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muso
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OK, I'll try to answer. I think your question relates to the greenhouse effect as it applies to longwave infrared radiation rather than the effect of the a solar flare hitting the Earth. Solar flares tend to cover a wide spectrum, so a whole lot of other variables come into play.
Think about the photons of longwave infrared being radiated from the Earth. As they travel up through the atmospheric column they can either go straight through into space, or if they happen to hit a greenhouse gas molecule, they are absorbed and re-radiated in a random direction.
In the lower atmosphere, the most significant greenhouse gas is water vapour, followed by carbon dioxide. Above a certain altitude, the water dewpoint is extremely low due to
the lower temperature, and carbon dioxide becomes the dominant greenhouse gas.
Now it's more complex than that, because the vast majority of radiation comes from the atmosphere itself. The energy is largely transferred from the Earth's surface to the atmosphere and clouds by thermal convection processes rather than radiation, because most of the IR radiated from the Earth's surface is absorbed. Convective process account for roughly ten times the energy transfer of radiation in the lower atmosphere.
As the LWIR photons travel up through the atmospheric column, several variables change which affect the proportion of radiation that ends up in space.
Without going much further, can you see that the same convection factors don't apply in the same way when the radiation is incident from a solar flare. In terms of the action of greenhouse gases in the upper atmosphere, it's pretty similar, although the geometry is different.
Does that make sense so far?
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