shankar1729
commented
1 month ago It appears that createXSF does not read the embed center at all, and even if it did, it's unclear how to use that in writing the XSF file, which only takes lattice vectors for the scalar fields and not an offset.
This may be easier to control with the X3D visualization techniques we introduced for the BEAST electrochemistry workshops: see ase_ext.tbz2 linked from https://beast-echem.org/workshops/2024/ for example. The code may still need tweaking to work with arbitrary embed centers, but is more manageable than XSF (and my horrendous old octave createXSF code that I can barely read now!).
Hello Prof. Sundararaman,
I'm trying to visualize solvent cavities in CANDLE using the createXSF script. I can see that it shifts the array to be centered at the coulomb truncation embed, but it seems the arrays for double-grid quantities are not centered there. For example, on this Ag (211) slab the atoms and data appear completely unaligned in x and z (y is symmetric):
It seems like the fluid is centered on to the center of the normal grid in some cases, but in others it's still a bit off. Centering the above gives:
While it's trivial to shift this to align with the atoms by eye, it's difficult to do so in a standardized way for all of the cavities I want to compare. Is there any way I can systematically determine the center of the fluid outputs from input/output?