Refactor thermo

CHANGELOG.md

@@ -4,17 +4,25 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [0.3.1]
+
+### Changed
+
+- Moved `quacc.custodian` to `quacc.calculators.custodian`
+- Renamed `quacc.thermo.ideal_gas` to `quacc.thermo.run_ideal_gas`
+- Renamed `quacc.schemas.ase.summarize_thermo` to `quacc.schemas.ase.summarize_igt_thermo`
+
 ## [0.3.0]
 
 ### Changed
 
 - Changed default `SCRATCH_DIR` from `/tmp` to `Path.cwd() / .scratch`
+- Refactored decorator handling to be more concise
+- Renamed `[optimizers]` extras to `[sella]`
 - Moved `quacc.utils.wflows` into `quacc.wflow.decorators` and `quacc.wflow.prefect`
 - Moved `quacc.utils.db` into `quacc.wflow.db`
 - Moved `quacc.utils.calc` to `quacc.runners.calc`
 - Moved `quacc.presets` to `quacc.calculators.presets`
-- Refactored decorator handling to be more concise
-- Renamed `[optimizers]` extras to `[sella]`
 
 ### Fixed
 

src/quacc/recipes/lj/core.py

@@ -12,12 +12,12 @@
 
 from quacc import job
 from quacc.runners.calc import run_ase_opt, run_ase_vib, run_calc
-from quacc.runners.thermo import ideal_gas
+from quacc.runners.thermo import run_ideal_gas
 from quacc.schemas import fetch_atoms
 from quacc.schemas.ase import (
+    summarize_igt_thermo,
     summarize_opt_run,
     summarize_run,
-    summarize_thermo,
     summarize_vib_run,
 )
 from quacc.utils.dicts import merge_dicts
@@ -183,8 +183,8 @@ def freq_job(
         vibrations, additional_fields={"name": "LJ Frequency"}
     )
 
-    igt = ideal_gas(atoms, vibrations.get_frequencies(), energy=energy)
-    vib_summary["thermo"] = summarize_thermo(
+    igt = run_ideal_gas(atoms, vibrations.get_frequencies(), energy=energy)
+    vib_summary["thermo"] = summarize_igt_thermo(
         igt,
         temperature=temperature,
         pressure=pressure,

src/quacc/recipes/newtonnet/core.py

@@ -11,12 +11,12 @@
 
 from quacc import SETTINGS, job
 from quacc.runners.calc import run_ase_opt, run_calc
-from quacc.runners.thermo import ideal_gas
+from quacc.runners.thermo import run_ideal_gas
 from quacc.schemas import fetch_atoms
 from quacc.schemas.ase import (
+    summarize_igt_thermo,
     summarize_opt_run,
     summarize_run,
-    summarize_thermo,
     summarize_vib_run,
 )
 from quacc.utils.dicts import merge_dicts
@@ -225,8 +225,8 @@ def freq_job(
         vib, additional_fields={"name": "ASE Vibrations Analysis"}
     )
 
-    igt = ideal_gas(final_atoms, vib.get_frequencies(), energy=energy)
-    summary["thermo"] = summarize_thermo(
+    igt = run_ideal_gas(final_atoms, vib.get_frequencies(), energy=energy)
+    summary["thermo"] = summarize_igt_thermo(
         igt,
         temperature=temperature,
         pressure=pressure,

src/quacc/recipes/tblite/core.py

@@ -8,12 +8,12 @@
 
 from quacc import job
 from quacc.runners.calc import run_ase_opt, run_ase_vib, run_calc
-from quacc.runners.thermo import ideal_gas
+from quacc.runners.thermo import run_ideal_gas
 from quacc.schemas import fetch_atoms
 from quacc.schemas.ase import (
+    summarize_igt_thermo,
     summarize_opt_run,
     summarize_run,
-    summarize_thermo,
     summarize_vib_run,
 )
 from quacc.utils.dicts import merge_dicts
@@ -196,7 +196,7 @@ def freq_job(
     -------
     FreqSchema
         Dictionary of results from [quacc.schemas.ase.summarize_vib_run] and
-        [quacc.schemas.ase.summarize_thermo][]
+        [quacc.schemas.ase.summarize_igt_thermo][]
     """
     atoms = fetch_atoms(atoms)
     vib_kwargs = vib_kwargs or {}
@@ -210,8 +210,8 @@ def freq_job(
         vibrations, additional_fields={"name": "TBLite Frequency"}
     )
 
-    igt = ideal_gas(atoms, vibrations.get_frequencies(), energy=energy)
-    vib_summary["thermo"] = summarize_thermo(
+    igt = run_ideal_gas(atoms, vibrations.get_frequencies(), energy=energy)
+    vib_summary["thermo"] = summarize_igt_thermo(
         igt,
         temperature=temperature,
         pressure=pressure,

src/quacc/runners/thermo.py

@@ -15,7 +15,7 @@
     from ase import Atoms
 
 
-def ideal_gas(
+def run_ideal_gas(
     atoms: Atoms,
     vib_freqs: list[float | complex],
     energy: float = 0.0,

src/quacc/schemas/ase.py

@@ -767,7 +767,7 @@ def summarize_vib_run(
     return task_doc
 
 
-def summarize_thermo(
+def summarize_igt_thermo(
     igt: IdealGasThermo,
     temperature: float = 298.15,
     pressure: float = 1.0,

tests/runners/test_thermo.py

@@ -3,24 +3,24 @@
 from ase.calculators.emt import EMT
 from ase.units import invcm
 
-from quacc.runners.thermo import ideal_gas
+from quacc.runners.thermo import run_ideal_gas
 
 
-def test_ideal_gas():
+def test_run_ideal_gas():
     co2 = molecule("CO2")
-    igt = ideal_gas(co2, [526, 526, 1480, 2565], spin_multiplicity=2)
+    igt = run_ideal_gas(co2, [526, 526, 1480, 2565], spin_multiplicity=2)
     assert igt.geometry == "linear"
     assert igt.spin == 0.5
 
     co2 = molecule("CO2")
     co2.calc = EMT()
     co2.calc.results["magmom"] = 1.0
-    igt = ideal_gas(co2, [526, 526, 1480, 2565])
+    igt = run_ideal_gas(co2, [526, 526, 1480, 2565])
     assert igt.spin == 0.5
     assert igt.get_ZPE_correction() == pytest.approx(2548.5 * invcm)
 
     co2 = molecule("CO2")
     co2.calc = EMT()
     co2.calc.results["magmom"] = 1.0
-    igt = ideal_gas(co2, [-12, 526, 526, 1480, 2565])
+    igt = run_ideal_gas(co2, [-12, 526, 526, 1480, 2565])
     assert igt.get_ZPE_correction() == pytest.approx(2548.5 * invcm)

tests/schemas/test_ase.py

@@ -14,9 +14,9 @@
 from monty.json import MontyDecoder, jsanitize
 
 from quacc.schemas.ase import (
+    summarize_igt_thermo,
     summarize_opt_run,
     summarize_run,
-    summarize_thermo,
     summarize_vib_run,
 )
 
@@ -284,13 +284,13 @@ def test_summarize_vib_run(tmpdir):
     assert len(results["results"]["vib_energies"]) == 6
 
 
-def test_summarize_thermo(tmpdir):
+def test_summarize_igt_thermo(tmpdir):
     tmpdir.chdir()
 
     # Make sure metadata is made
     atoms = molecule("N2")
     igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)
-    results = summarize_thermo(igt)
+    results = summarize_igt_thermo(igt)
     assert results["natoms"] == len(atoms)
     assert results["atoms"] == atoms
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
@@ -301,15 +301,15 @@ def test_summarize_thermo(tmpdir):
     # Test DB
     atoms = molecule("N2")
     igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)
-    summarize_thermo(igt)
+    summarize_igt_thermo(igt)
     store = MemoryStore()
-    summarize_thermo(igt, store=store)
+    summarize_igt_thermo(igt, store=store)
     assert store.count() == 1
 
     # Test remove_empties
     atoms = molecule("N2")
     igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)
-    results = summarize_thermo(igt, remove_empties=True)
+    results = summarize_igt_thermo(igt, remove_empties=True)
     assert results["natoms"] == len(atoms)
     assert results["atoms"] == atoms
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
@@ -322,7 +322,7 @@ def test_summarize_thermo(tmpdir):
     igt = IdealGasThermo(
         [0.0, 0.34], "linear", atoms=atoms, potentialenergy=-1, spin=0, symmetrynumber=2
     )
-    results = summarize_thermo(igt)
+    results = summarize_igt_thermo(igt)
     assert results["natoms"] == len(atoms)
     assert results["atoms"] == atoms
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
@@ -336,7 +336,7 @@ def test_summarize_thermo(tmpdir):
     igt = IdealGasThermo(
         [0.0, 0.34], "linear", atoms=atoms, potentialenergy=-1, spin=0, symmetrynumber=2
     )
-    results = summarize_thermo(igt)
+    results = summarize_igt_thermo(igt)
     assert results.get("atoms_info", {}) != {}
     assert results["atoms_info"].get("test_dict", None) == {"hi": "there", "foo": "bar"}
     assert results["atoms"].info.get("test_dict", None) == {"hi": "there", "foo": "bar"}
@@ -365,7 +365,7 @@ def test_summarize_thermo(tmpdir):
         spin=0.5,
         symmetrynumber=6,
     )
-    results = summarize_thermo(igt, temperature=1000.0, pressure=20.0)
+    results = summarize_igt_thermo(igt, temperature=1000.0, pressure=20.0)
     assert results["natoms"] == len(atoms)
     assert results["atoms"] == atoms
     assert len(results["parameters_thermo"]["vib_energies"]) == 6
@@ -387,7 +387,7 @@ def test_summarize_thermo(tmpdir):
     MontyDecoder().process_decoded(d)
 
     with pytest.raises(ValueError):
-        summarize_thermo(igt, charge_and_multiplicity=[0, 1])
+        summarize_igt_thermo(igt, charge_and_multiplicity=[0, 1])
 
 
 def test_errors(tmpdir):