from sella import Sella
from ase.build import molecule
from ase.calculators.emt import EMT
atoms = molecule("N2")
atoms.calc = EMT()
opt = Sella(atoms)
opt.run()
The same error happens with LennardJones as the calculator instead of EMT.
Traceback
ValueError Traceback (most recent call last)Cell In[1], line 8
6 atoms.calc = EMT()
7 opt = Sella(atoms)
----> 8 opt.run()
File ~\miniconda\envs\test\Lib\site-packages\ase\optimize\optimize.py:430, in Optimizer.run(self, fmax, steps)
415 """Run optimizer.
416
417 Parameters
(...)
427 True if the forces on atoms are converged.
428 """
429 self.fmax = fmax
--> 430 return Dynamics.run(self, steps=steps)
File ~\miniconda\envs\test\Lib\site-packages\ase\optimize\optimize.py:275, in Dynamics.run(self, steps)
257 def run(self, steps=DEFAULT_MAX_STEPS):
258 """Run dynamics algorithm.
259
260 This method will return when the forces on all individual
(...)
272 True if the forces on atoms are converged.
273 """
--> 275 for converged in Dynamics.irun(self, steps=steps):
276 pass
277 return converged
File ~\miniconda\envs\test\Lib\site-packages\ase\optimize\optimize.py:246, in Dynamics.irun(self, steps)
243 # run the algorithm until converged or max_steps reached
244 while not is_converged and self.nsteps < self.max_steps:
245 # compute the next step
--> 246 self.step()
247 self.nsteps += 1
249 # log the step
File ~\github\sella\sella\optimize\optimize.py:248, in Sella.step(self)
247 def step(self):
--> 248 s, smag = self._predict_step()
250 # Determine if we need to call the eigensolver, then step
251 if self.nsteps_since_diag >= self.diag_every_n:
File ~\github\sella\sella\optimize\optimize.py:227, in Sella._predict_step(self)
225 self.pes.calculate_hessian()
226 else:
--> 227 self.pes.diag(**self.diagkwargs)
228 self.nsteps_since_diag = -1
229 self.initialized = True
File ~\github\sella\sella\peswrapper.py:269, in PES.diag(self, gamma, threepoint, maxiter)
266 Hproj = NumericalHessian(self._calc_eg, self.get_x(), self.get_g(),
267 self.eta, threepoint, Ufree)
268 Hc = self.get_Hc()
--> 269 rayleigh_ritz(Hproj - Ufree.T @ Hc @ Ufree, gamma, P, v0=v0,
270 method=self.eigensolver,
271 maxiter=maxiter)
273 # Extract eigensolver iterates
274 Vs = Hproj.Vs
File ~\github\sella\sella\eigensolvers.py:58, in rayleigh_ritz(A, gamma, P, B, v0, vref, vreftol, method, maxiter)
56 while True:
57 Atilde = V.T @ (symmetrize_Y(V, AV, symm=symm))
---> 58 lams, vecs = eigh(Atilde, V.T @ B @ V)
59 nneg = max(1, np.sum(lams < 0))
60 # Rotate our subspace V to be diagonal in A.
61 # This is not strictly necessary but it makes our lives easier later
File ~\miniconda\envs\test\Lib\site-packages\scipy\linalg\_decomp.py:458, in eigh(a, b, lower, eigvals_only, overwrite_a, overwrite_b, type, check_finite, subset_by_index, subset_by_value, driver)
454 if driver not in drv_str:
455 raise ValueError('"{}" is unknown. Possible values are "None", "{}".'
456 ''.format(driver, '", "'.join(drv_str[1:]))) --> 458 a1 = _asarray_validated(a, check_finite=check_finite)
459 if len(a1.shape) != 2 or a1.shape[0] != a1.shape[1]:
460 raise ValueError('expected square "a" matrix')
File ~\miniconda\envs\test\Lib\site-packages\scipy\_lib\_util.py:321, in _asarray_validated(a, check_finite, sparse_ok, objects_ok, mask_ok, as_inexact)
319 raise ValueError('masked arrays are not supported')
320 toarray = np.asarray_chkfinite if check_finite else np.asarray
--> 321 a = toarray(a)
322 if not objects_ok:
323 if a.dtype is np.dtype('O'):
File ~\miniconda\envs\test\Lib\site-packages\numpy\lib\_function_base_impl.py:649, in asarray_chkfinite(a, dtype, order)
647 a = asarray(a, dtype=dtype, order=order)
648 if a.dtype.char in typecodes['AllFloat'] and not np.isfinite(a).all():
--> 649 raise ValueError(
650 "array must not contain infs or NaNs")
651 return a
ValueError: array must not contain infs or NaNs
The following simple example does not seem to work, and I'm not 100% sure why.
Reproduction
The same error happens with
LennardJonesas the calculator instead ofEMT.Traceback