Xmolout Workflow
Direct command workflow for xmolout file utilities.
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: trim-xmolout
Trim an xmolout file to a lighter format containing only atom type and x/y/z coordinates.
This command is useful when full xmolout output is too large for quick inspection or downstream
tools that support reading atomic positions (not other variables like velocities, molecule numbers, etc.which may be written to the xmolout file using ixmolo keyword in the control file). It writes a reduced output file and does not modify
the input file in place.
Examples
1. Trim a specific xmolout file to a named output:
reaxkit trim-xmolout --file xmolout --output xmolout_trimmed
2. Trim using a custom output filename:
reaxkit trim-xmolout --output xmolout_light
Arguments
Input and file selection
| Flag | Required | Default | Help | Choices |
|---|---|---|---|---|
--file |
No | xmolout | Input xmolout file. Example: --file runs/job1/xmolout, which reads that trajectory/output file as input. |
Outputs and plots
| Flag | Required | Default | Help | Choices |
|---|---|---|---|---|
--output |
No | xmolout_trimmed | Output trimmed xmolout file. Example: --output xmolout_light, which writes the reduced-content file with that 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. |
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.