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Phonon thermostat#349

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Alexsp32 wants to merge 82 commits intomainNQCD/NQCDynamics.jl:mainfrom phonon-thermostatNQCD/NQCDynamics.jl:phonon-thermostatCopy head branch name to clipboard

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Commits

Commits on Jan 19, 2024

• Modified O steps to accept temperature per total system or per atom

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• Modified O steps to accept temperature as vector for whole system

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• Added Thermostat and Simulation logic to handle temperature assignment.

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Commits on Jan 22, 2024

• CompositeModels now get a calculator

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• And now it should load

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Commits on Jan 23, 2024

• Integrator steps aren't happy.

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• Integrator troubleshooting

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• Maybe can't combine @.. and @. in any form?

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• Integrators should now be happy

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• Add DynamicsOutputs for temperature and first image

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• Thermostats should now show what they are nicely

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Commits on Jan 26, 2024

• Fixed broken Temperature output

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• Fixed temperature input again

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• Forgot another thing

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Commits on Jan 31, 2024

• Changed new DynamicsOutputs

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• Testing for conditions OutputQuantiseDiatomic.

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Commits on Feb 1, 2024

• Debug info for saving outputs

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Commits on Feb 7, 2024

• Remove debug stuff

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• First attempt at simulation-aware VelocityBoltzmann

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• Made a mistake using mobileatoms.

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Commits on Feb 12, 2024

• OutputTemperature now works.

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Commits on Apr 18, 2024

• Add batch evaluation support for MACEModel

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• Version bump to ensure correct NQCModels branch installed

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• Support batched Ring polymer evaluation with MACEModel

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Commits on Apr 24, 2024

• Allow testing with MACEModel NQCModels build

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Commits on Apr 26, 2024

• Include docs for MACEModels

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• Logic update to get_desorption_frame to fix #342

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Commits on May 3, 2024

• Fixed calculator methods for MACEModels

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Commits on May 21, 2024

• Update to newest main

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• Merge postprocessing

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• Properly incorporate rigid rotator energies

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• Add OutputFinalKineticEnergy for whole system

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• Add OutputSubsetFinalKineticEnergy for part of system

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• Add subset kinetic temperature output type.

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• DynamicsOutputs formatting improvements

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Commits on May 22, 2024

• Remove ref to missing file

  

  Alexander Spears (Mobile)

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• Function definition mistakes

  

  Alexander Spears (Mobile)

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• Remove reexport of QuantiseDiatomic

  

  Alexander Spears (Mobile)

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• More function definition syntax mistakes

  

  Alexander Spears (Mobile)

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• struct definition mistake

  

  Alexander Spears (Mobile)

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• FakeSolution needs prob field

  

  Alexander Spears (Mobile)

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• Forgot to export new output functions

  

  Alexander Spears (Mobile)

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• Add final time point output

  

  Alexander Spears (Mobile)

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• Add desorption snapshot output

  

  Alexander Spears (Mobile)

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Commits on May 23, 2024

• Add full DiffEq solution output

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• Typo in function def

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  d1d5482

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• Fix a few output function errors

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• Fix more output function errors

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• Forgot to include surface normal in distance criterion

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• Hopefully fix broadcasting

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• But maybe it works now

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• cba fixing broadcast, list comp instead

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• Forgot to remove .

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Commits on May 28, 2024

• Temperatures should get velocity, not positions

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Commits on Jun 25, 2024

• Add OutputSolution as alias of OutputEverything

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Commits on Jul 11, 2024

• Fixed mistake in desorption check logic that caused crash

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Commits on Jul 22, 2024

• Prototype for energy distribution analysis

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• Updated translation energy calculation

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Commits on Jul 23, 2024

• Desorption criterion updated with debug and fallback distance option

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Commits on Jul 24, 2024

• Rotation energy off by factor of angular momentum

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• Fixed small bug in 53ad3db

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Commits on Aug 1, 2024

• MACEModel to separate package. Added extension for calculator batching.

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• Version bump, Julia≥1.9 due to extensions, add MACEModels.jl weakdep

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• Update docs with MACEModels

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Commits on Aug 2, 2024

• PyCall -> PythonCall in tests

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Commits on Aug 20, 2024

• Merge current main state

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Commits on Aug 21, 2024

• Remove duplicate DynamicsOutput

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Commits on Aug 22, 2024

• Add behaviour for OutputDesorptionTrajectory for very early onset

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Commits on Aug 28, 2024

• Rotation energy calculated from J, quantisation failures return missing

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Commits on Oct 14, 2024

• Add noise output function

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• Forgot function export

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• More weird desorption logic

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Commits on Oct 16, 2024

• How did it work before?

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Commits on Dec 2, 2024

• Update docs

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• CHANGE BACK WITH PR - preview docs render

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• Wikilinks for a few more types

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Commits on Dec 3, 2024

• Small docs updates

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• Add RingPolymerSimulation with CompositeModel

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• Fix typo

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• chance back docs render

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• Merge branch 'mace-ring-polymer' into phonon-thermostat

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• Revert mistakes in project

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