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Neighbors Workflow

CLI workflow for center atoms and their four nearest neighbors.

Command: get-wurtzite-neighbors

Find the four nearest selected neighbors around every selected center atom.

Use this command to inspect the geometric input to the wurtzite-polarity calculation without calculating polarity. Neighbor assignment uses distances rather than fort.7 bond connectivity. It writes centers.csv and neighbors.csv with atom IDs, species, coordinates, minimum-image bond vectors, distances, proton proximity, and dynamic or formal charges.

Examples

  1. AlN with automatically detected ReaxFF charges:
     reaxkit get-wurtzite-neighbors --center Al --neighbor N

  2. Require the lightweight ReaxFF fort.7 charge stream:
     reaxkit get-wurtzite-neighbors --engine reaxff --charge-source reaxff

  3. ZnO with formal charges and an explicit output directory:
     reaxkit get-wurtzite-neighbors --center Zn --neighbor O --charge-source formal --formal-charge Zn=2 O=-2

Arguments

Scientific choices

Flag Required Default Help Choices
--center, --cation No Al Choose center species. Example: --center Zn Mg, analyzes both Zn- and Mg-centered sites.
--neighbor, --anion No N Choose neighbor species. Example: --neighbor O, assigns the four nearest oxygen atoms.
--proton No H Choose proton-like species for proximity grouping. Example: --proton H, tests nearby hydrogen atoms.
--charge-source No auto Choose dynamic or formal charges. Formal mode has no implicit species fallback and requires --formal-charge for every center and neighbor. Example: --charge-source formal --formal-charge Al=3 N=-3 H=1. auto, reaxff, formal
--formal-charge No Assign species-specific formal charges. Example: --formal-charge Al=3 N=-3 H=1, uses +3, -3, and +1 elementary charges.
--neighbor-cutoff No 3.0 Set the maximum center-neighbor distance in angstrom. Example: --neighbor-cutoff 2.5, excludes candidates farther than 2.5 angstrom.
--proton-cutoff No 2.0 Set the proton-proximity radius in angstrom. Example: --proton-cutoff 1.8, marks centers within 1.8 angstrom of H.
--c-axis No 0.0, 0.0, 1.0 Set the Cartesian polar-axis direction. Example: --c-axis 0 0 1, projects bonds along z.
--periodic No xyz Choose periodic lattice directions. Example: --periodic xy, wraps neighbors across a and b only. none, x, y, z, xy, xz, yz, xyz
--cell-lengths No Override cell lengths in angstrom. Example: --cell-lengths 10 10 16, uses that cell for every frame.
--cell-angles No 90.0, 90.0, 90.0 Set angles for --cell-lengths in degrees. Example: --cell-angles 90 90 120, defines a hexagonal cell.
--frames No Select zero-based source frames. Example: --frames 0:101:10, includes frames 0 through 100 every 10 frames.
--every No 1 Stride the selected frames. Example: --every 5, keeps every fifth selected frame.

Input and file selection

Flag Required Default Help Choices
--engine No Select the input adapter. Example: --engine reaxff, bypasses engine auto-detection. reaxff, ams, lammps
--input No . Set the path used for engine detection. Example: --input ./run, inspects ./run.
--run-dir No . Set the fallback simulation directory. Example: --run-dir ./run, resolves default files there.
--fort7 No fort.7 Select the ReaxFF charge file. Example: --fort7 ./run/fort.7, streams charges from that file.
--fort78 No fort.78 Select the applied-field file. Example: --fort78 ./run/fort.78, reads field samples from that file.
--xmolout No xmolout Select the coordinate and atom-name trajectory. Example: --xmolout ./run/xmolout, reads that trajectory.
--summary No Select optional simulation metadata. Example: --summary ./run/summary.txt, reads metadata from that file.

Outputs and plots

Flag Required Default Help Choices
--output-dir No Choose the CSV output directory. Example: --output-dir ./neighbors, writes centers.csv and neighbors.csv there.
--detail-format No Optional detail format (default: Parquet; legacy: CSV). parquet, csv

Execution

Flag Required Default Help Choices
--execution No auto Execution backend; unsupported backends fall back to serial with a logged reason. auto, serial, threads, processes
--workers No 0 Frame workers: auto or N (default: auto).
--chunk-size No 0 Maximum in-flight frames: auto or N.

Storage and cache

Flag Required Default Help Choices
--run-id No Run identifier for run-scoped layout. Example: --run-id run_91ac0e, which reuses that run identifier.
--project-root No reaxkit_workspace Project root that contains inputs/, data/, analysis/, etc. Example: --project-root ./workspace, which stores run artifacts there.
--analysis-id No Optional analysis artifact id; defaults to run id. Example: --analysis-id comparison-a, which names the analysis artifact explicitly.
--input-cache, --no-input-cache No True Reuse parsed input frames across commands (default: enabled; use --no-input-cache to force source reads for reproducibility checks or benchmarks). Example: --no-input-cache, which reloads frames from their source files.
--frame-cache-max-gb No 10.0 Maximum workspace frame-cache size in GiB (default: 10; use 0 for unlimited). Example: --frame-cache-max-gb 20, which caps cached frames at 20 GiB.
--output-profile No standard Select the shared artifact policy. Standard writes declared default outputs; minimal keeps core tables; full and legacy include optional details. Default: standard. Example: --output-profile full, which includes declared optional detail tables. minimal, standard, full, legacy

Diagnostics and compatibility

Flag Required Default Help Choices
-h, --help No show this help message and exit
--help-all, --all-flags No Show every option, grouped by purpose.
--log No quiet Choose console logging detail. Example: --log verbose, prints diagnostic progress information. verbose, quiet

Common Runtime and Presentation Arguments

These are shared workflow-level CLI flags added before command-specific options, covering runtime context (engine/input/storage) and output presentation/export behavior.

Each command table above includes its shared and inherited options.