nebmake.py error

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pkluijtmans
Posts: 3
Joined: Fri Oct 06, 2023 1:54 pm

nebmake.py error

Post by pkluijtmans »

Dear Graeme,

I am trying to do nonlinear interpolations with the nebmake.py, but it I get nan values for all images. My input POSCARs as initial and final image are below. 1 tetrahedron makes a 180 degree rotation, the tetrahedron with Sulphur number 14 as the centre atom, and the two structures are indistinguishable. The indices of the 4 rotating O atoms, are correct with the rotation. But when I use nebmake.py I get images will all positions of atoms in the structure as NaN. And the following lines appear immediately after calling nebmake.py:
/usr/lib/python2.7/site-packages/ase/neb.py:327: RuntimeWarning: divide by zero encountered in divide
e = 0.5 * (dd**2 / d4).sum()
/usr/lib/python2.7/site-packages/ase/neb.py:328: RuntimeWarning: divide by zero encountered in divide
f = -2 * ((dd * (1 - 2 * dd / d) / d**5)[..., np.newaxis] * D).sum(0)
/usr/lib/python2.7/site-packages/ase/neb.py:328: RuntimeWarning: invalid value encountered in multiply
f = -2 * ((dd * (1 - 2 * dd / d) / d**5)[..., np.newaxis] * D).sum(0)
/usr/lib/python2.7/site-packages/ase/neb.py:272: RuntimeWarning: invalid value encountered in double_scalars
f -= ft / tt * tangent
/usr/lib/python2.7/site-packages/ase/neb.py:274: RuntimeWarning: invalid value encountered in double_scalars
t2 * self.k[i], tangent) / tt * tangent

I guess the divide by zero results in NaN, but I do not get why this happens. The POSCARS look fine to me. Thanks in advance!
Attachments
Archief.zip
initial and final POSCAR
(14.83 KiB) Downloaded 1007 times
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