Your code contains a lot of lines of the form
averagecurrentH2(isnan(averagecurrentH2))=0;
When I run your entire code in debugging mode I see that many of these lines are active; in other words, many of the calculations are returning NaN and then returning 0. I suspect that you don't really want all these NaN values, and that something is going wrong with your calculation, and that is why fmincon gets stuck.
FYI, I set a 0 objective function
fun = @(x)0;
I suggest that you debug your nonlinear constraint function. And also, when that is debugged, set your objective to the square of the difference, not the absolute value of the difference:
error = norm((averagecurrentCO2+averagecurrentCO+averagecurrentC2H4+averagecurrentC2H6+averagecurrentO2+averagecurrentPOF3+averagecurrentH2) - 1e-3)^2;
% not
error=abs((averagecurrentCO2+averagecurrentCO+averagecurrentC2H4+averagecurrentC2H6+averagecurrentO2+averagecurrentPOF3+averagecurrentH2)-1*10^-3);
Alan Weiss
MATLAB mathematical toolbox documentation
