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What I mean is that I know a charge controller regulates the voltage and current into your batteries to protect them (and CC's can incorporate MPPT's to extract more from your solar panels), but do the MPPT CC's take ALL the energy you could generate from the PV panels and put all of that energy in the batteries (neglecting efficiency here because that is irrelevant for the purpose of this question)? Or do they also tone down the rate at which the batteries get charged as they get close to maximum capacity (I know the CC will stop charging the battery once it reaches full capacity).

For example, would the below be something that could happen?

A theoretical PV system could generate 12 watts with an MPPT CC at a given moment in time. If the batteries were at 5% charge, they could accept a charging rate of 12 watts, BUT since the batteries are at 75% charge, they can only be charged at a rate of 7 watts, so the MPPT CC sets the PV panels at 7 watts, thus losing you 5 watts from your PV panels.

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    \$\begingroup\$ MPPT means maximum power point tracking. If the maximum power point power is greater than the required charge power, then the charge controller will not operate at the maximum power point. Think about it, power has to go somewhere (thermodynamics). If it is not stored in the battery, it would just have to be converted to heat. So it is better to let the solar panel operate outside the MPPT point once that situation occurs. \$\endgroup\$ – mkeith Jun 28 '17 at 20:18
  • \$\begingroup\$ I get that. This is more of a question about how batteries work. From what you said, it sounds as though the rate at which they can be charged does drop down as they get closer to maximum capacity. I take it my best option would be to have enough storage space where this wouldn't be an issue and the MPPT CC would never need to drop below the maximum power point, right? \$\endgroup\$ – MechE Jun 28 '17 at 20:20
  • \$\begingroup\$ Depends on what you are trying to maximize. Realistically, there may be times when the output of the panels is simply not needed. I wouldn't just increase my batteries to avoid idle capacity. Keep in mind that the daily available energy from the panels may vary seasonally depending on where you are. Maybe a better option is to think of things to do with the power when excess is available. Run pool or pond pumps or something. \$\endgroup\$ – mkeith Jun 28 '17 at 20:35
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An MPPT controller is effectively a buck/boost converter that tries to present the optimum load to the solar panels in order to maximize the harvested energy while supplying the harvested energy at the voltage required by the load. At times, the solar panels will produce more energy than what can be used by the load. At other times, the load could consume more energy than the panels can produce.

An MPPT controller that is charging batteries is primarily monitoring and controlling the voltage to the battery. There is a standard temperature compensated charge profile for flooded and AGM batteries that it will follow as the state of charge of the battery progresses.

If the battery is deeply discharged, the battery will attempt to draw more current from the controller. If the solar panels are not producing enough energy to supply the current the battery could draw, the MPPT controller will effectively restrict the current drawn in order to keep the necessary charge voltage across the battery. This has the effect of slowing down the charge rate while still allowing the batteries to continue to charge.

If the solar panels are not producing enough energy for the controller to deliver the correct charging voltage, say in the early morning, then the charge controller will not charge the battery at all. In this case, potential energy from the solar panels is being wasted.

If the solar panels are producing more energy than the batteries require for charging, as when the battery is nearly fully charged, then the controller only needs to keep the right charge voltage since the batteries will not draw all available current. In this case, energy that the solar panels could have produced is not being used by the batteries. Therefore potential energy is being wasted.

In very hot climates, the charger may have to suspend charging all together if the batteries are too warm. In this case potential energy from the panels is being wasted.

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Lead and lithium batteries finish their recommended charging on a constant voltage, reducing current regime, with termination at a current threshhold. Both these chemistries therefore can absorb less power at the end of their charge. Nickel batteries can be run at a high charge rate throughout and terminate on temperature rise or voltage plateau/drop.

If the potential output of your solar panel is larger than the batteries can absorb at any time, then you'll just have to 'waste' that power, by not using it. Unless of course you can find another use for the spare power, like powering a bitcoin miner, or pumping water uphill.

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