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Use global counter in thermostats #3884
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Commits on Sep 3, 2020
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core: Use seed+salt in key of Philox
In the previous implementation, thermostat noise for different seeds was correlated, the seed just shifted the sequence. For example with seed offset X, the cross-correlation used to have a peak at lag X. Co-authored-by: Jean-Noël Grad <[email protected]>
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core: Use a single global counter for RNGs
Co-authored-by: Jean-Noël Grad <[email protected]>
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core: Use Philox infrastructure for SD thermostat
The SD external library uses Philox internally for both the CPU and GPU implementations. SD now uses the global counter instead of the simulation time divided by the time step, which are both mutable and can lead to correlated sequences when changed by the user.
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core: Make statistical unit tests faster
Remove overhead from the std::function wrapper and heap allocation.
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core: Make statistical unit tests faster
Reduce sample sizes and increase tolerances.
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Commits on Sep 4, 2020
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core: Move global counter to the integrator
This counter is incremented by the integrator and is completely dissociated from the thermostat infrastructure.
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core: Forward integrator_counter state by parameter
Pass the current value of the integrator_counter to the force kernels as a parameter instead of relying on external linkage. There are two exceptions: thermalized bonds and constraints, which were not designed to be extensible in this way, and still rely on external linkage.
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core: Break integrator/thermostat cyclic dependency
Header file thermostat.hpp no longer includes integrate.hpp.
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core: Remove temporary variable
Fixes clang-analyzer-deadcode.DeadStores warning.
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