MATLAB: Nearly identical code, hugely different runtimes

optimizationstrange run errors

Hi all,
I've got a weird situation going on. I have the following code:
if true
for ii = 2:natom 
  tcheck = 1; 
         while tcheck ~= 0
             tcheck = 0; 
             lx =  rand*lxmax;
             ly =  rand*lymax;
             lz =  rand*lzmax;
               for jj = 1:ii-1
                   x12 = lx-x(jj);
                   y12 = ly-y(jj);
                   z12 = lz-z(jj);
            %

                   x12 = x12-lxmax* round(x12/lxmax);
                   y12 = y12-lymax* round(y12/lymax);
                   z12 = z12-lzmax* round(y12/lzmax);
            %
                   dist = sqrt(x12^2 +y12^2 + z12^2);
                   if dist <= rmax
                        tcheck =tcheck +1; 
                        break
                   end
               end
           end
           x(ii) = lx;
           y(ii) = ly;
           z(ii) = lz;  
    ii
  endif true
natom=4000 and x,y,z are vectors of length 4000. lxmax, lymax, and lzmax are all equal at 40.5 which is what I have "cubesize" set to in the next code. In general you can assume the parameters controlling the iteration process are the same for both.
I am trying to incorporate this code into another program and rewrote it as such:
if true
for i=2:natoms
        while flag ~= 0
            flag=0;
            xtemp=rand*cubesize;
            ytemp=rand*cubesize;
            ztemp=rand*cubesize;
              for j=1:i-1
                  xvec=xtemp-store(j,3);
                  yvec=ytemp-store(j,4);
                  zvec=ztemp-store(j,5);
                  xvec = xvec-cubesize* round(xvec/cubesize);
                  yvec = zvec-cubesize* round(yvec/cubesize);
                  zvec = zvec-cubesize* round(zvec/cubesize);
                  dist=sqrt(xvec^2+yvec^2+zvec^2);
                  if dist <= moldia
                      flag=1;
                      break;
                  end
              end
          end
      store(i,2)=i;
      store(i,3)=xtemp;
      store(i,4)=ytemp;
      store(i,5)=ztemp;
      flag=1;
      i
  end
endif true
This code takes a HUGE amount more time to run. What gives? One speeds its way to i=3500 or so in a matter of seconds. The other craws to i=700 or so and then bogs. I even tried swapping out and storing everything in single vectors first with no effect.
The first code was inside a function, so I tried putting my entire new script inside a dummy function to no effect.
Thanks, Nathan

Best Answer

You should be pre-allocating the storage of the variables you are assigning in to. You might not use them all, but you can calculate a maximum possible occupancy and you can shrink the variables afterwards.
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