I'm posting this here as an answer so that if anyone else runs into the same problem, they can get it clarified.
After searching endlessly (because the SIESTA to BoltzTraP2 interface provided by the developers failed), I figured it out by myself. What happened was a problem of the k-point output file from SIESTA not being what BoltzTraP2 expects.
If you are ...
You mentioned DFT, which is typically used to calculate the electronic energy at zero temperature. You can adjust the geometry until this electronic energy is lowest, but then you might ask why for a given pressure, if you increase the temperature, a substance's geometry changes, perhaps from an ordered lattice, to a disordered liquid, to a bunch of ...
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 ...
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
Perhaps not the most detailed answer, since I'm not hugely familiar with the precise functionality/details that would be involved, but GPAW does seem to have the functionality.
Caveat: The GPAW docs are currently undergoing a fairly complete overhaul, so the link may be dead in the medium/long-term future, but as of the writing of this answer, it works.