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DeepSIM changes.  #284

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@iandobbie

With the paper draft there is a branch containing the last running setup from DeepSIM. The changes are minimal and probably worth integrating.

David picked out dstoychev@5a297ff as the only change, I found a couple more minor edits, but also related to the Alpao DM.

I suggest that we try to discover why the system needed to duplicate the 131st entry. Sounds like an obscure library bug, although 131st is a pretty strange number. As this is the only system that utilized this hardware it is likely to be a useful change that we need to find the cause for.

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