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In order to address the issue of the alpha values being inconsistent with complex geometry, one of two different approaches can be applied. The first way is to perform two more passes with a full screen quad with the alpha value of the desired alpha of the shadow stencil. The first pass uses a blend mode of Reverse Subtract, a source blend of One and a destination blend of One. This will take any alpha values less than the desired alpha value, and clamp them to zero. Provided all the alpha values are less than the desired alpha value set, this leaves you with pure zeros in the shadowed areas, and 1 - desired alpha values in the un-shadowed areas.
The second pass of the stencil normalization process. Here the shadows are set to the desired alpha value, and the unshadowed areas are back to 1.
The second pass adds the desired alpha back to the alpha buffer by using a blend operation of Add, a source blend of One and a destination blend of One. This will give shadowed areas the desired alpha, and un-shadowed areas a value of one. This is effectively a Max operation.
While the iPhone supports the Max operation, I personally have not had success yet getting the operation to work. Theoretically, however, the two above passes could be replaced with a single Max operation that effectively does what the two passes do, with less fill rate.
Now that the alpha stencil is built up, the shadows can be applied. This requires one final pass with a full screen quad colored the desired shadow color with an alpha of 1. The blend operation is Add, the source blend is Zero, and the destination blend is Destination Alpha. Also, the color operation should be Modulate in order to darken the affected areas of the scene.
The scene with shadows applied.
Using the alpha buffer for these sorts of tricks is a long standing tradition among those that grew up building the love hate relationship with fixed function pipelines. Mobile platforms for some of us are a blast from the past, where we again get to trick limited hardware to do things we want it to do, in order to obtain stunning visuals. The result: Dynamic Shadows on the iPhone, despite its imposed limitations.
To sum up, we can accomplish stencil quality shadows with a clear pass, up to six stencil building passes, two normalization passes, and an application pass. If fill rate isn't a concern, it's a viable solution to runtime shadows on the iPhone. I've implemented this solution in the Ogre 3D engine version 1.7 and tested it in their Shadows Sample on the iPhone. It will be available in the Ogre 3D distribution at a future date.