I am newly using STAN and trying to get acquainted and understand the type of errors expected when running the model. Of the errors I have got was after setting one of flows (nutrient/substance concentration) to zero, and when the calculation is done STAN gives one error that it shouldnt be less than zero (the calculated value is negative and very small - 10^27). How to avoid this error if I'm certain that no nutrient/Substance goes into that flow? Plus I have the uncertainties of all the flows and STAN reconciles to calculate accordingly.
You can ignore errors with regard to these very small negative values as they are actually zero. They are due to rounding errors near machine precision. You can avoid them by setting those quantities manually to zero where you are sure that they are zero.
Under "Extras > Options > Number formats > lowest absolut value > 0" you can set the threshold of values that should be displayed as zero in your flow diagram. But you will get these error messages anyway.