Differences

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+Capacitors are essentially very large gates.  Say for example that one wants a capacitor to ground.  In a metal gate CMOS process this can be done by simply creating a well and putting a large M1 over the well.  For example, if one wants a capacitor to ground, you could create a large P well and then put metal on top.  The P well is connected to ground and M1 to the desired connection.  Example metal gate CMOS capacitor (ST 24C02):
+{{:mcmaster:capacitor:metal_gate_st_24c02_hf2.jpg?300|}}
+{{:mcmaster:capacitor:metal_gate_st_24c02_hf1.jpg?300|}}
+Note the much smaller gate capacitors below and the body contacts below the capacitors.  It seems to me these capacitors as above would be isolated but M2 tied them together in parallel.  I am not clear why.
+I haven't seen many multi-metal capacitors although I have no idea why you couldn't.  It might be that the distance between M1 and active is less than the distance between M1 and say M2 such that the capacitance is much higher.