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This PR closes #152 by adding a sentinel file to indicate full completion for repex simulations. This avoids restart issues when a system file is written with an update time stamp, but the simulation crashes (or is killed) during trajectory reconstruction. Cleanup is only performed when the
.donefile is written, allowing recovery from partially written final checkpoints.I've also removed a small redundant attribute from the
DynamicsCacheto reduce the memory footprint. This variable can be created in scope, i.e. there is no need to store it.