Geometry Optimisations

I have actually managed to get the crystallographic cell parameters and fractional coordinates, and the calculation seems to be proceeding fine (forces are not greater than 10^-15 a.u.). If anyone finds this useful, the bash script is below. But I haven't tested it with any other spacegroup yet, just the 64th one.

#!/bin/bash outfile="$1" [ ! -f "$outfile" ] && echo "File not found!" && exit 5 [ -z "$(grep -e 'FINAL OPTIMIZED GEOMETRY' "$outfile")" ] && echo "The geometry optimization did not finish!" && exit 3 cat "$outfile" | sed -n '/^ *FINAL OPTIMIZED GEOMETRY/,/TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT END/p' | grep -A 2 -e '^ *CRYSTALLOGRAPHIC CELL' | tail -1 | sed 's@ \+@\n@g' | uniq | grep -v -e '^ *$' -e '^90.0000' > "${outfile%out}gem" fractionals="$(cat "$outfile" | sed -n '/^ *FINAL OPTIMIZED GEOMETRY/,/TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT END/p' | sed -n '/^ *COORDINATES IN THE CRYSTALLOGRAPHIC CELL/,/^ *$/p' | sed '1,3d;$d')" echo "$fractionals" | wc -l >> "${outfile%out}gem" echo "$fractionals" | gawk '{printf " %2d\t% 2.12e\t% 2.12e\t% 2.12e\n",$3,$5,$6,$7}' >> "${outfile%out}gem"

Hi,

The FINALRUN option works fine in P-CRYSTAL: that sentence in the Manual must be a leftover from the past, sorry for that.

Can you elaborate on how the optimized structures are unreasonable? Is it just for the underestimation of the computed band gap or also for some structural aspects? In this case, it would help if you could show us the "expected" structure, as well as the one you obtain from the optimization.

Hi,

Jefferson Maul has run a few tests and indeed we were able to reproduce the odd behavior you've been experiencing. Those negative values for the electron population of the vacancy are indeed very strange and may be suggestive of a basis set unbalance. It seems that whenever basis functions are left on the vacant site (either with your initial ATOMSUBS approach or with the more "canonical" GHOSTS approach) those functions are much "needed" by surrounding atoms.

We have found a possible way forward for your system through the use of the ATOMREMO option. With this option, you create the vacancy by removing the selected atom alongside its basis functions. For instance, we have used this approach to study Oxygen vacancies in CaSnO3 here.

We have used this approach on your system (on a smaller supercell to be able to run the tests more efficiently) and the geometry optimization went well. See the attached output file as a guide.

Hope this helps,

GiacomoAmbrogio Great! It works now! Thanks a lot!

Thank you very much. Now it works without any issue. I was not aware of the necessity to change this parameter as I did not encounter any issue with other calculations I have done due to it being 0 0 0.

Hi Othmen!

I think that you have a problem in the geometry sections of your input files. When dealing with monoclinic structures, only one angle (beta) has to be specified as alfa and gamma are 90 by default, see page 22 of Crystal User's Manual. Furthermore, in input1 the atomic coordinates are missing, while in input2 94 atoms coordinates are written but you specified that 95 atoms are present.

Let me know if you have other problems 🙂

Thank you very much for the detailed explanation—this really helped clarify things for me! The plot and your explanation made it all very clear.

Many thanks for your detailed explanation and for checking the code — that definitely clarifies things. I really appreciate your help!

thank you