`SameFileError` when running sequential VASP jobs in the same directory

[Andrew-S-Rosen]

Describe the bug
When running a VASP Flow locally without creating new directories, I get back a SameFileError. This is not particularly surprising, but I am wondering if there is a better way for atomate2 to handle this. Perhaps we should just be overwriting the files that are there, like what would happen in a normal VASP job submitted without any workflow orchestration tool? The reason this came up was because I was troubleshooting by running jobs locally and did not bother to rely on create_folders=True when launching the calculations. This is with Atomate2 0.0.21.

from atomate2.vasp.jobs.matpes import MatPesGGAStaticMaker
from pymatgen.io.vasp.sets import MatPESStaticSet
from pymatgen.core import Structure
from jobflow import Flow
from jobflow import run_locally

structure = Structure.from_file("test.cif")

toy_input_set = MatPESStaticSet(user_incar_settings={"ENCUT": 400, "KSPACING": 0.5})
static1 = MatPesGGAStaticMaker(input_set_generator=toy_input_set).make(structure)

static2 = MatPesGGAStaticMaker(name="Test 2", input_set_generator=toy_input_set, copy_vasp_kwargs={"additional_vasp_files": ("WAVECAR",)}).make(static1.output.structure, prev_dir=static1.output.dir_name)

flow = Flow([static1, static2])

run_locally(flow)

Traceback (most recent call last):
  File "/u/rosen1/.local/lib/python3.11/site-packages/jobflow/managers/local.py", line 117, in _run_job
    response = job.run(store=store)
               ^^^^^^^^^^^^^^^^^^^^
  File "/u/rosen1/.local/lib/python3.11/site-packages/jobflow/core/job.py", line 604, in run
    response = function(*self.function_args, **self.function_kwargs)
               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/u/rosen1/.local/lib/python3.11/site-packages/atomate2/vasp/jobs/base.py", line 214, in make
    copy_vasp_outputs(prev_dir, **self.copy_vasp_kwargs)
  File "/u/rosen1/.local/lib/python3.11/site-packages/atomate2/utils/file_client.py", line 586, in gen_file_client
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/u/rosen1/.local/lib/python3.11/site-packages/atomate2/vasp/files.py", line 89, in copy_vasp_outputs
    copy_files(
  File "/u/rosen1/.local/lib/python3.11/site-packages/atomate2/utils/file_client.py", line 588, in gen_file_client
    return func(*args, **kwargs)
           ^^^^^^^^^^^^^^^^^^^^^
  File "/u/rosen1/.local/lib/python3.11/site-packages/atomate2/common/files.py", line 73, in copy_files
    file_client.copy(from_file, to_file, src_host=src_host)
  File "/u/rosen1/.local/lib/python3.11/site-packages/atomate2/utils/file_client.py", line 240, in copy
    shutil.copy2(src_filename, dest_filename)
  File "/u/rosen1/.conda/envs/cms/lib/python3.11/shutil.py", line 448, in copy2
    copyfile(src, dst, follow_symlinks=follow_symlinks)
  File "/u/rosen1/.conda/envs/cms/lib/python3.11/shutil.py", line 236, in copyfile
    raise SameFileError("{!r} and {!r} are the same file".format(src, dst))
shutil.SameFileError: PosixPath('/work/nvme/bems/rosen1/test/test/INCAR.gz') and PosixPath('/work/nvme/bems/rosen1/test/test/INCAR.gz') are the same file

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