Merge pull request #122 from tawhai/generalised_surface_fitting

Generalised surface fitting
LungNoodle · Sep 1, 2022 · f69e4ff · f69e4ff
2 parents 44b992a + 336041d
commit f69e4ff
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Showing 28 changed files with 1,806 additions and 1,176 deletions.
diff --git a/src/bindings/c/CMakeLists.txt b/src/bindings/c/CMakeLists.txt
@@ -15,6 +15,7 @@ set(C_FORTRAN_LIB_SRCS
     imports.f90
     pressure_resistance_flow.f90
     species_transport.f90
+    surface_fitting.f90
     utils.f90
     ventilation.f90
     wave_transmission.f90
@@ -34,6 +35,7 @@ set(C_C_LIB_SRCS
     imports.c
     pressure_resistance_flow.c
     species_transport.c
+    surface_fitting.c
     utils.c
     ventilation.c
     wave_transmission.c
@@ -54,6 +56,7 @@ set(C_LIB_HDRS
   imports.h
   pressure_resistance_flow.h
   species_transport.h
+  surface_fitting.h
   utils.h
   ventilation.h
   wave_transmission.h

diff --git a/src/bindings/c/arrays.c b/src/bindings/c/arrays.c
@@ -1,9 +1,12 @@
 
 #include "arrays.h"
+#include "string.h"
 
 void set_node_field_value_c(int *row, int *col, double *value);
 
 void set_node_field_value(int row, int col, double value)
 {
   set_node_field_value_c(&row, &col, &value);
 }
+
+
diff --git a/src/bindings/c/arrays.f90 b/src/bindings/c/arrays.f90
@@ -26,5 +26,6 @@ subroutine set_node_field_value_c(row, col, value) bind(C, name="set_node_field_
 
   end subroutine set_node_field_value_c
 
+
 
 end module arrays_c
diff --git a/src/bindings/c/exports.c b/src/bindings/c/exports.c
@@ -4,29 +4,54 @@
 
 #include <string.h>
 
+void export_cubic_lagrange_2d_c(const char *EXFILE, int *exfile_len,
+				const char *group_name, int *group_name_len);
 void export_1d_elem_field_c(int *ne_field, const char *EXELEMFILE, int *EXELEMFILE_LEN,
-                            const char *group_name, int *group_name_len, const char *field_name, int *field_name_len );
-void export_1d_elem_geometry_c(const char *EXELEMFILE, int *EXELEMFILE_LEN, const char *name, int *name_len);
-void export_elem_geometry_2d_c(const char *EXELEMFILE, int *EXELEMFILE_LEN, const char *name, int *name_len, int *offset_elem, int *offset_node);
+                            const char *group_name, int *group_name_len,
+			    const char *field_name, int *field_name_len );
+void export_1d_elem_geometry_c(const char *EXELEMFILE, int *EXELEMFILE_LEN,
+			       const char *name, int *name_len);
+void export_elem_geometry_2d_c(const char *EXELEMFILE, int *EXELEMFILE_LEN,
+			       const char *name, int *name_len, int *offset_elem, int *offset_node);
 void export_node_field_c(int *nj_field, const char *EXNODEFIELD, int *EXNODEFIELD_LEN,
                          const char *name, int *name_len, const char *field_name, int *field_name_len);
-void export_elem_geometry_2d_c(const char *EXELEMFILE, int *EXELEMFILE_LEN, const char *name, int *name_len, int *offset_elem, int *offset_node);
-void export_terminal_solution_c(const char *EXNODEFILE, int *EXNODEFILE_LEN, const char *name, int *name_len);
-void export_terminal_perfusion_c(const char *EXNODEFILE, int *EXNODEFILE_LEN, const char *name, int *name_len);
-void export_node_geometry_c(const char *EXNODEFILE, int *EXNODEFILE_LEN, const char *name, int *name_len);
-void export_node_geometry_2d_c(const char *EXNODEFILE, int *EXNODEFILE_LEN, const char *name, int *name_len, int *offset);
-void export_data_geometry_c(const char *EXDATAFILE, int *EXDATAFILE_LEN, const char *name, int *name_len, int *offset);
+void export_elem_geometry_2d_c(const char *EXELEMFILE, int *EXELEMFILE_LEN,
+			       const char *name, int *name_len, int *offset_elem, int *offset_node);
+void export_terminal_solution_c(const char *EXNODEFILE, int *EXNODEFILE_LEN,
+				const char *name, int *name_len);
+void export_terminal_perfusion_c(const char *EXNODEFILE, int *EXNODEFILE_LEN,
+				 const char *name, int *name_len);
+void export_node_geometry_c(const char *EXNODEFILE, int *EXNODEFILE_LEN,
+			    const char *name, int *name_len);
+void export_node_geometry_2d_c(const char *EXNODEFILE, int *EXNODEFILE_LEN,
+			       const char *name, int *name_len, int *offset);
+void export_data_geometry_c(const char *EXDATAFILE, int *EXDATAFILE_LEN,
+			    const char *name, int *name_len, int *offset);
 void export_elem_field_c(const char *EXELEMFIELD, int *EXELEMFIELD_LEN,
-                         const char *name, int *name_len, const char *field_name, int *field_name_len);
-void export_terminal_ssgexch_c(const char *EXNODEFILE, int *filename_len, const char *name, int *name_len);
+                         const char *name, int *name_len, const char *field_name,
+			 int *field_name_len);
+void export_terminal_ssgexch_c(const char *EXNODEFILE, int *filename_len,
+			       const char *name, int *name_len);
+
+
+
+void export_cubic_lagrange_2d(const char *EXFILE, const char *group_name)
+{
+  int filename_len = strlen(EXFILE);
+  int group_name_len = strlen(group_name);
+
+  export_cubic_lagrange_2d_c(EXFILE, &filename_len, group_name, &group_name_len);
+}
 
-void export_1d_elem_field(int ne_field, const char *EXELEMFILE, const char *group_name, const char *field_name )
+void export_1d_elem_field(int ne_field, const char *EXELEMFILE,
+			  const char *group_name, const char *field_name )
 {
   int filename_len = strlen(EXELEMFILE);
   int group_name_len = strlen(group_name);
   int field_name_len = strlen(field_name);
 
-  export_1d_elem_field_c(&ne_field, EXELEMFILE, &filename_len, group_name, &group_name_len, field_name, &field_name_len);
+  export_1d_elem_field_c(&ne_field, EXELEMFILE, &filename_len, group_name,
+			 &group_name_len, field_name, &field_name_len);
 }
 
 void export_1d_elem_geometry(const char *EXELEMFILE, const char *name)
@@ -37,21 +62,25 @@ void export_1d_elem_geometry(const char *EXELEMFILE, const char *name)
   export_1d_elem_geometry_c(EXELEMFILE, &filename_len, name, &name_len);
 }
 
-void export_elem_geometry_2d(const char *EXELEMFILE, const char *name, int offset_elem, int offset_node)
+void export_elem_geometry_2d(const char *EXELEMFILE, const char *name,
+			     int offset_elem, int offset_node)
 {
   int filename_len = strlen(EXELEMFILE);
   int name_len = strlen(name);
 
-  export_elem_geometry_2d_c(EXELEMFILE, &filename_len, name, &name_len, &offset_elem, &offset_node);
+  export_elem_geometry_2d_c(EXELEMFILE, &filename_len, name, &name_len,
+			    &offset_elem, &offset_node);
 }
 
-void export_node_field(int nj_field, const char *EXNODEFIELD, const char *name, const char *field_name)
+void export_node_field(int nj_field, const char *EXNODEFIELD,
+		       const char *name, const char *field_name)
 {
   int filename_len = strlen(EXNODEFIELD);
   int name_len = strlen(name);
   int field_name_len = strlen(field_name);
 
-  export_node_field_c(&nj_field, EXNODEFIELD, &filename_len, name, &name_len, field_name, &field_name_len);
+  export_node_field_c(&nj_field, EXNODEFIELD, &filename_len, name,
+		      &name_len, field_name, &field_name_len);
 }
 
 void export_terminal_solution(const char *EXNODEFILE, const char *name)
@@ -108,6 +137,7 @@ void export_elem_field(const char *EXELEMFIELD, const char *name, const char *fi
   int name_len = strlen(name);
   int field_name_len = strlen(field_name);
 
-  export_elem_field_c(EXELEMFIELD, &filename_len, name, &name_len, field_name, &field_name_len);
+  export_elem_field_c(EXELEMFIELD, &filename_len, name, &name_len,
+		      field_name, &field_name_len);
 }
 
diff --git a/src/bindings/c/exports.f90 b/src/bindings/c/exports.f90
@@ -4,6 +4,30 @@ module exports_c
   private
 
 contains
+
+
+!!!################################################################
+
+  subroutine export_cubic_lagrange_2d_c(EXFILE, filename_len, group_name, group_name_len) &
+    bind(C, name="export_cubic_lagrange_2d_c")
+
+    use iso_c_binding, only: c_ptr
+    use utils_c, only: strncpy
+    use exports, only: export_cubic_lagrange_2d
+    use other_consts, only: MAX_STRING_LEN, MAX_FILENAME_LEN
+    implicit none
+    integer,intent(in) :: filename_len, group_name_len
+    type(c_ptr), value, intent(in) :: EXFILE, group_name
+    character(len=MAX_FILENAME_LEN) :: filename_f
+    character(len=MAX_STRING_LEN) :: group_name_f
+
+    call strncpy(filename_f, EXFILE, filename_len)
+    call strncpy(group_name_f, group_name, group_name_len)
+
+    call export_cubic_lagrange_2d(filename_f, group_name_f)
+
+  end subroutine export_cubic_lagrange_2d_c
+
 !!!################################################################
 
   subroutine export_1d_elem_field_c(ne_field, EXELEMFILE, filename_len, group_name, group_name_len, field_name, field_name_len) &

diff --git a/src/bindings/c/exports.h b/src/bindings/c/exports.h
@@ -4,6 +4,7 @@
 
 #include "symbol_export.h"
 
+SHO_PUBLIC void export_cubic_lagrange_2d(const char *EXFILE, const char *group_name);
 SHO_PUBLIC void export_1d_elem_field(int ne_field, const char *EXELEMFILE, const char *group_name, const char *field_name );
 SHO_PUBLIC void export_1d_elem_geometry(const char *EXELEMFILE, const char *name);
 SHO_PUBLIC void export_elem_geometry_2d(const char *EXELEMFILE, const char *name, int offset_elem, int offset_node);

diff --git a/src/bindings/c/gas_exchange.c b/src/bindings/c/gas_exchange.c
@@ -1,4 +1,3 @@
-
 #include "gas_exchange.h"
 
 void steadystate_gasexchange_c(double *c_art_o2, double *c_ven_o2,
@@ -11,4 +10,3 @@ void steadystate_gasexchange(double *c_art_o2, double *c_ven_o2,
 {
 	steadystate_gasexchange_c(c_art_o2, c_ven_o2, p_art_co2, p_art_o2, p_i_o2, p_ven_co2, p_ven_o2, shunt_fraction, VCO2, VO2);
 }
-
diff --git a/src/bindings/c/gas_exchange.f90 b/src/bindings/c/gas_exchange.f90
@@ -1,7 +1,7 @@
 module gas_exchange_c
   implicit none
   private
-
+  
 contains
   !!!######################################################################
   subroutine steadystate_gasexchange_c(c_art_o2,c_ven_o2,&
@@ -10,18 +10,18 @@ subroutine steadystate_gasexchange_c(c_art_o2,c_ven_o2,&
     use gas_exchange, only: steadystate_gasexchange
     use arrays,only: dp
     implicit none
-
+    
     !!! Parameter List
     real(dp),intent(in) :: p_i_o2,shunt_fraction,VCO2,VO2
     real(dp), intent(inout) :: c_art_o2,c_ven_o2,p_art_co2,p_art_o2,p_ven_o2,p_ven_co2
-
+    
     call steadystate_gasexchange(c_art_o2,c_ven_o2,&
-       p_art_co2,p_art_o2,p_i_o2,p_ven_co2,p_ven_o2,shunt_fraction,&
-       VCO2,VO2)
-
+         p_art_co2,p_art_o2,p_i_o2,p_ven_co2,p_ven_o2,shunt_fraction,&
+         VCO2,VO2)
+    
   end subroutine steadystate_gasexchange_c
-
-
-
+  
+  
+  
 end module gas_exchange_c
 
diff --git a/src/bindings/c/geometry.c b/src/bindings/c/geometry.c
@@ -12,6 +12,7 @@ void define_mesh_geometry_test_c(void);
 void define_node_geometry_c(const char *NODEFILE, int *filename_len);
 void define_node_geometry_2d_c(const char *NODEFILE, int *filename_len);
 void define_data_geometry_c(const char *DATAFILE, int *filename_len);
+void import_node_geometry_2d_c(const char *NODEFILE, int *filename_len);
 extern void make_data_grid_c(int *elemlist_len, int elemlist[], double *offset, double *spacing, const char *filename, int *filename_len, const char *groupname, int *groupname_len);
 extern void make_2d_vessel_from_1d_c(int *elemlist_len, int elemlist[]);
 void define_rad_from_file_c(const char *FIELDFILE, int *filename_len, const char *radius_type, int *radius_type_len);
@@ -21,7 +22,6 @@ void define_rad_from_geom_c(const char *order_system, int *order_system_len, dou
                             const char *group_type, int *group_type_len, const char *group_options, int *group_options_len);
 void element_connectivity_1d_c(void);
 void evaluate_ordering_c(void);
-void set_initial_volume_c(int *Gdirn, double *COV, double *total_volume, double *Rmax, double *Rmin);
 void volume_of_mesh_c(double *volume_model, double *volume_tree);
 void write_elem_geometry_2d_c(const char *ELEMFILE, int *filename_len);
 void write_geo_file_c(int *ntype, const char *GEOFILE, int *filename_len);
@@ -79,6 +79,12 @@ void define_data_geometry(const char *DATAFILE)
   define_data_geometry_c(DATAFILE, &filename_len);
 }
 
+void import_node_geometry_2d(const char *NODEFILE)
+{
+  int filename_len = (int)strlen(NODEFILE);
+  import_node_geometry_2d_c(NODEFILE, &filename_len);
+}
+
 void make_data_grid(int elemlist_len, int elemlist[], double offset, double spacing, const char *filename, const char *groupname)
 {
   int filename_len = (int)strlen(filename);
@@ -127,11 +133,6 @@ void evaluate_ordering()
   evaluate_ordering_c();
 }
 
-void set_initial_volume(int Gdirn, double COV, double total_volume, double Rmax, double Rmin)
-{
-  set_initial_volume_c(&Gdirn, &COV, &total_volume, &Rmax, &Rmin);
-}
-
 void volume_of_mesh(double *volume_model, double *volume_tree)
 {
   volume_of_mesh_c(volume_model, volume_tree);

diff --git a/src/bindings/c/geometry.f90 b/src/bindings/c/geometry.f90
@@ -127,6 +127,27 @@ subroutine define_node_geometry_c(NODEFILE, filename_len) bind(C, name="define_n
 
   end subroutine define_node_geometry_c
 
+!
+!###################################################################################
+!
+  subroutine import_node_geometry_2d_c(NODEFILE, filename_len) bind(C, name="import_node_geometry_2d_c")
+
+    use iso_c_binding, only: c_ptr
+    use utils_c, only: strncpy
+    use other_consts, only: MAX_FILENAME_LEN
+    use geometry, only: import_node_geometry_2d
+    implicit none
+
+    integer,intent(in) :: filename_len
+    type(c_ptr), value, intent(in) :: NODEFILE
+    character(len=MAX_FILENAME_LEN) :: filename_f
+
+    call strncpy(filename_f, NODEFILE, filename_len)
+
+    call import_node_geometry_2d(filename_f)
+
+  end subroutine import_node_geometry_2d_c
+
 !
 !###################################################################################
 !
@@ -285,25 +306,6 @@ subroutine evaluate_ordering_c() bind(C, name="evaluate_ordering_c")
 
   end subroutine evaluate_ordering_c
 
-!###################################################################################
-!
-!>*set_initial_volume:* assigns a volume to terminal units appended on a tree structure
-!>based on an assumption of a linear gradient in the gravitational direction with max
-!> min and COV values defined.
-  subroutine set_initial_volume_c(Gdirn, COV, total_volume, Rmax, Rmin) bind(C, name="set_initial_volume_c")
-
-    use geometry, only: set_initial_volume
-    use arrays, only: dp
-    implicit none
-
-    !     Parameter List
-    integer,intent(in) :: Gdirn
-    real(dp),intent(in) :: COV, total_volume, Rmax, Rmin
-
-    call set_initial_volume(Gdirn, COV, total_volume, Rmax, Rmin)
-
-  end subroutine set_initial_volume_c
-
 !
 !###################################################################################
 !

diff --git a/src/bindings/c/geometry.h b/src/bindings/c/geometry.h
@@ -13,6 +13,7 @@ SHO_PUBLIC void define_mesh_geometry_test();
 SHO_PUBLIC void define_node_geometry(const char *NODEFILE);
 SHO_PUBLIC void define_node_geometry_2d(const char *NODEFILE);
 SHO_PUBLIC void define_data_geometry(const char *DATAFILE);
+SHO_PUBLIC void import_node_geometry_2d(const char *NODEFILE);
 SHO_PUBLIC void make_data_grid(int elemlist_len, int elemlist[], double offset, double spacing, const char *filename, const char *groupname);
 SHO_PUBLIC void make_2d_vessel_from_1d(int elemlist_len, int elemlist[]);
 SHO_PUBLIC void define_rad_from_file(const char *FIELDFILE, const char *radius_type);
@@ -21,7 +22,6 @@ SHO_PUBLIC void define_rad_from_geom(const char *ORDER_SYSTEM, double CONTROL_PA
                                      double START_RAD, const char *GROUP_TYPE, const char *GROUP_OPTIONS);
 SHO_PUBLIC void element_connectivity_1d();
 SHO_PUBLIC void evaluate_ordering();
-SHO_PUBLIC void set_initial_volume(int Gdirn, double COV, double total_volume, double Rmax, double Rmin);
 SHO_PUBLIC void volume_of_mesh(double *volume_model, double *volume_tree);
 SHO_PUBLIC void write_elem_geometry_2d(const char *ELEMFILE);
 SHO_PUBLIC void write_geo_file(int ntype, const char *GEOFILE);

diff --git a/src/bindings/c/surface_fitting.c b/src/bindings/c/surface_fitting.c
@@ -2,12 +2,16 @@
 #include "string.h"
 
 void fit_surface_geometry_c(int *niterations,const char *fitting_file,int *fitting_file_len);
-
+void initialise_fit_mesh_c(void);
 
 void fit_surface_geometry(int niterations,const char *fitting_file)
 {
   int filename_len = strlen(fitting_file);
   fit_surface_geometry_c(&niterations, fitting_file, &filename_len);
 }
 
+void initialise_fit_mesh()
+{
+  initialise_fit_mesh_c();
+}
 
diff --git a/src/bindings/c/surface_fitting.f90 b/src/bindings/c/surface_fitting.f90
@@ -9,7 +9,7 @@ module surface_fitting_c
   subroutine fit_surface_geometry_c(niterations, fitting_file, filename_len) &
     bind(C, name="fit_surface_geometry_c")
 
-     use iso_c_binding, only: c_ptr
+    use iso_c_binding, only: c_ptr
     use utils_c, only: strncpy
     use other_consts, only: MAX_STRING_LEN, MAX_FILENAME_LEN
     use surface_fitting, only: fit_surface_geometry
@@ -27,4 +27,13 @@ end subroutine fit_surface_geometry_c
 
 !!!############################################################################
 
+  subroutine initialise_fit_mesh_c() bind(C, name="initialise_fit_mesh_c")
+    use surface_fitting, only: initialise_fit_mesh
+    implicit none
+
+    call initialise_fit_mesh
+
+  end subroutine initialise_fit_mesh_c
+
+!!!############################################################################
 end module surface_fitting_c
diff --git a/src/bindings/c/surface_fitting.h b/src/bindings/c/surface_fitting.h
@@ -4,5 +4,6 @@
 #include "symbol_export.h"
 
 SHO_PUBLIC void fit_surface_geometry(int niterations, const char *fitting_file);
+SHO_PUBLIC void initialise_fit_mesh();
 
 #endif /* AETHER_SURFACE_FITTING_H */
Original file line number	Diff line number	Diff line change
Expand Up		@@ -26,5 +26,6 @@ subroutine set_node_field_value_c(row, col, value) bind(C, name="set_node_field_

		end subroutine set_node_field_value_c



		end module arrays_c