Re: [Wien] DFT in biomedical research

-disordered-phases Just some quick thoughts though. ;) Kind regards, Michael Sluydts On 3/10/2021 2:45 PM, Laurence Marks wrote: I realize this is not really a W2k question, but anyway: is anyone aware of much use of DFT in biomedical research? _ Professor Laurence Marks "Research is to see

Re: [Wien] Is there any automate infrastructure supporting WIEN2k?

ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- dr. ir. Michael Sluydts Center for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9

Re: [Wien] Wien2k under bash/Ubuntu/Windows

Even though it's halloween, perhaps we should not take the horror too far. Op 31/10/2016 om 20:17 schreef Laurence Marks: Just for fun, has anyone tried compiling/using Wien2k in the Ubuntu distro that is part of the Windows 10 Anniversay release? -- dr. ir. Michael Sluydts Center

Re: [Wien] scf2forces

earch Fellow ABV-IIITM, Gwalior, India Mob. No. +91-9584499697 +91-8435727031 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archiv

Re: [Wien] Graphene bandstructure

minimum. Of course don't optimize the vacuum or you'll end up with graphite... Best regards, Michael Sluydts Op 22/12/2015 om 17:43 schreef Islam, Md F: Thanks, for your reply. I have used a vacuum of 30 bohr but I can try with larger vacuum to check if it makes any difference. Fhokrul

Re: [Wien] Reconstructed Si 100 surface

) must be passivated or not? Can we introduce dimers on both surfaces (top bottom). I am reading the paper ( http://pubs.acs.org/doi/pdf/10.1021/jp509095t ). What does it means P21, P22, P24 reconstructions? Many thanks On Sun, Jul 26, 2015 at 10:51 PM, Michael Sluydts michael.sluy...@ugent.be

Re: [Wien] negative value of U in solids

Hello Sandeep, A negative value of U for instance occurs in Ge. I was given this article before to explain this behavior: http://www.sbfisica.org.br/bjp/files/v36_286.pdf Note that the effective U = U-J. Best regards, Michael Sluydts sandeep schreef op 8/07/2015 om 18:49: Dear users

Re: [Wien] how to cut a surface

/usersguide.pdf Best regards, Michael Sluydts Fedor Bystrenko schreef op 25/06/2015 om 9:11: Hi, Are there any utils in WIEN package for supercell creation? I'm interested not just to enlarge the unit cell, but also to rotate it and cut a surface along some direction. For example, I take a unit

Re: [Wien] Problem when running MPI-parallel version of LAPW0

python #Machines file generator for WIEN2k #May 13th 2013 # #Michael Sluydts #Center for Molecular Modeling #Ghent University from collections import Counter import subprocess, os nodefile = subprocess.Popen('echo $PBS_NODEFILE',stdout=subprocess.PIPE,shell=True) nodefile = nodefile.communicate

Re: [Wien] Problem when running MPI-parallel version of LAPW0

Perhaps an important note: the python script is for a Torque PBS queuing system (based on $PBS_NODEFILE) Rémi Arras schreef op 22/10/2014 13:29: Dear Pr. Blaha, Dear Wien2k users, We tried to install the last version of Wien2k (14.1) on a supercomputer and we are facing some troubles with

Re: [Wien] octave problem, 2nd

object. It's indeed possible that some octave setting caused it to print the entire object before (maybe even version dependent). But proper accessing is done through the .pos . You'd have to check the octave manual for full details on this behavior. Hope I was of some help, Michael Sluydts

Re: [Wien] hi

Hello prof. Hakim, We have received your email. If you have any questions, feel free to share. Regards, Michael Sluydts Baaziz Hakim schreef op 17/09/2014 17:07: Prof. Dr : Baaziz Hakim Physics Department , University of M’sila B.P 166 Route ICHBILLIA 28000 M'Sila Algeria Tel : 213 35 54

Re: [Wien] Xcrygen compilation

Well in the meanwhile I finished my compilation (the binaries may be a slightly more user and time-friendly route). My conclusions: It seems that Tcl/Tk 8.6 they removed the result method from 'Tcl_Interp' which gets accessed quite a lot and makes it fail. The readme says it supports tcl =

Re: [Wien] Xcrygen compilation

Our local HPC team has been developing a framework called easybuild to quickly recompile various software. They save the configuration in python files called easyblocks. There is one for xcrysden. I'm however not sure if there were any remaining issues (and testing it again/making a new

Re: [Wien] Xcrygen compilation

(to xcrysden directory ?) * do python xcrysden.py N.B., I am probably missing some steps such as setting CC and other environmental variables.including destination. On Wed, Jul 16, 2014 at 12:48 PM, Michael Sluydts michael.sluy...@ugent.be mailto:michael.sluy...@ugent.be wrote: Our local HPC team

Re: [Wien] Parallel compilation installation

To add to Abraime's explanation, if you use the free -m command, if you check the -/+ buffers/cache line you can see how much is really free. -Michael Sluydts Luis Ogando schreef op 24/06/2014 13:33: Hi Abraime, If you are using something like top command in a terminal, do not worry about

Re: [Wien] [SPAM?]

again). Keep in mind that in literature you will often only find a U value which is then an effective U obtained as U-J. Regards, Michael Sluydts zahia ayat schreef op 9/06/2014 16:27: Please what are the steps used for GGA+U ? Because i need to use it. thank you

Re: [Wien] energy cutoff between core and valence electrons (ecut)

Hello Saurabh, Nothing is affected. Ecut is only used as a threshold, so as long as you don't cross any new level (at -7 or -26 in this case). You will notice no difference. Kind regards, Michael Sluydts saurabh samant schreef op 6/05/2014 22:28: Dear WIEN2k users, Plz refer to pg33

Re: [Wien] Errori in mini

Hello, Due to lack of information on what you are simulating and with which settings I think you will find more useful to perform the tests yourself where you vary the amount of CPUs used, that way you can see the actual difference. Kind regards, Michael Sluydts shamik chakrabarti

Re: [Wien] Regarding Bandstructure

Hello sikander, It's not a configuration file but a source code file, the can be found at $WIENROOT/SRC_spaghetti/spag.f I see that in wien2k 13 it's been updated to 9. If you change it you'll have to recompile spaghetti. Regards, Michael Sluydts sikandar azam schreef op 25/02/2014 10

Re: [Wien] Problem with structeditor for slabs

Thanks Robert, All slabs have now generated succesfully without any holes. Kind regards, Michael Sluydts Robert Laskowski schreef op 21/02/2014 3:18: Hi, cp attached file to $WIENROOT/SRC_structeditor/bin. thanks Robert On 20 February 2014 PM 10:17:55 Michael Sluydts wrote: Hello

Re: [Wien] Configuring SCRATCH variable for parallel computation

and not for actual user usage Maybe contact the person who set up this cluster and ask them what they recommend. Regards, Michael Sluydts César de la Fuente schreef op 13/02/2014 17:09: Hi, I 'm doing some tests in the Memento cluster of the University of Zaragoza on TiC system with a k

[Wien] Problem with x symmetry

struct are given below. Does anyone have any idea how to consistently fix this? x patchsymm does not fix the problem. Thanks, Michael Sluydts ATOM: 1 no hex-pointgroup found lm: == -- ERROR -- ERROR

Re: [Wien] Problem with x symmetry

numbers, that specific struct had gone through 12's sgroup which seems to have changed those from negative to positive and messed with the rotational matrices i assume. Thanks, Michael Sluydts Peter Blaha schreef op 27/01/2014 11:28: I do not have these problems with my version of symmetry

Re: [Wien] Help on AFM Structure Please help to remove my e-mail address on list Thanks

I'm not sure it's a good idea to teach antispam systems that the wien mailing list is spam. It may propagate depending on the setup. Regards, Michael Sluydts Masood Yousaf schreef op 21/01/2014 11:05: Respected Researcher If you find it so annoying just refer the emails to spam. In case you

Re: [Wien] XCrySDen error

Hello, I think you forgot to replace complete_path_to in your XCRYSDEN_TOP_DIR variable. It should be your local install path. Kind regards, Michael Sluydts ali betaouaf schreef op 1/18/2014 1:15 PM: Dear members, After installing XCrysden, and when I run, I see this message?? /home

Re: [Wien] (no subject)

Hello Ahmed, Locally you should be able to access it as http://127.0.0.1:7889 . Remotely you should use the ip or hostname the machine has in your network. Ensure no firewall such as iptables or apf is configured to block the service. Kind regards, Michael Sluydts ahmed amine schreef op

Re: [Wien] Wien2k data provenance

to init you can find the init command in the :log file at the top if you still have it. Regards, Michael Sluydts Taylor, Richard H. schreef op 2/12/2013 21:07: Dear Prof. Blaha and others, I am attempting to work backward from a Wien2k working directory to fully describe the simulation

Re: [Wien] mbj probem gap

over at the gamma point. Either way the band structure should give a closer hint as to what is happening. Regards, Michael Sluydts Op 13/09/2013 10:19, Amine Slassi schreef: Hi, I tried using mbj , I have running the calculation of materials pure ( supercell 2*2*2) I found that the gap

Re: [Wien] mbj probem gap

Hello, I would really start with plotting the band structures for both, so that you can see where the problem actually lies, as in what happens to the bands. The procedure is described in the manual. Regards, Michael Sluydts Op 13/09/2013 10:41, Amine Slassi schreef: Hi, I have found

Re: [Wien] Intel(R) Xeon Phi™ coprocessor

While I'm not sure how easily normal desktop benchmarks transfer to parallel processing through wien2k I usually look at the following benchmarks when comparing CPUs (and prices): http://cpubenchmark.net/high_end_cpus.html Best regards, Michael Sluydts Op 12/09/2013 15:43, Luis Ogando

Re: [Wien] Intel(R) Xeon Phi™ coprocessor

On 09/12/2013 03:46 PM, Michael Sluydts wrote: While I'm not sure how easily normal desktop benchmarks transfer to parallel processing through wien2k I usually look at the following benchmarks when comparing CPUs (and prices): http://cpubenchmark.net/high_end_cpus.html Best regards, Michael Sluydts

Re: [Wien] (no subject)

Hello, You can find info on QTL-B errors in the wien2k FAQ: http://www.wien2k.at/reg_user/faq/qtlb.html Regards, Michael Sluydts Op 8/09/2013 17:21, sikandar azam schreef: Hello Users I am facing the problem, when i am calculating the SCF, it give me this error Error in LAPW2 'l2main

Re: [Wien] Using TB-mbj functional in WIEN-2k

Hello, To expand the previous reply a bit, the manual lists the steps that init_mBJ_lapw follows which you must execute manually unless you are using version 13. Regards, Michael Sluydts Op 26/08/2013 12:00, t...@theochem.tuwien.ac.at schreef: Hi, In principle the steps are explained

Re: [Wien] l'approximation MBJ

, doesn't exist. It however details the exact steps that this program would execute and you can just follow the steps exactly as shown in that paragraph. If you have any more detailed questions you can always let us know. Kind regards, Michael Sluydts Op 11/08/2013 13:09, Sameh noui schreef: SVP

Re: [Wien] L'approximation MBJ

, Michael Sluydts Op 2/07/2013 10:55, Sameh noui schreef: SVP je cherche des documents sur l'approximation MBJ ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http

Re: [Wien] structeditor for creating a surface

layers again. Regards, Michael Sluydts Op 27/06/2013 8:44, Madhav Ghimire schreef: Dear Prof. Blaha, Thanks. Using x supercell, I could generate a 001 surface of Fe . But my current case is for 111 surface with 5 layers which is difficult to create using x supercell. In my current

Re: [Wien] Role of sgroup program

0.33 which may affect the output structure. You may wish to give us some more information on those errors you get if you don't switch to the sgroup-generated struct though since that does not seem normal to me in first instance. Regards, Michael Sluydts Op 24/06/2013 10:43, saurabh

Re: [Wien] make struct

Hello Mahdisa, You can either use a text editor and base your struct file on an existing one or use the wien2k structeditor with Octave (or Matlab) which will let you create, edit and save structures). Regards, Michael Sluydts Op 18/06/2013 12:01, MAHDI SALMANI HIRMAND schreef: Dear

Re: [Wien] Problem in making antiferromagnetic structure

Hello Santu, Normally if you change the 'Co' in the struct to 'Co1', 'Co2',... it will not try to merge the positions again, are you doing this already? Regards, Michael Sluydts Op 16/06/2013 10:21, Santu Baidya schreef: Dear wien2k users, I am using wien2k version WIEN2k_12.1 (Release

Re: [Wien] plane wave exhausted

Hello wasim, There's a patch that resolves this error. I can't immediately find it in the archives so I'll attach it. I'm not certain if there are any more elegant solutions remaining, if not then you'll have to add the patch and recompile. Regards, Michael Sluydts Op 14/06/2013 13:57

Re: [Wien] scp error

Hello, Is this maybe because the $SCRATCH variable points to your home directory? Maybe try pointing it to your dir if that is viable. export SCRATCH=/home/my_username/wien2k/case Good luck, Michael Sluydts Op 4/06/2013 11:19, Yundi Quan schreef: Hi, I'm working on a cluster 8 quadcore

Re: [Wien] RELATED TO STRUCTEDITOR

Hello Vishal, Try using mergestruct to merge slabs and movealla to make sure they're in the right position when merging. One of the rescale_c commands may be needed as well to make sure the cell dimensions are the same. Regards, Michael Sluydts Op 29/05/2013 5:39, vishal jain schreef

Re: [Wien] (no subject)

of the manual. Regards, Michael Sluydts Op 9/04/2013 12:32, wasim raja Mondal schreef: Dear wien2k community, I am beginner in wien2k. I am running Tic example from the wien2k manual. After doing the structure generation successfully when I am doing initialization I am facing this problem

Re: [Wien] no space left on device?

no experience with these (if they exist). Regards, Michael Sluydts Op 8/04/2013 10:50, ben abdallah houda schreef: Dear users, I already sent an email regarding my problem that I encountered during the execution of x opticc. the error is foundno space left on device. Someone can help me