[pre-commit.ci] auto fixes from pre-commit.com hooks

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theochem · Mar 5, 2024 · 0f3563d · 0f3563d
1 parent aa7bc77
commit 0f3563d
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Showing 4 changed files with 76 additions and 41 deletions.
diff --git a/atomdb/api.py b/atomdb/api.py
@@ -363,7 +363,9 @@ def load_all(elem, nexc=0, dataset=DEFAULT_DATASET, datapath=DEFAULT_DATAPATH):
         with open(file, "rb") as f:
             msg = unpack_msg(f)
         # Convert raw bytes back to numpy arrays, initialize the Species instance, store it
-        species.append(Species(**{k: frombuffer(v) if isinstance(v, bytes) else v for k, v in msg.items()}))
+        species.append(
+            Species(**{k: frombuffer(v) if isinstance(v, bytes) else v for k, v in msg.items()})
+        )
     return species
 
 

diff --git a/atomdb/datasets/uhf_augccpvdz/__init__.py b/atomdb/datasets/uhf_augccpvdz/__init__.py
@@ -94,9 +94,7 @@ def eval_orb_ked(one_density_matrix, basis, points, transform=None):
     "Adapted from Gbasis"
     orbt_ked = 0
     for orders in np.identity(3, dtype=int):
-        deriv_orb_eval_one = evaluate_deriv_basis(
-            basis, points, orders, transform=transform
-        )
+        deriv_orb_eval_one = evaluate_deriv_basis(basis, points, orders, transform=transform)
         deriv_orb_eval_two = deriv_orb_eval_one  # orders_one == orders_two
         density = one_density_matrix.dot(deriv_orb_eval_two)
         density *= deriv_orb_eval_one

diff --git a/atomdb/promolecule.py b/atomdb/promolecule.py
@@ -407,7 +407,10 @@ def make_promolecule(
     # Handle default multiplicity parameters
     if mults is None:
         # Force non-int charge to be integer here; it will be overwritten below.
-        mults = [MULTIPLICITIES[int(np.round(atnum - charge))] for (atnum, charge) in zip(atnums, charges)]
+        mults = [
+            MULTIPLICITIES[int(np.round(atnum - charge))]
+            for (atnum, charge) in zip(atnums, charges)
+        ]
 
     # Construct linear combination of species
     promol = Promolecule()
@@ -424,16 +427,18 @@ def make_promolecule(
                 promol.append(specie, coord, 1.0)
                 continue
             except FileNotFoundError:
-                warn("Unable to load species corresponding to `charge, mult`; "
-                     "generating species via linear combination of other species'")
+                warn(
+                    "Unable to load species corresponding to `charge, mult`; "
+                    "generating species via linear combination of other species'"
+                )
 
         # Non-integer charge and multiplicity
         #
         nelec = atnum - charge
         nspin = np.sign(mult) * (abs(mult) - 1)
         # Get all candidates for linear combination
         species_list = load_all(atom, dataset=dataset, datapath=datapath)
-        for specie in species_list[:len(species_list)]:
+        for specie in species_list[: len(species_list)]:
             if specie.nspin > 0:
                 specie_neg_spinpol = deepcopy(specie)
                 specie_neg_spinpol.spinpol = -1
@@ -445,11 +450,14 @@ def make_promolecule(
             energies = np.asarray([t.energy for t in ts], dtype=float)
             result = linprog(
                 energies,
-                A_eq=np.asarray([
-                    [1 for t in ts],
-                    [t.nelec for t in ts],
-                    [t.nspin * t.spinpol for t in ts],
-                ], dtype=float),
+                A_eq=np.asarray(
+                    [
+                        [1 for t in ts],
+                        [t.nelec for t in ts],
+                        [t.nspin * t.spinpol for t in ts],
+                    ],
+                    dtype=float,
+                ),
                 b_eq=np.asarray([1, nelec, nspin], dtype=float),
                 bounds=(0, 1),
             )
@@ -508,9 +516,15 @@ def _cart_to_bary(x0, y0, s1, s2, s3):
     r"""Helper function for computing barycentric coordinates."""
     x1, x2, x3 = s1.nelec, s2.nelec, s3.nelec
     y1, y2, y3 = s1.nspin, s2.nspin, s3.nspin
-    lambda1 = ((y2 - y3) * (x0 - x3) + (x3 - x2) * (y0 - y3) /
-               (y2 - y3) * (x1 - x3) + (x3 - x2) * (y1 - y3))
-    lambda2 = ((y3 - y1) * (x0 - x3) + (x1 - x3) * (y0 - y3) /
-               (y2 - y3) * (x1 - x3) + (x3 - x2) * (y1 - y3))
+    lambda1 = (
+        (y2 - y3) * (x0 - x3)
+        + (x3 - x2) * (y0 - y3) / (y2 - y3) * (x1 - x3)
+        + (x3 - x2) * (y1 - y3)
+    )
+    lambda2 = (
+        (y3 - y1) * (x0 - x3)
+        + (x1 - x3) * (y0 - y3) / (y2 - y3) * (x1 - x3)
+        + (x3 - x2) * (y1 - y3)
+    )
     lambda3 = 1 - lambda1 - lambda2
     return (lambda1, lambda2, lambda3)
diff --git a/atomdb/test/test_promolecule.py b/atomdb/test/test_promolecule.py
@@ -36,10 +36,13 @@
     pytest.param(
         {
             "atnums": [1, 1],
-            "coords": np.asarray([
-                [ 0.,  0.,  0.],
-                [ 0.,  0.,  1.],
-            ], dtype=float),
+            "coords": np.asarray(
+                [
+                    [0.0, 0.0, 0.0],
+                    [0.0, 0.0, 1.0],
+                ],
+                dtype=float,
+            ),
             "dataset": "slater",
         },
         id="H2 default charge/mult",
@@ -48,10 +51,13 @@
         {
             "atnums": [6, 6],
             "charges": [1, -1],
-            "coords": np.asarray([
-                [ 0.,  0.,  0.],
-                [ 0.,  0.,  1.],
-            ], dtype=float),
+            "coords": np.asarray(
+                [
+                    [0.0, 0.0, 0.0],
+                    [0.0, 0.0, 1.0],
+                ],
+                dtype=float,
+            ),
             "dataset": "slater",
         },
         id="C2 +/-1 charge, default mult",
@@ -61,10 +67,13 @@
             "atnums": [6, 6],
             "charges": [0.5, -0.5],
             "mults": [1, -1],
-            "coords": np.asarray([
-                [ 0.,  0.,  0.],
-                [ 0.,  0.,  1.],
-            ], dtype=float),
+            "coords": np.asarray(
+                [
+                    [0.0, 0.0, 0.0],
+                    [0.0, 0.0, 1.0],
+                ],
+                dtype=float,
+            ),
             "dataset": "slater",
         },
         id="C2 +/-0.5 charge",
@@ -74,9 +83,12 @@
             "atnums": [4],
             "charges": [1.2],
             "mults": [1.2],
-            "coords": np.asarray([
-                [ 0.,  0.,  0.],
-            ], dtype=float),
+            "coords": np.asarray(
+                [
+                    [0.0, 0.0, 0.0],
+                ],
+                dtype=float,
+            ),
             "dataset": "uhf_augccpvdz",
         },
         id="Be floating point charge/floating point mult",
@@ -86,9 +98,12 @@
             "atnums": [4],
             "charges": [1.2],
             "mults": [1],
-            "coords": np.asarray([
-                [ 0.,  0.,  0.],
-            ], dtype=float),
+            "coords": np.asarray(
+                [
+                    [0.0, 0.0, 0.0],
+                ],
+                dtype=float,
+            ),
             "dataset": "uhf_augccpvdz",
         },
         id="Be floating point charge/integer mult",
@@ -98,9 +113,12 @@
             "atnums": [4],
             "charges": [1.2],
             "mults": [-1.2],
-            "coords": np.asarray([
-                [ 0.,  0.,  0.],
-            ], dtype=float),
+            "coords": np.asarray(
+                [
+                    [0.0, 0.0, 0.0],
+                ],
+                dtype=float,
+            ),
             "dataset": "uhf_augccpvdz",
         },
         id="Be floating point charge/floating point mult (neg)",
@@ -110,9 +128,12 @@
             "atnums": [4],
             "charges": [1.2],
             "mults": [-1],
-            "coords": np.asarray([
-                [ 0.,  0.,  0.],
-            ], dtype=float),
+            "coords": np.asarray(
+                [
+                    [0.0, 0.0, 0.0],
+                ],
+                dtype=float,
+            ),
             "dataset": "uhf_augccpvdz",
         },
         id="Be floating point charge/integer mult (neg)",