I am trying to create a low pass filter with a cut-off frequency of 100Hz to retrieve a sine wave from a Fourier Square Wave. I am only able to achieve a sine wave with transients. How can I edit my filter design to achieve my desired output?
Where is your filter math? RC for -3db at 100HZ is 10K/160nF. Or you can swap the RC values to be 16K/100nF. I would keep R >= 10K to avoid loading the summing op-amp, as the inverting input is treated as a virtual ground. From what I see you could increase the value of all resistors by a factor of 10.
The triangle output may be from using R values that are too low for the op-amp to drive. If 1.59K becomes 15.9K, then your 1uF capacitor needs to be just 100nF, avoiding the need for aluminum or tantalum capacitors. R6 becomes 15.9K which avoids loading the output of the op-amp. For LM324 normal minimum load is about 2.2K ohm.
Your program maybe interpreting values the way a real LM324 op-amp would see them.