Make it pretty

ipi/engine/initializer.py

@@ -360,9 +360,13 @@ def init_stage1(self, simul):
         """
 
         if simul.beads.nbeads == 0:
-            fpos = fmom = fmass = flab = fcell = (
-                False  # we don't have an explicitly defined beads object yet
-            )
+            fpos = (
+                fmom
+            ) = (
+                fmass
+            ) = (
+                flab
+            ) = fcell = False  # we don't have an explicitly defined beads object yet
         else:
             fpos = fmom = fmass = flab = fcell = True
 

ipi/engine/motion/geop.py

@@ -481,9 +481,9 @@ def step(self, step=None):
 
             # Restore dimensionality of d and invhessian
             self.d[:, self.gm.fixatoms_mask] = masked_d
-            self.invhessian[np.ix_(self.gm.fixatoms_mask, self.gm.fixatoms_mask)] = (
-                masked_invhessian
-            )
+            self.invhessian[
+                np.ix_(self.gm.fixatoms_mask, self.gm.fixatoms_mask)
+            ] = masked_invhessian
 
         else:
             fdf0 = (self.old_u, -self.old_f)
@@ -576,9 +576,9 @@ def step(self, step=None):
             )
 
             # Restore dimensionality of the hessian
-            self.hessian[np.ix_(self.gm.fixatoms_mask, self.gm.fixatoms_mask)] = (
-                masked_hessian
-            )
+            self.hessian[
+                np.ix_(self.gm.fixatoms_mask, self.gm.fixatoms_mask)
+            ] = masked_hessian
         else:
             # Make one step. ( A step is finished when a movement is accepted)
             BFGSTRM(
@@ -794,9 +794,9 @@ def step(self, step=None):
             )
 
             # Restore dimensionality of the invhessian
-            self.invhessian[np.ix_(self.gm.fixatoms_mask, self.gm.fixatoms_mask)] = (
-                masked_invhessian
-            )
+            self.invhessian[
+                np.ix_(self.gm.fixatoms_mask, self.gm.fixatoms_mask)
+            ] = masked_invhessian
 
         else:
             fdf0 = (self.old_u, -self.old_f)

ipi/engine/motion/instanton.py

@@ -400,7 +400,7 @@ def evaluate(self):
         e = self.pot.copy()
         g = -self.f.copy()
 
-        e = e * (self.coef[1:,0] + self.coef[:-1,0]) / 2
+        e = e * (self.coef[1:, 0] + self.coef[:-1, 0]) / 2
         g = g * (self.coef[1:] + self.coef[:-1]) / 2
         return e, g
 
@@ -670,7 +670,7 @@ def evaluate(self):
         e += e_friction
         g += g_friction
 
-        e = e * (self.coef[1:,0] + self.coef[:-1,0]) / 2
+        e = e * (self.coef[1:, 0] + self.coef[:-1, 0]) / 2
         g = g * (self.coef[1:] + self.coef[:-1]) / 2
 
         return e, g
@@ -865,10 +865,10 @@ class Mapper(object):
     It also handles fixatoms"""
 
     def __init__(self):
-        """Initializes object for Mapper. 
+        """Initializes object for Mapper.
         This class is inteded to combine several mappers and provide
         the actual Mapper that will be used by the optimizers."""
-        
+
         self.sm = SpringMapper()
         self.gm = PesMapper()
 
@@ -1758,7 +1758,7 @@ def step(self, step=None):
             h_up_band[-1, :] += -np.ones(h_up_band.shape[1]) * lamb
             d_x = alpha * invmul_banded(h_up_band, f)
         else:
-            h_test = (h_test - np.eye(h_test.shape[0]) * lamb)
+            h_test = h_test - np.eye(h_test.shape[0]) * lamb
             d_x = alpha * np.linalg.solve(h_test, f)
 
         d_x.shape = self.fix.fixbeads.q.shape

ipi/interfaces/sockets.py

@@ -939,7 +939,9 @@ def dispatch_free_client(self, fc, match_ids="any", send_threads=[]):
             # makes sure the request is marked as running and the client included in the jobs list
             fc.locked = fc.lastreq is r["id"]
 
-            r["offset"] = (
+            r[
+                "offset"
+            ] = (
                 self.offset
             )  # transmits with the request an offset value for the energy (typically zero)
 

ipi/utils/parsing.py

@@ -50,9 +50,14 @@ def read_output(filename):
         match = header_pattern.match(line)
         if match:
             # Extracting matched groups
-            col_type, start_col, end_col, property_name, units, description = (
-                match.groups()
-            )
+            (
+                col_type,
+                start_col,
+                end_col,
+                property_name,
+                units,
+                description,
+            ) = match.groups()
             col_info = f"{start_col}-{end_col}" if end_col else start_col
             properties[col_info] = {
                 "name": property_name,

tools/py/energy_ppi.py

@@ -152,7 +152,9 @@ def totalEnergy(prefix, temp, ss=0):
                         rc[:] - q[j, i * 3 : i * 3 + 3], f[j, i * 3 : i * 3 + 3]
                     )
 
-            ePA *= 0.5 * nbeads * (Constants.kb * temperature) ** 2 / Constants.hbar**2
+            ePA *= (
+                0.5 * nbeads * (Constants.kb * temperature) ** 2 / Constants.hbar**2
+            )
             ePA += 0.5 * nbeads * (3 * natoms) * Constants.kb * temperature + U
             f2ePA = f2 * ePA
             eVir /= 2.0 * nbeads