Fort83 Workflow
Direct command workflow for extracting optimized force fields from fort.83.
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: extract-optimized-ffield
Extract the optimized force-field block from a fort.83 file.
This command scans for the Error force field marker and writes everything after that
marker to a separate output file. Use it to recover the trained/optimized force field
from optimization output.
Examples
1. Extract from a specific `fort.83` file with explicit output name:
reaxkit get-optimized-ffield --fort83 fort.83 --output fort83_optimized_ffield
2. Extract using a custom output filename:
reaxkit get-optimized-ffield --output trained_ffield
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--fort83 |
No |
fort.83 |
Path to fort.83. Example: --fort83 runs/job1/fort.83, which reads that optimization output file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output |
No |
fort83_optimized_ffield |
Output path for the extracted force field. Example: --output trained_ffield, which writes extracted parameters to that filename. |
|
--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. |
|
Command: get-optimized-ffield
Extract the optimized force-field block from a fort.83 file.
This command scans for the Error force field marker and writes everything after that
marker to a separate output file. Use it to recover the trained/optimized force field
from optimization output.
Examples
1. Extract from a specific `fort.83` file with explicit output name:
reaxkit get-optimized-ffield --fort83 fort.83 --output fort83_optimized_ffield
2. Extract using a custom output filename:
reaxkit get-optimized-ffield --output trained_ffield
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--fort83 |
No |
fort.83 |
Path to fort.83. Example: --fort83 runs/job1/fort.83, which reads that optimization output file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output |
No |
fort83_optimized_ffield |
Output path for the extracted force field. Example: --output trained_ffield, which writes extracted parameters to that filename. |
|
--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. |
|
Command: get-optimized-force-field-fort83
Extract the optimized force-field block from a fort.83 file.
This command scans for the Error force field marker and writes everything after that
marker to a separate output file. Use it to recover the trained/optimized force field
from optimization output.
Examples
1. Extract from a specific `fort.83` file with explicit output name:
reaxkit get-optimized-ffield --fort83 fort.83 --output fort83_optimized_ffield
2. Extract using a custom output filename:
reaxkit get-optimized-ffield --output trained_ffield
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--fort83 |
No |
fort.83 |
Path to fort.83. Example: --fort83 runs/job1/fort.83, which reads that optimization output file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output |
No |
fort83_optimized_ffield |
Output path for the extracted force field. Example: --output trained_ffield, which writes extracted parameters to that filename. |
|
--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. |
|
Command: get-optimized-ffield-fort83
Extract the optimized force-field block from a fort.83 file.
This command scans for the Error force field marker and writes everything after that
marker to a separate output file. Use it to recover the trained/optimized force field
from optimization output.
Examples
1. Extract from a specific `fort.83` file with explicit output name:
reaxkit get-optimized-ffield --fort83 fort.83 --output fort83_optimized_ffield
2. Extract using a custom output filename:
reaxkit get-optimized-ffield --output trained_ffield
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--fort83 |
No |
fort.83 |
Path to fort.83. Example: --fort83 runs/job1/fort.83, which reads that optimization output file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output |
No |
fort83_optimized_ffield |
Output path for the extracted force field. Example: --output trained_ffield, which writes extracted parameters to that filename. |
|
--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.