Can 3.3VDC , 5VDC and 9VDC share a common ground. As in on a breadboard top row is 3.3VDC the next 5VDC then drop down to 3rd row for 9VDC and the bottom row be the common ground. This would be great with the large Adafruit breadboard with the 4 terminals. I would also like to place a diode in the 2nd to 5th holes in each column to prevent fly-back is that a good idea?
Great question and the short answer is YES! In order for your design to maintain a completed circuit, it is necessary for the powered devices to share a common ground. Lets say you have a GPS, a Boarduino, and a Solenoid in your circuit prototyping some sort of crazy Portal Turret. Each one of these devices require different voltage levels, while all communicating with the Arduino. In order for this communication to take place, each device will need to share a common ground in addition to some level-shifting circuitry. This level-shifting circuity allows for devices operating at different voltage levels to communicate. Typically a 3.3V device can talk to a 5V device without any problem. Although when a 5V device tries to talk to a 3.3V device, it needs to communicate through a buffer that shifts the HIGH/LOW levels into a range that doesn’t damage the 3.3V devices circuitry. **Below is a representative schematic. You will need to choose appropriate regulators/supplies to meet the requirements of your components…especially solenoids.
With regards to your flyback question: Flyback protection diodes are typically used in circuits containing inductive loads, like a relay, solenoid or motor. The diode acts to protect the power circuity from voltage spikes produced when the inductive load sees a drop or loss of power. Adafruit has nice diagram illustrating a method for controlling a solenoid with an Arduino, as shown below:
I hope this has helped to answer your question and good luck setting up your breadboard!
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