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How we can avoid the un wanted pulses generated at the output of the PID controller

I think your gains are off.  It's unusual to have a negative value only for the derivative gain, and the derivative gain is huge compared to the other gains.  Conversely the integral time is relatively large meaning it will have little effect (remember, that's a time in minutes).  The PID Toolkit Manual has instructions for tuning a PID loop manually.  For a fast-responding system that can tolerate some oscillation you'll want to try the closed-loop Ziegler-Nichols approach.  For a slow system like a large oven, there's a Ziegler-Nichols open-loop method or the similar Cohen-Coon approach.  Note that for the closed-loop approach the manual refers to Proportional Band, which is standard terminology but also somewhat confusing.  Where the manual says that the P gain should be 2.00PBu, this is the same as saying that the P gain should be K/2.

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