Merge branch 'master' of github.com:zadorlab/sella

sella/internal.py

@@ -750,7 +750,7 @@ def _find_mic(self, indices: Tuple[int, ...]) -> np.ndarray:
         ])
 
         for dx, ncvec in zip(dxs, ncvecs):
-            vlen = np.infty
+            vlen = np.inf
             for neighbor in self._get_neighbors(dx):
                 trial = np.linalg.norm(dx + neighbor @ self.atoms.cell)
                 if trial < vlen:
@@ -1393,10 +1393,13 @@ def find_all_bonds(
                             self.add_bond((i, j), ts)
                         except DuplicateInternalError:
                             continue
-                        c10y[i, nbonds[i]] = j
-                        nbonds[i] += 1
-                        c10y[j, nbonds[j]] = i
-                        nbonds[j] += 1
+                        if nbonds[i] < max_bonds and nbonds[j] < max_bonds:
+                            c10y[i, nbonds[i]] = j
+                            nbonds[i] += 1
+                            c10y[j, nbonds[j]] = i
+                            nbonds[j] += 1
+                        else:
+                            pass
             first_run = False
             scale *= 1.05
 

sella/optimize/irc.py

@@ -24,7 +24,6 @@ def __init__(
         logfile: str = '-',
         trajectory: Optional[Union[str, TrajectoryWriter]] = None,
         master: Optional[bool] = None,
-        force_consistent: bool = False,
         ninner_iter: int = 10,
         irctol: float = 1e-2,
         dx: float = 0.1,
@@ -41,7 +40,6 @@ def __init__(
             logfile=logfile,
             trajectory=trajectory,
             master=master,
-            force_consistent=force_consistent,
         )
         self.ninner_iter = ninner_iter
         self.irctol = irctol

sella/optimize/optimize.py

@@ -44,7 +44,6 @@ def __init__(
         logfile: str = '-',
         trajectory: Union[str, Trajectory] = None,
         master: bool = None,
-        force_consistent: bool = False,
         delta0: float = None,
         sigma_inc: float = None,
         sigma_dec: float = None,
@@ -98,8 +97,7 @@ def __init__(
         self.rs = get_restricted_step(rs)
         Optimizer.__init__(self, atoms, restart=restart,
                            logfile=logfile, trajectory=asetraj,
-                           master=master,
-                           force_consistent=force_consistent)
+                           master=master)
 
         if delta0 is None:
             delta0 = default['delta0']
@@ -154,7 +152,7 @@ def __init__(
         self.xi = 1.
         self.nsteps_per_diag = nsteps_per_diag
         self.nsteps_since_diag = 0
-        self.diag_every_n = np.infty if diag_every_n is None else diag_every_n
+        self.diag_every_n = np.inf if diag_every_n is None else diag_every_n
 
     def initialize_pes(
         self,

sella/optimize/stepper.py

@@ -56,7 +56,7 @@ def get_s(self, alpha: float) -> Tuple[np.ndarray, np.ndarray]:
 class QuasiNewton(BaseStepper):
     alpha0 = 0.
     alphamin = 0.
-    alphamax = np.infty
+    alphamax = np.inf
     slope = -1
     synonyms = [
         'qn',

sella/py.typed

@@ -0,0 +1 @@
+