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Difference between wrfinput and initial wrfout

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I have been performing some experiments with WRF model by perturbing some variables in the wrfinput file, specifically T, U, V and P to create an ensemble of different initial conditions. I observed that the P fields in the wrfout file corresponding to the initial time of the forecast were different from its corresponding fields in the wrfinput file. Is there any process that modifies the initial conditions before starting the simulation?
Which version of WRF are you running? For older version of WRF, yes we do know there existed differences. However, for newer version like WRFV4, I believe P in wrfinput should be the same as that in the first time of wrfout.
If you run older version, can you switch to new version of WRF?