function [Solver,Mesh]=FemMatrixAssembly2(Physic,Material,Mesh,...
    Port1Mesh,Port1Solver,Port2Mesh,Port2Solver)


%process maxwell's equations
tic
epsilonr=Material.epsilonr-1i*Material.sigma*Material.temp;
[A,Mesh.Edges,Mesh.EdgesOfElements,Dof]=PhysicMatrixAssembly2(Mesh.Nodes,Mesh.Elements,...
    Mesh.Domains,Physic.lam0,epsilonr,Material.mur,Port1Solver.gamma);
b=complex(zeros(Dof,1));
disp('The time taken of matrix assmebly for maxwell equations');
toc

%process boundary mesh
tic
el2no=Mesh.Elements';
f1=el2no([1 1 1 2],:);
f2=el2no([2 2 3 3],:);
f3=el2no([3 4 4 4],:);
f_array=[f1(:) f2(:) f3(:)];
[Faces,~,FacesOfElements]=unique(f_array,'rows');
Mesh.AllFaces=Faces;
Mesh.FacesOfElements=FacesOfElements;
addDof=0;

%process port1 boundary condition
Port1Mesh.FacesConn=GetBFacesConn(Port1Mesh.OldFaces,Faces,FacesOfElements);
[A,b,addDof]=PortBCMatrixAssembly2(A,b,Mesh.Nodes,Mesh.Elements,Mesh.EdgesOfElements,...
    Mesh.Domains,Material.mur,Port1Mesh,Port1Solver,Dof,addDof);

%process port2 boundary condition
Port2Mesh.FacesConn=GetBFacesConn(Port2Mesh.OldFaces,Faces,FacesOfElements);
[A,b,addDof]=PortBCMatrixAssembly2(A,b,Mesh.Nodes,Mesh.Elements,Mesh.EdgesOfElements,...
    Mesh.Domains,Material.mur,Port2Mesh,Port2Solver,Dof,addDof);
addDof(1)=[];
disp('The time taken of processing port boundary condition');
toc

%process PEC boundary condition 
%not currently implemented
[PECFaces,~]=GetBFaces(Mesh.Faces,Mesh.FacesIndex,Physic.PEC);
fl2no=PECFaces';
n1=fl2no([1 1 2],:);
n2=fl2no([2 3 3],:);
fl_fd2no_array=[n1(:) n2(:)];
PECEdges=unique(fl_fd2no_array,'rows');
PECInd=find(ismember(Mesh.Edges,PECEdges,'rows'));
Free_ind=1:(Dof+sum(addDof));
Free_ind(PECInd)=[];
A=A(Free_ind,Free_ind);
b=b(Free_ind);

%solving
tic
[P,R,C] = equilibrate(A);
newA=R*P*A*C;
newb=R*P*b;
xx=newA\newb;
xx=C*xx;
Solver.err=norm(A*xx-b);
Solver.condA=condest(newA);

%processing PEC
for i=1:length(PECInd)-1
    n=PECInd(i);
    xx=[xx(1:n-1,:);zeros(1,1);xx(n:end,:)];
end
i=length(PECInd);
n=PECInd(i);
if n<=length(xx)
    xx=[xx(1:n-1,:);zeros(1,1);xx(n:end,:)];
else
    xx=[xx(1:n-1,:);zeros(1,1);];
end
%compute the electric field
Solver.Et=xx(1:Dof);
Solver.Dof=Dof;
Solver.e1=xx(Dof+1);
Solver.e2=xx(Dof+2);
disp('The time taken of solving');
toc

%Reconstructing electric field Ex,Ey,Ez and normE
tic
[Solver.Ex,Solver.Ey,Solver.Ez,Solver.normE]=GetBWExEyEz(1,...
    Mesh.Nodes,Mesh.Elements,Mesh.EdgesOfElements,Solver.Et,Port1Solver.gamma);
disp('The time taken of post-processing');
toc

end