Kopple2 Workflow
Direct command workflow for generating kopple2 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: gen_template_kopple2
Write a template kopple2 file for ReaxFF workflows.
This command generates a starter kopple2 file only. It does not run simulation steps
or modify existing run outputs. Use the generated template as a base and adjust values
for your target system.
Examples
1. Generate a template using default output name ('kopple2'):
reaxkit gen_template_kopple2
2. Generate a template with a custom filename:
reaxkit gen_template_kopple2 --output kopple2.template
3. Generate a template and also copy it to the current directory:
reaxkit gen_template_kopple2 --output kopple2.template --copy-to-dot
Arguments
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output |
No |
kopple2 |
Output filename to write under /input/. Example: --output kopple2.template, which writes the template using that filename. |
|
--copy-to-dot |
No |
False |
Also copy generated output to the 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. |
|
Command: make-kopple2
Write a template kopple2 file for ReaxFF workflows.
This command generates a starter kopple2 file only. It does not run simulation steps
or modify existing run outputs. Use the generated template as a base and adjust values
for your target system.
Examples
1. Generate a template using default output name ('kopple2'):
reaxkit gen_template_kopple2
2. Generate a template with a custom filename:
reaxkit gen_template_kopple2 --output kopple2.template
3. Generate a template and also copy it to the current directory:
reaxkit gen_template_kopple2 --output kopple2.template --copy-to-dot
Arguments
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output |
No |
kopple2 |
Output filename to write under /input/. Example: --output kopple2.template, which writes the template using that filename. |
|
--copy-to-dot |
No |
False |
Also copy generated output to the 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.