%MODEL class definition
%
%   Usage:
%      md = model(varargin)

classdef model
	properties (SetAccess=public) %Model fields
		% {{{
		%Careful here: no other class should be used as default value this is a bug of matlab
		mesh             = 0;
		mask             = 0;

		geometry         = 0;
		constants        = 0;
		surfaceforcings  = 0;
		basalforcings    = 0;
		materials        = 0;
		friction         = 0;
		flowequation     = 0;
		timestepping     = 0;
		initialization   = 0;
		rifts            = 0;

		debug            = 0;
		verbose          = 0;
		settings         = 0;
		solver           = 0;
		cluster          = 0;

		balancethickness = 0;
		diagnostic       = 0;
		groundingline    = 0;
		hydrology        = 0;
		prognostic       = 0;
		thermal          = 0;
		steadystate      = 0;
		transient        = 0;

		autodiff         = 0;
		flaim            = 0;
		inversion        = 0;
		qmu              = 0;

		results          = 0;
		radaroverlay     = 0;
		miscellaneous    = 0;
		private          = 0;

		%}}}
	end
	methods (Static)
		function md = loadobj(md) % {{{
			% This function is directly called by matlab when a model object is
			% loaded. If the input is a struct it is an old version of model and
			% old fields must be recovered (make sure they are in the deprecated
			% model properties)

			if verLessThan('matlab','7.9'),
				disp('Warning: your matlab version is old and there is a risk that load does not work correctly');
				disp('         if the model is not loaded correctly, rename temporarily loadobj so that matlab does not use it');

				% This is a Matlab bug: all the fields of md have their default value
				% Example of error message:
				% Warning: Error loading an object of class 'model':
				% Undefined function or method 'exist' for input arguments of type 'cell'
				%
				% This has been fixed in MATLAB 7.9 (R2009b) and later versions
			end

			if isstruct(md)
				disp('Recovering model object from a previous version');
				md = structtomodel(model,md);
			end

			%2012 August 4th
			if isa(md.materials,'materials'),
				disp('Recovering old materials');
				if numel(md.materials.rheology_Z)==1 & isnan(md.materials.rheology_Z),
					md.materials=matice(md.materials);
				else
					md.materials=matdamageice(md.materials);
				end
			end
			%2012 June 28th
			if sum(sum(isnan(md.mesh.edges)))>0
				disp('Update model edges from previous version');
				md.mesh.edges(isnan(md.mesh.edges))=-1;
			end

		end% }}}
	end
	methods
		function md = model(varargin) % {{{

			switch nargin
				case 0
					md=setdefaultparameters(md);
				otherwise
					error('model constructor error message: 0 of 1 argument only in input.');
				end
		end
		%}}}
		function md = checkmessage(md,string) % {{{
			if(nargout~=1) error('wrong usage, model must be an output'); end
			disp(['model not consistent: ' string]);
			md.private.isconsistent=false;
		end
		%}}}
		function md = collapse(md)% {{{
			%COLLAPSE - collapses a 3d mesh into a 2d mesh
			%
			%   This routine collapses a 3d model into a 2d model
			%   and collapses all the fileds of the 3d model by
			%   taking their depth-averaged values
			%
			%   Usage:
			%      md=collapse(md)
			%
			%   See also: EXTRUDE, MODELEXTRACT

			%Check that the model is really a 3d model
			if ~md.mesh.dimension==3,
				error('collapse error message: only 3d mesh can be collapsed')
			end

			%Start with changing alle the fields from the 3d mesh 

			%drag is limited to nodes that are on the bedrock.
			md.friction.coefficient=project2d(md,md.friction.coefficient,1);

			%p and q (same deal, except for element that are on the bedrock: )
			md.friction.p=project2d(md,md.friction.p,1);
			md.friction.q=project2d(md,md.friction.q,1);

			%observations
			if ~isnan(md.inversion.vx_obs), md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers); end;
			if ~isnan(md.inversion.vy_obs), md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers); end;
			if ~isnan(md.inversion.vel_obs), md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers); end;
			if ~isnan(md.inversion.cost_functions_coefficients), md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers); end;
			if numel(md.inversion.min_parameters)>1, md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers); end;
			if numel(md.inversion.max_parameters)>1, md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers); end;
			if ~isnan(md.surfaceforcings.mass_balance),
				md.surfaceforcings.mass_balance=project2d(md,md.surfaceforcings.mass_balance,md.mesh.numberoflayers); 
			end;
			if ~isnan(md.balancethickness.thickening_rate), md.balancethickness.thickening_rate=project2d(md,md.balancethickness.thickening_rate,md.mesh.numberoflayers); end;

			%results
			if ~isnan(md.initialization.vx),md.initialization.vx=DepthAverage(md,md.initialization.vx);end;
			if ~isnan(md.initialization.vy),md.initialization.vy=DepthAverage(md,md.initialization.vy);end;
			if ~isnan(md.initialization.vz),md.initialization.vz=DepthAverage(md,md.initialization.vz);end;
			if ~isnan(md.initialization.vel),md.initialization.vel=DepthAverage(md,md.initialization.vel);end;
			if ~isnan(md.initialization.temperature),md.initialization.temperature=DepthAverage(md,md.initialization.temperature);end;

			%bedinfo and surface info
			md.mesh.elementonbed=ones(md.mesh.numberofelements2d,1);
			md.mesh.elementonsurface=ones(md.mesh.numberofelements2d,1);
			md.mesh.vertexonbed=ones(md.mesh.numberofvertices2d,1);
			md.mesh.vertexonsurface=ones(md.mesh.numberofvertices2d,1);

			%elementstype
			if ~isnan(md.flowequation.element_equation)
				md.flowequation.element_equation=project2d(md,md.flowequation.element_equation,1);
				md.flowequation.vertex_equation=project2d(md,md.flowequation.vertex_equation,1);
				md.flowequation.bordermacayeal=project2d(md,md.flowequation.bordermacayeal,1);
				md.flowequation.borderpattyn=project2d(md,md.flowequation.borderpattyn,1);
				md.flowequation.borderstokes=project2d(md,md.flowequation.borderstokes,1);
			end	

			%boundary conditions
			md.diagnostic.spcvx=project2d(md,md.diagnostic.spcvx,md.mesh.numberoflayers);
			md.diagnostic.spcvy=project2d(md,md.diagnostic.spcvy,md.mesh.numberoflayers);
			md.diagnostic.spcvz=project2d(md,md.diagnostic.spcvz,md.mesh.numberoflayers);
			md.diagnostic.referential=project2d(md,md.diagnostic.referential,md.mesh.numberoflayers);
			md.prognostic.spcthickness=project2d(md,md.prognostic.spcthickness,md.mesh.numberoflayers);
			md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);

			%Extrusion of Neumann BC
			if ~isnan(md.diagnostic.icefront),
				numberofneumann2d=size(md.diagnostic.icefront,1)/(md.mesh.numberoflayers-1);
				md.diagnostic.icefront=[md.diagnostic.icefront(1:numberofneumann2d,1:2) md.diagnostic.icefront(1:numberofneumann2d,5:6)]; %Add two columns on the first layer 
			end

			%materials
			md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
			md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
			if isa(md.materials,'matdamageice')
				md.materials.rheology_Z=DepthAverage(md,md.materials.rheology_Z);
			end

			%special for thermal modeling:
			md.basalforcings.melting_rate=project2d(md,md.basalforcings.melting_rate,1); 
			md.basalforcings.geothermalflux=project2d(md,md.basalforcings.geothermalflux,1); %bedrock only gets geothermal flux

			%update of connectivity matrix
			md.mesh.average_vertex_connectivity=25;

			%Collapse the mesh
			nodes2d=md.mesh.numberofvertices2d;
			elements2d=md.mesh.numberofelements2d;

			%parameters
			md.geometry.surface=project2d(md,md.geometry.surface,1);
			md.geometry.thickness=project2d(md,md.geometry.thickness,1);
			md.geometry.bed=project2d(md,md.geometry.bed,1);
			md.geometry.bathymetry=project2d(md,md.geometry.bathymetry,1);
			md.mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
			md.mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);
			md.mask.elementonfloatingice=project2d(md,md.mask.elementonfloatingice,1);
			md.mask.vertexonfloatingice=project2d(md,md.mask.vertexonfloatingice,1);
			md.mask.elementongroundedice=project2d(md,md.mask.elementongroundedice,1);
			md.mask.vertexongroundedice=project2d(md,md.mask.vertexongroundedice,1);
			md.mask.elementonwater=project2d(md,md.mask.elementonwater,1);
			md.mask.vertexonwater=project2d(md,md.mask.vertexonwater,1);

			%lat long
			if numel(md.mesh.lat) ==md.mesh.numberofvertices,  md.mesh.lat=project2d(md,md.mesh.lat,1); end
			if numel(md.mesh.long)==md.mesh.numberofvertices, md.mesh.long=project2d(md,md.mesh.long,1); end

			%Initialize with the 2d mesh
			md.mesh.x=md.mesh.x2d;
			md.mesh.y=md.mesh.y2d;
			md.mesh.z=zeros(size(md.mesh.x2d));
			md.mesh.numberofvertices=md.mesh.numberofvertices2d;
			md.mesh.numberofelements=md.mesh.numberofelements2d;
			md.mesh.elements=md.mesh.elements2d;

			%Keep a trace of lower and upper nodes
			md.mesh.lowervertex=NaN;
			md.mesh.uppervertex=NaN;
			md.mesh.lowerelements=NaN;
			md.mesh.upperelements=NaN;

			%Remove old mesh 
			md.mesh.x2d=NaN;
			md.mesh.y2d=NaN;
			md.mesh.elements2d=NaN;
			md.mesh.numberofelements2d=md.mesh.numberofelements;
			md.mesh.numberofvertices2d=md.mesh.numberofvertices;
			md.mesh.numberoflayers=0;

			%Update mesh type
			md.mesh.dimension=2;
		end % }}}
		function md2 = extract(md,area) % {{{
			%extract - extract a model according to an Argus contour or flag list
			%
			%   This routine extracts a submodel from a bigger model with respect to a given contour
			%   md must be followed by the corresponding exp file or flags list
			%   It can either be a domain file (argus type, .exp extension), or an array of element flags. 
			%   If user wants every element outside the domain to be 
			%   extract2d, add '~' to the name of the domain file (ex: '~Pattyn.exp');
			%   an empty string '' will be considered as an empty domain
			%   a string 'all' will be considered as the entire domain
			%
			%   Usage:
			%      md2=extract(md,area);
			%
			%   Examples:
			%      md2=extract(md,'Domain.exp');
			%      md2=extract(md,md.mask.elementonfloatingice);
			%
			%   See also: EXTRUDE, COLLAPSE

			%copy model
			md1=md;

			%some checks
			if ((nargin~=2) | (nargout~=1)),
				help extract
				error('extract error message: bad usage');
			end

			%get elements that are inside area
			flag_elem=FlagElements(md1,area);
			if ~any(flag_elem),
				error('extracted model is empty');
			end

			%kick out all elements with 3 dirichlets
			spc_elem=find(~flag_elem);
			spc_node=sort(unique(md1.mesh.elements(spc_elem,:)));
			flag=ones(md1.mesh.numberofvertices,1);
			flag(spc_node)=0;
			pos=find(sum(flag(md1.mesh.elements),2)==0);
			flag_elem(pos)=0;

			%extracted elements and nodes lists
			pos_elem=find(flag_elem);
			pos_node=sort(unique(md1.mesh.elements(pos_elem,:)));

			%keep track of some fields
			numberofvertices1=md1.mesh.numberofvertices;
			numberofelements1=md1.mesh.numberofelements;
			numberofvertices2=length(pos_node);
			numberofelements2=length(pos_elem);
			flag_node=zeros(numberofvertices1,1);
			flag_node(pos_node)=1;

			%Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
			Pelem=zeros(numberofelements1,1);
			Pelem(pos_elem)=[1:numberofelements2]';
			Pnode=zeros(numberofvertices1,1);
			Pnode(pos_node)=[1:numberofvertices2]';

			%renumber the elements (some nodes won't exist anymore)
			elements_1=md1.mesh.elements;
			elements_2=elements_1(pos_elem,:);
			elements_2(:,1)=Pnode(elements_2(:,1));
			elements_2(:,2)=Pnode(elements_2(:,2));
			elements_2(:,3)=Pnode(elements_2(:,3));
			if md1.mesh.dimension==3,
				elements_2(:,4)=Pnode(elements_2(:,4));
				elements_2(:,5)=Pnode(elements_2(:,5));
				elements_2(:,6)=Pnode(elements_2(:,6));
			end

			%OK, now create the new model!

			%take every field from model
			md2=md1;

			%automatically modify fields

			%loop over model fields
			model_fields=fields(md1);
			for i=1:length(model_fields),
				%get field
				field=md1.(model_fields{i});
				fieldsize=size(field);
				if isobject(field), %recursive call
					object_fields=fields(md1.(model_fields{i}));
					for j=1:length(object_fields),
						%get field
						field=md1.(model_fields{i}).(object_fields{j});
						fieldsize=size(field);
						%size = number of nodes * n
						if fieldsize(1)==numberofvertices1
							md2.(model_fields{i}).(object_fields{j})=field(pos_node,:);
						elseif (fieldsize(1)==numberofvertices1+1)
							md2.(model_fields{i}).(object_fields{j})=[field(pos_node,:); field(end,:)];
						%size = number of elements * n
						elseif fieldsize(1)==numberofelements1
							md2.(model_fields{i}).(object_fields{j})=field(pos_elem,:);
						end
					end
				else
					%size = number of nodes * n
					if fieldsize(1)==numberofvertices1
						md2.(model_fields{i})=field(pos_node,:);
					elseif (fieldsize(1)==numberofvertices1+1)
						md2.(model_fields{i})=[field(pos_node,:); field(end,:)];
					%size = number of elements * n
					elseif fieldsize(1)==numberofelements1
						md2.(model_fields{i})=field(pos_elem,:);
					end
				end
			end

			%modify some specific fields

			%Mesh
			md2.mesh.numberofelements=numberofelements2;
			md2.mesh.numberofvertices=numberofvertices2;
			md2.mesh.elements=elements_2;

			%mesh.uppervertex mesh.lowervertex
			if md1.mesh.dimension==3
				md2.mesh.uppervertex=md1.mesh.uppervertex(pos_node);
				pos=find(~isnan(md2.mesh.uppervertex));
				md2.mesh.uppervertex(pos)=Pnode(md2.mesh.uppervertex(pos));

				md2.mesh.lowervertex=md1.mesh.lowervertex(pos_node);
				pos=find(~isnan(md2.mesh.lowervertex));
				md2.mesh.lowervertex(pos)=Pnode(md2.mesh.lowervertex(pos));

				md2.mesh.upperelements=md1.mesh.upperelements(pos_elem);
				pos=find(~isnan(md2.mesh.upperelements));
				md2.mesh.upperelements(pos)=Pelem(md2.mesh.upperelements(pos));

				md2.mesh.lowerelements=md1.mesh.lowerelements(pos_elem);
				pos=find(~isnan(md2.mesh.lowerelements));
				md2.mesh.lowerelements(pos)=Pelem(md2.mesh.lowerelements(pos));
			end

			%Initial 2d mesh 
			if md1.mesh.dimension==3
				flag_elem_2d=flag_elem(1:md1.mesh.numberofelements2d);
				pos_elem_2d=find(flag_elem_2d);
				flag_node_2d=flag_node(1:md1.mesh.numberofvertices2d);
				pos_node_2d=find(flag_node_2d);

				md2.mesh.numberofelements2d=length(pos_elem_2d);
				md2.mesh.numberofvertices2d=length(pos_node_2d);
				md2.mesh.elements2d=md1.mesh.elements2d(pos_elem_2d,:);
				md2.mesh.elements2d(:,1)=Pnode(md2.mesh.elements2d(:,1));
				md2.mesh.elements2d(:,2)=Pnode(md2.mesh.elements2d(:,2));
				md2.mesh.elements2d(:,3)=Pnode(md2.mesh.elements2d(:,3));

				md2.mesh.x2d=md1.mesh.x(pos_node_2d);
				md2.mesh.y2d=md1.mesh.y(pos_node_2d);
			end

			%Edges
			if size(md2.mesh.edges,2)>1, %do not use ~isnan because there are some NaNs...
				%renumber first two columns
				pos=find(md2.mesh.edges(:,4)~=-1);
				md2.mesh.edges(:  ,1)=Pnode(md2.mesh.edges(:,1));
				md2.mesh.edges(:  ,2)=Pnode(md2.mesh.edges(:,2));
				md2.mesh.edges(:  ,3)=Pelem(md2.mesh.edges(:,3));
				md2.mesh.edges(pos,4)=Pelem(md2.mesh.edges(pos,4));
				%remove edges when the 2 vertices are not in the domain.
				md2.mesh.edges=md2.mesh.edges(find(md2.mesh.edges(:,1) & md2.mesh.edges(:,2)),:);
				%Replace all zeros by -1 in the last two columns
				pos=find(md2.mesh.edges(:,3)==0);
				md2.mesh.edges(pos,3)=-1;
				pos=find(md2.mesh.edges(:,4)==0);
				md2.mesh.edges(pos,4)=-1;
				%Invert -1 on the third column with last column (Also invert first two columns!!)
				pos=find(md2.mesh.edges(:,3)==-1);
				md2.mesh.edges(pos,3)=md2.mesh.edges(pos,4);
				md2.mesh.edges(pos,4)=-1;
				values=md2.mesh.edges(pos,2);
				md2.mesh.edges(pos,2)=md2.mesh.edges(pos,1);
				md2.mesh.edges(pos,1)=values;
				%Finally remove edges that do not belong to any element
				pos=find(md2.mesh.edges(:,3)==-1 & md2.mesh.edges(:,4)==-1);
				md2.mesh.edges(pos,:)=[];
			end

			%Penalties
			if ~isnan(md2.diagnostic.vertex_pairing),
				for i=1:size(md1.diagnostic.vertex_pairing,1);
					md2.diagnostic.vertex_pairing(i,:)=Pnode(md1.diagnostic.vertex_pairing(i,:));
				end
				md2.diagnostic.vertex_pairing=md2.diagnostic.vertex_pairing(find(md2.diagnostic.vertex_pairing(:,1)),:);
			end
			if ~isnan(md2.prognostic.vertex_pairing),
				for i=1:size(md1.prognostic.vertex_pairing,1);
					md2.prognostic.vertex_pairing(i,:)=Pnode(md1.prognostic.vertex_pairing(i,:));
				end
				md2.prognostic.vertex_pairing=md2.prognostic.vertex_pairing(find(md2.prognostic.vertex_pairing(:,1)),:);
			end

			%recreate segments
			if md1.mesh.dimension==2
				md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
				md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
				md2.mesh.segments=contourenvelope(md2);
				md2.mesh.vertexonboundary=zeros(numberofvertices2,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
			else
				%First do the connectivity for the contourenvelope in 2d
				md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements2d,md2.mesh.numberofvertices2d);
				md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements2d,md2.mesh.vertexconnectivity);
				md2.mesh.segments=contourenvelope(md2);
				md2.mesh.vertexonboundary=zeros(numberofvertices2/md2.mesh.numberoflayers,1); md2.mesh.vertexonboundary(md2.mesh.segments(:,1:2))=1;
				md2.mesh.vertexonboundary=repmat(md2.mesh.vertexonboundary,md2.mesh.numberoflayers,1);
				%Then do it for 3d as usual
				md2.mesh.vertexconnectivity=NodeConnectivity(md2.mesh.elements,md2.mesh.numberofvertices);
				md2.mesh.elementconnectivity=ElementConnectivity(md2.mesh.elements,md2.mesh.vertexconnectivity);
			end

			%Boundary conditions: Dirichlets on new boundary
			%Catch the elements that have not been extracted
			orphans_elem=find(~flag_elem);
			orphans_node=unique(md1.mesh.elements(orphans_elem,:))';
			%Figure out which node are on the boundary between md2 and md1
			nodestoflag1=intersect(orphans_node,pos_node);
			nodestoflag2=Pnode(nodestoflag1);
			if numel(md1.diagnostic.spcvx)>1 & numel(md1.diagnostic.spcvy)>2 & numel(md1.diagnostic.spcvz)>2,
				if numel(md1.inversion.vx_obs)>1 & numel(md1.inversion.vy_obs)>1
					md2.diagnostic.spcvx(nodestoflag2)=md2.inversion.vx_obs(nodestoflag2); 
					md2.diagnostic.spcvy(nodestoflag2)=md2.inversion.vy_obs(nodestoflag2);
				else
					md2.diagnostic.spcvx(nodestoflag2)=NaN;
					md2.diagnostic.spcvy(nodestoflag2)=NaN;
					disp(' ')
					disp('!! extract warning: spc values should be checked !!')
					disp(' ')
				end
				%put 0 for vz
				md2.diagnostic.spcvz(nodestoflag2)=0;
			end
			if ~isnan(md1.thermal.spctemperature),
				md2.thermal.spctemperature(nodestoflag2,1)=1;
			end

			%Diagnostic
			if ~isnan(md2.diagnostic.icefront)
				md2.diagnostic.icefront(:,1)=Pnode(md1.diagnostic.icefront(:,1)); 
				md2.diagnostic.icefront(:,2)=Pnode(md1.diagnostic.icefront(:,2)); 
				md2.diagnostic.icefront(:,end-1)=Pelem(md1.diagnostic.icefront(:,end-1));
				if md1.mesh.dimension==3
					md2.diagnostic.icefront(:,3)=Pnode(md1.diagnostic.icefront(:,3)); 
					md2.diagnostic.icefront(:,4)=Pnode(md1.diagnostic.icefront(:,4)); 
				end
				md2.diagnostic.icefront=md2.diagnostic.icefront(find(md2.diagnostic.icefront(:,1) & md2.diagnostic.icefront(:,2) & md2.diagnostic.icefront(:,end)),:);
			end

			%Results fields
			if isstruct(md1.results),
				md2.results=struct();
				solutionfields=fields(md1.results);
				for i=1:length(solutionfields),
					%get subfields
					solutionsubfields=fields(md1.results.(solutionfields{i}));
					for j=1:length(solutionsubfields),
						field=md1.results.(solutionfields{i}).(solutionsubfields{j});
						if length(field)==numberofvertices1,
							md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_node);
						elseif length(field)==numberofelements1,
							md2.results.(solutionfields{i}).(solutionsubfields{j})=field(pos_elem);
						else
							md2.results.(solutionfields{i}).(solutionsubfields{j})=field;
						end
					end
				end
			end

			%Keep track of pos_node and pos_elem
			md2.mesh.extractedvertices=pos_node;
			md2.mesh.extractedelements=pos_elem;
		end % }}}
		function md = extrude(md,varargin) % {{{
			%EXTRUDE - vertically extrude a 2d mesh
			%
			%   vertically extrude a 2d mesh and create corresponding 3d mesh.
			%   The vertical distribution can:
			%    - follow a polynomial law
			%    - follow two polynomial laws, one for the lower part and one for the upper part of the mesh
			%    - be discribed by a list of coefficients (between 0 and 1)
			%   
			%
			%   Usage:
			%      md=extrude(md,numlayers,extrusionexponent);
			%      md=extrude(md,numlayers,lowerexponent,upperexponent);
			%      md=extrude(md,listofcoefficients);
			%
			%   Example:
			%      md=extrude(md,8,3);
			%      md=extrude(md,8,3,2);
			%      md=extrude(md,[0 0.2 0.5 0.7 0.9 0.95 1]);
			%
			%   See also: MODELEXTRACT, COLLAPSE

			%some checks on list of arguments
			if ((nargin>4) | (nargin<2) | (nargout~=1)),
				help extrude;
				error('extrude error message');
			end

			%Extrude the mesh
			if nargin==2, %list of coefficients
				clist=varargin{1};
				if any(clist<0) | any(clist>1),
					error('extrusioncoefficients must be between 0 and 1');
				end
				extrusionlist=sort(unique([clist(:);0;1]));
				numlayers=length(extrusionlist);
			elseif nargin==3, %one polynomial law
				if varargin{2}<=0,
					help extrude;
					error('extrusionexponent must be >=0');
				end
				numlayers=varargin{1};
				extrusionlist=((0:1:numlayers-1)/(numlayers-1)).^varargin{2};
			elseif nargin==4, %two polynomial laws
				numlayers=varargin{1};
				lowerexp=varargin{2};
				upperexp=varargin{3};

				if varargin{2}<=0 | varargin{3}<=0,
					help extrude;
					error('lower and upper extrusionexponents must be >=0');
				end

				lowerextrusionlist=[(0:2/(numlayers-1):1).^lowerexp]/2;
				upperextrusionlist=[(0:2/(numlayers-1):1).^upperexp]/2;
				extrusionlist=sort(unique([lowerextrusionlist 1-upperextrusionlist]));

			end

			if numlayers<2,
				error('number of layers should be at least 2');
			end
			if md.mesh.dimension==3,
				error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
			end

			%Initialize with the 2d mesh
			x3d=[]; 
			y3d=[];
			z3d=[];  %the lower node is on the bed
			thickness3d=md.geometry.thickness; %thickness and bed for these nodes
			bed3d=md.geometry.bed;

			%Create the new layers
			for i=1:numlayers,
				x3d=[x3d; md.mesh.x]; 
				y3d=[y3d; md.mesh.y];
				%nodes are distributed between bed and surface accordingly to the given exponent
				z3d=[z3d; bed3d+thickness3d*extrusionlist(i)]; 
			end
			number_nodes3d=size(x3d,1); %number of 3d nodes for the non extruded part of the mesh

			%Extrude elements 
			elements3d=[];
			for i=1:numlayers-1,
				elements3d=[elements3d;[md.mesh.elements+(i-1)*md.mesh.numberofvertices md.mesh.elements+i*md.mesh.numberofvertices]]; %Create the elements of the 3d mesh for the non extruded part
			end
			number_el3d=size(elements3d,1); %number of 3d nodes for the non extruded part of the mesh

			%Keep a trace of lower and upper nodes
			mesh.lowervertex=NaN*ones(number_nodes3d,1);
			mesh.uppervertex=NaN*ones(number_nodes3d,1);
			mesh.lowervertex(md.mesh.numberofvertices+1:end)=1:(numlayers-1)*md.mesh.numberofvertices;
			mesh.uppervertex(1:(numlayers-1)*md.mesh.numberofvertices)=md.mesh.numberofvertices+1:number_nodes3d;
			md.mesh.lowervertex=mesh.lowervertex;
			md.mesh.uppervertex=mesh.uppervertex;

			%same for lower and upper elements
			mesh.lowerelements=NaN*ones(number_el3d,1);
			mesh.upperelements=NaN*ones(number_el3d,1);
			mesh.lowerelements(md.mesh.numberofelements+1:end)=1:(numlayers-2)*md.mesh.numberofelements;
			mesh.upperelements(1:(numlayers-2)*md.mesh.numberofelements)=md.mesh.numberofelements+1:(numlayers-1)*md.mesh.numberofelements;
			md.mesh.lowerelements=mesh.lowerelements;
			md.mesh.upperelements=mesh.upperelements;

			%Save old mesh 
			md.mesh.x2d=md.mesh.x;
			md.mesh.y2d=md.mesh.y;
			md.mesh.elements2d=md.mesh.elements;
			md.mesh.numberofelements2d=md.mesh.numberofelements;
			md.mesh.numberofvertices2d=md.mesh.numberofvertices;

			%Update mesh type
			md.mesh.dimension=3;

			%Build global 3d mesh 
			md.mesh.elements=elements3d;
			md.mesh.x=x3d;
			md.mesh.y=y3d;
			md.mesh.z=z3d;
			md.mesh.numberofelements=number_el3d;
			md.mesh.numberofvertices=number_nodes3d;
			md.mesh.numberoflayers=numlayers;

			%Ok, now deal with the other fields from the 2d mesh:

			%lat long
			md.mesh.lat=project3d(md,'vector',md.mesh.lat,'type','node');
			md.mesh.long=project3d(md,'vector',md.mesh.long,'type','node');

			%drag coefficient is limited to nodes that are on the bedrock.
			md.friction.coefficient=project3d(md,'vector',md.friction.coefficient,'type','node','layer',1);

			%p and q (same deal, except for element that are on the bedrock: )
			md.friction.p=project3d(md,'vector',md.friction.p,'type','element');
			md.friction.q=project3d(md,'vector',md.friction.q,'type','element');

			%observations
			md.inversion.vx_obs=project3d(md,'vector',md.inversion.vx_obs,'type','node');
			md.inversion.vy_obs=project3d(md,'vector',md.inversion.vy_obs,'type','node');
			md.inversion.vel_obs=project3d(md,'vector',md.inversion.vel_obs,'type','node');
			md.surfaceforcings.mass_balance=project3d(md,'vector',md.surfaceforcings.mass_balance,'type','node');
			md.surfaceforcings.precipitation=project3d(md,'vector',md.surfaceforcings.precipitation,'type','node');
			md.balancethickness.thickening_rate=project3d(md,'vector',md.balancethickness.thickening_rate,'type','node');
			md.surfaceforcings.monthlytemperatures=project3d(md,'vector',md.surfaceforcings.monthlytemperatures,'type','node');

			%results
			if ~isnan(md.initialization.vx),md.initialization.vx=project3d(md,'vector',md.initialization.vx,'type','node');end;
			if ~isnan(md.initialization.vy),md.initialization.vy=project3d(md,'vector',md.initialization.vy,'type','node');end;
			if ~isnan(md.initialization.vz),md.initialization.vz=project3d(md,'vector',md.initialization.vz,'type','node');end;
			if ~isnan(md.initialization.vel),md.initialization.vel=project3d(md,'vector',md.initialization.vel,'type','node');end;
			if ~isnan(md.initialization.temperature),md.initialization.temperature=project3d(md,'vector',md.initialization.temperature,'type','node');end;
			if ~isnan(md.initialization.waterfraction),md.initialization.waterfraction=project3d(md,'vector',md.initialization.waterfraction,'type','node');end;

			%bedinfo and surface info
			md.mesh.elementonbed=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',1);
			md.mesh.elementonsurface=project3d(md,'vector',ones(md.mesh.numberofelements2d,1),'type','element','layer',md.mesh.numberoflayers-1);
			md.mesh.vertexonbed=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',1);
			md.mesh.vertexonsurface=project3d(md,'vector',ones(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);

			%elementstype
			if ~isnan(md.flowequation.element_equation)
				oldelements_type=md.flowequation.element_equation;
				md.flowequation.element_equation=zeros(number_el3d,1);
				md.flowequation.element_equation=project3d(md,'vector',oldelements_type,'type','element');
			end

			%verticestype
			if ~isnan(md.flowequation.vertex_equation)
				oldvertices_type=md.flowequation.vertex_equation;
				md.flowequation.vertex_equation=zeros(number_nodes3d,1);
				md.flowequation.vertex_equation=project3d(md,'vector',oldvertices_type,'type','node');
			end
			md.flowequation.bordermacayeal=project3d(md,'vector',md.flowequation.bordermacayeal,'type','node');
			md.flowequation.borderpattyn=project3d(md,'vector',md.flowequation.borderpattyn,'type','node');
			md.flowequation.borderstokes=project3d(md,'vector',md.flowequation.borderstokes,'type','node');

			%boundary conditions
			md.diagnostic.spcvx=project3d(md,'vector',md.diagnostic.spcvx,'type','node');
			md.diagnostic.spcvy=project3d(md,'vector',md.diagnostic.spcvy,'type','node');
			md.diagnostic.spcvz=project3d(md,'vector',md.diagnostic.spcvz,'type','node');
			md.thermal.spctemperature=project3d(md,'vector',md.thermal.spctemperature,'type','node','layer',md.mesh.numberoflayers,'padding',NaN);
			md.prognostic.spcthickness=project3d(md,'vector',md.prognostic.spcthickness,'type','node');
			md.balancethickness.spcthickness=project3d(md,'vector',md.balancethickness.spcthickness,'type','node');
			md.diagnostic.referential=project3d(md,'vector',md.diagnostic.referential,'type','node');

			%in 3d, pressureload: [node1 node2 node3 node4 element]
			pressureload_layer1=[md.diagnostic.icefront(:,1:2)  md.diagnostic.icefront(:,2)+md.mesh.numberofvertices2d  md.diagnostic.icefront(:,1)+md.mesh.numberofvertices2d  md.diagnostic.icefront(:,3:4)]; %Add two columns on the first layer 
			pressureload=[];
			for i=1:numlayers-1,
				pressureload=[pressureload ;pressureload_layer1(:,1:4)+(i-1)*md.mesh.numberofvertices2d pressureload_layer1(:,5)+(i-1)*md.mesh.numberofelements2d pressureload_layer1(:,6)];
			end
			md.diagnostic.icefront=pressureload;

			%connectivity
			md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1);
			md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
			for i=2:numlayers-1,
				md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)...
					=md.mesh.elementconnectivity((i-1)*md.mesh.numberofelements2d+1:(i)*md.mesh.numberofelements2d,:)+md.mesh.numberofelements2d;
			end
			md.mesh.elementconnectivity(find(isnan(md.mesh.elementconnectivity)))=0;

			%materials
			md.materials.rheology_B=project3d(md,'vector',md.materials.rheology_B,'type','node');
			md.materials.rheology_n=project3d(md,'vector',md.materials.rheology_n,'type','element');
			if isa(md.materials,'matdamageice')
				md.materials.rheology_Z=project3d(md,'vector',md.materials.rheology_Z,'type','node');
			end

			%parameters
			md.geometry.surface=project3d(md,'vector',md.geometry.surface,'type','node');
			md.geometry.thickness=project3d(md,'vector',md.geometry.thickness,'type','node');
			md.geometry.hydrostatic_ratio=project3d(md,'vector',md.geometry.hydrostatic_ratio,'type','node');
			md.geometry.bed=project3d(md,'vector',md.geometry.bed,'type','node');
			md.geometry.bathymetry=project3d(md,'vector',md.geometry.bathymetry,'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');
			md.mask.elementongroundedice=project3d(md,'vector',md.mask.elementongroundedice,'type','element');
			md.mask.vertexongroundedice=project3d(md,'vector',md.mask.vertexongroundedice,'type','node');
			md.mask.elementonwater=project3d(md,'vector',md.mask.elementonwater,'type','element');
			md.mask.vertexonwater=project3d(md,'vector',md.mask.vertexonwater,'type','node');
			if ~isnan(md.inversion.cost_functions_coefficients),md.inversion.cost_functions_coefficients=project3d(md,'vector',md.inversion.cost_functions_coefficients,'type','node');end;
			if ~isnan(md.inversion.min_parameters),md.inversion.min_parameters=project3d(md,'vector',md.inversion.min_parameters,'type','node');end;
			if ~isnan(md.inversion.max_parameters),md.inversion.max_parameters=project3d(md,'vector',md.inversion.max_parameters,'type','node');end;
			if ~isnan(md.qmu.partition),md.qmu.partition=project3d(md,'vector',md.qmu.partition','type','node');end
			if(md.surfaceforcings.isdelta18o),md.surfaceforcings.temperatures_lgm=project3d(md,'vector',md.surfaceforcings.temperatures_lgm,'type','node');end
			if(md.surfaceforcings.isdelta18o),md.surfaceforcings.temperatures_presentday=project3d(md,'vector',md.surfaceforcings.temperatures_presentday,'type','node');end
			if(md.surfaceforcings.isdelta18o),md.surfaceforcings.precipitations_presentday=project3d(md,'vector',md.surfaceforcings.precipitations_presentday,'type','node');end

			%Put lithostatic pressure if there is an existing pressure
			if ~isnan(md.initialization.pressure),
				md.initialization.pressure=md.constants.g*md.materials.rho_ice*(md.geometry.surface-md.mesh.z);
			end

			%special for thermal modeling:
			md.basalforcings.melting_rate=project3d(md,'vector',md.basalforcings.melting_rate,'type','node','layer',1); 
			if ~isnan(md.basalforcings.geothermalflux)
				md.basalforcings.geothermalflux=project3d(md,'vector',md.basalforcings.geothermalflux,'type','node','layer',1); %bedrock only gets geothermal flux
			end

			%increase connectivity if less than 25:
			if md.mesh.average_vertex_connectivity<=25,
				md.mesh.average_vertex_connectivity=100;
			end
			end % }}}
		function md = structtomodel(md,structmd) % {{{

			if ~isstruct(structmd) error('input model is not a structure'); end

			%loaded model is a struct, initialize output and recover all fields
			md = structtoobj(model,structmd);

			%Old field now classes
			if (isfield(structmd,'timestepping') & isnumeric(md.timestepping)), md.timestepping=timestepping(); end
			if (isfield(structmd,'mask') & isnumeric(md.mask)),md.mask=mask(); end

			%Field name change
			if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
			if isfield(structmd,'p'), md.friction.p=structmd.p; end
			if isfield(structmd,'q'), md.friction.q=structmd.p; end
			if isfield(structmd,'melting'), md.basalforcings.melting_rate=structmd.melting; end
			if isfield(structmd,'melting_rate'), md.basalforcings.melting_rate=structmd.melting_rate; end
			if isfield(structmd,'accumulation'), md.surfaceforcings.mass_balance=structmd.accumulation; end
			if isfield(structmd,'numberofgrids'), md.mesh.numberofvertices=structmd.numberofgrids; end
			if isfield(structmd,'numberofgrids2d'), md.mesh.numberofvertices2d=structmd.numberofgrids2d; end
			if isfield(structmd,'uppergrids'), md.mesh.uppervertex=structmd.uppergrids; end
			if isfield(structmd,'lowergrids'), md.mesh.lowervertex=structmd.lowergrids; end
			if isfield(structmd,'gridonbed'), md.mesh.vertexonbed=structmd.gridonbed; end
			if isfield(structmd,'gridonsurface'), md.mesh.vertexonsurface=structmd.gridonsurface; end
			if isfield(structmd,'extractedgrids'), md.mesh.extractedvertices=structmd.extractedgrids; end
			if isfield(structmd,'gridoniceshelf'), md.mask.vertexonfloatingice=structmd.gridoniceshelf; end
			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.mesh.vertexonboundary=structmd.gridonboundary; end
			if isfield(structmd,'petscoptions') & ~isempty(structmd.petscoptions), md.solver=structmd.petscoptions; end
			if isfield(structmd,'g'), md.constants.g=structmd.g; end
			if isfield(structmd,'yts'), md.constants.yts=structmd.yts; end
			if isfield(structmd,'surface_mass_balance'), md.surfaceforcings.mass_balance=structmd.surface_mass_balance; end
			if isfield(structmd,'basal_melting_rate'), md.basalforcings.melting_rate=structmd.basal_melting_rate; end
			if isfield(structmd,'basal_melting_rate_correction'), md.basalforcings.melting_rate_correction=structmd.basal_melting_rate_correction; end
			if isfield(structmd,'geothermalflux'), md.basalforcings.geothermalflux=structmd.geothermalflux; end
			if isfield(structmd,'drag'), md.friction.coefficient=structmd.drag; end
			if isfield(structmd,'drag_coefficient'), md.friction.coefficient=structmd.drag_coefficient; end
			if isfield(structmd,'drag_p'), md.friction.p=structmd.drag_p; end
			if isfield(structmd,'drag_q'), md.friction.q=structmd.drag_q; end
			if isfield(structmd,'riftproperties'), %old implementation
				md.rifts=rifts();
				md.rifts.riftproperties=structmd.riftproperties; 
				md.rifts.riftstruct=structmd.rifts;
				md.rifts.riftproperties=structmd.riftinfo;
			end
			if isfield(structmd,'bamg'), md.private.bamg=structmd.bamg; end
			if isfield(structmd,'lowmem'), md.settings.lowmem=structmd.lowmem; end
			if isfield(structmd,'io_gather'), md.settings.io_gather=structmd.io_gather; end
			if isfield(structmd,'spcwatercolumn'), md.hydrology.spcwatercolumn=structmd.spcwatercolumn; end
			if isfield(structmd,'hydro_n'), md.hydrology.n=structmd.hydro_n; end
			if isfield(structmd,'hydro_p'), md.hydrology.p=structmd.hydro_p; end
			if isfield(structmd,'hydro_q'), md.hydrology.q=structmd.hydro_q; end
			if isfield(structmd,'hydro_CR'), md.hydrology.CR=structmd.hydro_CR; end
			if isfield(structmd,'hydro_kn'), md.hydrology.kn=structmd.hydro_kn; end
			if isfield(structmd,'spctemperature'), md.thermal.spctemperature=structmd.spctemperature; end
			if isfield(structmd,'min_thermal_constraints'), md.thermal.penalty_threshold=structmd.min_thermal_constraints; end
			if isfield(structmd,'artificial_diffusivity'), md.thermal.stabilization=structmd.artificial_diffusivity; end
			if isfield(structmd,'max_nonlinear_iterations'), md.thermal.maxiter=structmd.max_nonlinear_iterations; end
			if isfield(structmd,'stabilize_constraints'), md.thermal.penalty_lock=structmd.stabilize_constraints; end
			if isfield(structmd,'penalty_offset'), md.thermal.penalty_factor=structmd.penalty_offset; end
			if isfield(structmd,'name'), md.miscellaneous.name=structmd.name; end
			if isfield(structmd,'notes'), md.miscellaneous.notes=structmd.notes; end
			if isfield(structmd,'dummy'), md.miscellaneous.dummy=structmd.dummy; end
			if isfield(structmd,'dt'), md.timestepping.time_step=structmd.dt; end
			if isfield(structmd,'ndt'), md.timestepping.final_time=structmd.ndt; end
			if isfield(structmd,'time_adapt'), md.timestepping.time_adapt=structmd.time_adapt; end
			if isfield(structmd,'cfl_coefficient'), md.timestepping.cfl_coefficient=structmd.cfl_coefficient; end
			if isfield(structmd,'spcthickness'), md.prognostic.spcthickness=structmd.spcthickness; end
			if isfield(structmd,'artificial_diffusivity'), md.prognostic.stabilization=structmd.artificial_diffusivity; end
			if isfield(structmd,'hydrostatic_adjustment'), md.prognostic.hydrostatic_adjustment=structmd.hydrostatic_adjustment; end
			if isfield(structmd,'penalties'), md.prognostic.vertex_pairing=structmd.penalties; end
			if isfield(structmd,'penalty_offset'), md.prognostic.penalty_factor=structmd.penalty_offset; end
			if isfield(structmd,'B'), md.materials.rheology_B=structmd.B; end
			if isfield(structmd,'n'), md.materials.rheology_n=structmd.n; end
			if isfield(structmd,'rheology_B'), md.materials.rheology_B=structmd.rheology_B; end
			if isfield(structmd,'rheology_n'), md.materials.rheology_n=structmd.rheology_n; end
			if isfield(structmd,'elementoniceshelf'), md.mask.elementonfloatingice=structmd.elementoniceshelf; end
			if isfield(structmd,'elementonicesheet'), md.mask.elementongroundedice=structmd.elementonicesheet; end
			if isfield(structmd,'elementonwater'), md.mask.elementonwater=structmd.elementonwater; end
			if isfield(structmd,'nodeoniceshelf'), md.mask.vertexonfloatingice=structmd.nodeoniceshelf; end
			if isfield(structmd,'nodeonicesheet'), md.mask.vertexongroundedice=structmd.nodeonicesheet; end
			if isfield(structmd,'nodeonwater'), md.mask.vertexonwater=structmd.nodeonwater; end
			if isfield(structmd,'spcthickness'), md.balancethickness.spcthickness=structmd.spcthickness; end
			if isfield(structmd,'artificial_diffusivity'), md.balancethickness.stabilization=structmd.artificial_diffusivity; end
			if isfield(structmd,'dhdt'), md.balancethickness.thickening_rate=structmd.dhdt; end
			if isfield(structmd,'ismacayealpattyn'), md.flowequation.ismacayealpattyn=structmd.ismacayealpattyn; end
			if isfield(structmd,'ishutter'), md.flowequation.ishutter=structmd.ishutter; end
			if isfield(structmd,'isstokes'), md.flowequation.isstokes=structmd.isstokes; end
			if isfield(structmd,'elements_type'), md.flowequation.element_equation=structmd.elements_type; end
			if isfield(structmd,'vertices_type'), md.flowequation.vertex_equation=structmd.vertices_type; end
			if isfield(structmd,'eps_rel'), md.steadystate.reltol=structmd.eps_rel; end
			if isfield(structmd,'max_steadystate_iterations'), md.steadystate.maxiter=structmd.max_steadystate_iterations; end
			if isfield(structmd,'isdiagnostic'), md.transient.isdiagnostic=structmd.isdiagnostic; end
			if isfield(structmd,'isprognostic'), md.transient.isprognostic=structmd.isprognostic; end
			if isfield(structmd,'isthermal'), md.transient.isthermal=structmd.isthermal; end
			if isfield(structmd,'control_analysis'), md.inversion.iscontrol=structmd.control_analysis; end
			if isfield(structmd,'weights'), md.inversion.cost_functions_coefficients=structmd.weights; end
			if isfield(structmd,'nsteps'), md.inversion.nsteps=structmd.nsteps; end
			if isfield(structmd,'maxiter_per_step'), md.inversion.maxiter_per_step=structmd.maxiter_per_step; end
			if isfield(structmd,'cm_min'), md.inversion.min_parameters=structmd.cm_min; end
			if isfield(structmd,'cm_max'), md.inversion.max_parameters=structmd.cm_max; end
			if isfield(structmd,'vx_obs'), md.inversion.vx_obs=structmd.vx_obs; end
			if isfield(structmd,'vy_obs'), md.inversion.vy_obs=structmd.vy_obs; end
			if isfield(structmd,'vel_obs'), md.inversion.vel_obs=structmd.vel_obs; end
			if isfield(structmd,'thickness_obs'), md.inversion.thickness_obs=structmd.thickness_obs; end
			if isfield(structmd,'vx'), md.initialization.vx=structmd.vx; end
			if isfield(structmd,'vy'), md.initialization.vy=structmd.vy; end
			if isfield(structmd,'vz'), md.initialization.vz=structmd.vz; end
			if isfield(structmd,'vel'), md.initialization.vel=structmd.vel; end
			if isfield(structmd,'pressure'), md.initialization.pressure=structmd.pressure; end
			if isfield(structmd,'temperature'), md.initialization.temperature=structmd.temperature; end
			if isfield(structmd,'waterfraction'), md.initialization.waterfraction=structmd.waterfraction; end
			if isfield(structmd,'watercolumn'), md.initialization.watercolumn=structmd.watercolumn; end
			if isfield(structmd,'surface'), md.geometry.surface=structmd.surface; end
			if isfield(structmd,'bed'), md.geometry.bed=structmd.bed; end
			if isfield(structmd,'thickness'), md.geometry.thickness=structmd.thickness; end
			if isfield(structmd,'bathymetry'), md.geometry.bathymetry=structmd.bathymetry; end
			if isfield(structmd,'thickness_coeff'), md.geometry.hydrostatic_ratio=structmd.thickness_coeff; end
			if isfield(structmd,'connectivity'), md.mesh.average_vertex_connectivity=structmd.connectivity; end
			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,'long'), md.mesh.long=structmd.long; end
			if isfield(structmd,'segments'), md.mesh.segments=structmd.segments; end
			if isfield(structmd,'segmentmarkers'), md.mesh.segmentmarkers=structmd.segmentmarkers; end
			if isfield(structmd,'dim'), md.mesh.dimension=structmd.dim; end
			if isfield(structmd,'numlayers'), md.mesh.numberoflayers=structmd.numlayers; end
			if isfield(structmd,'numberofelements'), md.mesh.numberofelements=structmd.numberofelements; end
			if isfield(structmd,'numberofvertices'), md.mesh.numberofvertices=structmd.numberofvertices; end
			if isfield(structmd,'numberofnodes'), md.mesh.numberofvertices=structmd.numberofnodes; end
			if isfield(structmd,'numberofedges'), md.mesh.numberofedges=structmd.numberofedges; end
			if isfield(structmd,'numberofelements2d'), md.mesh.numberofelements2d=structmd.numberofelements2d; end
			if isfield(structmd,'numberofnodes2d'), md.mesh.numberofvertices2d=structmd.numberofnodes2d; end
			if isfield(structmd,'nodeconnectivity'), md.mesh.vertexconnectivity=structmd.nodeconnectivity; end
			if isfield(structmd,'elementconnectivity'), md.mesh.elementconnectivity=structmd.elementconnectivity; end
			if isfield(structmd,'uppernodes'), md.mesh.uppervertex=structmd.uppernodes; end
			if isfield(structmd,'lowernodes'), md.mesh.lowervertex=structmd.lowernodes; end
			if isfield(structmd,'upperelements'), md.mesh.upperelements=structmd.upperelements; end
			if isfield(structmd,'lowerelements'), md.mesh.lowerelements=structmd.lowerelements; end
			if isfield(structmd,'elementonbed'), md.mesh.elementonbed=structmd.elementonbed; end
			if isfield(structmd,'elementonsurface'), md.mesh.elementonsurface=structmd.elementonsurface; end
			if isfield(structmd,'nodeonsurface'), md.mesh.vertexonsurface=structmd.nodeonsurface; end
			if isfield(structmd,'nodeonbed'), md.mesh.vertexonbed=structmd.nodeonbed; end
			if isfield(structmd,'elements2d'), md.mesh.elements2d=structmd.elements2d; end
			if isfield(structmd,'y2d'), md.mesh.y2d=structmd.y2d; end
			if isfield(structmd,'x2d'), md.mesh.x2d=structmd.x2d; end
			if isfield(structmd,'elements'), md.mesh.elements=structmd.elements; end
			if isfield(structmd,'edges'), 
				md.mesh.edges=structmd.edges; 
				md.mesh.edges(isnan(md.mesh.edges))=-1;
			end
			if isfield(structmd,'y'), md.mesh.y=structmd.y; end
			if isfield(structmd,'x'), md.mesh.x=structmd.x; end
			if isfield(structmd,'z'), md.mesh.z=structmd.z; end
			if isfield(structmd,'mask'), md.flaim.criterion=structmd.mask; end
			if isfield(structmd,'pressureload'), md.diagnostic.icefront=structmd.pressureload; end
			if isfield(structmd,'diagnostic_ref'), md.diagnostic.referential=structmd.diagnostic_ref; end
			if isfield(structmd,'npart'); md.qmu.numberofpartitions=structmd.npart; end
			if isfield(structmd,'part'); md.qmu.partition=structmd.part; end

			%Field changes
			if (isfield(structmd,'type') & ischar(structmd.type)), 
				if strcmpi(structmd.type,'2d'), md.mesh.dimension=2; end
				if strcmpi(structmd.type,'3d'), md.mesh.dimension=3; end
			end
			if isnumeric(md.verbose),
				md.verbose=verbose;
			end
			if size(md.diagnostic.icefront,2)==3 || size(md.diagnostic.icefront,2)==5,
				front=md.diagnostic.icefront;
				md.diagnostic.icefront=[front 1*md.mask.elementonfloatingice(front(:,end))];
			end
			if isfield(structmd,'spcvelocity'), 
				md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1);
				md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1);
				md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1);
				pos=find(structmd.spcvelocity(:,1)); md.diagnostic.spcvx(pos)=structmd.spcvelocity(pos,4); 
				pos=find(structmd.spcvelocity(:,2)); md.diagnostic.spcvy(pos)=structmd.spcvelocity(pos,5); 
				pos=find(structmd.spcvelocity(:,3)); md.diagnostic.spcvz(pos)=structmd.spcvelocity(pos,6); 
			end
			if isfield(structmd,'spcvx'), 
				md.diagnostic.spcvx=NaN*ones(md.mesh.numberofvertices,1);
				pos=find(~isnan(structmd.spcvx)); md.diagnostic.spcvx(pos)=structmd.spcvx(pos); 
			end
			if isfield(structmd,'spcvy'),
				md.diagnostic.spcvy=NaN*ones(md.mesh.numberofvertices,1);
				pos=find(~isnan(structmd.spcvy)); md.diagnostic.spcvy(pos)=structmd.spcvy(pos);     
			end
			if isfield(structmd,'spcvz'),
				md.diagnostic.spcvz=NaN*ones(md.mesh.numberofvertices,1);
				pos=find(~isnan(structmd.spcvz)); md.diagnostic.spcvz(pos)=structmd.spcvz(pos);     
			end
			if ~isempty(structmd.pressureload) & ismember(structmd.pressureload(end,end),[118 119 120]),
				pos=find(structmd.pressureload(:,end)==120); md.diagnostic.icefront(pos,end)=0;
				pos=find(structmd.pressureload(:,end)==118); md.diagnostic.icefront(pos,end)=1;
				pos=find(structmd.pressureload(:,end)==119); md.diagnostic.icefront(pos,end)=2;
			end
			if isfield(structmd,'elements_type') & structmd.elements_type(end,end)>50,
				pos=find(structmd.elements_type==59); md.flowequation.element_equation(pos,end)=0;
				pos=find(structmd.elements_type==55); md.flowequation.element_equation(pos,end)=1;
				pos=find(structmd.elements_type==56); md.flowequation.element_equation(pos,end)=2;
				pos=find(structmd.elements_type==60); md.flowequation.element_equation(pos,end)=3;
				pos=find(structmd.elements_type==62); md.flowequation.element_equation(pos,end)=4;
				pos=find(structmd.elements_type==57); md.flowequation.element_equation(pos,end)=5;
				pos=find(structmd.elements_type==58); md.flowequation.element_equation(pos,end)=6;
				pos=find(structmd.elements_type==61); md.flowequation.element_equation(pos,end)=7;
			end
			if isfield(structmd,'vertices_type') & structmd.vertices_type(end,end)>50,
				pos=find(structmd.vertices_type==59); md.flowequation.vertex_equation(pos,end)=0;
				pos=find(structmd.vertices_type==55); md.flowequation.vertex_equation(pos,end)=1;
				pos=find(structmd.vertices_type==56); md.flowequation.vertex_equation(pos,end)=2;
				pos=find(structmd.vertices_type==60); md.flowequation.vertex_equation(pos,end)=3;
				pos=find(structmd.vertices_type==62); md.flowequation.vertex_equation(pos,end)=4;
				pos=find(structmd.vertices_type==57); md.flowequation.vertex_equation(pos,end)=5;
				pos=find(structmd.vertices_type==58); md.flowequation.vertex_equation(pos,end)=6;
				pos=find(structmd.vertices_type==61); md.flowequation.vertex_equation(pos,end)=7;
			end
			if isfield(structmd,'rheology_law') & isnumeric(structmd.rheology_law),
				if (structmd.rheology_law==272), md.materials.rheology_law='None';      end
				if (structmd.rheology_law==368), md.materials.rheology_law='Paterson';  end
				if (structmd.rheology_law==369), md.materials.rheology_law='Arrhenius'; end
			end
			if isfield(structmd,'groundingline_migration') & isnumeric(structmd.groundingline_migration),
				if (structmd.groundingline_migration==272), md.groundingline.migration='None';      end
				if (structmd.groundingline_migration==273), md.groundingline.migration='AgressiveMigration';  end
				if (structmd.groundingline_migration==274), md.groundingline.migration='SoftMigration'; end
			end
			if isfield(structmd,'control_type') & isnumeric(structmd.control_type),
				if (structmd.control_type==143), md.inversion.control_parameters={'FrictionCoefficient'}; end
				if (structmd.control_type==190), md.inversion.control_parameters={'RheologyBbar'}; end
				if (structmd.control_type==147), md.inversion.control_parameters={'Thickeningrate'}; end
			end
			if isfield(structmd,'cm_responses') & ismember(structmd.cm_responses(end,end),[165:170 383 388 389]),
				pos=find(structmd.cm_responses==166); md.inversion.cost_functions(pos)=101;
				pos=find(structmd.cm_responses==167); md.inversion.cost_functions(pos)=102;
				pos=find(structmd.cm_responses==168); md.inversion.cost_functions(pos)=103;
				pos=find(structmd.cm_responses==169); md.inversion.cost_functions(pos)=104;
				pos=find(structmd.cm_responses==170); md.inversion.cost_functions(pos)=105;
				pos=find(structmd.cm_responses==165); md.inversion.cost_functions(pos)=201;
				pos=find(structmd.cm_responses==389); md.inversion.cost_functions(pos)=501;
				pos=find(structmd.cm_responses==388); md.inversion.cost_functions(pos)=502;
				pos=find(structmd.cm_responses==382); md.inversion.cost_functions(pos)=503;
			end

			if isfield(structmd,'artificial_diffusivity') & structmd.artificial_diffusivity==2,
					md.thermal.stabilization=2;
					md.prognostic.stabilization=1;
					md.balancethickness.stabilization=1;
			end
			if isnumeric(md.prognostic.hydrostatic_adjustment)
				if md.prognostic.hydrostatic_adjustment==269,
					md.prognostic.hydrostatic_adjustment='Incremental';
				else
					md.prognostic.hydrostatic_adjustment='Absolute';
				end
			end

			%New fields
			if ~isfield(structmd,'upperelements');
				md.mesh.upperelements=transpose(1:md.mesh.numberofelements)+md.mesh.numberofelements2d;
				md.mesh.upperelements(end-md.mesh.numberofelements2d+1:end)=NaN;
			end
			if ~isfield(structmd,'lowerelements');
				md.mesh.lowerelements=transpose(1:md.mesh.numberofelements)-md.mesh.numberofelements2d;
				md.mesh.lowerelements(1:md.mesh.numberofelements2d)=NaN;
			end

			if ~isfield(structmd,'diagnostic_ref');
				md.diagnostic.referential=NaN*ones(md.mesh.numberofvertices,6);
			end

		end% }}}
		function md = setdefaultparameters(md) % {{{

			%initialize subclasses
			md.mesh             = mesh();
			md.mask             = mask();
			md.constants        = constants();
			md.geometry         = geometry();
			md.initialization   = initialization();
			md.surfaceforcings  = surfaceforcings();
			md.basalforcings    = basalforcings();
			md.friction         = friction();
			md.rifts            = rifts();
			md.timestepping     = timestepping();
			md.groundingline    = groundingline();
			md.materials        = matice();
			md.flowequation     = flowequation();
			md.debug            = debug();
			md.verbose          = verbose('solution',true,'qmu',true,'control',true);
			md.settings         = settings();
			md.solver           = solver();
			if ismumps(),
				md.solver           = addoptions(md.solver,DiagnosticVertAnalysisEnum(),mumpsoptions());
			else
				md.solver           = addoptions(md.solver,DiagnosticVertAnalysisEnum(),iluasmoptions());
			end
			md.cluster          = generic();
			md.balancethickness = balancethickness();
			md.diagnostic       = diagnostic();
			md.hydrology        = hydrology();
			md.prognostic       = prognostic();
			md.thermal          = thermal();
			md.steadystate      = steadystate();
			md.transient        = transient();
			md.autodiff         = autodiff();
			md.flaim            = flaim();
			md.inversion        = inversion();
			md.qmu              = qmu();
			md.radaroverlay     = radaroverlay();
			md.results          = struct();
			md.miscellaneous    = miscellaneous();
			md.private          = private();
		end
		%}}}
		function disp(obj) % {{{
			disp(sprintf('%19s: %-22s -- %s','mesh'            ,['[1x1 ' class(obj.mesh) ']'],'mesh properties'));
			disp(sprintf('%19s: %-22s -- %s','mask'            ,['[1x1 ' class(obj.mask) ']'],'defines grounded and floating elements'));
			disp(sprintf('%19s: %-22s -- %s','geometry'        ,['[1x1 ' class(obj.geometry) ']'],'surface elevation, bedrock topography, ice thickness,...'));
			disp(sprintf('%19s: %-22s -- %s','constants'       ,['[1x1 ' class(obj.constants) ']'],'physical constants'));
			disp(sprintf('%19s: %-22s -- %s','surfaceforcings' ,['[1x1 ' class(obj.surfaceforcings) ']'],'surface forcings'));
			disp(sprintf('%19s: %-22s -- %s','basalforcings'   ,['[1x1 ' class(obj.basalforcings) ']'],'bed forcings'));
			disp(sprintf('%19s: %-22s -- %s','materials'       ,['[1x1 ' class(obj.materials) ']'],'material properties'));
			disp(sprintf('%19s: %-22s -- %s','friction'        ,['[1x1 ' class(obj.friction) ']'],'basal friction/drag properties'));
			disp(sprintf('%19s: %-22s -- %s','flowequation'    ,['[1x1 ' class(obj.flowequation) ']'],'flow equations'));
			disp(sprintf('%19s: %-22s -- %s','timestepping'    ,['[1x1 ' class(obj.timestepping) ']'],'time stepping for transient models'));
			disp(sprintf('%19s: %-22s -- %s','initialization'  ,['[1x1 ' class(obj.initialization) ']'],'initial guess/state'));
			disp(sprintf('%19s: %-22s -- %s','rifts'           ,['[1x1 ' class(obj.rifts) ']'],'rifts properties'));
			disp(sprintf('%19s: %-22s -- %s','debug'           ,['[1x1 ' class(obj.debug) ']'],'debugging tools (valgrind, gprof)'));
			disp(sprintf('%19s: %-22s -- %s','verbose'         ,['[1x1 ' class(obj.verbose) ']'],'verbosity level in solve'));
			disp(sprintf('%19s: %-22s -- %s','settings'        ,['[1x1 ' class(obj.settings) ']'],'settings properties'));
			disp(sprintf('%19s: %-22s -- %s','solver'          ,['[1x1 ' class(obj.solver) ']'],'PETSc options for each solution'));
			disp(sprintf('%19s: %-22s -- %s','cluster'         ,['[1x1 ' class(obj.cluster) ']'],'cluster parameters (number of cpus...)'));
			disp(sprintf('%19s: %-22s -- %s','balancethickness',['[1x1 ' class(obj.balancethickness) ']'],'parameters for balancethickness solution'));
			disp(sprintf('%19s: %-22s -- %s','diagnostic'      ,['[1x1 ' class(obj.diagnostic) ']'],'parameters for diagnostic solution'));
			disp(sprintf('%19s: %-22s -- %s','groundingline'   ,['[1x1 ' class(obj.groundingline) ']'],'parameters for groundingline solution'));
			disp(sprintf('%19s: %-22s -- %s','hydrology'       ,['[1x1 ' class(obj.hydrology) ']'],'parameters for hydrology solution'));
			disp(sprintf('%19s: %-22s -- %s','prognostic'      ,['[1x1 ' class(obj.prognostic) ']'],'parameters for prognostic solution'));
			disp(sprintf('%19s: %-22s -- %s','thermal'         ,['[1x1 ' class(obj.thermal) ']'],'parameters for thermal solution'));
			disp(sprintf('%19s: %-22s -- %s','steadystate'     ,['[1x1 ' class(obj.steadystate) ']'],'parameters for steadystate solution'));
			disp(sprintf('%19s: %-22s -- %s','transient'       ,['[1x1 ' class(obj.transient) ']'],'parameters for transient solution'));
			disp(sprintf('%19s: %-22s -- %s','autodiff'        ,['[1x1 ' class(obj.autodiff) ']'],'automatic differentiation parameters'));
			disp(sprintf('%19s: %-22s -- %s','flaim'           ,['[1x1 ' class(obj.flaim) ']'],'flaim parameters'));
			disp(sprintf('%19s: %-22s -- %s','inversion'       ,['[1x1 ' class(obj.inversion) ']'],'parameters for inverse methods'));
			disp(sprintf('%19s: %-22s -- %s','qmu'             ,['[1x1 ' class(obj.qmu) ']'],'dakota properties'));
			disp(sprintf('%19s: %-22s -- %s','results'         ,['[1x1 ' class(obj.results) ']'],'model results'));
			disp(sprintf('%19s: %-22s -- %s','radaroverlay'    ,['[1x1 ' class(obj.radaroverlay) ']'],'radar image for plot overlay'));
			disp(sprintf('%19s: %-22s -- %s','miscellaneous'   ,['[1x1 ' class(obj.miscellaneous) ']'],'miscellaneous fields'));
		end % }}}
	end
 end
