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Opls cleanup #143

Merged
merged 20 commits into from
Jul 12, 2023
Merged

Opls cleanup #143

merged 20 commits into from
Jul 12, 2023

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aklemenz
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In preparation for the upcoming paper on matscipy, I implemented tests and examples for the opls module.

aklemenz and others added 20 commits January 5, 2023 11:51
@aklemenz
BUG: Incorrect handling of undefined cutoffs.
aac0974
@aklemenz
MAINT: pep8 improvements
ca9ef19
@aklemenz
DOC: Added documentation for OPLS module.
3f66ce9
@aklemenz
TST: Added tests for OPLS module.
7d38cd3
@aklemenz
TST: Added tests for io.opls.py
ebeed98
@aklemenz
Documentation and cleanup in io.opls.py
d6d00f2
@aklemenz
MAINT: python3 compatibility and input data type of "assertArrayAlmos…
5b82817 
…tEqual"
@aklemenz
Simplified tests
60f3095
@aklemenz
Added examples for opls module
841ea39
@aklemenz
removed useless file
31e2239
@aklemenz
Included tests of opls module
dc9327b
@aklemenz
ENH:
a92a833 
- Enable modification of LJ and Coulomb cutoffs from scripts
- Enable LJ pairs A-B with manually set parameters without geometric mixing of parameters for A and B
@aklemenz
BUG: Added missing unit conversion
736db6e
@aklemenz
ENH: Added a function to restore all interactions from a LAMMPS run.
60ac466
@aklemenz
MAINT: Refactoring of the read routine for LAMMPS input/output files.
94e23d9
@aklemenz
BUG: Incorrect handling of unused LJ pairs.
c266707
@aklemenz
MAINT: Adapting tests to refactored IO routines.
a51af5f
@aklemenz
MAINT: Test failed due to forgotten write instruction.
61c222a
@aklemenz
BUG: Incorrect handling of LJ pairs in some special situations.
51c91a4
@jameskermode
Merge branch 'master' into opls-cleanup
fc44790
@jameskermode
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Failing test in test_neighbours.py is also failing in master so we should fix it there, and then can go ahead and merge this.

@jameskermode
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@pastewka did you figure out the neighbour list problem? If that is fixed in master then I guess this is fine to merge too?

@pastewka
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Yes it's fixed in master. Will merge this.

@pastewka pastewka merged commit f0ee07b into master Jul 12, 2023
18 of 19 checks passed
@pastewka pastewka deleted the opls-cleanup branch July 12, 2023 15:47
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@jameskermode jameskermode jameskermode approved these changes

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3 participants
@aklemenz @jameskermode @pastewka