ABINIT Tutorial Interatomic Distance of Hydrogens

Abinit Tutorial Interatomic Distance of Hydrogens

A simple tutorial we can investigate with ESTEST is taken from the ABINIT webpages is the calculation of the interatomic distance between two hydrogen atoms and looking at the total energy to estimate the optimal bond length. The original ABINIT tutorial is Lesson 1.2
http://www.abinit.org/documentation/helpfiles/for-v6.6/tutorial/lesson_1.html#12. In section 1.2.c we are asked to simulate two hydrogen atoms whose interatomic distance are adjusted from 1.0 bohr to 2.0 bohr in steps of 0.05 bohr. This gives us twenty simulations that we upload to ESTEST.

  1. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS00.xml
  2. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS01.xml
  3. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS02.xml
  4. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS03.xml
  5. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS04.xml
  6. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS05.xml
  7. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS06.xml
  8. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS07.xml
  9. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS08.xml
  10. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS09.xml
  11. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS10.xml
  12. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS11.xml
  13. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS12.xml
  14. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS13.xml
  15. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS14.xml
  16. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS15.xml
  17. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS16.xml
  18. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS17.xml
  19. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS18.xml
  20. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS19.xml
  21. yuangm/abinit2qbox/hdimer_bondlength/abinit/t12_DS20.xml

If we compare them, it is easy to inspect which simulation corresponding to a particular interatomic distance produces the minimum total energy.

We can post-process this data set to produce a plot of the distance between the hydrogen atoms versus the total energy explicitly by using the ESTEST plugins atom_distance, energy_components, and combining their outputs to input to the google_scatter_plot plugin. The output of google_scatter_plot is shown below

You can download the input XML for the google_scatter_plot plugin here.