Many large negative frequencies


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I think your main problem is that the geometry you specified for the frequency calculation is not at a minimum (or any stationary point), at least according to the test calculation I ran. Edo's input included an optimization before the frequency calculation so even though he specified the same geometry, it was optimized before doing the frequency calculation.

As a side note, as the documentation states, analytical second derivatives of the Minnesota functionals are not implemented so any frequency calculation with them will be numerical (i.e. in this case task dft freq and task dft freq numerical will do the exact same calculation).