Charge Field Workflow
CLI workflow for selected-atom charges versus applied electric field.
Command: get_charge_vs_electric_field
Export and plot selected-atom dynamic charges alongside an iteration-matched applied electric field.
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--atom-numbers, --atom-ids |
Yes |
|
|
|
--frames |
No |
|
Frames, e.g. 0:101:10. |
|
--every |
No |
1 |
Keep every Nth frame. |
|
--field-direction |
No |
z |
Applied-field component to correlate (default: z). |
x, y, z |
| Flag |
Required |
Default |
Help |
Choices |
--engine |
No |
|
|
reaxff, ams, lammps |
--input |
No |
. |
Input path used for engine detection. |
|
--run-dir |
No |
. |
Fallback simulation directory. |
|
--fort7 |
No |
fort.7 |
Dynamic-charge source. |
|
--fort78 |
No |
fort.78 |
Applied electric-field source. |
|
--xmolout |
No |
xmolout |
Per-frame atom identity source. |
|
--control |
No |
control |
Control file used to derive time. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--x-axis, --xaxis |
No |
frame |
Horizontal plot axis. |
frame, iter, time |
--dpi |
No |
180 |
Plot resolution in dots per inch. |
|
--output-dir |
No |
|
CSV and plots output directory. |
|
--export |
No |
|
Optional CSV output path. |
|
--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 |
|
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.