Change the order of if-statements in critical algo

First change is to make sure, if there is LinAlg error then
to discontinue.
If the density is zero, then discontinue
if the gradient isn't zero, then discontinue.

chemtools/topology/critical.py

@@ -142,19 +142,23 @@ def find_critical_points(self):
  (self._coords is not None and index < len(self._coords)):
  try:
  coord = self._root_vector_func(point.copy())
+ # add critical point if it is new and it doesn't contain any
+ if not (
+ np.any([np.linalg.norm(coord - cp.coordinate) < 1.e-3 for cp in self.cps])
+ and not np.any(np.isnan(coord))
+ ):
+ dens = self.func(coord)
+ # skip critical point if its density value is zero
+ if np.abs(dens) > 1.e-4:
+ grad = self.grad(coord)
+ # Make sure gradient is zero, as it's a critical point.
+ if np.all(np.abs(grad) < 1e-4):
+ # compute rank & signature of critical point
+ eigenvals, eigenvecs = np.linalg.eigh(self.hess(coord))
+ cp = CriticalPoint(coord, eigenvals, eigenvecs, 1e-4)
+ self._cps.setdefault((cp.rank[0], cp.signature[0]), []).append(cp)
  except np.linalg.LinAlgError as _:
  continue
- # add critical point if it is new
- if not np.any([np.linalg.norm(coord - cp.coordinate) < 1.e-3 for cp in self.cps]):
- dens = self.func(coord)
- grad = self.grad(coord)
- # skip critical point if its dens & grad are zero
- if abs(dens) < 1.e-4 and np.all(abs(grad) < 1.e-4):
- continue
- # compute rank & signature of critical point
- eigenvals, eigenvecs = np.linalg.eigh(self.hess(coord))
- cp = CriticalPoint(coord, eigenvals, eigenvecs, 1e-4)
- self._cps.setdefault((cp.rank[0], cp.signature[0]), []).append(cp)
  # check Poincare–Hopf equation
  if not self.poincare_hopf_equation:
  warnings.warn("Poincare–Hopf equation is not satisfied.", RuntimeWarning)
@@ -178,6 +182,7 @@ def _root_vector_func(self, guess, maxiter=5000):
  guess = guess - np.dot(np.linalg.inv(hess), grad[:, np.newaxis]).flatten()
  norm = np.linalg.norm(grad, axis=-1)
  niter += 1
+ # Sometimes guess returns [np.nan, np.nan, np.nan]
  return guess
 
  @staticmethod