@Catalyst2682 – I think there are two issues.
First, I would double-check the date specified by your script variable “edate”, which is used to define the script variable “MCIP_END” to ensure that the end date is actually 18 UTC 31 Jan 2016. You can check the file “namelist.mcip” that is generated by the script to see how “MCIP_END” was set. If you intend to explicitly set the start and end dates rather than use the script variables, then you need to uncomment (remove the # at the start of the line) where “MCIP_START” and “MCIP_END” are set to the dates you listed in your post, and comment out (add # to the start of the line) where “MCIP_START” and “MCIP_END” are set using the script variables “sdate” and “edate”.
Second, I’m not sure of the scientific implications of using data that are less frequent than hourly in the CCTM. You are processing MCIP with 3-hourly output, and I think the atmospheric changes should be captured at least hourly for the CCTM…which requires that you have hourly WRF output. That is a completely separate issue, but it is one that you should strongly consider, in my opinion, if you are planning to run the CCTM using this MCIP output.