"Special Facilities" is a term commonly used to describe a process or operation that benefits only a select or limited portion of a contractor's overall operations. Special facilities might include wind tunnels, space chambers, research vessels, testing labs, etc. The name or type of facility is not important. What is important is that the cost of operating the facilities does not benefit the entire operations equally and a method is needed to allocate costs to only benefiting cost objectives. Also, the cost need to be significant otherwise its fine to find a less precise way to account for its costs.
The cost related to specialized facilities consists of direct and indirect costs. For example, indirect costs related to a research vessel might include depreciation, maintenance and repairs, supplies, and general support salaries. While it is in use however, costs tend to spike because not you have the salaries of research scientists, vessel operators, food and other sustainment costs.
There are several ways to account for the costs of the research vessel or special facilities in general. The first is to charge the readily identifiable direct costs directly to the contract and then allocate the indirect costs to benefiting cost objectives on a 'usage' basis. Using our research vessel example, if the vessel is out on the high seas for 200 days per year, the indirect costs would be allocated over those 200 days and charged to the benefiting projects. This is probably the most equitable method though challenges when trying to forecast usage.
A second method is the same as the first except that indirect costs are charged to one of the existing indirect rates, perhaps an overhead rate. This method would be open to challenges by the Government so care would be necessary to ensure that it results in an equitable distribution of costs.
A third method would accumulate both direct and indirect costs and distributed to final cost objectives through one of the contractor's appropriate categories of indirect expense. This is the least precise method and should only be used if the costs are immaterial or the indirect rate allocation base approximates the special facility's usage.
Contract auditors are always looking for ways to 'improve' cost allocations, that is, finding alternate methods of allocating indirect costs that reduce costs to the Government. Whatever method a contractor chooses to allocate special facilities costs, needs to be supported by evidence that it results in equitable allocations to final cost objectives including Government contracts.