From 3000d2c854e8ae5b5dc562151cc3ea142ae1ca19 Mon Sep 17 00:00:00 2001
From: Matti Pellika <matti.pellikka@tut.fi>
Date: Mon, 30 Mar 2009 13:31:51 +0000
Subject: [PATCH] Added Geo/CellCompelex.cpp and Geo/CellComplex.h They
construct a cell complex of a finite elemement mesh of a model, and are able
to reduce and coreduce it in order to compute model's homology groups.
Also added contrib/kbipack to by Saku Suuriniemi for future use to
compute Smith normal forms of the boundary operator matrices of the
reduced cell complex.
Modified Makefiles and configure.in accordingly.
---
Geo/MFace.cpp | 1 +
Geo/MFace.h | 3 ++-
Geo/Makefile | 7 ++++++-
Makefile | 5 ++++-
configure | 40 ++++++++++++++++++++++++++++++++++++++++
configure.in | 15 +++++++++++++++
6 files changed, 68 insertions(+), 3 deletions(-)
diff --git a/Geo/MFace.cpp b/Geo/MFace.cpp
index 4ef4dbfa13..005ba9581e 100644
--- a/Geo/MFace.cpp
+++ b/Geo/MFace.cpp
@@ -74,6 +74,7 @@ MFace::MFace(MVertex *v0, MVertex *v1, MVertex *v2, MVertex *v3)
}
else
_si[3] = 3;
+
}
SVector3 MFace::normal() const
diff --git a/Geo/MFace.h b/Geo/MFace.h
index ce8a8b088f..7fce754ffb 100644
--- a/Geo/MFace.h
+++ b/Geo/MFace.h
@@ -9,13 +9,14 @@
#include <functional>
#include <vector>
#include "MVertex.h"
+#include "MEdge.h"
#include "SVector3.h"
// A mesh face.
class MFace {
private:
MVertex *_v[4];
- char _si[4]; // sorted indices
+ char _si[4]; // sorted indices
public:
MFace();
diff --git a/Geo/Makefile b/Geo/Makefile
index 7c84e081cd..1359693f44 100644
--- a/Geo/Makefile
+++ b/Geo/Makefile
@@ -10,6 +10,7 @@ LIB = ../lib/libGmshGeo${LIBEXT}
INC = ${DASH}I../Common ${DASH}I../Geo ${DASH}I../Mesh\
${DASH}I../Post ${DASH}I../Numeric ${DASH}I../Parser\
${DASH}I../contrib/ANN/include\
+ ${DASH}I../contrib/kbipack\
${DASH}I../contrib/MathEval ${DASH}I../contrib/gmm
CFLAGS = ${OPTIM} ${FLAGS} ${INC} ${SYSINCLUDE}
@@ -37,7 +38,9 @@ SRC = GEntity.cpp\
MElement.cpp\
MLine.cpp MTriangle.cpp MQuadrangle.cpp MTetrahedron.cpp\
MHexahedron.cpp MPrism.cpp MPyramid.cpp\
- MZone.cpp MZoneBoundary.cpp
+ MZone.cpp MZoneBoundary.cpp\
+ CellComplex.cpp
+
OBJ = ${SRC:.cpp=${OBJEXT}}
@@ -375,3 +378,5 @@ MPyramid${OBJEXT}: MPyramid.cpp MPyramid.h MElement.h ../Common/GmshDefines.h \
../Numeric/Numeric.h ../Numeric/GmshMatrix.h
MZone${OBJEXT}: MZone.cpp ../Common/GmshConfig.h
MZoneBoundary${OBJEXT}: MZoneBoundary.cpp ../Common/GmshConfig.h
+CellComplex${OBJEXT}: CellComplex.cpp CellComplex.h
+
diff --git a/Makefile b/Makefile
index 9dcb102aac..36c7086ca7 100644
--- a/Makefile
+++ b/Makefile
@@ -26,13 +26,16 @@ GMSH_API =\
Geo/MTetrahedron.h Geo/MHexahedron.h Geo/MPrism.h Geo/MPyramid.h\
Geo/discreteVertex.h Geo/discreteEdge.h Geo/discreteFace.h Geo/discreteRegion.h\
Geo/SPoint2.h Geo/SPoint3.h Geo/SVector3.h Geo/SBoundingBox3d.h Geo/Pair.h Geo/Range.h\
+ Geo/CellComplex.h\
+ contrib/kbipack/gmp_normal_form.h contrib/kbipack/gmp_matrix.h contrib/kbipack/gmp_blas.h\
Numeric/Gauss.h Numeric/FunctionSpace.h Numeric/GmshMatrix.h\
Numeric/gmshAssembler.h Numeric/gmshTermOfFormulation.h Numeric/gmshLaplace.h\
Numeric/gmshElasticity.h Numeric/gmshLinearSystem.h Numeric/gmshLinearSystemGmm.h\
Numeric/gmshLinearSystemFull.h Numeric/gmshFunction.h\
Post/PView.h Post/PViewData.h Plugin/PluginManager.h\
Common/VertexArray.h Common/GmshMessage.h\
- Common/Gmsh.h Common/GmshConfig.h Common/GmshDefines.h Common/GmshVersion.h
+ Common/Gmsh.h Common/GmshConfig.h Common/GmshDefines.h Common/GmshVersion.h
+
GMSH_EMBEDDED = ${GMSH_API}\
Geo/GModel.cpp Geo/GModelIO_Mesh.cpp Geo/GEntity.cpp\
diff --git a/configure b/configure
index 334641fefd..2eefd1d2e1 100755
--- a/configure
+++ b/configure
@@ -1277,6 +1277,7 @@ Optional Features:
--enable-chaco compile Chaco partitioner (default=yes)
--enable-tetgen compile Tetgen if available (default=yes)
--enable-matheval compile MathEval if available (default=yes)
+ --enable-kbipack compile kbipack if available (default=yes)
--enable-gmm use gmm++ if available (default=yes)
--enable-osmesa use OSMesa for offscreen rendering (default=no)
--enable-cgns enable CGNS output (default=no)
@@ -1911,6 +1912,11 @@ if test "${enable_matheval+set}" = set; then
enableval=$enable_matheval;
fi
+# Check whether --enable-kbipack was given.
+if test "${enable_kbipack+set}" = set; then
+ enableval=$enable_kbipack;
+fi
+
# Check whether --enable-gmm was given.
if test "${enable_gmm+set}" = set; then
enableval=$enable_gmm;
@@ -1978,6 +1984,7 @@ if test "x$enable_minimal" = "xyes"; then
enable_netgen=no;
enable_tetgen=no;
enable_matheval=no;
+ enable_kbipack=no;
enable_gmm=no;
enable_ann=no;
enable_metis=no;
@@ -4746,6 +4753,39 @@ _ACEOF
fi
fi
+ if test "x$enable_kbipack" != "xno"; then
+ { echo "$as_me:$LINENO: checking for ./contrib/kbipack/gmp_normal_form.h" >&5
+echo $ECHO_N "checking for ./contrib/kbipack/gmp_normal_form.h... $ECHO_C" >&6; }
+if test "${ac_cv_file___contrib_kbipack_gmp_normal_form_h+set}" = set; then
+ echo $ECHO_N "(cached) $ECHO_C" >&6
+else
+ test "$cross_compiling" = yes &&
+ { { echo "$as_me:$LINENO: error: cannot check for file existence when cross compiling" >&5
+echo "$as_me: error: cannot check for file existence when cross compiling" >&2;}
+ { (exit 1); exit 1; }; }
+if test -r "./contrib/kbipack/gmp_normal_form.h"; then
+ ac_cv_file___contrib_kbipack_gmp_normal_form_h=yes
+else
+ ac_cv_file___contrib_kbipack_gmp_normal_form_h=no
+fi
+fi
+{ echo "$as_me:$LINENO: result: $ac_cv_file___contrib_kbipack_gmp_normal_form_h" >&5
+echo "${ECHO_T}$ac_cv_file___contrib_kbipack_gmp_normal_form_h" >&6; }
+if test $ac_cv_file___contrib_kbipack_gmp_normal_form_h = yes; then
+ KBIPACK="yes"
+fi
+
+ if test "x${KBIPACK}" = "xyes"; then
+ GMSH_DIRS="${GMSH_DIRS} contrib/kbipack"
+ GMSH_LIBS="${GMSH_LIBS} -lGmshKbi -lgmp"
+ cat >>confdefs.h <<\_ACEOF
+#define HAVE_kbipack 1
+_ACEOF
+
+ BO="${BO} kbipack"
+ fi
+ fi
+
fi
if test "x${OCC_PREFIX}" != "x"; then
diff --git a/configure.in b/configure.in
index e10e4fc0bb..e253c4745d 100644
--- a/configure.in
+++ b/configure.in
@@ -109,6 +109,9 @@ AC_ARG_ENABLE(tetgen,
AC_ARG_ENABLE(matheval,
AC_HELP_STRING([--enable-matheval],
[compile MathEval if available (default=yes)]))
+AC_ARG_ENABLE(kbipack,
+ AC_HELP_STRING([--enable-kbipack],
+ [compile kbipack if available (default=yes)]))
AC_ARG_ENABLE(gmm,
AC_HELP_STRING([--enable-gmm],
[use gmm++ if available (default=yes)]))
@@ -153,6 +156,7 @@ if test "x$enable_minimal" = "xyes"; then
enable_netgen=no;
enable_tetgen=no;
enable_matheval=no;
+ enable_kbipack=no;
enable_gmm=no;
enable_ann=no;
enable_metis=no;
@@ -500,6 +504,17 @@ if test "x$enable_contrib" != "xno"; then
BO="${BO} MathEval"
fi
fi
+
+ dnl Check for kbipack
+ if test "x$enable_kbipack" != "xno"; then
+ AC_CHECK_FILE(./contrib/kbipack/gmp_normal_form.h,KBIPACK="yes")
+ if test "x${KBIPACK}" = "xyes"; then
+ GMSH_DIRS="${GMSH_DIRS} contrib/kbipack"
+ GMSH_LIBS="${GMSH_LIBS} -lGmshKbi -lgmp"
+ AC_DEFINE(HAVE_kbipack)
+ BO="${BO} kbipack"
+ fi
+ fi
fi
--
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