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gsd_rdf that can plot all_atoms #11

Merged
merged 68 commits into from
Nov 30, 2021
Merged

gsd_rdf that can plot all_atoms #11

merged 68 commits into from
Nov 30, 2021

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gwenwhite
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@gwenwhite gwenwhite commented Aug 29, 2021 •
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I created a function that will generate the RDF of all atoms (issue #10). Whenever A_name or B_name is set to None, that function is called upon within gsd_rdf.

The only issue is that it takes FOREVER to run with a full trajectory. Any ideas?

Made a new function that will plot rdf of all atom types. It is calle…
a68297d 
…d on in gsd_rdf when A_name or B_name is None.
@jennyfothergill jennyfothergill linked an issue Aug 30, 2021 that may be closed by this pull request
Be able to use all types in gsd_rdf #10
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jennyfothergill commented Aug 30, 2021 •
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Thanks, @gwenwhite !

The only issue is that it takes FOREVER to run with a full trajectory. Any ideas?

How big (box size, number of particles) is the system in your trajectory and what are you using for r_max? If you're not setting r_max, the default (just under half the box length) could be way too big.

Whenever A_name or B_name is set to None, that function is called upon within gsd_rdf.

I like that your addition is incorporated into gsd_rdf. By separating only the atom selection parts, I think we can reduce the amount of duplicate code in these two functions. (Having less duplicated code is nice when it's time to update a function because there's less to have to check, and the code is a little easier to read.)

EDIT: sorry I meant r_max not r_cut

@jennyfothergill jennyfothergill mentioned this pull request Sep 20, 2021
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thoughts from group meeting:
Only calculate neighborlist if using exclude bonded
RDF of molecule centers?

Gwen White and others added 22 commits September 30, 2021 19:33
temporary fix of making all atom rdf NOT exclude bonded
958269c
Merge branch 'master' of https://github.com/cmelab/cmeutils into gsd_…
887e25e 
…rdf/all-atom

Conflicts:
	cmeutils/structure.py
@jennyfothergill
code from bitbucket repo and new code to calculate quaternion
34cc2b6
@jennyfothergill
formattign
bc3df77
@jennyfothergill
add structure to init
00dfe2b
@jennyfothergill
calculate quaternion directly from vectors
585860d
@jennyfothergill
add rowan
748fdc9
@jennyfothergill
use rowan to compute quaternions
4986d57
@jennyfothergill
update docstring and add error handling
8ed689d
@jennyfothergill
add very basic test for get quaternions and switch to np.array_equal
db85637
@jennyfothergill @gwenwhite
Update environment.yml
3bd0c33 
Co-authored-by: gwenwhite <66272666+gwenwhite@users.noreply.github.com>
@chrisjonesBSU
create dynamics.py with msd from gsd functionality
a3fd3a9
@chrisjonesBSU
some syntax fixes
ca80a4c
@chrisjonesBSU
return complete msd object rather than array of data; set reset=False…
395d216 
… in compute
@chrisjonesBSU
pass images to freud msd; add functionality to include images when fi…
24415f9 
…nding atom pos
@chrisjonesBSU
add images list to msd func
bd9abc4
@chrisjonesBSU
pass in images to msd compute
e33908f
@chrisjonesBSU
syntax fix
f6b15e3
@chrisjonesBSU
change variable name to include underscore
cf5d5b8
@chrisjonesBSU
added a very simple unit test for msd_from_gsd
a0f919c
@chrisjonesBSU
add check for images of all zeros and throw warning
6c5c9a6
@chrisjonesBSU
option to write images to a gsd file, test to catch msd warning for n…
2ee81b6 
…o images
jennyfothergill
jennyfothergill reviewed Oct 25, 2021
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Getting close! Let me know if you need help with unit tests.

jennyfothergill
jennyfothergill reviewed Nov 30, 2021
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A couple minor formatting changes then LGTM!

@jennyfothergill jennyfothergill merged commit 5052ab4 into cmelab:master Nov 30, 2021
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@chrisjonesBSU chrisjonesBSU Awaiting requested review from chrisjonesBSU

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Be able to use all types in gsd_rdf
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@gwenwhite @jennyfothergill @chrisjonesBSU