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glotzerlab / hoomd-blue

Molecular dynamics and Monte Carlo soft matter simulation on GPUs.
http://glotzerlab.engin.umich.edu/hoomd-blue
BSD 3-Clause "New" or "Revised" License
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Remove deprecated: default global neighbor list #105

Closed joaander closed 8 years ago

joaander commented 8 years ago

Original report by Michael Howard (Bitbucket: mphoward, GitHub: mphoward).

The documentation says that default global neighbor lists may be removed in favor of the new explicit specification of neighbor list style. If this is the case, the things that would need to be cleaned up are:

  1. Remove the following:

    globals.neighbor_list
nlist._subscribe_global_nlist
nlist.set_params
nlist.reset_exclusions
nlist.benchmark
nlist.query_update_period

  2. Update all pair potentials to remove nlist=None as an option and remove any references to the default global neighbor list. There is probably a spot in charge.pppm that also needs this.

joaander commented 8 years ago

Original comment by Michael Howard (Bitbucket: mphoward, GitHub: mphoward).

Any thoughts / opinions on if this task should be done? On the one hand, it is convenient not to have to make a neighbor list for simple pair potentials. On the other hand, it is only a one-liner to create a neighbor list, and it forces the user to think carefully about how to use their neighbor lists effectively. If I am updating the neighbor list documentation (#141), it probably makes sense for me to also take care of this task at the same time, and then remove the discussion related to the global neighbor list wrappers from the docs (which are somewhat cumbersome anyway).

joaander commented 8 years ago

explicit is better than implicit. I say we go ahead with this plan.

I'm trying to make the time to get the sphinx docs up and running, but keep getting sidetracked by administrative tasks and travel. Hopefully tomorrow I can make enough forward progress on that so that I no longer hold you up.

joaander commented 8 years ago

Sphinx documentation is now fully in place on the 2.0 branch. To build the docs:

  1. make hoomd in a build directory ${build}.
  2. Add ${build} to your PYTHONPATH.
  3. Issue "make html" or "make latexpdf" in the source directory hoomd-blue/sphinx-docs.
joaander commented 8 years ago

Original comment by Michael Howard (Bitbucket: mphoward, GitHub: mphoward).

OK great, thanks! I'll attend to this next week.

joaander commented 8 years ago

Update python unit tests to proposed API

refs #105

joaander commented 8 years ago

Remove global neighbor list and wrappers

refs #105

joaander commented 8 years ago

Update python unit tests to proposed API

refs #105

joaander commented 8 years ago

Remove global neighbor list and wrappers

refs #105

joaander commented 8 years ago

Merged in mphoward/hoomd-blue/remove_global_nlist (pull request #173)

fixes #105

Remove global neighbor list