Jaguar Isomer Workflow
Workflow for creating Jaguar jobs from isomer representative folders.
Command: create-jaguar-isomer-jobs
Create Jaguar input files and Slurm submit scripts from detected isomer folders.
This workflow expects stage-1 per-isomer folders containing xmolout files.
It prepares jobs and can optionally call sbatch, but it does not track job completion
or diagnose Jaguar/runtime/license failures.
Examples
reaxkit create-jaguar-isomer-jobs --write-example-config slurm_job_config.yaml
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs --submit
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--isomer-dir |
No |
|
Directory containing per-isomer folders from detect-isomer-representatives --write-isomer-dirs. |
|
--hf-base |
No |
|
Jaguar hf_base.in template. This is molecular-system specific and must be reviewed. |
|
--job-config |
No |
|
Slurm/Jaguar YAML settings file. Use --write-example-config to create a template. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
jaguar_jobs |
Output directory for generated Jaguar job folders and manifest. |
|
--write-example-config |
No |
|
Write an editable Slurm/Jaguar YAML config template and exit. |
|
--detail-format |
No |
|
Optional detail format (default: Parquet; legacy: CSV). |
parquet, csv |
Execution
| Flag |
Required |
Default |
Help |
Choices |
--submit |
No |
False |
Submit generated jobs with sbatch. Submission success does not mean Jaguar completed successfully. |
|
--no-skip-completed |
No |
False |
Regenerate jobs even when an existing hf.out contains 'final geometry:'. |
|
--no-skip-queued |
No |
False |
With --submit, do not skip structures that already have a matching Slurm job name in squeue. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory or example config. |
|
--output-profile |
No |
standard |
Artifact profile (default: standard). |
standard, minimal, 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: create_jaguar_isomer_jobs
Create Jaguar input files and Slurm submit scripts from detected isomer folders.
This workflow expects stage-1 per-isomer folders containing xmolout files.
It prepares jobs and can optionally call sbatch, but it does not track job completion
or diagnose Jaguar/runtime/license failures.
Examples
reaxkit create-jaguar-isomer-jobs --write-example-config slurm_job_config.yaml
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs --submit
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--isomer-dir |
No |
|
Directory containing per-isomer folders from detect-isomer-representatives --write-isomer-dirs. |
|
--hf-base |
No |
|
Jaguar hf_base.in template. This is molecular-system specific and must be reviewed. |
|
--job-config |
No |
|
Slurm/Jaguar YAML settings file. Use --write-example-config to create a template. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
jaguar_jobs |
Output directory for generated Jaguar job folders and manifest. |
|
--write-example-config |
No |
|
Write an editable Slurm/Jaguar YAML config template and exit. |
|
--detail-format |
No |
|
Optional detail format (default: Parquet; legacy: CSV). |
parquet, csv |
Execution
| Flag |
Required |
Default |
Help |
Choices |
--submit |
No |
False |
Submit generated jobs with sbatch. Submission success does not mean Jaguar completed successfully. |
|
--no-skip-completed |
No |
False |
Regenerate jobs even when an existing hf.out contains 'final geometry:'. |
|
--no-skip-queued |
No |
False |
With --submit, do not skip structures that already have a matching Slurm job name in squeue. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory or example config. |
|
--output-profile |
No |
standard |
Artifact profile (default: standard). |
standard, minimal, 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-jaguar-isomer-jobs
Create Jaguar input files and Slurm submit scripts from detected isomer folders.
This workflow expects stage-1 per-isomer folders containing xmolout files.
It prepares jobs and can optionally call sbatch, but it does not track job completion
or diagnose Jaguar/runtime/license failures.
Examples
reaxkit create-jaguar-isomer-jobs --write-example-config slurm_job_config.yaml
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs --submit
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--isomer-dir |
No |
|
Directory containing per-isomer folders from detect-isomer-representatives --write-isomer-dirs. |
|
--hf-base |
No |
|
Jaguar hf_base.in template. This is molecular-system specific and must be reviewed. |
|
--job-config |
No |
|
Slurm/Jaguar YAML settings file. Use --write-example-config to create a template. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
jaguar_jobs |
Output directory for generated Jaguar job folders and manifest. |
|
--write-example-config |
No |
|
Write an editable Slurm/Jaguar YAML config template and exit. |
|
--detail-format |
No |
|
Optional detail format (default: Parquet; legacy: CSV). |
parquet, csv |
Execution
| Flag |
Required |
Default |
Help |
Choices |
--submit |
No |
False |
Submit generated jobs with sbatch. Submission success does not mean Jaguar completed successfully. |
|
--no-skip-completed |
No |
False |
Regenerate jobs even when an existing hf.out contains 'final geometry:'. |
|
--no-skip-queued |
No |
False |
With --submit, do not skip structures that already have a matching Slurm job name in squeue. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory or example config. |
|
--output-profile |
No |
standard |
Artifact profile (default: standard). |
standard, minimal, 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_jaguar_isomer_jobs
Create Jaguar input files and Slurm submit scripts from detected isomer folders.
This workflow expects stage-1 per-isomer folders containing xmolout files.
It prepares jobs and can optionally call sbatch, but it does not track job completion
or diagnose Jaguar/runtime/license failures.
Examples
reaxkit create-jaguar-isomer-jobs --write-example-config slurm_job_config.yaml
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs
reaxkit create-jaguar-isomer-jobs --isomer-dir isomer_outputs/isomers --hf-base hf_base.in --job-config slurm_job_config.yaml --output-dir jaguar_jobs --submit
Arguments
| Flag |
Required |
Default |
Help |
Choices |
--isomer-dir |
No |
|
Directory containing per-isomer folders from detect-isomer-representatives --write-isomer-dirs. |
|
--hf-base |
No |
|
Jaguar hf_base.in template. This is molecular-system specific and must be reviewed. |
|
--job-config |
No |
|
Slurm/Jaguar YAML settings file. Use --write-example-config to create a template. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
jaguar_jobs |
Output directory for generated Jaguar job folders and manifest. |
|
--write-example-config |
No |
|
Write an editable Slurm/Jaguar YAML config template and exit. |
|
--detail-format |
No |
|
Optional detail format (default: Parquet; legacy: CSV). |
parquet, csv |
Execution
| Flag |
Required |
Default |
Help |
Choices |
--submit |
No |
False |
Submit generated jobs with sbatch. Submission success does not mean Jaguar completed successfully. |
|
--no-skip-completed |
No |
False |
Regenerate jobs even when an existing hf.out contains 'final geometry:'. |
|
--no-skip-queued |
No |
False |
With --submit, do not skip structures that already have a matching Slurm job name in squeue. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory or example config. |
|
--output-profile |
No |
standard |
Artifact profile (default: standard). |
standard, minimal, 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.