Hi Rahul,
gdis can read pdb and write fdf. If you have an Ubuntu-based Linux, you
can just install it from the usual repositories. xyz does not contain
information about size and shape of the cell, but is otherwise an easier
starting point to do it manually (any editor with a "replace all"
function should allow you to do in NumberOfSpecies (rather than
NumberOfAtoms) steps).
Good luck,
Herbert
On 07/09/2019 01:19, RAHUL SURESH wrote:
Hi Herbert
I need the input in fdf format.
I have my input coordinates as PDB and xyz. In case of siesta, as the
coordinates must be terminated with atomic species number and my system
is having 700 atoms ( C N H ) it is too difficult to terminate them
manually. Any way I have to do it if there is no option left. So I wanna
know if it is possible to determine siesta accessible coordinates format.
Thank you
On Sat, 7 Sep, 2019, 1:38 AM Herbert Fruchtl,
<[email protected]
<mailto:[email protected]>> wrote:
Hi Rahul,
In what format do you have the coordinates? I have a program that
translates
between various periodic formats (fdf, VASP, CASTEP, Quantum
Espresso) that I
could send you. Some viewers (I use gdis) can save structures as
fdf. And then
there's ASE, which can read and write in a plethora of formats (but
you need to
now a bit of Python).
Cheers,
Herbert
On 05/09/2019 07:54, RAHUL SURESH wrote:
> Hi
>
> On a basic question- I am computing large-scale density
functional theory (DFT)
> calculations. The system has 700 atoms approx. Is there any
particular software
> to generate coordinates for siesta input to be included in %block
> atomiccoordinatesandatomicspecies?
>
> Or in case if I am reading the input from a file, say
"coordinate.data", should
> the coordinates be terminated with atomic species number?
>
> Thank you
> --
> /Regards,/
> /Rahul**/
--
Herbert Fruchtl
Senior Scientific Computing Officer
School of Chemistry, School of Mathematics and Statistics
University of St Andrews
--
The University of St Andrews is a charity registered in Scotland:
No SC013532
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