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Hi everyone,
Thanks for developing this nice software package! I was thinking about rewriting my not-so-organized MC code using this software package and was wondering if there is support for paral…
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Talking with Alexei Bazavov he pointed me to two possible techniques of interest. The first is [parallel tempering](https://pubs.rsc.org/en/content/articlehtml/2005/cp/b509983h) ([first paper](https:…
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We have a for loop over temperatures --> "parfor" (multiprocessing / multithreading).
Check that parallelizing does not yield performance loss compared to serial, can potentially happen for cheap s…
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Improve exploration of the configurational space via parallel tempering. A good introduction
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Earl, David J., and Michael W. Deem.
"Parallel tempering: Theory, applications, and new perspective…
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**Feature description**
Running PymcSampler as an internal sampler under the AdaptiveParallelTemperingSampler.
**Motivation/Application**
It seems like infrastructure is already in place for runn…
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**Describe the solution you'd like**
To be able to run multiple MCMC trajectories in parallel with different temperatures (saving individual trajectories) and swapping between temperatures. This shou…
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Hello Florian,
Thank you for open-sourcing such a great library that I am hoping to use for my research in theoretical seismology. I was wondering if i could ask a potentially dumb question here wi…
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in order to exploit PT better, assigning different starting points to the different chains would be good, as discussed here: https://github.com/ICB-DCM/pyPESTO/pull/268
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Hi,
This package looks great. I wonder if you have considered using the adaptation schemes from [Syed 2019](https://arxiv.org/abs/1905.02939) and [Syed 2021](https://arxiv.org/abs/2102.07720).
I…
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1 - Plotting free energy estimation seems to me a huge deltaG(target temp=302K), ~5000. Is it as a result from method or is it just a statistical estimation?
2 - I couldn't to reproduce the PMF g…
wever updated
7 years ago