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update smc documentation
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saratk1 committed Aug 24, 2023
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8 changes: 6 additions & 2 deletions docs/getting_started.rst
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Expand Up @@ -135,9 +135,13 @@ To perform a unidirectional Sequential Monte-Carlo (SMC) protocol, the following
sim=sim,
reference_samples=mm_samples,
nr_of_walkers=100,
nr_of_resampling_steps=1_000,
protocol_length=1_000
nr_of_resampling_steps=100,
save_endstates=True
)
Here, :code:`nr_of_walkers` indicates the number of walkers selected from the reference distribution, which are propagated for 1ps (:code:`nr_of_resampling_steps`, i.e. 1000 interpolation/resampling steps).
Here, :code:`nr_of_walkers` indicates the number of walkers selected from the reference distribution, which are propagated for 1ps (:code:`protocol_length`).
:code:`nr_of nr_of_resampling_steps` states that the walkers are resampled 100 times.
With the option :code:`save_endstates` samples at the end of the protocol can be saved.

Perform multiple protocols
~~~~~~~~~~~~~~~~~~~~~~
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