Isomer Trainset Workflow
Workflow for creating ReaxFF trainset files from completed isomer jobs.
Command: create-isomer-trainset
Create ReaxFF geo/trainset files from completed isomer jobs.
This workflow expects per-isomer job folders containing supported hf.out files.
Currently supported output format: Jaguar hf.out.
Incomplete or missing hf.out files are skipped by default and reported in the log.
Examples
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs --require-all-complete
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--weight |
No |
1.0 |
Weight for generated ENERGY trainset lines. |
|
--reference-composition |
No |
100.0 |
Composition value assigned to the lowest-energy reference structure. |
|
--temperature |
No |
273.0 |
Temperature used for relative composition. |
|
--gas-constant |
No |
1.987 |
Gas constant used for relative composition. |
|
--require-all-complete |
No |
False |
Fail if any isomer job folder is missing a completed hf.out. |
|
| Flag |
Required |
Default |
Help |
Choices |
--job-dir |
No |
isomer_jobs |
Directory containing per-isomer job folders. |
|
--geo-file |
No |
geo |
Output geo filename. |
|
--trainset-file |
No |
trainset.in |
Output trainset filename. |
|
--composition-file |
No |
composition.txt |
Output composition filename. |
|
--log-file |
No |
out_trainset_log.txt |
Output log filename. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_trainset |
Output directory for geo, trainset.in, composition.txt, and log files. |
|
--hf-output-name |
No |
hf.out |
Supported output filename inside each job folder. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory. |
|
--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_isomer_trainset
Create ReaxFF geo/trainset files from completed isomer jobs.
This workflow expects per-isomer job folders containing supported hf.out files.
Currently supported output format: Jaguar hf.out.
Incomplete or missing hf.out files are skipped by default and reported in the log.
Examples
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs --require-all-complete
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--weight |
No |
1.0 |
Weight for generated ENERGY trainset lines. |
|
--reference-composition |
No |
100.0 |
Composition value assigned to the lowest-energy reference structure. |
|
--temperature |
No |
273.0 |
Temperature used for relative composition. |
|
--gas-constant |
No |
1.987 |
Gas constant used for relative composition. |
|
--require-all-complete |
No |
False |
Fail if any isomer job folder is missing a completed hf.out. |
|
| Flag |
Required |
Default |
Help |
Choices |
--job-dir |
No |
isomer_jobs |
Directory containing per-isomer job folders. |
|
--geo-file |
No |
geo |
Output geo filename. |
|
--trainset-file |
No |
trainset.in |
Output trainset filename. |
|
--composition-file |
No |
composition.txt |
Output composition filename. |
|
--log-file |
No |
out_trainset_log.txt |
Output log filename. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_trainset |
Output directory for geo, trainset.in, composition.txt, and log files. |
|
--hf-output-name |
No |
hf.out |
Supported output filename inside each job folder. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory. |
|
--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-isomer-trainset
Create ReaxFF geo/trainset files from completed isomer jobs.
This workflow expects per-isomer job folders containing supported hf.out files.
Currently supported output format: Jaguar hf.out.
Incomplete or missing hf.out files are skipped by default and reported in the log.
Examples
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs --require-all-complete
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--weight |
No |
1.0 |
Weight for generated ENERGY trainset lines. |
|
--reference-composition |
No |
100.0 |
Composition value assigned to the lowest-energy reference structure. |
|
--temperature |
No |
273.0 |
Temperature used for relative composition. |
|
--gas-constant |
No |
1.987 |
Gas constant used for relative composition. |
|
--require-all-complete |
No |
False |
Fail if any isomer job folder is missing a completed hf.out. |
|
| Flag |
Required |
Default |
Help |
Choices |
--job-dir |
No |
isomer_jobs |
Directory containing per-isomer job folders. |
|
--geo-file |
No |
geo |
Output geo filename. |
|
--trainset-file |
No |
trainset.in |
Output trainset filename. |
|
--composition-file |
No |
composition.txt |
Output composition filename. |
|
--log-file |
No |
out_trainset_log.txt |
Output log filename. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_trainset |
Output directory for geo, trainset.in, composition.txt, and log files. |
|
--hf-output-name |
No |
hf.out |
Supported output filename inside each job folder. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory. |
|
--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_isomer_trainset
Create ReaxFF geo/trainset files from completed isomer jobs.
This workflow expects per-isomer job folders containing supported hf.out files.
Currently supported output format: Jaguar hf.out.
Incomplete or missing hf.out files are skipped by default and reported in the log.
Examples
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs
reaxkit create-isomer-trainset --job-dir isomer_jobs --output-dir trainset_outputs --require-all-complete
Arguments
Scientific choices
| Flag |
Required |
Default |
Help |
Choices |
--weight |
No |
1.0 |
Weight for generated ENERGY trainset lines. |
|
--reference-composition |
No |
100.0 |
Composition value assigned to the lowest-energy reference structure. |
|
--temperature |
No |
273.0 |
Temperature used for relative composition. |
|
--gas-constant |
No |
1.987 |
Gas constant used for relative composition. |
|
--require-all-complete |
No |
False |
Fail if any isomer job folder is missing a completed hf.out. |
|
| Flag |
Required |
Default |
Help |
Choices |
--job-dir |
No |
isomer_jobs |
Directory containing per-isomer job folders. |
|
--geo-file |
No |
geo |
Output geo filename. |
|
--trainset-file |
No |
trainset.in |
Output trainset filename. |
|
--composition-file |
No |
composition.txt |
Output composition filename. |
|
--log-file |
No |
out_trainset_log.txt |
Output log filename. |
|
Outputs and plots
| Flag |
Required |
Default |
Help |
Choices |
--output-dir |
No |
isomer_trainset |
Output directory for geo, trainset.in, composition.txt, and log files. |
|
--hf-output-name |
No |
hf.out |
Supported output filename inside each job folder. |
|
--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 |
--force |
No |
False |
Allow overwriting files in an existing non-empty output directory. |
|
--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.