Commit 114c1d41 authored by Peter Gottschling's avatar Peter Gottschling

Complete AMDiS tree moved to trunk/AMDiS.

parent fce86d10
This diff is collapsed.
28.03.2006: init file:
<myProblem>->output->serialize adapt info: 0/1
28.03.2006: FileWriterInterface changed:
writeFiles(double time, bool force) ->
writeFiles(AdaptInfo *adaptInfo, bool force)
27.03.2006: GERSMarker corrected
23.03.2006: BasisFunction::getDOFIndices() -> BasisFunction::getLocalIndices()
both functions do the same -> getDOFIndices depricated
15.03.2006: parallel AMDiS:
DualTraverse generalized
14.03.2006: parallel AMDiS:
MeshStructure.h and .cc added.
(-> transfer mesh tree via MPI)
13.03.2006: parallel AMDiS:
EmptyElementData.h added.
(-> marks elements belonging to processors myRank region)
Installation Instructions
*************************
Copyright (C) 1994, 1995, 1996, 1999, 2000, 2001, 2002, 2004, 2005 Free
Software Foundation, Inc.
This file is free documentation; the Free Software Foundation gives
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==================
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SUBDIRS = lib bin
EXTRA_DIST = demo
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================== Install AMDiS ===================
To install AMDiS run the following commands:
./configure --prefix=`pwd` [--enable-debug]
[--enable-intel]
[--with-mpi=<MPI-DIR>]
[--with-parmetis]
make install
Note that for debugging your application you should enable the flag
--enable-debug. If you do not need debugging information but, instead,
your application should run as fast as possible, do not set this flag.
The runtime will increase by factor 5 to 6 without --enable-debug!
================== Compile AMDiS on mars ===================
1) Load the Inter compiler:
module load icc
2) Change to the directory AMDiS/lib/ParMetis-3.1
3) Compile ParMETIS with:
make CC=icc LD=icc
4) Change to the AMDiS directory
5) Run the configure script:
./configure --prefix=`pwd` --enable-intel --enable-parmetis
You can also enabel --enable-debug. Enabling MPI using --with-mpi
does not work on mars and it is not necessary to use this parameter
to compile AMDiS with MPI on mars. Note taht is is also possible to
compile with gcc (just omit --enable-intel), but the result is less
performant. Compiling with the Intel compiler results in a huge
number of warnings. Just ignore them.
6) Start compiling with:
make install
7) To compile the demos you have to edit the Makefile in the demo
directory. At the beginning of the file you will find several
parameters, which you have to define in order to compiler the demos
properly.
================== Compile AMDiS on deimos ===================
1) Load MPI support for the GNU compiler:
module load openmpi
2) Change to the directory AMDiS/lib/ParMetis-3.1
3) Compile ParMETIS with:
make
4) Change to the AMDiS directory
5) Run the configure script:
./configure --prefix=`pwd` --with-mpi=/licsoft/libraries/openmpi/1.2.4/64bit --enable-parmetis
You may also enable --enable-debug.
6) Start compiling with:
make install
7) To compile the demos you have to edit the Makefile in the demo
directory. At the beginning of the file you will find several
parameters, which you have to define in order to compiler the demos
properly.
================== Remake AMDiS' make system ===================
If you have added a new source file or you want to change something
on the automake-system, you have to rerun the following commands:
libtoolize --copy --force
aclocal
autoconf
automake --copy --add-missing
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#include "CFE_Integration.h"
#include "Mesh.h"
#include "SurfaceQuadrature.h"
#include "Traverse.h"
#include "ScalableQuadrature.h"
#include "SubElInfo.h"
#include "SubPolytope.h"
double
CFE_Integration::integrate_onNegLs(ElementFunction<double> *f,
ElementLevelSet *elLS,
int deg,
Quadrature *q)
{
FUNCNAME("CFE_Integration::integrate_onNegLs()");
int dim = elLS->getDim();
double int_val = 0.0;
double el_int_val;
double subEl_int_val;
VectorOfFixVecs<DimVec<double> > *intersecPts;
SubPolytope *subPolytope;
int numIntersecPts;
int iq;
double val;
int numQuadPts;
int vertex_interior;
ScalableQuadrature *loc_scalQuad;
int numScalQuadPts;
bool subPolIsExterior = false;
int elStatus;
Mesh *mesh = elLS->getMesh();
// ===== Get quadratures. =====
if (!q) {
q = Quadrature::provideQuadrature(dim, deg);
}
numQuadPts = q->getNumPoints();
loc_scalQuad = NEW ScalableQuadrature(q);
numScalQuadPts = loc_scalQuad->getNumPoints();
// ===== Traverse mesh and calculate integral on each element. =====
TraverseStack stack;
ElInfo *loc_elInfo = stack.traverseFirst(mesh,
-1,
Mesh::CALL_LEAF_EL |
Mesh::FILL_COORDS |
Mesh::FILL_DET);
while(loc_elInfo) {
el_int_val = 0.0;
subEl_int_val = 0.0;
subPolIsExterior = false;
// Check whether current element is cut by the zero level set.
elStatus = elLS->createElementLevelSet(loc_elInfo);
if (elStatus == ElementLevelSet::LEVEL_SET_BOUNDARY) {
// -------------------------------------------------------------------
// Element is cut by the zero level set.
// -------------------------------------------------------------------
// Create subelements.
intersecPts = elLS->getElIntersecPoints();
numIntersecPts = elLS->getNumElIntersecPoints();
if (dim == 1 || (dim == 3 && numIntersecPts == 4)) {
// -----------------------------------------------------------------
// Subelement(s) are inside the domain with negative level set
// function value.
// Get vertex with negative level set function value.
for (int i=0; i<=dim; ++i) {
if (elLS->getElVertLevelSetVec(i) < 0) {
vertex_interior = i;
break;
}
}
subPolytope = NEW SubPolytope(loc_elInfo,
intersecPts,
numIntersecPts,
vertex_interior);
}
else {
// -----------------------------------------------------------------
// Subelement may be inside the domain with negative level set
// function value as well as inside the domain with positive
// function value.
//
// Whether a subelement is in the domain with negative or positive
// level set function values is checked by the level set function
// value of the first vertex of the subelement. (The subelements
// are created in such a way that this vertex always is a vertex
// of the element and not an intersection point. Thus the level set
// function value of this vertex really is unequal to zero.)
subPolytope = NEW SubPolytope(loc_elInfo,
intersecPts,
numIntersecPts,
0);
if(elLS->getVertexPos(subPolytope->getSubElement(0)->getLambda(0)) ==
ElementLevelSet::LEVEL_SET_EXTERIOR) {
subPolIsExterior = true;
}
}
elLS->setLevelSetDomain(ElementLevelSet::LEVEL_SET_INTERIOR);
// Calculate integral on subelement(s).
f->setElInfo(loc_elInfo);
for (std::vector<SubElInfo *>::iterator it =
subPolytope->getSubElementsBegin();
it != subPolytope->getSubElementsEnd();
it++) {
loc_scalQuad->scaleQuadrature(**it);
for (val = iq = 0; iq < numScalQuadPts; ++iq) {
val += loc_scalQuad->getWeight(iq)*(*f)(loc_scalQuad->getLambda(iq));
}
el_int_val += fabs((*it)->getDet()) * val;
}
// -------------------------------------------------------------------
// In case the subelement is in the domain with positive level set
// function values:
// Calculate the integral on the element part with negative
// level set function values by substracting the integral on the
// subelement from the integral on the complete element.
if (subPolIsExterior) {
subEl_int_val = el_int_val;
el_int_val = 0.0;