Author : Domenico Notaro
Mailto : domenico.not@gmail.com
Date : March 2016
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doc/: Code documentation -
include/: General include files -
lib/: Main library (to be generated) -
src/: Example sources1_uncoupled/: solve the uncoupled 1d and 3d problems2_singlebranch/: solve the coupling with single-vessel network3_Ybifurcation/: solve the problem with Y-shaped network4_primalmixed/: compare the output of primal and mixed solvers5_CFS/: simulate the flow of CSF in the brain
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config.mk: Specify the variable GETFEM_PREFIX for GetFEM++ library -
Doxyfile: Instruction to build the code documentation -
Makefile: Instruction to install the project (see INSTALLATION)
You need the open source finite element library "GetFEM++"
See http://download.gna.org/getfem/html/homepage
Version >= 4.2 is preferible
You must modify the path to the GetFEM library in config.mk:
GETFEM_PREFIX=/home/.../path/to/.../getfem
Alternatively, at MOX cluster use the module.sh file:
$ source module.sh
BEWARE: Recall to add the library path to LD_LIBRARY_PATH. Example:
$ export LD_LIBRARY_PATH=/home/...path/to.../getfem/lib
======================
Build the whole project with:
$ make
It first build the (static) library "libproblem3d1d" by calling
the Makefile in include/:
$ make -C include/
Then, it calls the inner makefiles provided for all examples.
It is also possible to build a single example, e.g. "1_uncoupled", with:
$ make library
$ make -C src/1_uncoupled
BEWARE: If you want non-optimized program type:
$ make DEBUG=yes
By defaul DEBUG=no.
The following macro are defined and exported
CPPFLAGS=-I../../include -I$(GETFEM_PREFIX)/include
CXXFLAGS=-std=c++11 -D=M3D1D_VERBOSE_
OPTFLAGS=-O3 -DNDEBUG -march=native
LDFLAGS=-L$(GETFEM_PREFIX)/lib
LIBRARIES=-lgetfem
Recall that any macro may be overrlued by specifying it when calling make. Example:
$ make CXXFLAGS+=-DSOMETHING OPTFLAGS=-g
======================
The documentation is produced by doxygen. The file Doxyfile contains the common doxygen configuration for all examples. Build the code documentation with:
$ make pdf
It first fills doc/ with code documentation ($ make doc) and then compile the .tex files to produce a portable file ($ pdflatex doc/latex/refman.tex). You can visualize the documentation with
$ evince doc/latex/refman.pdf
All examples are provided with a Makefile which accepts the following options:
- all : makes the example
- clean : as it says
- distclean : clean and also deletes temporary file and local doc directory Being "all" the first target of the makefile, to compile the examples is sufficient to type make. In addition the external Makefile (./Makefile) has the following options:
- doc : produces the documentation (html, tex)
- pdf : produces a guide in portable format
- library : build the library from files in include/
To run a specif example, go to the related subdirectory
$ cd src/3_Yshaped
Build the program
$ make
Execute the program with specific input
$ ./M3D1D input.param
Each program contains the file input.param that specifies
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Some flags to identify the particular example
- TEST_PARAM = 1 # import parameters in dimensionless form
- VTK_EXPORT = 1 # export results in vtk format
- ...
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The mesh
- For the 3D mesh you can either provide instruction to build a simple regular mesh (TEST_GEOMETRY = 1) or the absolute path to import a mesh pre-built with Gmsh (.gmsh)
- For the 1D mesh specify the path to the file of points (.pts). All examples come with a possible pts file
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GetFEM++ descriptors (FEM, ...)
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Problem parameters (dimensional or dimensionless)
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Boundary conditions. You can choose an arbitrary combination of Dirichlet-type conditions on pt and/or Robin-type conditions on the flux, namely:
% Faces: x=0 x=L y=0 y=L z=0 z=L
% BC labels (DIR / MIX)
BClabel = 'DIR DIR DIR DIR DIR DIR'
% BC values
BCvalue = '0.0 0.0 0.0 0.0 0.0 0.0'
BEWARE: All paths in file param must be ABSOLUTE
OS : Ubuntu 14.04 LTS 64-bit
Processor : Intel® Core™ i5-2410M CPU @ 2.30GHz × 4
Compiler : g++-4.8
GetFEM lib : 5.0