[Wien] Requesting gentle clarification on OMP_NUM_THREADS, run_lapw, volume optimisation and wien2k update.
Peter Blaha
peter.blaha at tuwien.ac.at
Tue Jun 20 09:46:04 CEST 2023
Usually, you would NEVER edit a cif file, unless you know very well the
corresponding rules.
You have two possibilities to modify a structure:
I 've seen that the cif file is from VESTA. VESTA allows you to remove
atoms, create larger cells, ....
Then export it as cif file and import it into WIEN2k. Then run the
symmetry programs nn, sgroup and symmetry.
Alternatively, convert the cif into a struct file and use the wien2k
tools (x supercell) and the structeditor to remove atoms.
In any case, it is your responsibility to create a "reasonable" model.
You cannot expect that I search the literature to find out the typical
vacancy concentration of HfO2. But it should be clear: for a 3% vacancy
concentration you need a supercell with about 30 oxygen atoms, .....
Am 20.06.2023 um 09:18 schrieb Pranjal Nandi:
>
> Dear Peter and Laurence,
>
> Thank you for your valuable inputs. I have some followup queries.
>
> 1. In the attached CIF file, I want to do DFT simulation on two
> situations. One when there is excess oxygen and one in less
> oxygen. However, I am confused as which part of the cif file I
> should modify/implement the changes
> 1. If I add a new line and add more oxygen, I am unsure of what I
> should set in other parameters such as label, occupancy,
> fract_x,y,z etc.
> 2. I am also confused on how many additions/removal can be
> considered as significant addition/reduction.
> 2. When I am adding/subtracting oxygen, for realistic results
> (matching simulation with lab experimental data), I should be
> doing the simulations on a large supercell or unit cell (for
> oxygen vacancies, I know that I should do a supercell as I cannot
> create it in the unit cell cif file)?
>
> Once again, thank you so much for your continuous support to the
> community.
>
> With warm regards,
>
> Pranjal
>
> *From:*Wien <wien-bounces at zeus.theochem.tuwien.ac.at> *On Behalf Of
> *Peter Blaha
> *Sent:* Thursday, June 15, 2023 5:11 PM
> *To:* wien at zeus.theochem.tuwien.ac.at
> *Subject:* Re: [Wien] Requesting gentle clarification on
> OMP_NUM_THREADS, run_lapw, volume optimisation and wien2k update.
>
> In addition to what L. Marks has already said:
>
> A unit cell with 216 atoms should be run in mpi parallel mode. You
> won't have too many k-points probably, in particularly when doing
> position optimization.
>
> About OMP Laurence Marks has already answered. The Intel mkl does not
> scale to higher OMP numbers. But: Test it out yourself. Set
> OMP_NUM_TREADS to 1 and run one iteration. Check the dayfile how long
> it takes. Set it to 2,4,8,16 and check the timing .... You should see
> that lapw0 will benefit when you set it to 64 (for your 216 atom
> cell), but unfortunately not much speedup in lapw1/2 anymore.
>
> Update of WIEN2k: You should install wien2k into a new directory, thus
> you do not destroy the old installation. In addition, there is a
> "copy" function in siteconfig which would copy the old settings to the
> new installation. It is briefly described on the download page .and in
> the (new !) usersguide as well as in the "update" site of wien2k.
>
> Updating is strongly recommended since the new init_lapw has some
> automatic precision settings and you won't run your supercell with
> 1000 k-points .....
>
> Volume optimization for high vacancy concentration is ok. What you
> read in the UG concerns the stress tensor, which is only NREL.
>
> Hf-4f: No, these are core/semicore states. You don't need
> onsite-hybrid or LDA+U. However, depending on your RMTs you may be
> able to put them into the core by specifying a charge criterium
> instead of an energy (like init -ecut 0.999)
>
> I have some general queries and it would be great if you can
> kindly provide me your feedback.
>
>
>
>
> 1. I have 64 CPU (32 x 2) and more than 9 TB space and the system
> is dedicated entirely to do simulations on DFT. I was thinking
> to set the OMP_NUM_THREADS at 40 or 50 (even higher) to use
> the maximum potential of the computer. But in the guidebook,
> it is recommended that I do not set it higher than 8. May I
> please the reason for this recommendation?
>
>
> 2. Is there a code to run_lapw continuously till it reaches the
> convergence and not start it again after 40 cycles?
>
>
> 3. If I do a volume optimization for a single unit cell and then
> I create a supercell of the optimized structure. Does the
> supercell remains in optimized volume condition? Or it is
> recommended that I do a volume optimization for the supercell
> as well. Further is WIEN2k a reliable platform for volume
> optimization of HfO as in the guidebook on page 87 it mentions
> “The accuracy is thus limited to first and second row elements
> (maybe early 3d elements) and in particular for the 5d series
> and above, large errors may occur due to the neglect of
> (scalar-) relativistic corrections.”
>
>
> 4. Lastly, as it says on the website that it is highly
> recommended to update the WIEN2K version, I am unable to find
> the manual where I can follow the instructions to update the
> version. As I have not done any installation of WIEN2K (my
> past colleague installed the present version), I am worried
> that while upgrading I may commit some mistake. A guideline on
> updating would have been very helpful.
>
> Looking forward to your kind feedback.
>
> Thank you in advance.
>
> With warm regards,
>
> Pranjal
>
>
>
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> --
> -----------------------------------------------------------------------
> Peter Blaha, Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
> Phone: +43-158801165300
> Email:peter.blaha at tuwien.ac.at
> WWW:http://www.imc.tuwien.ac.at WIEN2k:http://www.wien2k.at
> -------------------------------------------------------------------------
>
>
> Aquest missatge, i els fitxers adjunts que hi pugui haver, pot
> contenir informació confidencial o protegida legalment i s’adreça
> exclusivament a la persona o entitat destinatària. Si no consteu com a
> destinatari final o no teniu l’encàrrec de rebre’l, no esteu
> autoritzat a llegir-lo, retenir-lo, modificar-lo, distribuir-lo,
> copiar-lo ni a revelar-ne el contingut. Si l’heu rebut per error,
> informeu-ne el remitent i elimineu del sistema tant el missatge com
> els fitxers adjunts que hi pugui haver.
>
> Este mensaje, y los ficheros adjuntos que pueda incluir, puede
> contener información confidencial o legalmente protegida y está
> exclusivamente dirigido a la persona o entidad destinataria. Si usted
> no consta como destinatario final ni es la persona encargada de
> recibirlo, no está autorizado a leerlo, retenerlo, modificarlo,
> distribuirlo o copiarlo, ni a revelar su contenido. Si lo ha recibido
> por error, informe de ello al remitente y elimine del sistema tanto el
> mensaje como los ficheros adjuntos que pueda contener.
>
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--
-----------------------------------------------------------------------
Peter Blaha, Inst. f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-158801165300
Email:peter.blaha at tuwien.ac.at
WWW:http://www.imc.tuwien.ac.at WIEN2k:http://www.wien2k.at
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