Re: [Wien] DFT in biomedical research
Hey Laurence, Not sure if you're specifically thinking of solid-state, but typical biochemistry applications are common. For instance DFT and AI for drug discovery: https://www.technologyreview.com/10-breakthrough-technologies/2020/#ai-discovered-molecules Studies of initial polymer reactions, functional groups of proteins and so on also spring to mind or to try and get dynamic properties/spectroscopy of (parts of) very small proteins. In the end also DFT components to make forcefields or machine learning potentials for all kinds of applications are also very relevant nowadays (by sampling subsystems of larger ones). Colleague of mine used to study oxygen transport in lipid membranes with the NIH, not ab initio MD, but i can imagine the ML potential approach may be interesting. https://molmod.ugent.be/publications/permeability-membranes-liquid-ordered-and-liquid-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 what everybody else has seen, and to think what nobody else has thought", Albert Szent-Györgyi www.numis.northwestern.edu <http://www.numis.northwestern.edu> ___ 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-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)9 264 66 19 https://molmod.ugent.be ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Is there any automate infrastructure supporting WIEN2k?
Hey Min Lin, Peter and other wien2k users, In the past our in-house software Queue Manager has been used to automate wien2k calculations. It has workflow management, error fixing workflow support and a web interface, as well as some possibility for automated machine learning predictions which can be used to reprioritize calculations (so-called active learning). Nowadays the code has been restructured somewhat and we have not yet converted the wien2k scripts into our new module format. This should not be super difficult, but may require a little bit of copy pasting and testing. So if you or anyone else is interested to give this a try, please feel free to contact me. (Thomas Ruh, no time probably? :) ) Some information: An older presentation: https://1drv.ms/p/s!AjcJxUxn5c5rj-J04lwsgs6L7PH_Vg My PhD thesis with a wien2k example on Si/Ge point defects and an older function manual: https://1drv.ms/b/s!AjcJxUxn5c5rj-ll0_9g80r85pbIlw Some info in my PhD presentation too: https://www.youtube.com/watch?v=6ueXoqJgpZ0 Some things have been cleaned up a bit since the above resources were created, but the core functionality remains the same, with some additional machine learning. Kind regards, Michael On 02-Jul-19 6:07 PM, Peter Blaha wrote: No, not really as far as I know. You have to use the wien2k scripts, tutorials and/or the graphical user interface w2web, which teaches you how to perform certain tasks. There is a fairly old interface called "runwien" by a spanish group, but I've never used it myself nor do I know if it would be compatible with the latest version. Anyway, it was on github: https://github.com/aoterodelaroza/runwien/blob/master/doc/user-guide.txt Am 02.07.2019 um 14:01 schrieb 林敏: Dear WIEN2k expert, Is there any automate infrastructure supporting WIEN2k? Just like AiiDA supporting VASP, QE, CP2K, etc. Best wishes. Min Lin, Chemistry Department, Xiamen University, China. Email: lin...@stu.xmu.edu.cn ___ 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-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)9 264 66 19 https://molmod.ugent.be ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9 264 66 19 https://molmod.ugent.be ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] scf2forces
At risk of stating the obvious: the fact that the folder is called win2k and not wien2k also seems mildly suspicious. On 2/16/2016 2:28 PM, Gavin Abo wrote: If you do "ls ~/home/IITJHOME/ambeshst/win2k13mpi/phonopy-1.10.0/lib64/python", does it show files like api_gruneisen.py? If the files like that are in the python folder in the lib64 directory, then your .bashrc looks fine. On my system, they are under lib instead of lib64: username@computername:~$ ls ~/phonopy-1.10.0/lib/python/phonopy api_gruneisen.py api_qha.pyc harmonic _phonopy.so units.pyc api_gruneisen.pyc cui __init__.py qha version.py api_phonopy.py file_IO.py __init__.pyc _spglib.so version.pyc api_phonopy.pycfile_IO.pyc interface structure api_qha.py gruneisenphononunits.py In the error message, it looks like it is pointing to the wrong location (/home/IITJHOME/ambeshst/win2k13mpi/phonopy), when it should be pointing to "/home/IITJHOME/ambeshst/win2k13mpi/phonopy-1.10.0/lib64/python". Do "echo $PYTHONPATH", is it pointing to the right location? On my system, it is pointing to "/home/username/phonopy-1.10.0/lib/python": username@computername:~$ echo $PYTHONPATH :/home/username/phonopy-1.10.0/lib/python After adding export lines to .bashrc and saving the changes, did you reload the .bashrc (using "source ~/.bashrc" or open and use a new terminal)? On 2/16/2016 2:49 AM, Rajneesh Chaurasiya wrote: I have modified the file according to your suggestion but still there is same error... Traceback (most recent call last): File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ? from phonopy import * ImportError: No module named phonopy I am attaching the .bashrc file so please check whether this is correct or not.. please suggest your suggestion.. On Sat, Feb 13, 2016 at 12:38 PM, Rajneesh Chaurasiya <rajnano2...@gmail.com> wrote: Dear Gavin, I have installed newer version of phonopy package https://sourceforge.net/projects/phonopy/files/phonopy/phonopy-1.10/phonopy-1.10.0.tar.gz/download and it required the scf2forces which i get from http://www.wien2k.at/reg_user/unsupported/ but it showing the error, which i have seen in the previous message. but as per your suggestion if i use he experimental support option in Phonopy 1.10.0 [ http://atztogo.github.io/phonopy/wien2k.html#wien2k-interface ]: means phonopy --wien2k -f case-001.scf case-002.scf then it showing error some error. Traceback (most recent call last): File "/home/IITJHOME/ambeshst/win2k13mpi/phonopy", line 40, in ? from phonopy import * ImportError: No module named phonopy so i dont know that the installed phonopy is compatible with the wien2k or not. please give me your ideas why this is happening. -- Thanks & Regards Rajneesh Chaurasiya Junior Research 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- ir. Michael Sluydts Center for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9 264 66 19 https://molmod.ugent.be ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Graphene bandstructure
While I haven't done any graphene calculations, one of the typical issues in bandgap discrepancies is also the existence of strain. Ensure your lateral lattice parameters are optimized using your current functional so that you're certain you are looking at the band structure of the energetic 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 From: wien-boun...@zeus.theochem.tuwien.ac.at [wien-boun...@zeus.theochem.tuwien.ac.at] On Behalf Of t...@theochem.tuwien.ac.at [t...@theochem.tuwien.ac.at] Sent: Tuesday, December 22, 2015 10:20 AM To: A Mailing list for WIEN2k users Subject: Re: [Wien] Graphene bandstructure Hi, For graphene, you need to add vacuum in the z-direction in order to avoid interactions between the periodically repeated monolayers. Maybe the vacuum that you used is not large enough. F. Tran On Tue, 22 Dec 2015, Islam, Md F wrote: Hi, I am trying to do a bandstructure calculation of graphene to check if I can reproduce results discussed in literature (I am using a unit cell of 2 atoms). With spin-orbit coupling, there should be a gap of the order of few micro-eV and without spin-orbit, there should not be any gap at Dirac point. But I am getting a gap of meV even without spin-orbit. I tried both GGA and LDA with very dense mesh but the gap does not close. So I am wondering if anyone have any suggestion about how to do it in Wien2k. Thanks, Fhokrul ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- ir. Michael Sluydts Center for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9 264 66 19 https://molmod.ugent.be ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Reconstructed Si 100 surface
It is recommended to make both your slab surfaces identical where possible. The p21, p22 and p24 refer to the type of supercell used to represent the surface. Since you are using a periodic model you are imposing a strong symmetry on the surface, not all reconstructions can be made within your unit cell, indeed for your dimer you will need a 2x1 expansion, i.e. two cells next to eachother along the a axis. The symbols (and possible angles) represent the shape and rotation of the resulting cell (in this case p=primitive, c=centered). You can find more info in for instance: Introduction to Solid State Physics - Kittel - about the description of cells and Density Functional Theory: A Practical Introduction - Sholl and Steckel - for the basics of how to model surfaces Muhammad Sajjad schreef op 27/07/2015 om 10:51: Dear Delamora and Michael Many thanks for informative suggestions. I am intended to study electronic properties of Si (100) of thickness 1 nm. I am asked to introduce dimers instead of using H. But my question is one surface of the Si 100 must be passivated by hydrogen or not?Like If ones introduce dimer on the top (maximum Z) then bottom (minimum Z) 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 mailto:michael.sluy...@ugent.be wrote: Muhammad, When you move the two Si atoms with the dangling bond towards eachother you will create a dimer on the surface, no extra passivation by H atoms is needed, just ensure you make your slab symmetric where possible. If you google Si recontructions you should find very exact geometrical information since this has been done many times before. Best regards, Michael Sluydts Muhammad Sajjad schreef op 26/07/2015 om 17:59: Thank you Pablo But I am required to connect two Si atoms at the surface to reduce one dangling bond and then put H or may be H is not needed if both of the dangling bonds have possibility of omitting. I am reading the paper but could not understand although Fig. 2 is looking easy to understand. WHat is 2*1 or 2*2 or 2*4 ? are the super-cells like 2*1*1 or 2*2*1 etc. On Sun, Jul 26, 2015 at 6:22 PM, delamora delam...@unam.mx mailto:delam...@unam.mx wrote: This is the same that I simplified and symmetized. If you are going to add H then you need set the space group as P1 (#1) so the H can move freely and not in a symmetrical path. Now, if you use my proposed structure then you can put inversion (SG P-1, #2) and add two H, one on each surface, but in a symmetric way. Other thing, maybe my proposed structure is too small and your structure is ok, but I would symmetrize as I explained in an earlier message. Pablo *De:* wien-boun...@zeus.theochem.tuwien.ac.at mailto:wien-boun...@zeus.theochem.tuwien.ac.at wien-boun...@zeus.theochem.tuwien.ac.at mailto:wien-boun...@zeus.theochem.tuwien.ac.at en nombre de Muhammad Sajjad sajja...@gmail.com mailto:sajja...@gmail.com *Enviado:* domingo, 26 de julio de 2015 04:44 a. m. *Para:* wien *Asunto:* [Wien] Reconstructed Si 100 surface Dear Users Kindly guide me how to reconstruct Si 100 layer? The Si 100 structure is attached here with. It has two dangling bonds on both surfaces (Top and Bottom). My intension is to keep one dangling bond on the top and bottom surfaces that will be saturated by H addition. -- Kind Regards Muhammad Sajjad Post Doctoral Fellow KAUST, KSA. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 -- Kind Regards Muhammad Sajjad Post Doctoral Fellow KAUST, KSA. ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 -- ir. Michael Sluydts Center for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9 264 66 19 https://molmod.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! It may not be appropriate to post this question here, Did any one encounter negative value of U in solids (compounds) ? if so explain its origin and quote related concepts. Kindly explain the origin and experimental supports if any? ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- ir. Michael Sluydts Center for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9 264 66 19 https://molmod.ugent.be ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] how to cut a surface
There is a structeditor package provided with wien2k which is capable of performing these tasks. It uses the open source matlab equivalent octave and allows you to script the generation of surfaces (this can be useful when you want to generate many labs with different slab or vacuum thickness using a for loop). This also means you can extend it with your own functions, though there are some other packages available online with some additional functionalities (grain boundaries, etc). For the structeditor see section 9.26 in the user guide: http://www.wien2k.at/reg_user/textbooks/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 cell of wurzite SiC and want to create a surface with [10-10] orientation. Another question is how to rotate a crystal cell to a given angle along one axis. Any advices/ papers/algorithms are appreciated. Regards, Fedor Bystrenko ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html -- ir. Michael Sluydts Center for Molecular Modeling Ghent University Technologiepark 903 9052 Zwijnaarde, Belgium tel. +32 (0)9 264 66 19 https://molmod.ugent.be ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Problem when running MPI-parallel version of LAPW0
Hello Rémi,
While I'm not sure this is the (only) problem, in our setup we also give
mpirun the machines file:
setenv WIEN_MPIRUN mpirun -np _NP_ -machinefile _HOSTS_ _EXEC_
which I generate based on a 1 k-point per node setup with the following
python script:
/wienhybrid
#!/usr/bin/env 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()[0].strip()
nodefile = open(nodefile,'r')
machines = nodefile.readlines()
nodefile.close()
node = ''
corecount=Counter()
#gather cores per nodes
for core in machines:
node = core.split('.')[0]
corecount[node] += 1
#if there are more nodes than k-points we must redistribute the
remaining cores
#count the irreducible kpoints
IBZ = int(subprocess.Popen('wc -l ' + os.getcwd().split('/')[-1] +
'.klist',stdout=subprocess.PIPE,shell=True).communicate()[0])-2
corerank = corecount.most_common()
alloc = Counter()
total = Counter()
nodemap = []
#pick out the largest nodes and redivide the remaining ones by adding
the largest leftover node to the k-point with least allocated cores
for node,cores in corerank:
if len(alloc) IBZ:
alloc[node] += cores
total[node] += cores
else:
lowcore = total.most_common()[-1][0]
total[lowcore] += cores
nodemap.append((node,lowcore))
#give lapw0 all cores
machinesfile = 'lapw0: ' + corecount.keys()[0] + ':' +
str(corecount[corecount.keys()[0]]) + '\n'
#for node in corecount.keys():
#machinesfile += node + ':' + str(corecount[node]) + ' '
#machinesfile += '\n'
#machinesfile = ''
for node in alloc.keys():
#allocate main node
machinesfile += '1:' + node + ':' + str(alloc[node])
#machinesfile += '1:' + node
#for i in range(1,alloc[node]):
#machinesfile += ' ' + node
#distribute leftover nodes
extra = [x for x,y in nodemap if y == node]
for ext in extra:
#machinesfile += ' ' + ext + ':' + str(corecount[ext])
for i in range(1,corecount[ext]):
machinesfile+=' ' + ext
machinesfile += '\n'
#If your nodes do not all have the same specifications you may have to
change the weights above 1: and the granularity below, if you use a
residue machine you should remove extrafine and add the residue
configuration
machinesfile += 'granularity:1\nextrafine:1\n'
#if you have memory issues or a limited bandwidth between nodes try
uncommenting the following line (can always try it and see if it speeds
things up)
#machinesfile += 'lapw2 vector split:2\n'
machines = file('.machines','w')
machines.write(machinesfile)
machines.close()
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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 the MPI parallel version. 1)lapw0 is running correctly in sequential, but crashes systematically when the parallel option is activated (independently of the number of cores we use): lapw0 -p(16:08:13) starting parallel lapw0 at lun. sept. 29 16:08:13 CEST 2014 .machine0 : 4 processors Child id1 SIGSEGV Child id2 SIGSEGV Child id3 SIGSEGV Child id0 SIGSEGV **lapw0 crashed! 0.029u 0.036s 0:50.91 0.0%0+0k 5248+104io 17pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed stop error w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault Child with myid of1has an error 'Unknown' - SIGSEGV Child id1 SIGSEGV application called MPI_Abort(MPI_COMM_WORLD, 0) - process 1 **lapw0 crashed! cat: No match.0.027u 0.034s 1:33.13 0.0%0+0k 5200+96io 16pf+0w error: command/eos3/p1229/remir/INSTALLATION_WIEN/14.1/lapw0para -up -c lapw0.deffailed 2) lapw2 also crashes sometimes when MPI parallelization is used. Sequential or k-parallel runs are ok, and contrary to lapw0, the error does not occur for all cases (we did not notice any problem when testing the mpi benchmark with lapw1): w2k_dispatch_signal(): received: Segmentation fault application called MPI_Abort(MPI_COMM_WORLD, 768) - process 0 Our system is a Bullx DLC Cluster (LInux Red Hat+ Intel Ivybridge) and we use the compiler(+mkl) intel/14.0.2.144 and intelmpi/4.1.3.049. The batch Scheduler is SLURM. Here are the settings and the options we used for the installation : OPTIONS: current:FOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -traceback current:FPOPT:-FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML -Dmkl_scalapack -traceback -xAVX current:FFTW_OPT:-DFFTW3 -I/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/include current:FFTW_LIBS:-lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:LDFLAGS:$(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread current:DPARALLEL:'-DParallel' current:R_LIBS:-lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread current:RP_LIBS:-mkl=cluster -lfftw3_mpi -lfftw3 -L/users/p1229/remir/INSTALLATION_WIEN/fftw-3.3.4-Intel_MPI/lib current:MPIRUN:mpirun -np _NP_ _EXEC_ current:MKL_TARGET_ARCH:intel64 PARALLEL_OPTIONS: setenv TASKSET no setenv USE_REMOTE 1 setenv MPI_REMOTE 1 setenv WIEN_GRANULARITY 1 setenv WIEN_MPIRUN mpirun -np _NP_ _EXEC_ Any suggestions which could help us to solve this problem would be greatly appreciated. Best regards, Rémi Arras ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] octave problem, 2nd
Hello John,
You should be able to access the struct like an object in a typical
programming language.
s1.pos for positions
s1.pos(1,:) for the first row
s1.pos(:,1) for the first column
s1.a(1) for the first lattice coordinate and such
What you're seeing now is a referral to the entire 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
John Rundgren schreef op 17/09/2014 14:02:
Dear Wien2k team,
SRC_structeditor/doc/readme.txt shows on pages 1-2 how the octave
statement
s1=loadstruct(GaAs.struct)
generates all thinkable coordinates of the structure. But when I
changed to Ubuntu14 the s1 coordinates remained invisible.
From Gavin Abo I gratefully got a hint to write
print_struct_array_contents(1)
s1=loadstruct(GaAs.struct),
giving readable coordinates wrapped in brackets as shown below.
Remarkably, Ubuntu14-octave has not completely forgotten the
readme.txt instructions:
s2=makeprimitive(s1)
and
s3=makeconventional(s1)
write out coordinates as earlier without brackets.
How can one get around the write-out confusion?
Best, John Rundgren
s1 =
1x1 struct array containing the fields:
a =
{
[1,1] =
10.683945000 10.683945000 10.683945000
}
alpha =
{
[1,1] =
90 90 90
}
aname =
{
[1,1] =
Ga
As
}
jrj =
{
[1,1] =
781
781
}
lat2car =
{
[1,1] =
10.68394500.000 0.000
0.000 10.6839450 0.000
0.0000.000 10.6839450
}
brlat =
{
[1,1] =
0.000 5.3419725 5.3419725
5.3419725 0.000 5.3419725
5.3419725 5.3419725 0.000
}
lattic =
{
[1,1] = F
}
nat =
{
[1,1] = 2
}
pos =
{
[1,1] =
0.000 0.000 0.000
0.250 0.250 0.250
}
r0 =
{
[1,1] =
5.00e-05
5.00e-05
}
rmt =
{
[1,1] =
2
2
}
zz =
{
[1,1] =
31
33
}
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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 17 26 - Mobil : 213 771525993 ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 = 8.4 so practically this means you have to use 8.4 or 8.5 . Also, I think when our HPC team installed it they disabled Bwidget, I currently didn't and see that the text sometimes seems a bit (vertically) misaligned. Gavin Abo schreef op 17/07/2014 0:09: Correction: xcConfigure.sh should be in the scripts folder not the bin folder. On 7/16/2014 4:04 PM, Gavin Abo wrote: Can you tell us what kind of systems this happens on and what the errors are? The information might be helpful to others. I had xcrysden-1.5.53-linux_x86_64-semishared.tar.gz installed on a ubuntu 64 bit 14.04 LTS system. I just downloaded xcrysden-1.5.60-linux_x86_64-semishared.tar.gz from the xcrysden website, extracted it with tar xvf xcrysden-1.5.60-linux_x86_64-semishared.tar.gz, removed the xcrysden block in .bashrc for 1.5.53, ran xcConfigure.sh in the bin folder of the xcrysden installation to create a new xcrysden block for 1.5.60 in .bashrc, reloaded the new .bashrc settings (by closing terminal and opening a new one), and finally I ran xcrysden. It opens fine without any errors, but maybe I have to do other things to encounter the problems that you refer to. Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Xcrygen compilation
Yeah, it takes some getting used to (and may take too much time if only used for xcrysden). I've only used it a few times myself, it does work nicely for wien2k (with some tweaks of the public easyblock for 13). Practically you first need to install easybuild itself, which has an eb command that builds the software into a specific path (and organizes it by software, version, toolchain). It takes an 'easyconfig' file as input which contains more info on toolchains and patches used for the compilation, while the easyblock defines the more detailed instructions (like input for siteconfig for wien). It then builds the software (and makes a module file i think). The source it finds in some standard directory but there are command-line options to change all the source and destination folders etc. They have a reference site here: http://hpcugent.github.io/easybuild/, the slides there link to other pages in their wiki. Like I said this may be time-inefficient though and I'm not sure if the xcrysden install worked fully. The version they tried it on was 1.5.53, I myself always continued to used an old version in my account (1.5.21) (for which I don't think I did anything special). The combination of easyblock/easyconfig and the patch in the easyconfig folder may give some hints about what exactly they did. Since I need to build it again myself, maybe I'll give it a try tomorrow. The easyconfig and patch are here: https://github.com/hpcugent/easybuild-easyconfigs/tree/master/easybuild/easyconfigs/x/XCrySDen example for wien2k 12.1 install easyblock: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/w/wien2k.py easyconfig: https://github.com/hpcugent/easybuild-easyconfigs/blob/master/easybuild/easyconfigs/w/WIEN2k/WIEN2k-12.1-ictce-4.0.6.eb (when using easybuild itself these things get downloaded with it) Laurence Marks schreef op 16/07/2014 20:34: While I can probably fight my way around installing easyblocks, it would be useful for the general user if a bit more information was provided (by you or your local HPC team). For instance, I suspect it is something like: * Download the easyblocks module from http://hpcugent.github.com/easybuild (what else is needed ?) * cd to the directory (unzip ?) and do python setup.py install'' (is root access needed ?) * Download the script xcrysden (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 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 compile has been on my to do list). The easyblock can be found here: https://github.com/hpcugent/easybuild-easyblocks/blob/master/easybuild/easyblocks/x/xcrysden.py Laurence Marks schreef op 16/07/2014 19:41: Has anyone worked through a .configure (or similar) script for Xcrygen. The shared semishared versions on the web page are not that compatible with recent systems, and I hate (am too lazy) to start editing makefiles by hand. -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 -- Professor Laurence Marks Department of Materials Science and Engineering Northwestern University www.numis.northwestern.edu http://www.numis.northwestern.edu 1-847-491-3996 Co-Editor, Acta Cryst A Research is to see what everybody else has seen, and to think what nobody else has thought Albert Szent-Gyorgi ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 the Mem: row. You have to look ate the %MEM column. All the best, Luis 2014-06-23 13:03 GMT-03:00 Brahim ABRAIME b.abra...@gmail.com mailto:b.abra...@gmail.com: The memory RAM in use of the machines does not decrease when we kill the processes of Wien2k on the CPU Ans suggestions please ? Le 17 juin 2014 22:10, Gavin Abo gs...@crimson.ua.edu mailto:gs...@crimson.ua.edu a écrit : what about the environment in which we must mention the list of machines that will run parallel computing? If you are using a single PC, you should be able to use edit .machines in the menu of w2web. See section 5.5.4 The .machines file in the Wien2k 13.1 usersguide [http://www.wien2k.at/reg_user/textbooks/usersguide.pdf], which describes the content of the .machines file. I also find the University of Texas slides at the following link useful: https://www.xsede.org/documents/10157/305826/ecss_hliu_051012.pdf If you are using a cluster, you should talk to your system administer(s), because they should know everything about your cluster system and should be able to help you create the best configuration for your system (something we know nothing about it). There is a webpage in FAQ on the Wien2k website that can help with that: http://www.wien2k.at/reg_user/faq/pbs.html I also want to know the parameters for multi threading I think there was some previous discussion on threading. Search the mail archive at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/ For example, try searching with the keyword: OMP_NUM_THREADS ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] [SPAM?]
Hello, You can find details in the user manual paragraph 4.5.6 Orbital potentials p48 . You will have to get your U/J either from the literature or by fitting to experiment. There are also ways to determine it ab initio via linear response which I have little experience with (see literature 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 ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 of DFT and family of lapw methods, 2nd ed. by S.cottenier. For Ag atom ecut was modified to -7.5 Ry to treat the 4s states as valence electrons. Is the calculation or any of the properties is affected if we change the ecut to -8 or -9 or any value between 3D and 4S orbitals (-7 to -26 Ry). Thanking you, yours sincerely, Saurabh Samant ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 schreef op 4/04/2014 17:02: Dear Prof. Blaha Sir, To continue from your last suggestions we have noticed the timing of a single iteration. It is 10 minutes for 16 atoms/unit cell calculation. Sir, do you think that this speed is ok considering our system having 16 cpus?.. Yes of course for we have to go for k-parallization. Looking forwards to your comments and suggestion. With regards, On 3 Apr 2014 18:04, shamik chakrabarti shamik...@gmail.com mailto:shamik...@gmail.com wrote: Dear wien2k users, We are working on a Li based silicate materials. We are trying to do simultaneous optimization of lattice parameters and atomic coordinates. For that we are using Option 6 in volume optimize program while edited optimized.job to perform simultaneous force minimization. The calculation was run smoothly up to 2 structures i.e, case_abc_1.0 and case_abc_2.0. Then due to power failure the calculation was remain stopped for several hours.. We restarted the calculation by putting # to the two lines corresponding to 1st and 2nd structure in optimize.job...such that the calculation starts from the structure case_abc_3.0However, while running for 3rd structure the following display came in show dayfile option. ERROR status in case_abc___3.0 mini 004035D9 Unknown Unknown Unknown libc.so.6 00349521ECDD Unknown Unknown Unknown mini 004036E6 Unknown Unknown Unknown mini 00412AA6 MAIN__ 25 mini.f mini 0040C6AB haupt_593 haupt.f mini 0041A39F wrtscf_ 23 wrtscf.f mini 00451F5A Unknown Unknown Unknown mini 00453C1E Unknown Unknown Unknown Image PCRoutine LineSource forrtl: severe (64): input conversion error, unit -5, file Internal Formatted Read 3.887u 0.013s 0:03.90 99.7%0+0k 0+11912io 0pf+0w DSTART ENDS 3.879u 0.008s 0:03.88 99.7%0+0k 0+11904io 0pf+0w DSTART ENDS 3.879u 0.011s 0:03.89 99.7%0+0k 0+11904io 0pf+0w DSTART ENDS clmextrapol_lapw has generated a new case.clmdn 0.196u 0.007s 0:00.20 95.0%0+0k 0+8032io 0pf+0w 3.888u 0.015s 0:03.90 99.7%0+0k 0+13528io 0pf+0w DSTART ENDS running dstart in single mode clmextrapol_lapw has generated a new case.clmup 0.196u 0.010s 0:00.20 100.0%0+0k 0+8032io 0pf+0w 3.929u 0.020s 0:03.94 100.0%0+0k 0+13528io 0pf+0w DSTART ENDS running dstart in single mode clmextrapol_lapw has generated a new case.clmsum 0.195u 0.004s 0:00.20 95.0%0+0k 0+8032io 0pf+0w 3.923u 0.017s 0:03.94 99.7%0+0k 0+13528io 0pf+0w DSTART ENDS running dstart in single mode 3.888u 0.003s 0:03.89 99.7%0+0k 0+11904io 0pf+0w DSTART ENDS 3.895u 0.010s 0:03.91 99.7%0+0k 0+11904io 0pf+0w DSTART ENDS 3.934u 0.010s 0:03.94 100.0%0+0k 0+11912io 0pf+0w DSTART ENDS we are using wien2k 13.1 What could be the possible reasons for this error?.any response in this regard will be fruitful for us. Thanks in advance. with regards, -- Shamik Chakrabarti Senior Research Fellow Dept. of Physics Meteorology Material Processing Solid State Ionics Lab IIT Kharagpur Kharagpur 721302 INDIA ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 10:02:
Dear All
I have problem in calculating the band structure, so i saw this email
on the wien2k site
Thank you very much for this report and the analysis.
It will be updated in the next version of WIEN2k.
Am 16.01.2012 18:30, schrieb Muechler, Lukas:
/ Hey everyone,
//
// I've bee having an issue with plotting the bandstructure of large
supercells with SOC, as can also be found in the Mailingslist for several cases.
//
// The error that occurs is as follows
//
// number of k-points read in case.vector= (something)
// forrtl: severe (174): SIGSEGV, segmentation fault occurred
//
// I noticed that this only occurs when systems with a large number of bands
are used, so I looked intospagh.f and found this:
//
-
// !
// !.ALL K-VECTORS HAVE BEEN READ; SEARCH FOR K-POINT WITH SMALLEST
// ! NUMBER OF EIGENVALUES
// !
//200 continue
// nu_min=999
// write(*,*) 'number of k-points read in case.vector=',n_kpt
// do 205 j=1,n_kpt
//if (n_ene(j).lt.nu_min) then
// nu_min=n_ene(j)
// k_min=j
//endif
//205 continue
// write(6,*) 'smallest number eigenvalues at k=',k_min,' (',
// k_name(k_min),')'
// write(6,*) ' =',nu_min
//
-
//
// Since the program stops at this point and the number of bands in my case
(heavy atoms) is larger than 999, I increased it to 1500 and now it works.
// The bandstructure looks good aswell, so I think this number should be
higher than 999.
//
// Best,
//
// Lukas Muechler/
/
/
/
/
But in my calculations i couldn't find this/ /spagh.f file.So please can some
one help me that how i can reach to this file.
Regard
Sikander
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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 everyone,
I'm trying to generate a series of (110) surface slabs of varying
thickness for a zincblende crystal. I'm doing this using the
structeditor functions in an octave script (and have done this with
both wien2k (11), 12 and 13).
At certain thicknesses of the slab a problem occurs, which I've seen
in the past for other systems, where it appears to make a diagonal cut
at the bottom of the slab along a {001} direction. Does anyone by any
chance have a patch to resolve this? I know ways around it myself but
being able to use the provided functions directly would be nice.
I've added the bulk struct and octave script needed to reproduce the
problem below.
Thanks,
Michael Sluydts
bulk.struct
blebleble
F LATTICE,NONEQUIV.ATOMS 2 216 F-43m
MODE OF CALC=RELA unit=bohr
10.847217 10.847217 10.847217 90.00 90.00 90.00
ATOM -1: X=0. Y=0. Z=0.
MULT= 1 ISPLIT=15
Zn NPT= 781 R0=.5 RMT= 2.0 Z: 30.0
LOCAL ROT MATRIX:1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
ATOM -2: X=0.2500 Y=0.2500 Z=0.2500
MULT= 1 ISPLIT=15
Se NPT= 781 R0=.5 RMT= 2.0 Z: 34.0
LOCAL ROT MATRIX:1.000 0.000 0.000
0.000 1.000 0.000
0.000 0.000 1.000
0 NUMBER OF SYMMETRY OPERATIONS
script.m
bulk = makeconventional(loadstruct('bulk.struct'));
surf = makesurface(bulk,[1 1 0],2,(bulk.a(3)/2*sin(pi/4))*10+0.01,37.8);
savestruct(makeprimitive(surf),['bug.struct'],0);
--
==
Dr. Robert Laskowski
Senior Scientist, Materials Science Engineering Department
Institute of High Performance Computing, A*STAR
1 Fusionopolis Way, #16-16, Connexis, Singapore 138632
Tel(Off): +65. 64191493 Fax: +65. 64632536
=
IHPC Values :: Impact :: Honesty :: Performance :: Co-operation
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Re: [Wien] Configuring SCRATCH variable for parallel computation
Hello César, To perform parallel calculations you do need a shared directory between all nodes. As you have described '/home' appears to be a form of shared storage. What its intention is, is of course not well-known to us. If it is shared there is no direct reason it cannot function for wien, however the problems that might occur are: -the connection to the shared storage is too slow - if it is not meant to transfer files from and to during a calculation -there is not enough space - if it is just meant for temporary storage and user settings -the /home is meant as a login system 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- 100k pts , 4 nodes with 64 CPUs per node. It is a system that does not share RAM and hard disks between nodes during calculations. Initially the parallel computation with Wien2k stopped in the first cycle because a file system problem. The variable $ SCRATCH point to the local hard disks of each node used in the parallel computation. Fortunately I was able to finish the calculation re-directing the variable $ SCRATCH to /home directory that it is shared by all nodes. The calculation finish fine and it is correct, but I think that something is wrong. Wien2k not seems to be originally designed for a parallel calculation using /home as SCARTCH. Is it correct to use the /home directory as SCRATCH in Wien2k ? , Can this cause problems in the OS of Memento's cluster or in future wien2k calculations?. In fact, I'm having other problems with wien2k in other systems but I'm not sure if it is because SCRATCH points to /home directory or not. Thank you for your attention and appreciate any comment. Sincerely, Dr. César de la Fuente. Depto. de Física de la Materia Condensada. Edificio Torres-Quevedo EINA-Universidad de Zaragoza. C/María de Luna 3, 50018-Zaragoza (SPAIN). ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
[Wien] Problem with x symmetry
Hello everyone, I've been studying a set of similar structures (semiconductor defects) which, each time, I first relax with min_lapw after which I do another static run. Once in a while the relaxation gives me a structure which no longer passes through x symmetry. The error and an example 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: (multiplicity of atom 1 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 1 ISYM: 0 NSYM 6 ERROR: Check your struct file withx sgroup -- ERROR -- ATOM: 2 no hex-pointgroup found lm: == -- ERROR -- ERROR: (multiplicity of atom 2 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 3 ISYM: 0 NSYM 6 ERROR: Check your struct file withx sgroup -- ERROR -- ATOM: 3 no hex-pointgroup found lm: == -- ERROR -- ERROR: (multiplicity of atom 3 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 6 ISYM: 0 NSYM 6 ERROR: Check your struct file withx sgroup -- ERROR -- octavetmp R 20 160 R3m RELA 30.796412 30.796412 37.717748 90.00 90.00120.00 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 4 Ga1NPT= 781 R0=0.5000 RMT=1.5200 Z: 31.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 2: X=0.12462802 Y=0.37401410 Z=0.12462802 MULT= 3 ISPLIT= 8 2: X=0.12462802 Y=0.12462802 Z=0.37401410 2: X=0.37401410 Y=0.12462802 Z=0.12462802 Ge1NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 3: X=0.62493876 Y=0.37487342 Z=0.12467773 MULT= 6 ISPLIT= 8 3: X=0.12467773 Y=0.62493876 Z=0.37487342 3: X=0.37487342 Y=0.12467773 Z=0.62493876 3: X=0.37487342 Y=0.62493876 Z=0.12467773 3: X=0.62493876 Y=0.12467773 Z=0.37487342 3: X=0.12467773 Y=0.37487342 Z=0.62493876 Ge2NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 4: X=0.62492215 Y=0.37475633 Z=0.62492215 MULT= 3 ISPLIT= 8 4: X=0.62492215 Y=0.62492215 Z=0.37475633 4: X=0.37475633 Y=0.62492215 Z=0.62492215 Ge3NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 5: X=0.12201757 Y=0.87800148 Z=0.12201757 MULT= 3 ISPLIT= 8 5: X=0.12201757 Y=0.12201757 Z=0.87800148 5: X=0.87800148 Y=0.12201757 Z=0.12201757 Ge4NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 6: X=0.62573282 Y=0.87502487 Z=0.12480892 MULT= 6 ISPLIT= 8 6: X=0.12480892 Y=0.62573282 Z=0.87502487 6: X=0.87502487 Y=0.12480892 Z=0.62573282 6: X=0.87502487 Y=0.62573282 Z=0.12480892 6: X=0.62573282 Y=0.12480892 Z=0.87502487 6: X=0.12480892 Y=0.87502487 Z=0.62573282 Ge5NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 7: X=0.62500264 Y=0.87521103 Z=0.62500264 MULT= 3 ISPLIT= 8 7: X=0.62500264 Y=0.62500264 Z=0.87521103 7: X=0.87521103 Y=0.62500264 Z=0.62500264 Ge6NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 8: X=0.49974584 Y=0.99967116 Z=0.99967116 MULT= 3 ISPLIT= 8 8: X=0.99967116 Y=0.49974584 Z=0.99967116 8: X=0.99967116 Y
Re: [Wien] Problem with x symmetry
The original calculation was done with a patched 12.1 for consistency reasons. I *thought* I used 13's x symmetry when testing this morning. However, it would seem that the module did not swap properly. Having retested with 13 it seems to work now. I've also looked into the positive atom 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. It does not produce any error and runs fine, finding all symmetries. However, I very much doubt that the struct file you attached is from min_lapw ??? It has POSITIVE atomic numbers and WRONG local rotation matrices ?? Are you using the latest WIEN2k version ? On 01/27/2014 10:44 AM, Michael Sluydts wrote: Hello everyone, I've been studying a set of similar structures (semiconductor defects) which, each time, I first relax with min_lapw after which I do another static run. Once in a while the relaxation gives me a structure which no longer passes through x symmetry. The error and an example 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: (multiplicity of atom 1 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 1 ISYM: 0 NSYM 6 ERROR: Check your struct file withx sgroup -- ERROR -- ATOM: 2 no hex-pointgroup found lm: == -- ERROR -- ERROR: (multiplicity of atom 2 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 3 ISYM: 0 NSYM 6 ERROR: Check your struct file withx sgroup -- ERROR -- ATOM: 3 no hex-pointgroup found lm: == -- ERROR -- ERROR: (multiplicity of atom 3 )*(number of pointgroup-operations) ERROR: is NOT = (number of spacegroup-operations) ERROR: MULT: 6 ISYM: 0 NSYM 6 ERROR: Check your struct file withx sgroup -- ERROR -- octavetmp R 20 160 R3m RELA 30.796412 30.796412 37.717748 90.00 90.00120.00 ATOM 1: X=0. Y=0. Z=0. MULT= 1 ISPLIT= 4 Ga1NPT= 781 R0=0.5000 RMT=1.5200 Z: 31.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 2: X=0.12462802 Y=0.37401410 Z=0.12462802 MULT= 3 ISPLIT= 8 2: X=0.12462802 Y=0.12462802 Z=0.37401410 2: X=0.37401410 Y=0.12462802 Z=0.12462802 Ge1NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 3: X=0.62493876 Y=0.37487342 Z=0.12467773 MULT= 6 ISPLIT= 8 3: X=0.12467773 Y=0.62493876 Z=0.37487342 3: X=0.37487342 Y=0.12467773 Z=0.62493876 3: X=0.37487342 Y=0.62493876 Z=0.12467773 3: X=0.62493876 Y=0.12467773 Z=0.37487342 3: X=0.12467773 Y=0.37487342 Z=0.62493876 Ge2NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 4: X=0.62492215 Y=0.37475633 Z=0.62492215 MULT= 3 ISPLIT= 8 4: X=0.62492215 Y=0.62492215 Z=0.37475633 4: X=0.37475633 Y=0.62492215 Z=0.62492215 Ge3NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 5: X=0.12201757 Y=0.87800148 Z=0.12201757 MULT= 3 ISPLIT= 8 5: X=0.12201757 Y=0.12201757 Z=0.87800148 5: X=0.87800148 Y=0.12201757 Z=0.12201757 Ge4NPT= 781 R0=0.5000 RMT=2. Z: 32.0 LOCAL ROT MATRIX:1.000 0.000 0.000 0.000 1.000 0.000 0.000 0.000 1.000 ATOM 6: X=0.62573282 Y=0.87502487 Z=0.12480892 MULT= 6 ISPLIT= 8 6: X=0.12480892 Y=0.62573282 Z=0.87502487 6: X=0.87502487 Y
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 change your mind in future then you can un-spam the emails from wien mailing list. Best wishes Masood On Tuesday, January 21, 2014 5:48 AM, Gavin Abo gs...@crimson.ua.edu wrote: You used the online tool to unsubscribe at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien and it doesn't work? On 1/20/2014 5:39 PM, shch...@itri.org.tw mailto:shch...@itri.org.tw wrote: Dear Peter, Could you help me to cancell my e-mail address on your list? I receviced a lot of discussion message and I dont need them. Thanks, Shan Haw Chiou Ph. D. Senior Researcher ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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/ali13btf/Bureau/XCrySDen-1.5.17-bin-semishared/xcrysden: 160: .: Can't open /complete_path_to/XCrySDen-1.5.17-src-all/scripts/xcLib.sh Where is the problem?! Cordially ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 4/12/2013 20:39: *hello dear users i'm using WIEN2k 13 with opensuse 12.3 i have a problem, firefox can not open w2web don't recognize my w2web server so i try to re install w2web hello dear users i'm using WIEN2k 13 with opensuse 12.3 i have a problem, firefox can not open w2web don't recognize my w2web server so i try to re install w2web using * linux-9nov:~ # rm -r ~/.w2web linux-9nov:~ # w2web ### # w2web starter # # Copyright (C) 2001 luitz.at # ### hostname: Name or service not known w2web installer on host linux-9nov.site ### # w2web installer # # Copyright (C) 2001 luitz.at # ### Checking for Installation in /root/.w2web/linux-9nov.site Creating /root/.w2web Creating /root/.w2web/linux-9nov.site conf directory does not exist - creating it. logs directory does not exist - creating it. sessions directory does not exist - creating it. tmp directory does not exist - creating it. Installing w2web files ... Please answer these questions for proper installaltion. Just press enter for the default value of (in brackets). Please enter the username: [admin] Please enter the password: [password] admin:password Remember these. You will need them when you log in. Select the port to run on: [7890] 7889 Running on port 7889 Please enter this system's hostname: [linux-9nov.site] Using linux-9nov.site Is this your master node?: [y] y Installing... Attempting to start now... Trying to start /root/WIEN2k/SRC_w2web/bin/w2web hostname: Name or service not known w2web server started, now point your web browser to http://linux-9nov.site:7889 done. linux-9nov:~ # *i found the same thing * * Firefox can't find the server at www.linux-9nov.site.* * * *what to do now ?* * * *thank you in advance* ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Wien2k data provenance
Hello Richard, In outputst at the bottom there'll be a final list of orbitals with a T/F value in the core-state column. Where it switches from true to false is where the ecut was set, an exact value is not recorded as far as I know. If you want to check the value you yourself provided 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 provenance. I have run into some trouble in attempting to extract the core/valence cuttoff value (default set to -6.0 Ry). I assume this should be recorded somewhere but I have had no luck finding it. Any direction would be appreciated. Regards, Richard Taylor -- Richard Taylor, PhD National Institute of Standards and Technology Tel: (301) 975-5122 ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] mbj probem gap
Hello Amine, Have you taken a closer look at the band structure of the GGA and mBJ results? If you get the gap out of the scf files, depending on your k-mesh sometimes you can miss some data. For instance if you use a k-mesh that does not include the gamma point and there is a sharp cross 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 is Eg = 3 eV, and as I made doping of this materails the gap is become Eg = -99.99 eV ( metalic) , (note that with only GGA I don't found this problem. just with MBJ) Cordially ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 this problem just with doping in mBj ( for pure not problem), I look at analys scf. Cordially *De :* Michael Sluydts michael.sluy...@ugent.be *À :* A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at *Envoyé le :* Vendredi 13 septembre 2013 9h32 *Objet :* Re: [Wien] mbj probem gap Hello Amine, Have you taken a closer look at the band structure of the GGA and mBJ results? If you get the gap out of the scf files, depending on your k-mesh sometimes you can miss some data. For instance if you use a k-mesh that does not include the gamma point and there is a sharp cross 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 is Eg = 3 eV, and as I made doping of this materails the gap is become Eg = -99.99 eV ( metalic) , (note that with only GGA I don't found this problem. just with MBJ) Cordially ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 schreef: Dear Prof. Blaha, Thank you very much for the explanations. They will be very useful !! All the best, Luis 2013/9/12 Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at This depends a lot on what you want to do and how much money you have. The single-core speed of a fast I7 is at least as good (or faster) than most Xeons, and they are MUCH cheaper. So for all systems up to 64-100 atoms/cell, where you need several k-points, a small cluster of I7 cpus /4 cores, or more expensive 6 core) (with GB-network and a common NFS file system) is for sure the fastest platform and in particular has by FAR the best price/performance ratio (One powerful I7 computer may cost about 1000 Euro). For bigger clusters, a drawback can be the large space to put all PCs on a big shelf ), but if you have less than 1 Euros, this is probably the best choice. However, Xeons can be coupled (2-4 Xeons) to a single multicore computer (eg. 16 cores), which may work with mpi and can be used to handle systems up to 200-300 atoms. They also can be bought in small boxes and may fit in a single 19 inch cabinet. But of course such systems are much more expensive. From what I said above it should be clear, that it is completely useless to buy a single 4 core Xeon computer. The next step would be to buy an Infiniband switch+cards and couple your PCs with this fast network to a powerful multinode mpi-cluster. Since the switch/cards are fairly expensive, on usually takes here Xeons as platform. However, you need to know how to install/configure the software properly. I've seen such clusters even in computing centers, which were completely useless, because the network/mpi was instable and jobs would crash randomly every couple of hours . Our strategy: i) We have a GB-networked cluster with Intel I7 computers (which we maintain our-self and this cluster includes also all the user- workstations) and do all the calculations for systems up to 64 atoms/cell on these systems. 2) For bigger systems we go to our University computer-center and run there with a PBS queuing system. This has the advantage that we do not need to care about the installation of the infiniband network nor the mpi-infrastructure (but we use always intel-mpi together with ifort/mkl). On 09/11/2013 06:31 PM, Luis Ogando wrote: Dear Prof. Blaha, Just for curiosity, what processor did you buy ? Is the Xeon family better than the i7 one for WIEN2k calculations ? All the best, Luis 2013/9/11 Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at I don't know what latest means. We use the latest one installed on our supercomputers (4.1.1.036) I have not seen any significant change with mpi in the last years. PS: I just got info that we have now a new ifort available for download ... On 09/11/2013 05:00 PM, Laurence Marks wrote: Thanks. One thing I will add/ask concerning the parallelization, the latest impi seems to be substantially better -- have you tried it? I have not just noticed this with Wien2k, but I am told that others have seen improvements in other codes. On Wed, Sep 11, 2013 at 9:42 AM, Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at wrote: Before buying a couple of new computers, I was asking myself the same question and discussed this with some people of our computing departments. The conclusions: a) potentially very good, but in practice very questionable, because for most application you cannot get out the real speed (10 times faster than an Intel I7). This is true, even for many lapack/mkl subroutines where it should work better. They told me to wait, until the mkl becomes better
Re: [Wien] Intel(R) Xeon Phi™ coprocessor
Should probably also note with that page that the high end AMD CPUs are typically much cheaper, but they tend to have double the cores with nearly the same power usage per core (so double the power) compared to an i7 or xeon, at continuous operation this can lead to a painful power bill, possibly aggrevated by heat generation requiring more active cooling (though I don't remember data on the temperatures). Op 12/09/2013 17:33, Peter Blaha schreef: Nice page, although of course what for wien2k matters is the performance for lapack/blas calls for a diagonalization/matrix-matrix multiplication. Anyway, you can see that Intel Core i7-3930K @ 3.20GHz is pretty high ranked and costs(560$) just a quarter of the top Intel Xeon E5-2687W @ 3.10GHz (1930$), while its performance is only 15% less than the top value. And of course, this may change every couple of month 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 Op 12/09/2013 15:43, Luis Ogando schreef: Dear Prof. Blaha, Thank you very much for the explanations. They will be very useful !! All the best, Luis 2013/9/12 Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at This depends a lot on what you want to do and how much money you have. The single-core speed of a fast I7 is at least as good (or faster) than most Xeons, and they are MUCH cheaper. So for all systems up to 64-100 atoms/cell, where you need several k-points, a small cluster of I7 cpus /4 cores, or more expensive 6 core) (with GB-network and a common NFS file system) is for sure the fastest platform and in particular has by FAR the best price/performance ratio (One powerful I7 computer may cost about 1000 Euro). For bigger clusters, a drawback can be the large space to put all PCs on a big shelf ), but if you have less than 1 Euros, this is probably the best choice. However, Xeons can be coupled (2-4 Xeons) to a single multicore computer (eg. 16 cores), which may work with mpi and can be used to handle systems up to 200-300 atoms. They also can be bought in small boxes and may fit in a single 19 inch cabinet. But of course such systems are much more expensive. From what I said above it should be clear, that it is completely useless to buy a single 4 core Xeon computer. The next step would be to buy an Infiniband switch+cards and couple your PCs with this fast network to a powerful multinode mpi-cluster. Since the switch/cards are fairly expensive, on usually takes here Xeons as platform. However, you need to know how to install/configure the software properly. I've seen such clusters even in computing centers, which were completely useless, because the network/mpi was instable and jobs would crash randomly every couple of hours . Our strategy: i) We have a GB-networked cluster with Intel I7 computers (which we maintain our-self and this cluster includes also all the user- workstations) and do all the calculations for systems up to 64 atoms/cell on these systems. 2) For bigger systems we go to our University computer-center and run there with a PBS queuing system. This has the advantage that we do not need to care about the installation of the infiniband network nor the mpi-infrastructure (but we use always intel-mpi together with ifort/mkl). On 09/11/2013 06:31 PM, Luis Ogando wrote: Dear Prof. Blaha, Just for curiosity, what processor did you buy ? Is the Xeon family better than the i7 one for WIEN2k calculations ? All the best, Luis 2013/9/11 Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at I don't know what latest means. We use the latest one installed on our supercomputers (4.1.1.036) I have not seen any significant change with mpi in the last years. PS: I just got info that we have now a new ifort available for download ... On 09/11/2013 05:00 PM, Laurence Marks wrote: Thanks. One thing I will add/ask concerning the parallelization, the latest impi seems to be substantially better -- have you tried it? I have not just noticed this with Wien2k, but I am told that others have seen improvements in other codes. On Wed, Sep 11, 2013 at 9:42 AM
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' - QTL-B.GT.15., Ghostbands, check scf files please some one help me, thanks in advance. with regards sikander ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 in the user's guide which is in your WIEN2k directory. F. Tran On Mon, 26 Aug 2013, david yang wrote: Dear Prof. Blaha and WIEN2k user, I am an extensive user of WIEN-2k and currently I am using version 12.1 . I am trying to calculate band gap of few oxides in WIEN2k using TB-mbj functinal , but i am not aware of the steps involved. (I tried checking in the mailing list but did not get much insight) In WIEN2k 12.1 there is no such executable as init_mbj_lapw . So I am not sure how to start my calculation. Any suggestion and small insight in this regards with be highly helpful. Thank you all in advance Regards David yang Ph D student NUS Singapore ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] l'approximation MBJ
Hello, It's best to send questions in english to get more replies (since many won't speak french). You can find all the steps for running an mBJ calculation in the manual starting at page 54 (paragraph 4.5.9). It will however refer to the program init_mbj_lapw which, as far as I'm aware, 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 j'aimerai bien savoir comment faire pour utiliser l'approximation MBJ sous le code wien2k ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] L'approximation MBJ
Bonjour, Vous pouvez trouver l'information sur mBJ sur page 53 du manuel de wien2k, mais je pense que vous devez suivre les phases de la programma init_mbj_lapw manuellement parce que init_mbj_lapw n'existe pas. Si vous posez votre question en anglais il'y a plus de réponses. Regards, 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://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] structeditor for creating a surface
Hello Madhav, The thickness of the slab will vary depending on the interplanar distance for that surface. Usually you can do this more accurately by using an expression based on the bulk lattice constants. For instance: bulk = loadstruct(...) surface = makesurface(bulk,1,bulk.a(3)/2,20.0) where bulk.a(3) will be half the lattice constant in the z direction. You may have to add 0.001 or something so that it does not cut off the uppermost atoms (most likely there's a smaller or greater than somewhere that could benefit from an equals sign). So surface = makesurface(bulk,1,bulk.a(3)/2+0.001,20.0) Also make sure your number of atoms is always correct since for more exotic surfaces sometimes the structeditor eats a few atoms somewhere at the bottom of the slab where the 001 direction used to be... Which is then usually easily fixed by making a bit thicker slab and removing 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 structure, I need to create a vacuum of 20 Ang. on the fifth layer. So I was not sure whether the thickness of the material [30.0] selection in sr=makesurface (s,1,30.0,20.0) is OK for Fe. It will be great if you could confirm sr=makesurface (s,1,30.0,20.0) on structeditor is OK. Best regards Madhav On Thu, Jun 27, 2013 at 3:27 PM, Peter Blaha pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at wrote: It is up to you, how thick (how many layers) you want to make your slab. The thicker the better, but soon you will run out of computer power. PS: For a (001) surface the programx supercell is probably easier to use. There you would be asked for the number of cells along x,y,z and with 1x1x2 (3,4,5..) you can create slabs with different thickness. PS: On 06/27/2013 03:48 AM, Madhav Ghimire wrote: Dear Robert and wien2k users, I am creating a surface using structeditor program which required octave enironment, I came across sr=makesurface(s,n,ind,depth,vac) which creates surface for a given unitcell where: s input structure n normal vector (in lattice coordinates) ind an index of an atom which should be in (0 0 0) *depth thickness of the material* vac thickness of the vacuum layer example: sr=makesurface(s,[0 0 1],1,30.0,20.0) Now my doubt is: How shall I realize the thickness of the particular material (for example Fe) I mean can I choose it manually (any number) or I need to know the proper thickness of the material. If so, can anyone help where I can find the thickness information of the material. Thanks in advance Madhav ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-165300 tel:%2B43-1-58801-165300 FAX: +43-1-58801-165982 tel:%2B43-1-58801-165982 Email: bl...@theochem.tuwien.ac.at mailto:bl...@theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ -- ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at mailto:Wien@zeus.theochem.tuwien.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 ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] Role of sgroup program
Hello Saurabh, Sgroup will try to find the smallest primitive cell by maximizing the symmetry. This gives you the same structure. Since this lowers the amount of inequivalent positions it does reduce the freedom (so if you want to give one of them a slight nudge and break the symmetry you may not be able to do that within the higher symmetrical spacegroup). You should also make sure the struct files you are feeding into sgroup have sufficient decimals in their positions for instance a position at 1/3 may not be recognised when you feed sgroup 0.3330 but will be recognized 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 samant schreef: Dear Peter Blaha WIEN2k users, I am using WIEN2k 12.1 version. During initialization through w2web while viewing outputsgroup we can accept either the case.struct file generated by sgroup (which changes the position coordinates of the atoms in the primitive cell) or keep our original file. According to UG default is the latter one. Does they both refer to same structure? For TiC both cases run without error. Does the properties calculated from both structure file should be same? For some complicated compunds e.g. spinel compounds #227 fd-3m, we have to accept the struct file generated by sgroup to run an error free SCF. It changes the position coordinates of the atoms in the primitive cell whose original input was origin choice 2 of space group fd-3m .Does it still refer to the same structure but with a different primitive cell Thanks in advance, with regards, Saurabh Samanta ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 Wien2k users, Is it possible to make struct file of Wien2k within Terminal not W2web? Yours, Mahdisa ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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 22/7/2012) to make a case.struc file to do anti ferromagnetic calculation. The compound I am strudying has magnetic ion Co with multiplicity 4 . What I have to do is to make Co ions inequivalent. But when I am doing so wien2k is not taking that structure and it is trying to go back to its normal one. But when I am using WIEN2k_07 version I am not getting this problem. Here it also told me to go back to its normal one but If I donot want that it accepts the new structure. Could any one please tell what to do in new version WIEN2k_12.1 to get the antiferromagnetic structure. I do antiferromagnetic calculation by making Co ions inequivalent in case.struc file. Thanks in advamce. Santu Baidya SRF, CMPMS SNBNCBS *The happiest people do not always have the best of all,* * they simply appreciate what they find on their way!!! SANTU * ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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, wasim raja Mondal schreef: Dear wien2k experts, I am running one peroskite structure. Initially I was facing dtsrt error. But with the help from Lyudmila I have solved the problem and there is no error in the initialization process. But when I am running scf I am getting the following error: Error in LAPW1 'LOPW' - Plane waves exhausted The possible reason for the this error is: (1) Increase the RK max value (2) see the precession for the atomic position which is sensitive for space group 194. For example 0.33367 should be o.3337 (3) change lo+apw. possibility 1 and 2 I have done. For (1) I have set rk value up to 9.5 and for (2) I have carefully checked. But I am getting same error. For the third I have not checked because I donot know how to do this. I am using wien2k_12. I am attaching the structure file and *.rsp file. ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html SUBROUTINE LOPW(NAT) ! use matrices, only: HSROWS, KZZ, XK, YK, ZK use lolog, only : nlo, ilo use lstapw, only : NV use rotmat, only: ROTIJ, ROTLOC use struk, only : POS, MULT, NDF use parallel, only: myid,abort_parallel IMPLICIT NONE INCLUDE 'param.inc' ! !Scalar Arguments ! INTEGERNAT ! ! .. ! !generates the LAPW (K+G)-vector for local orbitals ! ! .. ! !Locals ! INTEGERIA1, IEQ, IIX, INDEX, J, K, KOFF, L, LM, LMDN INTEGERLMUP, LMX, N, NATX, NATXX, NB, NBM INTEGERJLO,ipass DOUBLE PRECISION HL, RKGM, SX, TPI, check DOUBLE PRECISION ROTV1(3), ROTV2(3), VEC(3) COMPLEX*16 CC ! COMPLEX*16 HH((LOMAX+1)**2*NDF,(LOMAX+1)**2*NDF) COMPLEX*16 HH((2*LOMAX+1)*48,(2*LOMAX+1)*48) COMPLEX*16 SF(NDF), YL(0:(LOMAX+1)**2) !,nv:HSROWS) ! !External Subroutines ! EXTERNAL ROTATE, YLM ! !Intrinsic Functions ! INTRINSIC ATAN, DCMPLX, DCONJG, EXP, SQRT ! ! ** Maybe Experiment ** DOUBLE PRECISION VEC2(3), TMP1, TMP2 ! TPI = 8.0D+0*ATAN(1.0D+0) ! check=2.0D-2 ipass=0 1continue check=check/2.d0 KOFF = NV IA1 = 0 DO 140 N = 1, NAT DO 130 L = 0, LOMAX !IF (LOOR(L,N)) THEN do jlo=1,ilo(l,n) LMDN = L*L + 1 LMUP = (L+1)*(L+1) INDEX = 0 NB = 0 NBM = MULT(N)*(1+LMUP-LMDN) DO 120 IEQ = 1, MULT(N) DO 110 LM = LMDN, LMUP NB = NB + 1 K = KOFF + NB 10CONTINUE INDEX = INDEX + 1 IF (INDEX .GT. NV) GOTO 900 ! WRITE (6,*) 'INDEX,K,N,L,IEQ,LM',INDEX,K,N,L,IEQ,LM KZZ(1,K) = KZZ(1,INDEX) KZZ(2,K) = KZZ(2,INDEX) KZZ(3,K) = KZZ(3,INDEX) XK(K) = XK(INDEX) YK(K) = YK(INDEX) ZK(K) = ZK(INDEX) RKGM = SQRT(XK(K)*XK(K)+YK(K)*YK(K)+ZK(K)*ZK(K)) IF (NBM .NE. 1) THEN DO 20 NATX = 1, MULT(N) NATXX = IA1 + NATX SX = KZZ(1,K)*POS(1,NATXX) + KZZ(2,K)*POS(2,NATXX) + KZZ(3,K)*POS(3,NATXX) ! SF(NATX) = EXP(DCMPLX(0.0D+0,TPI*SX)) SF(NATX) = DCMPLX(DCOS(TPI*SX),DSIN(TPI*SX)) 20 CONTINUE IIX = 0 DO 50 NATX = 1, MULT(N) IF (RKGM .LE. 1.0D-5) THEN DO 30 LMX = LMDN, LMUP !YL(LMX-1,K) = (0.0D+0,0.0D+0) YL(LMX-1) = 0.0D0 30 CONTINUE ! YL(0,K) = (1.0D+0,0.0D+0) YL(0) = 1.D0 ELSE VEC(1) = XK(K) VEC(2) = YK(K) VEC(3) = ZK(K) CALL ROTATE(VEC,ROTIJ(1,1,IA1+NATX),ROTV1
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 nodes. Nodes are called n001, n002, n003, n004... I use torque PBS queue system. When I submit a job using a bash file, the default directory is always my home directory. Therefore, at the beginning of my bash file, I always add a line 'cd /home/my_username/wien2k/case'. This works for scf calculations. However, when I use x lapw2 -qtl -band -p to calculate the band structure or x lapw2 -qtl -p to calculate the DOS, I always encounter the following error message: scp: .//case.vector_1 not found scp: .//case.vector_2 not found ... It seems scp is looking for case.vector_1 in my home directory rather than my working directory, even though I've added the line 'cd /home/my_username/case' in my bash file. This problem only occurs with using x lapw2 -qtl -p. I used to do scf calculation in serial and then use x lapw2 -qtl. But I'm wondering whether there is a workaround. Thanks. ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
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: Dear all, I successfully made desire surface using STRUCTEDITOR. It is possible to add different slabs one by one using matrix command?. I want to make multilayer structure Fe/Co/Al on Si(100) by using STRUCTEDITOR. Thanks regards Vishal Jain ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] (no subject)
Hello wasim, I4m not quite sure what happens by default but you should make sure that the wien directory is added to your global path (and that it is correct). Does /home/naushad/software/ contain the wien files or is it maybe a subdirectory /home/naushad/software/wien for instance then you could for instance do export WIENROOT= /home/naushad/software/wien and export PATH=$PATH:$WIENROOT (if you're working in bash) and it should find it. Maybe do echo $WIENROOT and echo $PATH to see what your current values are. A full overview of environment values can be found in section 11.4 of the manual. Regards, Michael Sluydts Op 9/04/2013 12:32, wasim raja Mondal schreef: Dear wien2k community, I am beginner in wien2k. I am running Tic example from the wien2k manual. After doing the structure generation successfully when I am doing initialization I am facing this problem: please help me. /home/naushad/software/nn: Command not found. 0.0u 0.0s 0:00.00 0.0% 0+0k 0+0io 0pf+0w error: command /home/naushad/software/nn nn.def failed ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ Wien mailing list Wien@zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien SEARCH the MAILING-LIST at: http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
Re: [Wien] no space left on device?
Hello dr. Abdallah, The first thing I would do is check the partition/drive which you use as scratch directory ($SCRATCH). You should have this defined in either your .bash_profile/.bashrc or the script you use to run wien calculations (if there is one). If you are using a simple setup you will most likely just have one hard drive. In this case, anywhere on the drive, type df -h. This will tell you the total size and what you have currently used. Most likely you will see that the main partition (being the largest) will be nearly full. In this case you will have to clean up some files and/or get a bigger drive. removing files in the SCRATCH directory can help. (If you don't know the setting, search for the files with vector in their name, could just be the calculation directory). Maybe someone else knows if you can stop wien from writing out certain files, but I have 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 to solve? I'll be very grateful. This is very urgent. thank you for your cooperation. Dr Houda Ben Abdallah Laboratory of condensed matter. Departement of Physics. Faculty of Sciences, Tunis. Tunisia ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html ___ 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-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html
