From ad20604e7a55732ab677a9e50341653bca43d670 Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Tue, 11 Jun 2024 18:08:35 +0100
Subject: [PATCH 01/35] Modify VASP recipes for vibrational analysis

---
 src/quacc/recipes/vasp/_base.py | 36 ++++++++++++++++-
 src/quacc/recipes/vasp/core.py  | 72 +++++++++++++++++++++++++++++++--
 2 files changed, 103 insertions(+), 5 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index bb3bcbe08d..a36540dc97 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -5,9 +5,11 @@
 from typing import TYPE_CHECKING
 
 from quacc.calculators.vasp import Vasp
-from quacc.runners.ase import run_calc, run_opt
+from quacc.runners.ase import run_calc, run_opt, run_vib
 from quacc.schemas.vasp import summarize_vasp_opt_run, vasp_summarize_run
+from quacc.schemas.ase import summarize_vib_and_thermo
 from quacc.utils.dicts import recursive_dict_merge
+from quacc.runners.thermo import run_ideal_gas
 
 if TYPE_CHECKING:
     from typing import Any
@@ -17,6 +19,7 @@
     from quacc.runners.ase import OptParams
     from quacc.schemas._aliases.vasp import VaspASEOptSchema, VaspSchema
     from quacc.utils.files import Filenames, SourceDirectory
+    from quacc.schemas._aliases.ase import VibThermoSchema
 
 
 def run_and_summarize(
@@ -120,3 +123,34 @@ def run_and_summarize_opt(
         report_mp_corrections=report_mp_corrections,
         additional_fields=additional_fields,
     )
+
+def run_and_summarize_vib_and_thermo(
+    atoms: Atoms,
+    energy: float = 0.0,
+    temperature: float = 298.15,
+    pressure: float = 1.0,
+    preset: str | None = None,
+    calc_defaults: dict[str, Any] | None = None,
+    calc_swaps: dict[str, Any] | None = None,
+    vib_kwargs: dict[str, Any] | None = None,
+    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
+) -> VibThermoSchema:
+    """
+    Base job function for VASP recipes with ASE vibrational analysis.
+)
+    """
+
+    # Set defaults    
+    calc_flags = recursive_dict_merge(calc_defaults, calc_swaps)
+
+    atoms.calc = Vasp(atoms, preset=preset, **calc_flags)
+    vibrations = run_vib(atoms, vib_kwargs=vib_kwargs, copy_files=copy_files)
+    igt = run_ideal_gas(atoms, vibrations.get_frequencies(), energy=energy)
+
+    return summarize_vib_and_thermo(
+        vibrations,
+        igt,
+        temperature=temperature,
+        pressure=pressure,
+        additional_fields={"name": "VASP Frequency and Thermo"},
+    )
\ No newline at end of file
diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index a3697ab116..57ec643ae3 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -10,17 +10,16 @@
 from pymatgen.io.vasp import Vasprun
 
 from quacc import flow, job
-from quacc.recipes.vasp._base import run_and_summarize, run_and_summarize_opt
+from quacc.recipes.vasp._base import run_and_summarize, run_and_summarize_opt, run_and_summarize_vib_and_thermo
 
 if TYPE_CHECKING:
     from typing import Any
 
     from ase.atoms import Atoms
-
-    from quacc.runners.ase import OptParams
+    from quacc.runners.ase import OptParams, VibKwargs
     from quacc.schemas._aliases.vasp import VaspASEOptSchema, VaspSchema
     from quacc.utils.files import Filenames, SourceDirectory
-
+    from quacc.schemas._aliases.ase import VibThermoSchema
 
 @job
 def static_job(
@@ -316,3 +315,68 @@ def non_scf_job(
         additional_fields={"name": "VASP Non-SCF"},
         copy_files={prev_dir: ["CHGCAR*", "WAVECAR*"]},
     )
+
+@job
+def freq_job(
+    atoms: Atoms,
+    preset: str | None = "BulkSet",
+    energy: float = 0.0,
+    temperature: float = 298.15,
+    pressure: float = 1.0,
+    vib_kwargs: VibKwargs | None = None,
+    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
+    **calc_kwargs,
+) -> VibThermoSchema:
+    """
+    Run a frequency job and calculate thermochemistry.
+
+    Parameters
+    ----------
+    atoms
+        Atoms object
+    preset 
+        Preset to use from `quacc.calculators.vasp.presets`.
+    energy
+        Potential energy in eV. If 0, then the output is just the correction.
+    temperature
+        Temperature in Kelvins.
+    pressure
+        Pressure in bar.
+    vib_kwargs
+        Dictionary of kwargs for the [ase.vibrations.Vibrations][] class.
+    copy_files
+        Files to copy (and decompress) from source to the runtime directory.
+    **calc_kwargs
+        Custom kwargs for the Vasp calculator. Set a value to
+        `None` to remove a pre-existing key entirely. For a list of available
+        keys, refer to [quacc.calculators.vasp.vasp.Vasp][].
+
+    Returns
+    -------
+    VibThermoSchema
+        Dictionary of results, specified in [quacc.schemas.ase.summarize_vib_and_thermo][].
+        See the type-hint for the data structure.
+    """
+    calc_defaults = {
+        "ediff": 1e-8,
+        "ibrion": -1,
+        "isym": 0,
+        "algo": "all",
+        "lcharg": False,
+        "lwave": True,
+        "nsw": 0,
+    }
+    vib_kwargs = vib_kwargs or {}
+
+    return run_and_summarize_vib_and_thermo(
+        atoms,
+        energy=energy,
+        temperature=temperature,
+        pressure=pressure,
+        preset=preset,
+        calc_defaults=calc_defaults,
+        calc_swaps=calc_kwargs,
+        vib_kwargs=vib_kwargs,
+        copy_files=copy_files,
+        additional_fields={"name": "VASP Frequency and Thermo"},
+    )

From 3000881135b37f909fab0f1b18f36d13d155bb4b Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Wed, 12 Jun 2024 11:10:36 +0100
Subject: [PATCH 02/35] Recipe to compute vibrational frequency

---
 src/quacc/recipes/vasp/_base.py               | 33 +++++++++++++++++--
 src/quacc/recipes/vasp/core.py                |  3 ++
 .../vasp_recipes/mocked/test_vasp_recipes.py  | 12 +++++++
 3 files changed, 46 insertions(+), 2 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index a36540dc97..170cb60396 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -134,10 +134,39 @@ def run_and_summarize_vib_and_thermo(
     calc_swaps: dict[str, Any] | None = None,
     vib_kwargs: dict[str, Any] | None = None,
     copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
+    additional_fields: dict[str, Any] | None = None,
 ) -> VibThermoSchema:
     """
     Base job function for VASP recipes with ASE vibrational analysis.
-)
+
+    Parameters
+    ----------
+    atoms
+        Atoms object
+    energy
+        Energy of the system
+    temperature
+        Temperature of the system
+    pressure
+        Pressure of the system
+    preset  
+        Preset to use from `quacc.calculators.vasp.presets`.
+    calc_defaults
+        Default parameters for the recipe.
+    calc_swaps
+        Dictionary of custom kwargs for the Vasp calculator. Set a value to
+        `None` to remove a pre-existing key entirely. For a list of available
+        keys, refer to [quacc.calculators.vasp.vasp.Vasp][].
+    vib_kwargs
+        Dictionary of custom kwargs for [quacc.runners.ase.run_vib][]
+    copy_files
+        Files to copy (and decompress) from source to the runtime directory.
+
+    Returns
+    -------
+    VibThermoSchema
+        Dictionary of results, specified in [quacc.schemas.ase.summarize_vib_and_thermo][].
+        See the type-hint for the data structure.
     """
 
     # Set defaults    
@@ -152,5 +181,5 @@ def run_and_summarize_vib_and_thermo(
         igt,
         temperature=temperature,
         pressure=pressure,
-        additional_fields={"name": "VASP Frequency and Thermo"},
+        additional_fields=additional_fields,
     )
\ No newline at end of file
diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index 57ec643ae3..5148bdd5c0 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -361,10 +361,13 @@ def freq_job(
         "ediff": 1e-8,
         "ibrion": -1,
         "isym": 0,
+        "istart": 1,
         "algo": "all",
         "lcharg": False,
         "lwave": True,
         "nsw": 0,
+        "ismear": 0,
+        "sigma": 0.05
     }
     vib_kwargs = vib_kwargs or {}
 
diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index 95321405ef..f0400646b1 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -23,6 +23,7 @@
     non_scf_job,
     relax_job,
     static_job,
+    freq_job
 )
 from quacc.recipes.vasp.mp import (
     mp_gga_relax_flow,
@@ -848,3 +849,14 @@ def test_mp_relax_flow_custom(tmp_path, patch_nonmetallic_taskdoc):
             job_params={"mp_metagga_relax_job": {"nsw": 0}},
         )
         assert output["relax2"]["parameters"]["nsw"] == 0
+
+
+def test_freq_job():
+    atoms = molecule("H2")
+    atoms.pbc = True
+    atoms.set_cell([3,3,3])
+    output = freq_job(atoms, kpts = (1,1,1))
+    assert output["parameters"]["ediff"] == 1e-08
+    assert output["parameters"]["sigma"] == 0.05
+    assert output["parameters"]["ismear"] == 0
+    assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)

From 78e567ba050d04489a415a1c670e049377d3c383 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 12 Jun 2024 16:03:56 +0000
Subject: [PATCH 03/35] pre-commit auto-fixes

---
 src/quacc/recipes/vasp/_base.py                     | 13 +++++++++----
 src/quacc/recipes/vasp/core.py                      |  6 ++++--
 .../vasp_recipes/mocked/test_vasp_recipes.py        |  6 +++---
 3 files changed, 16 insertions(+), 9 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index 3a1a85b805..c3f51c93cd 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -124,6 +124,7 @@ def run_and_summarize_opt(
         additional_fields=additional_fields,
     )
 
+
 def run_and_summarize_vib_and_thermo(
     atoms: Atoms,
     energy: float = 0.0,
@@ -149,7 +150,7 @@ def run_and_summarize_vib_and_thermo(
         Temperature of the system
     pressure
         Pressure of the system
-    preset  
+    preset
         Preset to use from `quacc.calculators.vasp.presets`.
     calc_defaults
         Default parameters for the recipe.
@@ -173,8 +174,12 @@ def run_and_summarize_vib_and_thermo(
     calc_flags = recursive_dict_merge(calc_defaults, calc_swaps)
 
     calc = Vasp(atoms, preset=preset, **calc_flags)
-    vibrations = Runner(atoms, calc, copy_files=copy_files).run_vib(vib_kwargs=vib_kwargs)
-    igt = ThermoRunner(atoms, vibrations.get_frequencies(), energy=energy).run_ideal_gas()
+    vibrations = Runner(atoms, calc, copy_files=copy_files).run_vib(
+        vib_kwargs=vib_kwargs
+    )
+    igt = ThermoRunner(
+        atoms, vibrations.get_frequencies(), energy=energy
+    ).run_ideal_gas()
 
     return summarize_vib_and_thermo(
         vibrations,
@@ -182,4 +187,4 @@ def run_and_summarize_vib_and_thermo(
         temperature=temperature,
         pressure=pressure,
         additional_fields=additional_fields,
-    )
\ No newline at end of file
+    )
diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index cfd30d6e03..f7342fd9a2 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -30,6 +30,7 @@
     )
     from quacc.utils.files import Filenames, SourceDirectory
 
+
 @job
 def static_job(
     atoms: Atoms,
@@ -325,6 +326,7 @@ def non_scf_job(
         copy_files={prev_dir: ["CHGCAR*", "WAVECAR*"]},
     )
 
+
 @job
 def freq_job(
     atoms: Atoms,
@@ -343,7 +345,7 @@ def freq_job(
     ----------
     atoms
         Atoms object
-    preset 
+    preset
         Preset to use from `quacc.calculators.vasp.presets`.
     energy
         Potential energy in eV. If 0, then the output is just the correction.
@@ -376,7 +378,7 @@ def freq_job(
         "lwave": True,
         "nsw": 0,
         "ismear": 0,
-        "sigma": 0.05
+        "sigma": 0.05,
     }
     vib_kwargs = vib_kwargs or {}
 
diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index f0400646b1..d87505633c 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -20,10 +20,10 @@
 from quacc.recipes.vasp.core import (
     ase_relax_job,
     double_relax_flow,
+    freq_job,
     non_scf_job,
     relax_job,
     static_job,
-    freq_job
 )
 from quacc.recipes.vasp.mp import (
     mp_gga_relax_flow,
@@ -854,8 +854,8 @@ def test_mp_relax_flow_custom(tmp_path, patch_nonmetallic_taskdoc):
 def test_freq_job():
     atoms = molecule("H2")
     atoms.pbc = True
-    atoms.set_cell([3,3,3])
-    output = freq_job(atoms, kpts = (1,1,1))
+    atoms.set_cell([3, 3, 3])
+    output = freq_job(atoms, kpts=(1, 1, 1))
     assert output["parameters"]["ediff"] == 1e-08
     assert output["parameters"]["sigma"] == 0.05
     assert output["parameters"]["ismear"] == 0

From c90696072bc5dddd636c3c315bbdf4cdf6c6b3a2 Mon Sep 17 00:00:00 2001
From: Andrew Rosen <asrosen93@gmail.com>
Date: Wed, 12 Jun 2024 09:06:39 -0700
Subject: [PATCH 04/35] fix docs

---
 src/quacc/recipes/vasp/_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index 3a1a85b805..e124407e00 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -158,7 +158,7 @@ def run_and_summarize_vib_and_thermo(
         `None` to remove a pre-existing key entirely. For a list of available
         keys, refer to [quacc.calculators.vasp.vasp.Vasp][].
     vib_kwargs
-        Dictionary of custom kwargs for [quacc.runners.ase.run_vib][]
+        Dictionary of custom kwargs for [quacc.runners.ase.Runner.run_vib][]
     copy_files
         Files to copy (and decompress) from source to the runtime directory.
 

From a9e4ea5a9c6476e5ab0d669701cf37aacfe5a8c2 Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Wed, 12 Jun 2024 17:44:09 +0100
Subject: [PATCH 05/35] new_defaults

---
 src/quacc/recipes/vasp/core.py | 5 -----
 1 file changed, 5 deletions(-)

diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index f7342fd9a2..6d54fd3a20 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -370,15 +370,10 @@ def freq_job(
     """
     calc_defaults = {
         "ediff": 1e-8,
-        "ibrion": -1,
         "isym": 0,
-        "istart": 1,
-        "algo": "all",
         "lcharg": False,
         "lwave": True,
         "nsw": 0,
-        "ismear": 0,
-        "sigma": 0.05,
     }
     vib_kwargs = vib_kwargs or {}
 

From 48e584f65e5556001eddbac5080b8e4f09d63617 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 12 Jun 2024 16:45:33 +0000
Subject: [PATCH 06/35] pre-commit auto-fixes

---
 src/quacc/recipes/vasp/core.py | 8 +-------
 1 file changed, 1 insertion(+), 7 deletions(-)

diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index 6d54fd3a20..8a98e8b1c9 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -368,13 +368,7 @@ def freq_job(
         Dictionary of results, specified in [quacc.schemas.ase.summarize_vib_and_thermo][].
         See the type-hint for the data structure.
     """
-    calc_defaults = {
-        "ediff": 1e-8,
-        "isym": 0,
-        "lcharg": False,
-        "lwave": True,
-        "nsw": 0,
-    }
+    calc_defaults = {"ediff": 1e-8, "isym": 0, "lcharg": False, "lwave": True, "nsw": 0}
     vib_kwargs = vib_kwargs or {}
 
     return run_and_summarize_vib_and_thermo(

From eacce405d50b9569447bef02398741679ad0fa9c Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Mon, 24 Jun 2024 11:39:05 +0100
Subject: [PATCH 07/35] Incorporate Harmonic approximation analysis

---
 docs/about/contributors.md                    |  1 +
 docs/user/recipes/recipes_list.md             |  1 +
 src/quacc/recipes/vasp/_base.py               | 17 ++--
 src/quacc/recipes/vasp/core.py                |  4 +-
 src/quacc/runners/thermo.py                   | 22 +++++-
 src/quacc/schemas/ase.py                      | 79 ++++++++++++++++---
 .../vasp_recipes/mocked/test_vasp_recipes.py  |  2 +-
 tests/core/runners/test_thermo.py             | 10 +++
 tests/core/schemas/test_ase.py                | 27 ++++++-
 9 files changed, 144 insertions(+), 19 deletions(-)

diff --git a/docs/about/contributors.md b/docs/about/contributors.md
index b5dbf78fd3..3dc99f7083 100644
--- a/docs/about/contributors.md
+++ b/docs/about/contributors.md
@@ -28,6 +28,7 @@ Additional contributions were made by the individuals listed [here](https://gith
 - [@yw-fang](https://github.com/yw-fang): VASP Non-SCF recipe
 - [@espottesmith](http://github.com/espottesmith): Some ORCA and Q-Chem workflows, mostly re: IRC
 - [@honghuikim](https://github.com/honghuikim): Dynamic changing of quacc settings with workflow engines
+- [@benshi97](https://github.com/benshi97): VASP frequency recipe
 
 ## Inspiration
 
diff --git a/docs/user/recipes/recipes_list.md b/docs/user/recipes/recipes_list.md
index 9085e09417..484a8ab2f3 100644
--- a/docs/user/recipes/recipes_list.md
+++ b/docs/user/recipes/recipes_list.md
@@ -251,6 +251,7 @@ The list of available quacc recipes is shown below. The "Req'd Extras" column sp
 | VASP Non-SCF                    | `#!Python @job`  | [quacc.recipes.vasp.core.non_scf_job][]         |              |
 | VASP Slab Static                | `#!Python @job`  | [quacc.recipes.vasp.slabs.static_job][]         |              |
 | VASP Slab Relax                 | `#!Python @job`  | [quacc.recipes.vasp.slabs.relax_job][]          |              |
+| VASP Frequency                  | `#!Python @job`  | [quacc.recipes.vasp.slabs.freq_job][]          |              |
 | VASP Bulk to Slabs              | `#!Python @flow` | [quacc.recipes.vasp.slabs.bulk_to_slabs_flow][] |              |
 | VASP Slab to Adsorbates         | `#!Python @flow` | [quacc.recipes.vasp.slabs.slab_to_ads_flow][]   |              |
 | VASP MP GGA Relax               | `#!Python @job`  | [quacc.recipes.vasp.mp.mp_gga_relax_job][]      | `quacc[mp]`  |
diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index 3ab6f67413..5e9a0a5817 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -12,7 +12,7 @@
 from quacc.utils.dicts import recursive_dict_merge
 
 if TYPE_CHECKING:
-    from typing import Any
+    from typing import Any, Literal
 
     from ase.atoms import Atoms
 
@@ -130,6 +130,7 @@ def run_and_summarize_vib_and_thermo(
     energy: float = 0.0,
     temperature: float = 298.15,
     pressure: float = 1.0,
+    thermo_method: Literal["ideal_gas", "harmonic"] = "ideal_gas",
     preset: str | None = None,
     calc_defaults: dict[str, Any] | None = None,
     calc_swaps: dict[str, Any] | None = None,
@@ -177,13 +178,19 @@ def run_and_summarize_vib_and_thermo(
     vibrations = Runner(atoms, calc, copy_files=copy_files).run_vib(
         vib_kwargs=vib_kwargs
     )
-    igt = ThermoRunner(
-        atoms, vibrations.get_frequencies(), energy=energy
-    ).run_ideal_gas()
+    if thermo_method == "harmonic":
+        thermo_analysis = ThermoRunner(
+            atoms, vibrations.get_frequencies(), energy=energy
+        ).run_harmonic()
+    elif thermo_method == "ideal_gas":
+        thermo_analysis = ThermoRunner(
+            atoms, vibrations.get_frequencies(), energy=energy
+        ).run_ideal_gas()
+
 
     return summarize_vib_and_thermo(
         vibrations,
-        igt,
+        thermo_analysis,
         temperature=temperature,
         pressure=pressure,
         additional_fields=additional_fields,
diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index 8a98e8b1c9..2ff7a4ae7c 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -334,6 +334,7 @@ def freq_job(
     energy: float = 0.0,
     temperature: float = 298.15,
     pressure: float = 1.0,
+    thermo_method: Literal["harmonic","ideal_gas"] = "ideal_gas",
     vib_kwargs: VibKwargs | None = None,
     copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
     **calc_kwargs,
@@ -368,7 +369,7 @@ def freq_job(
         Dictionary of results, specified in [quacc.schemas.ase.summarize_vib_and_thermo][].
         See the type-hint for the data structure.
     """
-    calc_defaults = {"ediff": 1e-8, "isym": 0, "lcharg": False, "lwave": True, "nsw": 0}
+    calc_defaults = {"ediff": 1e-7, "isym": 0, "lcharg": False, "lwave": True, "nsw": 0}
     vib_kwargs = vib_kwargs or {}
 
     return run_and_summarize_vib_and_thermo(
@@ -376,6 +377,7 @@ def freq_job(
         energy=energy,
         temperature=temperature,
         pressure=pressure,
+        thermo_method=thermo_method,
         preset=preset,
         calc_defaults=calc_defaults,
         calc_swaps=calc_kwargs,
diff --git a/src/quacc/runners/thermo.py b/src/quacc/runners/thermo.py
index 3a9c2c9034..afb11b78fd 100644
--- a/src/quacc/runners/thermo.py
+++ b/src/quacc/runners/thermo.py
@@ -7,7 +7,7 @@
 
 import numpy as np
 from ase import units
-from ase.thermochemistry import IdealGasThermo
+from ase.thermochemistry import IdealGasThermo, HarmonicThermo
 from emmet.core.symmetry import PointGroupData
 from pymatgen.io.ase import AseAtomsAdaptor
 
@@ -103,3 +103,23 @@ def run_ideal_gas(self, spin_multiplicity: int | None = None) -> IdealGasThermo:
             spin=spin,
             ignore_imag_modes=True,
         )
+    
+    def run_harmonic_thermo(self) -> HarmonicThermo:
+        """
+        Create a HarmonicThermo object for a molecule from a given vibrational analysis.
+        This works for free gases, solids and adsorbates.
+
+        Returns
+        -------
+        HarmonicThermo object
+        """
+
+        # Ensure all negative modes are made complex
+        for i, f in enumerate(self.vib_freqs):
+            if not isinstance(f, complex) and f < 0:
+                self.vib_freqs[i] = complex(0 - f * 1j)
+
+        # Convert vibrational frequencies to energies
+        vib_energies = [f * units.invcm for f in self.vib_freqs]
+
+        return HarmonicThermo(vib_energies=vib_energies, potentialenergy=self.energy, ignore_imag_modes=True)
diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index 33d18bc048..e3c0823d81 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -23,7 +23,7 @@
     from ase.atoms import Atoms
     from ase.io import Trajectory
     from ase.optimize.optimize import Optimizer
-    from ase.thermochemistry import IdealGasThermo
+    from ase.thermochemistry import IdealGasThermo, HarmonicThermo
     from maggma.core import Store
 
     from quacc.schemas._aliases.ase import (
@@ -215,7 +215,7 @@ def summarize_opt_run(
 
 def summarize_vib_and_thermo(
     vib: Vibrations,
-    igt: IdealGasThermo,
+    thermo_analysis: IdealGasThermo | HarmonicThermo,
     temperature: float = 298.15,
     pressure: float = 1.0,
     charge_and_multiplicity: tuple[int, int] | None = None,
@@ -230,8 +230,8 @@ def summarize_vib_and_thermo(
     ----------
     vib
         ASE Vibrations object.
-    igt
-        ASE IdealGasThermo object.
+    thermo_analysis
+        ASE IdealGasThermo or HarmonicThermo object.
     temperature
         Temperature in Kelvins.
     pressure
@@ -255,12 +255,20 @@ def summarize_vib_and_thermo(
     vib_task_doc = _summarize_vib_run(
         vib, charge_and_multiplicity=charge_and_multiplicity
     )
-    thermo_task_doc = _summarize_ideal_gas_thermo(
-        igt,
-        temperature=temperature,
-        pressure=pressure,
-        charge_and_multiplicity=charge_and_multiplicity,
-    )
+
+    if isinstance(thermo_analysis, HarmonicThermo):
+        thermo_task_doc = _summarize_harmonic_thermo(
+            ht=thermo_analysis,
+            temperature=temperature,
+            pressure=pressure,
+        )
+    elif isinstance(thermo_analysis, IdealGasThermo):
+        thermo_task_doc = _summarize_ideal_gas_thermo(
+            igt=thermo_analysis,
+            temperature=temperature,
+            pressure=pressure,
+            charge_and_multiplicity=charge_and_multiplicity,
+        )
 
     unsorted_task_doc = recursive_dict_merge(
         vib_task_doc, thermo_task_doc, additional_fields
@@ -437,3 +445,54 @@ def _summarize_ideal_gas_thermo(
     )
 
     return atoms_metadata | inputs | results
+
+def _summarize_harmonic_thermo(
+    ht: HarmonicThermo,
+    temperature: float = 298.15,
+    pressure: float = 1.0,
+) -> ThermoSchema:
+    """
+    Get tabulated results from an ASE HarmonicThermo object and store them in a
+    database-friendly format.
+
+    Parameters
+    ----------
+    ht
+        ASE HarmonicThermo object.
+    temperature
+        Temperature in Kelvins.
+    pressure
+        Pressure in bar.
+
+    Returns
+    -------
+    ThermoSchema
+        Dictionary representation of the task document
+    """
+    settings = get_settings()
+
+    inputs = {
+        "parameters_thermo": {
+            "temperature": temperature,
+            "pressure": pressure,
+            "vib_freqs": [e / units.invcm for e in ht.vib_energies],
+            "vib_energies": ht.vib_energies.tolist(),
+            "n_imag": ht.n_imag,
+        }
+    }
+
+    results = {
+        "results": {
+            "energy": ht.potentialenergy,
+            "helmholtz_energy": ht.get_helmholtz_energy(temperature, verbose=settings.DEBUG),
+            "internal_energy": ht.get_internal_energy(temperature, verbose=settings.DEBUG),
+            "entropy": ht.get_entropy(
+                temperature, verbose=settings.DEBUG
+            ),
+            "zpe": ht.get_ZPE_correction(),
+        }
+    }
+
+    atoms_metadata = {}
+
+    return atoms_metadata | inputs | results
\ No newline at end of file
diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index 31bc07217e..9055d2ba71 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -855,7 +855,7 @@ def test_mp_relax_flow_custom(tmp_path, patch_nonmetallic_taskdoc):
 def test_freq_job():
     atoms = molecule("H2")
     atoms.pbc = True
-    atoms.set_cell([3, 3, 3])
+    atoms.center(vacuum=1)
     output = freq_job(atoms, kpts=(1, 1, 1))
     assert output["parameters"]["ediff"] == 1e-08
     assert output["parameters"]["sigma"] == 0.05
diff --git a/tests/core/runners/test_thermo.py b/tests/core/runners/test_thermo.py
index b81d02b235..7ccb87f96f 100644
--- a/tests/core/runners/test_thermo.py
+++ b/tests/core/runners/test_thermo.py
@@ -26,3 +26,13 @@ def test_run_ideal_gas():
     co2.calc.results["magmom"] = 1.0
     igt = ThermoRunner(co2, [-12, 526, 526, 1480, 2565]).run_ideal_gas()
     assert igt.get_ZPE_correction() == pytest.approx(2548.5 * invcm)
+
+
+def test_run_harmonic_thermo():
+    co2 = molecule("CO2")
+    ht = ThermoRunner(co2, [526, 526, 1480, 2565]).run_harmonic_thermo()
+    assert ht.get_ZPE_correction() == pytest.approx(2548.5 * invcm)
+
+    co2 = molecule("CO2")
+    ht = ThermoRunner(co2, [-12, 526, 526, 1480, 2565]).run_harmonic_thermo()
+    assert ht.get_ZPE_correction() == pytest.approx(2548.5 * invcm)
\ No newline at end of file
diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index 34b98fd284..2035ca09d9 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -5,11 +5,13 @@
 from pathlib import Path
 
 import pytest
+
+from numpy.testing import assert_allclose as assert_close
 from ase.build import bulk, molecule
 from ase.calculators.emt import EMT
 from ase.io import read
 from ase.optimize import BFGS
-from ase.thermochemistry import IdealGasThermo
+from ase.thermochemistry import IdealGasThermo, HarmonicThermo
 from ase.units import invcm
 from ase.vibrations import Vibrations
 from maggma.stores import MemoryStore
@@ -18,6 +20,7 @@
 
 from quacc.schemas.ase import (
     _summarize_ideal_gas_thermo,
+    _summarize_harmonic_thermo,
     _summarize_vib_run,
     summarize_opt_run,
     summarize_run,
@@ -345,6 +348,28 @@ def test_summarize_ideal_gas_thermo(tmp_path, monkeypatch):
         _summarize_ideal_gas_thermo(igt, charge_and_multiplicity=[0, 1])
 
 
+def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
+    monkeypatch.chdir(tmp_path)
+
+    # Make sure metadata is made
+    ht = HarmonicThermo([0.34])
+    results = _summarize_harmonic_thermo(ht)
+    assert results["parameters_thermo"]["vib_energies"] == [0.34]
+    assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
+    assert results["results"]["energy"] == 0
+    assert_close(results["results"]["helmholtz_energy"], 0.16999995401497991,rtol=1e-5)
+    assert_close(results["results"]["internal_energy"], 0.1700006085385999,rtol=1e-5)
+    assert_close(results["results"]["entropy"], 2.1952829783392438e-09,rtol=1e-5)
+    assert_close(results["results"]["zpe"], 0.17,rtol=1e-5)
+
+
+    # test document can be jsanitized and decoded
+    d = jsanitize(results, strict=True, enum_values=True)
+    MontyDecoder().process_decoded(d)
+
+
+
+
 def test_errors(tmp_path, monkeypatch):
     monkeypatch.chdir(tmp_path)
 

From 128cdeb67de2800728061798d044de15f48eb9bd Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 24 Jun 2024 10:39:17 +0000
Subject: [PATCH 08/35] pre-commit auto-fixes

---
 src/quacc/recipes/vasp/_base.py   |  1 -
 src/quacc/recipes/vasp/core.py    |  2 +-
 src/quacc/runners/thermo.py       | 10 +++++++---
 src/quacc/schemas/ase.py          | 21 ++++++++++-----------
 tests/core/runners/test_thermo.py |  2 +-
 tests/core/schemas/test_ase.py    | 18 +++++++-----------
 6 files changed, 26 insertions(+), 28 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index 5e9a0a5817..e3644cb7a6 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -187,7 +187,6 @@ def run_and_summarize_vib_and_thermo(
             atoms, vibrations.get_frequencies(), energy=energy
         ).run_ideal_gas()
 
-
     return summarize_vib_and_thermo(
         vibrations,
         thermo_analysis,
diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index 2ff7a4ae7c..8dee078388 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -334,7 +334,7 @@ def freq_job(
     energy: float = 0.0,
     temperature: float = 298.15,
     pressure: float = 1.0,
-    thermo_method: Literal["harmonic","ideal_gas"] = "ideal_gas",
+    thermo_method: Literal["harmonic", "ideal_gas"] = "ideal_gas",
     vib_kwargs: VibKwargs | None = None,
     copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
     **calc_kwargs,
diff --git a/src/quacc/runners/thermo.py b/src/quacc/runners/thermo.py
index afb11b78fd..09113b9ed2 100644
--- a/src/quacc/runners/thermo.py
+++ b/src/quacc/runners/thermo.py
@@ -7,7 +7,7 @@
 
 import numpy as np
 from ase import units
-from ase.thermochemistry import IdealGasThermo, HarmonicThermo
+from ase.thermochemistry import HarmonicThermo, IdealGasThermo
 from emmet.core.symmetry import PointGroupData
 from pymatgen.io.ase import AseAtomsAdaptor
 
@@ -103,7 +103,7 @@ def run_ideal_gas(self, spin_multiplicity: int | None = None) -> IdealGasThermo:
             spin=spin,
             ignore_imag_modes=True,
         )
-    
+
     def run_harmonic_thermo(self) -> HarmonicThermo:
         """
         Create a HarmonicThermo object for a molecule from a given vibrational analysis.
@@ -122,4 +122,8 @@ def run_harmonic_thermo(self) -> HarmonicThermo:
         # Convert vibrational frequencies to energies
         vib_energies = [f * units.invcm for f in self.vib_freqs]
 
-        return HarmonicThermo(vib_energies=vib_energies, potentialenergy=self.energy, ignore_imag_modes=True)
+        return HarmonicThermo(
+            vib_energies=vib_energies,
+            potentialenergy=self.energy,
+            ignore_imag_modes=True,
+        )
diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index e3c0823d81..49b5a5f9f5 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -7,6 +7,7 @@
 import numpy as np
 from ase import units
 from ase.io import read
+from ase.thermochemistry import HarmonicThermo, IdealGasThermo
 from ase.vibrations import Vibrations
 from ase.vibrations.data import VibrationsData
 
@@ -23,7 +24,6 @@
     from ase.atoms import Atoms
     from ase.io import Trajectory
     from ase.optimize.optimize import Optimizer
-    from ase.thermochemistry import IdealGasThermo, HarmonicThermo
     from maggma.core import Store
 
     from quacc.schemas._aliases.ase import (
@@ -258,9 +258,7 @@ def summarize_vib_and_thermo(
 
     if isinstance(thermo_analysis, HarmonicThermo):
         thermo_task_doc = _summarize_harmonic_thermo(
-            ht=thermo_analysis,
-            temperature=temperature,
-            pressure=pressure,
+            ht=thermo_analysis, temperature=temperature, pressure=pressure
         )
     elif isinstance(thermo_analysis, IdealGasThermo):
         thermo_task_doc = _summarize_ideal_gas_thermo(
@@ -446,10 +444,9 @@ def _summarize_ideal_gas_thermo(
 
     return atoms_metadata | inputs | results
 
+
 def _summarize_harmonic_thermo(
-    ht: HarmonicThermo,
-    temperature: float = 298.15,
-    pressure: float = 1.0,
+    ht: HarmonicThermo, temperature: float = 298.15, pressure: float = 1.0
 ) -> ThermoSchema:
     """
     Get tabulated results from an ASE HarmonicThermo object and store them in a
@@ -484,15 +481,17 @@ def _summarize_harmonic_thermo(
     results = {
         "results": {
             "energy": ht.potentialenergy,
-            "helmholtz_energy": ht.get_helmholtz_energy(temperature, verbose=settings.DEBUG),
-            "internal_energy": ht.get_internal_energy(temperature, verbose=settings.DEBUG),
-            "entropy": ht.get_entropy(
+            "helmholtz_energy": ht.get_helmholtz_energy(
+                temperature, verbose=settings.DEBUG
+            ),
+            "internal_energy": ht.get_internal_energy(
                 temperature, verbose=settings.DEBUG
             ),
+            "entropy": ht.get_entropy(temperature, verbose=settings.DEBUG),
             "zpe": ht.get_ZPE_correction(),
         }
     }
 
     atoms_metadata = {}
 
-    return atoms_metadata | inputs | results
\ No newline at end of file
+    return atoms_metadata | inputs | results
diff --git a/tests/core/runners/test_thermo.py b/tests/core/runners/test_thermo.py
index 7ccb87f96f..722cd36888 100644
--- a/tests/core/runners/test_thermo.py
+++ b/tests/core/runners/test_thermo.py
@@ -35,4 +35,4 @@ def test_run_harmonic_thermo():
 
     co2 = molecule("CO2")
     ht = ThermoRunner(co2, [-12, 526, 526, 1480, 2565]).run_harmonic_thermo()
-    assert ht.get_ZPE_correction() == pytest.approx(2548.5 * invcm)
\ No newline at end of file
+    assert ht.get_ZPE_correction() == pytest.approx(2548.5 * invcm)
diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index 2035ca09d9..54717053f4 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -5,22 +5,21 @@
 from pathlib import Path
 
 import pytest
-
-from numpy.testing import assert_allclose as assert_close
 from ase.build import bulk, molecule
 from ase.calculators.emt import EMT
 from ase.io import read
 from ase.optimize import BFGS
-from ase.thermochemistry import IdealGasThermo, HarmonicThermo
+from ase.thermochemistry import HarmonicThermo, IdealGasThermo
 from ase.units import invcm
 from ase.vibrations import Vibrations
 from maggma.stores import MemoryStore
 from monty.json import MontyDecoder, jsanitize
 from monty.serialization import loadfn
+from numpy.testing import assert_allclose as assert_close
 
 from quacc.schemas.ase import (
-    _summarize_ideal_gas_thermo,
     _summarize_harmonic_thermo,
+    _summarize_ideal_gas_thermo,
     _summarize_vib_run,
     summarize_opt_run,
     summarize_run,
@@ -357,19 +356,16 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0
-    assert_close(results["results"]["helmholtz_energy"], 0.16999995401497991,rtol=1e-5)
-    assert_close(results["results"]["internal_energy"], 0.1700006085385999,rtol=1e-5)
-    assert_close(results["results"]["entropy"], 2.1952829783392438e-09,rtol=1e-5)
-    assert_close(results["results"]["zpe"], 0.17,rtol=1e-5)
-
+    assert_close(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
+    assert_close(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
+    assert_close(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
+    assert_close(results["results"]["zpe"], 0.17, rtol=1e-5)
 
     # test document can be jsanitized and decoded
     d = jsanitize(results, strict=True, enum_values=True)
     MontyDecoder().process_decoded(d)
 
 
-
-
 def test_errors(tmp_path, monkeypatch):
     monkeypatch.chdir(tmp_path)
 

From 0d3436d409cb3432c006f74f9f2397ad2833bf63 Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Mon, 24 Jun 2024 11:43:00 +0100
Subject: [PATCH 09/35] Fix recipe docs

---
 docs/user/recipes/recipes_list.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/docs/user/recipes/recipes_list.md b/docs/user/recipes/recipes_list.md
index 484a8ab2f3..a9e9623b57 100644
--- a/docs/user/recipes/recipes_list.md
+++ b/docs/user/recipes/recipes_list.md
@@ -251,7 +251,7 @@ The list of available quacc recipes is shown below. The "Req'd Extras" column sp
 | VASP Non-SCF                    | `#!Python @job`  | [quacc.recipes.vasp.core.non_scf_job][]         |              |
 | VASP Slab Static                | `#!Python @job`  | [quacc.recipes.vasp.slabs.static_job][]         |              |
 | VASP Slab Relax                 | `#!Python @job`  | [quacc.recipes.vasp.slabs.relax_job][]          |              |
-| VASP Frequency                  | `#!Python @job`  | [quacc.recipes.vasp.slabs.freq_job][]          |              |
+| VASP Frequency                  | `#!Python @job`  | [quacc.recipes.vasp.core.freq_job][]          |              |
 | VASP Bulk to Slabs              | `#!Python @flow` | [quacc.recipes.vasp.slabs.bulk_to_slabs_flow][] |              |
 | VASP Slab to Adsorbates         | `#!Python @flow` | [quacc.recipes.vasp.slabs.slab_to_ads_flow][]   |              |
 | VASP MP GGA Relax               | `#!Python @job`  | [quacc.recipes.vasp.mp.mp_gga_relax_job][]      | `quacc[mp]`  |

From 44626fb1dd6ef4e1e34c90966b0534c75a9393bc Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Mon, 24 Jun 2024 11:49:26 +0100
Subject: [PATCH 10/35] Update tests

---
 tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index 9055d2ba71..b76062ecd8 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -857,7 +857,5 @@ def test_freq_job():
     atoms.pbc = True
     atoms.center(vacuum=1)
     output = freq_job(atoms, kpts=(1, 1, 1))
-    assert output["parameters"]["ediff"] == 1e-08
-    assert output["parameters"]["sigma"] == 0.05
-    assert output["parameters"]["ismear"] == 0
+    assert output["parameters"]["ediff"] == 1e-07
     assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)

From 97b38442bcad612176511c87499fd0b96851bc39 Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Fri, 28 Jun 2024 18:26:09 +0200
Subject: [PATCH 11/35] Better documentation and unit tests

---
 src/quacc/recipes/vasp/_base.py               | 13 +++++--
 src/quacc/recipes/vasp/core.py                |  2 +
 src/quacc/runners/thermo.py                   |  1 +
 src/quacc/schemas/ase.py                      | 13 +++++--
 src/quacc/schemas/vasp.py                     |  2 +-
 .../vasp_recipes/mocked/test_vasp_recipes.py  | 15 +++++++
 tests/core/schemas/test_ase.py                | 39 ++++++++++++++++++-
 7 files changed, 76 insertions(+), 9 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index e3644cb7a6..beb63e8ad9 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -135,8 +135,8 @@ def run_and_summarize_vib_and_thermo(
     calc_defaults: dict[str, Any] | None = None,
     calc_swaps: dict[str, Any] | None = None,
     vib_kwargs: dict[str, Any] | None = None,
-    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
     additional_fields: dict[str, Any] | None = None,
+    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None
 ) -> VibThermoSchema:
     """
     Base job function for VASP recipes with ASE vibrational analysis.
@@ -151,6 +151,8 @@ def run_and_summarize_vib_and_thermo(
         Temperature of the system
     pressure
         Pressure of the system
+    thermo_method
+        Method to use for thermochemistry. Options are "harmonic" or "ideal_gas".
     preset
         Preset to use from `quacc.calculators.vasp.presets`.
     calc_defaults
@@ -161,6 +163,8 @@ def run_and_summarize_vib_and_thermo(
         keys, refer to [quacc.calculators.vasp.vasp.Vasp][].
     vib_kwargs
         Dictionary of custom kwargs for [quacc.runners.ase.Runner.run_vib][]
+    additional_fields
+        Additional fields to supply to the summarizer.
     copy_files
         Files to copy (and decompress) from source to the runtime directory.
 
@@ -181,15 +185,16 @@ def run_and_summarize_vib_and_thermo(
     if thermo_method == "harmonic":
         thermo_analysis = ThermoRunner(
             atoms, vibrations.get_frequencies(), energy=energy
-        ).run_harmonic()
+        ).run_harmonic_thermo()
     elif thermo_method == "ideal_gas":
         thermo_analysis = ThermoRunner(
             atoms, vibrations.get_frequencies(), energy=energy
         ).run_ideal_gas()
 
     return summarize_vib_and_thermo(
-        vibrations,
-        thermo_analysis,
+        vib = vibrations,
+        thermo_analysis = thermo_analysis,
+        atoms = atoms,
         temperature=temperature,
         pressure=pressure,
         additional_fields=additional_fields,
diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index 8dee078388..2b39f1bd00 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -354,6 +354,8 @@ def freq_job(
         Temperature in Kelvins.
     pressure
         Pressure in bar.
+    thermo_method
+        Method to use for thermochemistry. Options are "harmonic" or "ideal_gas".
     vib_kwargs
         Dictionary of kwargs for the [ase.vibrations.Vibrations][] class.
     copy_files
diff --git a/src/quacc/runners/thermo.py b/src/quacc/runners/thermo.py
index 09113b9ed2..2fe2a840bb 100644
--- a/src/quacc/runners/thermo.py
+++ b/src/quacc/runners/thermo.py
@@ -112,6 +112,7 @@ def run_harmonic_thermo(self) -> HarmonicThermo:
         Returns
         -------
         HarmonicThermo object
+            The ASE `HarmonicThermo` object.
         """
 
         # Ensure all negative modes are made complex
diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index 49b5a5f9f5..123a747efe 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -216,6 +216,7 @@ def summarize_opt_run(
 def summarize_vib_and_thermo(
     vib: Vibrations,
     thermo_analysis: IdealGasThermo | HarmonicThermo,
+    atoms: Atoms | None = None,
     temperature: float = 298.15,
     pressure: float = 1.0,
     charge_and_multiplicity: tuple[int, int] | None = None,
@@ -232,6 +233,8 @@ def summarize_vib_and_thermo(
         ASE Vibrations object.
     thermo_analysis
         ASE IdealGasThermo or HarmonicThermo object.
+    atoms
+        ASE Atoms object following a calculation.
     temperature
         Temperature in Kelvins.
     pressure
@@ -258,7 +261,7 @@ def summarize_vib_and_thermo(
 
     if isinstance(thermo_analysis, HarmonicThermo):
         thermo_task_doc = _summarize_harmonic_thermo(
-            ht=thermo_analysis, temperature=temperature, pressure=pressure
+            atoms=atoms, ht=thermo_analysis, temperature=temperature, pressure=pressure
         )
     elif isinstance(thermo_analysis, IdealGasThermo):
         thermo_task_doc = _summarize_ideal_gas_thermo(
@@ -446,6 +449,7 @@ def _summarize_ideal_gas_thermo(
 
 
 def _summarize_harmonic_thermo(
+    atoms: Atoms,
     ht: HarmonicThermo, temperature: float = 298.15, pressure: float = 1.0
 ) -> ThermoSchema:
     """
@@ -454,6 +458,8 @@ def _summarize_harmonic_thermo(
 
     Parameters
     ----------
+    atoms
+        ASE Atoms object used for the vibrational frequency calculation.
     ht
         ASE HarmonicThermo object.
     temperature
@@ -492,6 +498,7 @@ def _summarize_harmonic_thermo(
         }
     }
 
-    atoms_metadata = {}
-
+    atoms_metadata = atoms_to_metadata(
+        atoms
+    )
     return atoms_metadata | inputs | results
diff --git a/src/quacc/schemas/vasp.py b/src/quacc/schemas/vasp.py
index 75d11e97de..c08878c4ac 100644
--- a/src/quacc/schemas/vasp.py
+++ b/src/quacc/schemas/vasp.py
@@ -233,7 +233,7 @@ def summarize_vasp_opt_run(
         store=None,
     )
     vasp_summary = vasp_summarize_run(
-        final_atoms,
+        input_atoms = input_atoms,
         directory=directory,
         move_magmoms=move_magmoms,
         run_bader=run_bader,
diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index b76062ecd8..283a5e1498 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -853,9 +853,24 @@ def test_mp_relax_flow_custom(tmp_path, patch_nonmetallic_taskdoc):
 
 
 def test_freq_job():
+    atoms = molecule("H2")
+    atoms.pbc = True
+    atoms.center(vacuum=1)
+    output = freq_job(atoms, kpts=(1, 1, 1), thermo_method='harmonic')
+    assert output["parameters"]["ediff"] == 1e-07
+    # Check that "sigma" (only used in ideal_gas) isn't a key in parameters_thermo
+    assert "sigma" not in output["parameters_thermo"]
+    assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)
+
+
     atoms = molecule("H2")
     atoms.pbc = True
     atoms.center(vacuum=1)
     output = freq_job(atoms, kpts=(1, 1, 1))
     assert output["parameters"]["ediff"] == 1e-07
+    # Check that parmeters_thermo contains
+    assert output["parameters_thermo"]["sigma"] == 2.0
     assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)
+    assert len(output["results"]["vib_freqs"]) == 3 * len(atoms) - 5
+
+
diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index 54717053f4..13c3cc5345 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -23,6 +23,7 @@
     _summarize_vib_run,
     summarize_opt_run,
     summarize_run,
+    summarize_vib_and_thermo
 )
 
 FILE_DIR = Path(__file__).parent
@@ -349,10 +350,11 @@ def test_summarize_ideal_gas_thermo(tmp_path, monkeypatch):
 
 def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
     monkeypatch.chdir(tmp_path)
+    atoms = molecule("H2")
 
     # Make sure metadata is made
     ht = HarmonicThermo([0.34])
-    results = _summarize_harmonic_thermo(ht)
+    results = _summarize_harmonic_thermo(atoms=atoms, ht = ht)
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0
@@ -365,6 +367,41 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
     d = jsanitize(results, strict=True, enum_values=True)
     MontyDecoder().process_decoded(d)
 
+def test_summarize_vib_and_thermo(tmp_path,monkeypatch):
+    monkeypatch.chdir(tmp_path)
+
+    # Test harmonic thermo for the thermo_analysis procedure
+    atoms = molecule("H2")
+    atoms.calc = EMT()
+
+    ht = HarmonicThermo([0.34])
+    vib = Vibrations(atoms)
+    vib.run()
+    results = summarize_vib_and_thermo(vib=vib,thermo_analysis=ht,atoms=atoms)
+
+    assert results["parameters_thermo"]["vib_energies"] == [0.34]
+    assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
+    assert results["results"]["energy"] == 0
+    assert_close(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
+    assert_close(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
+    assert_close(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
+    assert_close(results["results"]["zpe"], 0.17, rtol=1e-5)
+
+    # Test ideal gas thermo for the thermo_analysis procedure
+    atoms = molecule("N2")
+    atoms.calc = EMT()
+    igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)
+    results = summarize_vib_and_thermo(vib=None,thermo_analysis=igt,atoms=atoms)
+
+    assert results["natoms"] == len(atoms)
+    assert results["atoms"] == atoms
+    assert results["parameters_thermo"]["vib_energies"] == [0.34]
+    assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
+    assert results["results"]["energy"] == 0
+    assert "pymatgen_version" in results["builder_meta"]
+
+    
+
 
 def test_errors(tmp_path, monkeypatch):
     monkeypatch.chdir(tmp_path)

From 0c6d06711386eacca877fe212f26f7d6e59a98fa Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 28 Jun 2024 16:27:04 +0000
Subject: [PATCH 12/35] pre-commit auto-fixes

---
 src/quacc/recipes/vasp/_base.py                     |  8 ++++----
 src/quacc/schemas/ase.py                            |  7 ++-----
 src/quacc/schemas/vasp.py                           |  2 +-
 .../vasp_recipes/mocked/test_vasp_recipes.py        |  5 +----
 tests/core/schemas/test_ase.py                      | 13 ++++++-------
 5 files changed, 14 insertions(+), 21 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index beb63e8ad9..c3fb0b3ee2 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -136,7 +136,7 @@ def run_and_summarize_vib_and_thermo(
     calc_swaps: dict[str, Any] | None = None,
     vib_kwargs: dict[str, Any] | None = None,
     additional_fields: dict[str, Any] | None = None,
-    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None
+    copy_files: SourceDirectory | dict[SourceDirectory, Filenames] | None = None,
 ) -> VibThermoSchema:
     """
     Base job function for VASP recipes with ASE vibrational analysis.
@@ -192,9 +192,9 @@ def run_and_summarize_vib_and_thermo(
         ).run_ideal_gas()
 
     return summarize_vib_and_thermo(
-        vib = vibrations,
-        thermo_analysis = thermo_analysis,
-        atoms = atoms,
+        vib=vibrations,
+        thermo_analysis=thermo_analysis,
+        atoms=atoms,
         temperature=temperature,
         pressure=pressure,
         additional_fields=additional_fields,
diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index ccf0696a7d..3b3a57d4b0 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -523,8 +523,7 @@ def _summarize_ideal_gas_thermo(
 
 
 def _summarize_harmonic_thermo(
-    atoms: Atoms,
-    ht: HarmonicThermo, temperature: float = 298.15, pressure: float = 1.0
+    atoms: Atoms, ht: HarmonicThermo, temperature: float = 298.15, pressure: float = 1.0
 ) -> ThermoSchema:
     """
     Get tabulated results from an ASE HarmonicThermo object and store them in a
@@ -572,7 +571,5 @@ def _summarize_harmonic_thermo(
         }
     }
 
-    atoms_metadata = atoms_to_metadata(
-        atoms
-    )
+    atoms_metadata = atoms_to_metadata(atoms)
     return atoms_metadata | inputs | results
diff --git a/src/quacc/schemas/vasp.py b/src/quacc/schemas/vasp.py
index c08878c4ac..0ad177f525 100644
--- a/src/quacc/schemas/vasp.py
+++ b/src/quacc/schemas/vasp.py
@@ -233,7 +233,7 @@ def summarize_vasp_opt_run(
         store=None,
     )
     vasp_summary = vasp_summarize_run(
-        input_atoms = input_atoms,
+        input_atoms=input_atoms,
         directory=directory,
         move_magmoms=move_magmoms,
         run_bader=run_bader,
diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index 283a5e1498..187e9624a3 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -856,13 +856,12 @@ def test_freq_job():
     atoms = molecule("H2")
     atoms.pbc = True
     atoms.center(vacuum=1)
-    output = freq_job(atoms, kpts=(1, 1, 1), thermo_method='harmonic')
+    output = freq_job(atoms, kpts=(1, 1, 1), thermo_method="harmonic")
     assert output["parameters"]["ediff"] == 1e-07
     # Check that "sigma" (only used in ideal_gas) isn't a key in parameters_thermo
     assert "sigma" not in output["parameters_thermo"]
     assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)
 
-
     atoms = molecule("H2")
     atoms.pbc = True
     atoms.center(vacuum=1)
@@ -872,5 +871,3 @@ def test_freq_job():
     assert output["parameters_thermo"]["sigma"] == 2.0
     assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)
     assert len(output["results"]["vib_freqs"]) == 3 * len(atoms) - 5
-
-
diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index 13c3cc5345..6f2c2f5b9f 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -23,7 +23,7 @@
     _summarize_vib_run,
     summarize_opt_run,
     summarize_run,
-    summarize_vib_and_thermo
+    summarize_vib_and_thermo,
 )
 
 FILE_DIR = Path(__file__).parent
@@ -354,7 +354,7 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
 
     # Make sure metadata is made
     ht = HarmonicThermo([0.34])
-    results = _summarize_harmonic_thermo(atoms=atoms, ht = ht)
+    results = _summarize_harmonic_thermo(atoms=atoms, ht=ht)
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0
@@ -367,7 +367,8 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
     d = jsanitize(results, strict=True, enum_values=True)
     MontyDecoder().process_decoded(d)
 
-def test_summarize_vib_and_thermo(tmp_path,monkeypatch):
+
+def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     monkeypatch.chdir(tmp_path)
 
     # Test harmonic thermo for the thermo_analysis procedure
@@ -377,7 +378,7 @@ def test_summarize_vib_and_thermo(tmp_path,monkeypatch):
     ht = HarmonicThermo([0.34])
     vib = Vibrations(atoms)
     vib.run()
-    results = summarize_vib_and_thermo(vib=vib,thermo_analysis=ht,atoms=atoms)
+    results = summarize_vib_and_thermo(vib=vib, thermo_analysis=ht, atoms=atoms)
 
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
@@ -391,7 +392,7 @@ def test_summarize_vib_and_thermo(tmp_path,monkeypatch):
     atoms = molecule("N2")
     atoms.calc = EMT()
     igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)
-    results = summarize_vib_and_thermo(vib=None,thermo_analysis=igt,atoms=atoms)
+    results = summarize_vib_and_thermo(vib=None, thermo_analysis=igt, atoms=atoms)
 
     assert results["natoms"] == len(atoms)
     assert results["atoms"] == atoms
@@ -400,8 +401,6 @@ def test_summarize_vib_and_thermo(tmp_path,monkeypatch):
     assert results["results"]["energy"] == 0
     assert "pymatgen_version" in results["builder_meta"]
 
-    
-
 
 def test_errors(tmp_path, monkeypatch):
     monkeypatch.chdir(tmp_path)

From 7616a6c34ed66cb0ee239248f41496f6f317a414 Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Fri, 28 Jun 2024 18:32:02 +0200
Subject: [PATCH 13/35] Fix vasp schema mistake

---
 src/quacc/schemas/vasp.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/src/quacc/schemas/vasp.py b/src/quacc/schemas/vasp.py
index 0ad177f525..37742a46de 100644
--- a/src/quacc/schemas/vasp.py
+++ b/src/quacc/schemas/vasp.py
@@ -233,7 +233,6 @@ def summarize_vasp_opt_run(
         store=None,
     )
     vasp_summary = vasp_summarize_run(
-        input_atoms=input_atoms,
         directory=directory,
         move_magmoms=move_magmoms,
         run_bader=run_bader,

From 4ad811af044cf020dd543c735bc46dece6cc9ede Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 20:30:05 -0700
Subject: [PATCH 14/35] Slight refactor to reduce code duplication

---
 src/quacc/recipes/vasp/_base.py | 11 +++++------
 1 file changed, 5 insertions(+), 6 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index c3fb0b3ee2..994c1abb57 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -182,14 +182,13 @@ def run_and_summarize_vib_and_thermo(
     vibrations = Runner(atoms, calc, copy_files=copy_files).run_vib(
         vib_kwargs=vib_kwargs
     )
-    if thermo_method == "harmonic":
-        thermo_analysis = ThermoRunner(
+    thermo_runner = ThermoRunner(
             atoms, vibrations.get_frequencies(), energy=energy
-        ).run_harmonic_thermo()
+        )
+    if thermo_method == "harmonic":
+        thermo_analysis = thermo_runner.run_harmonic_thermo()
     elif thermo_method == "ideal_gas":
-        thermo_analysis = ThermoRunner(
-            atoms, vibrations.get_frequencies(), energy=energy
-        ).run_ideal_gas()
+        thermo_analysis = thermo_runner.run_ideal_gas()
 
     return summarize_vib_and_thermo(
         vib=vibrations,

From 9af030b64a429edaf9e53c1b334324225ec68bbe Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jun 2024 03:30:12 +0000
Subject: [PATCH 15/35] pre-commit auto-fixes

---
 src/quacc/recipes/vasp/_base.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index 994c1abb57..a5ba634391 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -182,9 +182,7 @@ def run_and_summarize_vib_and_thermo(
     vibrations = Runner(atoms, calc, copy_files=copy_files).run_vib(
         vib_kwargs=vib_kwargs
     )
-    thermo_runner = ThermoRunner(
-            atoms, vibrations.get_frequencies(), energy=energy
-        )
+    thermo_runner = ThermoRunner(atoms, vibrations.get_frequencies(), energy=energy)
     if thermo_method == "harmonic":
         thermo_analysis = thermo_runner.run_harmonic_thermo()
     elif thermo_method == "ideal_gas":

From 8823d34cdb5925cbb8d88bd311b96606cdf7727a Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 20:37:52 -0700
Subject: [PATCH 16/35] Slight cleanup

---
 src/quacc/schemas/ase.py | 24 ++++++++++++------------
 1 file changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index 3b3a57d4b0..1fac1dc97c 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -335,11 +335,11 @@ def summarize_vib_and_thermo(
 
     if isinstance(thermo_analysis, HarmonicThermo):
         thermo_task_doc = _summarize_harmonic_thermo(
-            atoms=atoms, ht=thermo_analysis, temperature=temperature, pressure=pressure
+            atoms, thermo_analysis, temperature=temperature, pressure=pressure
         )
     elif isinstance(thermo_analysis, IdealGasThermo):
         thermo_task_doc = _summarize_ideal_gas_thermo(
-            igt=thermo_analysis,
+            thermo_analysis,
             temperature=temperature,
             pressure=pressure,
             charge_and_multiplicity=charge_and_multiplicity,
@@ -523,7 +523,7 @@ def _summarize_ideal_gas_thermo(
 
 
 def _summarize_harmonic_thermo(
-    atoms: Atoms, ht: HarmonicThermo, temperature: float = 298.15, pressure: float = 1.0
+    atoms: Atoms, harmonic_thermo: HarmonicThermo, temperature: float = 298.15, pressure: float = 1.0
 ) -> ThermoSchema:
     """
     Get tabulated results from an ASE HarmonicThermo object and store them in a
@@ -533,7 +533,7 @@ def _summarize_harmonic_thermo(
     ----------
     atoms
         ASE Atoms object used for the vibrational frequency calculation.
-    ht
+    harmonic_thermo
         ASE HarmonicThermo object.
     temperature
         Temperature in Kelvins.
@@ -551,23 +551,23 @@ def _summarize_harmonic_thermo(
         "parameters_thermo": {
             "temperature": temperature,
             "pressure": pressure,
-            "vib_freqs": [e / units.invcm for e in ht.vib_energies],
-            "vib_energies": ht.vib_energies.tolist(),
-            "n_imag": ht.n_imag,
+            "vib_freqs": [e / units.invcm for e in harmonic_thermo.vib_energies],
+            "vib_energies": harmonic_thermo.vib_energies.tolist(),
+            "n_imag": harmonic_thermo.n_imag,
         }
     }
 
     results = {
         "results": {
-            "energy": ht.potentialenergy,
-            "helmholtz_energy": ht.get_helmholtz_energy(
+            "energy": harmonic_thermo.potentialenergy,
+            "helmholtz_energy": harmonic_thermo.get_helmholtz_energy(
                 temperature, verbose=settings.DEBUG
             ),
-            "internal_energy": ht.get_internal_energy(
+            "internal_energy": harmonic_thermo.get_internal_energy(
                 temperature, verbose=settings.DEBUG
             ),
-            "entropy": ht.get_entropy(temperature, verbose=settings.DEBUG),
-            "zpe": ht.get_ZPE_correction(),
+            "entropy": harmonic_thermo.get_entropy(temperature, verbose=settings.DEBUG),
+            "zpe": harmonic_thermo.get_ZPE_correction(),
         }
     }
 

From 9f59d1da3f21f2573d4e9dc80adcddfb9b125148 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 29 Jun 2024 03:37:59 +0000
Subject: [PATCH 17/35] pre-commit auto-fixes

---
 src/quacc/schemas/ase.py | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index 1fac1dc97c..5938e405b2 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -523,7 +523,10 @@ def _summarize_ideal_gas_thermo(
 
 
 def _summarize_harmonic_thermo(
-    atoms: Atoms, harmonic_thermo: HarmonicThermo, temperature: float = 298.15, pressure: float = 1.0
+    atoms: Atoms,
+    harmonic_thermo: HarmonicThermo,
+    temperature: float = 298.15,
+    pressure: float = 1.0,
 ) -> ThermoSchema:
     """
     Get tabulated results from an ASE HarmonicThermo object and store them in a

From 39fe02d92f5837d6c82ba20bbd75dfa63fb04c66 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 20:44:13 -0700
Subject: [PATCH 18/35] Update test_ase.py

---
 tests/core/schemas/test_ase.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index 6f2c2f5b9f..b00fa785d3 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -354,7 +354,7 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
 
     # Make sure metadata is made
     ht = HarmonicThermo([0.34])
-    results = _summarize_harmonic_thermo(atoms=atoms, ht=ht)
+    results = _summarize_harmonic_thermo(atoms, ht)
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0

From 21a40861b980d33c3f7ecba16d31e909951133bf Mon Sep 17 00:00:00 2001
From: Andrew Rosen <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 20:59:50 -0700
Subject: [PATCH 19/35] Fix schema

---
 src/quacc/schemas/ase.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index 5938e405b2..522e505fc0 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -12,7 +12,7 @@
 from ase.vibrations.data import VibrationsData
 
 from quacc import __version__, get_settings
-from quacc.atoms.core import get_final_atoms_from_dynamics
+from quacc.atoms.core import copy_atoms, get_final_atoms_from_dynamics
 from quacc.schemas.atoms import atoms_to_metadata
 from quacc.schemas.prep import prep_next_run
 from quacc.utils.dicts import finalize_dict, recursive_dict_merge
@@ -515,8 +515,10 @@ def _summarize_ideal_gas_thermo(
         )
         raise ValueError(msg)
 
+    atoms_no_pbcs = copy_atoms(igt.atoms)
+    atoms_no_pbcs.pbc = False
     atoms_metadata = atoms_to_metadata(
-        igt.atoms, charge_and_multiplicity=charge_and_multiplicity
+        atoms_no_pbcs, charge_and_multiplicity=charge_and_multiplicity
     )
 
     return atoms_metadata | inputs | results

From 61d28a6c018bbff2f384498b9c8bb1e8fae4d93c Mon Sep 17 00:00:00 2001
From: Andrew Rosen <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 21:03:09 -0700
Subject: [PATCH 20/35] fix

---
 src/quacc/runners/thermo.py | 7 ++++++-
 src/quacc/schemas/ase.py    | 6 ++----
 2 files changed, 8 insertions(+), 5 deletions(-)

diff --git a/src/quacc/runners/thermo.py b/src/quacc/runners/thermo.py
index 2fe2a840bb..6586f1c089 100644
--- a/src/quacc/runners/thermo.py
+++ b/src/quacc/runners/thermo.py
@@ -11,6 +11,8 @@
 from emmet.core.symmetry import PointGroupData
 from pymatgen.io.ase import AseAtomsAdaptor
 
+from quacc.atoms.core import copy_atoms
+
 if TYPE_CHECKING:
     from ase.atoms import Atoms
 
@@ -53,6 +55,9 @@ def run_ideal_gas(self, spin_multiplicity: int | None = None) -> IdealGasThermo:
         -------
         IdealGasThermo object
         """
+        atoms_no_pbc = copy_atoms(self.atoms)
+        atoms_no_pbc.set_pbc(False)
+
         # Ensure all negative modes are made complex
         for i, f in enumerate(self.vib_freqs):
             if not isinstance(f, complex) and f < 0:
@@ -83,7 +88,7 @@ def run_ideal_gas(self, spin_multiplicity: int | None = None) -> IdealGasThermo:
 
         # Get symmetry for later use
         natoms = len(self.atoms)
-        mol = AseAtomsAdaptor().get_molecule(self.atoms, charge_spin_check=False)
+        mol = AseAtomsAdaptor().get_molecule(atoms_no_pbc, charge_spin_check=False)
         point_group_data = PointGroupData().from_molecule(mol)
 
         # Get the geometry
diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index 522e505fc0..5938e405b2 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -12,7 +12,7 @@
 from ase.vibrations.data import VibrationsData
 
 from quacc import __version__, get_settings
-from quacc.atoms.core import copy_atoms, get_final_atoms_from_dynamics
+from quacc.atoms.core import get_final_atoms_from_dynamics
 from quacc.schemas.atoms import atoms_to_metadata
 from quacc.schemas.prep import prep_next_run
 from quacc.utils.dicts import finalize_dict, recursive_dict_merge
@@ -515,10 +515,8 @@ def _summarize_ideal_gas_thermo(
         )
         raise ValueError(msg)
 
-    atoms_no_pbcs = copy_atoms(igt.atoms)
-    atoms_no_pbcs.pbc = False
     atoms_metadata = atoms_to_metadata(
-        atoms_no_pbcs, charge_and_multiplicity=charge_and_multiplicity
+        igt.atoms, charge_and_multiplicity=charge_and_multiplicity
     )
 
     return atoms_metadata | inputs | results

From f5ba21f665152ed0b1bdee8ec72a9db1bd7a003d Mon Sep 17 00:00:00 2001
From: Andrew Rosen <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 21:03:46 -0700
Subject: [PATCH 21/35] cleanup

---
 src/quacc/runners/thermo.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/quacc/runners/thermo.py b/src/quacc/runners/thermo.py
index 6586f1c089..6a2e873602 100644
--- a/src/quacc/runners/thermo.py
+++ b/src/quacc/runners/thermo.py
@@ -55,8 +55,6 @@ def run_ideal_gas(self, spin_multiplicity: int | None = None) -> IdealGasThermo:
         -------
         IdealGasThermo object
         """
-        atoms_no_pbc = copy_atoms(self.atoms)
-        atoms_no_pbc.set_pbc(False)
 
         # Ensure all negative modes are made complex
         for i, f in enumerate(self.vib_freqs):
@@ -87,11 +85,13 @@ def run_ideal_gas(self, spin_multiplicity: int | None = None) -> IdealGasThermo:
             spin = 0
 
         # Get symmetry for later use
-        natoms = len(self.atoms)
+        atoms_no_pbc = copy_atoms(self.atoms)
+        atoms_no_pbc.set_pbc(False)
         mol = AseAtomsAdaptor().get_molecule(atoms_no_pbc, charge_spin_check=False)
         point_group_data = PointGroupData().from_molecule(mol)
 
         # Get the geometry
+        natoms = len(self.atoms)
         if natoms == 1:
             geometry = "monatomic"
         elif point_group_data.linear:

From 997d13241165a557a221ed879a34033f723a516f Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 21:10:43 -0700
Subject: [PATCH 22/35] Update test_vasp_recipes.py

---
 tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index 187e9624a3..eeabc373af 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -856,7 +856,9 @@ def test_freq_job():
     atoms = molecule("H2")
     atoms.pbc = True
     atoms.center(vacuum=1)
-    output = freq_job(atoms, kpts=(1, 1, 1), thermo_method="harmonic")
+    relaxed_atoms = relax_job(atoms)["atoms"]
+
+    output = freq_job(relaxed_atoms, kpts=(1, 1, 1), thermo_method="harmonic")
     assert output["parameters"]["ediff"] == 1e-07
     # Check that "sigma" (only used in ideal_gas) isn't a key in parameters_thermo
     assert "sigma" not in output["parameters_thermo"]
@@ -865,7 +867,7 @@ def test_freq_job():
     atoms = molecule("H2")
     atoms.pbc = True
     atoms.center(vacuum=1)
-    output = freq_job(atoms, kpts=(1, 1, 1))
+    output = freq_job(relaxed_atoms, kpts=(1, 1, 1))
     assert output["parameters"]["ediff"] == 1e-07
     # Check that parmeters_thermo contains
     assert output["parameters_thermo"]["sigma"] == 2.0

From 1a50f1f74e0014700595fa36e7290fe764859b6f Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 21:11:20 -0700
Subject: [PATCH 23/35] Update thermo.py

---
 src/quacc/runners/thermo.py | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/src/quacc/runners/thermo.py b/src/quacc/runners/thermo.py
index 6a2e873602..b8fe8680a4 100644
--- a/src/quacc/runners/thermo.py
+++ b/src/quacc/runners/thermo.py
@@ -11,8 +11,6 @@
 from emmet.core.symmetry import PointGroupData
 from pymatgen.io.ase import AseAtomsAdaptor
 
-from quacc.atoms.core import copy_atoms
-
 if TYPE_CHECKING:
     from ase.atoms import Atoms
 
@@ -85,9 +83,7 @@ def run_ideal_gas(self, spin_multiplicity: int | None = None) -> IdealGasThermo:
             spin = 0
 
         # Get symmetry for later use
-        atoms_no_pbc = copy_atoms(self.atoms)
-        atoms_no_pbc.set_pbc(False)
-        mol = AseAtomsAdaptor().get_molecule(atoms_no_pbc, charge_spin_check=False)
+        mol = AseAtomsAdaptor().get_molecule(self.atoms, charge_spin_check=False)
         point_group_data = PointGroupData().from_molecule(mol)
 
         # Get the geometry

From 6ed278f64fd382a9ab4e3fe55a013ae90957e082 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 28 Jun 2024 21:16:27 -0700
Subject: [PATCH 24/35] Update test_vasp_recipes.py

---
 .../core/recipes/vasp_recipes/mocked/test_vasp_recipes.py | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index eeabc373af..a861e636a3 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -856,18 +856,14 @@ def test_freq_job():
     atoms = molecule("H2")
     atoms.pbc = True
     atoms.center(vacuum=1)
-    relaxed_atoms = relax_job(atoms)["atoms"]
 
-    output = freq_job(relaxed_atoms, kpts=(1, 1, 1), thermo_method="harmonic")
+    output = freq_job(atoms, kpts=(1, 1, 1), thermo_method="harmonic")
     assert output["parameters"]["ediff"] == 1e-07
     # Check that "sigma" (only used in ideal_gas) isn't a key in parameters_thermo
     assert "sigma" not in output["parameters_thermo"]
     assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)
 
-    atoms = molecule("H2")
-    atoms.pbc = True
-    atoms.center(vacuum=1)
-    output = freq_job(relaxed_atoms, kpts=(1, 1, 1))
+    output = freq_job(atoms, kpts=(1, 1, 1))
     assert output["parameters"]["ediff"] == 1e-07
     # Check that parmeters_thermo contains
     assert output["parameters_thermo"]["sigma"] == 2.0

From d62da1bb0e7dd77d6a8d49694f571899a8436475 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 1 Jul 2024 15:47:31 +0000
Subject: [PATCH 25/35] pre-commit auto-fixes

---
 src/quacc/recipes/vasp/_base.py | 3 ++-
 src/quacc/recipes/vasp/core.py  | 4 +++-
 2 files changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index 25fb9521ae..810b6dfda4 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -21,7 +21,8 @@
         OptParams,
         SourceDirectory,
         VaspASEOptSchema,
-        VaspSchema,VibThermoSchema,
+        VaspSchema,
+        VibThermoSchema,
     )
 
 
diff --git a/src/quacc/recipes/vasp/core.py b/src/quacc/recipes/vasp/core.py
index cba53b1834..52797c73c5 100644
--- a/src/quacc/recipes/vasp/core.py
+++ b/src/quacc/recipes/vasp/core.py
@@ -28,7 +28,9 @@
         OptParams,
         SourceDirectory,
         VaspASEOptSchema,
-        VaspSchema,VibThermoSchema,VibKwargs
+        VaspSchema,
+        VibKwargs,
+        VibThermoSchema,
     )
 
 

From 0a6141dabcdd0626b84f1192142896a77b702630 Mon Sep 17 00:00:00 2001
From: benshi97 <bxs21@cam.ac.uk>
Date: Wed, 24 Jul 2024 18:23:27 +0100
Subject: [PATCH 26/35] Fix tests

---
 tests/core/schemas/test_ase.py | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index b00fa785d3..e8d0734c92 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -392,7 +392,9 @@ def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     atoms = molecule("N2")
     atoms.calc = EMT()
     igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)
-    results = summarize_vib_and_thermo(vib=None, thermo_analysis=igt, atoms=atoms)
+    vib = Vibrations(atoms)
+    vib.run()
+    results = summarize_vib_and_thermo(vib=vib, thermo_analysis=igt, atoms=atoms)
 
     assert results["natoms"] == len(atoms)
     assert results["atoms"] == atoms

From 678b2a20b8057c7ac5b4fa67f0ab4e927f359384 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Wed, 24 Jul 2024 15:01:36 -0400
Subject: [PATCH 27/35] Update vasp.py

---
 src/quacc/schemas/vasp.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/src/quacc/schemas/vasp.py b/src/quacc/schemas/vasp.py
index 59ff154bfb..eaf9a96b6c 100644
--- a/src/quacc/schemas/vasp.py
+++ b/src/quacc/schemas/vasp.py
@@ -233,6 +233,7 @@ def summarize_vasp_opt_run(
         store=None,
     )
     vasp_summary = vasp_summarize_run(
+        final_atoms,
         directory=directory,
         move_magmoms=move_magmoms,
         run_bader=run_bader,

From 2664ba00482582b3155669824c86f1ae6aeadfe7 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 26 Jul 2024 10:50:26 -0400
Subject: [PATCH 28/35] Update variable name

---
 src/quacc/schemas/ase.py | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/src/quacc/schemas/ase.py b/src/quacc/schemas/ase.py
index 2aa85ea61d..37e97e6537 100644
--- a/src/quacc/schemas/ase.py
+++ b/src/quacc/schemas/ase.py
@@ -288,7 +288,7 @@ def summarize_md_run(
 
 def summarize_vib_and_thermo(
     vib: Vibrations,
-    thermo_analysis: IdealGasThermo | HarmonicThermo,
+    thermo_object: IdealGasThermo | HarmonicThermo,
     atoms: Atoms | None = None,
     temperature: float = 298.15,
     pressure: float = 1.0,
@@ -304,7 +304,7 @@ def summarize_vib_and_thermo(
     ----------
     vib
         ASE Vibrations object.
-    thermo_analysis
+    thermo_object
         ASE IdealGasThermo or HarmonicThermo object.
     atoms
         ASE Atoms object following a calculation.
@@ -332,13 +332,13 @@ def summarize_vib_and_thermo(
         vib, charge_and_multiplicity=charge_and_multiplicity
     )
 
-    if isinstance(thermo_analysis, HarmonicThermo):
+    if isinstance(thermo_object, HarmonicThermo):
         thermo_task_doc = _summarize_harmonic_thermo(
-            atoms, thermo_analysis, temperature=temperature, pressure=pressure
+            atoms, thermo_object, temperature=temperature, pressure=pressure
         )
-    elif isinstance(thermo_analysis, IdealGasThermo):
+    elif isinstance(thermo_object, IdealGasThermo):
         thermo_task_doc = _summarize_ideal_gas_thermo(
-            thermo_analysis,
+            thermo_object,
             temperature=temperature,
             pressure=pressure,
             charge_and_multiplicity=charge_and_multiplicity,

From 41f15656a3cc14760c4d50eb8210959dea14398d Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 26 Jul 2024 10:52:07 -0400
Subject: [PATCH 29/35] Remove typo

---
 tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
index a861e636a3..443d1f08a0 100644
--- a/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
+++ b/tests/core/recipes/vasp_recipes/mocked/test_vasp_recipes.py
@@ -865,7 +865,6 @@ def test_freq_job():
 
     output = freq_job(atoms, kpts=(1, 1, 1))
     assert output["parameters"]["ediff"] == 1e-07
-    # Check that parmeters_thermo contains
     assert output["parameters_thermo"]["sigma"] == 2.0
     assert len(output["results"]["vib_freqs_raw"]) == 3 * len(atoms)
     assert len(output["results"]["vib_freqs"]) == 3 * len(atoms) - 5

From 6036a4c90ea04b93e9e78163149011cb957a8030 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 26 Jul 2024 10:57:42 -0400
Subject: [PATCH 30/35] Update test_ase.py

---
 tests/core/schemas/test_ase.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index e8d0734c92..35671b8844 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -378,7 +378,7 @@ def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     ht = HarmonicThermo([0.34])
     vib = Vibrations(atoms)
     vib.run()
-    results = summarize_vib_and_thermo(vib=vib, thermo_analysis=ht, atoms=atoms)
+    results = summarize_vib_and_thermo(vib, ht, atoms=atoms)
 
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
@@ -394,7 +394,7 @@ def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)
     vib = Vibrations(atoms)
     vib.run()
-    results = summarize_vib_and_thermo(vib=vib, thermo_analysis=igt, atoms=atoms)
+    results = summarize_vib_and_thermo(vib, igt, atoms=atoms)
 
     assert results["natoms"] == len(atoms)
     assert results["atoms"] == atoms

From eca59870d326f4107acac9e46e7fc38daef6dd59 Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 26 Jul 2024 11:16:40 -0400
Subject: [PATCH 31/35] Update _base.py

---
 src/quacc/recipes/vasp/_base.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index 810b6dfda4..a01da50315 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -188,13 +188,13 @@ def run_and_summarize_vib_and_thermo(
     )
     thermo_runner = ThermoRunner(atoms, vibrations.get_frequencies(), energy=energy)
     if thermo_method == "harmonic":
-        thermo_analysis = thermo_runner.run_harmonic_thermo()
+        thermo_object = thermo_runner.run_harmonic_thermo()
     elif thermo_method == "ideal_gas":
-        thermo_analysis = thermo_runner.run_ideal_gas()
+        thermo_object = thermo_runner.run_ideal_gas()
 
     return summarize_vib_and_thermo(
         vib=vibrations,
-        thermo_analysis=thermo_analysis,
+        thermo_object,
         atoms=atoms,
         temperature=temperature,
         pressure=pressure,

From cd937a95c3626879b3e4532d658a09125c2b254f Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 26 Jul 2024 11:17:07 -0400
Subject: [PATCH 32/35] Update _base.py

---
 src/quacc/recipes/vasp/_base.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/quacc/recipes/vasp/_base.py b/src/quacc/recipes/vasp/_base.py
index a01da50315..59ea4809a7 100644
--- a/src/quacc/recipes/vasp/_base.py
+++ b/src/quacc/recipes/vasp/_base.py
@@ -193,7 +193,7 @@ def run_and_summarize_vib_and_thermo(
         thermo_object = thermo_runner.run_ideal_gas()
 
     return summarize_vib_and_thermo(
-        vib=vibrations,
+        vibrations,
         thermo_object,
         atoms=atoms,
         temperature=temperature,

From 4d030cbf8a36e29943a2c77ffc6e189724becd0f Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 26 Jul 2024 11:17:32 -0400
Subject: [PATCH 33/35] Update test_ase.py

---
 tests/core/schemas/test_ase.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index 35671b8844..befc81cd85 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -371,7 +371,7 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
 def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     monkeypatch.chdir(tmp_path)
 
-    # Test harmonic thermo for the thermo_analysis procedure
+    # Test harmonic thermo
     atoms = molecule("H2")
     atoms.calc = EMT()
 
@@ -388,7 +388,7 @@ def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     assert_close(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
     assert_close(results["results"]["zpe"], 0.17, rtol=1e-5)
 
-    # Test ideal gas thermo for the thermo_analysis procedure
+    # Test ideal gas thermo
     atoms = molecule("N2")
     atoms.calc = EMT()
     igt = IdealGasThermo([0.34], "linear", atoms=atoms, spin=0, symmetrynumber=2)

From 77c446fccdc16c233874125d9e584325b831cfeb Mon Sep 17 00:00:00 2001
From: "Andrew S. Rosen" <asrosen93@gmail.com>
Date: Fri, 26 Jul 2024 11:18:23 -0400
Subject: [PATCH 34/35] Update test_ase.py

---
 tests/core/schemas/test_ase.py | 18 +++++++++---------
 1 file changed, 9 insertions(+), 9 deletions(-)

diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index befc81cd85..5c182594d8 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -15,7 +15,7 @@
 from maggma.stores import MemoryStore
 from monty.json import MontyDecoder, jsanitize
 from monty.serialization import loadfn
-from numpy.testing import assert_allclose as assert_close
+from numpy.testing import assert_allclose
 
 from quacc.schemas.ase import (
     _summarize_harmonic_thermo,
@@ -358,10 +358,10 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0
-    assert_close(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
-    assert_close(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
-    assert_close(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
-    assert_close(results["results"]["zpe"], 0.17, rtol=1e-5)
+    assert_allclose(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
+    assert_allclose(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
+    assert_allclose(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
+    assert_allclose(results["results"]["zpe"], 0.17, rtol=1e-5)
 
     # test document can be jsanitized and decoded
     d = jsanitize(results, strict=True, enum_values=True)
@@ -383,10 +383,10 @@ def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0
-    assert_close(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
-    assert_close(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
-    assert_close(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
-    assert_close(results["results"]["zpe"], 0.17, rtol=1e-5)
+    assert_allclose(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
+    assert_allclose(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
+    assert_allclose(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
+    assert_allclose(results["results"]["zpe"], 0.17, rtol=1e-5)
 
     # Test ideal gas thermo
     atoms = molecule("N2")

From 2416a2831ad997991333fa220a76e2a0c401cd72 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 26 Jul 2024 15:18:30 +0000
Subject: [PATCH 35/35] pre-commit auto-fixes

---
 tests/core/schemas/test_ase.py | 16 ++++++++++++----
 1 file changed, 12 insertions(+), 4 deletions(-)

diff --git a/tests/core/schemas/test_ase.py b/tests/core/schemas/test_ase.py
index 5c182594d8..80568c9e36 100644
--- a/tests/core/schemas/test_ase.py
+++ b/tests/core/schemas/test_ase.py
@@ -358,8 +358,12 @@ def test_summarize_harmonic_thermo(tmp_path, monkeypatch):
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0
-    assert_allclose(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
-    assert_allclose(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
+    assert_allclose(
+        results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5
+    )
+    assert_allclose(
+        results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5
+    )
     assert_allclose(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
     assert_allclose(results["results"]["zpe"], 0.17, rtol=1e-5)
 
@@ -383,8 +387,12 @@ def test_summarize_vib_and_thermo(tmp_path, monkeypatch):
     assert results["parameters_thermo"]["vib_energies"] == [0.34]
     assert results["parameters_thermo"]["vib_freqs"] == [0.34 / invcm]
     assert results["results"]["energy"] == 0
-    assert_allclose(results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5)
-    assert_allclose(results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5)
+    assert_allclose(
+        results["results"]["helmholtz_energy"], 0.16999995401497991, rtol=1e-5
+    )
+    assert_allclose(
+        results["results"]["internal_energy"], 0.1700006085385999, rtol=1e-5
+    )
     assert_allclose(results["results"]["entropy"], 2.1952829783392438e-09, rtol=1e-5)
     assert_allclose(results["results"]["zpe"], 0.17, rtol=1e-5)