Less than the cylinder height. You could make TDC & BDC greater than the cylinder height if you want to. Just keep us all posted on how it turns out if that's what you decide to do.
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I recommend that TDC occur at the upper limit of the cylinder stroke, and that BDC occur at the lower limit. But I will consider other options, if there are any.
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it depends on your compression ratio needed. At the top = tdc, you have the minimum space into which the air is compressed. At the bottom = bdc you have the largest space. The ratoit between these volumes = compression ratio.
so if you have a cylinder with a tdc gap of 1 cm and the bottom bdc of 10 cm that means all the air in that 10 cm space is squeezed into the 1 cm space = a 10:1 compression ratio. Now the pressure might be ten times if the air stays cool, but air gets hot and the pressure might be higher than 10 times as much.
Due to heating, if they want higher compression rations than 8 or so, they often use a series of cylinders, each one smaller and higher pressure than the last as pressure and volume change inversely. Often they have coolers between the stages to reduce the temperature(interstage cooler).