Great point, I had not considered that. You are correct that HEC-RAS 6.1 still uses FHWA for inlet-controlled culverts. I’m adding the relevant info from the online manual should anyone else come across this post:
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The culvert hydraulic computations in HEC-RAS are similar to the bridge hydraulic computations, except the Federal Highway Administration’s (FHWA) standard equations for culvert hydraulics under inlet control are used to compute the losses through the structure (when a culvert is under inlet control conditions). Outlet control hydraulics are handled by balancing the energy equation from downstream to upstream.
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Regarding the mysterious error message, it is separate from the old “invert is lower than connected cells” error. I know this because I redrew the culvert, did not get that error message, but DID then get the “invert is lower” message (or whatever the wording is). So I am still not sure about the original error message.