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choderalab / yank

An open, extensible Python framework for GPU-accelerated alchemical free energy calculations.
http://getyank.org
MIT License
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unknown parameter number_of_iterations #956

Closed dprada closed 6 years ago

dprada commented 6 years ago

Yank 0.21 (omnia channel -conda-) does not recognize the yaml option 'number_of_iterations'.

In Yank 0.20 this option was introduced in the dictionary template_options with the line 1207 of experiment.py:

        template_options.update(utils.get_keyword_args(repex.ReplicaExchange.__init__))

This fact makes the examples not functional. I hope this helps to keep the stable version usable for the new users experimenting with yank.

Thanks a lot.

Lnaden commented 6 years ago

YANK 0.21.0 was a significant refactor of YANK's code base which included a generalization of the sampling scheme introducing a generic, fixed state MultiStateSampler; the Hamiltonian Replica Exchange sampler ReplicaExchangeSampler; and the single-replica state jumping self-adjusted mixture sampling SAMSSampler. As part of this generalization, the YAML files were changed to include two additional blocks samplers and mcmc which control sampler-specific and Markov Chain Monte Carlo-specific options, respectively.

We decided to move a couple options such as number_of_iterations from the general options block to their respective samplers and mcmc blocks to avoid ambiguity since multiple samplers can now be provided. The samplers and mcmc blocks are fully optional and a default set of options will be chosen if you do not specify them, and to facilitate backwards-like behavior, we renamed the option in the primary options block to default_number_of_iterations. If you want to restore the previous behavior, simply exchange number_of_iterations with default_number_of_iterations in your options block, although we encourage experimentation with the new blocks as well.

See http://getyank.org/latest/yamlpages/samplers.html for more information about the new block and look over the changelog to see how YANK's structure has changed in 0.21.0

dprada commented 6 years ago

Thanks for your kind reply! I am going to have a look.

jchodera commented 6 years ago

Our apologies for the ever-changing API! We hope this is very close to a final stable release! Things should be much more stable once the initial preprint is posted!

dprada commented 6 years ago

No need to apologize. You are doing a great effort and a fantastic job. I had to look more in detail before opening the issue. Thanks.