Charges Workflow

Direct command workflow for generating charges 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_charges

Write a template charges file for ReaxFF workflows. This command generates a starter charges file only. It does not run simulation steps or apply charges to an existing trajectory/run. Use the generated file as a base, then edit it according to your system and workflow requirements.

Examples

---

  1. Generate a template using default output name ('charges'):
   reaxkit gen_template_charges

  2. Generate a template with a custom filename:
   reaxkit gen_template_charges --output charges.template

  3. Generate a template and also copy it to the current directory:
   reaxkit gen_template_charges --output charges.template --copy-to-dot

Arguments

Outputs and plots

Flag	Required	Default	Help	Choices
--output	No	charges	Output filename to write under /input/
--copy-to-dot	No	False	Also copy generated output to the current directory.
--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-charges

Write a template charges file for ReaxFF workflows. This command generates a starter charges file only. It does not run simulation steps or apply charges to an existing trajectory/run. Use the generated file as a base, then edit it according to your system and workflow requirements.

Examples

---

  1. Generate a template using default output name ('charges'):
   reaxkit gen_template_charges

  2. Generate a template with a custom filename:
   reaxkit gen_template_charges --output charges.template

  3. Generate a template and also copy it to the current directory:
   reaxkit gen_template_charges --output charges.template --copy-to-dot

Arguments

Outputs and plots

Flag	Required	Default	Help	Choices
--output	No	charges	Output filename to write under /input/
--copy-to-dot	No	False	Also copy generated output to the current directory.
--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.