substitute

Your code should make some changes to ini1 if some of the elements in the qth column are less than 0.01. Here is a little self-contained example:

inn = { 1, 0.001, 0, 2, 3 };
ini1 = 999*ones(rows(inn), 1);
q = 1;

print "before substute, ini1 = " ini1;
ini1[.,q]=substute(ini1[.,q], inn[.,q]-0.01.<0, 1);
print "after substute, ini1 = " ini1;

The output from this code is:

before substute, ini1 = 
       999.00000 
       999.00000 
       999.00000 
       999.00000 
       999.00000 
after substute, ini1 = 
       999.00000 
       1.0000000 
       1.0000000 
       999.00000 
       999.00000 

I might try calculating the separate input on another line of code and then take a look at it to see if it has any 1's in it, like this:

mask = (inn[.,q] - 0.01) .< 0;
print mask;
ini1[.,q]=substute(ini1[.,q], mask, 1);

If there are no 1's in the print out of mask then that is the problem.