fix the check point number when restarting the simulation

After MR !1251 (merged), the check point of the initial condition for restarting simulation is not output and m_nchk is not increased by 1. For example, if the restart file has ChkFileNum 10 and Time 1, the output chk files after restarting the simulation is

old version ChkFileNum	old version Time	new ChkFileNum	new Time
10	1	no	no
11	1.1	10	1.1
12	1.2	11	1.2

This makes the ChkFileNum of the restarting simulation different from previous simulations. I am not sure if we can revert the modification of this part or fix the ChkFileNum like this

old version ChkFileNum	old version Time	current MR ChkFileNum	current MR Time
10	1	no	no
11	1.1	11	1.1
12	1.2	12	1.2