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Glue #1

Merged
merged 22 commits into from
Mar 20, 2021
Merged

Glue #1

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19f43d6
added packages
eschmidt42 Feb 2, 2021
a3f4b6a
added the finnis-sinclair variant of glue type potentials
eschmidt42 Feb 2, 2021
5b805ff
added documentation
eschmidt42 Feb 3, 2021
8942490
expanded potential energy and force tests to all vacancy free bcc cry…
eschmidt42 Feb 3, 2021
87e7d82
added potential energy and force checks for bcc crystal with a single…
eschmidt42 Feb 7, 2021
52f46b8
added tests for the finnis-sinclair type of glue potentials
eschmidt42 Feb 14, 2021
dd0881c
added section to run a longer simulation for the documentation
eschmidt42 Feb 14, 2021
221b690
added fields for forces, velocities and glue densities in Simulation
eschmidt42 Mar 10, 2021
eaacf33
refactored glue forces to work as general_inters
eschmidt42 Mar 10, 2021
a9d7ef1
modified potential_energy to pre-compute glue densities, if necessary
eschmidt42 Mar 10, 2021
fd93544
modified accelerations to allow for glue density update and calculati…
eschmidt42 Mar 10, 2021
95b9635
added GlueDensityLogger, VelocityLogger and ForcesLogger
eschmidt42 Mar 10, 2021
36457e0
fixed copy-paste error
eschmidt42 Mar 10, 2021
1808489
added ForwardDiff
eschmidt42 Mar 12, 2021
057b9a6
refactored reducing redundancy and replacing manually implemented der…
eschmidt42 Mar 12, 2021
acf7ce8
updated algebraic signs
eschmidt42 Mar 15, 2021
b99aca3
added convenience function to easily generate variables for the Finni…
eschmidt42 Mar 16, 2021
fd7cb6f
refactored the ground state energy, forces and vacancy formation ener…
eschmidt42 Mar 16, 2021
f80004e
refactored fs.ipynb: removed superfluous tests and reduced the math t…
eschmidt42 Mar 16, 2021
275c296
removed superfluous enumerate
eschmidt42 Mar 17, 2021
b136903
added docstrings
eschmidt42 Mar 17, 2021
931f214
cleaned
eschmidt42 Mar 17, 2021
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5 changes: 5 additions & 0 deletions Project.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -7,9 +7,14 @@ version = "0.2.1"
BioStructures = "de9282ab-8554-53be-b2d6-f6c222edabfc"
CUDA = "052768ef-5323-5732-b1bb-66c8b64840ba"
Colors = "5ae59095-9a9b-59fe-a467-6f913c188581"
Crystal = "3c6eccdf-2a89-4c24-a1d4-ff210daa8476"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
Distributions = "31c24e10-a181-5473-b8eb-7969acd0382f"
ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
KernelDensity = "5ab0869b-81aa-558d-bb23-cbf5423bbe9b"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Makie = "ee78f7c6-11fb-53f2-987a-cfe4a2b5a57a"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
ProgressMeter = "92933f4c-e287-5a05-a399-4b506db050ca"
Reexport = "189a3867-3050-52da-a836-e630ba90ab69"
Requires = "ae029012-a4dd-5104-9daa-d747884805df"
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