New port: math/moab: Component for representing and evaluating mesh data

9 files changed, 226 insertions, 0 deletions

diff --git a/math/Makefile b/math/Makefile
index aa0c72ac8e60..351573594dc5 100644
--- a/math/Makefile
+++ b/math/Makefile
@@ -353,6 +353,7 @@
     SUBDIR += miracl
     SUBDIR += mkl-dnn
     SUBDIR += mlpack
+    SUBDIR += moab
     SUBDIR += moo
     SUBDIR += mosesdecoder
     SUBDIR += mpc
diff --git a/math/moab/Makefile b/math/moab/Makefile
new file mode 100644
index 000000000000..fe36c191b46e
--- /dev/null
+++ b/math/moab/Makefile
@@ -0,0 +1,26 @@
+# $FreeBSD$
+
+PORTNAME=	moab
+DISTVERSION=	4.6.3
+CATEGORIES=	math
+MASTER_SITES=	http://ftp.mcs.anl.gov/pub/fathom/
+
+MAINTAINER=	yuri@FreeBSD.org
+COMMENT=	Component for representing and evaluating mesh data
+
+LICENSE=	BSD2CLAUSE
+xLICENSE_FILE=	${WRKSRC}/LICENSE.txt
+
+LIB_DEPENDS=	libhdf5.so:science/hdf5 \
+		libnetcdf.so:science/netcdf
+
+USES=		autoreconf gmake libtool localbase:ldflags
+GNU_CONFIGURE=	yes
+CONFIGURE_ARGS=	--disable-static --with-netcdf=${LOCALBASE}
+USE_LDCONFIG=	yes
+
+OPTIONS_DEFINE=	DOCS
+
+PORTDOCS=	*
+
+.include <bsd.port.mk>
diff --git a/math/moab/distinfo b/math/moab/distinfo
new file mode 100644
index 000000000000..e6b9701ae78d
--- /dev/null
+++ b/math/moab/distinfo
@@ -0,0 +1,3 @@
+TIMESTAMP = 1541374760
+SHA256 (moab-4.6.3.tar.gz) = a25933254a05013811d3769e5d96b01cc7b5d67026acacbaae4f3568ce18fd7f
+SIZE (moab-4.6.3.tar.gz) = 21861257
diff --git a/math/moab/files/patch-configure.ac b/math/moab/files/patch-configure.ac
new file mode 100644
index 000000000000..6d6a7718c8fe
--- /dev/null
+++ b/math/moab/files/patch-configure.ac
@@ -0,0 +1,12 @@
+--- configure.ac.orig	2018-11-05 00:30:52 UTC
++++ configure.ac
+@@ -31,7 +31,8 @@ LIBS="$LIBS -lm"
+ 
+ AC_PROG_LN_S
+ AC_PROG_MAKE_SET
+-AC_DISABLE_SHARED
++AC_ENABLE_SHARED
++AC_DISABLE_STATIC
+ AC_PROG_LIBTOOL
+ FATHOM_COMPILER_FLAGS
+ m4_ifdef([AM_SILENT_RULES],[
diff --git a/math/moab/files/patch-src_io_NCHelper.cpp b/math/moab/files/patch-src_io_NCHelper.cpp
new file mode 100644
index 000000000000..1a00dedf38c6
--- /dev/null
+++ b/math/moab/files/patch-src_io_NCHelper.cpp
@@ -0,0 +1,11 @@
+--- src/io/NCHelper.cpp.orig	2018-11-05 01:48:41 UTC
++++ src/io/NCHelper.cpp
+@@ -714,7 +714,7 @@ ErrorCode NCHelper::get_tag_to_set(ReadN
+       rval = mbImpl->tag_get_handle(tag_name.str().c_str(), 0, MB_TYPE_INTEGER, tagh, MB_TAG_CREAT | MB_TAG_SPARSE | MB_TAG_VARLEN);
+       break;
+     default:
+-      std::cerr << "Unrecognized data type for tag " << tag_name << std::endl;
++      std::cerr << "Unrecognized data type for tag " << tag_name.str() << std::endl;
+       rval = MB_FAILURE;
+   }
+ 
diff --git a/math/moab/files/patch-src_io_ReadABAQUS.cpp b/math/moab/files/patch-src_io_ReadABAQUS.cpp
new file mode 100644
index 000000000000..335fd11e5769
--- /dev/null
+++ b/math/moab/files/patch-src_io_ReadABAQUS.cpp
@@ -0,0 +1,11 @@
+--- src/io/ReadABAQUS.cpp.orig	2018-11-04 23:41:08 UTC
++++ src/io/ReadABAQUS.cpp
+@@ -105,7 +105,7 @@ void ReadABAQUS::reset()
+ ReadABAQUS::~ReadABAQUS() 
+ {
+   mdbImpl->release_interface(readMeshIface);
+-  if (NULL != abFile)
++  if (abFile.is_open())
+     abFile.close();
+ }
+ 
diff --git a/math/moab/files/patch-src_io_WriteNCDF.cpp b/math/moab/files/patch-src_io_WriteNCDF.cpp
new file mode 100644
index 000000000000..36e804036893
--- /dev/null
+++ b/math/moab/files/patch-src_io_WriteNCDF.cpp
@@ -0,0 +1,13 @@
+--- src/io/WriteNCDF.cpp.orig	2018-11-05 01:47:40 UTC
++++ src/io/WriteNCDF.cpp
+@@ -154,8 +154,8 @@ void WriteNCDF::time_and_date(char* time
+    strftime(date_string, TIME_STR_LEN, "%m/%d/%Y", local_time);
+ 
+      // terminate with NULL character
+-   time_string[10] = (char)NULL;
+-   date_string[10] = (char)NULL;
++   time_string[10] = (char)0;
++   date_string[10] = (char)0;
+ }
+ 
+ ErrorCode WriteNCDF::write_file(const char *exodus_file_name, 
diff --git a/math/moab/pkg-descr b/math/moab/pkg-descr
new file mode 100644
index 000000000000..4b44baa85061
--- /dev/null
+++ b/math/moab/pkg-descr
@@ -0,0 +1,15 @@
+The Mesh-Oriented datABase (MOAB) is a component for representing and evaluating
+mesh data. MOAB can store structured and unstructured mesh, consisting of
+elements in the finite element zoo plus polygons and polyhedra. The functional
+interface to MOAB is simple yet powerful, allowing the representation of many
+types of metadata commonly found on the mesh. MOAB is optimized for efficiency
+in space and time, based on access to mesh in chunks rather than through
+individual entities, while also versatile enough to support individual entity
+access. The MOAB library can naturally represent finite element and other types
+of mesh data. Various types of meta-data are often used in conjunction with
+a mesh. Examples include boundary condition groupings, material types, and
+provenance information for the mesh. Because the data model used in MOAB is so
+abstract, conventions are useful for describing how meta-data is stored into
+that data model.
+
+WWW: http://sigma.mcs.anl.gov/moab-library/
diff --git a/math/moab/pkg-plist b/math/moab/pkg-plist
new file mode 100644
index 000000000000..7a07eb78fa11
--- /dev/null
+++ b/math/moab/pkg-plist
@@ -0,0 +1,134 @@
+bin/dagmc_preproc
+bin/h5minfo
+bin/h5mvalidate
+bin/hexmodops
+bin/mbconvert
+bin/mbdepth
+bin/mbgsets
+bin/mbmem
+bin/mbsize
+bin/mbskin
+bin/mbsurfplot
+bin/mbtagprop
+bin/spheredecomp
+include/DagMC.hpp
+include/MBAdaptiveKDTree.hpp
+include/MBBSPTree.hpp
+include/MBBSPTreePoly.hpp
+include/MBCN.h
+include/MBCN.hpp
+include/MBCN_protos.h
+include/MBCartVect.hpp
+include/MBCore.hpp
+include/MBEntityHandle.h
+include/MBEntityType.h
+include/MBForward.hpp
+include/MBGeomUtil.hpp
+include/MBInterface.hpp
+include/MBOrientedBoxTreeTool.hpp
+include/MBParallelComm.hpp
+include/MBParallelData.hpp
+include/MBProcConfig.hpp
+include/MBRange.hpp
+include/MBReadUtilIface.hpp
+include/MBReaderIface.hpp
+include/MBReaderWriterSet.hpp
+include/MBSkinner.hpp
+include/MBTagConventions.hpp
+include/MBTypes.h
+include/MBUnknownInterface.hpp
+include/MBUtil.hpp
+include/MBVersion.h
+include/MBWriteUtilIface.hpp
+include/MBWriterIface.hpp
+include/MBiMesh.hpp
+include/MBmpi.h
+include/MOAB_FCDefs.h
+include/iBase.h
+include/iBase_f.h
+include/iMesh.h
+include/iMesh_extensions.h
+include/iMesh_extensions_protos.h
+include/iMesh_f.h
+include/iMesh_protos.h
+include/moab/AdaptiveKDTree.hpp
+include/moab/BSPTree.hpp
+include/moab/BSPTreePoly.hpp
+include/moab/BVHTree.hpp
+include/moab/BoundBox.hpp
+include/moab/CN.hpp
+include/moab/CartVect.hpp
+include/moab/Compiler.hpp
+include/moab/Core.hpp
+include/moab/CpuTimer.hpp
+include/moab/DualTool.hpp
+include/moab/ElemEvaluator.hpp
+include/moab/EntityHandle.hpp
+include/moab/EntityType.hpp
+include/moab/Error.hpp
+include/moab/ExoIIInterface.hpp
+include/moab/FBEngine.hpp
+include/moab/FileOptions.hpp
+include/moab/FindPtFuncs.h
+include/moab/Forward.hpp
+include/moab/GeomTopoTool.hpp
+include/moab/GeomUtil.hpp
+include/moab/HigherOrderFactory.hpp
+include/moab/HomXform.hpp
+include/moab/Interface.hpp
+include/moab/LinearHex.hpp
+include/moab/LinearQuad.hpp
+include/moab/LinearTet.hpp
+include/moab/LinearTri.hpp
+include/moab/LloydSmoother.hpp
+include/moab/Matrix3.hpp
+include/moab/MergeMesh.hpp
+include/moab/MeshTopoUtil.hpp
+include/moab/OrientedBoxTreeTool.hpp
+include/moab/ProgOptions.hpp
+include/moab/QuadraticHex.hpp
+include/moab/Range.hpp
+include/moab/RangeMap.hpp
+include/moab/ReadUtilIface.hpp
+include/moab/ReaderIface.hpp
+include/moab/ReaderWriterSet.hpp
+include/moab/ReorderTool.hpp
+include/moab/ScdInterface.hpp
+include/moab/SetIterator.hpp
+include/moab/Skinner.hpp
+include/moab/SpatialLocator.hpp
+include/moab/SpatialLocatorTimes.hpp
+include/moab/SpectralMeshTool.hpp
+include/moab/Tree.hpp
+include/moab/TreeStats.hpp
+include/moab/TupleList.hpp
+include/moab/Types.hpp
+include/moab/UnknownInterface.hpp
+include/moab/Util.hpp
+include/moab/Version.h
+include/moab/WriteUtilIface.hpp
+include/moab/WriterIface.hpp
+include/moab/point_locater/element_maps/linear_hex_map.hpp
+include/moab/point_locater/element_maps/linear_tet_map.hpp
+include/moab/point_locater/element_maps/quadratic_hex_map.hpp
+include/moab/point_locater/element_maps/spectral_hex_map.hpp
+include/moab/point_locater/io.hpp
+include/moab/point_locater/parametrizer.hpp
+include/moab/point_locater/point_locater.hpp
+include/moab/point_locater/tree/bvh_tree.hpp
+include/moab/point_locater/tree/common_tree.hpp
+include/moab/point_locater/tree/element_tree.hpp
+lib/MOABConfig.cmake
+lib/iMesh-Defs.inc
+lib/libMOAB.so
+lib/libMOAB.so.0
+lib/libMOAB.so.0.0.0
+lib/libdagmc.so
+lib/libdagmc.so.0
+lib/libdagmc.so.0.0.0
+lib/libiMesh.so
+lib/libiMesh.so.0
+lib/libiMesh.so.0.0.0
+lib/moab.config
+lib/moab.make
+man/man1/mbconvert.1.gz