Geometry Optimisations

esmuigors said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:

About the manual extraction – do I understand correctly that I should take the primitive and not crystallographic cell parameters?! The input in the .d12 file is in crystallographic cell, isn't it?

Hi esmuigors,
If you want to proceed with the manual extraction of the geometry you should copy the Crystallographic cell lattice parameters required by the space group you are working with (e.g. Monoclinic will require you a, b, c and β, while a cubic only the a lattice vector), the only exception to this are P lattices where the primitive and crystallographic coincide. Accordingly, also the fractionary coordinate you will copy should be the one of the Crystallographic cell, but you should copy only the atoms present in the asymmetric unit of your system identified by a T in the FINAL OPTIMIZED GEOMETRY print in the .out file, I will include here below an example to better clarify.

FINAL OPTIMIZED GEOMETRY - DIMENSIONALITY OF THE SYSTEM 3 (NON PERIODIC DIRECTION: LATTICE PARAMETER FORMALLY SET TO 500) ******************************************************************************* LATTICE PARAMETERS (ANGSTROMS AND DEGREES) - BOHR = 0.5291772083 ANGSTROM PRIMITIVE CELL - CENTRING CODE 6/0 VOLUME= 62.890767 - DENSITY 13.512 g/cm^3 A B C ALPHA BETA GAMMA 6.02167869 6.02167869 6.02167869 147.475653 147.475653 46.660012 ******************************************************************************* ATOMS IN THE ASYMMETRIC UNIT 2 - ATOMS IN THE UNIT CELL: 4 ATOM X/A Y/B Z/C ******************************************************************************* 1 T 273 TA -2.420755613827E-03 -2.420755613827E-03 4.983867094700E-20 2 F 273 TA -2.524207556138E-01 2.475792443862E-01 -5.000000000000E-01 3 T 233 AS 4.184207556138E-01 4.184207556138E-01 -2.220446049250E-16 4 F 233 AS 1.684207556138E-01 -3.315792443862E-01 -5.000000000000E-01 TRANSFORMATION MATRIX PRIMITIVE-CRYSTALLOGRAPHIC CELL 0.0000 1.0000 1.0000 1.0000 0.0000 1.0000 1.0000 1.0000 0.0000 ******************************************************************************* CRYSTALLOGRAPHIC CELL (VOLUME= 125.78153367) A B C ALPHA BETA GAMMA 3.37253732 3.37253732 11.05868170 90.000000 90.000000 90.000000 COORDINATES IN THE CRYSTALLOGRAPHIC CELL ATOM X/A Y/B Z/C ******************************************************************************* 1 T 273 TA -1.956455588613E-19 2.296201495291E-19 -2.420755613827E-03 2 F 273 TA -5.000000000000E-01 2.084229456032E-17 -2.524207556138E-01 3 T 233 AS 5.000000000000E-01 5.000000000000E-01 -8.157924438617E-02 4 F 233 AS -5.117515658395E-17 -5.000000000000E-01 -3.315792443862E-01

In this example you'll have to extract from the second geometry print (i.e. Crystallographic cell) the a and c lattice parameters, given the Tetragonal lattice, alongside the fractionary coordinate of atoms 1 and 3.

esmuigors said in Unexpectedly cannot get the geometry after optimization: KEYWORD EXTPRT NOT ALLOWED:

Are there any workarounds to persuade the script to actually copy the fort.34 file?

In this regards, I don't have your script, but it should be sufficient to add to your script something along these lines in the section where all the files are copied back to your working folder:

if [ -e fort.34 ] then cp fort.34 $HERE/$INPUTFILE.f34 fi

in this case $HERE=$PWD, while $INPUTFILE is the variable corresponding to your input name.

I hope this helps.

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