Isomer Workflow
File workflow for coarse isomer representative detection.
Command: detect-isomer-representatives
Detect coarse target-formula isomer representatives using canonical ReaxKit data.
For this file workflow, ReaxFF fort.7 and xmolout are first loaded through ReaxFFAdapter
as ConnectivityTrajectoryData, then the engine-independent analyzer is executed.
The target formula, prefix, and legacy folder behavior are read from control_params.
Examples
reaxkit detect-isomer-representatives --fort7 fort.7 --xmolout xmolout --control control_params --output-dir isomer_outputs
reaxkit detect-isomer-representatives --output-dir isomer_outputs --max-representatives 10
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--max-representatives |
No |
|
Optional cap on representatives, limiting downstream Jaguar jobs. |
|
| Flag |
Required |
Default |
Help |
Choices |
--fort7 |
No |
fort.7 |
Input ReaxFF fort.7 file. |
|
--xmolout |
No |
xmolout |
Input ReaxFF xmolout file. |
|
--control |
No |
control_params |
Input legacy control_params file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_outputs |
Output directory for xmolout_isomers, isomer_run_log.txt, and optional isomer folders. |
|
--write-isomer-dirs |
No |
False |
Force writing per-isomer folders under output-dir/isomers. |
|
--no-isomer-dirs |
No |
False |
Disable per-isomer folders even when control_params has isomer_run=2. |
|
--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 |
--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: detect_isomer_representatives
Detect coarse target-formula isomer representatives using canonical ReaxKit data.
For this file workflow, ReaxFF fort.7 and xmolout are first loaded through ReaxFFAdapter
as ConnectivityTrajectoryData, then the engine-independent analyzer is executed.
The target formula, prefix, and legacy folder behavior are read from control_params.
Examples
reaxkit detect-isomer-representatives --fort7 fort.7 --xmolout xmolout --control control_params --output-dir isomer_outputs
reaxkit detect-isomer-representatives --output-dir isomer_outputs --max-representatives 10
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--max-representatives |
No |
|
Optional cap on representatives, limiting downstream Jaguar jobs. |
|
| Flag |
Required |
Default |
Help |
Choices |
--fort7 |
No |
fort.7 |
Input ReaxFF fort.7 file. |
|
--xmolout |
No |
xmolout |
Input ReaxFF xmolout file. |
|
--control |
No |
control_params |
Input legacy control_params file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_outputs |
Output directory for xmolout_isomers, isomer_run_log.txt, and optional isomer folders. |
|
--write-isomer-dirs |
No |
False |
Force writing per-isomer folders under output-dir/isomers. |
|
--no-isomer-dirs |
No |
False |
Disable per-isomer folders even when control_params has isomer_run=2. |
|
--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 |
--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: detect-isomers
Detect coarse target-formula isomer representatives using canonical ReaxKit data.
For this file workflow, ReaxFF fort.7 and xmolout are first loaded through ReaxFFAdapter
as ConnectivityTrajectoryData, then the engine-independent analyzer is executed.
The target formula, prefix, and legacy folder behavior are read from control_params.
Examples
reaxkit detect-isomer-representatives --fort7 fort.7 --xmolout xmolout --control control_params --output-dir isomer_outputs
reaxkit detect-isomer-representatives --output-dir isomer_outputs --max-representatives 10
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--max-representatives |
No |
|
Optional cap on representatives, limiting downstream Jaguar jobs. |
|
| Flag |
Required |
Default |
Help |
Choices |
--fort7 |
No |
fort.7 |
Input ReaxFF fort.7 file. |
|
--xmolout |
No |
xmolout |
Input ReaxFF xmolout file. |
|
--control |
No |
control_params |
Input legacy control_params file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_outputs |
Output directory for xmolout_isomers, isomer_run_log.txt, and optional isomer folders. |
|
--write-isomer-dirs |
No |
False |
Force writing per-isomer folders under output-dir/isomers. |
|
--no-isomer-dirs |
No |
False |
Disable per-isomer folders even when control_params has isomer_run=2. |
|
--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 |
--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: detect_isomers
Detect coarse target-formula isomer representatives using canonical ReaxKit data.
For this file workflow, ReaxFF fort.7 and xmolout are first loaded through ReaxFFAdapter
as ConnectivityTrajectoryData, then the engine-independent analyzer is executed.
The target formula, prefix, and legacy folder behavior are read from control_params.
Examples
reaxkit detect-isomer-representatives --fort7 fort.7 --xmolout xmolout --control control_params --output-dir isomer_outputs
reaxkit detect-isomer-representatives --output-dir isomer_outputs --max-representatives 10
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--max-representatives |
No |
|
Optional cap on representatives, limiting downstream Jaguar jobs. |
|
| Flag |
Required |
Default |
Help |
Choices |
--fort7 |
No |
fort.7 |
Input ReaxFF fort.7 file. |
|
--xmolout |
No |
xmolout |
Input ReaxFF xmolout file. |
|
--control |
No |
control_params |
Input legacy control_params file. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_outputs |
Output directory for xmolout_isomers, isomer_run_log.txt, and optional isomer folders. |
|
--write-isomer-dirs |
No |
False |
Force writing per-isomer folders under output-dir/isomers. |
|
--no-isomer-dirs |
No |
False |
Disable per-isomer folders even when control_params has isomer_run=2. |
|
--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 |
--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.