Settlement is a geotechnical problem. If the soil underneath is Sand, then liquefaction may occur. Liquefaction Potential Index (LPI) can be determined by empirical procedure or by lab test. If the soil is Clay, then consolidation may occur. This can be avoided by Vertical Drains or other method.

Settlement problem can be analyzed by Standard Penetration Test (SPT), or CPT etc. in-situ test.

Hope this helps.  

You can determine the settlement by an oedometer test.

Here you can find a list with geotechnical software:

http://www.ggsd.com/

and click on: Settlement analysis

For structure with raft foundation, the stress distribution will be more even, and the calculation can be simplified using spreadsheet for each soil layer. Soil data required for each layer includes E, E50, Cc, Cv from Consolidation test, and actual pore pressure and overburden pressure. Using this approach, only one value of settlement will be get for 1 set of soil layer data.

If a type of pile foundation used, distribution of stree will be more complicated. In this case, using FE 3D program such as PLAXIS 3D, or simplified model program using Mindlin Theory will be useful (NSETTLE3D). Using such software, we can get also contour of settlement to find maximum settlement location.