From my experience you have to consider this:
1) SAFETY: Safety requirements that you need in your system. N2 is an inert and H2 obviously not (LFL = 4% HFL=96-98%, low and high flammability limits).
If you require an ATEX atmosphere to avoid problems you have to check that your MFC is an ATEX instrument. This is important depending on the safety measures that you are working.
2) MATERIAL COMPATIBILITY: If you do not require this, just check that the materials of the MFC valve (joints, etc.) are suitable for H2, normally they are (it is not the case for CO2 that "eats" the joints if they are not of the proper material).
3) ACCURACY. The MFC are normally very precise, to use them you just need to calibrate them, to be accurate. To calibrate a MFC is easy, by using an up-side.down probete with water. You just need to record the volume moved by the H2 with time.
You can also calibrate them with a similar instrument that the one used for Gas Chromatography flows (with the bubble etc.).
The error expected, I think that is proportional to the ratio of densities between N2 and H2 that is aproximately 14. But it depends on the case.
The conversion is probably possible, although the flow capacity generally changes with the gas. It will depend on the actual system if that change is acceptable or not. Please check the Mass Flow Controller (MFC) technical literature for information on the appropriate conversion factors to find the flow capacity with the new gas.
A conversion factor can be used to calculate the mass flow values for the new gas, even if the MFC was calibrated for other gas (presumably for the previous gas). This conversion factor should adapt the previous relationship between signal and mass (or volumetric) flow, valid for the previous gas, to the new gas. Some inaccuracy is introduced with this approach, as for the best accuracy, the MFC should actually be re-calibrated with the new gas under typical operating conditions.
For the particular case of a MFC operating on the principle of heat transfer by sensing the temperature change along the heated section of a capillary tube, the output signal (V) would be given as: V = K·Cp·Qm = K·Cp·ρ·Qv, where K is a constant independent of the gas, Cp is the specific heat, ρ is the density (normal conditions), Qm is the mass flow and Qv the volumetric flow. The above mentioned conversion factor is obtained from this expression applied to both the gases. The change from N2 to H2 would actually lead to a small change on the volumetric flow readings for the same signal, because the product Cp·ρ is quite similar for both gases. For this type of MFC the error introduced by not re-calibrating the MFC with the new gas would reach around 3% if no correction is applied; while by applying the above mentioned conversion factor this error can be reduced to about 2%.
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