Dear Avogadro community,
I would like to be able to use Avogadro to plot atomic forces, since I could
not find anything about this in the archives or on the wiki I thought I
would ask it here.
There is already the ability in Avogadro to visualise forces (of the
internal force fields) during geometry optimisation.
However, I would like to be able to plot forces from an external calculation
(e.g. some other geometry optimisation or perhaps some molecular dynamics
run).
Ideally I would take some file with atoms and forces, perhaps like the
xyz-format, for example for benzene (CPMD output in a.u.)
# ATOM COORDINATES GRADIENTS (-FORCES)
> 1 C 8.0928 7.1721 9.4669 -2.615E-05 -2.365E-05 -4.308E-07
> 2 C 10.7329 7.1815 9.4673 1.622E-05 -1.182E-05 -6.480E-06
> 3 C 12.0445 9.4724 9.4646 2.381E-05 -2.595E-05 7.109E-07
> 4 C 10.7165 11.7538 9.4612 -3.304E-06 4.943E-05 9.874E-07
> 5 C 8.0766 11.7446 9.4611 1.678E-05 -6.206E-05 6.322E-06
> 6 C 6.7649 9.4537 9.4639 3.416E-06 2.201E-05 1.319E-05
> 7 H 7.0700 5.3850 9.4693 2.226E-05 1.444E-05 5.035E-06
> 8 H 7.0408 13.5245 9.4587 -2.785E-05 3.492E-05 -6.664E-07
> 9 H 11.7687 5.4017 9.4705 9.805E-06 5.655E-07 1.481E-05
> 10 H 4.7053 9.4462 9.4638 1.488E-06 -9.189E-06 1.782E-06
> 11 H 14.1040 9.4798 9.4652 -1.552E-05 -9.837E-07 4.701E-06
> 12 H 11.7396 13.5409 9.4587 -1.460E-05 -2.542E-05 -6.205E-06
Then after opening the file with Avogadro I would select forces and the
forces arrows would appear!
I would like to be able to choose a color and scale for the arrows.
This way I could plot different force fields and make comparisons for
example.
Currently I plot this (if saved as 'geo.xyz') simply with gnuplot
gnuplot> scale=1E4
gnuplot> spl 'geo.xyz' u 3:4:5 w p lt 0 pt 7 t 'atoms', '' u
> 3:4:5:(scale*$6):(scale*$7):(scale*$8) w vec lt 1 t 'forces'
But of course this is quite ugly and tedious, since it lacks bonds or other
visualisation options and I cannot visualise any dynamical processes.
So my questions are the following:
- Is there any way to do this in Avogadro already?
* If so, what did I miss? (file-format, Avogadro version, etc.)
* If not;
+ Could someone point me in the right direction for adding this
feature?
Perhaps commenting on the best (/easiest) way to implement this.
+ Is there anyone else interested in this feature??
Best regards,
Jaap
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