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I simulated three phase rectifier using a thyristor like so:

enter image description here

I get the expected result. But if I change the thyristors to IGBTs as shown below, it does not work.

enter image description here

Why do these two circuits behave differently?

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    \$\begingroup\$ how doesn't it work? what is the circuit you used. NOTE: I have a feeling I know what you did wrong but until you should exactly what you did... As a precursor... does it look like it is rectifying normally? \$\endgroup\$ – JonRB Nov 2 '15 at 12:25
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In the scr rectifier, you have given individual gate pulses viz PG1,PG2,PG3 etc. But in the IGBT, YOU HAVE given a common have signal to ask the 6 IGBTs. It will lead to a short circuit.

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IGBTs and SCRs behave completely differently.

SCRs block cathode-to-anode, and conduct anode-to-cathode when gated and forward biased.

IGBTs with antiparallel diodes conduct emitter to collector, block collector to emitter unless gated, and conduct collector to emitter when gated.

In your case, you're turning on the upper and lower IGBTs at the same time. This causes a short circuit across the DC bus, which will break something. It will definitely not rectify. If you were not turning on the IGBTs, the circuit would behave like a normal diode rectifier. SCRs don't have that problem, because even when gated on they don't reverse-conduct. (It's still not a great idea to gate them on when heavily reverse-biased though.)

I'd give you other recommendations, if you could describe what goal you are trying to achieve.

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