Index: /issm/trunk-jpl/src/m/miscellaneous/diagnostics.m
===================================================================
--- /issm/trunk-jpl/src/m/miscellaneous/diagnostics.m	(revision 21447)
+++ /issm/trunk-jpl/src/m/miscellaneous/diagnostics.m	(revision 21447)
@@ -0,0 +1,49 @@
+function diagnostics(md,varargin) 
+%DIAGNOSTICS: output all sort of information as shape files.
+
+	%process options: 
+	options=pairoptions(varargin{:});
+	path=getfieldvalue(options,'path','./');
+
+	%mesh:
+	if getfieldvalue(options,'mesh',0),
+		mesh2shp(md,[path '/mesh']);
+	end
+
+	%grounding line : 
+	if getfieldvalue(options,'gl',0),
+		contours=contourlevelzero(md,md.mask.groundedice_levelset,0);
+		expwrite(contours,[path '/groundingline.exp']);
+		exp2shp([path '/groundingline.shp'],[path '/groundingline.exp']);
+	end
+
+	%velocity: 
+	if exist(options,'vel'),
+		vel=getfieldvalue(options,'vel',md.initialization.vel);
+		xposting=getfieldvalue(options,'velposting',500);
+		yposting=getfieldvalue(options,'velposting',500);
+
+		xmin=min(md.mesh.x); ymax=max(md.mesh.y); 
+		ncols=(max(md.mesh.x)-min(md.mesh.x))/xposting+1;
+		nlines=(max(md.mesh.y)-min(md.mesh.y))/yposting+1;
+		
+		[xm,ym,vel]=InterpFromMeshToGrid(md.mesh.elements,md.mesh.x,md.mesh.y,vel,xmin,ymax,xposting,yposting,nlines,ncols,0);
+		vel=uint16(flipud(vel));
+
+		imwrite(vel,[path '/vel.tif'],'tiff');
+
+		string=sprintf('!gdal_translate -a_srs EPSG:3031 -a_ullr %g %g %g %g %s/vel.tif %s/velg.tif',...
+		min(md.mesh.x),max(md.mesh.y),max(md.mesh.x),min(md.mesh.y),path,path);
+		eval(string);
+
+	end
+
+	%hot spots: 
+	if getfieldvalue(options,'hotspots',0),
+		threshold=getfieldvalue(options,'threshold',5000);
+		i=getfieldvalue(options,'hotspotsi',length(md.results.TransientSolution));
+		pos=find(md.results.TransientSolution(i).Vel>threshold);
+		contour.x=md.mesh.x(pos); contour.y=md.mesh.y(pos); contour.density=1;
+		expwrite(contour,[path '/hotspots.exp']);
+		exp2shp([path '/hotspots.shp'],[path '/hotspots.exp']);
+	end