/scratch.global/bwaters/jobs/3dab4296-41af-46d1-81cd-f4240bbf2d82-007/TE_422664787246_001-and-MO_680820064987_001-1752098711/staged_job_files/repository/te/ElasticConstantsCubic_diamond_Re__TE_422664787246_001/../../td/ElasticConstantsCubic__TD_011862047401_006/runner:45: FutureWarning: Please use atoms.calc = calc self.slab.set_calculator(self.calculator) /scratch.global/bwaters/jobs/3dab4296-41af-46d1-81cd-f4240bbf2d82-007/TE_422664787246_001-and-MO_680820064987_001-1752098711/staged_job_files/repository/te/ElasticConstantsCubic_diamond_Re__TE_422664787246_001/../../td/ElasticConstantsCubic__TD_011862047401_006/runner:119: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) self.minscale = float( Traceback (most recent call last): File "/scratch.global/bwaters/jobs/3dab4296-41af-46d1-81cd-f4240bbf2d82-007/TE_422664787246_001-and-MO_680820064987_001-1752098711/staged_job_files/repository/te/ElasticConstantsCubic_diamond_Re__TE_422664787246_001/../../td/ElasticConstantsCubic__TD_011862047401_006/runner", line 248, in results = bulkmodulus.results() File "/scratch.global/bwaters/jobs/3dab4296-41af-46d1-81cd-f4240bbf2d82-007/TE_422664787246_001-and-MO_680820064987_001-1752098711/staged_job_files/repository/te/ElasticConstantsCubic_diamond_Re__TE_422664787246_001/../../td/ElasticConstantsCubic__TD_011862047401_006/runner", line 128, in results elastic_constants, info = hess(np.zeros(6, dtype=float)) File "/usr/local/lib/python3.10/dist-packages/numdifftools/core.py", line 538, in __call__ return super(Hessdiag, self).__call__(np.atleast_1d(x), *args, **kwds) File "/usr/local/lib/python3.10/dist-packages/numdifftools/core.py", line 288, in __call__ results, f_xi = self._derivative(x_i, args, kwds) File "/usr/local/lib/python3.10/dist-packages/numdifftools/core.py", line 238, in _derivative_nonzero_order results = [diff(f, fxi, x_i, h) for h in steps] File "/usr/local/lib/python3.10/dist-packages/numdifftools/core.py", line 238, in results = [diff(f, fxi, x_i, h) for h in steps] File "/usr/local/lib/python3.10/dist-packages/numdifftools/finite_difference.py", line 286, in _central_even - f(x - e_i + e_j) + f(x - e_i - e_j)) / (4. * hess[j, i]) File "/usr/local/lib/python3.10/dist-packages/numdifftools/core.py", line 257, in export_fun return fun(x, *args, **kwds) File "/scratch.global/bwaters/jobs/3dab4296-41af-46d1-81cd-f4240bbf2d82-007/TE_422664787246_001-and-MO_680820064987_001-1752098711/staged_job_files/repository/te/ElasticConstantsCubic_diamond_Re__TE_422664787246_001/../../td/ElasticConstantsCubic__TD_011862047401_006/runner", line 92, in energy_from_strain res = minimize( File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_minimize.py", line 733, in minimize res = _minimize_bfgs(fun, x0, args, jac, callback, **options) File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_optimize.py", line 1419, in _minimize_bfgs _line_search_wolfe12(f, myfprime, xk, pk, gfk, File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_optimize.py", line 1155, in _line_search_wolfe12 ret = line_search_wolfe1(f, fprime, xk, pk, gfk, File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_linesearch.py", line 93, in line_search_wolfe1 stp, fval, old_fval = scalar_search_wolfe1( File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_linesearch.py", line 170, in scalar_search_wolfe1 stp, phi1, phi0, task = dcsrch( File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_dcsrch.py", line 255, in __call__ phi1 = self.phi(stp) File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_linesearch.py", line 84, in phi return f(xk + s*pk, *args) File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_differentiable_functions.py", line 326, in fun self._update_fun() File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_differentiable_functions.py", line 295, in _update_fun fx = self._wrapped_fun(self.x) File "/usr/local/lib/python3.10/dist-packages/scipy/optimize/_differentiable_functions.py", line 21, in wrapped fx = fun(np.copy(x), *args) File "/scratch.global/bwaters/jobs/3dab4296-41af-46d1-81cd-f4240bbf2d82-007/TE_422664787246_001-and-MO_680820064987_001-1752098711/staged_job_files/repository/te/ElasticConstantsCubic_diamond_Re__TE_422664787246_001/../../td/ElasticConstantsCubic__TD_011862047401_006/runner", line 72, in get_energy_from_positions energy = self.slab.get_potential_energy() File "/usr/local/lib/python3.10/dist-packages/ase/atoms.py", line 772, in get_potential_energy energy = self._calc.get_potential_energy(self) File "/usr/local/lib/python3.10/dist-packages/ase/calculators/abc.py", line 26, in get_potential_energy return self.get_property(name, atoms) File "/usr/local/lib/python3.10/dist-packages/ase/calculators/calculator.py", line 515, in get_property self.calculate(atoms, [name], system_changes) File "/usr/local/lib/python3.10/dist-packages/ase/calculators/kim/kimmodel.py", line 289, in calculate self._update_neigh(atoms, self._species_map) File "/usr/local/lib/python3.10/dist-packages/ase/calculators/kim/neighborlist.py", line 456, in update self.build() File "/usr/local/lib/python3.10/dist-packages/ase/calculators/kim/kimpy_wrappers.py", line 110, in myfunc return check_call(func, *args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/ase/calculators/kim/kimpy_wrappers.py", line 101, in check_call return f(*args, **kwargs) File "/usr/local/lib/python3.10/dist-packages/ase/calculators/kim/neighborlist.py", line 371, in build return self.neigh.build( ValueError: cannot create std::vector larger than max_size() Command exited with non-zero status 1 {"realtime":3.27,"usertime":2.99,"systime":2.40,"memmax":107740,"memavg":0}