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Fix Bussi thermostat DOF count and add zero-KE guard - #57
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n_degrees_of_freedom was hardcoded to 3*len(atoms), which biases the target temperature upward when constraints (e.g. FixCom) remove DOF, and silently divides by zero if velocities haven't been set yet. Both fixes mirror ASE's own reference ase.md.bussi.Bussi implementation. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
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Summary
n_degrees_of_freedomused a hardcoded3 * len(atoms), biasing the target temperature upward whenever DOF-removing constraints (e.g.FixCom) are attached. Now usesatoms.get_number_of_degrees_of_freedom(), matching ASE's own referencease.md.bussi.Bussiimplementation.__init__that raisesValueErrorif the initial kinetic energy is ~0, to avoid a silent divide-by-zero/NaN when velocities haven't been set yet. Also matches ASE's reference implementation.Test plan
FixComconstraint and confirm the reported/sampled temperature matches target (previously biased ~1-33% high depending on system size)Bussiwith zero-velocity atoms raisesValueError🤖 Generated with Claude Code