I found a discrepancy on values of XLAT or XLONG variables between the first mother grid wrfout_d01 file and the following ones. (FLEXPART_WRF feels bad about it!).
There is no problem with inner domains.
Please check whether you have the problem, by typing similar UNIX commands with your own wrfout_d01 files:
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ncdump -f f -v XLONG wrfout_d01_2009-07-08_12:00:00 > X1.out
ncdump -f f -v XLONG wrfout_d01_2009-07-08_13:00:04 > X2.out
diff X1.out X2.out | more
where one of the wrfout file must be the first one.
here is the result of my diff command:
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< 5.918274, // XLONG(56,53,1)
> 5.918243, // XLONG(56,53,1)
which is a about a 3 meter error.
Thanks