Bug with overriding options on the command line

[seanfarley]

When overriding the NOUT and TIMESTEP variables, it seems that the output file is not written. It seems to be because the logic for determining whether or not to write the BOUT.dmp file is calculated before the command-line options are read.

I have not investigated this too much due to time but wanted to document it here. I will investivate after writing deadlines are finished.