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Changes CTPSimulation so that it doesn't break AthenaMP TCTs (ATLASRECTS-5018)

Peter Onyisi requested to merge ponyisi/athena:master-fix-ctpsim-mp into master

Changes CTPSimulation so that it doesn't break AthenaMP TCTs. It uses the deprecated beginRun() but this code needs a complete rewrite for AthenaMT anyway.

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