Changeset 9714

Timestamp:

09/09/11 07:28:59 (14 years ago)

Author:

Mathieu Morlighem

Message:

moved some stuff to mesh

Location:

issm/trunk

Files:

• src/m/classes/mesh.m (modified) (1 diff)
• src/m/classes/model/model.m (modified) (7 diffs)
• src/m/kml/kml_mesh_elem.m (modified) (3 diffs)
• src/m/kml/kml_mesh_write.m (modified) (2 diffs)
• src/m/kml/kml_part_edges.m (modified) (8 diffs)
• src/m/kml/kml_part_elems.m (modified) (3 diffs)
• src/m/kml/kml_part_flagedges.m (modified) (3 diffs)
• src/m/kml/kml_partitions.m (modified) (8 diffs)
• src/m/kml/kml_unsh_edges.m (modified) (3 diffs)
• src/m/model/bamg.m (modified) (2 diffs)
• src/m/model/collapse.m (modified) (1 diff)
• src/m/model/extrude.m (modified) (1 diff)
• src/m/model/ismodelselfconsistent.m (modified) (1 diff)
• src/m/model/kmlimagesc.m (modified) (2 diffs)
• src/m/model/mesh/meshconvert.m (modified) (2 diffs)
• src/m/model/mesh/meshnodensity.m (modified) (3 diffs)
• src/m/model/mesh/meshrefine.m (modified) (2 diffs)
• src/m/model/mesh/meshyams.m (modified) (2 diffs)
• src/m/model/mesh/reorder.m (modified) (1 diff)
• src/m/model/mesh/rifts/meshaddrifts.m (modified) (1 diff)
• src/m/model/mesh/rifts/meshprocessoutsiderifts.m (modified) (2 diffs)
• src/m/model/mesh/rifts/meshprocessrifts.m (modified) (2 diffs)
• src/m/model/mesh/rifts/meshyamsrecreateriftsegments.m (modified) (5 diffs)
• src/m/model/mesh/setmesh.m (modified) (3 diffs)
• src/m/model/modelextract.m (modified) (1 diff)
• src/m/model/outflow.m (modified) (1 diff)
• src/m/model/plot/applyoptions.m (modified) (2 diffs)
• src/m/model/plot/kmlgroundoverlay.m (modified) (2 diffs)
• src/m/model/plot/latlonoverlay.m (modified) (2 diffs)
• src/m/model/plot/plot_boundaries.m (modified) (1 diff)
• src/m/model/plot/plot_riftfraction.m (modified) (1 diff)
• src/m/model/plot/plot_riftnumbering.m (modified) (2 diffs)
• src/m/model/plot/plot_riftpenetration.m (modified) (2 diffs)
• src/m/model/plot/plot_riftrelvel.m (modified) (2 diffs)
• src/m/model/plot/plot_riftvel.m (modified) (2 diffs)
• src/m/model/plot/plot_segments.m (modified) (2 diffs)
• src/m/model/plot/processmesh.m (modified) (1 diff)
• src/m/model/plot/showregion.m (modified) (1 diff)
• src/m/model/radarpower.m (modified) (2 diffs)
• src/m/model/setmask2.m (modified) (2 diffs)
• src/m/solutions/flaim.m (modified) (3 diffs)
• src/m/utils/BC/SetIceSheetBC.m (modified) (1 diff)
• src/m/utils/BC/SetIceShelfBC.m (modified) (3 diffs)
• src/m/utils/BC/SetMarineIceSheetBC.m (modified) (2 diffs)
• src/m/utils/Mesh/argusmesh.m (modified) (1 diff)
• src/m/utils/Mesh/squaremesh.m (modified) (2 diffs)
• template (modified) (2 diffs)
• test/NightlyRun/test131.m (modified) (1 diff)
• test/NightlyRun/test132.m (modified) (1 diff)
• test/NightlyRun/test133.m (modified) (1 diff)
• test/NightlyRun/test134.m (modified) (1 diff)
• test/NightlyRun/test233.m (modified) (1 diff)
• test/NightlyRun/test234.m (modified) (1 diff)
• test/NightlyRun/test235.m (modified) (1 diff)
• test/NightlyRun/test236.m (modified) (1 diff)
• test/NightlyRun/test527.m (modified) (1 diff)
• test/NightlyRun/test625.m (modified) (1 diff)
• test/NightlyRun/test626.m (modified) (1 diff)
• test/Par/79North.par (modified) (1 diff)
• test/Par/RoundSheetShelf.par (modified) (1 diff)

issm/trunk/src/m/classes/mesh.m

@@ -9 +9 @@
                 extractedvertices           = modelfield('default',NaN,'marshall',false);
                 extractedelements           = modelfield('default',NaN,'marshall',false);
+                vertexonboundary            = modelfield('default',NaN,'marshall',false);
+                lat        = modelfield('default',NaN,'marshall',false);
+                long       = modelfield('default',NaN,'marshall',false);
+                hemisphere = modelfield('default',NaN,'marshall',false);
+                segments             = modelfield('default',NaN,'marshall',false);
+                segmentmarkers       = modelfield('default',NaN,'marshall',false);
         end
         methods

issm/trunk/src/m/classes/model/model.m

@@ -43 +43 @@
                  %FIXME: all other fields should belong to other classes
 
-                 %Mesh
                  dim                 = modelfield('default',0,'marshall',true,'format','Integer');
                  numberofelements    = modelfield('default',0,'marshall',true,'format','Integer');
@@ -55 +54 @@
                  edges               = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',3);
 
-                 %Initial 2d mesh 
                  numberofelements2d = modelfield('default',0,'marshall',true,'format','Integer');
                  numberofnodes2d    = modelfield('default',0,'marshall',true,'format','Integer');
@@ -62 +60 @@
                  y2d                = modelfield('default',NaN,'marshall',false);
 
-                 %latlon of the coorinates
-                 lat        = modelfield('default',NaN,'marshall',false);
-                 long       = modelfield('default',NaN,'marshall',false);
-                 hemisphere = modelfield('default',NaN,'marshall',false);
-
-                 %Penalties
-                 segments             = modelfield('default',NaN,'marshall',false);
-                 segmentmarkers       = modelfield('default',NaN,'marshall',false);
-
-                 %Projections
                  uppernodes           = modelfield('default',NaN,'marshall',false);
                  upperelements        = modelfield('default',NaN,'marshall',true,'format','DoubleMat','mattype',2);
@@ -77 +65 @@
                  lowernodes           = modelfield('default',NaN,'marshall',false);
 
-                 %Extrusion
                  numlayers         = modelfield('default',0,'marshall',true,'format','Integer');
                  elementonbed      = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',2);
@@ -83 +70 @@
                  nodeonbed         = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',1);
                  nodeonsurface     = modelfield('default',NaN,'marshall',true,'format','BooleanMat','mattype',1);
-
-                 %Boundary conditions
-                 nodeonboundary = modelfield('default',NaN,'marshall',false);
                  %}}}
          end
@@ -234 +218 @@
                          if isfield(structmd,'gridonicesheet'), md.mask.vertexongroundedice=structmd.gridonicesheet; end
                          if isfield(structmd,'gridonwater'), md.mask.vertexonwater=structmd.gridonwater; end
-                         if isfield(structmd,'gridonboundary'), md.nodeonboundary=structmd.gridonboundary; end
+                         if isfield(structmd,'gridonboundary'), md.mesh.vertexonboundary=structmd.gridonboundary; end
                          if isfield(structmd,'petscoptions'), md.solver=structmd.petscoptions; end
                          if isfield(structmd,'g'), md.constants.g=structmd.g; end
@@ -328 +312 @@
                          if isfield(structmd,'extractednodes'), md.mesh.extractedvertices=structmd.extractednodes; end
                          if isfield(structmd,'extractedelements'), md.mesh.extractedelements=structmd.extractedelements; end
+                         if isfield(structmd,'nodeonboundary'), md.mesh.vertexonboundary=structmd.nodeonboundary; end
+                         if isfield(structmd,'hemisphere'), md.mesh.hemisphere=structmd.hemisphere; end
+                         if isfield(structmd,'lat'), md.mesh.lat=structmd.lat; end
+                         if isfield(structmd,'lon'), md.mesh.lon=structmd.lon; end
+                         if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
+                         if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
 
                          %Field changes

issm/trunk/src/m/kml/kml_mesh_elem.m

@@ -61 +61 @@
 end
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
     if     ~exist('latsgn','var')
         error(['Missing ''latsgn'' parameter to calculate missing lat/long data.']);
@@ -69 +69 @@
     else
         display('Converting x/y data to lat/long data.');
-        [md.lat,md.long]=xy2ll(md.x,md.y,latsgn);
+        [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,latsgn);
     end
 end
@@ -160 +160 @@
 
     for j=1:size(md.elements,2)
-        kring.coords(j,:)=[md.long(md.elements(i,j)) md.lat(md.elements(i,j)) alt];
+        kring.coords(j,:)=[md.mesh.long(md.elements(i,j)) md.mesh.lat(md.elements(i,j)) alt];
     end
     kring.coords(end,:)=kring.coords(1,:);

issm/trunk/src/m/kml/kml_mesh_write.m

@@ -67 +67 @@
 end
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
     if     ~exist('latsgn','var')
         error(['Missing ''latsgn'' parameter to calculate missing lat/long data.']);
@@ -75 +75 @@
     else
         display('Converting x/y data to lat/long data.');
-        [md.lat,md.long]=xy2ll(md.x,md.y,latsgn);
+        [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,latsgn);
     end
 end

issm/trunk/src/m/kml/kml_part_edges.m

@@ -62 +62 @@
 end
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
     if     ~exist('latsgn','var')
         error(['Missing ''latsgn'' parameter to calculate missing lat/long data.']);
@@ -70 +70 @@
     else
         display('Converting x/y data to lat/long data.');
-        [md.lat,md.long]=xy2ll(md.x,md.y,latsgn);
+        [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,latsgn);
     end
 end
@@ -234 +234 @@
 %  if first edge, write out first node
                     if ~elast
-                        kline.coords(end+1,:)=[md.long(edgeper(j,1)) md.lat(edgeper(j,1)) alt];
+                        kline.coords(end+1,:)=[md.mesh.long(edgeper(j,1)) md.mesh.lat(edgeper(j,1)) alt];
                     end
-                    kline.coords(end+1,:)=[md.long(edgeper(j,2)) md.lat(edgeper(j,2)) alt];
+                    kline.coords(end+1,:)=[md.mesh.long(edgeper(j,2)) md.mesh.lat(edgeper(j,2)) alt];
                     elast=elemper(j);
                     nlast=edgeper(j,2);
@@ -323 +323 @@
 %  write out first node of first side for half-edge to midpoint
 %                                disp(['segment j=' int2str(j) ' unshared half edge from node ' int2str(elemp(ielem,nlast)) ' (node ' int2str(nlast) ') on side ' int2str(slast) ' from element ' int2str(ielem) ' written.'])
-                                kline.coords(end+1,:)=[md.long(elemp(ielem,nlast)) ...
-                                                       md.lat(elemp(ielem,nlast)) alt];
+                                kline.coords(end+1,:)=[md.mesh.long(elemp(ielem,nlast)) ...
+                                                       md.mesh.lat(elemp(ielem,nlast)) alt];
                             end
                             nlast=0;
                             
 %  write out midpoint of first side
-                            kline.coords(end+1,:)=[(md.long(elemp(ielem,slast))...
-                                                   +md.long(elemp(ielem,mod(slast,3)+1)))/2. ...
-                                                   (md.lat(elemp(ielem,slast))...
-                                                   +md.lat(elemp(ielem,mod(slast,3)+1)))/2. alt];
+                            kline.coords(end+1,:)=[(md.mesh.long(elemp(ielem,slast))...
+                                                   +md.mesh.long(elemp(ielem,mod(slast,3)+1)))/2. ...
+                                                   (md.mesh.lat(elemp(ielem,slast))...
+                                                   +md.mesh.lat(elemp(ielem,mod(slast,3)+1)))/2. alt];
                         end
 
@@ -371 +371 @@
 %  write out half-edge from current node to midpoint of unshared side
 %                            disp(['segment j=' int2str(j) ' unshared half edge from node ' int2str(elemp(ielem,nlast)) ' (node ' int2str(nlast) ') on side ' int2str(slast) ' from element ' int2str(ielem) ' written.'])
-                            kline.coords(end+1,:)=[(md.long(elemp(ielem,nlast))...
-                                                   +md.long(elemp(ielem,nnext)))/2. ...
-                                                   (md.lat(elemp(ielem,nlast))...
-                                                   +md.lat(elemp(ielem,nnext)))/2. alt];
+                            kline.coords(end+1,:)=[(md.mesh.long(elemp(ielem,nlast))...
+                                                   +md.mesh.long(elemp(ielem,nnext)))/2. ...
+                                                   (md.mesh.lat(elemp(ielem,nlast))...
+                                                   +md.mesh.lat(elemp(ielem,nnext)))/2. alt];
                             nlast=0;
 
@@ -404 +404 @@
 %  all different, so cut through centroid
 %                                disp(['element ielem=' int2str(ielem) ' centroid written.'])
-                                kline.coords(end+1,:)=[sum(md.long(elemp(ielem,:)))/3. ...
-                                                       sum(md.lat(elemp(ielem,:)))/3. alt];
+                                kline.coords(end+1,:)=[sum(md.mesh.long(elemp(ielem,:)))/3. ...
+                                                       sum(md.mesh.lat(elemp(ielem,:)))/3. alt];
                             end
 %  one node is in current partition, so cut off other two nodes
@@ -419 +419 @@
 %  write out midpoint of opposite side
 %                        disp(['segment j=' int2str(j) ' internal edge from side ' int2str(slast) ' to side ' int2str(snext) ' from element ' int2str(ielem) ' written.'])
-                        kline.coords(end+1,:)=[(md.long(elemp(ielem,snext))...
-                                               +md.long(elemp(ielem,mod(snext,3)+1)))/2. ...
-                                               (md.lat(elemp(ielem,snext))...
-                                               +md.lat(elemp(ielem,mod(snext,3)+1)))/2. alt];
+                        kline.coords(end+1,:)=[(md.mesh.long(elemp(ielem,snext))...
+                                               +md.mesh.long(elemp(ielem,mod(snext,3)+1)))/2. ...
+                                               (md.mesh.lat(elemp(ielem,snext))...
+                                               +md.mesh.lat(elemp(ielem,mod(snext,3)+1)))/2. alt];
                         elast=ielem;
                         nlast=0;
@@ -451 +451 @@
                             end
 %                            disp(['segment j=' int2str(j) ' unshared half edge on side ' int2str(slast) ' to node ' int2str(elemp(elast,nnext)) ' (node ' int2str(nnext) ') from element ' int2str(elast) ' written.'])
-                            kline.coords(end+1,:)=[md.long(elemp(elast,nnext)) ...
-                                                   md.lat(elemp(elast,nnext)) alt];
+                            kline.coords(end+1,:)=[md.mesh.long(elemp(elast,nnext)) ...
+                                                   md.mesh.lat(elemp(elast,nnext)) alt];
                             break
 %  if not unshared, advance perimeter list and watch for end

issm/trunk/src/m/kml/kml_part_elems.m

@@ -62 +62 @@
 end
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
     if     ~exist('latsgn','var')
         error(['Missing ''latsgn'' parameter to calculate missing lat/long data.']);
@@ -70 +70 @@
     else
         display('Converting x/y data to lat/long data.');
-        [md.lat,md.long]=xy2ll(md.x,md.y,latsgn);
+        [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,latsgn);
     end
 end
@@ -199 +199 @@
 
             for j=1:size(elem,2)
-                kring.coords(j,:)=[md.long(elem(i,j)) md.lat(elem(i,j)) alt];
+                kring.coords(j,:)=[md.mesh.long(elem(i,j)) md.mesh.lat(elem(i,j)) alt];
             end
             kring.coords(end,:)=kring.coords(1,:);

issm/trunk/src/m/kml/kml_part_flagedges.m

@@ -54 +54 @@
 end
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
     if     ~exist('latsgn','var')
         error(['Missing ''latsgn'' parameter to calculate missing lat/long data.']);
@@ -62 +62 @@
     else
         display('Converting x/y data to lat/long data.');
-        [md.lat,md.long]=xy2ll(md.x,md.y,latsgn);
+        [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,latsgn);
     end
 end
@@ -74 +74 @@
 if (~exist('prtplt','var') || strncmpi(prtplt,'on' ,2) || strncmpi(prtplt,'y',1)) && ...
     md.qmu.numberofpartitions
-    [latseg,lonseg]=flagedges(md.elements,md.lat,md.long,md.qmu.partition);
+    [latseg,lonseg]=flagedges(md.elements,md.mesh.lat,md.mesh.long,md.qmu.partition);
     kfold=kml_folder();
     kfold.name      ='Partition Segments';

issm/trunk/src/m/kml/kml_partitions.m

@@ -63 +63 @@
 end
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
     if     ~exist('latsgn','var')
         error(['Missing ''latsgn'' parameter to calculate missing lat/long data.']);
@@ -71 +71 @@
     else
         display('Converting x/y data to lat/long data.');
-        [md.lat,md.long]=xy2ll(md.x,md.y,latsgn);
+        [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,latsgn);
     end
 end
@@ -236 +236 @@
 %  if first edge, write out first node
                     if ~elast
-                        kring.coords(end+1,:)=[md.long(edgeper(j,1)) md.lat(edgeper(j,1)) alt];
+                        kring.coords(end+1,:)=[md.mesh.long(edgeper(j,1)) md.mesh.lat(edgeper(j,1)) alt];
                     end
-                    kring.coords(end+1,:)=[md.long(edgeper(j,2)) md.lat(edgeper(j,2)) alt];
+                    kring.coords(end+1,:)=[md.mesh.long(edgeper(j,2)) md.mesh.lat(edgeper(j,2)) alt];
                     elast=elemper(j);
                     nlast=edgeper(j,2);
@@ -325 +325 @@
 %  write out first node of first side for half-edge to midpoint
 %                                disp(['segment j=' int2str(j) ' unshared half edge from node ' int2str(elemp(ielem,nlast)) ' (node ' int2str(nlast) ') on side ' int2str(slast) ' from element ' int2str(ielem) ' written.'])
-                                kring.coords(end+1,:)=[md.long(elemp(ielem,nlast)) ...
-                                                       md.lat(elemp(ielem,nlast)) alt];
+                                kring.coords(end+1,:)=[md.mesh.long(elemp(ielem,nlast)) ...
+                                                       md.mesh.lat(elemp(ielem,nlast)) alt];
                             end
                             nlast=0;
                             
 %  write out midpoint of first side
-                            kring.coords(end+1,:)=[(md.long(elemp(ielem,slast))...
-                                                   +md.long(elemp(ielem,mod(slast,3)+1)))/2. ...
-                                                   (md.lat(elemp(ielem,slast))...
-                                                   +md.lat(elemp(ielem,mod(slast,3)+1)))/2. alt];
+                            kring.coords(end+1,:)=[(md.mesh.long(elemp(ielem,slast))...
+                                                   +md.mesh.long(elemp(ielem,mod(slast,3)+1)))/2. ...
+                                                   (md.mesh.lat(elemp(ielem,slast))...
+                                                   +md.mesh.lat(elemp(ielem,mod(slast,3)+1)))/2. alt];
                         end
 
@@ -373 +373 @@
 %  write out half-edge from current node to midpoint of unshared side
 %                            disp(['segment j=' int2str(j) ' unshared half edge from node ' int2str(elemp(ielem,nlast)) ' (node ' int2str(nlast) ') on side ' int2str(slast) ' from element ' int2str(ielem) ' written.'])
-                            kring.coords(end+1,:)=[(md.long(elemp(ielem,nlast))...
-                                                   +md.long(elemp(ielem,nnext)))/2. ...
-                                                   (md.lat(elemp(ielem,nlast))...
-                                                   +md.lat(elemp(ielem,nnext)))/2. alt];
+                            kring.coords(end+1,:)=[(md.mesh.long(elemp(ielem,nlast))...
+                                                   +md.mesh.long(elemp(ielem,nnext)))/2. ...
+                                                   (md.mesh.lat(elemp(ielem,nlast))...
+                                                   +md.mesh.lat(elemp(ielem,nnext)))/2. alt];
                             nlast=0;
 
@@ -406 +406 @@
 %  all different, so cut through centroid
 %                                disp(['element ielem=' int2str(ielem) ' centroid written.'])
-                                kring.coords(end+1,:)=[sum(md.long(elemp(ielem,:)))/3. ...
-                                                       sum(md.lat(elemp(ielem,:)))/3. alt];
+                                kring.coords(end+1,:)=[sum(md.mesh.long(elemp(ielem,:)))/3. ...
+                                                       sum(md.mesh.lat(elemp(ielem,:)))/3. alt];
                             end
 %  one node is in current partition, so cut off other two nodes
@@ -421 +421 @@
 %  write out midpoint of opposite side
 %                        disp(['segment j=' int2str(j) ' internal edge from side ' int2str(slast) ' to side ' int2str(snext) ' from element ' int2str(ielem) ' written.'])
-                        kring.coords(end+1,:)=[(md.long(elemp(ielem,snext))...
-                                               +md.long(elemp(ielem,mod(snext,3)+1)))/2. ...
-                                               (md.lat(elemp(ielem,snext))...
-                                               +md.lat(elemp(ielem,mod(snext,3)+1)))/2. alt];
+                        kring.coords(end+1,:)=[(md.mesh.long(elemp(ielem,snext))...
+                                               +md.mesh.long(elemp(ielem,mod(snext,3)+1)))/2. ...
+                                               (md.mesh.lat(elemp(ielem,snext))...
+                                               +md.mesh.lat(elemp(ielem,mod(snext,3)+1)))/2. alt];
                         elast=ielem;
                         nlast=0;
@@ -453 +453 @@
                             end
 %                            disp(['segment j=' int2str(j) ' unshared half edge on side ' int2str(slast) ' to node ' int2str(elemp(elast,nnext)) ' (node ' int2str(nnext) ') from element ' int2str(elast) ' written.'])
-                            kring.coords(end+1,:)=[md.long(elemp(elast,nnext)) ...
-                                                   md.lat(elemp(elast,nnext)) alt];
+                            kring.coords(end+1,:)=[md.mesh.long(elemp(elast,nnext)) ...
+                                                   md.mesh.lat(elemp(elast,nnext)) alt];
                             break
 %  if not unshared, advance perimeter list and watch for end

issm/trunk/src/m/kml/kml_unsh_edges.m

@@ -54 +54 @@
 end
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
     if     ~exist('latsgn','var')
         error(['Missing ''latsgn'' parameter to calculate missing lat/long data.']);
@@ -62 +62 @@
     else
         display('Converting x/y data to lat/long data.');
-        [md.lat,md.long]=xy2ll(md.x,md.y,latsgn);
+        [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,latsgn);
     end
 end
@@ -104 +104 @@
 
         for j=1:2
-            kline.coords(j,:)=[md.long(edgeuns(i,j)) md.lat(edgeuns(i,j)) alt];
+            kline.coords(j,:)=[md.mesh.long(edgeuns(i,j)) md.mesh.lat(edgeuns(i,j)) alt];
         end
 

issm/trunk/src/m/model/bamg.m

@@ -321 +321 @@
 md.elements=bamgmesh_out.Triangles(:,1:3);
 md.edges=bamgmesh_out.IssmEdges;
-md.segments=bamgmesh_out.IssmSegments(:,1:3);
-md.segmentmarkers=bamgmesh_out.IssmSegments(:,4);
+md.mesh.segments=bamgmesh_out.IssmSegments(:,1:3);
+md.mesh.segmentmarkers=bamgmesh_out.IssmSegments(:,4);
 
 %Fill in rest of fields:
@@ -334 +334 @@
 md.elementonbed=ones(md.numberofelements,1);
 md.elementonsurface=ones(md.numberofelements,1);
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 md.elementconnectivity=md.private.bamg.mesh.ElementConnectivity;
 md.elementconnectivity(find(isnan(md.elementconnectivity)))=0;

issm/trunk/src/m/model/collapse.m

@@ -83 +83 @@
 md.geometry.thickness=project2d(md,md.geometry.thickness,1);
 md.geometry.bed=project2d(md,md.geometry.bed,1);
-md.nodeonboundary=project2d(md,md.nodeonboundary,1);
+md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
 md.mask.elementonfloatingice=project2d(md,md.mask.elementonfloatingice,1);
 md.mask.vertexonfloatingice=project2d(md,md.mask.vertexonfloatingice,1);

issm/trunk/src/m/model/extrude.m

@@ -202 +202 @@
 md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
 md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'type','node');
-md.nodeonboundary=project3d(md,'vector',md.nodeonboundary,'type','node');
+md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');
 md.mask.elementonfloatingice=project3d(md,'vector',md.mask.elementonfloatingice,'type','element');
 md.mask.vertexonfloatingice=project3d(md,'vector',md.mask.vertexonfloatingice,'type','node');

issm/trunk/src/m/model/ismodelselfconsistent.m

@@ -151 +151 @@
                 message(['model not consistent: md.rifts should be a structure!']);
         end
-        if ~isempty(find(md.segmentmarkers>=2)),
+        if ~isempty(find(md.mesh.segmentmarkers>=2)),
                 %We have segments with rift markers, but no rift structure!
                 message(['model not consistent: model ' md.miscellaneous.name ' should be processed for rifts (run meshprocessrifts)!']);

issm/trunk/src/m/model/kmlimagesc.m

@@ -20 +20 @@
 fontsize=getfieldvalue(options,'fontsize',12);
 posting=getfieldvalue(options,'posting',.1);
-minlong=getfieldvalue(options,'minlong',min(md.long));
-maxlong=getfieldvalue(options,'maxlong',max(md.long));
-minlat=getfieldvalue(options,'minlat',min(md.lat));
-maxlat=getfieldvalue(options,'maxlat',max(md.lat));
+minlong=getfieldvalue(options,'minlong',min(md.mesh.long));
+maxlong=getfieldvalue(options,'maxlong',max(md.mesh.long));
+minlat=getfieldvalue(options,'minlat',min(md.mesh.lat));
+maxlat=getfieldvalue(options,'maxlat',max(md.mesh.lat));
 minfield=getfieldvalue(options,'minfield',min(field));
 maxfield=getfieldvalue(options,'maxfield',max(field));
 
 %do we have hemisphere setup?:
-if ~isstr(md.hemisphere),
-        error('md.hemisphere should be ''s'' or ''n''');
+if ~isstr(md.mesh.hemisphere),
+        error('md.mesh.hemisphere should be ''s'' or ''n''');
 end
 
-if strcmpi(md.hemisphere,'s'),
+if strcmpi(md.mesh.hemisphere,'s'),
         hemisphere=1;
         central_meridian=getfieldvalue(options,'central_meridian',45);
         standard_parallel=getfieldvalue(options,'standard_parallel',70);
-elseif strcmpi(md.hemisphere,'n'),
+elseif strcmpi(md.mesh.hemisphere,'n'),
         hemisphere=-1;
         central_meridian=getfieldvalue(options,'central_meridian',0);
         standard_parallel=getfieldvalue(options,'standard_parallel',71);
 else
-        error('md.hemisphere should be ''s'' or ''n''');
+        error('md.mesh.hemisphere should be ''s'' or ''n''');
 end
 
@@ -49 +49 @@
 
 %regrid to lat,long grid
-[x_m,y_m,field]=InterpFromMeshToGrid(md.elements,md.long,md.lat,field,minlong,maxlat,posting,posting,nlines,ncols,NaN);
+[x_m,y_m,field]=InterpFromMeshToGrid(md.elements,md.mesh.long,md.mesh.lat,field,minlong,maxlat,posting,posting,nlines,ncols,NaN);
 field=flipud(field);
 

issm/trunk/src/m/model/mesh/meshconvert.m

@@ -32 +32 @@
 md.elements=bamgmesh_out.Triangles(:,1:3);
 md.edges=bamgmesh_out.IssmEdges;
-md.segments=bamgmesh_out.IssmSegments(:,1:3);
-md.segmentmarkers=bamgmesh_out.IssmSegments(:,4);
+md.mesh.segments=bamgmesh_out.IssmSegments(:,1:3);
+md.mesh.segmentmarkers=bamgmesh_out.IssmSegments(:,4);
 
 %Fill in rest of fields:
@@ -45 +45 @@
 md.elementonbed=ones(md.numberofelements,1);
 md.elementonsurface=ones(md.numberofelements,1);
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;

issm/trunk/src/m/model/mesh/meshnodensity.m

@@ -25 +25 @@
 %Mesh using TriMeshNoDensity
 if strcmp(riftname,''),
-        [md.elements,md.x,md.y,md.segments,md.segmentmarkers]=TriMeshNoDensity(domainname);
+        [md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshNoDensity(domainname);
 else
         [elements,x,y,segments,segmentmarkers]=TriMeshNoDensity(domainname,riftname);
@@ -50 +50 @@
         md.y=y;
         md.elements=elements;
-        md.segments=segments;
-        md.segmentmarkers=segmentmarkers;
+        md.mesh.segments=segments;
+        md.mesh.segmentmarkers=segmentmarkers;
 end
 
@@ -58 +58 @@
 md.numberofnodes=length(md.x);
 md.z=zeros(md.numberofnodes,1);
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 md.nodeonbed=ones(md.numberofnodes,1);
 md.nodeonsurface=ones(md.numberofnodes,1);

issm/trunk/src/m/model/mesh/meshrefine.m

@@ -16 +16 @@
 
 %Refine using TriMeshRefine
-[md.elements,md.x,md.y,md.segments,md.segmentmarkers]=TriMeshRefine(md.elements,md.x,md.y,md.segments,md.segmentmarkers,areas,'yes');
+[md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMeshRefine(md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers,areas,'yes');
 
 %Fill in rest of fields:
@@ -22 +22 @@
 md.numberofnodes=length(md.x);
 md.z=zeros(md.numberofnodes,1);
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 md.nodeonbed=ones(md.numberofnodes,1);
 md.nodeonsurface=ones(md.numberofnodes,1);

issm/trunk/src/m/model/mesh/meshyams.m

@@ -97 +97 @@
                 md.nodeconnectivity=NodeConnectivity(md.elements,md.numberofnodes);
                 md.elementconnectivity=ElementConnectivity(md.elements,md.nodeconnectivity);
-                md.segments=findsegments(md);
+                md.mesh.segments=findsegments(md);
                 md=meshyamsrecreateriftsegments(md);
         end
@@ -110 +110 @@
 
 %recreate segments
-md.segments=findsegments(md);
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.segments=findsegments(md);
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 
 %Fill in rest of fields:

issm/trunk/src/m/model/mesh/reorder.m

@@ -21 +21 @@
 %update all fields
 md.elements=tnewnodes(md.elements(newelements,:));
-md.segments=[tnewnodes(md.segments(:,1)) tnewnodes(md.segments(:,2)) tnewelements(md.segments(:,3))];
+md.mesh.segments=[tnewnodes(md.mesh.segments(:,1)) tnewnodes(md.mesh.segments(:,2)) tnewelements(md.mesh.segments(:,3))];
 md.x=md.x(newnodes);
 md.y=md.y(newnodes);
 md.z=md.z(newnodes);
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;

issm/trunk/src/m/model/mesh/rifts/meshaddrifts.m

@@ -74 +74 @@
         end
         
-        md.segments(:,1:2)=nodeconv(md.segments(:,1:2));
-        md.segments(:,3)=elconv(md.segments(:,3));
+        md.mesh.segments(:,1:2)=nodeconv(md.mesh.segments(:,1:2));
+        md.mesh.segments(:,3)=elconv(md.mesh.segments(:,3));
 
 end
 
 %finish up "a la" mesh.h
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 md.nodeonbed=ones(md.numberofnodes,1);
 md.nodeonsurface=ones(md.numberofnodes,1);

issm/trunk/src/m/model/mesh/rifts/meshprocessoutsiderifts.m

@@ -68 +68 @@
 
                 %deal with segments
-                tipsegments=find((md.segments(:,1)==tip) | (md.segments(:,2)==tip));
+                tipsegments=find((md.mesh.segments(:,1)==tip) | (md.mesh.segments(:,2)==tip));
                 for  k=1:length(tipsegments),
                         segment_index=tipsegments(k);
-                        pos=find(md.segments(segment_index,1:2)~=tip);
-                        other_node=md.segments(segment_index,pos);
+                        pos=find(md.mesh.segments(segment_index,1:2)~=tip);
+                        other_node=md.mesh.segments(segment_index,pos);
                         if ~isconnected(md.elements,other_node,tip),
-                                pos=find(md.segments(segment_index,1:2)==tip);
-                                md.segments(segment_index,pos)=num;
+                                pos=find(md.mesh.segments(segment_index,1:2)==tip);
+                                md.mesh.segments(segment_index,pos)=num;
                         end
                 end
@@ -86 +86 @@
 md.numberofnodes=length(md.x);
 md.z=zeros(md.numberofnodes,1);
-md.nodeonboundary=zeros(length(md.x),1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(length(md.x),1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 md.rifts.numrifts=length(md.rifts.riftstruct);
 md.flowequation.element_equation=3*ones(md.numberofelements,1);

issm/trunk/src/m/model/mesh/rifts/meshprocessrifts.m

@@ -25 +25 @@
 
 %Call MEX file
-[md.elements,md.x,md.y,md.segments,md.segmentmarkers,md.rifts.riftstruct]=TriMeshProcessRifts(md.elements,md.x,md.y,md.segments,md.segmentmarkers);
+[md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers,md.rifts.riftstruct]=TriMeshProcessRifts(md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers);
 if ~isstruct(md.rifts.riftstruct),
         error('TriMeshProcessRifts did not find any rift');
@@ -34 +34 @@
 md.numberofnodes=length(md.x);
 md.z=zeros(md.numberofnodes,1);
-md.nodeonboundary=zeros(length(md.x),1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(length(md.x),1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 md.rifts.numrifts=length(md.rifts.riftstruct);
 md.flowequation.element_equation=3*ones(md.numberofelements,1);

issm/trunk/src/m/model/mesh/rifts/meshyamsrecreateriftsegments.m

@@ -11 +11 @@
 
                                 %find tip1 and tip2 for this rift, in the new mesh created by yams.
-                                pos=find_point(md.x(md.segments(:,1)),md.y(md.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2));
-                                tip1=md.segments(pos,1);
-                                pos=find_point(md.x(md.segments(:,1)),md.y(md.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2));
-                                tip2=md.segments(pos,1);
+                                pos=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2));
+                                tip1=md.mesh.segments(pos,1);
+                                pos=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2));
+                                tip2=md.mesh.segments(pos,1);
 
                                 %start from tip1, and build segments of this rift. 
-                                pos=find_point(md.x(md.segments(:,1)),md.y(md.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2));
+                                pos=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2));
                                 pos_record=[pos_record; pos];
-                                riftsegs=md.segments(pos,:);
+                                riftsegs=md.mesh.segments(pos,:);
                                 while 1,
                                         A=riftsegs(end,1); B=riftsegs(end,2); el=riftsegs(end,3);
                                         %find other segment that holds B.
-                                        pos=find(md.segments(:,1)==B);
+                                        pos=find(md.mesh.segments(:,1)==B);
                                         pos_record=[pos_record; pos];
-                                        riftsegs=[riftsegs; md.segments(pos,:)];
+                                        riftsegs=[riftsegs; md.mesh.segments(pos,:)];
                                         if riftsegs(end,2)==tip1, 
                                                 break;
@@ -39 +39 @@
 
                                 %find tip1 and tip2 for this rift, in the new mesh created by yams.
-                                pos1=find_point(md.x(md.segments(:,1)),md.y(md.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2));
-                                tip1=md.segments(pos1,1);
-                                pos2=find_point(md.x(md.segments(:,1)),md.y(md.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2));
-                                tip2=md.segments(pos2,1);
+                                pos1=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip1coordinates(1),rift.tip1coordinates(2));
+                                tip1=md.mesh.segments(pos1,1);
+                                pos2=find_point(md.x(md.mesh.segments(:,1)),md.y(md.mesh.segments(:,1)),rift.tip2coordinates(1),rift.tip2coordinates(2));
+                                tip2=md.mesh.segments(pos2,1);
                                 if length(tip1)==2,
                                         %swap.
@@ -53 +53 @@
 
                                 pos_record=[pos_record; pos];
-                                riftsegs=md.segments(pos,:);
+                                riftsegs=md.mesh.segments(pos,:);
                                 while 1,
                                         A=riftsegs(end,1); B=riftsegs(end,2); el=riftsegs(end,3);
                                         %find other segment that holds B.
-                                        pos=find(md.segments(:,1)==B);
+                                        pos=find(md.mesh.segments(:,1)==B);
                                         pos_record=[pos_record; pos];
-                                        riftsegs=[riftsegs; md.segments(pos,:)];
+                                        riftsegs=[riftsegs; md.mesh.segments(pos,:)];
                                         if ((riftsegs(end,2)==tip2(1)) | (riftsegs(end,2)==tip2(2))), 
                                                 %figure out which tip we reached
@@ -70 +70 @@
                                 pos=pos2(index);
                                 pos_record=[pos_record; pos];
-                                riftsegs=[riftsegs; md.segments(pos,:)];
+                                riftsegs=[riftsegs; md.mesh.segments(pos,:)];
                                 while 1,
                                         A=riftsegs(end,1); B=riftsegs(end,2); el=riftsegs(end,3);
                                         %find other segment that holds B.
-                                        pos=find(md.segments(:,1)==B);
+                                        pos=find(md.mesh.segments(:,1)==B);
                                         pos_record=[pos_record; pos];
-                                        riftsegs=[riftsegs; md.segments(pos,:)];
+                                        riftsegs=[riftsegs; md.mesh.segments(pos,:)];
                                         if riftsegs(end,2)==tip1, 
                                                 break;
@@ -88 +88 @@
         end
         %take out rift segments from segments
-        md.segments(pos_record,:)=[];
+        md.mesh.segments(pos_record,:)=[];

issm/trunk/src/m/model/mesh/setmesh.m

@@ -39 +39 @@
 %Mesh using TriMesh
 if strcmp(riftname,''),
-        [md.elements,md.x,md.y,md.segments,md.segmentmarkers]=TriMesh(domainname,area,'yes');
+        [md.elements,md.x,md.y,md.mesh.segments,md.mesh.segmentmarkers]=TriMesh(domainname,area,'yes');
 else
         [elements,x,y,segments,segmentmarkers]=TriMesh(domainname,riftname,area,'yes');
@@ -64 +64 @@
         md.y=y;
         md.elements=elements;
-        md.segments=segments;
-        md.segmentmarkers=segmentmarkers;
+        md.mesh.segments=segments;
+        md.mesh.segmentmarkers=segmentmarkers;
 end
 
@@ -72 +72 @@
 md.numberofnodes=length(md.x);
 md.z=zeros(md.numberofnodes,1);
-md.nodeonboundary=zeros(md.numberofnodes,1); md.nodeonboundary(md.segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1); md.mesh.vertexonboundary(md.mesh.segments(:,1:2))=1;
 md.nodeonbed=ones(md.numberofnodes,1);
 md.nodeonsurface=ones(md.numberofnodes,1);

issm/trunk/src/m/model/modelextract.m

@@ -206 +206 @@
                 md2.elementconnectivity=ElementConnectivity(md2.elements,md2.nodeconnectivity);
                 md2.segments=contourenvelope(md2);
-                md2.nodeonboundary=zeros(numberofnodes2,1); md2.nodeonboundary(md2.segments(:,1:2))=1;
+                md2.mesh.vertexonboundary=zeros(numberofnodes2,1); md2.nodeonboundary(md2.segments(:,1:2))=1;
         end
 

issm/trunk/src/m/model/outflow.m

@@ -5 +5 @@
 %      flag=outflow(md);
 
-A=md.segments(:,1);
-B=md.segments(:,2);
+A=md.mesh.segments(:,1);
+B=md.mesh.segments(:,2);
 Nx=-(md.y(A)-md.y(B));
 Ny=  md.x(A)-md.x(B);

issm/trunk/src/m/model/plot/applyoptions.m

@@ -9 +9 @@
 
 %some defaults
-if strcmpi(md.hemisphere,'n'), options=addfielddefault(options,'hemisphere','n'); 
-elseif strcmpi(md.hemisphere,'s'), options=addfielddefault(options,'hemisphere','s'); 
+if strcmpi(md.mesh.hemisphere,'n'), options=addfielddefault(options,'hemisphere','n'); 
+elseif strcmpi(md.mesh.hemisphere,'s'), options=addfielddefault(options,'hemisphere','s'); 
 end
 
@@ -410 +410 @@
         axis equal off
         %box off
-        if strcmpi(md.hemisphere,'n') | strcmpi(md.hemisphere,'north'),
+        if strcmpi(md.mesh.hemisphere,'n') | strcmpi(md.mesh.hemisphere,'north'),
                 A=expread([ issmdir() '/projects/Exp/GreenlandBoxFront.exp']);
                 [A.x A.y]=ll2xy(A.x,A.y,+1,45,70);
-        elseif strcmpi(md.hemisphere,'s') | strcmpi(md.hemisphere,'south'),
+        elseif strcmpi(md.mesh.hemisphere,'s') | strcmpi(md.mesh.hemisphere,'south'),
                 A=expread([ issmdir() '/projects/Exp/Antarctica.exp']);
         else

issm/trunk/src/m/model/plot/kmlgroundoverlay.m

@@ -12 +12 @@
 
 %first figure out if lat and long were computed!
-if (isempty(md.lat) | isempty(md.long)),
+if (isempty(md.mesh.lat) | isempty(md.mesh.long)),
         error('kmlgroundoverlay error message: project x,y onto lat,long fields of model!');
 end
@@ -28 +28 @@
 
 %figure out  min and max for lat and long of this image:
-west=min(md.long);
-east=max(md.long);
-south=min(md.lat);
-north=max(md.lat);
+west=min(md.mesh.long);
+east=max(md.mesh.long);
+south=min(md.mesh.lat);
+north=max(md.mesh.lat);
 
 %print image at high resolution

issm/trunk/src/m/model/plot/latlonoverlay.m

@@ -66 +66 @@
         latitudes =lat*ones(size(longitudes));
 
-        if strcmpi(md.hemisphere,'n'),
+        if strcmpi(md.mesh.hemisphere,'n'),
                 if lat<0, continue; end
                 [x,y]=ll2xy(latitudes,longitudes,+1,45,70);
-        elseif strcmpi(md.hemisphere,'s'),
+        elseif strcmpi(md.mesh.hemisphere,'s'),
                 if lat>0, continue; end
                 [x,y]=ll2xy(latitudes,longitudes,-1, 0,71);
@@ -105 +105 @@
 for lon=-180:lonstep:180
 
-        if strcmpi(md.hemisphere,'n'),
+        if strcmpi(md.mesh.hemisphere,'n'),
                 latitudes =0:resolution:90;
                 longitudes=lon*ones(size(latitudes));
                 [x,y]=ll2xy(latitudes,longitudes,+1,45,70);
-        elseif strcmpi(md.hemisphere,'s'),
+        elseif strcmpi(md.mesh.hemisphere,'s'),
                 latitudes =-90:resolution:0;
                 longitudes=lon*ones(size(latitudes));

issm/trunk/src/m/model/plot/plot_boundaries.m

@@ -15 +15 @@
 [x y z elements is2d isplanet]=processmesh(md,[],options);
 
-for i=1:size(md.segments,1),
-        plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'k.-');hold on;
+for i=1:size(md.mesh.segments,1),
+        plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'k.-');hold on;
 end
 

issm/trunk/src/m/model/plot/plot_riftfraction.m

@@ -19 +19 @@
 
 %plot mesh boundaries
-for i=1:size(md.segments,1),
-        h1=plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'k.-');
+for i=1:size(md.mesh.segments,1),
+        h1=plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'k.-');
 end
 

issm/trunk/src/m/model/plot/plot_riftnumbering.m

@@ -15 +15 @@
 
 %plot mesh boundaries
-for i=1:size(md.segments,1),
-        plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'k.-');
+for i=1:size(md.mesh.segments,1),
+        plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'k.-');
 end
 
@@ -24 +24 @@
 if isstruct(md.rifts.riftstruct),
         %plot mesh boundaries
-        for i=1:size(md.segments,1),
-                h1=plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'b-');
+        for i=1:size(md.mesh.segments,1),
+                h1=plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'b-');
         end
         for i=1:size(md.rifts.riftstruct,1),

issm/trunk/src/m/model/plot/plot_riftpenetration.m

@@ -14 +14 @@
 
 %plot mesh boundaries
-for i=1:size(md.segments,1),
-        plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'k-');
+for i=1:size(md.mesh.segments,1),
+        plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'k-');
 end
 
@@ -23 +23 @@
 if isstruct(md.rifts.riftstruct),
         %plot mesh boundaries
-        for i=1:size(md.segments,1),
-                h1=plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'b-');
+        for i=1:size(md.mesh.segments,1),
+                h1=plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'b-');
         end
         for i=1:size(md.rifts.riftstruct,1),

issm/trunk/src/m/model/plot/plot_riftrelvel.m

@@ -39 +39 @@
 
 %plot mesh boundaries
-for i=1:size(md.segments,1),
-        plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'k-');
+for i=1:size(md.mesh.segments,1),
+        plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'k-');
 end
 
@@ -59 +59 @@
 
 %plot mesh boundaries
-for i=1:size(md.segments,1),
-        h1=plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'b-');
+for i=1:size(md.mesh.segments,1),
+        h1=plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'b-');
 end
 for i=1:md.rifts.numrifts,

issm/trunk/src/m/model/plot/plot_riftvel.m

@@ -35 +35 @@
 
 %plot mesh boundaries
-for i=1:size(md.segments,1),
-        plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'k.-');
+for i=1:size(md.mesh.segments,1),
+        plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'k.-');
 end
 
@@ -53 +53 @@
 
 %plot mesh boundaries
-for i=1:size(md.segments,1),
-        h1=plot(x(md.segments(i,1:2)),y(md.segments(i,1:2)),'b-');
+for i=1:size(md.mesh.segments,1),
+        h1=plot(x(md.mesh.segments(i,1:2)),y(md.mesh.segments(i,1:2)),'b-');
 end
 

issm/trunk/src/m/model/plot/plot_segments.m

@@ -12 +12 @@
 %process mesh and data
 [x y z elements is2d isplanet]=processmesh(md,[],options);
-segments=md.segments;
+segments=md.mesh.segments;
 
 if (md.dim==2),
@@ -27 +27 @@
         if strcmpi(getfieldvalue(options,'segmentnumbering','off'),'on'),
                 text(sum(x(segments(:,1:2)),2)/2,sum(y(segments(:,1:2)),2)/2,sum(z(segments(:,1:2)),2)/2+1,...
-                        num2str(md.segmentmarkers),...
+                        num2str(md.mesh.segmentmarkers),...
                         'backgroundcolor',[0.8 0.9 0.8],'HorizontalAlignment','center','VerticalAlignment','middle');
         end

issm/trunk/src/m/model/plot/processmesh.m

@@ -21 +21 @@
                 y2d=md.y2d;
         else
-                x=md.long;
+                x=md.mesh.long;
                 x2d=md.x2d;
-                y=md.lat;
+                y=md.mesh.lat;
                 y2d=md.y2d;
         end

issm/trunk/src/m/model/plot/showregion.m

@@ -15 +15 @@
 axis equal off
 %box off
-if strcmpi(md.hemisphere,'n') | strcmpi(md.hemisphere,'north'),
+if strcmpi(md.mesh.hemisphere,'n') | strcmpi(md.mesh.hemisphere,'north'),
         A=expread([issmdir() 'projects/Exp/Greenland.exp']);
-elseif strcmpi(md.hemisphere,'s') | strcmpi(md.hemisphere,'south'),
+elseif strcmpi(md.mesh.hemisphere,'s') | strcmpi(md.mesh.hemisphere,'south'),
         A=expread([issmdir() '/projects/Exp/Antarctica.exp']);
 else

issm/trunk/src/m/model/radarpower.m

@@ -29 +29 @@
 %figure out if we should go look for Greenland or Antarctica geotiff, or if user provided one.
 if ~exist(options,'overlay_image'),
-        if strcmpi(md.hemisphere,'n'),
+        if strcmpi(md.mesh.hemisphere,'n'),
                 if ~exist([issmdir() '/projects/ModelData/MOG/mog150_greenland_map.jpg']),
                         error(['radarpower error message: file ' issmdir() '/projects/ModelData/MOG/mog150_greenland_map.jpg not found.']);
@@ -56 +56 @@
                 md.radaroverlay.y=(ymin:(ymax-ymin)/(size(md.radaroverlay.pwr,1)-1):ymax);
 
-        elseif strcmpi(md.hemisphere,'s'),
+        elseif strcmpi(md.mesh.hemisphere,'s'),
                 if highres,
                         if ~exist([issmdir() '/projects/ModelData/MosaicTiffRsat/amm125m_v2_200m.tif']),

issm/trunk/src/m/model/setmask2.m

@@ -120 +120 @@
 
 %call findsegments to build segment using THIS conectivity
-md.segments=findsegments(md,'elementconnectivity',elementconnectivity);
+md.mesh.segments=findsegments(md,'elementconnectivity',elementconnectivity);
 
 %some final checks: 
@@ -146 +146 @@
 md.mask.elementongroundedice=elementongroundedice;
 
-md.segmentmarkers(:)=1;
+md.mesh.segmentmarkers(:)=1;

issm/trunk/src/m/solutions/flaim.m

@@ -50 +50 @@
 %  calculate latitude and longitude, if necessary 
 
-if isempty(md.lat)  || ((numel(md.lat) == 1)  && isnan(md.lat)) || ...
-   isempty(md.long) || ((numel(md.long) == 1) && isnan(md.long))
+if isempty(md.mesh.lat)  || ((numel(md.mesh.lat) == 1)  && isnan(md.mesh.lat)) || ...
+   isempty(md.mesh.long) || ((numel(md.mesh.long) == 1) && isnan(md.mesh.long))
         if     ~isfield(options,'latsgn')
                 error(['Missing ''latsgn'' parameter to calculate missing lat/long values.']);
@@ -58 +58 @@
         else
                 display('Converting x/y values to lat/long values.');
-                [md.lat,md.long]=xy2ll(md.x,md.y,options.latsgn);
+                [md.mesh.lat,md.mesh.long]=xy2ll(md.x,md.y,options.latsgn);
         end
 end
@@ -80 +80 @@
 
 display('Calling KMLMeshWrite.');
-KMLMeshWrite(md.miscellaneous.name,md.miscellaneous.notes,md.elements,md.nodeconnectivity,md.lat,md.long,md.qmu.partition,md.flaim.criterion,options.cmap,filekml);
+KMLMeshWrite(md.miscellaneous.name,md.miscellaneous.notes,md.elements,md.nodeconnectivity,md.mesh.lat,md.mesh.long,md.qmu.partition,md.flaim.criterion,options.cmap,filekml);
 %  for testing
 %filekml='issm-split-geikie1-targets.kml';

issm/trunk/src/m/utils/BC/SetIceSheetBC.m

@@ -8 +8 @@
 
 %node on Dirichlet
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
 md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);

issm/trunk/src/m/utils/BC/SetIceShelfBC.m

@@ -20 +20 @@
         if ~exist(icefrontfile), error(['SetIceShelfBC error message: ice front file ' icefrontfile ' not found']); end
         nodeinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2);
-        nodeonicefront=double(md.nodeonboundary & nodeinsideicefront);
+        nodeonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront);
 elseif nargin==1,
         nodeonicefront=zeros(md.numberofnodes,1);
@@ -27 +27 @@
         error('bad usage');
 end
-pos=find(md.nodeonboundary & ~nodeonicefront);
+pos=find(md.mesh.vertexonboundary & ~nodeonicefront);
 md.diagnostic.spcvx=NaN*ones(md.numberofnodes,1);
 md.diagnostic.spcvy=NaN*ones(md.numberofnodes,1);
@@ -47 +47 @@
 %segment on Ice Front
 %segment on Neumann (Ice Front)
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2)));
+pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2)));
 if (md.dim==2)
-        pressureload=md.segments(pos,:);
+        pressureload=md.mesh.segments(pos,:);
 elseif md.dim==3
-        pressureload_layer1=[md.segments(pos,1:2)  md.segments(pos,2)+md.numberofnodes2d  md.segments(pos,1)+md.numberofnodes2d  md.segments(pos,3)];
+        pressureload_layer1=[md.mesh.segments(pos,1:2)  md.mesh.segments(pos,2)+md.numberofnodes2d  md.mesh.segments(pos,1)+md.numberofnodes2d  md.mesh.segments(pos,3)];
         pressureload=[];
         for i=1:md.numlayers-1,

issm/trunk/src/m/utils/BC/SetMarineIceSheetBC.m

@@ -24 +24 @@
         end
         nodeinsideicefront=ContourToMesh(md.elements,md.x,md.y,icefrontfile,'node',2);
-        vertexonicefront=double(md.nodeonboundary & nodeinsideicefront);
+        vertexonicefront=double(md.mesh.vertexonboundary & nodeinsideicefront);
 else
         %Guess where the ice front is
         vertexonfloatingice=zeros(md.numberofnodes,1);
         vertexonfloatingice(md.elements(find(md.mask.elementonfloatingice),:))=1;
-        vertexonicefront=double(md.nodeonboundary & vertexonfloatingice);
+        vertexonicefront=double(md.mesh.vertexonboundary & vertexonfloatingice);
 end
-pos=find(md.nodeonboundary & ~vertexonicefront);
+pos=find(md.mesh.vertexonboundary & ~vertexonicefront);
 if isempty(pos),
         warning('SetMarineIceSheetBC warning: ice front all around the glacier, no dirichlet found. Dirichlet must be added manually')
@@ -53 +53 @@
 
 md.hydrology.spcwatercolumn=zeros(md.numberofnodes,2);
-pos=find(md.nodeonboundary); 
+pos=find(md.mesh.vertexonboundary); 
 md.hydrology.spcwatercolumn(pos,1)=1;
 
 %segment on Neumann (Ice Front)
-pos=find(vertexonicefront(md.segments(:,1)) | vertexonicefront(md.segments(:,2)));
+pos=find(vertexonicefront(md.mesh.segments(:,1)) | vertexonicefront(md.mesh.segments(:,2)));
 if (md.dim==2)
-        pressureload=md.segments(pos,:);
+        pressureload=md.mesh.segments(pos,:);
 elseif md.dim==3
-        pressureload_layer1=[md.segments(pos,1:2)  md.segments(pos,2)+md.numberofnodes2d  md.segments(pos,1)+md.numberofnodes2d  md.segments(pos,3)];
+        pressureload_layer1=[md.mesh.segments(pos,1:2)  md.mesh.segments(pos,2)+md.numberofnodes2d  md.mesh.segments(pos,1)+md.numberofnodes2d  md.mesh.segments(pos,3)];
         pressureload=[];
         for i=1:md.numlayers-1,

issm/trunk/src/m/utils/Mesh/argusmesh.m

@@ -91 +91 @@
 
 %Add segments and nodes on boundary
-md.segments=findsegments(md);
-md.nodeonboundary=zeros(md.numberofnodes,1);
-md.nodeonboundary(md.segments(:,1))=1;
-md.nodeonboundary(md.segments(:,2))=1;
+md.mesh.segments=findsegments(md);
+md.mesh.vertexonboundary=zeros(md.numberofnodes,1);
+md.mesh.vertexonboundary(md.mesh.segments(:,1))=1;
+md.mesh.vertexonboundary(md.mesh.segments(:,2))=1;

issm/trunk/src/m/utils/Mesh/squaremesh.m

@@ -60 +60 @@
 md.z=zeros(nods,1);
 md.numberofnodes=nods;
-md.nodeonboundary=zeros(nods,1);md.nodeonboundary(segments(:,1:2))=1;
+md.mesh.vertexonboundary=zeros(nods,1);md.mesh.vertexonboundary(segments(:,1:2))=1;
 md.nodeonbed=ones(nods,1);
 md.nodeonsurface=ones(nods,1);
@@ -66 +66 @@
 %plug elements
 md.elements=index;
-md.segments=segments;
+md.mesh.segments=segments;
 md.numberofelements=nel;
 md.elementonbed=ones(nel,1);

issm/trunk/template

@@ -2 +2 @@
 
         projection
-                lat
-                long
-                hemisphere
-
           x
           y
@@ -34 +30 @@
           nodeconnectivity
           elementconnectivity
-          connectivity -> rename average_vertex_connectivity
-
-          segments
-          segmentmarkers
-          nodeonboundary
-
-          extractednodes
-          extractedelements
 }}}
 

issm/trunk/test/NightlyRun/test131.m

@@ -3 +3 @@
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 %Add boundary conditions on thickness on the border
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
 md=setflowequation(md,'macayeal','all');

issm/trunk/test/NightlyRun/test132.m

@@ -3 +3 @@
 md=parameterize(md,'../Par/SquareShelfConstrained.par');
 %Add boundary conditions on thickness on the border
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
 md=setflowequation(md,'macayeal','all');

issm/trunk/test/NightlyRun/test133.m

@@ -4 +4 @@
 md=extrude(md,5,1);
 %Add boundary conditions on thickness on the border
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
 md=setflowequation(md,'macayeal','all');

issm/trunk/test/NightlyRun/test134.m

@@ -4 +4 @@
 md=extrude(md,5,1);
 %Add boundary conditions on thickness on the border
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
 md=setflowequation(md,'macayeal','all');

issm/trunk/test/NightlyRun/test233.m

@@ -54 +54 @@
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:);
 diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
 md.diagnostic.icefront=diagnostic.icefront;

issm/trunk/test/NightlyRun/test234.m

@@ -54 +54 @@
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:);
 diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
 md.diagnostic.icefront=diagnostic.icefront;

issm/trunk/test/NightlyRun/test235.m

@@ -51 +51 @@
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:);
 diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
 md.diagnostic.icefront=diagnostic.icefront;

issm/trunk/test/NightlyRun/test236.m

@@ -51 +51 @@
 nodeonicefront=zeros(md.numberofnodes,1);
 pos=find(md.y==ymax); nodeonicefront(pos)=1;
-pos=find(nodeonicefront(md.segments(:,1)) | nodeonicefront(md.segments(:,2))); diagnostic.icefront=md.segments(pos,:);
+pos=find(nodeonicefront(md.mesh.segments(:,1)) | nodeonicefront(md.mesh.segments(:,2))); diagnostic.icefront=md.mesh.segments(pos,:);
 diagnostic.icefront=[diagnostic.icefront 1*md.mask.elementonfloatingice(diagnostic.icefront(:,end))];
 md.diagnostic.icefront=diagnostic.icefront;

issm/trunk/test/NightlyRun/test527.m

@@ -28 +28 @@
 %refine existing mesh 3
 hVertices=NaN*ones(md.numberofnodes,1);
-hVertices(find(md.nodeonboundary))=500;
+hVertices(find(md.mesh.vertexonboundary))=500;
 md2=bamg(md,'metric',md.miscellaneous.dummy,'hmin',1000,'hmax',20000,'gradation',3,'geometricalmetric',1,'anisomax',1,'hVertices',hVertices);
 x5=md2.x;

issm/trunk/test/NightlyRun/test625.m

@@ -7 +7 @@
 %Ice sheet only
 md=modelextract(md,md.mask.elementongroundedice);
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
 

issm/trunk/test/NightlyRun/test626.m

@@ -7 +7 @@
 %Ice sheet only
 md=modelextract(md,md.mask.elementongroundedice);
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
 

issm/trunk/test/Par/79North.par

@@ -44 +44 @@
 %Boundary conditions:
 md=SetMarineIceSheetBC(md);
-pos=find(md.nodeonboundary);
+pos=find(md.mesh.vertexonboundary);
 md.balancethickness.spcthickness(pos)=md.geometry.thickness(pos);
 md.prognostic.spcthickness(pos)=md.geometry.thickness(pos);

issm/trunk/test/Par/RoundSheetShelf.par

@@ -83 +83 @@
 md.diagnostic.spcvy(pos)=0;
 
-pressureload=md.segments;
+pressureload=md.mesh.segments;
 pressureload=[pressureload 1*md.mask.elementonfloatingice(pressureload(:,end)) + 0*md.mask.elementongroundedice(pressureload(:,end))];
 md.diagnostic.icefront=pressureload;