Hi Nick,
thank you for the suggestion.
Indeed, Inelastica offers a tool to convert cartesian geometry to a
z-matrix.
It also keeps the order of atoms and the output seems to be correct
(Siesta created xyz file looks correct).
Sadly, the constraints don't seem to work in the relaxations process.
I applied two constraints to a torsional angle, but Siesta doesn't
properly relax the system any longer. Instead it moves whole blocks of
atoms instead of moving it freely, which doesn't make sense. The atoms
with the constraints are the last ones in the list, so even if there is
a small bug, it shouldn't affect the previous atoms, but it seems to do.
To validate that I haven't done something fundamentally wrong, I tried
to add some other constraints, same effect. I also inverted the
constraints, resulting in a really rigid system.
For now I have to assume that the z-matrix implementation doesn't
properly work (using Siesta Trunk 4.31) . Maybe it's because I have a
too large molecule (62 atoms), I don't know.
Excerpt of my z-matrix:
ZM.UnitsLength Ang
ZM.UnitsAngle deg
%block Zmatrix
molecule
2 1 1 1 0.000000000 0.000000000 0.000000000 1 1 1
4 1 0 0 1.039279130 71.521282134 36.832905451 1 1 1
2 2 1 0 11.009927486 139.129013969 -32.140521098 1 1 1
4 3 2 1 1.093554670 25.282100120 -27.855292414 1 1 1
....
1 56 55 54 1.489603039 108.089831202 140.484983799 1 1 1
3 57 56 55 1.370454084 120.848946586 82.090094914 1 1 0
1 58 57 56 6.005719299 26.225299396 71.464457416 1 1 1
4 59 58 57 1.419017222 96.338481585 143.243659157 1 1 1
1 60 59 58 1.489368822 108.081952863 -8.484961798 1 1 1
3 61 60 59 1.361183653 121.028066969 82.120260295 1 1 0
cartesian
constants
variables
constraints
%endblock Zmatrix
best wishes,
Frank
On 07/17/2013 03:17 PM, Nick Papior Andersen wrote:
I have never tried it but Inelastica:
http://inelastica.sourceforge.net/ has routines for converting to a
zmatrix from a Cartesian geometry.
You could try that.
Kind regards Nick
2013/7/17 Frank Maier <[email protected]
<mailto:[email protected]>>
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
