Get Beta Workflow
Dedicated workflow for cell angle beta.
Command: get_beta
Get cell angle beta as a time series.
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--frames |
No |
|
Frame selector, for example --frames 0:20:2 or --frames 0,5,10. |
|
--every |
No |
1 |
Keep every Nth selected frame. |
|
--frame-source |
No |
|
Trajectory file whose headers define frame iterations when no control file exists. By default, the configured or sibling xmolout is used. |
|
--frame-count |
No |
|
Total trajectory frame count used to infer frame spacing only when neither a control file nor a trajectory frame source exists. |
|
| Flag |
Required |
Default |
Help |
Choices |
--engine |
No |
|
|
reaxff, ams, lammps |
--input |
No |
. |
Input file or directory used for engine detection. |
|
--run-dir |
No |
. |
Run directory used as a fallback for input discovery. |
|
--xmolout |
No |
xmolout |
Trajectory input path. |
|
--summary |
No |
|
Optional summary.txt input path. |
|
--control |
No |
control |
Control file used for frame (iout2) and time conversion. The default also searches beside the selected input files. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--plot |
No |
|
Plot all series together (single), in one multi-panel figure (subplot), or as one figure file per series (separate). |
single, subplot, separate |
--show |
No |
False |
|
|
--save |
No |
|
|
|
--export |
No |
|
|
|
--grid |
No |
|
Subplot grid such as 2x2. |
|
--xaxis |
No |
iter |
|
iter, frame, time |
--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 |
|
|
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.