Create Boltzmann velocity distributions from Simulations directly
#332
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
* Add OutputInitial DynamicsOutput
* Stopgap fix for failing unit tests based on memory allocation * Add allocation test debug messages * Fixed version logic to be defined for all Julia versions
- Added new DynamicsOutput: OutputDesorptionTrajectory #317 - Added new DynamicsOutput: OutputDesorptionAngle #317 - Created an `Analysis` submodule for common analysis functions - Add `Structure` submodule for common utility functions for atomic structure. * Add rudimentary tests for NQCDynamics.Structure * Improved method definitions, possible efficiency gain by using views * Add unit tests for diatomic analysis functions for desorption * Add "Analysis" group to unit testing * Added explanation for Structure module scope
|
Don't merge until dependent PRs are merged. |
reinimaurer1
approved these changes
Jul 22, 2024
…orrect atom freezing.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Fixes NQCD/NQCDistributions.jl#9 and requires NQCD/NQCDistributions.jl#12 and NQCD/NQCModels.jl#35 to be merged prior.
Since the
VelocityBoltzmannis dependent on the atomic masses, it makes sense to be able to pull both these and the overall dimensions from an existingSimulation. For consistency, a temperature must still be provided separately, but this is quick to do withSimulation.temperature(0).Also, initialising
VelocityBoltzmannfrom a simulation should check for any atoms not included inmobileatoms, as these should be initialised with zero velocity.