--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/+scheme/Hypsyst3d.m	Thu Oct 13 09:34:30 2016 +0200
@@ -0,0 +1,318 @@
+classdef Hypsyst3d < scheme.Scheme
+    properties
+        m % Number of points in each direction, possibly a vector
+        n %size of system
+        h % Grid spacing
+        x, y, z % Grid
+        X, Y, Z% Values of x and y for each grid point
+        Yx, Zx, Xy, Zy, Xz, Yz %Grid values for boundary surfaces
+        order % Order accuracy for the approximation
+        
+        D % non-stabalized scheme operator
+        A, B, C, E
+        
+        H % Discrete norm
+        % Norms in the x, y and z directions
+        Hxi,Hyi, Hzi % Kroneckerd norms. 1'*Hx*v corresponds to integration in the x dir.
+        I_x,I_y, I_z, I_N
+        e_w, e_e, e_s, e_n, e_b, e_t
+        params %parameters for the coeficient matrice
+    end
+    
+    
+    methods
+        function obj = Hypsyst3d(m, lim, order, A, B,C, E, params)
+            default_arg('E', [])
+            xlim = lim{1};
+            ylim = lim{2};
+            zlim = lim{3};
+            
+            if length(m) == 1
+                m = [m m m];
+            end
+            
+            obj.A=A;
+            obj.B=B;
+            obj.C=C;
+            obj.E=E;
+            m_x = m(1);
+            m_y = m(2);
+            m_z=m(3);
+            obj.params = params;
+            
+            ops_x = sbp.D2Standard(m_x,xlim,order);
+            ops_y = sbp.D2Standard(m_y,ylim,order);
+            ops_z = sbp.D2Standard(m_z,zlim,order);
+            
+            obj.x = ops_x.x;
+            obj.y = ops_y.x;
+            obj.z = ops_z.x;
+            
+            obj.X = kr(obj.x,ones(m_y,1),ones(m_z,1));%% Que pasa?
+            obj.Y = kr(ones(m_x,1),obj.y,ones(m_z,1));
+            obj.Z = kr(ones(m_x,1),ones(m_y,1),obj.z);
+            
+            obj.Yx=kr(obj.y,ones(m_z,1));
+            obj.Zx=kr(ones(m_y,1),obj.z);
+
+            obj.Xy=kr(obj.x,ones(m_z,1));
+            obj.Zy=kr(ones(m_x,1),obj.z);
+            
+            obj.Xz=kr(obj.x,ones(m_y,1));
+            obj.Yz=kr(ones(m_z,1),obj.y);
+            
+            Aevaluated = obj.evaluateCoefficientMatrix(A, obj.X, obj.Y,obj.Z);
+            Bevaluated = obj.evaluateCoefficientMatrix(B, obj.X, obj.Y,obj.Z);
+            Cevaluated = obj.evaluateCoefficientMatrix(C, obj.X, obj.Y,obj.Z);
+            Eevaluated = obj.evaluateCoefficientMatrix(E, obj.X, obj.Y,obj.Z);
+            
+            obj.n = length(A(obj.params,0,0,0));
+            
+            I_n = eye(obj.n);
+            I_x = speye(m_x);
+            obj.I_x = I_x;
+            I_y = speye(m_y);
+            obj.I_y = I_y;
+            I_z = speye(m_z);
+            obj.I_z = I_z;
+            
+            
+            D1_x = kr(I_n, ops_x.D1, I_y,I_z);
+            obj.Hxi = kr(I_n, ops_x.HI, I_y,I_z);
+            D1_y = kr(I_n, I_x, ops_y.D1,I_z);
+            obj.Hyi = kr(I_n, I_x, ops_y.HI,I_z);
+            D1_z = kr(I_n, I_x, I_y,ops_z.D1);
+            obj.Hzi = kr(I_n, I_x,I_y, ops_y.HI);
+            
+            obj.e_w = kr(I_n, ops_x.e_l, I_y,I_z);
+            obj.e_e = kr(I_n, ops_x.e_r, I_y,I_z);
+            obj.e_s = kr(I_n, I_x, ops_y.e_l,I_z);
+            obj.e_n = kr(I_n, I_x, ops_y.e_r,I_z);
+            obj.e_b = kr(I_n, I_x, I_y, ops_z.e_l);
+            obj.e_t = kr(I_n, I_x, I_y, ops_z.e_r);
+            
+            obj.m=m;
+            obj.h=[ops_x.h ops_y.h ops_x.h];
+            obj.order=order;
+            
+            obj.D=-Aevaluated*D1_x-Bevaluated*D1_y-Cevaluated*D1_z-Eevaluated;
+        end
+        
+        % Closure functions return the opertors applied to the own doamin to close the boundary
+        % Penalty functions return the opertors to force the solution. In the case of an interface it returns the operator applied to the other doamin.
+        %       boundary            is a string specifying the boundary e.g. 'l','r' or 'e','w','n','s'.
+        %       type                is a string specifying the type of boundary condition if there are several.
+        %       data                is a function returning the data that should be applied at the boundary.
+        function [closure, penalty] = boundary_condition(obj,boundary,type,L)
+            default_arg('type','char');
+            BM=boundary_matrices(obj,boundary);
+            
+            switch type
+                case{'c','char'}
+                    [closure,penalty]=boundary_condition_char(obj,BM);
+                case{'general'}
+                    [closure,penalty]=boundary_condition_general(obj,BM,boundary,L);
+                otherwise
+                    error('No such boundary condition')
+            end
+        end
+        
+        function [closure, penalty] = interface(obj,boundary,neighbour_scheme,neighbour_boundary)
+            error('An interface function does not exist yet');
+        end
+        
+        function N = size(obj)
+            N = obj.m;
+        end
+        
+        function [ret] = evaluateCoefficientMatrix(obj, mat, X, Y, Z)
+            params=obj.params;
+            side=max(length(X),length(Y));
+            if isa(mat,'function_handle')
+                [rows,cols]=size(mat(params,0,0,0));
+                matVec=mat(params,X',Y',Z');
+                matVec=sparse(matVec);
+            else
+                matVec=mat;
+                [rows,cols]=size(matVec);
+                side=max(length(X),length(Y));
+                cols=cols/side;
+            end
+            ret=kron(ones(rows,cols),speye(side));
+            
+            for ii=1:rows
+                for jj=1:cols
+                    ret((ii-1)*side+1:ii*side,(jj-1)*side+1:jj*side)=diag(matVec(ii,(jj-1)*side+1:jj*side));
+                end
+            end
+        end
+        
+        
+        function [BM]=boundary_matrices(obj,boundary)
+            params=obj.params;
+            
+            switch boundary
+                case {'w','W','west'}
+                    BM.e_=obj.e_w;
+                    mat=obj.A;
+                    BM.boundpos='l';
+                    BM.Hi=obj.Hxi;
+                    [BM.V,BM.Vi,BM.D,signVec]=obj.matrixDiag(mat,obj.X(1),obj.Yx,obj.Zx);
+                    BM.side=length(obj.Yx);
+                case {'e','E','east'}
+                    BM.e_=obj.e_e;
+                    mat=obj.A;
+                    BM.boundpos='r';
+                    BM.Hi=obj.Hxi;
+                    [BM.V,BM.Vi,BM.D,signVec]=obj.matrixDiag(mat,obj.X(end),obj.Yx,obj.Zx);
+                    BM.side=length(obj.Yx);
+                case {'s','S','south'}
+                    BM.e_=obj.e_s;
+                    mat=obj.B;
+                    BM.boundpos='l';
+                    BM.Hi=obj.Hyi;
+                    [BM.V,BM.Vi,BM.D,signVec]=obj.matrixDiag(mat,obj.Xy,obj.Y(1),obj.Zy);
+                    BM.side=length(obj.Xy);
+                case {'n','N','north'}
+                    BM.e_=obj.e_n;
+                    mat=obj.B;
+                    BM.boundpos='r';
+                    BM.Hi=obj.Hyi;
+                    [BM.V,BM.Vi,BM.D,signVec]=obj.matrixDiag(mat,obj.Xy,obj.Y(end),obj.Zy);
+                    BM.side=length(obj.Xy);
+                case{'b','B','Bottom'}
+                    BM.e_=obj.e_b;
+                    mat=obj.C;
+                    BM.boundpos='l';
+                    BM.Hi=obj.Hzi;
+                    [BM.V,BM.Vi,BM.D,signVec]=obj.matrixDiag(mat,obj.Xz,obj.Yz,obj.Z(1));
+                    BM.side=length(obj.Xz);
+                case{'t','T','Top'}
+                    BM.e_=obj.e_t;
+                    mat=obj.C;
+                    BM.boundpos='r';
+                    BM.Hi=obj.Hzi;
+                    [BM.V,BM.Vi,BM.D,signVec]=obj.matrixDiag(mat,obj.Xz,obj.Yz,obj.Z(end));
+                    BM.side=length(obj.Xz);
+            end
+            
+            BM.pos=signVec(1); BM.zeroval=signVec(2); BM.neg=signVec(3);
+        end
+        
+        
+        function [closure, penalty]=boundary_condition_char(obj,BM)
+            side = BM.side;
+            pos = BM.pos;
+            neg = BM.neg;
+            zeroval=BM.zeroval;
+            V = BM.V;
+            Vi = BM.Vi;
+            Hi=BM.Hi;
+            D=BM.D;
+            e_=BM.e_;
+            
+            switch BM.boundpos
+                case {'l'}
+                    tau=sparse(obj.n*side,pos);
+                    Vi_plus=Vi(1:pos,:);
+                    tau(1:pos,:)=-abs(D(1:pos,1:pos));
+                    closure=Hi*e_*V*tau*Vi_plus*e_';
+                    penalty=-Hi*e_*V*tau*Vi_plus;
+                case {'r'}
+                    tau=sparse(obj.n*side,neg);
+                    tau((pos+zeroval)+1:obj.n*side,:)=-abs(D((pos+zeroval)+1:obj.n*side,(pos+zeroval)+1:obj.n*side));
+                    Vi_minus=Vi((pos+zeroval)+1:obj.n*side,:);
+                    closure=Hi*e_*V*tau*Vi_minus*e_';
+                    penalty=-Hi*e_*V*tau*Vi_minus;
+            end
+        end
+        
+        
+        function [closure,penalty]=boundary_condition_general(obj,BM,boundary,L)
+            side = BM.side;
+            pos = BM.pos;
+            neg = BM.neg;
+            zeroval=BM.zeroval;
+            V = BM.V;
+            Vi = BM.Vi;
+            Hi=BM.Hi;
+            D=BM.D;
+            e_=BM.e_;
+            switch boundary
+                case {'w','W','west'}                    
+                    L=obj.evaluateCoefficientMatrix(L,obj.x(1),obj.Yx,obj.Zx);
+                case {'e','E','east'}
+                    L=obj.evaluateCoefficientMatrix(L,obj.x(end),obj.Yx,obj.Zx);
+                case {'s','S','south'}
+                    L=obj.evaluateCoefficientMatrix(L,obj.Xy,obj.y(1),obj.Zy);
+                case {'n','N','north'}
+                    L=obj.evaluateCoefficientMatrix(L,obj.Xy,obj.y(end),obj.Zy);
+                case {'b','B','bottom'}
+                     L=obj.evaluateCoefficientMatrix(L,obj.Xz,obj.Yz,obj.z(1));
+                case {'t','T','top'}   
+                    L=obj.evaluateCoefficientMatrix(L,obj.Xz,obj.Yz,obj.z(end));
+            end
+            
+            switch BM.boundpos
+                case {'l'}
+                    tau=sparse(obj.n*side,pos);
+                    Vi_plus=Vi(1:pos,:);
+                    Vi_minus=Vi(pos+zeroval+1:obj.n*side,:);
+                    V_plus=V(:,1:pos);
+                    V_minus=V(:,(pos+zeroval)+1:obj.n*side);
+                    
+                    tau(1:pos,:)=-abs(D(1:pos,1:pos));
+                    R=-inv(L*V_plus)*(L*V_minus);
+                    closure=Hi*e_*V*tau*(Vi_plus-R*Vi_minus)*e_';
+                    penalty=-Hi*e_*V*tau*inv(L*V_plus)*L;
+                case {'r'}
+                    tau=sparse(obj.n*side,neg);
+                    tau((pos+zeroval)+1:obj.n*side,:)=-abs(D((pos+zeroval)+1:obj.n*side,(pos+zeroval)+1:obj.n*side));
+                    Vi_plus=Vi(1:pos,:);
+                    Vi_minus=Vi((pos+zeroval)+1:obj.n*side,:);
+                    
+                    V_plus=V(:,1:pos);
+                    V_minus=V(:,(pos+zeroval)+1:obj.n*side);
+                    R=-inv(L*V_minus)*(L*V_plus);
+                    closure=Hi*e_*V*tau*(Vi_minus-R*Vi_plus)*e_';
+                    penalty=-Hi*e_*V*tau*inv(L*V_minus)*L;
+            end
+        end
+        
+        
+        function [V,Vi, D,signVec]=matrixDiag(obj,mat,x,y,z)
+            params=obj.params;
+            syms xs ys zs
+            [V, D]=eig(mat(params,xs,ys,zs));
+            xs=x;
+            ys=y;
+            zs=z;
+            
+            
+            side=max(length(x),length(y));
+            Dret=zeros(obj.n,side*obj.n);
+            Vret=zeros(obj.n,side*obj.n);
+            for ii=1:obj.n
+                for jj=1:obj.n
+                    Dret(jj,(ii-1)*side+1:side*ii)=eval(D(jj,ii));
+                    Vret(jj,(ii-1)*side+1:side*ii)=eval(V(jj,ii));
+                end
+            end
+            
+            D=sparse(Dret);
+            V=sparse(Vret);
+            V=obj.evaluateCoefficientMatrix(V,x,y,z);
+            D=obj.evaluateCoefficientMatrix(D,x,y,z);
+            DD=diag(D);
+            
+            poseig=(DD>0);
+            zeroeig=(DD==0);
+            negeig=(DD<0);
+            
+            D=diag([DD(poseig); DD(zeroeig); DD(negeig)]);
+            V=[V(:,poseig) V(:,zeroeig) V(:,negeig)];
+            Vi=inv(V);
+            signVec=[sum(poseig),sum(zeroeig),sum(negeig)];
+        end
+    end
+end
\ No newline at end of file