Code

Glue#1

Code

Merged

eschmidt42 merged 22 commits intomastereschmidt42/Molly.jl:masterfrom glueeschmidt42/Molly.jl:glueCopy head branch name to clipboardMar 20, 2021

+1,052-7

Commits

Commits on Feb 2, 2021

• added packages

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  19f43d6

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• added the finnis-sinclair variant of glue type potentials

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Commits on Feb 3, 2021

• added documentation

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  5b805ff

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• expanded potential energy and force tests to all vacancy free bcc crystals

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Commits on Feb 7, 2021

• added potential energy and force checks for bcc crystal with a single vacancy

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Commits on Feb 14, 2021

• added tests for the finnis-sinclair type of glue potentials

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• added section to run a longer simulation for the documentation

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Commits on Mar 10, 2021

• added fields for forces, velocities and glue densities in Simulation

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• refactored glue forces to work as general_inters

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• modified potential_energy to pre-compute glue densities, if necessary

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  a9d7ef1

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• modified accelerations to allow for glue density update and calculation of glue forces using the general_inters loop

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• added GlueDensityLogger, VelocityLogger and ForcesLogger

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  95b9635

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• fixed copy-paste error

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Commits on Mar 12, 2021

• added ForwardDiff

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• refactored reducing redundancy and replacing manually implemented derivates with FordwardDiff.derivate to re-use the non-derivative forms also used to successfully test ground state energies

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Commits on Mar 15, 2021

• updated algebraic signs

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Commits on Mar 16, 2021

• added convenience function to easily generate variables for the Finnis-Sinclair 1984 empirical model

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• refactored the ground state energy, forces and vacancy formation energy tests

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• refactored fs.ipynb: removed superfluous tests and reduced the math to the core components

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Commits on Mar 17, 2021

• removed superfluous enumerate

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• added docstrings

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• cleaned

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