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CST MWS is based on FIT, u can start your learn from two documents -- getting start and tutorials, in "documentation" fold which is direct in CST install fold.
CST is based on Finite Integration Technique. This method is similar to Finite Difference Time Domain Method; the main difference is that FIT solve maxwall equation in time domain in integral form while FDTD in differencial form. To understand the CST program you can serch for some paper on FDTD method (it is very popular)
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