Step 5. Analyze results of several calculations at once
When all the ammonia optimization jobs are finished, we can compare the results. The main conclusion that you will reach is that DZ (double zeta) basis set optimization, job name 'NH3.DZ.Large', leads to the planar ammonia molecule, which is an artefact. As covered in the preceding tutorials, you can optionally use several GUI modules to observe that:
- ADFmovie, which will show the geometry optimization
- ADFinput, which will open the (last) converged geometry
- ADFview, which will open the converged geometry and also would display various density maps in 3D
For example, let us use ADFview to demonstrate the results:
Select job NH3.DZ.Large in the ADFjobs window (should then be highlighted) Select SCM → View Select Fields → Grid → Fine Select Add → HOMO In the isosurface contour value field which appeared at the bottom, change the default '0.03' to '0.3' Type 'Ctrl-minus' several times, until the central N atom ball does not overlap strongly with the HOMO orbital.
Similarly, visualize HOMO of NH3 optimized in any basis set other than DZ (for example, from job NH3.DZP.Large)
What you will observe is that HOMO of ammonia does not have the anticipated sp3 hybridization, when DZ basis set is used (planar ammonia as optimized in DZ is to the left; pyramidal ammonia as optimized in DZP is to the right) :
Starting from ADF version 2008, an automated procedure to report results from a list of ADF jobs is available. This task is achieved via using the Report tool within ADFjobs. Below we will demonstrate how to do this for our set of completed NH3 molecule optimizations.
Go to the ADFjobs window Select Tools → New Report Template...
This will open up Report dialog. In the 'Report' field, you can choose the name for your report file and its format ('HTML' or 'Tab separated plain text'). The other fields ('General', 'Images', 'Results') contain various relevant options you can choose for preparing your report. Check boxes are marked in red against the options which will enter the report by default:
In the 'Report'/'Template name' field, type 'MyReport' In the 'Results' field check the non-default boxes against 'Dipole Moment' and 'Dipole Vector' Click 'OK'
The Report dialog will close, saving our template named 'MyReport'. Now we will generate actual report following the saved template:
In ADFjobs window, select all the finished jobs from the NH3 set Select Tools → Build MyReport Report
'Save As' dialog window will pop up, showing the 'report.html' default file name.
Choose your file name and location, then click 'Save'
Now ADF will scan through your job list and prepare the report. Finally the browser will start showing your report file (by default, named 'report.html'). Below, only the part of the HTML report is shown; if the font appears too small, the image below can be viewed in a separate window (for example, using Right-Click, and selecting 'View Image' from some browsers on Windows).
The Report tool created a table-like report of the results. We can clearly see that only for DZ basis optimization our NH3 molecule is planar, see the last 'row' of the report table. Above, we have selected to report dipole moment and dipole vector; these values show up in the two last columns. Obviously the dipole moment is zero only for the planar NH3 structure.
Congratulations, we are done with the ammonia optimization tutorial!
If you want to exit all the GUI modules at once: select SCM → Close All
