CONTCAR -> POSCAR check

[jmmshn]

Sometimes the CONTCAR file gets created by VASP but is empty. Not a big problem since we are copying the file first but would be a helpful error message if something went wrong. We can validate the CONTCAR before copying and throwing an error. https://github.com/materialsproject/atomate2/blob/d21bdac763595372c04db999fcaa71b155dae28c/src/atomate2/vasp/files.py#L101

[jmmshn]

UPDATE

For long running jobs using fireworks the following CLI script can be called from the cluster to restart the job from a fizzled state and just copy over the CONTCAR files.

#!/usr/bin/env python3
"""Restart fizzled jobs."""
import json
import logging
from pathlib import Path

import click
from fireworks import LaunchPad
from pymatgen.io.vasp.inputs import Poscar

logger = logging.getLogger(__name__)

LPAD = LaunchPad.auto_load()

def _get_fizzled(query=None):
    """Find the fizzed relaxation jobs.

    The atomate2 created fireworks for long running relaxation jobs should be simple.
    Basically `spec._tasks.0` should be the relaxation job.

        Args:
                query: query to use.  The basic query is already included.

        Returns:
                list: list of fizzled fireworks ids
    """
    fw_query = {
        "spec._tasks.0.job.function.@callable": "BaseVaspMaker.make",
        "state": "FIZZLED",
        "$or": [
            {"spec._tasks.0.job.function_args.0.@class": "Structure"},
            {"spec._tasks.0.job.function_args.0.@class": "OutputReference"},
        ],
    }
    fw_query.update(query or {})
    return LPAD.get_fw_ids(query=fw_query)

def _get_last_launch_dir(fw_id):
    """Get the last launch directory for a fizzled job.

    Args:
            fw_id: fireworks id

    Returns:
            str: last launch directory
    """
    return LPAD.get_fw_dict_by_id(fw_id)["launches"][-1]["launch_dir"]

def _read_contcar(dir_name):
    """Read the CONTCAR currently in the directory.

    Args:
            dir_name: directory to read CONTCAR from

    Returns:
            Structure: structure from CONTCAR
    """
    try:
        contcar = Poscar.from_file(Path(dir_name) / "CONTCAR")
    except Exception:
        contcar = None
    return contcar

def _update_fw_db(fw_id, structure):
    """Update the spec structure for a fizzled job.

    Args:
        fw_id: fireworks id
        structure: structure to update to
    """
    fw_dict = LPAD.get_fw_dict_by_id(fw_id)
    fw_dict["spec"]["_tasks"][0]["job"]["function_args"][0][
        "structure"
    ] = structure.as_dict()
    update_dict = {"_tasks.0.job.function_args.0": structure.as_dict()}
    LPAD.update_spec([fw_id], update_dict)

@click.command()
@click.option("-q", "--query", default={})
@click.option("-d", "--dry-run", is_flag=True)
def main(query, dry_run):
    """Run the CLI."""
    q = json.loads(query)
    fizzled = _get_fizzled(q)

    for fw_id in fizzled:
        dir_name = _get_last_launch_dir(fw_id)
        print(f"Reading CONTCAR for {fw_id} from {dir_name}")
        contcar = _read_contcar(dir_name)
        if contcar is not None:
            print(">>>>CONTCAR PARSED")
        if contcar is not None:
            # start the return first then update the db
            # this way the data from the failed calculation is kept
            if not dry_run:
                print(f"Rerun -- {fw_id}")
                LPAD.rerun_fw(fw_id)
                _update_fw_db(fw_id, contcar)

if __name__ == "__main__":
    main()

[utf]

Thanks for this code @jmmshn. What do you think about adding this as part of the command line utility for atomate2. So the command would be something like:

atm fireworks-continue ...

[jmmshn]

The only question I have is whether we can ensure the position of the structure argument

[matthewkuner]

I think this could easily be modified to enable people to run VASP jobs on preempt-able queues, as well. I'll work on that and get back if I get it functioning