some fixes

fluid/fluid_problem.c

@@ -192,6 +192,7 @@ static void f_boundary(WeakBoundary *wbnd, FluidProblem *problem,const double *n
     dun[iD] = 0;
     dunt[iD] = 0;
     unold += sold[U+iD]*n[iD];
+    if(vid>=0)
     unext += data[vid+iD]*n[iD];
     dcn += dc[iD]*n[iD];
     s_c += vid<0?0:(u[iD]-data[vid+iD])*n[iD];
@@ -1818,7 +1819,7 @@ void fluid_problem_local_adapt_mesh(FluidProblem *problem, double lcmax, double
         }
         read_the_tree(mesh, Tree, x_new, n_nodes_new, elements_new, n_elements_new, boundaries_new, boundary_tags_new, n_boundaries_new);
         
-        problem->map = (Tree_cell *) malloc(n_elements_new*sizeof(Tree_cell));
+        problem->map = malloc(n_elements_new*sizeof(Tree_cell*));
         problem->map2Tree = (int *) malloc(n_elements_new*sizeof(Tree_cell));
         get_the_mapping(Tree, problem->map, problem->map2Tree, problem->size_initial_mesh);
         
@@ -1843,16 +1844,16 @@ void fluid_problem_local_adapt_mesh(FluidProblem *problem, double lcmax, double
         int *boundaries_new = (int*) calloc(2*n_boundaries_new, sizeof(int));
         int *boundary_tags_new = (int*) malloc(n_boundaries_new*sizeof(int));
         
-        Tree_cell *map_new = (Tree_cell*) malloc(n_elements_new*sizeof(Tree_cell));
+        Tree_cell **map_new = malloc(n_elements_new*sizeof(Tree_cell*));
         int *map2Tree_new = (int*) malloc(n_elements_new*sizeof(Tree_cell));
         
         // initialize to zero
-        for (int n=0; n<mesh->n_elements; n++) {
+        for (int n=0; n<mesh->n_nodes; n++) {
             for (int ii=0; ii<3; ii++) {
                 x_new[n*3+ii]=mesh->x[n*3+ii];
             }
         }
-        for (int n=mesh->n_elements; n<n_elements_new; n++) {
+        for (int n=mesh->n_nodes; n<n_nodes_new; n++) {
             for (int ii=0; ii<3; ii++) {
                 x_new[n*3+ii]=0.;
             }
@@ -1860,7 +1861,7 @@ void fluid_problem_local_adapt_mesh(FluidProblem *problem, double lcmax, double
         
         deep_tree_create_the_data_structure(mesh, problem->Tree, x_new, n_nodes_new, elements_new, n_elements_new, boundaries_new, n_boundaries_new, boundary_tags_new, map_new, map2Tree_new, problem->size_initial_mesh);
         
-        //fluid_problem_set_elements(problem, n_nodes_new, x_new, n_elements_new, elements_new, n_boundaries_new, boundaries_new, boundary_tags_new, mesh->n_boundaries, mesh->boundary_names,1);
+        fluid_problem_set_elements(problem, n_nodes_new, x_new, n_elements_new, elements_new, n_boundaries_new, boundaries_new, boundary_tags_new, mesh->n_boundaries, mesh->boundary_names,1);
         
         /*char filename[128];
         sprintf(filename, "test_%d.msh",global_ind); global_ind++;
@@ -1868,15 +1869,14 @@ void fluid_problem_local_adapt_mesh(FluidProblem *problem, double lcmax, double
         mesh_write_msh(problem->mesh,ftmp);
         fclose(ftmp);*/
         
-        /*printf("HERE \n");
+        /*printf("HERE \n");*/
         problem->map = map_new;
-        problem->map2Tree = map2Tree_new;*/
+        problem->map2Tree = map2Tree_new;
         
-        /*free(elements_new);
+        free(elements_new);
         free(x_new);
         free(boundaries_new);
-        free(boundary_tags_new);*/
-        exit(1);
+        free(boundary_tags_new);
         
     }
     /*Mesh *mesh = problem->mesh;

fluid/fluid_problem.h

@@ -64,7 +64,7 @@ struct FluidProblem {
   Mesh *mesh;
   MeshTree *mesh_tree;
   Tree_cell *Tree;
-  Tree_cell *map;
+  Tree_cell **map;
   int *map2Tree;
   int size_initial_mesh;
   MeshBoundary *boundaries;

fluid/mesh.h

@@ -127,9 +127,7 @@ typedef struct Tree_cell
 {
     struct Tree_cell *children;
     struct Tree_cell *parent;
-    struct Tree_cell *nghb0;
-    struct Tree_cell *nghb1;
-    struct Tree_cell *nghb2;
+    struct Tree_cell *nghb[3];
     
     int tag;
     int bool_ref;
@@ -149,27 +147,27 @@ typedef struct Tree_cell
 void create_the_tree(Mesh *mesh, Tree_cell *Tree, double h_min, int *n_nodes_new, int *n_elements_new, int *delta_boundaries_new);
 void read_the_tree(Mesh *mesh, Tree_cell *Tree, double *x_new, int n_nodes_new, int *elements_new, int n_elements_new, int *boundaries_new, int *boundary_tags_new, int n_boundaries_new);
 
-void deep_tree_walk_tree(Mesh *mesh, Tree_cell *Tree, Tree_cell *map, int *map2Tree, int size, double h_min, int *n_nodes_new, int *n_elements_new, int *n_boundaries_new);
-void deep_tree_create_the_data_structure(Mesh *mesh, Tree_cell *Tree, double *x_new, int n_nodes_new, int *elements_new, int n_elements_new, int *boundaries_new, int n_boundaries_new, int *boundary_tags_new, Tree_cell *map_new, int *map2Tree_new, int size);
-void deep_tree_get_map(Tree_cell *current, Tree_cell *map_new, int *map2Tree_new, int *elt, int root);
+void deep_tree_walk_tree(Mesh *mesh, Tree_cell *Tree, Tree_cell **map, int *map2Tree, int size, double h_min, int *n_nodes_new, int *n_elements_new, int *n_boundaries_new);
+void deep_tree_create_the_data_structure(Mesh *mesh, Tree_cell *Tree, double *x_new, int n_nodes_new, int *elements_new, int n_elements_new, int *boundaries_new, int n_boundaries_new, int *boundary_tags_new, Tree_cell **map_new, int *map2Tree_new, int size);
+void deep_tree_get_map(Tree_cell *current, Tree_cell **map_new, int *map2Tree_new, int *elt, int root);
 
 void deep_tree_create_x_elt_bd(Mesh *mesh, Tree_cell *current, double *x_new, int *elements_new, int *boundaries_new, int *boundary_tags_new, int *ibd);
-void deep_tree_init_nghb_step1(Mesh *mesh, Tree_cell *map, Tree_cell *current);
-void deep_tree_init_nghb_step2(Mesh *mesh, Tree_cell *Tree, Tree_cell *map, int *map2Tree, Tree_cell *current);
-void deep_tree_transfert_nghb(Tree_cell *current, Tree_cell *tree_elt, int buffer, int bool_nghb0, int bool_nghb1);
+//void deep_tree_init_nghb_step1(Mesh *mesh, Tree_cell **map, Tree_cell *current);
+//void deep_tree_init_nghb_step2(Mesh *mesh, Tree_cell *Tree, Tree_cell **map, int *map2Tree, Tree_cell *current);
+//void deep_tree_transfert_nghb(Tree_cell *current, Tree_cell *tree_elt, int buffer, int bool_nghb0, int bool_nghb1);
 void deep_tree_transfer(Tree_cell *current, int iel);
 
-void deep_tree_set_bool_ref(Mesh *mesh, Tree_cell *current, double h_min);
+//void deep_tree_set_bool_ref(Mesh *mesh, Tree_cell *current, double h_min);
 void deep_tree_refinement(Mesh *mesh, Tree_cell *Tree, Tree_cell *current, double h_min, int *index, int *elt);
 void deep_tree_complete_the_refinement(Mesh *mesh, Tree_cell *Tree, Tree_cell *current, int *index, int *elt);
 void deep_tree_remove_illegale_refinement(Mesh *mesh, Tree_cell *Tree, Tree_cell *current, int *index, int *elt, int *ibd, int *num);
 
-void deep_tree_talk_2_neighbours(Tree_cell *map, Tree_cell *current, int iel, int *index);
+void deep_tree_talk_2_neighbours(Tree_cell **map, Tree_cell *current, int iel, int *index);
 void deep_tree_cut_into_4(Mesh *mesh, Tree_cell *Tree, Tree_cell *current, int iel, int *index, int *elt, int bool_2_transfert);
 void deep_tree_cut_into_2(Tree_cell *current, int *index, int *elt);
 void deep_tree_transform_into_4(Mesh *mesh, Tree_cell *Tree, Tree_cell *current, int *index, int *elt);
 void deep_tree_transfer_for_transform(Tree_cell *buf, int ii, Tree_cell *buf_nghb, int *index, int cut_edge, int save_tag1, int save_tag2);
-void deep_tree_green_refinement(Mesh *mesh, Tree_cell *Tree, Tree_cell *map, Tree_cell *current, int *map2Tree, int *index, int *elt);
+void deep_tree_green_refinement(Mesh *mesh, Tree_cell *Tree, Tree_cell *current, int *index, int *elt);
 
 
 int find_nghb(Mesh *mesh, int current, int n_edges, int neighbours[3], int nodes[6], int phys[3]);
@@ -185,7 +183,7 @@ int bool_2_nodes_no_children(Tree_cell *Tree, int iel);
 void cut_in_2(Tree_cell *Tree, int iel, int *elements_new, int *elt);
 void cut_in_4(Mesh *mesh, Tree_cell *Tree, int iel, double *x_new, int *elements_new, int *elt, int *boundaries_new, int *boundary_tags_new, int *ibd);
 
-void get_the_mapping(Tree_cell *Tree, Tree_cell *map, int *map2Tree, int size);
+void get_the_mapping(Tree_cell *Tree, Tree_cell **map, int *map2Tree, int size);
 
 void printing_post_processing_files(Mesh *mesh, int *elements_new, double *x_new, int *boundaries_new, int n_elements_new, int n_boundaries_new);
 void print_current(Tree_cell *current, int bool_print);