If you are merely interested in finding the displacements of atoms from the
initial atomic configuration you can use (disclaimer) my software package
sisl <https://github.com/zerothi/sisl>:
#### script
import sisl as s
geom_in = s.get_sile('RUN.fdf').read_geometry()
geom_out = s.get_sile('RUN.fdf').read_geometry(order=['XV'])
print(geom_out.xyz - geom_in.xyz)
### done
This will print, to stdout the displacements of each atom from the initial
configuration and the final configuration.
Den man. 2. jul. 2018 kl. 22.05 skrev Harsh Shah <[email protected]>:
> Thanks.
>
> Is there any particular software I can use for this?
>
> On Sat, 30 Jun 2018, 3:07 pm Mehdi Shamekhi, <[email protected]>
> wrote:
>
>> Define two matrix, first one the relaxed atom coordinates and second one
>> the initial atom coordinates.
>>
>> The differential will be the displacement of each atom.
>>
>> _______________________
>>
>> Mehdi Shamekhi
>> MSc student of Electrical Engineering
>> Department of Electrical Engineering
>> University of Zanjan, Zanjan, Iran
>>
>>
>>
>> On Fri, Jun 29, 2018 at 00:33, Harsh Shah <[email protected]> wrote:
>>
>> Thanks, I got the first part.
>>
>> Can you please elaborate on how can I find displacement by differential
>> of .fdf and .out coordinates.
>>
>>
>>
>> On Wed, Jun 27, 2018 at 3:05 PM Mehdi Shamekhi <[email protected]>
>> wrote:
>>
>> Hello
>>
>> In the last SCF of each CG step the dDmax must be less than what you have
>> defined in your .fdf file.
>>
>> dDmax is the DM.Tolerance.
>>
>> If it is less than the value you put in the .fdf file it has been
>> converged.
>>
>> outcoor: Relaxed or unrelaxed atomic coordinates is at the end of .out
>> file where you can find the atom displacement by differential of .fdf and
>> .out coordinates.
>>
>> Regards,
>> Mehdi
>>
>> _______________________
>>
>> Mehdi Shamekhi
>> MSc student of Electrical Engineering
>> Department of Electrical Engineering
>> University of Zanjan, Zanjan, Iran
>>
>>
>>
>> On Wed, Jun 27, 2018 at 00:42, Harsh Shah <[email protected]> wrote:
>>
>> Dear Siesta user,
>>
>> 1. How can I determine whether first energy minimization of a file
>> has converged or not and it has achieved force tolerance? I mean how can I
>> know from the output file/log file or any other file, if it has converged
>> or not and achieved the tolerance?
>> 2. How to calculate displacement of each atom?
>>
>> Regards,
>> Harsh Shah
>>
>>
>>
>>
--
Kind regards Nick
