Refactor runner module code

CHANGELOG.md

@@ -25,6 +25,8 @@ Changelog
 * Add `gcmc_batch_size` and `gcmc_num_attempts` options to set the number of GCMC trials evaluated in parallel per batch and in total per move, which were previously fixed at the defaults of the GCMC sampler. Both can be changed on restart, e.g. to reduce wasted trials when more than one is accepted per move [#246](https://github.com/OpenBioSim/somd2/pull/246).
 * Add adaptive replica exchange, enabled with `adaptive_repex`, which concentrates sampling on the lambda windows that are slowest to converge. Windows are ranked at checkpoints by the uncertainty they contribute to the free energy, and only the highest ranked are propagated and exchanged every cycle, with the rest joining every `adaptive_mix_interval` cycles [#247](https://github.com/OpenBioSim/somd2/pull/247).
 * Require `frame_frequency` to be a multiple of `gcmc_frequency` for GCMC simulations, so that every frame has a matching ghost water record. Previously some combinations silently saved frames without one [#247](https://github.com/OpenBioSim/somd2/pull/247).
+* Fixed the regular runner's final block when the `runtime` isn't a multiple of the `checkpoint_frequency`, which ran a single integration step rather than the remaining time, without GCMC moves. Each checkpoint now appends exactly the energies sampled since the last one, so energies are no longer duplicated, or lost on restart when `checkpoint_frequency` is zero. Blocks that aren't a whole number of GCMC or terminal flip intervals no longer overrun, and energy components are time stamped correctly after a restart [#248](https://github.com/OpenBioSim/somd2/pull/248).
+* Require the `runtime`, `checkpoint_frequency`, `energy_frequency`, `frame_frequency`, `gcmc_frequency` and `terminal_flip_frequency` to be multiples of the `timestep` for the regular runner, which runs in whole integration steps. GCMC and terminal flip moves now keep their frequency across checkpoints [#248](https://github.com/OpenBioSim/somd2/pull/248).
 
 [2026.2.0](https://github.com/openbiosim/somd2/compare/2026.1.0...2026.2.0) - Sep 2026
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src/somd2/_viewer/_data.py

@@ -249,7 +249,11 @@ def __setstate__(self, state):
 
 class _RepexUnpickler(_pickle.Unpickler):
     def find_class(self, module, name):
-        if module == "somd2.runner._repex" and name == "DynamicsCache":
+        # The cache moved to its own module, so older checkpoints use _repex.
+        if name == "DynamicsCache" and module in (
+            "somd2.runner._dynamics_cache",
+            "somd2.runner._repex",
+        ):
             return _RepexState
         return super().find_class(module, name)