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Hi Tasnova,
A process' Merit Order is similar to a priority number - it tells LEAP which processes to use first, second (third, fourth, etc...) to meet the electricity generation module's requirements in a given time slice. Have a look here for details:
http://www.energycommunity.org/WebHelpPro/Transformation/Merit_Order.htm
To your second question - capacity is not the same thing as generation, so a larger Exogenous Capacity does not necessarily imply that more crude oil will be processed. LEAP runs a module's processes to meet the module requirements. You can view these requirements in Results view by selecting the Oil Refining module with your mouse, and viewing Transformation: Requirements.
The exception is if you specify that a process should be run using the FullCapacity rule, in which case the process will be dispatched without regard for the module requirements (this is the cause of the diagnostic message you see when using the FullCapacity rule). For details on LEAP's dispatch rules, please see this help file:
http://www.energycommunity.org/WebHelpPro/Transformation/Process_Dispatch_Rules.htm
Hope this helps,
Taylor