Cleanup functions related to rotational velocity, improve sample input files#162
Cleanup functions related to rotational velocity, improve sample input files#162danielhollas merged 4 commits intomasterfrom
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@JanosJiri can you take a look? Thanks! Also, if there is anybody else that would perhaps be interesting in reviewing the code, let me know! (especially for simple refactoring like this, it might be nice for somebody to get familiar with the codebase). |
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## master #162 +/- ##
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+ Coverage 92.41% 92.42% +0.01%
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Files 43 43
Lines 6053 6063 +10
Branches 735 734 -1
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Misses 447 447
Partials 12 12
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JanosJiri
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I left just small suggestions/comments. No need to incorporate them.
| &nhcopt | ||
| temp=298.15, ! temperature [K] for Maxwell-Boltzmann sampling and thermostat | ||
| inose=1, ! Thermostating: Nose-Hoover 1, microcanonical 0,GLE 2 | ||
| nchain=4, ! number of nose-hoover chains |
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Just a comment: there are lots of deleted options. It might t be useful to have some brief manual for them. :)
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Yeah, I've deleted a bunch of options that the user should not generally touch, since these sample inputs are generally meant for first time users.
Note that ABIN's manual is currently available on Overleaf, but I haven't updated it in a long while. Some of these options are documented there though. Perhaps that is something we could work together when you are in Bristol. :-)
Currently, there is no one working on ABIN modifications but I will ask. |
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Cleaning up the
remove_rotationsfunctions, that we call at the beginning of the simulations to remove rotational velocity.Confusingly, we've also used the same function to print angular momentum along the MD simulations.
In this PR I decoupled the code to smaller functions to make this all less confusing.
Also tried to cleanup the sample input files to make them (hopefully) a little more accessible for first time users.
But MUCH more needs to be done in this area.