Command guide

Various tasks can be performed through the command line interface of PFD-kit. Here is a guide to the available commands.

Making perturbed structures

The initial structures for exploration can be generated by perturbing availiable frames. For example, ten perturbed structures for the diamond Si system can be prepared by the following command:

pfd perturb -n 10 dia_si.extxyz -c 0.03

The input file can be of any ase-compatible format. The perturbed frames are stored in pert_dia_si.extxyz.

Submitting a Workflow

To submit a workflow, navigate to the working directory and run:

pfd submit input.json

input.json contains workflow definitions. The workflow ID will be printed upon successful submission.

Checking status

To check the status of exploration, use:

pfd status input.json workflow_id

Restarting from a Checkpoint

To restart a workflow with modified input parameters, use:

pfd resubmit input.json old_workflow_id -u 0-100

This reuses the results of the first 100 steps of an old workflow. To list completed steps:

pfd resubmit input.json old_workflow_id -l

Downloading Results

To download the output model file, use:

pfd download input.json workflow_id

For advanced usage, download a specific step’s output:

pfd download input.json workflow_id -i 0 -d prep-run-train/input/models

List available download definitions:

pfd download input.json workflow_id -l

PFD-kit Command Arguments

Note: Use -h or --help to list all possible arguments for PFD-kit subcommands.

Subcommand: perturb

Usage:

pfd perturb [-h] [-n PERT_NUM] [-c CELL_PERT_FRACTION] [-d ATOM_PERT_DISTANCE] [-s ATOM_PERT_STYLE] [-a ATOM_PERT_PROB] [-r SUPERCELL [SUPERCELL ...]] ATOMS [ATOMS ...]

Arguments:

  • ATOMS: the structure files in ase-compatible format, support multiple files.

  • -n PERT_NUM, --pert-num PERT_NUM: the number of perturbed structures to be generated for each input structure. (default: 1)

  • -c CELL_PERT_FRACTION, --cell-pert-fraction CELL_PERT_FRACTION: the fraction of cell perturbation. (default: 0.05)

  • -d ATOM_PERT_DISTANCE, --atom-pert-distance ATOM_PERT_DISTANCE: the distance to perturb the atom. (default: 0.2)

  • -s ATOM_PERT_STYLE, --atom-pert-style ATOM_PERT_STYLE: the style of perturbation. (default: normal)

  • -a ATOM_PERT_PROB, --atom-pert-prob ATOM_PERT_PROB: the probability of perturbing each atom. (default: 1.0)

  • -r SUPERCELL [SUPERCELL ...], --supercell SUPERCELL [SUPERCELL ...]: the supercell replication, support int or 3 ints. (default: None)

Subcommand: submit

Usage:

pfd submit [-h] [-m] CONFIG

Arguments:

  • CONFIG: Path to the configuration script in json format.

  • -m, --monitoring: Monitor workflow progress and auto-download the output model upon successful completion.

Subcommand: status

Usage:

pfd status [-h] CONFIG ID

Arguments:

  • CONFIG: Path to the configuration script in json format.

  • ID: Workflow ID of an existing PFD workflow.

Subcommand: resubmit

Usage:

pfd resubmit [-h] [-m] CONFIG ID

Arguments:

  • CONFIG: Path to the configuration script in json format.

  • ID: Workflow ID of an existing PFD workflow.

  • -l, --list: List completed steps of an existing workflow.

  • -u, --reuse REUSE: Reuse completed steps from an existing workflow.

  • -f, --fold: Reuse dflow Steps in the workflow as a whole. For instance, failed LAMMPS tasks would be skipped in the resubmitted workflow if the prep-run-explore Steps it belongs to is asserted as successful.

  • -m, --monitoring: Monitor workflow progress and auto-download the output model upon successful completion.

Subcommand: download

Usage:

pfd download [-h] [-l] [-k KEYS] [-i ITERATIONS] [-d STEP_DEFINITIONS] [-p PREFIX] [-n] CONFIG ID

Arguments:

  • CONFIG: Path to the configuration script in json format.

  • ID: Workflow ID of an existing PFD workflow.

  • -k, --keys KEYS: Download artifacts by step key(s).

  • -d, --step-definitions STEP_DEFINITIONS: Download artifacts by step definitions.

  • -l, --list-supported: List all supported step definitions.

  • -i, --iterations ITERATIONS: Specify steps from which iterations are to be downloaded. Used in conjuntion with -d STEP_DEFINITIONS.

  • -p, --prefix PREFIX: Prefix for the download path.