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Fort7 Workflow

Direct command workflow for repairing corrupted fort.7 files.

This module implements CLI workflow orchestration for its command family, including argument parsing, request construction, execution dispatch, and result presentation handoff.

Usage context

  • Command routing: Resolve CLI aliases and normalized command names.
  • Task execution: Build request objects and invoke registered tasks.
  • Output handling: Forward results to table, plot, export, or report flows.

Command: repair_fort7

Repair corrupted fort.7 atom lines where fused integer columns break tokenization. This command rewrites a repaired output file while preserving lines that do not need changes. It is useful when malformed spacing/column fusion causes downstream parsing failures, which happen in +9999-atom-simulations using Standalone ReaxFF, in trajectory or analysis workflows.

Examples

  1. Repair a specific input file and write to a named output:
   reaxkit repair_fort7 --file fort.7 --output fort7_fixed

  2. Repair using custom output and also copy result to current directory:
   reaxkit repair_fort7 --output fort7_repaired --copy-to-dot

Arguments

Input and file selection

Flag Required Default Help Choices
--file No fort.7 Input fort.7 file. Example: --file runs/job1/fort.7, which reads that file as repair source.
--xmolout No xmolout Trajectory coordinates for resolving fused atom ids (default: ./xmolout; the file must exist).

Outputs and plots

Flag Required Default Help Choices
--output No fort7_fixed Output repaired fort.7 file. Example: --output fort7_repaired, which writes repaired content using that output name.
--copy-to-dot No False Also copy generated output to current directory. Example: --copy-to-dot, which keeps a convenience copy where you run the command.
--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.
--progress-every No 5000 Number of input lines between progress-bar updates (default: 5000).

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.