Changeset 902

Timestamp:

07/18/16 08:58:58 (8 years ago)

Author:

oabramkina

Message:

Sequential version of new functionalities for mesh connectivity:

edge_faces
face_edges
face_face.

Compilation error of version 900 resolved.

File:

• XIOS/trunk/src/io/nc4_data_output.cpp (modified) (11 diffs)

XIOS/trunk/src/io/nc4_data_output.cpp

@@ -450 +450 @@
       StdString domainName = domain->name;
       domain->assignMesh(domainName);
-      //domain->mesh->createMesh(domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
-      domain->mesh->createMeshEpsilon(domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
+      domain->mesh->createMesh(domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
+      //domain->mesh->createMeshEpsilon(server->intraComm, domain->lonvalue_srv, domain->latvalue_srv, domain->bounds_lon_srv, domain->bounds_lat_srv);
 
       StdString node_x = domainName + "_node_x";
@@ -463 +463 @@
       StdString face_y = domainName + "_face_y";
       StdString face_nodes = domainName + "_face_nodes";
+      StdString face_edges = domainName + "_face_edges";
+      StdString edge_faces = domainName + "_edge_face_links";
+      StdString face_faces = domainName + "_face_links";
 
       StdString dimNode = "n" + domainName + "_node";
@@ -487 +490 @@
             // Adding nodes
             if (domain->nvertex == 1)
+            {
+              if (!SuperClassWriter::varExist(node_x) || !SuperClassWriter::varExist(node_y))
+              {
+                SuperClassWriter::addDimension(dimNode, domain->ni_glo);
+                dim0.clear();
+                dim0.push_back(dimNode);
+                SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
+                SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
+                SuperClassWriter::addAttribute("longname_name", StdString("Longitude of mesh nodes."), &node_x);
+                SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
+                SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
+                SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
+                SuperClassWriter::addAttribute("longname_name", StdString("Latitude of mesh nodes."), &node_y);
+                SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
+              }
+            } // domain->nvertex == 1
+
+            // Adding edges and nodes, if nodes have not been defined previously
+            if (domain->nvertex == 2)
             {
               if (!SuperClassWriter::varExist(node_x) || !SuperClassWriter::varExist(node_y))
@@ -502 +524 @@
                 SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
               }
-            } // domain->nvertex == 1
-
-            // Adding edges and nodes, if nodes have not been defined previously
-            if (domain->nvertex == 2)
-            {
-              // Nodes
-              if (!SuperClassWriter::varExist(node_x) || !SuperClassWriter::varExist(node_y))
-              {
-                SuperClassWriter::addDimension(dimNode, domain->mesh->nbNodes);
-                dim0.clear();
-                dim0.push_back(dimNode);
-                SuperClassWriter::addVariable(node_x, NC_FLOAT, dim0);
-                SuperClassWriter::addAttribute("standard_name", StdString("longitude"), &node_x);
-                SuperClassWriter::addAttribute("longname_name", StdString("Longitude of mesh nodes."), &node_x);
-                SuperClassWriter::addAttribute("units", StdString("degrees_east"), &node_x);
-                SuperClassWriter::addVariable(node_y, NC_FLOAT, dim0);
-                SuperClassWriter::addAttribute("standard_name", StdString("latitude"), &node_y);
-                SuperClassWriter::addAttribute("longname_name", StdString("Latitude of mesh nodes."), &node_y);
-                SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
-              }
-              // Edges
               if (!SuperClassWriter::varExist(edge_x) || !SuperClassWriter::varExist(edge_y))
               {
@@ -566 +567 @@
                 SuperClassWriter::addAttribute("units", StdString("degrees_north"), &node_y);
               }
-              // Edges
               if (!SuperClassWriter::varExist(edge_x) || !SuperClassWriter::varExist(edge_y))
               {
@@ -590 +590 @@
                 SuperClassWriter::addAttribute("start_index", 0, &edge_nodes);
               }
-              // Faces
                 SuperClassWriter::addAttribute("face_coordinates", face_x + " " + face_y, &domainName);
                 SuperClassWriter::addAttribute("face_node_connectivity", face_nodes, &domainName);
@@ -612 +611 @@
                 SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its corner nodes."), &face_nodes);
                 SuperClassWriter::addAttribute("start_index", 0, &face_nodes);
+                dim0.clear();
+                dim0.push_back(dimFace);
+                dim0.push_back(dimVertex);
+                SuperClassWriter::addVariable(face_edges, NC_INT, dim0);
+                SuperClassWriter::addAttribute("cf_role", StdString("face_edge_connectivity"), &face_edges);
+                SuperClassWriter::addAttribute("long_name", StdString("Maps every face to its edges."), &face_edges);
+                SuperClassWriter::addAttribute("start_index", 0, &face_edges);
+                dim0.clear();
+                dim0.push_back(dimEdge);
+                dim0.push_back(dimTwo);
+                SuperClassWriter::addVariable(edge_faces, NC_INT, dim0);
+                SuperClassWriter::addAttribute("cf_role", StdString("edge_face connectivity"), &edge_faces);
+                SuperClassWriter::addAttribute("long_name", StdString("neighbor faces for edges"), &edge_faces);
+                SuperClassWriter::addAttribute("start_index", 0, &edge_faces);
+                SuperClassWriter::addAttribute("_FillValue", -999, &edge_faces);
+                SuperClassWriter::addAttribute("comment", StdString("missing neighbor faces are indicated using _FillValue"), &edge_faces);
+                dim0.clear();
+                dim0.push_back(dimFace);
+                dim0.push_back(dimVertex);
+                SuperClassWriter::addVariable(face_faces, NC_INT, dim0);
+                SuperClassWriter::addAttribute("cf_role", StdString("face_face connectivity"), &face_faces);
+                SuperClassWriter::addAttribute("long_name", StdString("Indicates which other faces neighbor each face"), &face_faces);
+                SuperClassWriter::addAttribute("start_index", 0, &face_faces);
+                SuperClassWriter::addAttribute("flag_values", -1, &face_faces);
+                SuperClassWriter::addAttribute("flag_meanings", StdString("out_of_mesh"), &face_faces);
             } // domain->nvertex > 2
 
             SuperClassWriter::definition_end();
+
+            std::vector<StdSize> start(1) ;
+            std::vector<StdSize> count(1) ;
+            if (domain->isEmpty())
+             {
+               start[0]=0 ;
+               count[0]=0 ;
+             }
+             else
+             {
+               start[0]=domain->zoom_ibegin_srv-domain->global_zoom_ibegin;
+               count[0]=domain->zoom_ni_srv ;
+             }
 
             if (!isWrittenDomain(domid))
@@ -620 +657 @@
               if (domain->nvertex == 1)
               {
-                SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0);
-                SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0);
+                SuperClassWriter::writeData(domain->mesh->node_lat, node_y, isCollective, 0, &start, &count);
+                SuperClassWriter::writeData(domain->mesh->node_lon, node_x, isCollective, 0, &start, &count);
               }
               else if (domain->nvertex == 2)
@@ -641 +678 @@
                 SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0);
                 SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes);
+                SuperClassWriter::writeData(domain->mesh->face_edges, face_edges);
+                SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces);
+                SuperClassWriter::writeData(domain->mesh->face_faces, face_faces);
               }
               setWrittenDomain(domid);
@@ -684 +724 @@
                 SuperClassWriter::writeData(domain->mesh->face_lon, face_x, isCollective, 0);
                 SuperClassWriter::writeData(domain->mesh->face_nodes, face_nodes);
+                SuperClassWriter::writeData(domain->mesh->face_edges, face_edges);
+                SuperClassWriter::writeData(domain->mesh->edge_faces, edge_faces);
+                SuperClassWriter::writeData(domain->mesh->face_faces, face_faces);
               }
             }// isWrittenDomain
@@ -736 +779 @@
 
          StdString appendDomid  = (singleDomain) ? "" : "_"+domid ;
-
 
          StdString dimXid = StdString("cell").append(appendDomid);