MAX);
+ }
+};
+
+template<typename GV, typename RF, typename Params, const int Phase>
+class PhiInitial_3pBubble :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PhiInitial_3pBubble<GV,RF,Params,Phase> >
+{
+ RF eps;
+ RF r;
+
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
+
+ PhiInitial_3pBubble(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,PhiInitial_3pBubble<GV,RF,Params,Phase> > (gv)
+ {
+ eps = params.eps;
+ r = params.initial.ptree.get("Radius",0.2);
+ }
+
+ inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
+ {
+ RF dist = std::sqrt((x[0]-0.5)*(x[0]-0.5)+(x[1]-0.5)*(x[1]-0.5));
+ RF rf = 0.5*(1+tanh(1/eps/sqrt(2)*(dist-r)));
+
+ if(Phase == 0)
+ {
+ y = 1-rf;
+ return;
+ }
+
+ RF fluid = 0.5*(1+tanh(1/eps/sqrt(2)*(x[1]-0.5)));
+ y=fluid*rf;
+ }
+};
+
+
//______________________________________________________________________________________________________________________
#include <dune/phasefield/boundary_fn.hh>
@@ -354,6 +531,45 @@ public:
};
+
+template<typename GV, typename RF, typename Params, int dim>
+class VelocityInitial_Channelflow :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,dim>,
+ VelocityInitial_Channelflow<GV,RF,Params,dim> >
+{
+ const Params_Time& time;
+ RF v;
+
+
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,dim> Traits;
+
+ typedef typename Traits::DomainType DomainType;
+ typedef typename Traits::RangeType RangeType;
+
+ VelocityInitial_Channelflow(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,VelocityInitial_Channelflow<GV,RF,Params,dim> > (gv)
+ , time(params.time)
+ {
+ v = params.initial.ptree.get("FlowV",(RF)0.1);
+ }
+
+ template <typename T>
+ void setTime(T t){
+ time = t;
+ }
+
+ inline void evaluateGlobal(const DomainType & x, RangeType & y) const
+ {
+ y = 0.0;
+ if(x[1]>1-GRID_EPS) //Flow boundary
+ {
+ y[0] = v;
+ }
+ }
+};
+
template<typename GV, typename RF, typename Params>
class UInitial_Inflow :
public Dune::PDELab::AnalyticGridFunctionBase<
@@ -368,8 +584,8 @@ public:
UInitial_Inflow(const GV & gv, const Params & params) :
Dune::PDELab::AnalyticGridFunctionBase<Traits,UInitial_Inflow<GV,RF,Params> > (gv)
{
- uConst = params.initial.ptree.get("uConst",(RF)1.0);
- uInflow = params.initial.ptree.get("uInflow",(RF)1.5);
+ uConst = params.initial.ptree.get("uConst",(RF)0.5);
+ uInflow = params.initial.ptree.get("uInflow",(RF)0.5);
}
inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
@@ -387,13 +603,14 @@ class PInitial_Inflow :
public Dune::PDELab::AnalyticGridFunctionBase<
Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PInitial_Inflow<GV,RF,Params> >
{
-
+ RF pConst;
public:
typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
PInitial_Inflow(const GV & gv, const Params & params) :
Dune::PDELab::AnalyticGridFunctionBase<Traits,PInitial_Inflow<GV,RF,Params> > (gv)
{
+ pConst = params.initial.ptree.get("pConst",(RF)0.01);
}
inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
@@ -401,7 +618,7 @@ public:
y = 0;
if(x[0]<1e-7)
{
- y=20;
+ y=pConst;
}
}
};
diff --git a/dune/phasefield/localoperator/fem_2p_cahnhilliard.hh b/dune/phasefield/localoperator/fem_2p_cahnhilliard.hh
new file mode 100644
index 0000000..e7745a5
--- /dev/null
+++ b/dune/phasefield/localoperator/fem_2p_cahnhilliard.hh
@@ -0,0 +1,84 @@
+#pragma once
+
+#include<dune/pdelab/common/quadraturerules.hh>
+#include<dune/pdelab/finiteelement/localbasiscache.hh>
+#include<dune/pdelab/localoperator/defaultimp.hh>
+#include<dune/pdelab/localoperator/pattern.hh>
+#include<dune/pdelab/localoperator/flags.hh>
+#include<dune/pdelab/localoperator/variablefactories.hh>
+#include<dune/pdelab/gridfunctionspace/gridfunctionspace.hh>
+
+#include<dune/phasefield/localoperator/fem_base_chns.hh>
+
+
+//Parameter class (for functions), FEM space and RangeField
+template<typename Param, typename CHGFS, typename CHContainer>
+class FEM_2P_CahnHilliard :
+ public Dune::PDELab::FullVolumePattern,
+ public Dune::PDELab::LocalOperatorDefaultFlags,
+ public Dune::PDELab::NumericalJacobianVolume<FEM_2P_CahnHilliard<Param, CHGFS, CHContainer> >,
+ public Dune::PDELab::NumericalJacobianApplyVolume<FEM_2P_CahnHilliard<Param, CHGFS, CHContainer> >
+{
+private:
+ typedef typename CHContainer::field_type RF;
+ typedef typename CHGFS::Traits::GridViewType::template Codim<0>::Entity ENTITY;
+
+ CHLocalBasisCache<CHGFS> chCache;
+
+ typedef GFS_LocalViewer<CHGFS, CHContainer, ENTITY, RF> CHLView;
+ mutable CHLView chOldLocal;
+
+ Param& param; // parameter functions
+
+public:
+ enum {doPatternVolume=true};
+ enum {doAlphaVolume=true};
+
+ //constructor
+ FEM_2P_CahnHilliard(Param& param_, CHGFS& chGfs_, CHContainer& chVOld_) :
+ chOldLocal(chGfs_,chVOld_),
+ param(param_)
+ {
+ }
+
+
+ template<typename EG, typename LFSU, typename X, typename LFSV, typename R>
+ void alpha_volume (const EG& eg, const LFSU& lfsu, const X& x, const LFSV& lfsv, R& r) const
+ {
+ //Quadrature Rule
+ const int dim = EG::Entity::dimension;
+ const int order = 5; //TODO: Choose more educated
+ auto rule = Dune::PDELab::quadratureRule(eg.geometry(), order);
+
+ chOldLocal.DoEvaluation(eg);
+
+ for(const auto& ip : rule)
+ {
+ const auto S = eg.geometry().jacobianInverseTransposed(ip.position());
+ auto factor = ip.weight()*eg.geometry().integrationElement(ip.position());
+
+ CHVariables_PFOld_Extension<RF,dim,LFSV> ch(chCache, ip.position(), lfsv, x.base(), chOldLocal.lv, S);
+
+
+
+ for (size_t i=0; i<ch.pfspace.size(); i++)
+ {
+
+ RF J1 = param.mobility.eval(ch.pf) * (ch.gradxi*ch.basis.gradphi[i][0]);
+
+ // integrate: (pf-pfold)*phi_i/delta_t + gradpf * grad phi_i + ...
+ r.accumulate(ch.pfspace,i,factor*(
+ (ch.pf-ch.pfOld)*ch.basis.phi[i]/param.time.dt
+ +J1
+ ));
+
+ r.accumulate(ch.xispace,i,factor*(
+ ch.xi*ch.basis.phi[i]
+ - 1/param.eps* param.dw.eval_d(ch.pf) *ch.basis.phi[i]
+ - param.eps * (ch.gradpf*ch.basis.gradphi[i][0])
+ ));
+ }
+ }
+ }
+
+};
diff --git a/dune/phasefield/localoperator/fem_3p_cahnhilliard.hh b/dune/phasefield/localoperator/fem_3p_cahnhilliard.hh
new file mode 100644
index 0000000..98b603b
--- /dev/null
+++ b/dune/phasefield/localoperator/fem_3p_cahnhilliard.hh
@@ -0,0 +1,95 @@
+#pragma once
+
+#include<dune/pdelab/common/quadraturerules.hh>
+#include<dune/pdelab/finiteelement/localbasiscache.hh>
+#include<dune/pdelab/localoperator/defaultimp.hh>
+#include<dune/pdelab/localoperator/pattern.hh>
+#include<dune/pdelab/localoperator/flags.hh>
+#include<dune/pdelab/localoperator/variablefactories.hh>
+#include<dune/pdelab/gridfunctionspace/gridfunctionspace.hh>
+
+#include<dune/phasefield/localoperator/fem_base_chns.hh>
+
+
+//Parameter class (for functions), FEM space and RangeField
+template<typename Param, typename CHGFS, typename CHContainer>
+class FEM_3P_CahnHilliard :
+ public Dune::PDELab::FullVolumePattern,
+ public Dune::PDELab::LocalOperatorDefaultFlags,
+ public Dune::PDELab::NumericalJacobianVolume<FEM_3P_CahnHilliard<Param, CHGFS, CHContainer> >,
+ public Dune::PDELab::NumericalJacobianApplyVolume<FEM_3P_CahnHilliard<Param, CHGFS, CHContainer> >
+{
+private:
+ typedef typename CHContainer::field_type RF;
+ typedef typename CHGFS::Traits::GridViewType::template Codim<0>::Entity ENTITY;
+
+ CHLocalBasisCache<CHGFS> chCache;
+
+ typedef GFS_LocalViewer<CHGFS, CHContainer, ENTITY, RF> CHLView;
+ mutable CHLView chOldLocal;
+
+ Param& param; // parameter functions
+
+public:
+ enum {doPatternVolume=true};
+ enum {doAlphaVolume=true};
+
+ //constructor
+ FEM_3P_CahnHilliard(Param& param_, CHGFS& chGfs_, CHContainer& chVOld_) :
+ chOldLocal(chGfs_,chVOld_),
+ param(param_)
+ {
+ }
+
+
+ template<typename EG, typename LFSU, typename X, typename LFSV, typename R>
+ void alpha_volume (const EG& eg, const LFSU& lfsu, const X& x, const LFSV& lfsv, R& r) const
+ {
+ //Quadrature Rule
+ const int dim = EG::Entity::dimension;
+ const int order = 5; //TODO: Choose more educated
+ auto rule = Dune::PDELab::quadratureRule(eg.geometry(), order);
+
+ chOldLocal.DoEvaluation(eg);
+
+ for(const auto& ip : rule)
+ {
+ const auto S = eg.geometry().jacobianInverseTransposed(ip.position());
+ auto factor = ip.weight()*eg.geometry().integrationElement(ip.position());
+
+ CHVariables_Threephase_PFOld_Extension<RF,dim,LFSV> ch(chCache, ip.position(), lfsv, x.base(), chOldLocal.lv, S);
+
+ RF pf3 = 1-ch.pf-ch.pf2;
+ RF xi3 = -param.tw.Sigma3*(ch.xi/param.tw.Sigma1 + ch.xi2/param.tw.Sigma2);
+
+ for (size_t i=0; i<ch.pfspace.size(); i++)
+ {
+ RF J1 = param.mobility.eval(ch.pf,ch.pf2,pf3)*param.eps/param.tw.Sigma1 * (ch.gradxi*ch.basis.gradphi[i][0]);
+
+ // integrate: (pf-pfold)*phi_i/delta_t + gradpf * grad phi_i + ...
+ r.accumulate(ch.pfspace,i,factor*(
+ (ch.pf-ch.pfOld)*ch.basis.phi[i]/param.time.dt
+ +J1
+ ));
+
+ r.accumulate(ch.pf2space,i,factor*(
+ (ch.pf2-ch.pf2Old)*ch.basis.phi[i]/param.time.dt
+ +param.mobility.eval(ch.pf,ch.pf2,pf3)*param.eps/param.tw.Sigma2 * (ch.gradxi2*ch.basis.gradphi[i][0])
+ ));
+
+ r.accumulate(ch.xispace,i,factor*(
+ ch.xi*ch.basis.phi[i]
+ - 1/param.eps* param.tw.eval_dpf1(ch.pf,ch.pf2,pf3) *ch.basis.phi[i]
+ - param.eps * param.tw.Sigma1* (ch.gradpf*ch.basis.gradphi[i][0])
+ ));
+
+ r.accumulate(ch.xi2space,i,factor*(
+ ch.xi2*ch.basis.phi[i]
+ - 1/param.eps* param.tw.eval_dpf2(ch.pf,ch.pf2,pf3) *ch.basis.phi[i]
+ - param.eps * param.tw.Sigma2* (ch.gradpf2*ch.basis.gradphi[i][0])
+ ));
+ }
+ }
+ }
+
+};
diff --git a/dune/phasefield/localoperator/fem_base_chns.hh b/dune/phasefield/localoperator/fem_base_chns.hh
index 33ece23..d01e62e 100644
--- a/dune/phasefield/localoperator/fem_base_chns.hh
+++ b/dune/phasefield/localoperator/fem_base_chns.hh
@@ -126,6 +126,34 @@ public:
}
};
+
+//_________________________________________________________________________________________________________________________
+
+template<typename RF, const int dim, typename CHLFS>
+class CHVariables_PFOld_Extension : public CHVariables<RF,dim,CHLFS>
+{
+public:
+
+
+ RF pfOld;
+ Dune::FieldVector<RF,dim> gradpfOld;
+
+
+ template<typename Pos, typename Cache, typename LV, typename S>
+ CHVariables_PFOld_Extension(const Cache& cache,
+ const Pos& position, const CHLFS& chLfs, const LV& lv, const LV& lvOld, S& s) :
+ CHVariables<RF,dim,CHLFS>(cache, position, chLfs, lv, s),
+ pfOld(0.0),
+ gradpfOld(0.0)
+ {
+ for (size_t i=0; i<this->pfspace.size(); i++)
+ {
+ pfOld += lvOld[this->pfspace.localIndex(i)]*this->basis.phi[i];
+ gradpfOld.axpy(lvOld[this->pfspace.localIndex(i)],this->basis.gradphi[i][0]);
+ }
+ }
+};
+
//_________________________________________________________________________________________________________________________
template<typename RF, const int dim, typename CHLFS>
@@ -202,6 +230,37 @@ public:
//_________________________________________________________________________________________________________________________
+template<typename RF, const int dim, typename CHLFS>
+class CHVariables_Threephase_PFOld_Extension : public CHVariables_Threephase_Extension<RF,dim,CHLFS>
+{
+public:
+
+ RF pfOld;
+ Dune::FieldVector<RF,dim> gradpfOld;
+ RF pf2Old;
+ Dune::FieldVector<RF,dim> gradpf2Old;
+
+
+ template<typename Pos, typename Cache, typename LV, typename S>
+ CHVariables_Threephase_PFOld_Extension(const Cache& cache,
+ const Pos& position, const CHLFS& chLfs, const LV& lv, const LV& lvOld, S& s) :
+ CHVariables_Threephase_Extension<RF,dim,CHLFS>(cache, position, chLfs, lv, s),
+ pfOld(0.0),
+ gradpfOld(0.0),
+ pf2Old(0.0),
+ gradpf2Old(0.0)
+ {
+ for (size_t i=0; i<this->pfspace.size(); i++)
+ {
+ pfOld += lvOld[this->pfspace.localIndex(i)]*this->basis.phi[i];
+ gradpfOld.axpy(lvOld[this->pfspace.localIndex(i)],this->basis.gradphi[i][0]);
+ pf2Old += lvOld[this->pf2space.localIndex(i)]*this->basis.phi[i];
+ gradpf2Old.axpy(lvOld[this->pf2space.localIndex(i)],this->basis.gradphi[i][0]);
+ }
+ }
+};
+
+
template<typename RF, const int dim, typename CHLFS>
class CHVariables_Threephase_U_PFOld_Extension : public CHVariables_Threephase_Extension<RF,dim,CHLFS>
{
diff --git a/dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh b/dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh
index c2e668d..2b072da 100644
--- a/dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh
+++ b/dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh
@@ -115,23 +115,34 @@ template<typename Param, typename CHGFS, typename CHContainer, typename NSGFS, t
//const auto v_nabla_v = v * jacv[k];
RF gradxi3k = -param.tw.Sigma3*(ch.gradxi[k]/param.tw.Sigma1 + ch.gradxi2[k]/param.tw.Sigma2);
RF S = 0;
- //S += xi1*(gradpf1[k]*pf_f - pf1 * gradpf_f[k])/pf_f;
- //S += xi1*(gradpf2[k]*pf_f - pf2 * gradpf_f[k])/pf_f;
- //S += 2*param.delta*(gradxi3k-gradxi2[k]-gradxi1[k]);
- S += ch.pf*ch.gradxi[k] + ch.pf2*ch.gradxi2[k];
+ S += - ch.xi2*(ch.gradpf[k]*pf_f - ch.pf * gradpf_f[k])/(pf_f*pf_f); //TODO!!!!!!! Other pf_f scaling!!!!!
+ S += - ch.xi *(ch.gradpf2[k]*pf_f - ch.pf2 * gradpf_f[k])/(pf_f*pf_f);
+ S += - 2*param.delta*pf3*(gradxi3k-ch.gradxi2[k]-ch.gradxi[k]);
+
+ //Stronger form - flow in interfaces possible
+ //S += -ch.pf*ch.gradxi[k] - ch.pf2*ch.gradxi2[k] - 2*param.delta*pf3*gradxi3k;
+
+ //Works but is not the one in the theory (same as above, w/o regularization)
+ //S += -ch.pf*ch.gradxi[k] - ch.pf2*ch.gradxi2[k];
+
S = S*param.SurfaceTensionScaling*ns.vbasis.phi[i];
r.accumulate(child(ns.vspace,k),i, ( rho_f_reg*(ns.v[k]-ns.vOld[k])*ns.vbasis.phi[i]/param.time.dt //TimeEvolution
- - ns.p * (pf_f*ns.vbasis.gradphi[i][0][k] + ns.vbasis.phi[i]*gradpf_f[k]) //Pressure
- + param.phys.mu * (ns.jacv[k]*ns.vbasis.gradphi[i][0]) //+vphi[i]*(jacv[k]*gradpf) ) //Viscosity
+ //- ns.p * (pf_f*ns.vbasis.gradphi[i][0][k] + ns.vbasis.phi[i]*gradpf_f[k]) //Pressure in weak form
+ + pf_f * (ns.gradp[k] * ns.vbasis.phi[i]) //Pressure in strong form
+ + param.phys.eval_mu(pf_f) * (ns.jacv[k]*ns.vbasis.gradphi[i][0]) //+vphi[i]*(jacv[k]*gradpf) ) //Viscosity
+ param.vDis.eval(pf_f)*ns.v[k]*ns.vbasis.phi[i] //Velocity Dissipation in Solid
//- rho*g[k]*vphi[i] //Gravitation
- + S //Surface Tension
+ - S //Surface Tension
)*factor);
-
- }
- }
- }
- }
+ if(k==0)
+ {
+ r.accumulate(child(ns.vspace,k),i, ( pf_f * (param.phys.outerMomentumXForce * ns.vbasis.phi[i]) // Momentum Forcing Term
+ )*factor);
+ }
+ } //for k
+ } // for i
+ } // for ip
+ } //alpha volume
};
diff --git a/dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh b/dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh
index f5914b7..84f8961 100644
--- a/dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh
+++ b/dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh
@@ -78,8 +78,9 @@ public:
for (size_t i=0; i<ch.pfspace.size(); i++)
{
- RF R1 = 0;//-param.tw.eval_q(ch.pf,ch.pf2,pf3)/param.eps*
- //(param.reaction.eval(ch.u)+param.phys.curvatureAlpha*(ch.xi-xi3))*phi[i];
+ RF Rspeed = std::max(param.tw.eval_q(ch.pf,ch.pf2,pf3) - 0.1, 0.0);
+ RF R1 = -Rspeed/param.eps*
+ (param.reaction.eval(ch.u)+param.phys.curvatureAlpha*(ch.xi-xi3))*ch.basis.phi[i];
RF J1 = param.mobility.eval(ch.pf,ch.pf2,pf3)*param.eps/param.tw.Sigma1 * (ch.gradxi*ch.basis.gradphi[i][0]);
// integrate: (pf-pfold)*phi_i/delta_t + gradpf * grad phi_i + ...
@@ -111,6 +112,8 @@ public:
));
// integrate (pf-pfold)*(u-uast)*phi_i/delta_t + pfold*(u-uold)*phi_i/delta_t + D*pf*gradu*grad phi_i = 0
+
+ Dune::FieldVector<RF, dim> xg = eg.geometry().global( ip.position() );
r.accumulate(ch.uspace,i,factor*(
//(u-param.uAst)*phi[i]/param.dt //For Testing
@@ -122,6 +125,12 @@ public:
//- pf_c*(u-param.phys.uAst)*(v*gradphi[i][0])
+ (pf_c*(ch.u-param.phys.uAst)*ns.div_v + (ch.u-param.phys.uAst)*(ch.gradpf*ns.v) + pf_c*(ch.gradu*ns.v) )*ch.basis.phi[i]
));
+ if(xg[0]<=0.1)
+ {
+ r.accumulate(ch.uspace,i,factor*(
+ 10*(ch.u-1.5)*ch.basis.phi[i] ));
+ }
+
}
}
}
diff --git a/language_tests/Fortran/CMakeCache.txt b/language_tests/Fortran/CMakeCache.txt
new file mode 100644
index 0000000..b22d0d5
--- /dev/null
+++ b/language_tests/Fortran/CMakeCache.txt
@@ -0,0 +1,287 @@
+# This is the CMakeCache file.
+# For build in directory: /usr/local/ssd/home/vonwolls/dumux/dune-phasefield/language_tests/Fortran
+# It was generated by CMake: /usr/bin/cmake
+# You can edit this file to change values found and used by cmake.
+# If you do not want to change any of the values, simply exit the editor.
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+# KEY is the name of a variable in the cache.
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+
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+
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+
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+//Flags used by the linker during Release with Debug Info builds.
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+//If set, runtime paths are not added when installing shared libraries,
+// but are added when building.
+CMAKE_SKIP_INSTALL_RPATH:BOOL=NO
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+//If set, runtime paths are not added when using shared libraries.
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+
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+CMAKE_MODULE_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_NM
+CMAKE_NM-ADVANCED:INTERNAL=1
+//number of local generators
+CMAKE_NUMBER_OF_MAKEFILES:INTERNAL=1
+//ADVANCED property for variable: CMAKE_OBJCOPY
+CMAKE_OBJCOPY-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_OBJDUMP
+CMAKE_OBJDUMP-ADVANCED:INTERNAL=1
+//Platform information initialized
+CMAKE_PLATFORM_INFO_INITIALIZED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_RANLIB
+CMAKE_RANLIB-ADVANCED:INTERNAL=1
+//Path to CMake installation.
+CMAKE_ROOT:INTERNAL=/usr/share/cmake-3.9
+//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS
+CMAKE_SHARED_LINKER_FLAGS-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_DEBUG
+CMAKE_SHARED_LINKER_FLAGS_DEBUG-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL
+CMAKE_SHARED_LINKER_FLAGS_MINSIZEREL-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_SHARED_LINKER_FLAGS_RELEASE
+CMAKE_SHARED_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
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+CMAKE_SHARED_LINKER_FLAGS_RELWITHDEBINFO-ADVANCED:INTERNAL=1
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+CMAKE_SKIP_INSTALL_RPATH-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_SKIP_RPATH
+CMAKE_SKIP_RPATH-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS
+CMAKE_STATIC_LINKER_FLAGS-ADVANCED:INTERNAL=1
+//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_DEBUG
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+//ADVANCED property for variable: CMAKE_STATIC_LINKER_FLAGS_RELEASE
+CMAKE_STATIC_LINKER_FLAGS_RELEASE-ADVANCED:INTERNAL=1
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diff --git a/language_tests/Fortran/CMakeLists.txt b/language_tests/Fortran/CMakeLists.txt
new file mode 100644
index 0000000..97bc95a
--- /dev/null
+++ b/language_tests/Fortran/CMakeLists.txt
@@ -0,0 +1,6 @@
+project(test NONE)
+ cmake_minimum_required(VERSION 2.8.0)
+ set (CMAKE_Fortran_FLAGS "")
+ set (CMAKE_EXE_LINKER_FLAGS "")
+ enable_language(Fortran OPTIONAL)
+
\ No newline at end of file
diff --git a/run-in-dune-env b/run-in-dune-env
new file mode 100755
index 0000000..a759bcd
--- /dev/null
+++ b/run-in-dune-env
@@ -0,0 +1,4 @@
+#!/bin/bash
+
+source /home/ians1/vonwolls/ssd_local/dumux/build-release/python_virtualenv/bin/activate
+"$@"
diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
index 9ca989c..751ad71 100644
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
@@ -5,3 +5,10 @@ add_subdirectory(test_3pchns_r)
add_subdirectory(test_2pchns_r)
add_subdirectory(test_contactpointdynamics)
add_subdirectory(summerschool)
+add_subdirectory(test_slipvelocity)
+add_subdirectory(test_hainesjump)
+add_subdirectory(test_periodic)
+add_subdirectory(paper_epsdelta)
+add_subdirectory(example_cahnhilliard)
+add_subdirectory(example_nucleus)
+add_subdirectory(paper_thinstrip_full)
diff --git a/src/dune-phasefield b/src/dune-phasefield
new file mode 100755
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diff --git a/src/example_cahnhilliard/2p_driver.hh b/src/example_cahnhilliard/2p_driver.hh
new file mode 100644
index 0000000..b78dfac
--- /dev/null
+++ b/src/example_cahnhilliard/2p_driver.hh
@@ -0,0 +1,202 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include <dune/phasefield/localoperator/fem_2p_cahnhilliard.hh>
+#include <dune/phasefield/localoperator/pf_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/ff_chns.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename GV, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_2p(Grid& grid, GV& gv, ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_ff< RF,
+ DoubleWell_poly<RF> ,
+ Mobility_Const<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_ff_chns<RF, ES, V_FEM, P_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+
+ typedef Bdry_ff_chns<2, Dune::PDELab::DirichletConstraintsParameters, // v_x, v_y
+ Dune::PDELab::NoDirichletConstraintsParameters, // p
+ Dune::PDELab::NoDirichletConstraintsParameters, // phi
+ Dune::PDELab::NoDirichletConstraintsParameters> // mu
+ Bdry;
+ Bdry bdry;
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_ff_chns< ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_SpinodalDecomposition<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters>> Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+
+ typedef FEM_2P_CahnHilliard<Parameters, CH_GFS, CH_V > CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_ff_chns<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+
+ // Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ //rInd0.refineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ rInd0.myRefineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //vtkwriter.write(param.time.t + i,Dune::VTK::ascii);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,600,200,3,1);
+
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+
+ int result = timestepManager.doOnlyCHTimestep(ch_newton,vtkwriter);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ //rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+ rInd.myRefineGrid(grid,gv,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,1);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/example_cahnhilliard/3p_driver.hh b/src/example_cahnhilliard/3p_driver.hh
new file mode 100644
index 0000000..1fc06d0
--- /dev/null
+++ b/src/example_cahnhilliard/3p_driver.hh
@@ -0,0 +1,215 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include <dune/phasefield/localoperator/fem_3p_cahnhilliard.hh>
+#include <dune/phasefield/localoperator/pf_3p_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/fff_chns.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename GV, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_3p(Grid& grid, GV& gv, ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ //typedef typename Grid::LeafGridView GV;
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ //GV gv = grid.leafGridView();
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_fff< RF,
+ TripleWell<RF,DoubleWell_poly<RF> >,
+ Mobility_Const<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_fff_chns<RF, ES, V_FEM, P_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+
+ typedef Bdry_fff_chns_compositeV_2d<Dune::PDELab::DirichletConstraintsParameters, //v_x
+ Dune::PDELab::DirichletConstraintsParameters, // v_y
+ Dune::PDELab::NoDirichletConstraintsParameters, // p
+ Dune::PDELab::NoDirichletConstraintsParameters, // phi1
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu1
+ Dune::PDELab::NoDirichletConstraintsParameters, // phi2
+ Dune::PDELab::NoDirichletConstraintsParameters> // mu2
+ Bdry;
+ Bdry bdry;
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_fff_chns< ZeroInitialVector<GV,RF,dim, Parameters>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_3pBubble<GV,RF,Parameters,0>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_3pBubble<GV,RF,Parameters,1>,
+ ZeroInitial<GV,RF,Parameters> > Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+
+ typedef FEM_3P_CahnHilliard<Parameters, CH_GFS, CH_V> CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_fff_chns<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+
+ // Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ //rInd0.refineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ rInd0.myRefineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //vtkwriter.write(param.time.t + i,Dune::VTK::ascii);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,600,200,3,1);
+
+
+ // Nonlinear solver
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+
+ int result = timestepManager.doOnlyCHTimestep(ch_newton,vtkwriter);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ rInd.myRefineGrid(grid,gv,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/example_cahnhilliard/CMakeLists.txt b/src/example_cahnhilliard/CMakeLists.txt
new file mode 100644
index 0000000..684fcbf
--- /dev/null
+++ b/src/example_cahnhilliard/CMakeLists.txt
@@ -0,0 +1,3 @@
+add_executable(ch2p_equation ch2p_equation.cc)
+add_executable(ch3p_equation ch3p_equation.cc)
+dune_symlink_to_source_files(FILES grids ch2p.ini ch3p.ini)
diff --git a/src/example_cahnhilliard/ch2p.ini b/src/example_cahnhilliard/ch2p.ini
new file mode 120000
index 0000000..a63fdea
--- /dev/null
+++ b/src/example_cahnhilliard/ch2p.ini
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard/ch2p.ini
\ No newline at end of file
diff --git a/src/example_cahnhilliard/ch2p_equation.cc b/src/example_cahnhilliard/ch2p_equation.cc
new file mode 100644
index 0000000..7d076ed
--- /dev/null
+++ b/src/example_cahnhilliard/ch2p_equation.cc
@@ -0,0 +1,165 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+
+// dunext includes
+#include <dune/xt/grid/view/periodic.hh>
+#include "2p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("ch2p.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+ /*Dune::GridFactory<Grid> factory;
+ if (helper.rank()==0)
+ Dune::GmshReader<Grid>::read(factory,filename,boundary_index_map,element_index_map,true,false);
+ Dune::GridFactory<Grid>::WorldMatrix matrix;
+ std::cout << "a" << std::endl;
+ matrix[0][0] = 1;
+ matrix[0][1] = 0;
+ matrix[1][1] = 1;
+ matrix[1][0] = 0;
+ std::cout << "b" << std::endl;
+ Dune::GridFactory<Grid>::WorldVector shift;
+ matrix[0] = 1;
+ matrix[1] = 0;
+ std::cout << "c" << std::endl;
+ factory.insertFaceTransformation(matrix,shift );
+ std::cout << "d" << std::endl;
+
+ std::shared_ptr<Grid> gridp(factory.createGrid());*/
+
+ Dune::GridFactory<Grid> factory;
+ Dune::GmshReader<Grid>::read(factory,filename,true,true);
+ Dune::GridFactory<Grid>::WorldMatrix matrix;
+ std::cout << "a" << std::endl;
+ matrix[0][0] = 1;
+ matrix[0][1] = 0;
+ matrix[1][1] = 1;
+ matrix[1][0] = 0;
+ std::cout << "b" << std::endl;
+ Dune::GridFactory<Grid>::WorldVector shift;
+ shift[0] = 1;
+ shift[1] = 0;
+ std::cout << "c" << std::endl;
+ factory.insertFaceTransformation(matrix,shift );
+
+ Dune::GridFactory<Grid>::WorldMatrix matrix2 = matrix;
+ Dune::GridFactory<Grid>::WorldVector shift2;
+ shift2[0] = 0;
+ shift2[1] = 1;
+ std::cout << "c2" << std::endl;
+ factory.insertFaceTransformation(matrix2,shift2 );
+
+
+
+ std::cout << "d" << std::endl;
+
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+
+ //Dune::GridPtr< Grid > gridp( filename );
+ std::cout << "i" << std::endl;
+
+
+
+ //gridp->globalRefine(refinement);
+ //gridp->loadBalance();
+ //std::cout << " after load balance /" << helper.rank() << "/ " << gridp->size(0) << std::endl;
+
+ typedef Grid::LeafGridView LGV;
+ std::bitset<2> periodic_directions(ptree.get("domain.periodic","00"));
+ typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv(gridp->leafGridView(),periodic_directions);
+
+ //typedef Grid::LeafGridView GV;
+ //GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_2p(*gridp, gv, es,vFem,pFem,phiFem, ptree, helper);
+ }
+
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
diff --git a/src/example_cahnhilliard/ch3p.ini b/src/example_cahnhilliard/ch3p.ini
new file mode 120000
index 0000000..9d9e9e2
--- /dev/null
+++ b/src/example_cahnhilliard/ch3p.ini
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_cahnhilliard/ch3p.ini
\ No newline at end of file
diff --git a/src/example_cahnhilliard/ch3p_equation.cc b/src/example_cahnhilliard/ch3p_equation.cc
new file mode 100644
index 0000000..a27f896
--- /dev/null
+++ b/src/example_cahnhilliard/ch3p_equation.cc
@@ -0,0 +1,151 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+
+// dunext includes
+#include <dune/xt/grid/view/periodic.hh>
+#include "3p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("ch3p.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+
+ std::bitset<2> periodic_directions(ptree.get("domain.periodic","00"));
+
+ Dune::GridFactory<Grid> factory;
+ Dune::GmshReader<Grid>::read(factory,filename,true,true);
+ Dune::GridFactory<Grid>::WorldMatrix matrix;
+ std::cout << "a" << std::endl;
+ matrix[0][0] = 1;
+ matrix[0][1] = 0;
+ matrix[1][1] = 1;
+ matrix[1][0] = 0;
+ std::cout << "b" << std::endl;
+ Dune::GridFactory<Grid>::WorldVector shift;
+ shift[0] = 1;
+ shift[1] = 0;
+ std::cout << "c" << std::endl;
+ if(periodic_directions[0])
+ {
+ factory.insertFaceTransformation(matrix,shift );
+ }
+
+ Dune::GridFactory<Grid>::WorldMatrix matrix2 = matrix;
+ Dune::GridFactory<Grid>::WorldVector shift2;
+ shift2[0] = 0;
+ shift2[1] = 1;
+ std::cout << "c2" << std::endl;
+ if(periodic_directions[1])
+ {
+ factory.insertFaceTransformation(matrix2,shift2 );
+ }
+
+
+
+ std::cout << "d" << std::endl;
+
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+ std::cout << "i" << std::endl;
+
+
+ //gridp->globalRefine(refinement);
+ //gridp->loadBalance();
+ //std::cout << " after load balance /" << helper.rank() << "/ " << gridp->size(0) << std::endl;
+
+ typedef Grid::LeafGridView LGV;
+ typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv(gridp->leafGridView(),periodic_directions);
+
+ //typedef Grid::LeafGridView GV;
+ //GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_3p(*gridp, gv, es,vFem,pFem,phiFem, ptree, helper);
+ }
+
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
diff --git a/src/example_cahnhilliard/grids/periodic.dgf b/src/example_cahnhilliard/grids/periodic.dgf
new file mode 100644
index 0000000..b9e8e57
--- /dev/null
+++ b/src/example_cahnhilliard/grids/periodic.dgf
@@ -0,0 +1,23 @@
+DGF
+
+INTERVAL
+0 0 % lower left corner
+1 1 % upper right corner
+8 8 % number of cells in each direction
+#
+
+PERIODICFACETRANSFORMATION
+1 0, 0 1 + 1 0 % make periodic in x-direction
+1 0, 0 1 + 0 1 % make periodic in y-direction
+#
+
+BOUNDARYDOMAIN
+DEFAULT 1
+#
+
+GRIDPARAMETER
+OVERLAP 0
+#
+
+#
+
diff --git a/src/example_cahnhilliard/grids/xperiodic.dgf b/src/example_cahnhilliard/grids/xperiodic.dgf
new file mode 100644
index 0000000..19762d4
--- /dev/null
+++ b/src/example_cahnhilliard/grids/xperiodic.dgf
@@ -0,0 +1,22 @@
+DGF
+
+INTERVAL
+0 0 % lower left corner
+1 1 % upper right corner
+8 8 % number of cells in each direction
+#
+
+PERIODICFACETRANSFORMATION
+1 0, 0 1 + 1 0 % make periodic in x-direction
+#
+
+BOUNDARYDOMAIN
+DEFAULT 1
+#
+
+GRIDPARAMETER
+OVERLAP 0
+#
+
+#
+
diff --git a/src/example_nucleus/3p_driver.hh b/src/example_nucleus/3p_driver.hh
new file mode 100644
index 0000000..ad95f6b
--- /dev/null
+++ b/src/example_nucleus/3p_driver.hh
@@ -0,0 +1,224 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include <dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh>
+#include <dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh>
+#include <dune/phasefield/localoperator/pf_3p_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/ffs_chns_r.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename GV, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_3p(Grid& grid, GV& gv, ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_ffs_r< RF,
+ TripleWell<RF,DoubleWell_limited< RF, DoubleWell_poly<RF>, Limiter_FakeDiverging<RF> > >,
+ Mobility_Const<RF>,
+ Reaction_Quadratic_Limited<RF>,
+ VelDissipation_Quadratic<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_ffs_chns_r<RF, ES, V_FEM, P_FEM, PHI_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+
+ typedef Bdry_ffs_chns_r_compositeV_2d<Dune::PDELab::DirichletConstraintsParameters, // v_x
+ Dune::PDELab::DirichletConstraintsParameters, // v_y
+ Dune::PDELab::NoDirichletConstraintsParameters, // p
+ Dune::PDELab::NoDirichletConstraintsParameters, // phi1
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu1
+ Dune::PDELab::NoDirichletConstraintsParameters, // phi2
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu2
+ Dune::PDELab::NoDirichletConstraintsParameters> // u
+ Bdry;
+ Bdry bdry;
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_ffs_chns_r< ZeroInitialVector<GV,RF,dim,Parameters>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_3pSphereAndDroplet<GV,RF,Parameters,0>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_3pSphereAndDroplet<GV,RF,Parameters,1>,
+ ZeroInitial<GV,RF,Parameters>,
+ ConstInitial<GV,RF,Parameters,CONST_INITIAL_U> > Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+// Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ //rInd0.refineGrid(grid,chV,nsV,gfs.ch,gfs.ns,1);
+ rInd0.myRefineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+ typedef FEM_FFS_CHNS_NavierStokes<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> NS_LOP;
+ NS_LOP nsLop(param, gfs.ch, chV, chVOld, gfs.ns, nsVOld);
+
+ typedef FEM_FFS_CHNS_R_CahnHilliard<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld, gfs.ns, nsV);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_ffs_chns_r<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+ typedef Dune::PDELab::GridOperator<NS_GFS,NS_GFS,NS_LOP,MBE,RF,RF,RF,typename GFS::NS_CC,typename GFS::NS_CC> NS_GO;
+ NS_GO nsGo(gfs.ns,gfs.nsCC,gfs.ns,gfs.nsCC,nsLop,mbe);
+
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,500,100,3,1);
+
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <NS_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> NS_LS; NS_LS ls_ns(nsGo,1000,200,3,1);
+
+ // Nonlinear solver
+ typedef Dune::PDELab::Newton<NS_GO,NS_LS,NS_V> PDESolver1;
+ PDESolver1 ns_newton(nsGo,nsV,ls_ns);
+ ns_newton.setParameters(ptree.sub("NS_Newton"));
+
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+
+ int result = timestepManager.doTimestep(ns_newton,ch_newton,vtkwriter);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ //rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+
+ rInd.myRefineGrid(grid,gv,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,1);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/example_nucleus/CMakeLists.txt b/src/example_nucleus/CMakeLists.txt
new file mode 100644
index 0000000..9a023c9
--- /dev/null
+++ b/src/example_nucleus/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_executable(nucleus_equation nucleus_equation.cc)
+dune_symlink_to_source_files(FILES grids chns.ini)
diff --git a/src/example_nucleus/chns.ini b/src/example_nucleus/chns.ini
new file mode 120000
index 0000000..dd6e491
--- /dev/null
+++ b/src/example_nucleus/chns.ini
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/example_nucleus/chns.ini
\ No newline at end of file
diff --git a/src/example_nucleus/nucleus_equation.cc b/src/example_nucleus/nucleus_equation.cc
new file mode 100644
index 0000000..3ba4d82
--- /dev/null
+++ b/src/example_nucleus/nucleus_equation.cc
@@ -0,0 +1,139 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+#include <dune/xt/grid/view/periodic.hh>
+#include "3p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("chns.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+
+
+ Dune::GridFactory<Grid> factory;
+ Dune::GmshReader<Grid>::read(factory,filename,true,true);
+ Dune::GridFactory<Grid>::WorldMatrix matrix;
+ std::cout << "a" << std::endl;
+ matrix[0][0] = 1;
+ matrix[0][1] = 0;
+ matrix[1][1] = 1;
+ matrix[1][0] = 0;
+ std::cout << "b" << std::endl;
+ Dune::GridFactory<Grid>::WorldVector shift;
+ shift[0] = 1;
+ shift[1] = 0;
+ std::cout << "c" << std::endl;
+ factory.insertFaceTransformation(matrix,shift );
+
+
+
+ std::cout << "d" << std::endl;
+
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+
+ //Dune::GridPtr< Grid > gridp( filename );
+ std::cout << "i" << std::endl;
+
+
+
+ //gridp->globalRefine(refinement);
+ //gridp->loadBalance();
+ //std::cout << " after load balance /" << helper.rank() << "/ " << gridp->size(0) << std::endl;
+
+ typedef Grid::LeafGridView LGV;
+ std::bitset<2> periodic_directions(ptree.get("domain.periodic","00"));
+ typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv(gridp->leafGridView(),periodic_directions);
+
+ //typedef Grid::LeafGridView GV;
+ //GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_3p(*gridp, gv, es,vFem,pFem,phiFem, ptree, helper);
+ }
+
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
diff --git a/src/paper_epsdelta/3p_driver.hh b/src/paper_epsdelta/3p_driver.hh
new file mode 100644
index 0000000..9006997
--- /dev/null
+++ b/src/paper_epsdelta/3p_driver.hh
@@ -0,0 +1,222 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include <dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh>
+#include <dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh>
+#include <dune/phasefield/localoperator/pf_3p_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/ffs_chns_r.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_3p (Grid& grid, const ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ typedef typename Grid::LeafGridView GV;
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv = grid.leafGridView();
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_ffs_r< RF,
+ TripleWell<RF,DoubleWell_limited< RF, DoubleWell_poly<RF>, Limiter_FakeDiverging<RF> > >,
+ Mobility_Const<RF>,
+ Reaction_None<RF>,
+ VelDissipation_Quadratic_Shifted<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_ffs_chns_r<RF, ES, V_FEM, P_FEM, PHI_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+
+ typedef Bdry_ffs_chns_r_compositeV_2d<InflowOutflow_v, // v_x
+ Dune::PDELab::DirichletConstraintsParameters, // v_y
+ InflowOutflow_p, // p
+ InflowOutflow_phi, // phi1
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu1
+ InflowOutflow_phi, // phi2
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu2
+ InflowOutflow_u> // u
+ Bdry;
+ Bdry bdry;
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_ffs_chns_r< VelocityInitial_Inflow<GV,RF,Parameters,dim>,
+ PInitial_Inflow<GV,RF,Parameters>,
+ PhiInitial_HainesJump<GV,RF,Parameters,0>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_HainesJump<GV,RF,Parameters,1>,
+ ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters> > Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+// Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ rInd0.refineGrid(grid,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+ typedef FEM_FFS_CHNS_NavierStokes<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> NS_LOP;
+ NS_LOP nsLop(param, gfs.ch, chV, chVOld, gfs.ns, nsVOld);
+
+ typedef FEM_FFS_CHNS_R_CahnHilliard<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld, gfs.ns, nsV);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_ffs_chns_r<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+ typedef Dune::PDELab::GridOperator<NS_GFS,NS_GFS,NS_LOP,MBE,RF,RF,RF,typename GFS::NS_CC,typename GFS::NS_CC> NS_GO;
+ NS_GO nsGo(gfs.ns,gfs.nsCC,gfs.ns,gfs.nsCC,nsLop,mbe);
+
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,500,100,3,0);
+
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <NS_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> NS_LS; NS_LS ls_ns(nsGo,1000,200,3,0);
+
+ // Nonlinear solver
+ typedef Dune::PDELab::Newton<NS_GO,NS_LS,NS_V> PDESolver1;
+ PDESolver1 ns_newton(nsGo,nsV,ls_ns);
+ ns_newton.setParameters(ptree.sub("NS_Newton"));
+
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+
+ int result = timestepManager.doTimestepToConvergence(ns_newton,ch_newton,vtkwriter,nsV,chV);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/paper_epsdelta/CMakeLists.txt b/src/paper_epsdelta/CMakeLists.txt
new file mode 100644
index 0000000..0a312cc
--- /dev/null
+++ b/src/paper_epsdelta/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_executable(epsdelta_equation epsdelta_equation.cc)
+dune_symlink_to_source_files(FILES grids chns.ini)
diff --git a/src/paper_epsdelta/chns.ini b/src/paper_epsdelta/chns.ini
new file mode 120000
index 0000000..e58eb79
--- /dev/null
+++ b/src/paper_epsdelta/chns.ini
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/paper_epsdelta/chns.ini
\ No newline at end of file
diff --git a/src/paper_epsdelta/epsdelta_equation.cc b/src/paper_epsdelta/epsdelta_equation.cc
new file mode 100644
index 0000000..b17ed0b
--- /dev/null
+++ b/src/paper_epsdelta/epsdelta_equation.cc
@@ -0,0 +1,116 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+
+#include "3p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("chns.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+ Dune::GridFactory<Grid> factory;
+ if (helper.rank()==0)
+ Dune::GmshReader<Grid>::read(factory,filename,boundary_index_map,element_index_map,true,false);
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+ //gridp->globalRefine(refinement);
+ //gridp->loadBalance();
+ //std::cout << " after load balance /" << helper.rank() << "/ " << gridp->size(0) << std::endl;
+
+ //typedef Grid::LeafGridView LGV;
+
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ //GV gv(gridp->leafGridView(),periodic_directions);
+
+ typedef Grid::LeafGridView GV;
+ GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 1;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_3p(*gridp, es,vFem,pFem,phiFem, ptree, helper);
+ }
+
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
diff --git a/src/paper_thinstrip_full/3p_driver.hh b/src/paper_thinstrip_full/3p_driver.hh
new file mode 100644
index 0000000..46ab1e9
--- /dev/null
+++ b/src/paper_thinstrip_full/3p_driver.hh
@@ -0,0 +1,225 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include "thinstrip_full_chns_r_cahnhilliard.hh"
+#include "thinstrip_full_chns_navierstokes.hh"
+#include <dune/phasefield/localoperator/pf_3p_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include "thinstrip_parameters.hh"
+#include "thinstrip_boundary.hh"
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/ffs_chns_r.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename GV, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_3p(Grid& grid, GV& gv, ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_thinstrip< RF,
+ TripleWell<RF,DoubleWell_limited< RF, DoubleWell_poly<RF>, Limiter_FakeDiverging<RF> > >,
+ Mobility_Const<RF>,
+ Reaction_Thinstrip<RF>,
+ VelDissipation_Quadratic<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_ffs_chns_r<RF, ES, V_FEM, P_FEM, PHI_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+ typedef DomainSize<RF> DS;
+ DS dS(0,param.YScaling,0,2,1e-8);
+ typedef Bdry_ffs_chns_r_compositeV_2d_Explicit_Domain<BottomBoundary<DS>, // v_x
+ AllBoundary<DS>, // v_y
+ LeftRightBoundary<DS>, // p
+ NoBoundary<DS>, // phi1
+ NoBoundary<DS>, // mu1
+ NoBoundary<DS>, // phi2
+ NoBoundary<DS>, // mu2
+ LeftBoundary<DS>> // u
+ Bdry;
+ Bdry bdry(dS);
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_ffs_chns_r< VelocityInitial_InOutFlow<GV,RF,Parameters,dim>,
+ PInitial_InOutFlow<GV,RF,Parameters>,
+ PhiInitial_Thinstrip_Layers<GV,RF,Parameters,0>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_Thinstrip_Layers<GV,RF,Parameters,1>,
+ ZeroInitial<GV,RF,Parameters>,
+ UInitial_Inflow<GV,RF,Parameters> > Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+// Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ //rInd0.refineGrid(grid,chV,nsV,gfs.ch,gfs.ns,1);
+ rInd0.myRefineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+ typedef THINSTRIP_FULL_CHNS_NavierStokes<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> NS_LOP;
+ NS_LOP nsLop(param, gfs.ch, chV, chVOld, gfs.ns, nsVOld);
+
+ typedef THINSTRIP_FULL_CHNS_R_CahnHilliard<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld, gfs.ns, nsV);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_ffs_chns_r<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+ typedef Dune::PDELab::GridOperator<NS_GFS,NS_GFS,NS_LOP,MBE,RF,RF,RF,typename GFS::NS_CC,typename GFS::NS_CC> NS_GO;
+ NS_GO nsGo(gfs.ns,gfs.nsCC,gfs.ns,gfs.nsCC,nsLop,mbe);
+
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,500,100,3,1);
+
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <NS_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> NS_LS; NS_LS ls_ns(nsGo,1000,200,3,1);
+
+ // Nonlinear solver
+ typedef Dune::PDELab::Newton<NS_GO,NS_LS,NS_V> PDESolver1;
+ PDESolver1 ns_newton(nsGo,nsV,ls_ns);
+ ns_newton.setParameters(ptree.sub("NS_Newton"));
+
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+
+ int result = timestepManager.doTimestep(ns_newton,ch_newton,vtkwriter);
+ //int result = timestepManager.doOnlyNSTimestep(ns_newton,vtkwriter);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ //rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+
+ rInd.myRefineGrid(grid,gv,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,1);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/paper_thinstrip_full/CMakeLists.txt b/src/paper_thinstrip_full/CMakeLists.txt
new file mode 100644
index 0000000..c75bcc5
--- /dev/null
+++ b/src/paper_thinstrip_full/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_executable(thinstrip_equation thinstrip_equation.cc)
+dune_symlink_to_source_files(FILES grids chns.ini)
diff --git a/src/paper_thinstrip_full/chns.ini b/src/paper_thinstrip_full/chns.ini
new file mode 100644
index 0000000..75f3777
--- /dev/null
+++ b/src/paper_thinstrip_full/chns.ini
@@ -0,0 +1,64 @@
+[Physics]
+uAst = 1
+D = 0.02
+rho1 = 1.0
+rho2 = 1.0
+mu=0.005
+ReactionRate=0.5
+#ReactionLimiter = 1000
+SurfaceTensionScaling=0.1
+VelDissipationRate = 1000
+CurvatureAlpha=0.001
+
+[domain]
+level = 0
+filename = grids/rectangle_periodic_coarse.msh
+YScalingFactor = 0.5
+YScaling = 0.5
+
+[output]
+filename = output2
+
+[Phasefield]
+eps=0.03
+delta=0.03
+DoubleWellDelta=0.05
+Mobility=0.01
+Sigma1=1
+Sigma2=1
+Sigma3=1
+
+[Time]
+tMax = 30
+dt = 0.015
+dtMax = 0.15
+dtMin = 0.0015
+#saveintervall = 0.5
+#dtIncreaseFactor=1.2
+#dtDecreaseFactor=0.5
+
+[Initial]
+# FlowVyy= 10# pConst/(Domain_width * mu)
+pConst=0.1
+uConst=0.5
+uInflow=0.3
+
+[Refinement]
+etaRefine = 0.2
+etaCoarsen = 0.1
+maxRefineLevel = 6
+minRefineLevel = -1
+
+[NS_Newton]
+ReassembleThreshold = 0.0
+LineSearchMaxIterations = 30
+MaxIterations = 30
+AbsoluteLimit = 1e-9
+Reduction = 1e-7
+VerbosityLevel = 1
+
+[Phasefield_Newton]
+ReassembleThreshold = 0.0
+LineSearchMaxIterations = 30
+MaxIterations = 30
+VerbosityLevel = 1
diff --git a/src/paper_thinstrip_full/thinstrip_boundary.hh b/src/paper_thinstrip_full/thinstrip_boundary.hh
new file mode 100644
index 0000000..1f511c2
--- /dev/null
+++ b/src/paper_thinstrip_full/thinstrip_boundary.hh
@@ -0,0 +1,211 @@
+
+#pragma once
+#include <cmath>
+#include <dune/pdelab/common/function.hh>
+#include <dune/pdelab/constraints/common/constraintsparameters.hh>
+
+#include <dune/phasefield/initial_fn.hh>
+
+#define GRID_TOP_THINSTRIP 1
+
+
+template<typename DomainSize>
+class LeftBoundary : public Dune::PDELab::DirichletConstraintsParameters
+{
+private:
+ const DomainSize ds;
+public:
+ LeftBoundary(const DomainSize d) : ds(d)
+ {
+ }
+
+ template<typename I>
+ bool isDirichlet(const I & intersection, const Dune::FieldVector<typename I::ctype, I::mydimension> & coord) const
+ {
+ Dune::FieldVector<typename I::ctype, I::coorddimension>
+ xg = intersection.geometry().global( coord );
+ if ( xg[0] > ds.domainEps)
+ {
+ return false;
+ }
+ return true;
+ }
+};
+
+template<typename DomainSize>
+class BottomBoundary : public Dune::PDELab::DirichletConstraintsParameters
+{
+private:
+ const DomainSize ds;
+public:
+ BottomBoundary(const DomainSize d) : ds(d)
+ {
+ }
+
+ template<typename I>
+ bool isDirichlet(const I & intersection, const Dune::FieldVector<typename I::ctype, I::mydimension> & coord) const
+ {
+ Dune::FieldVector<typename I::ctype, I::coorddimension>
+ xg = intersection.geometry().global( coord );
+ if ( xg[1]>ds.bottom + ds.domainEps)
+ {
+ return false;
+ }
+ return true;
+ }
+};
+
+template<typename DomainSize>
+class LeftRightBoundary : public Dune::PDELab::DirichletConstraintsParameters
+{
+private:
+ const DomainSize ds;
+public:
+ LeftRightBoundary(const DomainSize d) : ds(d)
+ {
+ }
+
+ template<typename I>
+ bool isDirichlet(const I & intersection, const Dune::FieldVector<typename I::ctype, I::mydimension> & coord) const
+ {
+ Dune::FieldVector<typename I::ctype, I::coorddimension>
+ xg = intersection.geometry().global( coord );
+ if (xg[1]>ds.bottom + ds.domainEps && xg[1]<ds.top - ds.domainEps)
+ {
+ return true;
+ }
+ return false;
+ }
+};
+
+template<typename DomainSize>
+class AllBoundary : public Dune::PDELab::DirichletConstraintsParameters
+{
+private:
+ const DomainSize ds;
+public:
+ AllBoundary(const DomainSize d) : ds(d)
+ {
+ }
+
+ template<typename I>
+ bool isDirichlet(const I & intersection, const Dune::FieldVector<typename I::ctype, I::mydimension> & coord) const
+ {
+ return true;
+ }
+};
+
+template<typename DomainSize>
+class NoBoundary : public Dune::PDELab::DirichletConstraintsParameters
+{
+private:
+ const DomainSize ds;
+public:
+ NoBoundary(const DomainSize d) : ds(d)
+ {
+ }
+
+ template<typename I>
+ bool isDirichlet(const I & intersection, const Dune::FieldVector<typename I::ctype, I::mydimension> & coord) const
+ {
+ return false;
+ }
+};
+
+template<typename GV, typename RF, typename Params, int dim>
+class VelocityInitial_InOutFlow :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,dim>,
+ VelocityInitial_InOutFlow<GV,RF,Params,dim> >
+{
+ const Params_Time& time;
+ RF v;
+ RF yS;
+
+
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,dim> Traits;
+
+ typedef typename Traits::DomainType DomainType;
+ typedef typename Traits::RangeType RangeType;
+
+ VelocityInitial_InOutFlow(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,VelocityInitial_InOutFlow<GV,RF,Params,dim> > (gv)
+ , time(params.time)
+ {
+ v = params.initial.ptree.get("pConst",(RF)0.01)/(params.YScaling*params.YScaling) /2 /*Domain Width*/ /params.phys.mu;
+ yS = params.YScaling;
+ }
+
+ template <typename T>
+ void setTime(T t){
+ time = t;
+ }
+
+ inline void evaluateGlobal(const DomainType & x, RangeType & y) const
+ {
+ y[0] = std::max(0.0, v/2.0*(x[1]-0.3*yS)*((2*GRID_TOP_THINSTRIP-0.3)*yS-x[1]));
+ }
+};
+
+template<typename GV, typename RF, typename Params>
+class PInitial_InOutFlow :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PInitial_InOutFlow<GV,RF,Params> >
+{
+ RF pConst;
+ RF yS;
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
+
+ PInitial_InOutFlow(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,PInitial_InOutFlow<GV,RF,Params> > (gv)
+ {
+ pConst = params.initial.ptree.get("pConst",(RF)0.01);
+ yS = params.YScaling;
+ }
+
+ inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
+ {
+ y = 0;
+ if(x[0]<1e-7)
+ {
+ y=pConst/(yS*yS);
+ }
+ }
+};
+
+template<typename GV, typename RF, typename Params, const int Phase>
+class PhiInitial_Thinstrip_Layers :
+ public Dune::PDELab::AnalyticGridFunctionBase<
+ Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1>, PhiInitial_Thinstrip_Layers<GV,RF,Params,Phase> >
+{
+ RF eps;
+ RF yS;
+ RF d1;
+ RF d2;
+
+public:
+ typedef Dune::PDELab::AnalyticGridFunctionTraits<GV,RF,1> Traits;
+
+ PhiInitial_Thinstrip_Layers(const GV & gv, const Params & params) :
+ Dune::PDELab::AnalyticGridFunctionBase<Traits,PhiInitial_Thinstrip_Layers<GV,RF,Params,Phase> > (gv)
+ {
+ eps = params.eps;
+ d1 = params.initial.ptree.get("d1",0.3);
+ d2 = params.initial.ptree.get("d1",0.3);
+ yS = params.YScaling;
+ }
+
+ inline void evaluateGlobal(const typename Traits::DomainType & x, typename Traits::RangeType & y) const
+ {
+ RF rf = 0.5*(1+tanh(1/eps/sqrt(2)*(x[1] - d1*yS)));
+ RF rf2 = 0.5*(1+tanh(1/eps/sqrt(2)*(x[1] - d1*yS - d2*yS)));
+ if(Phase == 1)
+ {
+ y = rf2;
+ return;
+ }
+ y=rf*(1-rf2);
+ }
+};
diff --git a/src/paper_thinstrip_full/thinstrip_equation.cc b/src/paper_thinstrip_full/thinstrip_equation.cc
new file mode 100644
index 0000000..f4f2c23
--- /dev/null
+++ b/src/paper_thinstrip_full/thinstrip_equation.cc
@@ -0,0 +1,139 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+#include <dune/grid/geometrygrid/grid.hh>
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+#include <dune/xt/grid/view/periodic.hh>
+#include "3p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+template<typename RF>
+class ExampleThinstripTransform
+ : public Dune :: AnalyticalCoordFunction< RF, 2, 2, ExampleThinstripTransform<RF> >
+{
+ typedef ExampleThinstripTransform<RF> This;
+ typedef Dune :: AnalyticalCoordFunction< RF, 2, 2, This > Base;
+ public:
+ typedef typename Base :: DomainVector DomainVector;
+ typedef typename Base :: RangeVector RangeVector;
+
+ const RF YS;
+
+ ExampleThinstripTransform(const RF YScalingFactor) : YS(YScalingFactor)
+ {
+ }
+
+ void evaluate ( const DomainVector &x, RangeVector &y ) const
+ {
+ y[ 0 ] = x[ 0 ];
+ y[ 1 ] = YS*x[ 1 ];
+ }
+};
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("chns.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+
+ Dune::GridFactory<Grid> factory;
+ Dune::GmshReader<Grid>::read(factory,filename,true,true);
+
+
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+
+ typedef Dune::GeometryGrid<Grid,ExampleThinstripTransform<double>> GGrid;
+ ExampleThinstripTransform<double>* tfp = new ExampleThinstripTransform<double>(ptree.get("domain.YScalingFactor",1.0));
+ std::shared_ptr<GGrid> ggridp(new GGrid(gridp.get(),tfp));
+
+ typedef GGrid::LeafGridView LGV;
+ std::bitset<2> periodic_directions(ptree.get("domain.periodic","00"));
+ typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv(ggridp->leafGridView(),periodic_directions);
+
+ //typedef Grid::LeafGridView GV;
+ //GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_3p(*ggridp, gv, es,vFem,pFem,phiFem, ptree, helper);
+ }
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
diff --git a/src/paper_thinstrip_full/thinstrip_full_chns_navierstokes.hh b/src/paper_thinstrip_full/thinstrip_full_chns_navierstokes.hh
new file mode 100644
index 0000000..ba0bc4b
--- /dev/null
+++ b/src/paper_thinstrip_full/thinstrip_full_chns_navierstokes.hh
@@ -0,0 +1,148 @@
+#pragma once
+
+#include<dune/pdelab/common/quadraturerules.hh>
+#include<dune/pdelab/finiteelement/localbasiscache.hh>
+#include<dune/pdelab/localoperator/defaultimp.hh>
+#include<dune/pdelab/localoperator/pattern.hh>
+#include<dune/pdelab/localoperator/flags.hh>
+#include<dune/pdelab/localoperator/variablefactories.hh>
+#include<dune/pdelab/gridfunctionspace/gridfunctionspace.hh>
+
+#include<dune/phasefield/localoperator/fem_base_chns.hh>
+
+
+
+
+template<typename Param, typename CHGFS, typename CHContainer, typename NSGFS, typename NSContainer>
+ class THINSTRIP_FULL_CHNS_NavierStokes :
+ public Dune::PDELab::FullVolumePattern,
+ public Dune::PDELab::LocalOperatorDefaultFlags,
+ public Dune::PDELab::NumericalJacobianVolume<THINSTRIP_FULL_CHNS_NavierStokes<Param, CHGFS, CHContainer, NSGFS, NSContainer> >,
+ public Dune::PDELab::NumericalJacobianApplyVolume<THINSTRIP_FULL_CHNS_NavierStokes<Param, CHGFS, CHContainer, NSGFS, NSContainer> >
+ {
+ private:
+ typedef typename CHContainer::field_type RF;
+ typedef typename NSGFS::Traits::GridViewType::template Codim<0>::Entity ENTITY;
+
+ CHLocalBasisCache<CHGFS> chCache;
+ VLocalBasisCache<NSGFS> vCache;
+ PLocalBasisCache<NSGFS> pCache;
+
+ typedef GFS_LocalViewer<CHGFS, CHContainer, ENTITY, RF> CHLView;
+ mutable CHLView chLocal;
+ //mutable CHLView chOldLocal;
+
+ typedef GFS_LocalViewer<NSGFS, NSContainer, ENTITY, RF> NSLView;
+ mutable NSLView nsOldLocal;
+
+ Param& param; // parameter functions
+
+ //FOR DETECTING ENTITY changes
+ typedef typename NSGFS::Traits::GridViewType::template Codim<0>::Entity ENT;
+ mutable ENT OldEnt;
+
+ public:
+
+
+ // pattern assembly flags
+ enum { doPatternVolume = true };
+
+ // residual assembly flags
+ enum { doAlphaVolume = true };
+ //enum { doLambdaVolume = true };
+
+
+
+ THINSTRIP_FULL_CHNS_NavierStokes (Param& param_, CHGFS& chGfs_, CHContainer& chV_, CHContainer& chVOld_,
+ NSGFS& nsGfs_, NSContainer& nsVOld_) :
+ chLocal(chGfs_,chV_),
+ //chOldLocal(chGfs_,chVOld_),
+ nsOldLocal(nsGfs_,nsVOld_),
+ param(param_)
+ {
+ }
+
+
+ template<typename EG, typename LFSU, typename X, typename LFSV, typename R>
+ void alpha_volume (const EG& eg, const LFSU& lfsu, const X& x, const LFSV& lfsv, R& r) const
+ {
+
+ //Quadrature Rule
+ const int dim = EG::Entity::dimension;
+ const int order = 5; //TODO: Choose more educated
+ auto rule = Dune::PDELab::quadratureRule(eg.geometry(), order);
+
+ chLocal.DoEvaluation(eg);
+ //chOldLocal.DoEvaluation(eg);
+ nsOldLocal.DoSubEvaluation(eg,child(nsOldLocal.lfs,Dune::Indices::_0));
+
+ for(const auto& ip : rule)
+ {
+ const auto S = eg.geometry().jacobianInverseTransposed(ip.position());
+ auto factor = ip.weight()*eg.geometry().integrationElement(ip.position());
+
+ CHVariables_Threephase_Extension<RF,dim,decltype(chLocal.lfs)> ch(chCache, ip.position(), chLocal.lfs, chLocal.lv, S);
+ NSVariables_P_VOld_Extension<RF,dim,LFSV> ns(vCache, pCache, ip.position(), lfsv, x.base(), nsOldLocal.lv, S);
+
+
+ RF pf3=1-ch.pf-ch.pf2;
+ RF pf_f=ch.pf+ch.pf2+2*param.delta*pf3;
+ Dune::FieldVector<RF,dim> gradpf_f(0.0);
+ gradpf_f.axpy((1-2*param.delta),ch.gradpf+ch.gradpf2);
+
+ RF rho_f=param.phys.rho_f(ch.pf,ch.pf2);
+ RF rho_f_reg = rho_f + (param.phys.rho_1+param.phys.rho_2)*param.delta;
+
+ for (size_t i=0; i<ns.pspace.size(); i++)
+ {
+ for(int k=0; k<dim; k++)
+ {
+ // integrate: (div v)*phi
+ //r.accumulate(ns.pspace,i, -1.0* pf_f*(v*gradphi[i][0])*factor); Weak form
+ r.accumulate(ns.pspace,i, -1.0 * (pf_f*ns.div_v + (gradpf_f*ns.v) )* ns.pbasis.phi[i] * factor);
+ }
+ }
+ for (size_t i=0; i<ns.vfemspace.size(); i++)
+ {
+ for(int k=0; k<dim; k++)
+ {
+ // integrate: ( (rho+rhoOld)/2 * v_n+1 - rhoOld * v_n)/dt * phi + nu * Dv_n+1 : D phi - p_n+1 div phi
+
+ //std::cout << (param.nu * (jacv[k]*gradvphi[i][0]) - p * gradvphi[i][0][k]
+ //- param.rho*g[k]*vphi[i] )*factor << std::endl;
+
+ //RF lambda = 3;
+ //const auto v_nabla_v = v * jacv[k];
+ RF gradxi3k = -param.tw.Sigma3*(ch.gradxi[k]/param.tw.Sigma1 + ch.gradxi2[k]/param.tw.Sigma2);
+ RF S = 0;
+ S += - ch.xi2*(ch.gradpf[k]*pf_f - ch.pf * gradpf_f[k])/(pf_f*pf_f); //TODO!!!!!!! Other pf_f scaling!!!!!
+ S += - ch.xi *(ch.gradpf2[k]*pf_f - ch.pf2 * gradpf_f[k])/(pf_f*pf_f);
+ S += - 2*param.delta*pf3*(gradxi3k-ch.gradxi2[k]-ch.gradxi[k]);
+
+ //Stronger form - flow in interfaces possible
+ //S += -ch.pf*ch.gradxi[k] - ch.pf2*ch.gradxi2[k] - 2*param.delta*pf3*gradxi3k;
+
+ //Works but is not the one in the theory (same as above, w/o regularization)
+ //S += -ch.pf*ch.gradxi[k] - ch.pf2*ch.gradxi2[k];
+
+ S = S*param.SurfaceTensionScaling*ns.vbasis.phi[i];
+
+ r.accumulate(child(ns.vspace,k),i, ( rho_f_reg*(ns.v[k]-ns.vOld[k])*ns.vbasis.phi[i]/param.time.dt //TimeEvolution
+ //- ns.p * (pf_f*ns.vbasis.gradphi[i][0][k] + ns.vbasis.phi[i]*gradpf_f[k]) //Pressure in weak form
+ + pf_f * (ns.gradp[k] * ns.vbasis.phi[i]) //Pressure in strong form
+ + param.phys.eval_mu(pf_f) * (ns.jacv[k]*ns.vbasis.gradphi[i][0]) //+vphi[i]*(jacv[k]*gradpf) ) //Viscosity
+ + param.vDis.eval(pf_f)*ns.v[k]*ns.vbasis.phi[i] //Velocity Dissipation in Solid
+ //- rho*g[k]*vphi[i] //Gravitation
+ - S //Surface Tension
+ )*factor);
+ if(k==0)
+ {
+ r.accumulate(child(ns.vspace,k),i, ( pf_f * (param.phys.outerMomentumXForce * ns.vbasis.phi[i]) // Momentum Forcing Term
+ )*factor);
+ }
+ } //for k
+ } // for i
+ } // for ip
+ } //alpha volume
+
+ };
diff --git a/src/paper_thinstrip_full/thinstrip_full_chns_r_cahnhilliard.hh b/src/paper_thinstrip_full/thinstrip_full_chns_r_cahnhilliard.hh
new file mode 100644
index 0000000..c254699
--- /dev/null
+++ b/src/paper_thinstrip_full/thinstrip_full_chns_r_cahnhilliard.hh
@@ -0,0 +1,132 @@
+#pragma once
+
+#include<dune/pdelab/common/quadraturerules.hh>
+#include<dune/pdelab/finiteelement/localbasiscache.hh>
+#include<dune/pdelab/localoperator/defaultimp.hh>
+#include<dune/pdelab/localoperator/pattern.hh>
+#include<dune/pdelab/localoperator/flags.hh>
+#include<dune/pdelab/localoperator/variablefactories.hh>
+#include<dune/pdelab/gridfunctionspace/gridfunctionspace.hh>
+
+#include<dune/phasefield/localoperator/fem_base_chns.hh>
+
+//Parameter class (for functions), FEM space and RangeField
+template<typename Param, typename CHGFS, typename CHContainer, typename NSGFS, typename NSContainer>
+class THINSTRIP_FULL_CHNS_R_CahnHilliard :
+ public Dune::PDELab::FullVolumePattern,
+ public Dune::PDELab::LocalOperatorDefaultFlags,
+ public Dune::PDELab::NumericalJacobianVolume<THINSTRIP_FULL_CHNS_R_CahnHilliard<Param, CHGFS, CHContainer, NSGFS, NSContainer> >,
+ public Dune::PDELab::NumericalJacobianApplyVolume<THINSTRIP_FULL_CHNS_R_CahnHilliard<Param, CHGFS, CHContainer, NSGFS, NSContainer> >
+{
+private:
+ typedef typename CHContainer::field_type RF;
+ typedef typename CHGFS::Traits::GridViewType::template Codim<0>::Entity ENTITY;
+
+ CHLocalBasisCache<CHGFS> chCache;
+ VLocalBasisCache<NSGFS> vCache;
+
+ typedef GFS_LocalViewer<CHGFS, CHContainer, ENTITY, RF> CHLView;
+ mutable CHLView chOldLocal;
+
+ typedef GFS_LocalViewer<NSGFS, NSContainer, ENTITY, RF> NSLView;
+ mutable NSLView nsLocal;
+
+
+ Param& param; // parameter functions
+
+public:
+ enum {doPatternVolume=true};
+ //enum {doLambdaVolume=true};
+ enum {doAlphaVolume=true};
+
+ //constructor
+ THINSTRIP_FULL_CHNS_R_CahnHilliard(Param& param_, CHGFS& chGfs_, CHContainer& chVOld_, NSGFS& nsGfs_, NSContainer& nsV) :
+ chOldLocal(chGfs_,chVOld_),
+ nsLocal(nsGfs_,nsV),
+ param(param_)
+ {
+ }
+
+
+ template<typename EG, typename LFSU, typename X, typename LFSV, typename R>
+ void alpha_volume (const EG& eg, const LFSU& lfsu, const X& x, const LFSV& lfsv, R& r) const
+ {
+ //Quadrature Rule
+ const int dim = EG::Entity::dimension;
+ const int order = 2; //TODO: Choose more educated
+ auto rule = Dune::PDELab::quadratureRule(eg.geometry(), order);
+
+ chOldLocal.DoEvaluation(eg);
+ //chOldLocal.DoEvaluation(eg);
+ nsLocal.DoSubEvaluation(eg,child(nsLocal.lfs,Dune::Indices::_0));
+
+ for(const auto& ip : rule)
+ {
+ const auto S = eg.geometry().jacobianInverseTransposed(ip.position());
+ auto factor = ip.weight()*eg.geometry().integrationElement(ip.position());
+
+ CHVariables_Threephase_U_PFOld_Extension<RF,dim,LFSV> ch(chCache, ip.position(), lfsv, x.base(),chOldLocal.lv, S);
+ NSVariables<RF,dim,decltype(nsLocal.lfs)> ns(vCache, ip.position(), nsLocal.lfs, nsLocal.lv, S);
+
+ RF pf3 = 1-ch.pf-ch.pf2;
+ RF xi3 = -param.tw.Sigma3*(ch.xi/param.tw.Sigma1 + ch.xi2/param.tw.Sigma2);
+
+ RF pf_c = ch.pf;
+ RF pf_c_Old = ch.pfOld;
+ RF pf_c_reg = pf_c+param.delta;
+ RF pf_c_reg_Old = pf_c_Old + param.delta;
+
+ for (size_t i=0; i<ch.pfspace.size(); i++)
+ {
+ RF Rspeed = std::max(param.tw.eval_q(ch.pf,ch.pf2,pf3) - 0.1, 0.0);
+ RF R1 = -Rspeed/param.eps*
+ (param.reaction.eval(ch.u)+param.phys.curvatureAlpha*(ch.xi-xi3))*ch.basis.phi[i];
+ RF J1 = param.mobility.eval(ch.pf,ch.pf2,pf3)*param.eps/param.tw.Sigma1 * (ch.gradxi*ch.basis.gradphi[i][0]);
+
+ // integrate: (pf-pfold)*phi_i/delta_t + gradpf * grad phi_i + ...
+ r.accumulate(ch.pfspace,i,factor*(
+ (ch.pf-ch.pfOld)*ch.basis.phi[i]/param.time.dt
+ +J1
+ +(ch.pf*ns.div_v + (ch.gradpf*ns.v))*ch.basis.phi[i]
+ //-pf1*(v*gradphi[i][0]) weak transport
+ -R1
+ ));
+
+ r.accumulate(ch.pf2space,i,factor*(
+ (ch.pf2-ch.pf2Old)*ch.basis.phi[i]/param.time.dt
+ +param.mobility.eval(ch.pf,ch.pf2,pf3)*param.eps/param.tw.Sigma2 * (ch.gradxi2*ch.basis.gradphi[i][0])
+ +(ch.pf2*ns.div_v + (ch.gradpf2*ns.v))*ch.basis.phi[i]
+ //-pf2*(v*gradphi[i][0])
+ ));
+
+ r.accumulate(ch.xispace,i,factor*(
+ ch.xi*ch.basis.phi[i]
+ - 1/param.eps* param.tw.eval_dpf1(ch.pf,ch.pf2,pf3) *ch.basis.phi[i]
+ - param.eps * param.tw.Sigma1* (ch.gradpf*ch.basis.gradphi[i][0])
+ ));
+
+ r.accumulate(ch.xi2space,i,factor*(
+ ch.xi2*ch.basis.phi[i]
+ - 1/param.eps* param.tw.eval_dpf2(ch.pf,ch.pf2,pf3) *ch.basis.phi[i]
+ - param.eps * param.tw.Sigma2* (ch.gradpf2*ch.basis.gradphi[i][0])
+ ));
+
+ // integrate (pf-pfold)*(u-uast)*phi_i/delta_t + pfold*(u-uold)*phi_i/delta_t + D*pf*gradu*grad phi_i = 0
+
+ //Dune::FieldVector<RF, dim> xg = eg.geometry().global( ip.position() );
+ r.accumulate(ch.uspace,i,factor*(
+
+ //(u-param.uAst)*phi[i]/param.dt //For Testing
+
+ (pf_c_reg-pf_c_reg_Old)*(ch.u-param.phys.uAst)*ch.basis.phi[i]/param.time.dt
+ + pf_c_reg_Old*(ch.u-ch.uOld)*ch.basis.phi[i]/param.time.dt
+ + param.phys.D*pf_c_reg_Old*(ch.gradu*ch.basis.gradphi[i][0])
+ + J1*(ch.u-param.phys.uAst)
+ //- pf_c*(u-param.phys.uAst)*(v*gradphi[i][0])
+ + (pf_c*(ch.u-param.phys.uAst)*ns.div_v + (ch.u-param.phys.uAst)*(ch.gradpf*ns.v) + pf_c*(ch.gradu*ns.v) )*ch.basis.phi[i]
+ ));
+ }
+ }
+ }
+
+};
diff --git a/src/paper_thinstrip_full/thinstrip_parameters.hh b/src/paper_thinstrip_full/thinstrip_parameters.hh
new file mode 100644
index 0000000..1a820a0
--- /dev/null
+++ b/src/paper_thinstrip_full/thinstrip_parameters.hh
@@ -0,0 +1,48 @@
+
+#pragma once
+
+#include <dune/phasefield/base_parameters.hh>
+
+
+template <typename Number, typename TW, typename Mobility, typename Reaction, typename VelDissipation>
+class Params_thinstrip : public Params_ffs_r<Number, TW, Mobility, Reaction, VelDissipation>
+{
+public:
+ const Number YScaling;
+
+ Params_thinstrip(const Dune::ParameterTree& ptree) :
+ Params_ffs_r<Number, TW, Mobility, Reaction, VelDissipation>(ptree),
+ YScaling(ptree.get("domain.YScaling",1.0))
+ {
+ ModifyParameters();
+ std::cout << "YScaling " << YScaling << " Eps " << this->eps << std::endl;
+ }
+
+ void ModifyParameters()
+ {
+ this->eps *= YScaling;
+ this->mobility.mobility *= YScaling*YScaling;
+ this->reaction.reactionRate *= YScaling;
+ this->vDis.velDissipationRate *= 1./(YScaling*YScaling);
+ }
+};
+
+
+template<typename Number>
+class Reaction_Thinstrip
+{
+public:
+ Number reactionRate;
+ Reaction_Thinstrip(const Dune::ParameterTree & param) :
+ reactionRate(param.get("ReactionRate",(Number)0.1))
+ {
+ }
+
+ Number eval( const Number& u) const
+ {
+ if(u<0)
+ return reactionRate*(0-0.5);
+ else
+ return reactionRate*(u-0.5);
+ }
+};
diff --git a/src/rectangle_periodic.geo b/src/rectangle_periodic.geo
index c427e57..8039dad 100644
--- a/src/rectangle_periodic.geo
+++ b/src/rectangle_periodic.geo
@@ -1,5 +1,5 @@
// mesh width associated with points
-lc = 0.02;
+lc = 0.03;
Point(1) = {0, 0, 0, lc};
Point(2) = {2, 0, 0, lc};
diff --git a/src/test_contactpointdynamics/3p_driver.hh b/src/test_contactpointdynamics/3p_driver.hh
index a8c8440..a7f4ff5 100644
--- a/src/test_contactpointdynamics/3p_driver.hh
+++ b/src/test_contactpointdynamics/3p_driver.hh
@@ -39,7 +39,7 @@ void driver_3p (Grid& grid, const ES& es, const V_FEM& vFem, const P_FEM pFem, c
TripleWell<RF,DoubleWell_limited< RF, DoubleWell_poly<RF>, Limiter_FakeDiverging<RF> > >,
Mobility_Const<RF>,
Reaction_None<RF>,
- VelDissipation_Quadratic<RF> > Parameters;
+ VelDissipation_Quadratic_Shifted<RF> > Parameters;
Parameters param(ptree);
TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
@@ -76,8 +76,6 @@ void driver_3p (Grid& grid, const ES& es, const V_FEM& vFem, const P_FEM pFem, c
using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
CH_V chV(gfs.ch);
NS_V nsV(gfs.ns);
- CH_V chVOld = chV;
- NS_V nsVOld = nsV;
//_________________________________________________________________________________________________________________________
//Initial Values
@@ -94,6 +92,26 @@ void driver_3p (Grid& grid, const ES& es, const V_FEM& vFem, const P_FEM pFem, c
Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
//_________________________________________________________________________________________________________________________
+// Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ rInd0.refineGrid(grid,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
// LocalOperators
typedef FEM_FFS_CHNS_NavierStokes<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> NS_LOP;
@@ -191,21 +209,7 @@ void driver_3p (Grid& grid, const ES& es, const V_FEM& vFem, const P_FEM pFem, c
RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
rInd.calculateIndicator(gv,chV,false);
rInd.markGrid(grid,2);
-
- printVector(chV,3,"chV");
- printVector(nsV,3,"nsV");
-
- // do refinement
- std::cout << "adapt grid and solution" << std::endl;
- auto chTransfer = transferSolutions(gfs.ch,4,chV,chVOld);
- auto nsTransfer = transferSolutions(gfs.ns,4,nsV,nsVOld);
- Dune::PDELab::adaptGrid(grid, chTransfer,nsTransfer);
- std::cout << "adapt grid and solution ended" << std::endl;
-
- printVector(chV,3,"chV");
- printVector(nsV,3,"nsV");
-
- //vtkwriter.write(timestepManager.t+1e-6,Dune::VTK::ascii);
+ rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
// recompute constraints
gfs.updateConstraintsContainer(bdry);
diff --git a/src/test_hainesjump/3p_driver.hh b/src/test_hainesjump/3p_driver.hh
new file mode 100644
index 0000000..f702d0e
--- /dev/null
+++ b/src/test_hainesjump/3p_driver.hh
@@ -0,0 +1,222 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include <dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh>
+#include <dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh>
+#include <dune/phasefield/localoperator/pf_3p_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/ffs_chns_r.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_3p (Grid& grid, const ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ typedef typename Grid::LeafGridView GV;
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv = grid.leafGridView();
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_ffs_r< RF,
+ TripleWell<RF,DoubleWell_limited< RF, DoubleWell_poly<RF>, Limiter_FakeDiverging<RF> > >,
+ Mobility_Const<RF>,
+ Reaction_None<RF>,
+ VelDissipation_Quadratic_Shifted<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_ffs_chns_r<RF, ES, V_FEM, P_FEM, PHI_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+
+ typedef Bdry_ffs_chns_r_compositeV_2d<InflowOutflow_v, // v_x
+ Dune::PDELab::DirichletConstraintsParameters, // v_y
+ InflowOutflow_p, // p
+ InflowOutflow_phi, // phi1
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu1
+ InflowOutflow_phi, // phi2
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu2
+ InflowOutflow_u> // u
+ Bdry;
+ Bdry bdry;
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_ffs_chns_r< VelocityInitial_Inflow<GV,RF,Parameters,dim>,
+ PInitial_Inflow<GV,RF,Parameters>,
+ PhiInitial_HainesJump<GV,RF,Parameters,0>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_HainesJump<GV,RF,Parameters,1>,
+ ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters> > Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+// Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ rInd0.refineGrid(grid,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+ typedef FEM_FFS_CHNS_NavierStokes<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> NS_LOP;
+ NS_LOP nsLop(param, gfs.ch, chV, chVOld, gfs.ns, nsVOld);
+
+ typedef FEM_FFS_CHNS_R_CahnHilliard<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld, gfs.ns, nsV);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_ffs_chns_r<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+ typedef Dune::PDELab::GridOperator<NS_GFS,NS_GFS,NS_LOP,MBE,RF,RF,RF,typename GFS::NS_CC,typename GFS::NS_CC> NS_GO;
+ NS_GO nsGo(gfs.ns,gfs.nsCC,gfs.ns,gfs.nsCC,nsLop,mbe);
+
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,500,100,3,1);
+
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <NS_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> NS_LS; NS_LS ls_ns(nsGo,1000,200,3,1);
+
+ // Nonlinear solver
+ typedef Dune::PDELab::Newton<NS_GO,NS_LS,NS_V> PDESolver1;
+ PDESolver1 ns_newton(nsGo,nsV,ls_ns);
+ ns_newton.setParameters(ptree.sub("NS_Newton"));
+
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+
+ int result = timestepManager.doTimestep(ns_newton,ch_newton,vtkwriter);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/test_hainesjump/CMakeLists.txt b/src/test_hainesjump/CMakeLists.txt
new file mode 100644
index 0000000..bddab54
--- /dev/null
+++ b/src/test_hainesjump/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_executable(h_equation h_equation.cc)
+dune_symlink_to_source_files(FILES grids chns.ini)
diff --git a/src/test_hainesjump/chns.ini b/src/test_hainesjump/chns.ini
new file mode 120000
index 0000000..544e65b
--- /dev/null
+++ b/src/test_hainesjump/chns.ini
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/test_hainesjump/chns.ini
\ No newline at end of file
diff --git a/src/test_hainesjump/h_equation.cc b/src/test_hainesjump/h_equation.cc
new file mode 100644
index 0000000..b17ed0b
--- /dev/null
+++ b/src/test_hainesjump/h_equation.cc
@@ -0,0 +1,116 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+
+#include "3p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("chns.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+ Dune::GridFactory<Grid> factory;
+ if (helper.rank()==0)
+ Dune::GmshReader<Grid>::read(factory,filename,boundary_index_map,element_index_map,true,false);
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+ //gridp->globalRefine(refinement);
+ //gridp->loadBalance();
+ //std::cout << " after load balance /" << helper.rank() << "/ " << gridp->size(0) << std::endl;
+
+ //typedef Grid::LeafGridView LGV;
+
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ //GV gv(gridp->leafGridView(),periodic_directions);
+
+ typedef Grid::LeafGridView GV;
+ GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 1;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_3p(*gridp, es,vFem,pFem,phiFem, ptree, helper);
+ }
+
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
diff --git a/src/test_periodic/3p_driver.hh b/src/test_periodic/3p_driver.hh
new file mode 100644
index 0000000..9d7821e
--- /dev/null
+++ b/src/test_periodic/3p_driver.hh
@@ -0,0 +1,279 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include <dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh>
+#include <dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh>
+#include <dune/phasefield/localoperator/pf_3p_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/ffs_chns_r.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename GV, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_3p(Grid& grid, GV& gv, ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ //typedef typename Grid::LeafGridView GV;
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ //GV gv = grid.leafGridView();
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_ffs_r< RF,
+ TripleWell<RF,DoubleWell_limited< RF, DoubleWell_poly<RF>, Limiter_FakeDiverging<RF> > >,
+ //TripleWell<RF,DoubleWell_poly<RF>>,
+ Mobility_Const<RF>,
+ Reaction_None<RF>,
+ VelDissipation_Quadratic<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_ffs_chns_r<RF, ES, V_FEM, P_FEM, PHI_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+
+ typedef Bdry_ffs_chns_r_compositeV_2d<InflowOutflow_v, // v_x
+ Dune::PDELab::DirichletConstraintsParameters, // v_y
+ InflowOutflow_p, // p
+ InflowOutflow_phi, // phi1
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu1
+ InflowOutflow_phi, // phi2
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu2
+ InflowOutflow_u> // u
+ Bdry;
+ Bdry bdry;
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_ffs_chns_r< VelocityInitial_Channelflow<GV,RF,Parameters,dim>,
+ PInitial_Inflow<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_3pSlipTest<GV,RF,Parameters,1>,
+ ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters> > Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+ typedef FEM_FFS_CHNS_NavierStokes<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> NS_LOP;
+ NS_LOP nsLop(param, gfs.ch, chV, chVOld, gfs.ns, nsVOld);
+
+ typedef FEM_FFS_CHNS_R_CahnHilliard<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld, gfs.ns, nsV);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_ffs_chns_r<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+
+/* // Refine Intial Values
+ for(int i=0; i<3; i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement0"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ rInd0.myRefineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ vtkwriter.write(param.time.t + i*0.001f,Dune::VTK::ascii);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ chVOld = chV;
+ nsVOld = nsV;*/
+
+ // Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ //rInd0.refineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ rInd0.myRefineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //vtkwriter.write(param.time.t + i,Dune::VTK::ascii);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+
+
+/* //Coarsening Test
+ // Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("RefinementTEST"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ rInd0.myRefineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ //rInd0.refineGrid(grid,gv,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ vtkwriter.write(100+ i,Dune::VTK::ascii);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ chVOld = chV;
+ nsVOld = nsV;*/
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+ typedef Dune::PDELab::GridOperator<NS_GFS,NS_GFS,NS_LOP,MBE,RF,RF,RF,typename GFS::NS_CC,typename GFS::NS_CC> NS_GO;
+ NS_GO nsGo(gfs.ns,gfs.nsCC,gfs.ns,gfs.nsCC,nsLop,mbe);
+
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,500,100,3,1);
+
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <NS_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> NS_LS; NS_LS ls_ns(nsGo,3000,500,3,1);
+
+ // Nonlinear solver
+ typedef Dune::PDELab::Newton<NS_GO,NS_LS,NS_V> PDESolver1;
+ PDESolver1 ns_newton(nsGo,nsV,ls_ns);
+ ns_newton.setParameters(ptree.sub("NS_Newton"));
+
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+ int result;
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+ //if(timestepManager.time.t < 0.05)
+ result = timestepManager.doOnlyCHTimestep(ch_newton,vtkwriter);
+ //else
+ // result = timestepManager.doOnlyNSTimestep(ns_newton,vtkwriter);
+ // result = timestepManager.doTimestep(ns_newton,ch_newton,vtkwriter);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ //rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/test_periodic/CMakeLists.txt b/src/test_periodic/CMakeLists.txt
new file mode 100644
index 0000000..8683ce1
--- /dev/null
+++ b/src/test_periodic/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_executable(p_equation p_equation.cc)
+dune_symlink_to_source_files(FILES grids chns.ini)
diff --git a/src/test_periodic/chns.ini b/src/test_periodic/chns.ini
new file mode 120000
index 0000000..fd9a161
--- /dev/null
+++ b/src/test_periodic/chns.ini
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/test_periodic/chns.ini
\ No newline at end of file
diff --git a/src/test_periodic/grids/periodic.dgf b/src/test_periodic/grids/periodic.dgf
new file mode 100644
index 0000000..b9e8e57
--- /dev/null
+++ b/src/test_periodic/grids/periodic.dgf
@@ -0,0 +1,23 @@
+DGF
+
+INTERVAL
+0 0 % lower left corner
+1 1 % upper right corner
+8 8 % number of cells in each direction
+#
+
+PERIODICFACETRANSFORMATION
+1 0, 0 1 + 1 0 % make periodic in x-direction
+1 0, 0 1 + 0 1 % make periodic in y-direction
+#
+
+BOUNDARYDOMAIN
+DEFAULT 1
+#
+
+GRIDPARAMETER
+OVERLAP 0
+#
+
+#
+
diff --git a/src/test_periodic/grids/xperiodic.dgf b/src/test_periodic/grids/xperiodic.dgf
new file mode 100644
index 0000000..19762d4
--- /dev/null
+++ b/src/test_periodic/grids/xperiodic.dgf
@@ -0,0 +1,22 @@
+DGF
+
+INTERVAL
+0 0 % lower left corner
+1 1 % upper right corner
+8 8 % number of cells in each direction
+#
+
+PERIODICFACETRANSFORMATION
+1 0, 0 1 + 1 0 % make periodic in x-direction
+#
+
+BOUNDARYDOMAIN
+DEFAULT 1
+#
+
+GRIDPARAMETER
+OVERLAP 0
+#
+
+#
+
diff --git a/src/test_periodic/p_equation.cc b/src/test_periodic/p_equation.cc
new file mode 100644
index 0000000..864ed4c
--- /dev/null
+++ b/src/test_periodic/p_equation.cc
@@ -0,0 +1,141 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+
+// dunext includes
+#include <dune/xt/grid/view/periodic.hh>
+#include "3p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("chns.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+
+
+ Dune::GridFactory<Grid> factory;
+ Dune::GmshReader<Grid>::read(factory,filename,true,true);
+ Dune::GridFactory<Grid>::WorldMatrix matrix;
+ std::cout << "a" << std::endl;
+ matrix[0][0] = 1;
+ matrix[0][1] = 0;
+ matrix[1][1] = 1;
+ matrix[1][0] = 0;
+ std::cout << "b" << std::endl;
+ Dune::GridFactory<Grid>::WorldVector shift;
+ shift[0] = 1;
+ shift[1] = 0;
+ std::cout << "c" << std::endl;
+ factory.insertFaceTransformation(matrix,shift );
+
+
+
+ std::cout << "d" << std::endl;
+
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+
+ //Dune::GridPtr< Grid > gridp( filename );
+ std::cout << "i" << std::endl;
+
+
+
+ //gridp->globalRefine(refinement);
+ //gridp->loadBalance();
+ //std::cout << " after load balance /" << helper.rank() << "/ " << gridp->size(0) << std::endl;
+
+ typedef Grid::LeafGridView LGV;
+ std::bitset<2> periodic_directions(ptree.get("domain.periodic","00"));
+ typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv(gridp->leafGridView(),periodic_directions);
+
+ //typedef Grid::LeafGridView GV;
+ //GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_3p(*gridp, gv, es,vFem,pFem,phiFem, ptree, helper);
+ }
+
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
diff --git a/src/test_slipvelocity/3p_driver.hh b/src/test_slipvelocity/3p_driver.hh
new file mode 100644
index 0000000..2b97ce9
--- /dev/null
+++ b/src/test_slipvelocity/3p_driver.hh
@@ -0,0 +1,222 @@
+#pragma once
+
+// C includes
+#include<sys/stat.h>
+// C++ includes
+#include<iostream>
+// Dune includes
+#include<dune/grid/io/file/vtk.hh>
+#include<dune/pdelab/newton/newton.hh>
+
+#include <dune/phasefield/localoperator/fem_ffs_chns_r_cahnhilliard.hh>
+#include <dune/phasefield/localoperator/fem_ffs_chns_navierstokes.hh>
+#include <dune/phasefield/localoperator/pf_3p_diff_estimator.hh>
+
+#include <dune/phasefield/utility/ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES.hh>
+
+#include <dune/phasefield/chns_base.hh>
+#include <dune/phasefield/ffs_chns_r.hh>
+#include <dune/phasefield/initial_fn.hh>
+#include <dune/phasefield/debug/vector_debug.hh>
+
+
+
+//_________________________________________________________________________________________________________________________
+
+template<typename Grid, typename ES, typename V_FEM, typename P_FEM, typename PHI_FEM>
+void driver_3p (Grid& grid, const ES& es, const V_FEM& vFem, const P_FEM pFem, const PHI_FEM& phiFem, Dune::ParameterTree& ptree, Dune::MPIHelper& helper)
+{
+
+ typedef typename Grid::LeafGridView GV;
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ GV gv = grid.leafGridView();
+ const int dim = GV::dimension;
+ typedef double RF;
+
+
+ typedef Params_ffs_r< RF,
+ TripleWell<RF,DoubleWell_limited< RF, DoubleWell_poly<RF>, Limiter_FakeDiverging<RF> > >,
+ Mobility_Const<RF>,
+ Reaction_None<RF>,
+ VelDissipation_Quadratic_Shifted<RF> > Parameters;
+ Parameters param(ptree);
+ TimestepManager timestepManager(ptree.sub("Time"),param.time,2);
+
+
+//_________________________________________________________________________________________________________________________
+// Make grid function spaces
+
+
+ typedef GFS_ffs_chns_r<RF, ES, V_FEM, P_FEM, PHI_FEM, PHI_FEM> GFS;
+ GFS gfs(es,vFem,pFem,phiFem,phiFem);
+ typedef typename GFS::NS NS_GFS;
+ typedef typename GFS::CH CH_GFS;
+
+
+ //_________________________________________________________________________________________________________________________
+ //Constraints
+
+ typedef Bdry_ffs_chns_r_compositeV_2d<InflowOutflow_v, // v_x
+ Dune::PDELab::DirichletConstraintsParameters, // v_y
+ InflowOutflow_p, // p
+ InflowOutflow_phi, // phi1
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu1
+ InflowOutflow_phi, // phi2
+ Dune::PDELab::NoDirichletConstraintsParameters, // mu2
+ InflowOutflow_u> // u
+ Bdry;
+ Bdry bdry;
+ gfs.updateConstraintsContainer(bdry);
+
+ //_________________________________________________________________________________________________________________________
+ //Coefficient vectors
+
+ using CH_V = Dune::PDELab::Backend::Vector<CH_GFS, RF>;
+ using NS_V = Dune::PDELab::Backend::Vector<NS_GFS, RF>;
+ CH_V chV(gfs.ch);
+ NS_V nsV(gfs.ns);
+
+ //_________________________________________________________________________________________________________________________
+ //Initial Values
+
+ typedef Ini_ffs_chns_r< VelocityInitial_Inflow<GV,RF,Parameters,dim>,
+ ZeroInitial<GV,RF,Parameters>,
+ PhiInitial_3pSlipTest<GV,RF,Parameters,0>,
+ ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters>,
+ ZeroInitial<GV,RF,Parameters> > Initial;
+ Initial initial(gv,param);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+
+ //_________________________________________________________________________________________________________________________
+// Refine Intial Values
+ for(int i=0; i<ptree.get("Refinement.maxRefineLevel",2); i++)
+ {
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND0;
+ RIND0 rInd0(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd0.calculateIndicator(gv,chV,false);
+ rInd0.markGrid(grid,2);
+ rInd0.refineGrid(grid,chV,nsV,gfs.ch,gfs.ns,1);
+ Dune::PDELab::interpolate(initial.iniCH , gfs.ch, chV);
+ Dune::PDELab::interpolate(initial.iniNS , gfs.ns, nsV);
+ }
+
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+
+ CH_V chVOld = chV;
+ NS_V nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+ // LocalOperators
+
+ typedef FEM_FFS_CHNS_NavierStokes<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> NS_LOP;
+ NS_LOP nsLop(param, gfs.ch, chV, chVOld, gfs.ns, nsVOld);
+
+ typedef FEM_FFS_CHNS_R_CahnHilliard<Parameters, CH_GFS, CH_V, NS_GFS, NS_V> CH_LOP;
+ CH_LOP chLop(param, gfs.ch, chVOld, gfs.ns, nsV);
+
+ typedef Dune::PDELab::ISTL::BCRSMatrixBackend<> MBE;
+ MBE mbe(10);// Maximal number of nonzeroes per row can be cross-checked by patternStatistics().
+
+
+ //_________________________________________________________________________________________________________________________
+ // Construct discrete Grid Functions
+ typedef DGF_ffs_chns_r<GFS, NS_V, CH_V> DGF;
+ DGF dgf(gfs, nsV, chV);
+
+ //_________________________________________________________________________________________________________________________
+ // prepare VTK writer
+ std::string filename=ptree.get("output.filename","output");
+ struct stat st;
+ if( stat( filename.c_str(), &st ) != 0 )
+ {
+ int stat = 0;
+ stat = mkdir(filename.c_str(),S_IRWXU|S_IRWXG|S_IRWXO);
+ if( stat != 0 && stat != -1)
+ std::cout << "Error: Cannot create directory " << filename << std::endl;
+ }
+ auto stationaryvtkwriter = std::make_shared<Dune::SubsamplingVTKWriter<GV> >(gv,0);
+ Dune::VTKSequenceWriter<GV> vtkwriter(stationaryvtkwriter,filename.c_str(),filename.c_str(),"");
+ dgf.addToVTKWriter(vtkwriter);
+
+ vtkwriter.write(param.time.t,Dune::VTK::ascii);
+
+//_________________________________________________________________________________________________________________________
+ printVector(chV,10,"chV");
+ printVector(nsV,10,"nsV");
+
+
+ //____________________________________________________________________________________________________________________
+ //int i_it=0;
+ chVOld = chV;
+ nsVOld = nsV;
+ while (!timestepManager.isFinished())
+ {
+
+ // Grid Operators
+ typedef Dune::PDELab::GridOperator<NS_GFS,NS_GFS,NS_LOP,MBE,RF,RF,RF,typename GFS::NS_CC,typename GFS::NS_CC> NS_GO;
+ NS_GO nsGo(gfs.ns,gfs.nsCC,gfs.ns,gfs.nsCC,nsLop,mbe);
+
+ typedef Dune::PDELab::GridOperator<CH_GFS,CH_GFS,CH_LOP,MBE,RF,RF,RF,typename GFS::CH_CC,typename GFS::CH_CC> CH_GO;
+ CH_GO chGo(gfs.ch,gfs.chCC,gfs.ch,gfs.chCC,chLop,mbe);
+
+ // Linear solver
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <CH_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> CH_LS; CH_LS ls_ch(chGo,500,100,3,1);
+
+ typedef ISTLBackend_NOVLP_BASE_PREC_FOR_GMRES
+ <NS_GO, Dune::SeqILU0, Dune::RestartedGMResSolver> NS_LS; NS_LS ls_ns(nsGo,1000,200,3,1);
+
+ // Nonlinear solver
+ typedef Dune::PDELab::Newton<NS_GO,NS_LS,NS_V> PDESolver1;
+ PDESolver1 ns_newton(nsGo,nsV,ls_ns);
+ ns_newton.setParameters(ptree.sub("NS_Newton"));
+
+ typedef Dune::PDELab::Newton<CH_GO,CH_LS,CH_V> PDESolver2;
+ PDESolver2 ch_newton(chGo,chV,ls_ch);
+ ch_newton.setParameters(ptree.sub("Phasefield_Newton"));
+
+ //_________________________________________________________________________________________________________________________
+ // do time step
+
+
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH, nsV, chV);
+
+ int result = timestepManager.doTimestep(ns_newton,ch_newton,vtkwriter);
+ if(result <0)
+ {
+ return;
+ }
+ else if(result == 0)
+ {
+ nsV = nsVOld;
+ chV = chVOld;
+ continue;
+ }
+
+ chVOld = chV;
+ nsVOld = nsV;
+
+ //_________________________________________________________________________________________________________________________
+
+ // mark elements for refinement
+ typedef RefinementIndicator<GV,RF,PF_3P_DIFF_ESTIMATOR<CH_GFS>,CH_GFS> RIND;
+ RIND rInd(gv,gfs.ch,ptree.sub("Refinement"));
+ rInd.calculateIndicator(gv,chV,false);
+ rInd.markGrid(grid,2);
+ rInd.refineGrid(grid,chV,chVOld,nsV,nsVOld,gfs.ch,gfs.ns,2);
+
+ // recompute constraints
+ gfs.updateConstraintsContainer(bdry);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsV,chV);
+ interpolateToBdry(gfs,initial.iniNS,initial.iniCH,nsVOld,chVOld);
+
+
+ //vtkwriter.write(timestepManager.t+2e-6,Dune::VTK::ascii);
+ }
+}
diff --git a/src/test_slipvelocity/CMakeLists.txt b/src/test_slipvelocity/CMakeLists.txt
new file mode 100644
index 0000000..a8a7117
--- /dev/null
+++ b/src/test_slipvelocity/CMakeLists.txt
@@ -0,0 +1,2 @@
+add_executable(s_equation s_equation.cc)
+dune_symlink_to_source_files(FILES grids chns.ini)
diff --git a/src/test_slipvelocity/chns.ini b/src/test_slipvelocity/chns.ini
new file mode 120000
index 0000000..6326ed5
--- /dev/null
+++ b/src/test_slipvelocity/chns.ini
@@ -0,0 +1 @@
+/home/ians1/vonwolls/ssd_local/dumux/dune-phasefield/src/test_slipvelocity/chns.ini
\ No newline at end of file
diff --git a/src/test_slipvelocity/s_equation.cc b/src/test_slipvelocity/s_equation.cc
new file mode 100644
index 0000000..b17ed0b
--- /dev/null
+++ b/src/test_slipvelocity/s_equation.cc
@@ -0,0 +1,116 @@
+#ifdef HAVE_CONFIG_H
+#include "config.h"
+#endif
+
+#include<iostream>
+// dune includes
+#include<dune/common/parallel/mpihelper.hh>
+#include<dune/common/parametertreeparser.hh>
+#include<dune/common/timer.hh>
+//#if HAVE_UG
+//#include<dune/grid/uggrid.hh>
+//#endif
+#if HAVE_DUNE_ALUGRID
+#include<dune/alugrid/grid.hh>
+#include<dune/alugrid/dgf.hh>
+#include<dune/grid/io/file/dgfparser/dgfparser.hh>
+#endif
+// pdelab includes
+#include<dune/pdelab/finiteelementmap/pkfem.hh>
+
+#include "3p_driver.hh"
+
+//===============================================================
+// Main program with grid setup
+//===============================================================
+
+
+
+
+int main(int argc, char** argv)
+{
+ #if !HAVE_SUPERLU
+ std::cout << "Error: These examples work only if SuperLU is available." << std::endl;
+ exit(1);
+ #endif
+
+ #if HAVE_UG
+ try{
+ // Maybe initialize Mpi
+ Dune::MPIHelper&
+ helper = Dune::MPIHelper::instance(argc, argv);
+ if(Dune::MPIHelper::isFake)
+ std::cout<< "This is a sequential program." << std::endl;
+ else
+ std::cout << "Parallel code run on "
+ << helper.size() << " process(es)" << std::endl;
+
+ // open ini file
+ Dune::ParameterTree ptree;
+ Dune::ParameterTreeParser ptreeparser;
+ ptreeparser.readINITree("chns.ini",ptree);
+ ptreeparser.readOptions(argc,argv,ptree);
+
+ // read ini file
+// const int dim = ptree.get<int>("grid.dim");
+ const int refinement = ptree.get<int>("domain.level");
+
+
+ if (true/*dim==2*/)
+ {
+
+ typedef Dune::ALUGrid<2,2,Dune::simplex,Dune::conforming> Grid;
+ //typedef Dune::UGGrid<2> Grid;
+ typedef Grid::ctype DF;
+
+ std::vector<int> boundary_index_map;
+ std::vector<int> element_index_map;
+
+ std::string filename = ptree.get("domain.filename",
+ "turbtube2d.msh");
+ Dune::GridFactory<Grid> factory;
+ if (helper.rank()==0)
+ Dune::GmshReader<Grid>::read(factory,filename,boundary_index_map,element_index_map,true,false);
+ std::shared_ptr<Grid> gridp(factory.createGrid());
+ //gridp->globalRefine(refinement);
+ //gridp->loadBalance();
+ //std::cout << " after load balance /" << helper.rank() << "/ " << gridp->size(0) << std::endl;
+
+ //typedef Grid::LeafGridView LGV;
+
+ //std::bitset<2> periodic_directions(std::string("01"));
+ //typedef Dune::XT::Grid::PeriodicGridView<LGV> GV;
+ //GV gv(gridp->leafGridView(),periodic_directions);
+
+ typedef Grid::LeafGridView GV;
+ GV gv = gridp->leafGridView();
+
+ std::cout << "OK" << std::endl;
+
+ using ES = Dune::PDELab::NonOverlappingEntitySet<GV>;
+ ES es(gv);
+
+ const int k = 2;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k> V_FEM;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,k-1> P_FEM;
+ const int l = 1;
+ typedef Dune::PDELab::PkLocalFiniteElementMap<ES,DF,double,l> PHI_FEM;
+
+ V_FEM vFem(es);
+ P_FEM pFem(es);
+ PHI_FEM phiFem(es);
+
+ driver_3p(*gridp, es,vFem,pFem,phiFem, ptree, helper);
+ }
+
+ }
+ catch (Dune::Exception &e){
+ std::cerr << "Dune reported error: " << e << std::endl;
+ return 1;
+ }
+ catch (...){
+ std::cerr << "Unknown exception thrown!" << std::endl;
+ return 1;
+ }
+ #endif
+}
--
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