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Use global counter in thermostats #3884

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Use global counter in thermostats #3884

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Commits on Sep 3, 2020

  1. utils: Fixed parameter type for uint64_t u32_to_u64

    @fweik @jngrad
    fweik authored and jngrad committed Sep 3, 2020
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  2. 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]>
    @fweik @jngrad
    fweik and jngrad committed Sep 3, 2020
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  3. core: Use a single global counter for RNGs 

    Co-authored-by: Jean-Noël Grad <[email protected]>
    @fweik @jngrad
    fweik and jngrad committed Sep 3, 2020
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  4. 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.
    @jngrad
    jngrad committed Sep 3, 2020
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  5. docs: Document unified thermostat infrastructure

    @jngrad
    jngrad committed Sep 3, 2020
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  6. core: Make statistical unit tests faster 

    Remove overhead from the std::function wrapper and heap allocation.
    @jngrad
    jngrad committed Sep 3, 2020
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  7. core: Make statistical unit tests faster 

    Reduce sample sizes and increase tolerances.
    @jngrad
    jngrad committed Sep 3, 2020
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Commits on Sep 4, 2020

  1. tests: Increase RNG checks tolerance

    @jngrad
    jngrad committed Sep 4, 2020
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  2. tests: Increase RNG checks tolerance

    @jngrad
    jngrad committed Sep 4, 2020
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  3. core: Move global counter to the integrator 

    This counter is incremented by the integrator and is completely
dissociated from the thermostat infrastructure.
    @jngrad
    jngrad committed Sep 4, 2020
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  4. 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.
    @jngrad
    jngrad committed Sep 4, 2020
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  5. core: Break integrator/thermostat cyclic dependency 

    Header file thermostat.hpp no longer includes integrate.hpp.
    @jngrad
    jngrad committed Sep 4, 2020
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  6. core: Use vector operations

    @jngrad
    jngrad committed Sep 4, 2020
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  7. core: Move NpT functions to dedicated file

    @jngrad
    jngrad committed Sep 4, 2020
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  8. core: Split thermostats from integrators

    @jngrad
    jngrad committed Sep 4, 2020
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  9. core: Remove temporary variable 

    Fixes clang-analyzer-deadcode.DeadStores warning.
    @jngrad
    jngrad committed Sep 4, 2020
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  10. core: Header cleanup

    @jngrad
    jngrad committed Sep 4, 2020
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