Add H5Fed.

.gitattributes

@@ -3,6 +3,31 @@
 /COPYRIGHT -text
 /ChangeLog -text
 /GNUmakefile.orig -text
+H5Fed/applications/gmsh2h5fed.cc -text
+H5Fed/applications/gmsh2h5fed.hh -text
+H5Fed/applications/makefile.am -text
+H5Fed/autogen.sh -text
+H5Fed/configure.ac -text
+H5Fed/grids/cube0.geo -text
+H5Fed/grids/cube0.msh -text
+H5Fed/grids/cubeincube.geo -text
+H5Fed/grids/cubeincube.msh -text
+H5Fed/grids/sphere.geo -text
+H5Fed/grids/sphere.msh -text
+H5Fed/libsrc/gmsh/gmsh.cc -text
+H5Fed/libsrc/gmsh/gmsh.hh -text
+H5Fed/libsrc/gmsh/gmshconst.hh -text
+H5Fed/libsrc/gmsh/gmshgrammar.hh -text
+H5Fed/libsrc/gmsh/gmshsemanticaction.hh -text
+H5Fed/libsrc/gmsh/makefile.am -text
+H5Fed/libsrc/h5fed/h5fed.cc -text
+H5Fed/libsrc/h5fed/h5fed.hh -text
+H5Fed/libsrc/h5fed/h5fedconst.hh -text
+H5Fed/libsrc/h5fed/makefile.am -text
+H5Fed/libsrc/makefile.am -text
+H5Fed/libsrc/stdincl/nonsciconst.h -text
+H5Fed/libsrc/stdincl/physicomath.h -text
+H5Fed/makefile.am -text
 /Makefile.am -text
 /Makefile.orig -text
 /NEWS -text

H5Fed/applications/gmsh2h5fed.hh

+// rights - 2006-, copyright benedikt oswald and patrick leidenberger, all rights reserved
+// project - phidias3d
+// file name - phidias3d.h
+// file type - c++ header file
+// objective - header file for the phidias3d visualization postprocessor
+// modified - 2006 jun 26, creation, benedikt oswald
+// modified - 2006 jun 28, 
+// modified - 2006 jul 30, Add include for command line argument parser
+//                         with boost::program_options, pl.
+// inheritance - 
+// feature - implements the phidias3d visualization postprocessor; the features
+// feature - will be (1) read VTK legacy formatted files (2) read HDF5/ELECTROMAGNETIC
+// feature - structures files (3) export VTK legacy formatted files (4) export
+// feature - data, both meshes and fields, throught the Renderman Interface
+// feature - routines.
+// required software - 
+
+
+/* include standard header files */
+#include <cmath>
+#include <complex>
+#include <string>
+#include <vector>
+#include <iostream>
+#include <iterator>
+#include <math.h>
+
+/* Include the files for rlog. */
+#include <rlog/rlog.h>
+#include <rlog/rloglocation.h>
+#include <rlog/Error.h>
+#include <rlog/RLogChannel.h>
+#include <rlog/StdioNode.h>
+// Include this if you want to log the time.
+#include <rlog/RLogTime.h>
+
+// Include the boost program program_options to parse the comand line
+// options.
+#include <boost/program_options.hpp>
+
+
+/* include standard proprietary header files */
+#include <nonsciconst.h>
+#include <physicomath.h>
+//#include <ristream.h>
+#include <gmsh.hh>
+
+// Include the Hdf5FiniteElementData API.
+#ifdef HAVE_HDF5
+  // Include the Hdf5FiniteElementData API.
+  #include <h5fed.hh>
+  // Include h5fed specific constants.
+  #include <h5fedconst.hh>
+#else
+  #warning No hdf5 lib found!!
+#endif
+
+
+
+#ifndef PHIDIAS3D_H_
+#define PHIDIAS3D_H_
+
+using namespace physicomath;
+using namespace nonsciconst;
+using namespace gmshtohdf5fed;
+
+
+
+#endif /*PHIDIAS3D_H_*/

H5Fed/applications/makefile.am

+## Makefile.am -- process this file with automake to produce Makefile.in
+##
+## authors   - benedikt oswald and patrick leidenberger
+## modified  - 2006 aug 21, patrick leidenberger, creation
+## modified  - 2006 aug 23, pl, adaped to changed directory structure.
+## modified  - 2006 aug 25, pl, adaped to changed directory structure.
+#
+## objective - automake input file for the gmsh directory
+## project   - gmsh2h5fed
+
+noinst_PROGRAMS = gmsh2h5fed
+
+gmsh2h5fed_SOURCES = gmsh2h5fed.cc
+gmsh2h5fed_DEPENDENCIES = ../libsrc/stdincl/nonsciconst.h      \
+                             ../libsrc/stdincl/physicomath.h      \
+                             ../libsrc/gmsh/gmsh.hh               \
+                             ../libsrc/gmsh/gmsh.cc               \
+                             ../libsrc/gmsh/gmshconst.hh          \
+                             ../libsrc/gmsh/gmshgrammar.hh        \
+                             ../libsrc/gmsh/gmshsemanticaction.hh \
+                             ../libsrc/h5fed/h5fed.hh             \
+                             ../libsrc/h5fed/h5fed.cc
+
+gmsh2h5fed_LDADD = @GMSH2H5FED_LIBS@
+
+#AM_CPPFLAGS = @AM_CPPFLAGS@

H5Fed/autogen.sh

+libtoolize -f && \
+aclocal && \
+autoconf && \
+autoheader && \
+automake --add-missing && \
+CC='mpicc' F9X='mpif90' CXX='mpiCC' ./configure --with-rlog=$HOME/extlib/rlog-1.3.7 --with-boost='' --with-hdf5=$HOME/extlib/hdf5-1.6.5 &&\
+make clean && \
+make all
+
+

H5Fed/configure.ac

+## Process this file with autoconf to produce a configure script
+##
+## author    - benedikt oswald and patrick leidenberger
+## modified  - 2006 aug 21, pl, creation.
+## modified  - 2006 aug 24, pl, add h5fed path.
+##
+## to do     : The rlog lib needs a -DRLOG_COMPONENT="some name", I don't know
+##             how tho do this so that the quotation marks are in the output
+##             stream as well, pl, 2006 jul 04.
+##
+## objective - develop input file for GNU autotools/configure
+## project   - H5Fed
+##
+
+AC_PREREQ(2.59)
+AC_COPYRIGHT([This configure script is copyright by Benedikt Oswald and Patrick Leidenberger, 2006])
+
+AC_INIT([gmshtohdf5fed], [1.0], [in case of problems mail to: benedikt.oswald@psi.ch or patrick.leidenberger@psi.ch])
+
+# library creation
+AC_PROG_LIBTOOL
+
+# standard macros
+AC_CONFIG_AUX_DIR(./)
+AM_INIT_AUTOMAKE
+AC_CONFIG_HEADER([./config.h:./config.in])
+
+# set cppflags to zero
+CPPFLAGS=""
+CFFLAGS=""
+CXXFLAGS=""
+
+# provide include directories
+AC_SUBST([AM_CPPFLAGS], '-I$(top_srcdir)/libsrc/stdincl -I$(top_srcdir)/libsrc/gmsh -I$(top_srcdir)/libsrc/h5fed')
+AC_SUBST([GMSH2H5FED_LIBS],'$(top_srcdir)/libsrc/gmsh/libgmsh.la $(top_srcdir)/libsrc/h5fed/libh5fed.la')
+
+# Make available external libraries
+AC_ARG_WITH(boost,
+            AC_HELP_STRING([--with-boost=PREFIX],
+            [prefix where the Boost libraries and include files are to be found]),
+						[BOOST_PREFIX=$withval
+						 LDFLAGS="-lz -lboost_program_options "])
+
+AC_ARG_WITH(rlog,
+            AC_HELP_STRING([--with-rlog=PREFIX],
+            [prefix where the rlog libraries and include files are to be found]),
+						[RLOG_PREFIX=$withval
+						 CPPFLAGS="-I"$RLOG_PREFIX"/include "${CPPFLAGS}
+						 LDFLAGS=$RLOG_PREFIX"/lib/librlog.la "${LDFLAGS}])
+
+AC_ARG_ENABLE(rlog-debug,
+              AC_HELP_STRING([--disable-rlog-debug],
+              [disable the debug output channel of rlog]),
+              [],
+              [CFFLAGS="-DUSE_RLOG_DEBUG_CHANNEL "${CFFLAGS}
+               CXXFLAGS="-DUSE_RLOG_DEBUG_CHANNEL "${CXXFLAGS}])
+
+AC_ARG_ENABLE(rlog-error,
+              AC_HELP_STRING([--disable-rlog-error],
+              [disable the error output channel of rlog]),
+              [],
+              [CFFLAGS="-DUSE_RLOG_ERROR_CHANNEL "${CFFLAGS}
+               CXXFLAGS="-DUSE_RLOG_ERROR_CHANNEL "${CXXFLAGS}])
+
+AC_ARG_ENABLE(rlog-info,
+              AC_HELP_STRING([--disable-rlog-info],
+              [disable the info output channel of rlog]),
+              [],
+              [CFFLAGS="-DUSE_RLOG_INFO_CHANNEL "${CFFLAGS}
+               CXXFLAGS="-DUSE_RLOG_INFO_CHANNEL "${CXXFLAGS}])
+
+AC_ARG_ENABLE(rlog-warning,
+              AC_HELP_STRING([--disable-rlog-warning],
+              [disable the warning output channel of rlog]),
+              [],
+              [CFFLAGS="-DUSE_RLOG_WARNING_CHANNEL "${CFFLAGS}
+               CXXFLAGS="-DUSE_RLOG_WARNING_CHANNEL "${CXXFLAGS}])
+
+AC_ARG_WITH(hdf5,
+            AC_HELP_STRING([--with-hdf5=PREFIX],
+            [prefix to hdf5 libraries and include files]),
+               [HDF5_PREFIX=$withval
+				 CPPFLAGS="-DHAVE_HDF5 -I"$HDF5_PREFIX"/include "${CPPFLAGS}
+			     LDFLAGS="-L"$HDF5_PREFIX"/lib -lhdf5 "${LDFLAGS}])
+#			     LDFLAGS=$HDF5_PREFIX"/lib/libhdf5.la "${LDFLAGS}])
+
+
+# Set C/C++ compiler flags.
+CPPFLAGS=${CPPFLAGS}
+CFFLAGS="-g3 "${CFFLAGS}
+CXXFLAGS="-g3 "${CXXFLAGS}
+
+AM_INIT_AUTOMAKE([1.9 foreign])
+
+AC_PROG_CC
+AC_PROG_MAKE_SET
+AC_PROG_INSTALL([install])
+
+AC_CONFIG_FILES([makefile
+                   applications/makefile
+                   libsrc/makefile
+                     libsrc/gmsh/makefile
+                   libsrc/h5fed/makefile])
+
+
+AC_OUTPUT

H5Fed/grids/cube0.geo

+// rights - 2002-2005, benedikt oswald, 
+// project - aq
+// file name - cube0.geo
+// file type - GMSH script file
+// objective - model cube fundamental cube
+// modified - 2005 jan 25, benedikt oswald, creation
+// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
+// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
+// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
+// modified - 2005 mar 22, benedikt oswald, adapted to model fundamental cube
+// inheritance - 
+// feature - models fundamental cube, used for benchmark calculations of a Hertzian dipole
+// feature - radiating into free space; the model uses standard physical domain tags;
+
+
+// 1 modeling constants
+
+lcl1=0.50;             // characteristic length in fractions of lambda@1 GHz for air domain
+lcl2=0.50;             // characteristic length in fractions of lambda@1 GHz for air domain
+
+lambda=0.30;           // wavelength of electromagntic wave at a frequency of 1 GHz
+
+lx=2.0;                // x dim of computational domain
+ly=2.0;                // y dim of computational domain
+lz=2.0;                // z dim of computational domain
+
+cx=0.5*lx;             // calculate center of computational domain
+cy=0.5*ly;             // calculate center of computational domain
+cz=0.5*lz;             // calculate center of computational domain
+
+
+// 1.2 Define physical material domains
+
+vacuum=609;                   // physical entity vacuum
+air=709;                      // physical entity air
+subsurface=809;               // physical entity subsurface
+pml=1301;                     // physical entity pml material
+icelens=4001;                 // physical entity icelens
+vacuum_background_bnd=12701;  // boundary to background, i.e. vacuum
+interelement_bnd=12702;       // interior boundary, separating different material domains
+
+
+
+// 2 Define cubes
+// 2.1.1 Define points of cube
+
+p0=newp; Point(p0) = {0.0, 0.0, 0.0, lambda * lcl1};
+p1=newp; Point(p1) = { lx, 0.0, 0.0, lambda * lcl1};
+p2=newp; Point(p2) = { lx,  ly, 0.0, lambda * lcl1};
+p3=newp; Point(p3) = {0.0,  ly, 0.0, lambda * lcl1};
+p4=newp; Point(p4) = {0.0, 0.0,  lz, lambda * lcl1};
+p5=newp; Point(p5) = { lx, 0.0,  lz, lambda * lcl1};
+p6=newp; Point(p6) = { lx,  ly,  lz, lambda * lcl1};
+p7=newp; Point(p7) = {0.0,  ly,  lz, lambda * lcl1};
+
+// 2.1.3 Define lines of cube
+
+// lower xy plane
+li0=newl; Line(li0) = {p0,p1};
+li1=newl; Line(li1) = {p1,p2};
+li2=newl; Line(li2) = {p2,p3};
+li3=newl; Line(li3) = {p3,p0};
+
+// upper xy plane
+li4=newl; Line(li4) = {p4,p5};
+li5=newl; Line(li5) = {p5,p6};
+li6=newl; Line(li6) = {p6,p7};
+li7=newl; Line(li7) = {p7,p4};
+
+// vertical lines
+li8=newl; Line(li8) = {p0,p4};
+li9=newl; Line(li9) = {p1,p5};
+li10=newl; Line(li10) = {p2,p6};
+li11=newl; Line(li11) = {p3,p7};
+
+
+// 2.1.5 Define line 6 line loops for the 6 faces of the cube
+
+lloop0= newreg; Line Loop(lloop0) = { li0, li1, li2, li3};
+lloop1= newreg; Line Loop(lloop1) = { li4, li5, li6, li7};
+
+lloop2= newreg; Line Loop(lloop2) = { li0, li9, -li4, -li8 };
+lloop3= newreg; Line Loop(lloop3) = { li1, li10, -li5, -li9};
+
+lloop4= newreg; Line Loop(lloop4) = { li2, li11, -li6, -li10};
+lloop5= newreg; Line Loop(lloop5) = { li3, li8,  -li7, -li11};
+
+
+// 2.1.7 define plane surfaces for the cube
+
+s0=news; Plane Surface(s0) = {lloop0};
+s1=news; Plane Surface(s1) = {lloop1};
+s2=news; Plane Surface(s2) = {lloop2};
+s3=news; Plane Surface(s3) = {lloop3};
+s4=news; Plane Surface(s4) = {lloop4};
+s5=news; Plane Surface(s5) = {lloop5};
+
+
+// 2.1.9 Define surface loops required for volume definition of the cube
+
+sloop0=newreg; Surface Loop(sloop0) ={s0,s1,s2,s3,s4,s5};
+
+// 2.1.10 Define volume of the cube
+
+v0=newv; Volume(v0) = {sloop0};
+
+// 3.0 define physical entitites
+
+Physical Point(vacuum_background_bnd) = {p0:p7};
+Physical Line(vacuum_background_bnd) = {li0:li11};
+Physical Surface(vacuum_background_bnd) = {s0:s5};
+Physical Volume(air) = {v0};
+
+

H5Fed/grids/cubeincube.geo

+// rights - 2002-2005, benedikt oswald, 
+// project - aq
+// file name - cubeincube.geo
+// file type - GMSH script file
+// objective - model cube in a cube mesh, useful for PML booundary conditions
+// modified - 2005 jan 25, benedikt oswald, creation
+// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
+// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
+// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
+// inheritance - 
+// feature - models a cube in a cube mesh, useful for PML booundary conditions;
+// feature - the PML boundary model is based on a 3D region with special electromagnetic
+// feature - material properties which guarantee, in theory, perfect absorption of incident
+// feature - electromagnetic waves independent of the angle between the wave vector
+// feature - and the boundary; in order to model the PML material domain a separate mesh
+// feature - region is created so that there is a clean boundary between the PML and
+// feature - and the air region.
+
+
+// 1 modeling constants
+
+lcair=0.90;            // characteristic length in fractions of lambda@1 GHz for air domain
+lcpml=0.70;            // characteristic length in fractions of lambda@1 GHz for PML region
+lambda=0.30;           // wavelength of electromagntic wave at a frequency of 1 GHz
+
+lx=1.0;                // x dim of computational domain
+ly=1.0;                // y dim of computational domain
+lz=1.0;                // z dim of computational domain
+
+cx=0.5*lx;             // calculate center of computational domain
+cy=0.5*ly;             // calculate center of computational domain
+cz=0.5*lz;             // calculate center of computational domain
+
+lpmlxl=0.1;            // thickness of PML region
+lpmlxh=0.1;            // thickness of PML region
+
+lpmlyl=0.1;            // thickness of PML region
+lpmlyh=0.1;            // thickness of PML region
+
+lpmlzl=0.1;            // thickness of PML region
+lpmlzh=0.1;            // thickness of PML region
+
+xminic=lpmlxl;          // x min of inner cube
+xmaxic=lx-lpmlxh;       // x max of inner cube
+yminic=lpmlyl;          // y min of inner cube
+ymaxic=ly-lpmlyh;       // y max of inner cube
+zminic=lpmlzl;          // z min of inner cube
+zmaxic=lz-lpmlzh;       // z max of inner cube
+
+// 1.2 Define physical material domains
+
+vacuum=609;                   // physical entity vacuum
+air=709;                      // physical entity air
+pml=1301;                     // physical entity pml material
+icelens=4001;                 // physical entity icelens
+vacuum_background_bnd=12701;  // boundary to background, i.e. vacuum
+interelement_bnd=12702;       // interior boundary, separating different material domains
+
+
+
+// 2 Define cubes
+// 2.1.1 Define points of outer cube
+
+p0=newp; Point(p0) = {0.0, 0.0, 0.0, lambda * lcpml};
+p1=newp; Point(p1) = { lx, 0.0, 0.0, lambda * lcpml};
+p2=newp; Point(p2) = { lx,  ly, 0.0, lambda * lcpml};
+p3=newp; Point(p3) = {0.0,  ly, 0.0, lambda * lcpml};
+p4=newp; Point(p4) = {0.0, 0.0,  lz, lambda * lcpml};
+p5=newp; Point(p5) = { lx, 0.0,  lz, lambda * lcpml};
+p6=newp; Point(p6) = { lx,  ly,  lz, lambda * lcpml};
+p7=newp; Point(p7) = {0.0,  ly,  lz, lambda * lcpml};
+
+// 2.1.2 Define points of inner cube
+
+p100=newp; Point(p100) = {xminic, yminic, zminic, lambda * lcair};
+p101=newp; Point(p101) = {xmaxic, yminic, zminic, lambda * lcair};
+p102=newp; Point(p102) = {xmaxic, ymaxic, zminic, lambda * lcair};
+p103=newp; Point(p103) = {xminic, ymaxic, zminic, lambda * lcair};
+
+p104=newp; Point(p104) = {xminic, yminic, zmaxic, lambda * lcair};
+p105=newp; Point(p105) = {xmaxic, yminic, zmaxic, lambda * lcair};
+p106=newp; Point(p106) = {xmaxic, ymaxic, zmaxic, lambda * lcair};
+p107=newp; Point(p107) = {xminic, ymaxic, zmaxic, lambda * lcair};
+
+
+// 2.1.3 Define lines of outer cube
+
+// lower xy plane
+li0=newl; Line(li0) = {p0,p1};
+li1=newl; Line(li1) = {p1,p2};
+li2=newl; Line(li2) = {p2,p3};
+li3=newl; Line(li3) = {p3,p0};
+
+// upper xy plane
+li4=newl; Line(li4) = {p4,p5};
+li5=newl; Line(li5) = {p5,p6};
+li6=newl; Line(li6) = {p6,p7};
+li7=newl; Line(li7) = {p7,p4};
+
+// vertical lines
+li8=newl; Line(li8) = {p0,p4};
+li9=newl; Line(li9) = {p1,p5};
+li10=newl; Line(li10) = {p2,p6};
+li11=newl; Line(li11) = {p3,p7};
+
+// 2.1.4 Define lines of outer cube
+
+// lower xy plane
+li100=newl; Line(li100) = {p100,p101};
+li101=newl; Line(li101) = {p101,p102};
+li102=newl; Line(li102) = {p102,p103};
+li103=newl; Line(li103) = {p103,p100};
+
+// upper xy plane
+li104=newl; Line(li104) = {p104,p105};
+li105=newl; Line(li105) = {p105,p106};
+li106=newl; Line(li106) = {p106,p107};
+li107=newl; Line(li107) = {p107,p104};
+
+// vertical lines
+li108=newl; Line(li108) = {p100,p104};
+li109=newl; Line(li109) = {p101,p105};
+li110=newl; Line(li110) = {p102,p106};
+li111=newl; Line(li111) = {p103,p107};
+
+
+// 2.1.5 Define line 6 line loops for the 6 faces of outer cube
+
+lloop0= newreg; Line Loop(lloop0) = { li0, li1, li2, li3};
+lloop1= newreg; Line Loop(lloop1) = { li4, li5, li6, li7};
+
+lloop2= newreg; Line Loop(lloop2) = { li0, li9, -li4, -li8 };
+lloop3= newreg; Line Loop(lloop3) = { li1, li10, -li5, -li9};
+
+lloop4= newreg; Line Loop(lloop4) = { li2, li11, -li6, -li10};
+lloop5= newreg; Line Loop(lloop5) = { li3, li8,  -li7, -li11};
+
+
+// 2.1.6 Define line 6 line loops for the 6 faces of inner cube
+
+lloop100= newreg; Line Loop(lloop100) = { li100, li101, li102, li103};
+lloop101= newreg; Line Loop(lloop101) = { li104, li105, li106, li107};
+
+lloop102= newreg; Line Loop(lloop102) = { li100, li109, -li104, -li108 };
+lloop103= newreg; Line Loop(lloop103) = { li101, li110, -li105, -li109};
+
+lloop104= newreg; Line Loop(lloop104) = { li102, li111, -li106, -li110};
+lloop105= newreg; Line Loop(lloop105) = { li103, li108, -li107, -li111};
+
+
+// 2.1.7 define plane surfaces for outer cube
+
+s0=news; Plane Surface(s0) = {lloop0};
+s1=news; Plane Surface(s1) = {lloop1};
+s2=news; Plane Surface(s2) = {lloop2};
+s3=news; Plane Surface(s3) = {lloop3};
+s4=news; Plane Surface(s4) = {lloop4};
+s5=news; Plane Surface(s5) = {lloop5};
+
+// 2.1.8 define plane surfaces for inner cube
+
+s100=news; Plane Surface(s100) = {lloop100};
+s101=news; Plane Surface(s101) = {lloop101};
+s102=news; Plane Surface(s102) = {lloop102};
+s103=news; Plane Surface(s103) = {lloop103};
+s104=news; Plane Surface(s104) = {lloop104};
+s105=news; Plane Surface(s105) = {lloop105};
+
+
+// 2.1.9 Define surface loops required for volume definition of outer cube
+
+sloop0=newreg; Surface Loop(sloop0) ={s0,s1,s2,s3,s4,s5};
+
+
+// 2.1.9 Define surface loops required for volume definition of inner cube
+
+sloop100=newreg; Surface Loop(sloop100) ={s100,s101,s102,s103,s104,s105};
+
+
+// 2.1.10 Define volume of outer cube
+
+v0=newv; Volume(v0) = {sloop0,sloop100};
+
+
+// 2.1.11 Define volume of inner cube
+
+v100=newv; Volume(v100) = {sloop100};
+
+
+// 3.0 define physical entitites
+
+Physical Point(vacuum_background_bnd) = {p0,p1,p2,p3,p4,p5,p6,p7};
+Physical Line(vacuum_background_bnd) = {li0,li1,li2,li3,li4,li5,li6,li7,li8,li9,li10,li11};
+//Physical Line Loop(vacuum_background_bnd) = {lloop0,lloop1,lloop2,lloop3,lloop4,lloop5};
+Physical Surface(vacuum_background_bnd) = {s0,s1,s2,s3,s4,s5};
+//Physical Surface Loop(vacuum_background_bnd) = {sloop0};
+Physical Volume(pml) = {v0};
+
+Physical Point(interelement_bnd) = {p100,p101,p102,p103,p104,p105,p106,p107};
+Physical Line(interelement_bnd) = {li100,li101,li102,li103,li104,li105,li106,li107,li108,li109,li110,li111};
+//Physical Line Loop(interelement_bnd) = {lloop100,lloop101,lloop102,lloop103,lloop104,lloop105};
+Physical Surface(interelement_bnd) = {s100,s101,s102,s103,s104,s105};
+//Physical Surface Loop(interelement_bnd) = {sloop100};
+Physical Volume(air) = {v100};
+
+

H5Fed/grids/sphere.geo

+// rights - 2002-2005, benedikt oswald, 
+// project - aq
+// file name - sphere.geo
+// file type - GMSH script file
+// objective - model cube in a cube, 2 spherical objects mesh to investigate sub lambda resolution capability 
+// modified - 2005 jan 25, benedikt oswald, creation
+// modified - 2005 jan 25, benedikt oswald, added background hexahedron, subsurface hexahedron
+// modified - 2005 feb 01, benedikt oswald, adapted to the simple.geo problem
+// modified - 2005 mar 08, benedikt oswald, adapted to the cube in cube geometry
+// modified - 2005 mar 09, benedikt oswald, adapted to cube in cube and spherical particle configuration
+// modified - 2005 mar 11, benedikt oswald, adapted to investigation of sub-lambda resolution capability
+// modified - 2005 mar 22, benedikt oswald, adapted to be based on reference background medium subLambda310.geo
+// modified - 2005 mar 23, benedikt oswald, adapted to model a microresonator geometry
+// modified - 2005 mar 29, benedikt oswald, adapted to model a high quality sphere for a Hertzian dipole benchmark
+// modified - 2005
+// inheritance - 
+// feature - models a microresonator geometry; a dielectric sphere within an air sphere; the dielectric
+// feature - sphere will be excited by a Hertzian dipole in the vicinity of the sphere;
+// feature - 
+
+
+// 1 modeling constants
+
+lcair=1.20;             // characteristic length in fractions of lambda@1 GHz for air domain
+lcsubsurface=1.20;      // characteristic length in fractions of lambda@1 GHz for subsurface domain
+lcil1=0.80;              // characteristic length in fractions of lambda@1 GHz for icelens region
+lcil2=0.40;              // characteristic length in fractions of lambda@1 GHz for icelens 2 region
+lambda=3.0e-1;          // wavelength of electromagntic wave at a frequency of 1 GHz
+
+lx=3.0;                 // x dim of computational domain
+ly=3.0;                 // y dim of computational domain
+lz=2.0;                 // z dim of computational domain
+
+cx=0.5*lx;              // calculate center of computational domain
+cy=0.5*ly;              // calculate center of computational domain
+cz=0.5*lz;              // calculate center of computational domain
+
+dxl=0.3;                // thickness of PML region
+dxh=0.3;                // thickness of PML region
+
+dyl=0.3;                // thickness of PML region
+dyh=0.3;                // thickness of PML region
+
+dzl=0.30;               // thickness of PML region
+dzh=0.60;               // thickness of PML region
+
+xminic=dxl;             // x min of inner cube
+xmaxic=lx-dxh;          // x max of inner cube
+yminic=dyl;             // y min of inner cube
+ymaxic=ly-dyh;          // y max of inner cube
+zminic=dzl;             // z min of inner cube
+zmaxic=lz-dzh;          // z max of inner cube
+
+dsx=0.10;               // x distance separating the two spherical scatterers
+dsy=0.00;               // y distance separating the two spherical scatterers
+dsz=0.00;               // z distance separating the two spherical scatterers
+
+r1=1.0;                    // radius of air sphere
+ilcx=0.0;                     // x center of air sphere
+ilcy=0.0;                     // y center of 
+ilcz=0.0;                     // z center of 
+
+r2=2.0e-6;                    // radius of dielectric sphere
+il2cx=0.0;                    // x center of dielectric sphere
+il2cy=0.0;                    // y center of dielectric sphere
+il2cz=0.0;                    // z center of dielectric sphere
+
+
+// 1.2 Define physical material domains
+
+vacuum=609;                   // physical entity vacuum
+air=709;                      // physical entity air
+subsurface=809;               // physical entity subsurface
+pml=1301;                     // physical entity pml material
+icelens1=4001;                // physical entity icelens
+icelens2=4003;                // physical entity icelens 2
+dielsphere=4005;              // physical entity dielectric sphere
+vacuum_background_bnd=12701;  // boundary to background, i.e. vacuum
+air_soil_bnd=12702;           // interior boundary, separating air and subsurface material
+soil_icelens1_bnd=12703;      // interior boundary, separating background subsurface from icelens particle
+soil_icelens2_bnd=12705;      // interior boundary, separating background subsurface from icelens 2 particle
+dielectric_sphere_bnd=12707;  // interior boundary, separting air background from dielectric sphere
+
+
+// 2.2.1 Define air sphere 1
+
+ilp1 = newp; Point(ilp1) = {ilcx,    ilcy,    ilcz,    lcil1 * lambda} ;
+ilp2 = newp; Point(ilp2) = {ilcx+r1, ilcy,    ilcz,    lcil1 * lambda} ;
+ilp3 = newp; Point(ilp3) = {ilcx,    ilcy+r1, ilcz,    lcil1 * lambda} ;
+ilp4 = newp; Point(ilp4) = {ilcx,    ilcy,    ilcz+r1, lcil1 * lambda} ;
+ilp5 = newp; Point(ilp5) = {ilcx-r1, ilcy,    ilcz,    lcil1 * lambda} ;
+ilp6 = newp; Point(ilp6) = {ilcx,    ilcy-r1, ilcz,    lcil1 * lambda} ;
+ilp7 = newp; Point(ilp7) = {ilcx,    ilcy,    ilcz-r1, lcil1 * lambda} ;
+
+ilc1 = newreg; Circle(ilc1) = {ilp2,ilp1,ilp7};
+ilc2 = newreg; Circle(ilc2) = {ilp7,ilp1,ilp5};
+ilc3 = newreg; Circle(ilc3) = {ilp5,ilp1,ilp4};
+ilc4 = newreg; Circle(ilc4) = {ilp4,ilp1,ilp2};
+ilc5 = newreg; Circle(ilc5) = {ilp2,ilp1,ilp3};
+ilc6 = newreg; Circle(ilc6) = {ilp3,ilp1,ilp5};
+ilc7 = newreg; Circle(ilc7) = {ilp5,ilp1,ilp6};
+ilc8 = newreg; Circle(ilc8) = {ilp6,ilp1,ilp2};
+ilc9 = newreg; Circle(ilc9) = {ilp7,ilp1,ilp3};
+ilc10 = newreg; Circle(ilc10) = {ilp3,ilp1,ilp4};
+ilc11 = newreg; Circle(ilc11) = {ilp4,ilp1,ilp6};
+ilc12 = newreg; Circle(ilc12) = {ilp6,ilp1,ilp7};
+
+// We need non-plane surfaces to define the spherical icelens:
+// here we use ruled surfaces, which can have 3 or 4
+// sides:
+
+ill1 = newreg; Line Loop(ill1) = {ilc5,ilc10,ilc4};   ilruls1=newreg; Ruled Surface(ilruls1) = {ill1};
+ill2 = newreg; Line Loop(ill2) = {ilc9,-ilc5,ilc1};   ilruls2=newreg; Ruled Surface(ilruls2) = {ill2};
+ill3 = newreg; Line Loop(ill3) = {ilc12,-ilc8,-ilc1}; ilruls3=newreg; Ruled Surface(ilruls3) = {ill3};
+ill4 = newreg; Line Loop(ill4) = {ilc8,-ilc4,ilc11};  ilruls4=newreg; Ruled Surface(ilruls4) = {ill4};
+ill5 = newreg; Line Loop(ill5) = {-ilc10,ilc6,ilc3};  ilruls5=newreg; Ruled Surface(ilruls5) = {ill5};
+ill6 = newreg; Line Loop(ill6) = {-ilc11,-ilc3,ilc7}; ilruls6=newreg; Ruled Surface(ilruls6) = {ill6};
+ill7 = newreg; Line Loop(ill7) = {-ilc2,-ilc7,-ilc12};ilruls7=newreg; Ruled Surface(ilruls7) = {ill7};
+ill8 = newreg; Line Loop(ill8) = {-ilc6,-ilc9,ilc2};  ilruls8=newreg; Ruled Surface(ilruls8) = {ill8};
+
+ilsloop0 = newreg; 
+Surface Loop(ilsloop0) = {ill8+1,ill5+1,ill1+1,ill2+1,ill3+1,ill7+1,ill6+1,ill4+1};
+
+
+// 2.3.3 Define volume of air sphere
+
+vil1=newv; Volume(vil1) = {ilsloop0};
+
+
+// 3.0 define physical entitites
+
+Physical Point(vacuum_background_bnd) = {ilp1,ilp2,ilp3,ilp4,ilp5,ilp6,ilp7};
+Physical Surface(vacuum_background_bnd) = {ilruls1,ilruls2,ilruls3,ilruls4,ilruls5,ilruls6,ilruls7,ilruls8};
+Physical Volume(air) = {vil1};
+

H5Fed/libsrc/gmsh/gmsh.cc

+// rights - 2006-, copyright patrick leidenberger and benedikt oswald,
+//                 all rights reserved
+// project   - gmsh2h5fed
+// file name - gmsh.cc
+// file type - c++ implementation file
+// objective - implement class for readind gmsh data files