Complete AMDiS tree moved to trunk/AMDiS.

AMDiS/ChangeLog

+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)
+

AMDiS/INSTALL

+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
+unlimited permission to copy, distribute and modify it.
+
+Basic Installation
+==================
+
+These are generic installation instructions.
+
+   The `configure' shell script attempts to guess correct values for
+various system-dependent variables used during compilation.  It uses
+those values to create a `Makefile' in each directory of the package.
+It may also create one or more `.h' files containing system-dependent
+definitions.  Finally, it creates a shell script `config.status' that
+you can run in the future to recreate the current configuration, and a
+file `config.log' containing compiler output (useful mainly for
+debugging `configure').
+
+   It can also use an optional file (typically called `config.cache'
+and enabled with `--cache-file=config.cache' or simply `-C') that saves
+the results of its tests to speed up reconfiguring.  (Caching is
+disabled by default to prevent problems with accidental use of stale
+cache files.)
+
+   If you need to do unusual things to compile the package, please try
+to figure out how `configure' could check whether to do them, and mail
+diffs or instructions to the address given in the `README' so they can
+be considered for the next release.  If you are using the cache, and at
+some point `config.cache' contains results you don't want to keep, you
+may remove or edit it.
+
+   The file `configure.ac' (or `configure.in') is used to create
+`configure' by a program called `autoconf'.  You only need
+`configure.ac' if you want to change it or regenerate `configure' using
+a newer version of `autoconf'.
+
+The simplest way to compile this package is:
+
+  1. `cd' to the directory containing the package's source code and type
+     `./configure' to configure the package for your system.  If you're
+     using `csh' on an old version of System V, you might need to type
+     `sh ./configure' instead to prevent `csh' from trying to execute
+     `configure' itself.
+
+     Running `configure' takes awhile.  While running, it prints some
+     messages telling which features it is checking for.
+
+  2. Type `make' to compile the package.
+
+  3. Optionally, type `make check' to run any self-tests that come with
+     the package.
+
+  4. Type `make install' to install the programs and any data files and
+     documentation.
+
+  5. You can remove the program binaries and object files from the
+     source code directory by typing `make clean'.  To also remove the
+     files that `configure' created (so you can compile the package for
+     a different kind of computer), type `make distclean'.  There is
+     also a `make maintainer-clean' target, but that is intended mainly
+     for the package's developers.  If you use it, you may have to get
+     all sorts of other programs in order to regenerate files that came
+     with the distribution.
+
+Compilers and Options
+=====================
+
+Some systems require unusual options for compilation or linking that the
+`configure' script does not know about.  Run `./configure --help' for
+details on some of the pertinent environment variables.
+
+   You can give `configure' initial values for configuration parameters
+by setting variables in the command line or in the environment.  Here
+is an example:
+
+     ./configure CC=c89 CFLAGS=-O2 LIBS=-lposix
+
+   *Note Defining Variables::, for more details.
+
+Compiling For Multiple Architectures
+====================================
+
+You can compile the package for more than one kind of computer at the
+same time, by placing the object files for each architecture in their
+own directory.  To do this, you must use a version of `make' that
+supports the `VPATH' variable, such as GNU `make'.  `cd' to the
+directory where you want the object files and executables to go and run
+the `configure' script.  `configure' automatically checks for the
+source code in the directory that `configure' is in and in `..'.
+
+   If you have to use a `make' that does not support the `VPATH'
+variable, you have to compile the package for one architecture at a
+time in the source code directory.  After you have installed the
+package for one architecture, use `make distclean' before reconfiguring
+for another architecture.
+
+Installation Names
+==================
+
+By default, `make install' installs the package's commands under
+`/usr/local/bin', include files under `/usr/local/include', etc.  You
+can specify an installation prefix other than `/usr/local' by giving
+`configure' the option `--prefix=PREFIX'.
+
+   You can specify separate installation prefixes for
+architecture-specific files and architecture-independent files.  If you
+pass the option `--exec-prefix=PREFIX' to `configure', the package uses
+PREFIX as the prefix for installing programs and libraries.
+Documentation and other data files still use the regular prefix.
+
+   In addition, if you use an unusual directory layout you can give
+options like `--bindir=DIR' to specify different values for particular
+kinds of files.  Run `configure --help' for a list of the directories
+you can set and what kinds of files go in them.
+
+   If the package supports it, you can cause programs to be installed
+with an extra prefix or suffix on their names by giving `configure' the
+option `--program-prefix=PREFIX' or `--program-suffix=SUFFIX'.
+
+Optional Features
+=================
+
+Some packages pay attention to `--enable-FEATURE' options to
+`configure', where FEATURE indicates an optional part of the package.
+They may also pay attention to `--with-PACKAGE' options, where PACKAGE
+is something like `gnu-as' or `x' (for the X Window System).  The
+`README' should mention any `--enable-' and `--with-' options that the
+package recognizes.
+
+   For packages that use the X Window System, `configure' can usually
+find the X include and library files automatically, but if it doesn't,
+you can use the `configure' options `--x-includes=DIR' and
+`--x-libraries=DIR' to specify their locations.
+
+Specifying the System Type
+==========================
+
+There may be some features `configure' cannot figure out automatically,
+but needs to determine by the type of machine the package will run on.
+Usually, assuming the package is built to be run on the _same_
+architectures, `configure' can figure that out, but if it prints a
+message saying it cannot guess the machine type, give it the
+`--build=TYPE' option.  TYPE can either be a short name for the system
+type, such as `sun4', or a canonical name which has the form:
+
+     CPU-COMPANY-SYSTEM
+
+where SYSTEM can have one of these forms:
+
+     OS KERNEL-OS
+
+   See the file `config.sub' for the possible values of each field.  If
+`config.sub' isn't included in this package, then this package doesn't
+need to know the machine type.
+
+   If you are _building_ compiler tools for cross-compiling, you should
+use the option `--target=TYPE' to select the type of system they will
+produce code for.
+
+   If you want to _use_ a cross compiler, that generates code for a
+platform different from the build platform, you should specify the
+"host" platform (i.e., that on which the generated programs will
+eventually be run) with `--host=TYPE'.
+
+Sharing Defaults
+================
+
+If you want to set default values for `configure' scripts to share, you
+can create a site shell script called `config.site' that gives default
+values for variables like `CC', `cache_file', and `prefix'.
+`configure' looks for `PREFIX/share/config.site' if it exists, then
+`PREFIX/etc/config.site' if it exists.  Or, you can set the
+`CONFIG_SITE' environment variable to the location of the site script.
+A warning: not all `configure' scripts look for a site script.
+
+Defining Variables
+==================
+
+Variables not defined in a site shell script can be set in the
+environment passed to `configure'.  However, some packages may run
+configure again during the build, and the customized values of these
+variables may be lost.  In order to avoid this problem, you should set
+them in the `configure' command line, using `VAR=value'.  For example:
+
+     ./configure CC=/usr/local2/bin/gcc
+
+causes the specified `gcc' to be used as the C compiler (unless it is
+overridden in the site shell script).  Here is a another example:
+
+     /bin/bash ./configure CONFIG_SHELL=/bin/bash
+
+Here the `CONFIG_SHELL=/bin/bash' operand causes subsequent
+configuration-related scripts to be executed by `/bin/bash'.
+
+`configure' Invocation
+======================
+
+`configure' recognizes the following options to control how it operates.
+
+`--help'
+`-h'
+     Print a summary of the options to `configure', and exit.
+
+`--version'
+`-V'
+     Print the version of Autoconf used to generate the `configure'
+     script, and exit.
+
+`--cache-file=FILE'
+     Enable the cache: use and save the results of the tests in FILE,
+     traditionally `config.cache'.  FILE defaults to `/dev/null' to
+     disable caching.
+
+`--config-cache'
+`-C'
+     Alias for `--cache-file=config.cache'.
+
+`--quiet'
+`--silent'
+`-q'
+     Do not print messages saying which checks are being made.  To
+     suppress all normal output, redirect it to `/dev/null' (any error
+     messages will still be shown).
+
+`--srcdir=DIR'
+     Look for the package's source code in directory DIR.  Usually
+     `configure' can determine that directory automatically.
+
+`configure' also accepts some other, not widely useful, options.  Run
+`configure --help' for more details.
+

AMDiS/Makefile.am

+SUBDIRS = lib bin
+
+EXTRA_DIST = demo

AMDiS/README

+================== 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

AMDiS/compositeFEM/src/CFE_Integration.cc

+#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;
+