Atomic simulation environment can do this with the following line of logic.
Calculate the number of nearest neighbors for all atoms
Select the undercoordinated atoms
Calculate the direction away from the neighbors (sum vectors from
neighbor->atom and normalize)
Add your atom to cover the dangling bonds, such as H, in direction
of calculated vector
This error has been resolved now. Though I am not an expert but here are few thoughts. There may be several reasons for this error:
This error might appear due to numerical instability from overlapping atoms.
As mentioned by @Phil Hasnip, if the S-matrix eigenvalues are really small.
Some pseudopotential may not fit with calculation, USPP giving non-...
The effective mass is related to the second derivative of the E-k curve as
So an accurate value of effective mass requires an accurate dispersion curve at all k points. If enough k values are not taken to plot the curve, plotting tools will interpolate the values to have a smooth curve, and the values may vary significantly from the actual values. This may ...