Studying a surface
This lesson was created for an earlier version of BigDFT, from before the change to the yaml input format. A new version of the tutorial has not yet been created. In the meantime, bigdft-tool can be used to convert from the old input file format to the yaml format.
Surface calculations with an ideal monolayer of water molecules
The purpose of this lesson is to introduce the surface calculation, the output of different scalar field like the local potential and to add an electric field.
Defining a surface configuration
The boundary conditions are specified in the position file. No other parameters are necessary to be changed. To do it, modify the second line of the XYZ posinp.xyz file to write the keyword surface like in this example:
3 angstroem surface 3.5 1.0 3.0 O 1.5 0.0 1.5 H 0.7285 0.620919 1.5 H 2.2715 0.620919 1.5
Three floats are required after the surface keyword to define the bounding box in x, y and z direction. In BigDFT, the direction perpendicular to the surface must be the y direction. The box size in that one is then irrelevant (ignored by the code).
The example above describes a mono layer of water molecules. This un-realistic example is used to easily illustrate the capability of BigDFT to exactly compute the local potential, even in the case of an internal dipolar moment.
Exercise: run BigDFT for the given atomic configuration.
The convergence is still good and calculation terminates within 13 iterations. One can notice also the y free direction in the screen output when looking at the Poisson solver output, giving a box dimensions of 40x163x36 in grid spacings.
Plot the potential values
It is possible to output scalar fields like the different potentials (Hartree, external (ionic) and local) after the last electronic convergence. To do this, set the third number of the eleventh line of input.dft to 2:
0 0 2 InputPsiId, output_wf, output_grid
Exercise: rerun the previous calculation to give a look to the local potential. A file local_potential_avg_y will be generated in the data directory and contains the projection along the y axis of the local potential (i.e.Hartree plus ionic).
One can see the existence of a dipolar moment due to the displacement between the center of mass of negative charges and positive charges. The plot shows the quality of the Poisson solver calculation introducing no artifact or necessary accordance at boundaries.
Add an electric field
Thanks to the Green function treatment in the Poisson solver, we've seen that's it's possible to exactly treat the dipolar moment in a box, add a charge (cf. <a href="H1B_grid_cv.html" target="_blank" >previous tutorial</a>) but it is also possible to add an electric field. To do this, set the second value of the fourth line of input.dft:
0 0.0 0.010 0.0 charge of the system, Electric field
The unit for the electric field is hartree per bohr and the direction of the field is always the y direction (even for non surface calculations).
Exercise: rerun the previous calculation with an electric field of 0.01Ht/bohr.
The local potential is bent by the field as expected.