Index: /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.m
===================================================================
--- /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.m	(revision 19055)
+++ /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.m	(revision 19055)
@@ -0,0 +1,151 @@
+
+function export_netCDF(md,filename)	
+	
+%Now going on Real treatment
+	if exist(filename),
+		disp(sprintf('File %s allready exist', filename));
+		prompt = 'Give a new name or "delete" to replace: ';
+		newname = input(prompt,'s');
+		if strcmp(newname,'delete')
+			delete(filename)
+		else
+			disp(sprintf('New file name is %s ', newname));
+			filename=newname
+	  end
+  end
+	%open file and write description
+	mode = netcdf.getConstant('NETCDF4');
+	mode = bitor(mode,netcdf.getConstant('NOCLOBBER'));%NOCLOBBER to avoid overwrite
+	ncid = netcdf.create(filename,mode);
+	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Title',['Results for run ' md.miscellaneous.name]);
+	netcdf.putAtt(ncid,netcdf.getConstant('NC_GLOBAL'),'Date',['Created ' datestr(now)]);
+	
+	%gather geometry and timestepping as dimensions
+	Duration=md.timestepping.final_time-md.timestepping.start_time;
+	if Duration>0 && md.timestepping.time_step*md.settings.output_frequency>0,
+		StepNum=Duration/(md.timestepping.time_step*md.settings.output_frequency);
+	else
+		StepNum=1;
+  end							
+ 
+	%define netcdf dimensions
+	DimSize(1).index=netcdf.defDim(ncid,'EltNum',md.mesh.numberofelements);
+	DimSize(2).index=netcdf.defDim(ncid,'VertNum',md.mesh.numberofvertices);
+	DimSize(3).index=netcdf.defDim(ncid,'VertperElt',size(md.mesh.elements,2));
+	
+	for i=1:length(DimSize),
+		[DimSize(i).name,DimSize(i).value]=netcdf.inqDim(ncid,DimSize(i).index);
+		DimValue(i)=DimSize(i).value;% putting vallues in an array for
+                                 % further use
+  end
+ 
+	%Needs a first turn arround for var def
+ 
+	%get all model classes and create respective groups
+	groups=fieldnames(md);
+	for i=1:length(groups),
+		%disp(sprintf('group name in tree %s ',groups{i}));
+		groupID=netcdf.defGrp(ncid,groups{i});
+		%In each group gather the fields of the class
+		groupfields=fields(md.(groups{i}));
+		%Special treatment for the results
+		if strcmp(groups(i),'results'),
+			for j=1:length(groupfields)%looping on the different solutions
+				%disp(sprintf('=====Field name in tree %s ',groupfields{j}));
+				if length(md.results.(groupfields{j}))>1,
+					%the solution have several timestep get last timesteps and output frequency
+					last_step = length(md.results.(groupfields{j}));
+					step_freq = md.settings.output_frequency;
+					%grab first time step
+					subfields=fields(md.results.(groupfields{j})(1));
+					for k=1:length(subfields),
+						netcdf.putAtt(groupID,netcdf.getConstant('NC_GLOBAL'),'classtype','results');
+						if ~strcmp(subfields(k),'errlog') && ~strcmp(subfields(k),'outlog') && ~strcmp(subfields(k),'SolutionType'),
+							disp(sprintf('==========SubField name in tree %s ',subfields{k}));
+							Var=md.results.(groupfields{1})(1).(subfields{k});
+							[truc,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,subfields{k},DimSize,DimValue);
+							%CreateVar(Var,True,last_step,step_freq)
+			      end
+		      end
+				elseif length(md.results.(groupfields{j}))==1,
+					%only one timestep
+					subfields=fields(md.results.(groupfields{j}));
+					for k=1:length(subfields),
+						disp(sprintf('==========SubField name in tree %s ',subfields{k}));
+						netcdf.putAtt(groupID,netcdf.getConstant('GLOBAL'),'classtype','results');
+						if ~strcmp(subfields(k),'errlog') && ~strcmp(subfields(k),'outlog') && ~strcmp(subfields(k),'SolutionType'),
+							Var=md.results.(groupfields{1})(1).(subfields{k});
+							[truc,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,subfields{k},DimSize,DimValue);
+			      end
+		      end
+				else
+					print 'Result format not suported'
+		    end
+	    end
+		else
+			for j=1:length(groupfields),
+				disp(sprintf('=====Field name in tree %s ',groupfields{j}));
+				netcdf.putAtt(groupID,netcdf.getConstant('GLOBAL'),'classtype',class(md.(groups{i})));
+				Var=md.(groups{i}).(groupfields{j});
+				[truc,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,groupfields{j},DimSize,DimValue);
+	    end
+	  end	
+  end
+	netcdf.close(ncid);
+end
+
+function [varclass,DimSize,DimValue]=DefCreateVar(ncid,Var,groupID,field,DimSize,DimValue)
+	varclass=class(Var);
+	varsize=size(Var);
+	varlength=length(Var);
+	if isa(Var,'logical'),
+		if Var,
+			LogicString='True';
+		else,
+			LogicString='False';
+  	end
+		netcdf.putAtt(groupID,netcdf.getConstant('GLOBAL'),field,LogicString);
+	elseif isa(Var,'char'),
+		netcdf.putAtt(groupID,netcdf.getConstant('GLOBAL'),field,Var);
+	elseif isa(Var,'double'), %dealing with arrays
+		[dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue);
+ 		varid = netcdf.defVar(groupID,field,'double',dims);
+		if length(Var)==0,
+			netcdf.putVar(groupID,varid,NaN);
+		else
+			netcdf.putVar(groupID,varid,Var);
+  	end
+	elseif isa(Var,'cell'),
+		disp(sprintf('no support for class %s for field %s so far',varclass,field));
+	elseif isa(Var,'struct'),
+		disp(sprintf('no support for class %s for field %s so far',varclass,field));
+	else
+		disp(sprintf('no support for class %s of field %s',varclass,field));
+  end
+	return
+end
+
+function [dims,DimSize,DimValue]=GetDims(ncid,Var,groupID,field,DimSize,DimValue)
+	dims=[];
+	varlength=length(Var);
+	varsize=size(Var);
+	MatOrVec=varsize>1; %checking if we have a matrix (1 1) are vector (1 0)
+	for i=1:sum(MatOrVec), %loop on the number of (non 1) dimensions
+		currentdim=varsize(i);
+		dimexist=DimValue==currentdim;
+		if sum(dimexist)==0, %dimension is new to us, need to create it
+			dimname=strcat(field,int2str(i));
+			dimindex=length(DimSize)+1;
+			DimSize(dimindex).index=netcdf.defDim(ncid,dimname,currentdim);
+			[DimSize(dimindex).name,DimSize(dimindex).value]=netcdf.inqDim(ncid,DimSize(dimindex).index);
+			dims(i)=DimSize(dimindex).index;
+			DimValue(dimindex)=currentdim;
+		else
+			dimindex=find(dimexist);
+			if DimSize(dimindex).value~=currentdim,
+				error('Indexation problem with the dimension structure')
+  	  end
+	  end
+		dims(i)=DimSize(dimindex).index;
+  end
+end
Index: /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.py
===================================================================
--- /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.py	(revision 19054)
+++ /issm/trunk-jpl/src/m/contrib/netCDF/export_netCDF.py	(revision 19055)
@@ -14,14 +14,14 @@
 	def GetDim(var,shape,i,istime):
 		output=[]
-		for dim in range(0,i):
-			if type(shape[0])==int:
+		for dim in range(0,i): #loop on the dimensions
+			if type(shape[0])==int: 
 				try:
-					output=output+[str(DimDict[shape[dim]])]
-				except KeyError:
+					output=output+[str(DimDict[shape[dim]])] #test if the dimension allready exist
+				except KeyError: #if not create it
 					if (shape[dim])>1:
-						NewDim=NCData.createDimension(str(field),(shape[dim]))
-						DimDict[len(NewDim)]=str(field)
+						NewDim=NCData.createDimension(str(field)+str(dim),(shape[dim]))
+						DimDict[len(NewDim)]=str(field)+str(dim)
 						output=output+[str(DimDict[shape[dim]])]
-						print 'Defining dimension ' +str(shape[dim]) +' for '+str(field)
+						print 'Defining dimension ' +str(shape[dim]) +' for '+str(field)+str(dim)
 			elif type(shape[0])==str:#dealling with a dictionnary
 				try:
@@ -129,24 +129,8 @@
 	VertNum=NCData.createDimension('VertNum',md.mesh.numberofvertices)
 	VertperElt=NCData.createDimension('VertperElt',numpy.shape(md.mesh.elements)[1])
-	if type(md.mesh) is mesh2d:
-		DimNum=NCData.createDimension('DimNum',2)
-	elif type(md.mesh) is mesh3dprisms:
-		DimNum=NCData.createDimension('DimNum',3)
-	else:
-		print 'I can not get the Dimension of the problem'
-	EdgeNum=NCData.createDimension('EdgeNum',md.mesh.numberofedges)
-	Time=NCData.createDimension('Time',StepNum)
-	SegNum=NCData.createDimension('SegNum',numpy.shape(md.mesh.segmentmarkers)[0])
-	InvSteps=NCData.createDimension('InvSteps',md.inversion.nsteps)
-	DictDim=NCData.createDimension('DictDim',2)
 
 	DimDict = {len(EltNum):'EltNum',
 						 len(VertNum):'VertNum',
-						 len(VertperElt):'VertperElt',
-						 len(DimNum):'DimNum',
-						 len(EdgeNum):'EdgeNum',
-						 len(Time):'Time',
-						 len(SegNum):'SegNum',
-						 len(InvSteps):'InvSteps'}
+						 len(VertperElt):'VertperElt'}
 
 	TypeDict = {float:'f8',