Commands
BespokeFit provides a full command line interface to its major features under
the alias openff-bespoke
. The CLI is organised into sub-commands similar to
conda
, GROMACS, git
and apt
. This CLI is self-documenting via the --help
switch which is available on any subcommand:
openff-bespoke --help
openff-bespoke executor launch --help
See the quick start guide for examples of using the CLI.
openff-bespoke
The root group for all CLI commands.
openff-bespoke [OPTIONS] COMMAND [ARGS]...
cache
Commands to manually update the qc data cache.
openff-bespoke cache [OPTIONS] COMMAND [ARGS]...
update
The main worker function which updates the redis cache with qcsubmit results objects.
openff-bespoke cache update [OPTIONS]
Options
- --qcf-datatype <qcf_datatype>
The type of dataset to cache.
- Default
torsion
- Options
torsion | optimization | hessian
- --qcf-address <qcf_address>
The address of the QCFractal server to pull the dataset from.
- Default
api.qcarchive.molssi.org:443
- --qcf-config <qcf_config>
The path to a QCFractal config file containing the address username and password.
combine
Combine force fields from local files and task ids.
openff-bespoke combine [OPTIONS]
Options
executor
Commands for interacting with a bespoke executor.
openff-bespoke executor [OPTIONS] COMMAND [ARGS]...
launch
Launch a bespoke executor.
openff-bespoke executor launch [OPTIONS]
Options
- --directory <directory>
Required The directory to store any working and log files in
- Default
bespoke-executor
- --n-fragmenter-workers <n_fragmenter_workers>
The number of fragmentation workers to spawn
- Default
1
- --qc-compute-n-cores <qc_compute_n_cores>
The maximum number of cores ( / CPUs) to reserve per QC compute worker. The actual number of cores utilised will depend on the type of QC calculation being performed. If no value is specified, all CPUs will be made available to each worker.
list
List the ids of any bespoke optimizations.
openff-bespoke executor list [OPTIONS]
Options
retrieve
Retrieve the current output of a bespoke optimization.
openff-bespoke executor retrieve [OPTIONS]
Options
run
Run bespoke optimization using a temporary executor.
If you are running many bespoke optimizations it is recommended that you first launch a bespoke executor using the launch command and then submit the optimizations to it using the submit command.
openff-bespoke executor run [OPTIONS]
Options
- --workflow <workflow_name>
The name of the built-in bespoke fitting workflow to use.
- Options
default | debug
- --workflow-file <workflow_file_name>
The path to a serialized bespoke workflow factory that encodes the bespoke fitting workflow to use.
- --output-force-field <output_force_field_path>
The (optional) path [.offxml] to save the bespoke force field to if the fit succeeded
- --target-torsion <target_torsion_smirks>
The SMIRKS pattern(s) that should be used to identify the bonds in the input molecule to generate bespoke torsions around if requested. It must only match the two atoms involved in the central bond. This argument can be specified multiple times if you wish to provide multiple patterns.
- --default-qc-spec <default_qc_spec>
The program, method, and basis to use by default when performing any QC calculations, e.g. –default-qc-spec xtb gfn2xtb none. If no basis is required to be specified for a particular method (e.g. for ANI or XTB) then ‘none’ should be specified.
- --directory <directory>
The directory to store any working and log files in. By default all files and logs will be stored in a temporary directory and deleted when the command exists.
- --n-fragmenter-workers <n_fragmenter_workers>
The number of fragmentation workers to spawn
- Default
1
- --qc-compute-n-cores <qc_compute_n_cores>
The maximum number of cores ( / CPUs) to reserve per QC compute worker. The actual number of cores utilised will depend on the type of QC calculation being performed. If no value is specified, all CPUs will be made available to each worker.
submit
Submit a new bespoke optimization to a running executor.
openff-bespoke executor submit [OPTIONS]
Options
- --workflow <workflow_name>
The name of the built-in bespoke fitting workflow to use.
- Options
default | debug
- --workflow-file <workflow_file_name>
The path to a serialized bespoke workflow factory that encodes the bespoke fitting workflow to use.
- --save-submission-info, --no-save-submission-info
If the submission table printed in the terminal, which maps input molecules to an optimization ID, should be saved to a csv file.
- --target-torsion <target_torsion_smirks>
The SMIRKS pattern(s) that should be used to identify the bonds in the input molecule to generate bespoke torsions around if requested. It must only match the two atoms involved in the central bond. This argument can be specified multiple times if you wish to provide multiple patterns.
watch
Watch the status of a bespoke optimization.
openff-bespoke executor watch [OPTIONS]
Options
launch-worker
Launch a single worker of the requested type in the main process.
Used to connect workers to a remote bespokefit server.
Note:
By default bespokefit will automatically use all cores and memory made available to the worker which should be declared in the job submission script. To change these defaults see the settings BEFLOW_QC_COMPUTE_WORKER_N_CORES & BEFLOW_QC_COMPUTE_WORKER_MAX_MEM.
Args:
worker_type: The alias name of the worker type which should be started.
openff-bespoke launch-worker [OPTIONS]
Options
prepare
Prepare an optimizations’ input files based on its schema.
openff-bespoke prepare [OPTIONS]
Options