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improved automation #6

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improved automation #6

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@orbeckst orbeckst commented Sep 2, 2018

@lvanderf 's improvements (fix #4)

  • OPM integration
  • automation
  • various fixes

Probably requires extensive review and careful rebasing because some changes were manually incorporated into develop already. The PR is made available so that the code is visible.

Lennard van der Feltz added 30 commits August 23, 2013 13:03
… ImportError if MDAnalysis is not present. Also added comments.
…o changed pdb2dat to make use of default from argparse.
…th membrane references removed. As a result alterations were made to membrane.py and io.py and a new template was introduced. setup.py altered to include new script. Still need to check output, update documentation, and possibly refactor code.
… of a membrane-free class. Updated email in init.py
…es.py. Corrected logger name for electrostatics.py(formerly membrane.py)
…ses where no options are submitted to 1dgraph.py
Lennard van der Feltz added 30 commits April 3, 2014 12:55
…specifications. Also leaned up some io references(corrected to bpio)
…populate_default to work with both placeion and cfg_template scripts.
…Parameters call to include additional options for compatibility with new populate defaults function.
…tting.py with the option to use seaborn to improve plot quality.
…t fixes include membraneless bp runs and the addition of support for runs larger than 10k points.
…at files using z interpolation of energies
…e to datalgebra and added object algebra to datarray objects.
…ssages for when attempting unreasonable manipulations.
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merge Lennard's code
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