Add XYZFileReduction for writing trajectory positions to (ext)XYZ files by Copilot · Pull Request #473 · NQCD/NQCDynamics.jl

Copilot · 2026-03-20T07:10:01Z

Adds XYZFileReduction, enabling run_dynamics to write trajectory positions directly to XYZ files for visualization — analogous to FileReduction for HDF5.

Changes

src/Ensembles/reductions.jl: New XYZFileReduction struct:
- Takes a filename and simulation object (for atom types and cell info)
- Writes one file per trajectory: output_1.xyz, output_2.xyz, etc.
- Dispatches on cell type: PeriodicCell → extXYZ via NQCBase.write_extxyz (includes lattice/PBC); all other cells (e.g., InfiniteCell) → plain XYZ with positions in Ångströms
- Non-.xyz/.extxyz extensions are coerced to .xyz
src/Ensembles/run_dynamics.jl: Adds precompile-step cleanup for XYZFileReduction files (mirrors existing FileReduction handling)
src/Ensembles/Ensembles.jl: Exports XYZFileReduction
test/Ensembles/reductions.jl: Tests for single/multi-trajectory output, file format validation, and extension normalization

Usage

sim = Simulation(Atoms([:H, :C]), model; cell=PeriodicCell(...))
run_dynamics(sim, (0.0, 100.0), distribution;
    output = OutputPosition,
    reduction = XYZFileReduction("traj.xyz", sim),
    trajectories = 10,
)
# Writes traj_1.xyz ... traj_10.xyz in extXYZ format

Requires OutputPosition to be included in the output tuple.

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This section details on the original issue you should resolve

<issue_title>Add output for (ext)XYZ files</issue_title>
<issue_description>Could be implemented like the FileReduction to take positions (and velocities) and output them to XYZ files for easier visualisation. </issue_description>

Comments on the Issue (you are @copilot in this section)
@reinimaurer1 Doesn't write_extxyz in NQCBase already do that? https://github.com/NQCD/NQCBase.jl/blob/933e805a43f8ed27d44dfac5d8459f0c956de351/src/io/extxyz.jl#L5
would it make sense for us to interface to ExtXYZ.jl?
https://github.com/libAtoms/ExtXYZ.jl</comment_new>
<comment_new>@Alexsp32
Yes, but we could add support to do this straight from run_dynamics, like the FileReduction which outputs data in HDF5 format. </comment_new>

Fixes Add output for (ext)XYZ files #334

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Co-authored-by: Alexsp32 <39826690+Alexsp32@users.noreply.github.com>

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Copilot AI assigned Copilot and Alexsp32 Mar 20, 2026

Copilot started work on behalf of Alexsp32 March 20, 2026 07:10 View session

Add XYZFileReduction for trajectory output to (ext)XYZ files

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Co-authored-by: Alexsp32 <39826690+Alexsp32@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Add output for (ext)XYZ files~~ Add XYZFileReduction for writing trajectory positions to (ext)XYZ files Mar 20, 2026

Copilot AI requested a review from Alexsp32 March 20, 2026 07:29

Copilot finished work on behalf of Alexsp32 March 20, 2026 07:29

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Add XYZFileReduction for writing trajectory positions to (ext)XYZ files#473

Add XYZFileReduction for writing trajectory positions to (ext)XYZ files#473
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Copilot AI commented Mar 20, 2026 •

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Copilot AI commented Mar 20, 2026 •

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