added tests for frequency and molecule optimization

tests/qchem/conftest.py

@@ -160,9 +160,16 @@ def check_qin(
     ref_qin_path = ref_path / "inputs" / "mol.qin.gz"
     ref_qin = QCInput.from_file(ref_qin_path)
     script_directory = Path(__file__).resolve().parent
-    user_qin_path = script_directory / "mol.qin.gz"
-    user_qin = QCInput.from_file(user_qin_path)
     # defaults = {"sym_ignore": True, "symmetry": False, "xc_grid": 3}
+    job_name = ref_path.stem
+    print(f"The job name is {job_name}")
+    if job_name == "water_single_point":
+        user_qin_path = script_directory / "sp.qin.gz"
+    elif job_name == "water_optimization":
+        user_qin_path = script_directory / "opt.qin.gz"
+    elif job_name == "water_frequency":
+        user_qin_path = script_directory / "freq.qin.gz"
+    user_qin = QCInput.from_file(user_qin_path)
 
     keys_to_check = (
         set(user_qin.as_dict()) if qin_settings is None else set(qin_settings)

tests/qchem/jobs/test_core.py

@@ -2,6 +2,7 @@
 import sys
 from pathlib import Path
 
+import numpy as np
 from emmet.core.qc_tasks import TaskDoc
 
 # from emmet.core.vasp.calculation import IonicStep, VaspObject
@@ -15,9 +16,7 @@
 from pymatgen.core.structure import Molecule
 from pytest import approx
 
-from atomate2.qchem.jobs.core import (
-    SinglePointMaker,
-)
+from atomate2.qchem.jobs.core import FreqMaker, OptMaker, SinglePointMaker
 
 curr_dir = Path(os.path.dirname(sys.argv[0]))
 
@@ -26,15 +25,14 @@
 
 # Construct the full path
 mol_path = curr_dir / file_name
-H2O_structure = Molecule.from_file(mol_path)
-# print(H2O_structure)
+H2O_structure = Molecule.from_file(file_name)
 
 
 def test_single_point_maker(mock_qchem, clean_dir, structure=H2O_structure):
     # jstore = jobflow.SETTINGS.JOB_STORE
 
     # mapping from job name to directory containing test files
-    ref_paths = {"single_point": "single_point"}
+    ref_paths = {"single_point": "water_single_point"}
 
     # settings passed to fake_run_vasp; adjust these to check for certain INCAR settings
     # fake_run_qchem_kwargs = {"single_point": {"qin_settings": None}}
@@ -45,19 +43,74 @@ def test_single_point_maker(mock_qchem, clean_dir, structure=H2O_structure):
 
     # generate job
     job = SinglePointMaker().make(structure)
-    print(job.__dict__)
-    print(job)
 
     # run the flow or job and ensure that it finished running successfully
     responses = run_locally(job, create_folders=True, ensure_success=True)
 
     # validate job outputs
     output1 = responses[job.uuid][1].output
-    print(output1.output)
     assert isinstance(output1, TaskDoc)
     assert output1.output.final_energy == approx(-76.4451488262)
 
-    # with jstore.additional_stores["data"] as s:
-    #     doc = s.query_one({"job_uuid": job.uuid})
-    # dd = doc["data"]
-    # assert dd["@class"] == "Chgcar"
+
+def test_opt_maker(mock_qchem, clean_dir, structure=H2O_structure):
+    ref_paths = {"optimization": "water_optimization"}
+    fake_run_qchem_kwargs = {}
+    mock_qchem(ref_paths, fake_run_qchem_kwargs)
+
+    job = OptMaker().make(structure)
+
+    responses = run_locally(job, create_folders=True, ensure_success=True)
+    opt_geometry = {
+        "@module": "pymatgen.core.structure",
+        "@class": "Molecule",
+        "charge": 0,
+        "spin_multiplicity": 1,
+        "sites": [
+            {
+                "name": "O",
+                "species": [{"element": "O", "occu": 1}],
+                "xyz": [-0.8001136722, 2.2241304324, -0.0128020517],
+                "properties": {},
+                "label": "O",
+            },
+            {
+                "name": "H",
+                "species": [{"element": "H", "occu": 1}],
+                "xyz": [0.1605037895, 2.195300528, 0.0211059581],
+                "properties": {},
+                "label": "H",
+            },
+            {
+                "name": "H",
+                "species": [{"element": "H", "occu": 1}],
+                "xyz": [-1.0782701173, 1.6278690395, 0.6883760935],
+                "properties": {},
+                "label": "H",
+            },
+        ],
+        "properties": {},
+    }
+
+    output1 = responses[job.uuid][1].output
+    assert isinstance(output1, TaskDoc)
+    assert sorted(opt_geometry.items()) == sorted(
+        output1.output.optimized_molecule.as_dict().items()
+    )
+    assert output1.output.final_energy == approx(-76.450849061819)
+
+
+def test_freq(mock_qchem, clean_dir, structure=H2O_structure):
+    ref_paths = {"frequency": "water_frequency"}
+    fake_run_qchem_kwargs = {}
+    mock_qchem(ref_paths, fake_run_qchem_kwargs)
+
+    job = FreqMaker().make(structure)
+
+    responses = run_locally(job, create_folders=True, ensure_success=True)
+    ref_freqs = np.array([1643.03, 3446.82, 3524.32])
+    output1 = responses[job.uuid][1].output
+    assert np.array_equal(
+        np.array(output1.calcs_reversed[0].output.frequencies), ref_freqs
+    )
+    assert output1.output.final_energy == approx(-76.449405011)