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Mixed Finite Element Methods for Coupled 3D/1D Fluid Problems

Politecnico di Milano (ITALY)

Author : Domenico Notaro

Mailto : [email protected]

Date : March 2016

How to install and run the program

THE PACKAGE

  • doc/ : Code documentation

  • include/ : General include files

  • lib/ : Main library (to be generated)

  • src/ : Example sources

    • 1_uncoupled/ : solve the uncoupled 1d and 3d problems
    • 2_singlebranch/ : solve the coupling with single-vessel network
    • 3_Ybifurcation/ : solve the problem with Y-shaped network
    • 4_primalmixed/ : compare the output of primal and mixed solvers
    • 5_CFS/ : simulate the flow of CSF in the brain

  • 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)

INSTALLATION

Prerequisites

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

======================

Installation

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

======================

Documentation

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

MAKE OPTIONS

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/

RUN EXAMPLES

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

  • Some flags to identify the particular example

    • TEST_PARAM = 1 # import parameters in dimensionless form
    • VTK_EXPORT = 1 # export results in vtk format
    • ...

  • 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

  • GetFEM++ descriptors (FEM, ...)

  • Problem parameters (dimensional or dimensionless)

  • 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

DEV ENVIRONMENT

OS : Ubuntu 14.04 LTS 64-bit

Processor : Intel® Core™ i5-2410M CPU @ 2.30GHz × 4

Compiler : g++-4.8

GetFEM lib : 5.0