//MODEL class definition
//
//   Usage:
//      md = new model()

function model () {
	//methods
		this.disp = function() { //{{{
			console.log(sprintf("class model echo: "));
			console.log(sprintf("//19s: //-22s -- //s","mesh"            ,"[1x1 " + typeof(this.mesh) + "]","mesh properties"));
			console.log(sprintf("//19s: //-22s -- //s","mask"            ,"[1x1 " + typeof(this.mask) + "]","defines grounded and floating elements"));
			console.log(sprintf("//19s: //-22s -- //s","geometry"        ,"[1x1 " + typeof(this.geometry) + "]","surface elevation, bedrock topography, ice thickness,..."));
			console.log(sprintf("//19s: //-22s -- //s","constants"       ,"[1x1 " + typeof(this.constants) + "]","physical constants"));
			console.log(sprintf("//19s: //-22s -- //s","smb"             ,"[1x1 " + typeof(this.smb) + "]","surface mass balance"));
			console.log(sprintf("//19s: //-22s -- //s","basalforcings"   ,"[1x1 " + typeof(this.basalforcings) + "]","bed forcings"));
			console.log(sprintf("//19s: //-22s -- //s","materials"       ,"[1x1 " + typeof(this.materials) + "]","material properties"));
			console.log(sprintf("//19s: //-22s -- //s","damage"          ,"[1x1 " + typeof(this.damage) + "]","parameters for damage evolution solution"));
			console.log(sprintf("//19s: //-22s -- //s","friction"        ,"[1x1 " + typeof(this.friction) + "]","basal friction/drag properties"));
			console.log(sprintf("//19s: //-22s -- //s","flowequation"    ,"[1x1 " + typeof(this.flowequation) + "]","flow equations"));
			console.log(sprintf("//19s: //-22s -- //s","timestepping"    ,"[1x1 " + typeof(this.timestepping) + "]","time stepping for trans models"));
			console.log(sprintf("//19s: //-22s -- //s","initialization"  ,"[1x1 " + typeof(this.initialization) + "]","initial guess/state"));
			console.log(sprintf("//19s: //-22s -- //s","rifts"           ,"[1x1 " + typeof(this.rifts) + "]","rifts properties"));
			console.log(sprintf("//19s: //-22s -- //s","slr"             ,"[1x1 " + typeof(this.slr) + "]","slr forcings"));
			console.log(sprintf("//19s: //-22s -- //s","dsl"             ,"[1x1 " + typeof(this.dsl) + "]","dynamic sea level"));
			console.log(sprintf("//19s: //-22s -- //s","debug"           ,"[1x1 " + typeof(this.debug) + "]","debugging tools (valgrind, gprof)"));
			console.log(sprintf("//19s: //-22s -- //s","verbose"         ,"[1x1 " + typeof(this.verbose) + "]","verbosity level in solve"));
			console.log(sprintf("//19s: //-22s -- //s","settings"        ,"[1x1 " + typeof(this.settings) + "]","settings properties"));
			console.log(sprintf("//19s: //-22s -- //s","toolkits"        ,"[1x1 " + typeof(this.toolkits) + "]","PETSc options for each solution"));
			console.log(sprintf("//19s: //-22s -- //s","cluster"         ,"[1x1 " + typeof(this.cluster) + "]","cluster parameters (number of cpus...)"));
			console.log(sprintf("//19s: //-22s -- //s","balancethickness","[1x1 " + typeof(this.balancethickness) + "]","parameters for balancethickness solution"));
			console.log(sprintf("//19s: //-22s -- //s","stressbalance"   ,"[1x1 " + typeof(this.stressbalance) + "]","parameters for stressbalance solution"));
			console.log(sprintf("//19s: //-22s -- //s","groundingline"   ,"[1x1 " + typeof(this.groundingline) + "]","parameters for groundingline solution"));
			console.log(sprintf("//19s: //-22s -- //s","hydrology"       ,"[1x1 " + typeof(this.hydrology) + "]","parameters for hydrology solution"));
			console.log(sprintf("//19s: //-22s -- //s","masstransport"   ,"[1x1 " + typeof(this.masstransport) + "]","parameters for masstransport solution"));
			console.log(sprintf("//19s: //-22s -- //s","thermal"         ,"[1x1 " + typeof(this.thermal) + "]","parameters for thermal solution"));
			console.log(sprintf("//19s: //-22s -- //s","steadystate"     ,"[1x1 " + typeof(this.steadystate) + "]","parameters for steadystate solution"));
			console.log(sprintf("//19s: //-22s -- //s","trans"           ,"[1x1 " + typeof(this.trans) + "]","parameters for trans solution"));
			console.log(sprintf("//19s: //-22s -- //s","levelset"        ,"[1x1 " + typeof(this.levelset) + "]","parameters for moving boundaries (level-set method)"));
			console.log(sprintf("//19s: //-22s -- //s","calving"         ,"[1x1 " + typeof(this.calving) + "]","parameters for calving"));
			console.log(sprintf("//19s: //-22s -- //s","gia"             ,"[1x1 " + typeof(this.gia) + "]","parameters for gia solution"));
			console.log(sprintf("//19s: //-22s -- //s","love"            ,"[1x1 " + typeof(this.love) + "]","parameters for love solution"));
			console.log(sprintf("//19s: //-22s -- //s","esa"             ,"[1x1 " + typeof(this.esa) + "]","parameters for elastic adjustment solution"));
			console.log(sprintf("//19s: //-22s -- //s","autodiff"        ,"[1x1 " + typeof(this.autodiff) + "]","automatic differentiation parameters"));
			console.log(sprintf("//19s: //-22s -- //s","inversion"       ,"[1x1 " + typeof(this.inversion) + "]","parameters for inverse methods"));
			console.log(sprintf("//19s: //-22s -- //s","qmu"             ,"[1x1 " + typeof(this.qmu) + "]","dakota properties"));
			console.log(sprintf("//19s: //-22s -- //s","amr"             ,"[1x1 " + typeof(this.amr) + "]","adaptive mesh refinement properties"));
			console.log(sprintf("//19s: //-22s -- //s","outputdefinition","[1x1 " + typeof(this.outputdefinition) + "]","output definition"));
			console.log(sprintf("//19s: //-22s -- //s","results"         ,"[1x1 " + typeof(this.results) + "]","model results"));
			console.log(sprintf("//19s: //-22s -- //s","radaroverlay"    ,"[1x1 " + typeof(this.radaroverlay) + "]","radar image for plot overlay"));
			console.log(sprintf("//19s: //-22s -- //s","miscellaneous"   ,"[1x1 " + typeof(this.miscellaneous) + "]","miscellaneous fields"));
		} //}}}
		this.setdefaultparameters = function () { // {{{

			//initialize subclasses
			this.mesh             = new mesh2d();
			this.mask             = new mask();
			this.constants        = new constants();
			this.geometry         = new geometry();
			this.smb              = new SMBforcing();
			this.basalforcings    = new basalforcings();
			this.materials        = new matice();
			this.damage           = new damage();
			this.friction         = new friction();
			this.flowequation     = new flowequation();
			this.timestepping     = new timestepping();
			this.initialization   = new initialization();
			this.rifts            = new rifts();
			this.slr              = new slr();
			this.dsl              = new dsl();

			this.debug            = new debug();
			this.verbose          = new verbose();
			this.settings         = new issmsettings();
			this.toolkits         = new toolkits();
			this.cluster          = new local();

			this.balancethickness = new balancethickness();
			this.stressbalance    = new stressbalance();
			this.groundingline    = new groundingline();
			this.hydrology        = new hydrologyshreve();
			this.masstransport    = new masstransport();
			this.thermal          = new thermal();
			this.steadystate      = new steadystate();
			this.trans            = new trans();
			this.levelset         = new levelset();
			this.calving          = new calving();
			this.gia              = new giaivins();
			this.love             = new fourierlove();
			this.esa              = new esa();
			this.autodiff         = new autodiff();
			this.inversion        = new inversion();
			this.qmu              = new qmu();
			this.amr					 = new amr();
			this.radaroverlay     = new radaroverlay();
			this.results          = {};
			this.outputdefinition = new outputdefinition();
			this.radaroverlay     = new radaroverlay();
			this.miscellaneous    = new miscellaneous();
			this.priv             = new priv();
		} //}}}
		this.checkmessage = function(string){ //{{{
			console.log('model not consistent: ' + string);
			this.priv.isconsistent=false;
		} //}}}
		this.fix = function(){ //{{{

			for (var field in this){

				//Some properties do not need to be fixed
				if (field == 'results' | field =='radaroverlay' | field == 'toolkits' | field =='cluster' | field == 'priv') continue;

				//Check that current field is a class
				if(typeof this[field] == 'function'){
					continue;
				}

				//Fix current object
				this[field].fix(this);
			}

		} //}}}
		this.extrude = function(md) { //{{{
			//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 described 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,15,1.3);
			//      md=extrude(md,15,1.3,1.2);
			//      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
			var argc = arguments.length;
			var extrusionlist;
			var numlayers;
			
			if ((argc > 4) | (argc < 2)) {
				throw "extrude error message";
			}

			//Extrude the mesh
			if (argc==2) { //list of coefficients
				clist=arguments[0];
				if (ArrayAnyBelowStrict(clist,0) || ArrayAnyAboveStrict(clist,1)) {
					throw 'extrusioncoefficients must be between 0 and 1';
				}
				extrusionlist=ArraySort(ArrayUnique(clist.push(0,1)));
				numlayers=extrusionlist.length;
			} else if (argc==3) { //one polynomial law
				if (arguments[1]<=0) {
					throw 'extrusionexponent must be >=0';
				}
				numlayers=arguments[1];
				extrusionlist = [];
				for (var i = 0; i < numlayers; i++) {
					extrusionlist.push(Math.pow(i/(numlayers-1), arguments[2]));
				}
			} else if (argc==4) { //two polynomial laws
				numlayers=arguments[1];
				var lowerexp=arguments[2];
				var upperexp=arguments[3];

				if (arguments[2]<=0 || arguments[3]<=0) {
					throw 'lower and upper extrusionexponents must be >=0';
				}

				var lowerextrusionlist = [];
				for (var i = 0; i <= 1; i += (2/(numlayers-1))) {
					lowerextrusionlist.push(Math.pow(i, lowerexp)/2)
				}
				var upperextrusionlist = [];
				for (var i = 0; i <= 1; i += (2/(numlayers-1))) {
					upperextrusionlist.push(1-Math.pow(i, upperexp)/2)
				}
				extrusionlist=ArrayConcat(lowerextrusionlist,upperextrusionlist);
				extrusionlist=ArraySort(ArrayUnique(extrusionlist.push(1)));
			}

			if (numlayers<2) {
				console.error('number of layers should be at least 2');
			}
			if (md.mesh.domaintype() === '3D') {
				console.error('Cannot extrude a 3d mesh (extrude cannot be called more than once)');
			}

			//Initialize with the 2d mesh
			var mesh2d = md.mesh;
			md.mesh=new mesh3dprisms();
			md.mesh.x                           = mesh2d.x;
			md.mesh.y                           = mesh2d.y;
			md.mesh.elements                    = mesh2d.elements;
			md.mesh.numberofelements            = mesh2d.numberofelements;
			md.mesh.numberofvertices            = mesh2d.numberofvertices;

			md.mesh.lat                         = mesh2d.lat;
			md.mesh.long                        = mesh2d.long;
			md.mesh.epsg                        = mesh2d.epsg;
			md.mesh.scale_factor                = mesh2d.scale_factor;

			md.mesh.vertexonboundary            = mesh2d.vertexonboundary;
			md.mesh.vertexconnectivity          = mesh2d.vertexconnectivity;
			md.mesh.elementconnectivity         = mesh2d.elementconnectivity;
			md.mesh.average_vertex_connectivity = mesh2d.average_vertex_connectivity;

			md.mesh.extractedvertices           = mesh2d.extractedvertices;
			md.mesh.extractedelements           = mesh2d.extractedelements;

			var x3d=new Float64Array(); 
			var y3d=new Float64Array();
			var z3d=new Float64Array();  //the lower node is on the bed
			var thickness3d=md.geometry.thickness; //thickness and bed for these nodes
			var bed3d=md.geometry.base;

			//Create the new layers
			//Dimensions of x/y/z3d: md.mesh.numberofvertices * numlayers, 1
			for (var i = 1; i <= numlayers; i++) {
				x3d=ArrayConcat(x3d, md.mesh.x); 
				y3d=ArrayConcat(y3d, md.mesh.y); 
				//nodes are distributed between bed and surface accordingly to the given exponent
				z3d=ArrayConcat(z3d, FloatFix(thickness3d.map(function(value,index) { return bed3d[index] + value * extrusionlist[i-1]; }), thickness3d.length)); 
			}
			var number_nodes3d=x3d.length; //number of 3d nodes for the non extruded part of the mesh

			//Extrude elements 
			//Create the elements of the 3d mesh for the non extruded part
			//Dimensions of elements3d: md.mesh.numberofelements * (numlayers - 1), 6
			var elements3d=[];
			var elements_prisms=[];
			for (var i = 1; i < numlayers; i++) {
				for (var j = 0; j < md.mesh.numberofelements; j++) {
					elements_prisms = [];
					for (var k = 0, offset = (i - 1) * md.mesh.numberofvertices; k < 3; k++) {
						elements_prisms.push(md.mesh.elements[j][k]+offset);
					}
					for (var k = 0, offset = i * md.mesh.numberofvertices; k < 3; k++) {
						elements_prisms.push(md.mesh.elements[j][k]+offset);
					}
					elements3d.push(elements_prisms);
				}				
			}
			number_el3d=elements3d.length; //number of 3d nodes for the non extruded part of the mesh

			//Keep a trace of lower and upper nodes
			var lowervertex = NewArrayFill(number_nodes3d, NaN);
			var uppervertex = NewArrayFill(number_nodes3d, NaN);
			//Set first layer to NaN and start count from 1 at next layer (i = md.mesh.numberofvertices+1)
			for (var i = md.mesh.numberofvertices, k = 1; i < lowervertex.length; i++, k++) {
				lowervertex[i] = k;
			};
			//Set last layer to NaN and start count from md.mesh.numberofvertices+1 at first layer (i = 1)
			for (var i = 0, k = md.mesh.numberofvertices+1; i < (numlayers-1)*md.mesh.numberofvertices; i++, k++) {
				uppervertex[i] = k;
			};
			md.mesh.lowervertex=lowervertex;
			md.mesh.uppervertex=uppervertex;

			//same for lower and upper elements
			var lowerelements = NewArrayFill(number_el3d, NaN);
			var upperelements = NewArrayFill(number_el3d, NaN);
			//Set first layer to NaN and start count from 1 at next layer (i = md.mesh.numberofelements+1)
			for (var i = md.mesh.numberofelements, k = 1; i < lowerelements.length; i++, k++) {
				lowerelements[i] = k;
			};
			//Set last 2 layers to NaN and start count from md.mesh.numberofvertices+1 at first layer (i = 1)
			for (var i = 0, k = md.mesh.numberofelements + 1; i < (numlayers-2)*md.mesh.numberofelements; i++, k++) {
				upperelements[i] = k;
			};
			md.mesh.lowerelements=lowerelements;
			md.mesh.upperelements=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;

			//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:

			//bedinfo and surface info
			md.mesh.vertexonbase=project3d(md,'vector',NewArrayFill(md.mesh.numberofvertices2d,1),'type','node','layer',1);
			md.mesh.vertexonsurface=project3d(md,'vector',NewArrayFill(md.mesh.numberofvertices2d,1),'type','node','layer',md.mesh.numberoflayers);
			md.mesh.vertexonboundary=project3d(md,'vector',md.mesh.vertexonboundary,'type','node');

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

			md.geometry=md.geometry.extrude(md);
			md.friction=md.friction.extrude(md);
			md.inversion=md.inversion.extrude(md);
			md.smb=md.smb.extrude(md);
			md.initialization=md.initialization.extrude(md);

			md.flowequation=md.flowequation.extrude(md);
			md.stressbalance=md.stressbalance.extrude(md);
			md.thermal=md.thermal.extrude(md);
			md.masstransport=md.masstransport.extrude(md);
			md.levelset=md.levelset.extrude(md);
			md.calving=md.calving.extrude(md);
			md.hydrology = md.hydrology.extrude(md);

			//connectivity
			if (!ArrayAnyNaN(md.mesh.elementconnectivity)) {
				//md.mesh.elementconnectivity=repmat(md.mesh.elementconnectivity,numlayers-1,1); //Replicate the matrix across numlayers-1 
				var temparr = [];
				for (var i = 0; i < numlayers - 1; i++) {
					temparr = ArrayConcat(temparr, md.mesh.elementconnectivity);
				}
				md.mesh.elementconnectivity = temparr;
		
				//md.mesh.elementconnectivity(find(md.mesh.elementconnectivity==0))=NaN;
				var indices = ArrayFind(md.mesh.elementconnectivity, 0);
				for (var i = 0; i < indices.length; i++) {
					md.mesh.elementconnectivity[i] = NaN;
				};
		
				for (var i = 2; i < numlayers; i++) {
					//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;
					for (var j = (i-1)*md.mesh.numberofelements2d; j <= (i)*md.mesh.numberofelements2d-1; j++) {
						for (var k = 0; k < 3; k++) {
							md.mesh.elementconnectivity[j][k] += md.mesh.numberofelements2d;
						}
					}
				}
				md.mesh.elementconnectivity = md.mesh.elementconnectivity.map(function(value) { return (Number.isNaN(value)) ? 0 : value; });
			}

			md.materials=md.materials.extrude(md);
			md.damage=md.damage.extrude(md);
			md.mask=md.mask.extrude(md);
			md.qmu=md.qmu.extrude(md);
			md.basalforcings=md.basalforcings.extrude(md);

			//increase connectivity if less than 25:
			if (md.mesh.average_vertex_connectivity<=25) {
				md.mesh.average_vertex_connectivity=100;
			}
		} //}}}
		this.extract = function(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: '~HO.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');
			//
			//   See also: EXTRUDE, COLLAPSE

			//some checks on list of arguments
			var argc = arguments.length;

			if (!((argc == 2) | (argc == 1))) {
				throw "extract error message: bad usage";
			}
			
			//get elements that are inside area
			flag_elem=FlagElements(this,area);

			if (!ArrayAnyEqual(flag_elem,1))throw "extracted model is empty!"

			/*kick out all elements with 3 dirichlets: actually, not so fast, not good for javscript usually.
			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
			var pos_elem = ArrayFind(flag_elem,1);
			var dup_nodes= new Array(pos_elem.length*3);
			for(var i=0;i<pos_elem.length;i++){
				dup_nodes[3*i]=md.mesh.elements[pos_elem[i]][0]-1;
				dup_nodes[3*i+1]=md.mesh.elements[pos_elem[i]][1]-1;
				dup_nodes[3*i+2]=md.mesh.elements[pos_elem[i]][2]-1;
			}
			pos_node=ArrayUnique(dup_nodes); pos_node=ArraySort(pos_node);

			//keep track of some fields
			var numberofvertices1=md.mesh.numberofvertices;
			var numberofelements1=md.mesh.numberofelements;
			var numberofvertices2=pos_node.length;
			var numberofelements2=pos_elem.length;
			var flag_node=NewArrayFill(numberofvertices1,0);
			for (var i=0;i<pos_node.length;i++)flag_node[pos_node[i]]=1;

			//Create Pelem and Pnode (transform old nodes in new nodes and same thing for the elements)
			Pelem=NewArrayFill(numberofelements1,0);
			for (var i=0;i<numberofelements2;i++) Pelem[pos_elem[i]]=i;
			Pnode=NewArrayFill(numberofvertices1,0);
			for (var i=0;i<numberofvertices2;i++) Pnode[pos_node[i]]=i;
			//renumber the elements (some nodes won't exist anymore)
			var elements_2=NewArrayFill2D(numberofelements2,3,0);
			for (var i=0;i<numberofelements2;i++){
				for (var j=0;j<3;j++){
					elements_2[i][j]=Pnode[md.mesh.elements[i][j]-1]+1;
				}
			}
			
			/*if isa(md.mesh,'mesh3dprisms'),
				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
			var md2=md.deepcopy(md);
			//var md2=new model(); md2.mesh=new mesh3dsurface();
			
			//deal with mesh: {{{
			md2.mesh.numberofvertices=numberofvertices2;
			md2.mesh.numberofelements=numberofelements2;
			md2.mesh.elements=elements_2;

			md2.mesh.x=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.mesh.x[i]=md.mesh.x[pos_node[i]];
			md2.mesh.y=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.mesh.y[i]=md.mesh.y[pos_node[i]];
			md2.mesh.z=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.mesh.z[i]=md.mesh.z[pos_node[i]];
			md2.mesh.lat=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.mesh.lat[i]=md.mesh.lat[pos_node[i]];
			md2.mesh.long=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.mesh.long[i]=md.mesh.long[pos_node[i]];
			md2.mesh.r=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.mesh.r[i]=md.mesh.r[pos_node[i]];
			//}}}
			//deal with geometry: {{{
			md2.geometry.base=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.geometry.base[i]=md.geometry.base[pos_node[i]];
			md2.geometry.thickness=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.geometry.thickness[i]=md.geometry.thickness[pos_node[i]];
			md2.geometry.surface=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.geometry.surface[i]=md.geometry.surface[pos_node[i]];
			md2.geometry.bed=new Array(numberofvertices2); for (var i=0;i<numberofvertices2;i++)md2.geometry.bed[i]=md.geometry.bed[pos_node[i]];
			//}}}

			//Keep track of pos_node and pos_elem
			for (var i=0;i<md2.mesh.numberofvertices;i++)pos_node[i]=pos_node[i]+1;
			for (var i=0;i<md2.mesh.numberofelements;i++)pos_elem[i]=pos_elem[i]+1;
			md2.mesh.extractedvertices=pos_node;
			md2.mesh.extractedelements=pos_elem;

			return md2;



			//automatically modify fields

			//loop over model fields
			//model_fields=fields(md);





		} //}}}
		this.collapse = function(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.elementtype() !== 'Penta') {
				console.error('collapse error message: only 3d mesh can be collapsed')
			}

			// Start with changing all the fields from the 3d mesh 

			// dealing with the friction law
			// drag is limited to nodes that are on the bedrock.
			if (md.friction.classname() === 'friction') {
				md.friction.coefficient=project2d(md,md.friction.coefficient,1);
				md.friction.p=project2d(md,md.friction.p,1);
				md.friction.q=project2d(md,md.friction.q,1);
			} else if (md.friction.classname() === 'frictionhydro') {
				md.friction.q=project2d(md,md.friction.q,1);
				md.friction.C=project2d(md,md.friction.C,1);
				md.friction.As=project2d(md,md.friction.As,1);
				md.friction.effective_pressure=project2d(md,md.friction.effective_pressure,1);
			} else if (md.friction.classname() === 'frictionwaterlayer') {
				md.friction.coefficient=project2d(md,md.friction.coefficient,1);
				md.friction.p=project2d(md,md.friction.p,1);
				md.friction.q=project2d(md,md.friction.q,1);
				md.friction.water_layer=project2d(md,md.friction.water_layer,1);
			} else if (md.friction.classname() === 'frictionweertman') {
				md.friction.C=project2d(md,md.friction.C,1);
				md.friction.m=project2d(md,md.friction.m,1);
			} else if (md.friction.classname() === 'frictionweertmantemp') {
				md.friction.C=project2d(md,md.friction.C,1);
				md.friction.m=project2d(md,md.friction.m,1);
			} else {
				disp('friction type not supported');
			}

			// observations
			if (!Number.isNaN(md.inversion.vx_obs))
				md.inversion.vx_obs=project2d(md,md.inversion.vx_obs,md.mesh.numberoflayers);

			if (!Number.isNaN(md.inversion.vy_obs))
				md.inversion.vy_obs=project2d(md,md.inversion.vy_obs,md.mesh.numberoflayers);

			if (!Number.isNaN(md.inversion.vel_obs))
				md.inversion.vel_obs=project2d(md,md.inversion.vel_obs,md.mesh.numberoflayers);

			if (!Number.isNaN(md.inversion.cost_functions_coefficients))
				md.inversion.cost_functions_coefficients=project2d(md,md.inversion.cost_functions_coefficients,md.mesh.numberoflayers);

			if (numel(md.inversion.min_parameters)>1)
				md.inversion.min_parameters=project2d(md,md.inversion.min_parameters,md.mesh.numberoflayers);

			if (numel(md.inversion.max_parameters)>1) 
				md.inversion.max_parameters=project2d(md,md.inversion.max_parameters,md.mesh.numberoflayers);

			if (md.smb.classname() === 'SMBforcing' && !Number.isNaN(md.smb.mass_balance)) {
				md.smb.mass_balance=project2d(md,md.smb.mass_balance,md.mesh.numberoflayers);
			} else if (md.smb.classname() === 'SMBhenning' && !Number.isNaN(md.smb.smbref)) {
				md.smb.smbref=project2d(md,md.smb.smbref,md.mesh.numberoflayers);
			}

			// results
			if (!Number.isNaN(md.initialization.vx))
				md.initialization.vx=DepthAverage(md,md.initialization.vx);
			if (!Number.isNaN(md.initialization.vy))
				md.initialization.vy=DepthAverage(md,md.initialization.vy);
			if (!Number.isNaN(md.initialization.vz))
				md.initialization.vz=DepthAverage(md,md.initialization.vz);
			if (!Number.isNaN(md.initialization.vel))
				md.initialization.vel=DepthAverage(md,md.initialization.vel);
			if (!Number.isNaN(md.initialization.temperature))
				md.initialization.temperature=DepthAverage(md,md.initialization.temperature);
			if (!Number.isNaN(md.initialization.pressure))
				md.initialization.pressure=project2d(md,md.initialization.pressure,1);
			if (!Number.isNaN(md.initialization.sediment_head))
				md.initialization.sediment_head=project2d(md,md.initialization.sediment_head,1);
			if (!Number.isNaN(md.initialization.epl_head))
				md.initialization.epl_head=project2d(md,md.initialization.epl_head,1);
			if (!Number.isNaN(md.initialization.epl_thickness))
				md.initialization.epl_thickness=project2d(md,md.initialization.epl_thickness,1);

			// giaivins
			if (!Number.isNaN(md.gia.mantle_viscosity))
				md.gia.mantle_viscosity=project2d(md,md.gia.mantle_viscosity,1);
			if (!Number.isNaN(md.gia.lithosphere_thickness))
				md.gia.lithosphere_thickness=project2d(md,md.gia.lithosphere_thickness,1);

			// elementstype
			if (!Number.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.borderSSA=project2d(md,md.flowequation.borderSSA,1);
				md.flowequation.borderHO=project2d(md,md.flowequation.borderHO,1);
				md.flowequation.borderFS=project2d(md,md.flowequation.borderFS,1);
			}

			// boundary conditions
			md.stressbalance.spcvx=project2d(md,md.stressbalance.spcvx,md.mesh.numberoflayers);
			md.stressbalance.spcvy=project2d(md,md.stressbalance.spcvy,md.mesh.numberoflayers);
			md.stressbalance.spcvz=project2d(md,md.stressbalance.spcvz,md.mesh.numberoflayers);
			md.stressbalance.referential=project2d(md,md.stressbalance.referential,md.mesh.numberoflayers);
			md.stressbalance.loadingforce=project2d(md,md.stressbalance.loadingforce,md.mesh.numberoflayers);
			md.masstransport.spcthickness=project2d(md,md.masstransport.spcthickness,md.mesh.numberoflayers);
			if (!Number.isNaN(md.damage.spcdamage))
				md.damage.spcdamage=project2d(md,md.damage.spcdamage,md.mesh.numberoflayers);
			md.thermal.spctemperature=project2d(md,md.thermal.spctemperature,md.mesh.numberoflayers);

			// Hydrologydc variables
			if (md.hydrology.classname() === 'hydrologydc') {
				md.hydrology.spcsediment_head=project2d(md,md.hydrology.spcsediment_head,1);
				md.hydrology.mask_eplactive_node=project2d(md,md.hydrology.mask_eplactive_node,1);
				md.hydrology.sediment_transmitivity=project2d(md,md.hydrology.sediment_transmitivity,1);
				md.hydrology.basal_moulin_input=project2d(md,md.hydrology.basal_moulin_input,1);

				if(md.hydrology.isefficientlayer==1)
					md.hydrology.spcepl_head=project2d(md,md.hydrology.spcepl_head,1);
			}
			
			// materials
			md.materials.rheology_B=DepthAverage(md,md.materials.rheology_B);
			md.materials.rheology_n=project2d(md,md.materials.rheology_n,1);
			
			// damage: 
			if (md.damage.isdamage)
				md.damage.D=DepthAverage(md,md.damage.D);

			// special for thermal modeling:
			if (!Number.isNaN(md.basalforcings.groundedice_melting_rate))
				md.basalforcings.groundedice_melting_rate=project2d(md,md.basalforcings.groundedice_melting_rate,1); 

			if (!Number.isNaN(md.basalforcings.floatingice_melting_rate))
				md.basalforcings.floatingice_melting_rate=project2d(md,md.basalforcings.floatingice_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
			var nodes2d=md.mesh.numberofvertices2d;
			var 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.base=project2d(md,md.geometry.base,1);
			if (!Number.isNaN(md.geometry.bed))
				md.geometry.bed=project2d(md,md.geometry.bed,1);

			if (!Number.isNaN(md.mask.groundedice_levelset))
				md.mask.groundedice_levelset=project2d(md,md.mask.groundedice_levelset,1);

			if (!Number.isNaN(md.mask.ice_levelset))
				md.mask.ice_levelset=project2d(md,md.mask.ice_levelset,1);

			// lat long
			if (numel(md.mesh.lat) === md.mesh.numberofvertices)
				md.mesh.lat=project2d(md,md.mesh.lat,1);
			if (numel(md.mesh.long) === md.mesh.numberofvertices)
				md.mesh.long=project2d(md,md.mesh.long,1);
			if (numel(md.mesh.scale_factor) === md.mesh.numberofvertices)
				md.mesh.scale_factor=project2d(md,md.mesh.scale_factor,1);

			// Initialize with the 2d mesh
			var mesh = new mesh2d();
			mesh.x=md.mesh.x2d;
			mesh.y=md.mesh.y2d;
			mesh.numberofvertices=md.mesh.numberofvertices2d;
			mesh.numberofelements=md.mesh.numberofelements2d;
			mesh.elements=md.mesh.elements2d;

			if (!Number.isNaN(md.mesh.vertexonboundary))
				mesh.vertexonboundary=project2d(md,md.mesh.vertexonboundary,1);
			if (!Number.isNaN(md.mesh.elementconnectivity))
				mesh.elementconnectivity=project2d(md,md.mesh.elementconnectivity,1);

			md.mesh=mesh;
			md.mesh.vertexconnectivity=NodeConnectivity(md.mesh.elements,md.mesh.numberofvertices);
			md.mesh.elementconnectivity=ElementConnectivity(md.mesh.elements,md.mesh.vertexconnectivity);
			md.mesh.segments=contourenvelope(md.mesh);

			return md;
		} /*}}}*/
		this.deepCopy = function(md) { //{{{
			/*
			 *DEEPCOPY - returns a deep copy of the model.
			 *
			 *   This routine creates a new model with new objects 
			 *   for each corresponding object in the original model,
			 *   so that changes in one do not affect the other.
			 *
			 *   Usage:
			 *	 md1=deepCopy(md)
			 *
			 */
			function recursiveDeepCopy(obj) {
				var returnValue;

				switch (typeof obj) {
					case "object":
						if (obj === null) {
							// null => null
							returnValue = null;
						} else {
							switch (toString.call(obj)) {
								case "[object Array]":
									// It's an array, create a new array with deep copies of the entries
									returnValue = obj.map(recursiveDeepCopy);
									break;
								default:
									// Some other kind of object, deep-copy its properties into a new object
									returnValue = Object.keys(obj).reduce(function(prev, key) {
										prev[key] = recursiveDeepCopy(obj[key]);
										return prev;
									}, {});
									break;
							}
						}
						break;
					default:
						// It's a primitive, copy via assignment
						returnValue = obj;
						break;
				}
				return returnValue;
			}
			
			return recursiveDeepCopy(md);
		} /*}}}*/
	//properties
	// {{{
		//Careful here: no other class should be used as default value this is a bug of matlab
		this.mesh             = 0;
		this.mask             = 0;

		this.geometry         = 0;
		this.constants        = 0;
		this.smb              = 0;
		this.basalforcings    = 0;
		this.materials        = 0;
		this.damage           = 0;
		this.friction         = 0;
		this.flowequation     = 0;
		this.timestepping     = 0;
		this.initialization   = 0;
		this.rifts            = 0;
		this.slr              = 0;
		this.dsl              = 0;

		this.debug            = 0;
		this.verbose          = 0;
		this.settings         = 0;
		this.toolkits         = 0;
		this.cluster          = 0;

		this.balancethickness = 0;
		this.stressbalance    = 0;
		this.groundingline    = 0;
		this.hydrology        = 0;
		this.masstransport    = 0;
		this.thermal          = 0;
		this.steadystate      = 0;
		this.trans            = 0;
		this.levelset         = 0;
		this.calving          = 0;
		this.love             = 0;
		this.gia              = 0;
		this.esa              = 0;

		this.autodiff         = 0;
		this.inversion        = 0;
		this.qmu              = 0;
		this.amr					 = 0;

		this.results          = 0;
		this.outputdefinition = 0;
		this.radaroverlay     = 0;
		this.miscellaneous    = 0;
		this.priv             = 0;

		//set default values for fields
		this.setdefaultparameters();

		//}}}
}
