Geometry optimisation is working well by itself, but there is a bug in the qmmm example:
/home/animal/Packages/pyberny/berny/Math.py:129: RuntimeWarning: divide by zero encountered in double_scalars
x = x-fx/dxf
/home/animal/Packages/pyberny/berny/berny.py:182: RuntimeWarning: invalid value encountered in multiply
return norm(np.linalg.solve(l*eye(H.shape[0])-H, g))-trust
Traceback (most recent call last):
File "10-with_qmmm.py", line 24, in <module>
mol1 = berny_solver.optimize(mf)
File "/home/animal/Packages/pyscf/pyscf/geomopt/berny_solver.py", line 63, in optimize
optimizer.send((energy, gradients))
File "/home/animal/Packages/pyberny/berny/berny.py", line 36, in Berny
converged = algo.step(energy, gradients, log=log)
File "/home/animal/Packages/pyberny/berny/berny.py", line 94, in step
dot(proj, s.interpolated.g), H_proj, s.weights, s.trust, log=log
File "/home/animal/Packages/pyberny/berny/berny.py", line 183, in quadratic_step
l = Math.findroot(steplength, ev[0]) # minimization on sphere
File "/home/animal/Packages/pyberny/berny/Math.py", line 136, in findroot
raise FindrootException()
berny.Math.FindrootException
This is the issue reported by pyscf https://github.com/sunqm/pyscf/issues/147
Geometry optimisation is working well by itself, but there is a bug in the qmmm example: