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This report documents modifications to the U.S. Geological Survey's modular three-dimensional finite-difference groundwater flow model used for a regional aquifer-system analysis of the Columbia Plateau. The changes were needed because the aquifer system includes unconformities, deep canyons, and steeply dipping structural barriers that could not be represented realistically by the existing model. The modifications permit flow from a cell in any layer to a cell in any other adjacent layer; allow a cell that has been cut completely through by a canyon to remain in the model by setting the branch conductance to zero only on specified cell walls; simulate barriers to lateral groundwater flow by reducing the branch conductance only on specified cell walls; and allow use of a convergent grid. The concepts and mathematical basis for these modifications are described. The changes in the data-input items for this modified model, compared with those of the existing modular model, are described.

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There are five files containing source codes of the flow model and post-processors. Input for the flow model is stored in 51 files and grouped into 16 categories, one for each of the packages of the model except its utility package. Model output is in 18 files. The postprocessors have four files, two with input control and two with output. Five command-input files compile and load the flow model, run it, and run the postprocessors .