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Currently, I have a digital circuit running parallel to a LED to measure if it is driven high, with a zener clipper circuit to clip the voltage to 3.3v (max safe for microcontroller).

Current circuit is: this

This senses if S2 is closed but does not check if S1 is closed.

I want to have a digital circuit that checks if both S1 and S2 are closed.

Thanks in advance

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schematic

simulate this circuit – Schematic created using CircuitLab

Figure 1. Opto-isolator to detect current flow in LED circuit.

The problem with your circuit is that with S1 and S2 open both ends of LED2 are floating and your GPIO input will be too so the logic level will be undefined.

A simple solution is to monitor the current in the LED circuit. This can be achieved with an opto-isolator as shown in Figure 1.

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