Allow for thread-safe execution (#1780)

## Summary of Changes

This PR adds a new quacc setting, `CHDIR`, that will allow the user to
specify whether any `os.chdir` calls are made, thereby allowing for
multiple jobs to be run on a single Python process.

Closes #1641.

### Checklist

- [X] I have read the ["Guidelines"
section](https://quantum-accelerators.github.io/quacc/dev/contributing.html#guidelines)
of the contributing guide. Don't lie! 😉
- [X] My PR is on a custom branch and is _not_ named `main`.
- [X] I have used `black`, `isort`, and `ruff` as described in the
[style
guide](https://quantum-accelerators.github.io/quacc/dev/contributing.html#style).
- [X] I have added relevant, comprehensive [unit
tests](https://quantum-accelerators.github.io/quacc/dev/contributing.html#unit-tests).

### Notes

- Your PR will likely not be merged without proper and thorough tests.
- If you are an external contributor, you will see a comment from
[@buildbot-princeton](https://github.com/buildbot-princeton). This is
solely for the maintainers.
- When your code is ready for review, ping one of the [active
maintainers](https://quantum-accelerators.github.io/quacc/about/contributors.html#active-maintainers).

---------

Co-authored-by: deepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>

src/quacc/runners/prep.py

@@ -81,7 +81,8 @@ def calc_setup(
     # for all threads in the current process. However, elsewhere in the code,
     # we use absolute paths to avoid issues. We keep this here for now because some
     # old ASE calculators do not support the `directory` keyword argument.
-    os.chdir(tmpdir)
+    if SETTINGS.CHDIR:
+        os.chdir(tmpdir)
 
     return tmpdir, job_results_dir
 
@@ -126,7 +127,8 @@ def calc_cleanup(atoms: Atoms, tmpdir: Path | str, job_results_dir: Path | str)
     # for all threads in the current process. However, elsewhere in the code,
     # we use absolute paths to avoid issues. We keep this here for now because some
     # old ASE calculators do not support the `directory` keyword argument.
-    os.chdir(job_results_dir)
+    if SETTINGS.CHDIR:
+        os.chdir(job_results_dir)
 
     # Gzip files in tmpdir
     if SETTINGS.GZIP_FILES:

src/quacc/settings.py

@@ -103,6 +103,20 @@ class QuaccSettings(BaseSettings):
             """
         ),
     )
+    CHDIR: bool = Field(
+        True,
+        description=(
+            """
+            Whether quacc will make `os.chdir` calls to change the working directory
+            to be the location where the calculation is run. By default, we leave this
+            as `True` because not all ASE calculators properly support a `directory`
+            parameter. In most cases, this is fine, but it breaks thread safety.
+            If you need to run multiple, parallel calculations in a single Python process,
+            such as in a multithreaded job execution mode, then this setting needs
+            to be `False`. Note that not all calculators properly support this, however.
+            """
+        ),
+    )
     GZIP_FILES: bool = Field(
         True, description="Whether generated files should be gzip'd."
     )

tests/core/recipes/lj_recipes/test_lj_recipes.py

@@ -93,3 +93,18 @@ def test_freq_job(tmp_path, monkeypatch):
     assert len(output["results"]["vib_freqs"]) == 3 * len(atoms) - 6
     assert len(output["parameters_thermo"]["vib_freqs"]) == 3 * len(atoms) - 6
     assert output["parameters_thermo"]["n_imag"] == 0
+
+
+def test_freq_job_threads(tmp_path, monkeypatch):
+    monkeypatch.chdir(tmp_path)
+
+    SETTINGS.CHDIR = False
+
+    atoms = molecule("H2O")
+
+    output = freq_job(relax_job(atoms)["atoms"])
+    assert output["natoms"] == len(atoms)
+    assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)
+    assert output["parameters_thermo"]["n_imag"] == 0
+
+    SETTINGS.CHDIR = DEFAULT_SETTINGS.CHDIR = True

tests/parsl/test_emt_recipes.py

@@ -4,12 +4,19 @@
 
 from ase.build import bulk
 
+from quacc import SETTINGS
 from quacc.recipes.emt.core import relax_job  # skipcq: PYL-C0412
 from quacc.recipes.emt.slabs import bulk_to_slabs_flow  # skipcq: PYL-C0412
 
+DEFAULT_SETTINGS = SETTINGS.model_copy()
 
-def test_parsl_functools(tmp_path, monkeypatch):
+
+@pytest.mark.parametrize("chdir", [True, False])
+def test_parsl_functools(tmp_path, monkeypatch, chdir):
     monkeypatch.chdir(tmp_path)
+
+    SETTINGS.CHDIR = chdir
+
     atoms = bulk("Cu")
     result = bulk_to_slabs_flow(
         atoms, job_params={"relax_job": {"opt_params": {"fmax": 0.1}}}, run_static=False
@@ -18,27 +25,39 @@ def test_parsl_functools(tmp_path, monkeypatch):
     assert "atoms" in result[-1]
     assert result[-1]["fmax"] == 0.1
 
+    SETTINGS.CHDIR = DEFAULT_SETTINGS.CHDIR
+
 
-def test_phonon_flow(tmp_path, monkeypatch):
+@pytest.mark.parametrize("chdir", [True, False])
+def test_phonon_flow(tmp_path, monkeypatch, chdir):
     pytest.importorskip("phonopy")
     from quacc.recipes.emt.phonons import phonon_flow
 
+    SETTINGS.CHDIR = chdir
+
     monkeypatch.chdir(tmp_path)
     atoms = bulk("Cu")
     output = phonon_flow(atoms)
     assert output.result()["results"]["thermal_properties"]["temperatures"].shape == (
         101,
     )
 
+    SETTINGS.CHDIR = DEFAULT_SETTINGS.CHDIR
+
 
-def test_phonon_flow_multistep(tmp_path, monkeypatch):
+@pytest.mark.parametrize("chdir", [True, False])
+def test_phonon_flow_multistep(tmp_path, monkeypatch, chdir):
     pytest.importorskip("phonopy")
     from quacc.recipes.emt.phonons import phonon_flow
 
+    SETTINGS.CHDIR = chdir
+
     monkeypatch.chdir(tmp_path)
     atoms = bulk("Cu")
     relaxed = relax_job(atoms)
     output = phonon_flow(relaxed["atoms"])
     assert output.result()["results"]["thermal_properties"]["temperatures"].shape == (
         101,
     )
+
+    SETTINGS.CHDIR = DEFAULT_SETTINGS.CHDIR