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The EMI filter after the rectifier will be less effective specially for common mode noise.
The main source of conducted EMIs in this motor driver is the inverter. Therefore placing the EMI filter after the rectifier may be effective for conducted EMI in differential mode. However high frequency EMI may bypass the filter using alternative paths on PCB, chassis, capacitive coupling between IGBT module and heatsink, etc.
The rectifier causes low frequency harmonics which may be reduced with low frequency filters, harmonic filters, PFC... However it is not a big source of high frequency EMIs.
In option 2 the EMI filter is not connected to chassis / earth, this may reduce its common mode noise rejection.
If you intend to have some EMI/EMC certification or meet some standard I would recommend to go for option 1.
I don't think there is any simple math to calculate the change in effectiveness as many parameters are involved... I would suggest to perform an EMI test using LSIN as you mentioned.
If you want to simplify the 3 phase filter, you could split the filter in two... placing the "differential stage" in the DC bus side (after the bridge rectifier) and the "common mode stage" before the rectifier. It is common to have LC filters between rectifier and inverter. By the way, do you have power factor requirements?
I should have said, is there a mathematical way or a study paper that discusses the effect of EMI filter when it is placed after the bridge rectifier (on the DC bus side)?
This isn't for a new design. In the past designs that I have done, I have used a full blown (one or two stage) filter with both common and differential mode chokes before the bridge rectifier. However, I have recently come across some other designs that have used just a common mode choke after the bridge rectifier on the DC bus side (as in the attached figure). Reading more into it, I understand that if the EMI requirements aren't stringent, you can get away by designing a common mode choke that also has an effect on the differential noise. This is done with very wide winding spacing that generates the leakage inductance needed to provide
this differential inductance. However, I am quite sure in these designs that I am looking at, the designer just used a off-the-shelf common mode choke. Which made me think, how can ballpark the filter's effectiveness.