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

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

flowermd/library/forcefields.py

@@ -601,17 +601,17 @@ def __init__(
         lpar,
         lperp,
         r_cut,
-        #bond_k,
-        #bond_r0,
+        # bond_k,
+        # bond_r0,
         angle_k=None,
         angle_theta0=None,
     ):
         self.epsilon = epsilon
         self.lperp = lperp
         self.lpar = lpar
         self.r_cut = r_cut
-        #self.bond_k = bond_k
-        #self.bond_r0 = bond_r0
+        # self.bond_k = bond_k
+        # self.bond_r0 = bond_r0
         self.angle_k = angle_k
         self.angle_theta0 = angle_theta0
         hoomd_forces = self._create_forcefield()
@@ -620,10 +620,10 @@ def __init__(
     def _create_forcefield(self):
         forces = []
         # Bonds
-        #bond = hoomd.md.bond.Harmonic()
-        #bond.params["A-A"] = dict(k=self.bond_k, r0=self.bond_r0)
-        #bond.params["B-B"] = dict(k=0, r0=self.lpar)
-        #forces.append(bond)
+        # bond = hoomd.md.bond.Harmonic()
+        # bond.params["A-A"] = dict(k=self.bond_k, r0=self.bond_r0)
+        # bond.params["B-B"] = dict(k=0, r0=self.lpar)
+        # forces.append(bond)
 
         # Angles
         if all([self.angle_k, self.angle_theta0]):

flowermd/library/polymers.py

@@ -314,7 +314,7 @@ def _build(self, length):
         # Build up ellipsoid bead
         bead = mb.Compound(name="ellipsoid")
         head = mb.Compound(
-            pos=(0, 0, self.lpar), name="_H", mass=self.bead_mass / 2 
+            pos=(0, 0, self.lpar), name="_H", mass=self.bead_mass / 2
         )
         center = mb.Compound(pos=(0, 0, 0), name="_C", mass=self.bead_mass / 2)
         bead.add([center, head])

flowermd/utils/constraints.py

@@ -10,15 +10,20 @@ def set_bond_constraints(snapshot, bond_type, constrain_value, tolerance=1e-5):
     constraint_values = []
     constraint_groups = []
     bond_type_id = snapshot.bonds.types.index(bond_type)
-    bond_indices = np.where(snapshot.bonds.typeid == np.array(bond_type_id))[0].astype(int)
+    bond_indices = np.where(snapshot.bonds.typeid == np.array(bond_type_id))[
+        0
+    ].astype(int)
     for idx in bond_indices:
         group = snapshot.bonds.group[idx]
-        bond_len = np.linalg.norm(snapshot.particles.position[group[1]] - snapshot.particles.position[group[0]])
+        bond_len = np.linalg.norm(
+            snapshot.particles.position[group[1]]
+            - snapshot.particles.position[group[0]]
+        )
         if not np.isclose(constrain_value, bond_len, atol=tolerance):
             raise ValueError("Values found not within the given tolerance")
         constraint_values.append(constrain_value)
         constraint_groups.append(group)
-    
+
     snapshot.constraints.N = len(constraint_values)
     snapshot.constraints.value = constraint_values
     snapshot.constraints.group = constraint_groups