Analysis functions for diatomic molecules. #329
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Alexsp32
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Alexsp32
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Jan 15, 2024
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Need to re-work several bits of this PR since they're very memory-inefficient and some edge cases aren't covered. |
I've merged in various changes to decrease the memory footprint of |
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Nicely done! |
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| module Structure | |||
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can you please create a markdown file for structure.md in docs/API to explain in a few sentences what this module is about
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I've slightly improved docs here.
reinimaurer1
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Apr 12, 2024
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@wgst there are a few new functions that could be useful for you |
Alexsp32
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Apr 15, 2024
- 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
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Feb 21, 2025
…332) * Add Simulation-aware VelocityBoltzmann with support for frozen atoms. * Forgot to add new file * Basic docs * Forgot second arg in mobileatoms call * Add OutputInitial DynamicsOutput (#337) * Add OutputInitial DynamicsOutput * Fix allocation-based unit tests (#336) * 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 * Analysis functions for diatomic molecules. (#329) - 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 * Add unit tests and fix a mistake * Wrong path for test asset * Add DynamicalDistribution constructor from Simulation, add test for correct atom freezing. --------- Co-authored-by: Reinhard Maurer <r.maurer@warwick.ac.uk>
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Changes:
DynamicsOutputsfor Desorption Angles and DynamicsVariables during desorption (New DynamicsOutputs: OutputDesorptionTrajectory, OutputDesorptionAngle #317)Structuresubmodule.Analysissubmodule to contain functions needed for more complex analysis of MD trajectories.