Index: /issm/trunk-jpl/src/m/classes/mesh3dsurface.m
===================================================================
--- /issm/trunk-jpl/src/m/classes/mesh3dsurface.m	(revision 19076)
+++ /issm/trunk-jpl/src/m/classes/mesh3dsurface.m	(revision 19076)
@@ -0,0 +1,211 @@
+%MESH3DSURFACE class definition
+%
+%   Usage:
+%      mesh3dsurface=mesh3dsurface();
+
+classdef mesh3dsurface
+	properties (SetAccess=public) 
+		x                           = NaN;
+		y                           = NaN;
+		z                           = NaN;
+		elements                    = NaN;
+		numberofelements            = 0;
+		numberofvertices            = 0;
+		numberofedges               = 0;
+
+		lat                         = NaN;
+		long                        = NaN;
+		r                           = NaN;
+
+		vertexonboundary            = NaN;
+		edges                       = NaN;
+		segments                    = NaN;
+		segmentmarkers              = NaN;
+		vertexconnectivity          = NaN;
+		elementconnectivity         = NaN;
+		average_vertex_connectivity = 0;
+
+		extractedvertices           = NaN;
+		extractedelements           = NaN;
+	end
+	methods (Static)
+		function self = loadobj(self) % {{{
+			% This function is directly called by matlab when a model selfect is
+			% loaded. Update old properties here
+
+			%2014 Oct. 1st
+			if isstruct(self),
+				oldself=self;
+				%Assign property values from struct
+				self=structtoobj(mesh3dsurface(),oldself);
+				if isfield(oldself,'hemisphere'),
+					disp('md.mesh.hemisphere has been automatically converted to EPSG code');
+					if strcmpi(oldself.hemisphere,'n'),
+						self.epsg=3413;
+					else
+						self.epsg=3031;
+					end
+				end
+			end
+
+		end% }}}
+	end
+	methods
+		function self = mesh3dsurface(varargin) % {{{
+			switch nargin
+				case 0
+					self=setdefaultparameters(self);
+				case 1
+					self=mesh3dsurface();
+					object=varargin{1};
+					fields=fieldnames(object);
+					for i=1:length(fields)
+						field=fields{i};
+						if ismember(field,properties('mesh3dsurface')),
+							self.(field)=object.(field);
+						end
+					end
+				otherwise
+					error('constructor not supported');
+			end
+		end % }}}
+		function obj = setdefaultparameters(obj) % {{{
+
+			%the connectivity is the averaged number of nodes linked to a
+			%given node through an edge. This connectivity is used to initially
+			%allocate memory to the stiffness matrix. A value of 16 seems to
+			%give a good memory/time ration. This value can be checked in
+			%trunk/test/Miscellaneous/runme.m
+			obj.average_vertex_connectivity=25;
+		end % }}}
+		function md = checkconsistency(obj,md,solution,analyses) % {{{
+
+			md = checkfield(md,'fieldname','mesh.x','NaN',1,'size',[md.mesh.numberofvertices 1]);
+			md = checkfield(md,'fieldname','mesh.y','NaN',1,'size',[md.mesh.numberofvertices 1]);
+			md = checkfield(md,'fieldname','mesh.z','NaN',1,'size',[md.mesh.numberofvertices 1]);
+			md = checkfield(md,'fieldname','mesh.lat','NaN',1,'size',[md.mesh.numberofvertices 1]);
+			md = checkfield(md,'fieldname','mesh.long','NaN',1,'size',[md.mesh.numberofvertices 1]);
+			md = checkfield(md,'fieldname','mesh.r','NaN',1,'size',[md.mesh.numberofvertices 1]);
+			md = checkfield(md,'fieldname','mesh.elements','NaN',1,'>',0,'values',1:md.mesh.numberofvertices);
+			md = checkfield(md,'fieldname','mesh.elements','size',[md.mesh.numberofelements 3]);
+			if any(~ismember(1:md.mesh.numberofvertices,sort(unique(md.mesh.elements(:)))));
+				md = checkmessage(md,'orphan nodes have been found. Check the mesh outline');
+			end
+			md = checkfield(md,'fieldname','mesh.numberofelements','>',0);
+			md = checkfield(md,'fieldname','mesh.numberofvertices','>',0);
+			md = checkfield(md,'fieldname','mesh.average_vertex_connectivity','>=',9,'message','''mesh.average_vertex_connectivity'' should be at least 9 in 2d');
+
+			switch(solution),
+				case ThermalSolutionEnum(),
+					md = checkmessage(md,'thermal not supported for 2d mesh');
+			end
+		end % }}}
+		function disp(obj) % {{{
+			disp(sprintf('   2D tria Mesh (horizontal):')); 
+
+			disp(sprintf('\n      Elements and vertices:'));
+			fielddisplay(obj,'numberofelements','number of elements');
+			fielddisplay(obj,'numberofvertices','number of vertices');
+			fielddisplay(obj,'elements','vertex indices of the mesh elements');
+			fielddisplay(obj,'x','vertices x coordinate [m]');
+			fielddisplay(obj,'y','vertices y coordinate [m]');
+			fielddisplay(obj,'z','vertices z coordinate [m]');
+			fielddisplay(obj,'lat','vertices latitude [degrees]');
+			fielddisplay(obj,'long','vertices longitude [degrees]');
+			fielddisplay(obj,'r','vertices radius [m]');
+			
+			fielddisplay(obj,'edges','edges of the 2d mesh (vertex1 vertex2 element1 element2)');
+			fielddisplay(obj,'numberofedges','number of edges of the 2d mesh');
+
+			disp(sprintf('\n      Properties:'));
+			fielddisplay(obj,'vertexonboundary','vertices on the boundary of the domain flag list');
+			fielddisplay(obj,'segments','edges on domain boundary (vertex1 vertex2 element)');
+			fielddisplay(obj,'segmentmarkers','number associated to each segment');
+			fielddisplay(obj,'vertexconnectivity','list of vertices connected to vertex_i');
+			fielddisplay(obj,'elementconnectivity','list of vertices connected to element_i');
+			fielddisplay(obj,'average_vertex_connectivity','average number of vertices connected to one vertex');
+
+			disp(sprintf('\n      Extracted model:'));
+			fielddisplay(obj,'extractedvertices','vertices extracted from the model');
+			fielddisplay(obj,'extractedelements','elements extracted from the model'); 
+		end % }}}
+		function createxml(obj,fid) % {{{
+			fprintf(fid, '<!-- #D surface Mesh -->\n');
+
+			%elements and vertices
+			fprintf(fid,'%s\n%s\n%s\n','<frame key="1" label="Elements and vertices">','<section name="mesh" />');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n','  <parameter key ="numberofelements" type="',class(obj.numberofelements),'" default="',convert2str(obj.numberofelements),'">','     <section name="mesh" />','     <help> number of elements </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n','  <parameter key ="numberofvertices" type="',class(obj.numberofvertices),'" default="',convert2str(obj.numberofvertices),'">','     <section name="mesh" />','     <help> number of vertices </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n','  <parameter key ="elements" type="',class(obj.elements),'" default="',convert2str(obj.elements),'">','     <section name="mesh" />','     <help> vertex indices of the mesh elements </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="x" type="',class(obj.x),'" default="',convert2str(obj.x),'">','     <section name="mesh" />','     <help> vertices x coordinate [m] </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="y" type="',class(obj.y),'" default="',convert2str(obj.y),'">','     <section name="mesh" />','     <help> vertices y coordinate [m] </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="edges" type="',class(obj.edges),'" default="',convert2str(obj.edges),'">','     <section name="mesh" />','     <help> edges of the 2d mesh (vertex1 vertex2 element1 element2) </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="numberofedges" type="',class(obj.numberofedges),'" default="',convert2str(obj.numberofedges),'">','     <section name="mesh" />','     <help> number of edges of the 2d mesh </help>','  </parameter>');
+			fprintf(fid,'%s\n%s\n','</frame>');
+
+			% properties
+			fprintf(fid,'%s\n%s\n%s\n','<frame key="2" label="Properties">','<section name="mesh" />');             
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="vertexonboundary" type="',class(obj.vertexonboundary),'" default="',convert2str(obj.vertexonboundary),'">','     <section name="mesh" />','     <help> vertices on the boundary of the domain flag list </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="segments" type="',class(obj.segments),'" default="',convert2str(obj.segments),'">','     <section name="mesh" />','     <help> edges on domain boundary (vertex1 vertex2 element) </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="segmentmarkers" type="',class(obj.segmentmarkers),'" default="',convert2str(obj.segmentmarkers),'">','     <section name="mesh" />','     <help> number associated to each segment </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="vertexconnectivity" type="',class(obj.vertexconnectivity),'" default="',convert2str(obj.vertexconnectivity),'">','     <section name="mesh" />','     <help> list of vertices connected to vertex_i </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="elementconnectivity" type="',class(obj.elementconnectivity),'" default="',convert2str(obj.elementconnectivity),'">','     <section name="mesh" />','     <help> list of vertices connected to element_i </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="average_vertex_connectivity" type="',class(obj.average_vertex_connectivity),'" default="',convert2str(obj.average_vertex_connectivity),'">','     <section name="mesh" />','     <help> average number of vertices connected to one vertex </help>','  </parameter>');
+			fprintf(fid,'%s\n%s\n','</frame>');
+
+			%extracted model
+			fprintf(fid,'%s\n%s\n%s\n','<frame key="3" label="Extracted Model">','<section name="mesh" />'); 
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="extractedvertices" type="',class(obj.extractedvertices),'" default="',convert2str(obj.extractedvertices),'">','     <section name="mesh" />','     <help> vertices extracted from the model </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="extractedelements" type="',class(obj.extractedelements),'" default="',convert2str(obj.extractedelements),'">','     <section name="mesh" />','     <help> elements extracted from the model </help>','  </parameter>');
+			fprintf(fid,'%s\n%s\n','</frame>');
+
+			%projection
+			fprintf(fid,'%s\n%s\n%s\n','<frame key="4" label="Projection">','<section name="mesh" />'); 
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="lat" type="',class(obj.lat),'" default="',convert2str(obj.lat),'">','     <section name="mesh" />','     <help> vertices latitude [degrees] </help>','  </parameter>');
+			fprintf(fid,'%s%s%s%s%s\n%s\n%s\n%s\n','  <parameter key ="long" type="',class(obj.long),'" default="',convert2str(obj.long),'">','     <section name="mesh" />','     <help> verticies longitude [degrees] </help>','  </parameter>');
+			% choice (epsg) 'n' or 's'
+			fprintf(fid,'%s\n%s\n%s\n','  <parameter key ="epsg" type="alternative" optional="false">','     <section name="mesh" />','     <help> Indicate epsg ''n'' or ''s'' </help>');
+			fprintf(fid,'%s\n','       <option value="n" type="string" default="true"> </option>');
+			fprintf(fid,'%s\n','       <option value="s" type="string" default="false"> </option>');
+			fprintf(fid,'%s\n','  </parameter>');
+			fprintf(fid,'%s\n%s\n','</frame>');
+
+		end % }}}
+		function marshall(obj,md,fid) % {{{
+			WriteData(fid,'enum',DomainTypeEnum(),'data',StringToEnum(['Domain' domaintype(obj)]),'format','Integer');
+			WriteData(fid,'enum',DomainDimensionEnum(),'data',dimension(obj),'format','Integer');
+			WriteData(fid,'enum',MeshElementtypeEnum(),'data',StringToEnum(elementtype(obj)),'format','Integer');
+			WriteData(fid,'object',obj,'class','mesh','fieldname','x','format','DoubleMat','mattype',1);
+			WriteData(fid,'object',obj,'class','mesh','fieldname','y','format','DoubleMat','mattype',1);
+			WriteData(fid,'object',obj,'class','mesh','fieldname','z','format','DoubleMat','mattype',1);
+			WriteData(fid,'object',obj,'class','mesh','fieldname','lat','format','DoubleMat','mattype',1);
+			WriteData(fid,'object',obj,'class','mesh','fieldname','long','format','DoubleMat','mattype',1);
+			WriteData(fid,'object',obj,'class','mesh','fieldname','r','format','DoubleMat','mattype',1);
+			WriteData(fid,'enum',MeshZEnum(),'data',zeros(obj.numberofvertices,1),'format','DoubleMat','mattype',1);
+			WriteData(fid,'object',obj,'class','mesh','fieldname','elements','format','DoubleMat','mattype',2);
+			WriteData(fid,'object',obj,'class','mesh','fieldname','numberofelements','format','Integer');
+			WriteData(fid,'object',obj,'class','mesh','fieldname','numberofvertices','format','Integer');
+			WriteData(fid,'object',obj,'class','mesh','fieldname','average_vertex_connectivity','format','Integer');
+			WriteData(fid,'object',obj,'class','mesh','fieldname','vertexonboundary','format','DoubleMat','mattype',1);
+		end % }}}
+		function t = domaintype(obj) % {{{
+			t = '3Dsurface';
+		end % }}}
+		function d = dimension(obj) % {{{
+			d = 2;
+		end % }}}
+		function s = elementtype(obj) % {{{
+			s = 'Tria';
+		end % }}}
+		function [x y z elements is2d isplanet] = processmesh(self,options) % {{{
+
+			isplanet = 1;
+			is2d     = 0;
+
+			elements = self.elements;
+			x        = self.x;
+			y        = self.y;
+			z        = self.z;
+		end % }}}
+	end
+end