Add Libgmsh support/ flboundadapt

Makefile.in

@@ -104,6 +104,9 @@ endif
 ifneq (@HAVE_PETSC33@,yes)
 	EXCLUDE_TAGS := $(EXCLUDE_TAGS) -e petsc33
 endif
+ifneq (@HAVE_LIBGMSH@,yes)
+	EXCLUDE_TAGS := $(EXCLUDE_TAGS) -e libgmsh
+endif
 
 .SUFFIXES: .f90 .F90 .c .cpp .o .a
 

configure

@@ -672,6 +672,7 @@ INSTALL_SCRIPT
 INSTALL_PROGRAM
 UNROLL_LOOPS
 OPENMP_CXXFLAGS
+HAVE_LIBGMSH
 LAPACK_LIBS
 BLAS_LIBS
 HAVE_CGAL
@@ -734,7 +735,6 @@ infodir
 docdir
 oldincludedir
 includedir
-runstatedir
 localstatedir
 sharedstatedir
 sysconfdir
@@ -850,7 +850,6 @@ datadir='${datarootdir}'
 sysconfdir='${prefix}/etc'
 sharedstatedir='${prefix}/com'
 localstatedir='${prefix}/var'
-runstatedir='${localstatedir}/run'
 includedir='${prefix}/include'
 oldincludedir='/usr/include'
 docdir='${datarootdir}/doc/${PACKAGE_TARNAME}'
@@ -1103,15 +1102,6 @@ do
   | -silent | --silent | --silen | --sile | --sil)
     silent=yes ;;
 
-  -runstatedir | --runstatedir | --runstatedi | --runstated \
-  | --runstate | --runstat | --runsta | --runst | --runs \
-  | --run | --ru | --r)
-    ac_prev=runstatedir ;;
-  -runstatedir=* | --runstatedir=* | --runstatedi=* | --runstated=* \
-  | --runstate=* | --runstat=* | --runsta=* | --runst=* | --runs=* \
-  | --run=* | --ru=* | --r=*)
-    runstatedir=$ac_optarg ;;
-
   -sbindir | --sbindir | --sbindi | --sbind | --sbin | --sbi | --sb)
     ac_prev=sbindir ;;
   -sbindir=* | --sbindir=* | --sbindi=* | --sbind=* | --sbin=* \
@@ -1249,7 +1239,7 @@ fi
 for ac_var in	exec_prefix prefix bindir sbindir libexecdir datarootdir \
 		datadir sysconfdir sharedstatedir localstatedir includedir \
 		oldincludedir docdir infodir htmldir dvidir pdfdir psdir \
-		libdir localedir mandir runstatedir
+		libdir localedir mandir
 do
   eval ac_val=\$$ac_var
   # Remove trailing slashes.
@@ -1402,7 +1392,6 @@ Fine tuning of the installation directories:
   --sysconfdir=DIR        read-only single-machine data [PREFIX/etc]
   --sharedstatedir=DIR    modifiable architecture-independent data [PREFIX/com]
   --localstatedir=DIR     modifiable single-machine data [PREFIX/var]
-  --runstatedir=DIR       modifiable per-process data [LOCALSTATEDIR/run]
   --libdir=DIR            object code libraries [EPREFIX/lib]
   --includedir=DIR        C header files [PREFIX/include]
   --oldincludedir=DIR     C header files for non-gcc [/usr/include]
@@ -9928,6 +9917,119 @@ if test "$have_udunits" = "yes"; then
 #define HAVE_LIBUDUNITS 1
 EOF
 fi
+{ $as_echo "$as_me:${as_lineno-$LINENO}: checking Checking for libGmsh support" >&5
+$as_echo_n "checking Checking for libGmsh support... " >&6; }
+ac_ext=cpp
+ac_cpp='$CXXCPP $CPPFLAGS'
+ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CXX -o conftest$ac_exeext $CXXFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_cxx_compiler_gnu
+
+LIBS_bck="$LIBS"
+LIBS="-lGmsh"
+cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+  #include <gmsh/Gmsh.h>
+
+#ifdef F77_DUMMY_MAIN
+
+#  ifdef __cplusplus
+     extern "C"
+#  endif
+   int F77_DUMMY_MAIN() { return 1; }
+
+#endif
+#ifdef FC_DUMMY_MAIN
+#ifndef FC_DUMMY_MAIN_EQ_F77
+#  ifdef __cplusplus
+     extern "C"
+#  endif
+   int FC_DUMMY_MAIN() { return 1; }
+#endif
+#endif
+int
+main ()
+{
+
+  GmshInitialize ();
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+  { $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+  LIBS="$LIBS $LIBS_bck"
+  $as_echo "#define HAVE_LIBGMSH 1" >>confdefs.h
+
+  HAVE_LIBGMSH="yes"
+
+else
+
+  LIBS="-lgmsh"
+  cat confdefs.h - <<_ACEOF >conftest.$ac_ext
+/* end confdefs.h.  */
+
+	#include <gmsh/Gmsh.h>
+#ifdef F77_DUMMY_MAIN
+
+#  ifdef __cplusplus
+     extern "C"
+#  endif
+   int F77_DUMMY_MAIN() { return 1; }
+
+#endif
+#ifdef FC_DUMMY_MAIN
+#ifndef FC_DUMMY_MAIN_EQ_F77
+#  ifdef __cplusplus
+     extern "C"
+#  endif
+   int FC_DUMMY_MAIN() { return 1; }
+#endif
+#endif
+int
+main ()
+{
+
+  	GmshInitialize ();
+
+  ;
+  return 0;
+}
+_ACEOF
+if ac_fn_cxx_try_link "$LINENO"; then :
+
+	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: yes" >&5
+$as_echo "yes" >&6; }
+   	LIBS="$LIBS $LIBS_bck"
+  	$as_echo "#define HAVE_LIBGMSH 1" >>confdefs.h
+
+	HAVE_LIBGMSH="yes"
+
+else
+
+        HAVE_LIBGMSH="no"
+  	{ $as_echo "$as_me:${as_lineno-$LINENO}: result: no" >&5
+$as_echo "no" >&6; }
+  	LIBS="$LIBS_bck"
+
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+
+fi
+rm -f core conftest.err conftest.$ac_objext \
+    conftest$ac_exeext conftest.$ac_ext
+
+ac_ext=c
+ac_cpp='$CPP $CPPFLAGS'
+ac_compile='$CC -c $CFLAGS $CPPFLAGS conftest.$ac_ext >&5'
+ac_link='$CC -o conftest$ac_exeext $CFLAGS $CPPFLAGS $LDFLAGS conftest.$ac_ext $LIBS >&5'
+ac_compiler_gnu=$ac_cv_c_compiler_gnu
+
 
 # Check whether --enable-openmp was given.
 if test "${enable_openmp+set}" = set; then :
@@ -13877,7 +13979,7 @@ fi
 
 #####
 #
-LIBS="$LIBS -L./lib"
+LIB="$LIBS -L./lib"
 
 ##############################################################
 # Stream I/O

configure.in

@@ -305,6 +305,37 @@ if test "$have_udunits" = "yes"; then
 #define HAVE_LIBUDUNITS 1
 EOF
 fi
+AC_MSG_CHECKING([Checking for libGmsh support])
+AC_LANG_PUSH([C++])
+LIBS_bck="$LIBS"
+LIBS="-lGmsh"
+AC_TRY_LINK([
+  #include <gmsh/Gmsh.h>
+  ],[
+  GmshInitialize ();
+  ],[
+  AC_MSG_RESULT([yes])
+  LIBS="$LIBS $LIBS_bck"
+  AC_DEFINE(HAVE_LIBGMSH, [1])
+  HAVE_LIBGMSH="yes"	
+  ],[
+  LIBS="-lgmsh"
+  AC_TRY_LINK([
+	#include <gmsh/Gmsh.h>],[
+  	GmshInitialize ();
+  	],[
+	AC_MSG_RESULT([yes])
+   	LIBS="$LIBS $LIBS_bck"
+  	AC_DEFINE(HAVE_LIBGMSH, [1])
+	HAVE_LIBGMSH="yes"	
+  	],[
+        HAVE_LIBGMSH="no"	
+  	AC_MSG_RESULT([no])
+  	LIBS="$LIBS_bck"
+  	])
+  ])
+AC_SUBST(HAVE_LIBGMSH)
+AC_LANG_POP([C++])
 
 AC_ARG_ENABLE(openmp,
     [AC_HELP_STRING([--enable-openmp],
@@ -1067,7 +1098,7 @@ fi
 
 #####
 #
-LIBS="$LIBS -L./lib"
+LIB="$LIBS -L./lib"
 
 ##############################################################
 # Stream I/O

femtools/Field_Options.F90

@@ -98,7 +98,7 @@ module field_options
      & extract_pressure_mesh, extract_velocity_mesh, &
      & postprocess_periodic_mesh, get_diagnostic_coordinate_field, &
      & get_nodal_coordinate_field, extract_prognostic_pressure, &
-     & extract_prognostic_velocity
+     & extract_prognostic_velocity, get_surface_ids
 
   integer, parameter, public :: FIELD_EQUATION_UNKNOWN                   = 0, &
                                 FIELD_EQUATION_ADVECTIONDIFFUSION        = 1, &
@@ -1337,4 +1337,25 @@ function extract_prognostic_velocity(state, stat) result(vfield)
 
   end function extract_prognostic_velocity
 
+  subroutine get_surface_ids(bc_path, mesh, surface_ids)
+    character(len=*), intent(in) ::  bc_path
+    type(mesh_type) :: mesh
+    integer, dimension(:), allocatable, intent(out) :: surface_ids
+    integer shape_option(2)
+    character(len = OPTION_PATH_LEN) :: surface_names
+    character(len = FIELD_NAME_LEN), dimension(:), allocatable :: name_list
+
+    if (have_option(bc_path//"/surface_ids")) then
+       shape_option=option_shape(bc_path//"/surface_ids")
+       allocate(surface_ids(1:shape_option(1)))
+       call get_option(bc_path//"/surface_ids", surface_ids)
+    else if (have_option(bc_path//"/surface_names")) then
+       call get_option(bc_path//"/surface_names", surface_names)
+       call tokenize(trim(surface_names), name_list, ",")
+       allocate(surface_ids(size(name_list)))
+       call get_surface_ids_from_names(mesh, name_list, surface_ids)
+    end if
+
+  end subroutine get_surface_ids
+
 end module field_options

femtools/Fields_Allocates.F90

@@ -538,6 +538,11 @@ subroutine deallocate_mesh(mesh)
        deallocate(mesh%element_halos)
     end if
 
+    if (associated(mesh%surface_names)) then
+       deallocate(mesh%surface_names)
+       nullify(mesh%surface_names)
+    end if
+
     call deallocate_faces(mesh)
 
     if(associated(mesh%subdomain_mesh)) then
@@ -1097,6 +1102,10 @@ function make_mesh (model, shape, continuity, name) &
             size(mesh%faces%surface_node_list), name='Surface'//trim(mesh%name))
 #endif
     end if
+    if (associated(model%surface_names)) then
+       allocate(mesh%surface_names(size(model%surface_names)))
+       mesh%surface_names(:) = model%surface_names(:)
+    end if
     call addref(mesh)
 
   end function make_mesh

femtools/Fields_Base.F90

@@ -367,7 +367,8 @@ module fields_base
 	    extract_scalar_field_from_tensor_field, ele_curl_at_quad,&
 	    eval_shape, ele_jacobian_at_quad, ele_div_at_quad_tensor,&
 	    ele_2d_curl_at_quad, getsndgln, local_coords_matrix,&
-            local_coords_interpolation
+            local_coords_interpolation, set_surface_names, &
+            get_surface_ids_from_names
 
 contains
 
@@ -4199,4 +4200,39 @@ subroutine write_minmax_tensor(tfield, field_expression)
 
   end subroutine write_minmax_tensor
 
+  subroutine set_surface_names(mesh, names, ids)
+    type(mesh_type), intent(inout) :: mesh
+    character(len=*), intent(in) :: names(:)
+    integer, intent(in) :: ids(:)
+
+    integer :: i
+
+    allocate(mesh%surface_names(size(ids)))
+
+    do i=1, size(ids)
+       mesh%surface_names(i)%id = ids(i)
+       mesh%surface_names(i)%name = names(i)
+    end do
+  end subroutine set_surface_names
+
+  subroutine get_surface_ids_from_names(mesh, names, ids)
+    type(mesh_type), intent(in) :: mesh
+    character(len=*), intent(in) :: names(:)
+    integer, intent(out) :: ids(:)
+
+    integer :: i, j
+
+    ids = -1
+
+    do i=1, size(ids)
+       do j=1, size(mesh%surface_names)
+          if (trim(mesh%surface_names(j)%name) == trim(names(i))) then
+             ids(i) = mesh%surface_names(j)%id
+             exit
+          end if
+       end do
+    end do
+
+  end subroutine get_surface_ids_from_names
+
 end module fields_base

femtools/Fields_Data_Types.F90

@@ -50,6 +50,11 @@ module fields_data_types
   integer, public, parameter :: FIELD_TYPE_NORMAL=0, FIELD_TYPE_CONSTANT=1, FIELD_TYPE_PYTHON=2, &
     FIELD_TYPE_DEFERRED=3
 
+  type surface_name
+     integer :: id
+     character (len=FIELD_NAME_LEN) :: name
+  end type surface_name
+
   type adjacency_cache
     type(csr_sparsity), pointer :: nnlist => null()
     type(csr_sparsity), pointer :: nelist => null()
@@ -89,6 +94,8 @@ module fields_data_types
      !! A list of ids marking different parts of the mesh
      !! so that initial conditions can be associated with it.
      integer, dimension(:), pointer :: region_ids=>null()
+     !! list mapping surface names to ids
+     type(surface_name), dimension(:), pointer :: surface_names=>null()
      !! Halo information for parallel simulations.
      type(halo_type), dimension(:), pointer :: halos=>null()
      type(halo_type), dimension(:), pointer :: element_halos=>null()