Hi everyone,
I currently try to run Siesta using the Z-Matrix input in order to add
more flexible constraints to my simulation.
But my main problem is the creation of the Z-Matrix. I have up to 100
Atoms, so building it from hand is nearly impossible.
I tried the program Aten, which allows me to convert the Cartesian
coordinates to a z-matrix format by maintaining the atom order. The
z-matrix however seems to be broken, at least the following Cartesian
coordinates produced by Siesta are garbage. It also stores all values in
variables and somehow Siesta doesn't accept them as variables.
I also tried Avogadro and its Gaussian export function which also gives
me a z-matrix, but it reshuffles the atoms and so adding defined
constraints to the angles between specific atoms is not possible any longer.
All in all does Siesta also use its own implementation in the Z-Matrix
format (different column order, first three rows require additional
informations, ...)
So how do you create your Z-matrix?
What programs can you recommend?
Or have you written your own script to convert xyz to z-matrix and might
share it?
Best wishes,
Frank
