Look in parfeap/usolve.F for
call KSPGetTolerances (kspsol,p_rtol,p_atol,p_dtol,p_maxit,
& ierr)
if(pmaxit.le.0) then
pmaxit = p_maxit
endif
call KSPSetTolerances (kspsol, itol, atol, dtol,pmaxit,
& ierr) ! From command data
We only utilize the maximum iterations parameter from the command line. The rest are ignored in favor of the ones set using FEAP's TOLerance command (see pp. 488-490 of the user manual). If you want to use the command line options, you can pass the values read by KSPGetTolerances into KSPSetTolerances but make sure to add some logic so that the FEAP values are used if you have not set them on the command line.
btw, section 4.3.2 of the PETSc manual discusses such options. Others are also discussed in the PETSc manual.