Matlab Program running very slow

Hi All,

I have a function that assigns a matrix 400*400 element value based on another 400*400 matrix element value. It can not be simply done by matrix_A=matrix_B. I do it elementwise.

The program runs super slow. I used a double loop to call the function. Anybody has suggestion/advice on the issue? I posted my codes as below just for reference. Thanks a million in advance.

iInd=zeros((nqubits-1)*nqubits,1); 
jInd=zeros((nqubits-1)*nqubits,1); 
val=zeros((nqubits-1)*nqubits,1)
elementNum=1; 
%add coupling
for i=1:1:(num-1)
    for j=i:1:num
        if interaction(i,j) ~=0
            %J=zeros(nqubits,nqubits)
            H=zeros(1,nqubits)
            varindex1=getvarindex(i,var_size);
            varindex2=getvarindex(j,var_size);
            
            if varindex1==1
                startnum1=0
                varstartnum1=0
            else
                startnum1=0
                varstartnum1=0
                 for k=1:1:(varindex1-1)
                    startnum1=startnum1+var_size(k)-1
                    varstartnum1=varstartnum1+var_size(k)
                 end
            end
             
              if varindex2==1
                startnum2=0
                varstartnum2=0
              else
                startnum2=0
                varstartnum2=0
                 for k=1:1:(varindex2-1)
                    startnum2=startnum2+var_size(k)-1
                    varstartnum2=varstartnum2+var_size(k)
                 end
              end
            
              if (i-varstartnum1) ==1
                  if (j-varstartnum2)==1
                      %J(startnum1+1,startnum2+1)=1
                      iInd(elementNum)=startnum1+1;
                      jInd(elementNum)=startnum2+1;
                      val(elementNum)=1;
                      elementNum=elementNum+1;
                      H(startnum1+1)=1
                      H(startnum2+1)=1
                  elseif (j-varstartnum2)==var_size(varindex2)
                       m=var_size(varindex2)
                       %J(startnum1+1,startnum2+m-1)=-1
                       iInd(elementNum)=startnum1+1;
                       jInd(elementNum)=startnum2+m-1;
                       val(elementNum)=-1;
                       elementNum=elementNum+1;
                       H(startnum1+1)=1
                       H(startnum2+m-1)=-1
                  else
                       % k1=i-varstartnum1
                        k2=j-varstartnum2
                        %J(startnum1+1,startnum2+k2)=1
                        iInd(elementNum)=startnum1+1;
                        iInd(elementNum+1)=startnum1+1;
                        jInd(elementNum)=startnum2+k2;
                        jInd(elementNum+1)=startnum2+k2-1;
                        val(elementNum)=1;
                        val(elementNum+1)=-1;
                        elementNum=elementNum+2;
                        %J(startnum1+1,startnum2+k2-1)=-1
                        H(startnum2+k2)=1
                        H(startnum2+k2-1)=-1
                  end
              elseif (i-varstartnum1)==var_size(varindex1)
                      m1=var_size(varindex1)
                  if (j-varstartnum2)==1
                      %J(startnum1+m1-1,startnum2+1)=-1
                      iInd(elementNum)=startnum1+m1-1;
                      jInd(elementNum)=startnum2+1;
                      val(elementNum)=-1;
                      elementNum=elementNum+1;
                      H(startnum1+m1-1)=-1
                      H(startnum2+1)=1
                  elseif (j-varstartnum2)==var_size(varindex2)
                      m2=var_size(varindex2)
                      %J(startnum1+m1-1,startnum2+m2-1)=1
                      iInd(elementNum)=startnum1+m1-1;
                      jInd(elementNum)=startnum2+m2-1;
                      val(elementNum)=1;
                      elementNum=elementNum+1;
                      H(startnum1+m1-1)=-1
                      H(startnum2+m2-1)=-1
                  else
                      k2=j-varstartnum2
                      %J(startnum1+m1-1,startnum2+k2)=-1
                      %J(startnum1+m1-1,startnum2+k2-1)=1
                      iInd(elementNum)=startnum1+m1-1;
                        iInd(elementNum+1)=startnum1+m1-1;
                        jInd(elementNum)=startnum2+k2;
                        jInd(elementNum+1)=startnum2+k2-1;
                        val(elementNum)=-1;
                        val(elementNum+1)=1;
                        elementNum=elementNum+2;
                      H(startnum2+k2)=1
                      H(startnum2+k2-1)=-1
                  end
              else
                  k1=i-varstartnum1
                  if (j-varstartnum2)==1
                      %J(startnum1+k1,startnum2+1)=1
                      %J(startnum1+k1-1,startnum2+1)=-1
                      iInd(elementNum)=startnum1+k1;
                        iInd(elementNum+1)=startnum1+k1-1;
                        jInd(elementNum)=startnum2+1;
                        jInd(elementNum+1)=startnum2+1;
                        val(elementNum)=1;
                        val(elementNum+1)=-1;
                        elementNum=elementNum+2;
                      H(startnum1+k1)=1
                      H(startnum1+k1-1)=-1
                  elseif (j-varstartnum2)==var_size(varindex2)
                      m2=var_size(varindex2)
                      %J(startnum1+k1,startnum2+m2-1)=-1
                      %J(startnum1+k1-1,startnum2+m2-1)=1
                      iInd(elementNum)=startnum1+k1;
                        iInd(elementNum+1)=startnum1+k1-1;
                        jInd(elementNum)=startnum2+m2-1;
                        jInd(elementNum+1)=startnum2+m2-1;
                        val(elementNum)=-1;
                        val(elementNum+1)=1;
                        elementNum=elementNum+2;
                      H(startnum1+k1)=1
                      H(startnum1+k1-1)=-1
                  else
                      k2=j-varstartnum2
                      %J(startnum1+k1,startnum2+k2)=1
                      %J(startnum1+k1,startnum2+k2-1)=-1
                      iInd(elementNum)=startnum1+k1;
                        iInd(elementNum+1)=startnum1+k1;
                        jInd(elementNum)=startnum2+k2;
                        jInd(elementNum+1)=startnum2+k2-1;
                        val(elementNum)=1;
                        val(elementNum+1)=-1;
                        elementNum=elementNum+2;
                      J(startnum1+k1-1,startnum2+k2)=-1
                      J(startnum1+k1-1,startnum2+k2-1)=1
                  end
              end
              
        end
        
        H=1/4*H*interaction(i,j);
        H_prob=H_prob+H;
        
        iInd=iInd(1:elementNum-1); % remove extra entries
        jInd=jInd(1:elementNum-1); % remove extra entries
        val=val(1:elementNum-1); % list of values (all ones in this case)
        J=sparse(iInd,jInd,val,nqubits,nqubits);
        J=1/4*J*interaction(i,j);
        J_prob=J_prob+J;
    end
end