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Adding a Glue Type / N-Body Empirical Potential - the Finnis-Sinclair 1984 potential for single element systems #32
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19f43d6
added packages
eschmidt42 a3f4b6a
added the finnis-sinclair variant of glue type potentials
eschmidt42 5b805ff
added documentation
eschmidt42 8942490
expanded potential energy and force tests to all vacancy free bcc cry…
eschmidt42 87e7d82
added potential energy and force checks for bcc crystal with a single…
eschmidt42 52f46b8
added tests for the finnis-sinclair type of glue potentials
eschmidt42 dd0881c
added section to run a longer simulation for the documentation
eschmidt42 221b690
added fields for forces, velocities and glue densities in Simulation
eschmidt42 eaacf33
refactored glue forces to work as general_inters
eschmidt42 a9d7ef1
modified potential_energy to pre-compute glue densities, if necessary
eschmidt42 fd93544
modified accelerations to allow for glue density update and calculati…
eschmidt42 95b9635
added GlueDensityLogger, VelocityLogger and ForcesLogger
eschmidt42 36457e0
fixed copy-paste error
eschmidt42 1808489
added ForwardDiff
eschmidt42 057b9a6
refactored reducing redundancy and replacing manually implemented der…
eschmidt42 acf7ce8
updated algebraic signs
eschmidt42 b99aca3
added convenience function to easily generate variables for the Finni…
eschmidt42 fd7cb6f
refactored the ground state energy, forces and vacancy formation ener…
eschmidt42 f80004e
refactored fs.ipynb: removed superfluous tests and reduced the math t…
eschmidt42 275c296
removed superfluous enumerate
eschmidt42 b136903
added docstrings
eschmidt42 931f214
cleaned
eschmidt42 4e2c73b
removed cell
eschmidt42 f88c5b2
removing comments
eschmidt42 3982887
Merge branch 'hotfix-removing-comments'
eschmidt42 b472fd9
Merge pull request #1 from eschmidt42/glue
eschmidt42 ee4d487
resolved merge conflict
eschmidt42 5a81002
replaced ForwardDiff.derivate with analytical derivatives and added k…
eschmidt42 c0d37fa
removed f comment in docstrings
eschmidt42 a71dc51
replaced dataframes with dicts
eschmidt42 4b55ae4
replaced another derivative forgotten earlier
eschmidt42 b332f60
updated tests
eschmidt42 825f1ad
minor change to improve readability of ForceLogger
eschmidt42 d646f9b
removed DataFrames reference
eschmidt42 945ddb0
removed DataFrames and Plots reference
eschmidt42 115adf2
relocated packages from Molly.jl to docs
eschmidt42 30a54b2
made notebook compatible with changes in in src/interactions/glue_fs.jl
eschmidt42 331cc70
removed because relocated to ./docs
eschmidt42 d87b4c6
removed superfluous cells
eschmidt42 bbc47f1
adjusted glue tests to changes in Crystal.jl and introduced more name…
eschmidt42 d073ef8
updated test: switched from Crystal to SingleCrystal package
eschmidt42 fbf2629
switched toml from Crystal to SingleCrystal
eschmidt42 d95cfbe
switched to toml SingleCrystal.jl
eschmidt42 b276156
updated notebook to work with the new data structure of the potential…
eschmidt42 71522fe
removed ForwardDiff
eschmidt42 b9ece8d
removed empty spaces and updated doc strings
eschmidt42 d1f113a
rm SingleCrystal package as direct dependency
eschmidt42 05d1990
replaced abstract types in structs
eschmidt42 12c5a31
wrapped glue tests in a testset
eschmidt42 996ed6e
kind of resolved conflict
eschmidt42 3b9ce51
welp...
eschmidt42 076ad3d
adjusted to renaming of Simnulation struct
eschmidt42 d2b3375
updated test to new Simulation
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,6 +1,10 @@ | ||
| [deps] | ||
| DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0" | ||
| Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4" | ||
| Molly = "aa0f7f06-fcc0-5ec4-a7f3-a573f33f9c4c" | ||
| Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80" | ||
| SingleCrystal = "3c6eccdf-2a89-4c24-a1d4-ff210daa8476" | ||
| Test = "8dfed614-e22c-5e08-85e1-65c5234f0b40" | ||
|
|
||
| [compat] | ||
| Documenter = "0.25" | ||
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The plots in the documentation could be generated during the docs build, but it would be ideal to use the same package for all the plots (preferably one of the Makie backends). @jgreener64 One idea would be to use
CairoMakie, but it might also be possible to useWGLMakie(it would be a bit more complex, but we get interactive plots). For this to work, thevisualizefunction should be available withAbstractPlotting. A more elegant solution would be to use recipes, butAbstractPlottingis not a light dependency right now.There was a problem hiding this comment.
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It would indeed be better to use the same plotting package throughout, though at the minute the code in the docs is not run during the docs build and Makie plots are pasted as images into the doc files.
It would be good if the docs notebook appeared in the docs - perhaps it could go in the examples section as markdown. Then these docs dependencies can be removed until we deal with doctests later, as the examples can assume that users have the package installed.
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Tried using
Makiebefore but had some problem I can't remember.Plotsis mostly required for thedocs/fs.ipynbnotebook. Can try to replacePlotsthere though if required.