Re: [Wien] DFT in biomedical research

[Michael Sluydts]

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>

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

[Michael Sluydts]

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








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

[Michael Sluydts]

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?




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Re: [Wien] scf2forces

[Michael Sluydts]

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 
 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



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Re: [Wien] Graphene bandstructure

[Michael Sluydts]

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
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Re: [Wien] Reconstructed Si 100 surface

[Michael Sluydts]

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 
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 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>
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> en nombre
de Muhammad Sajjad 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.

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-- 
Kind Regards

Muhammad Sajjad
Post Doctoral Fellow
KAUST, KSA.


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Re: [Wien] Reconstructed Si 100 surface

[Michael Sluydts]

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 <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>
mailto:wien-boun...@zeus.theochem.tuwien.ac.at>> en nombre de
Muhammad Sajjad 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.

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--
Kind Regards
Muhammad Sajjad
Post Doctoral Fellow
KAUST, KSA.


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Re: [Wien] negative value of U in solids

[Michael Sluydts]

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?"




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Re: [Wien] how to cut a surface

[Michael Sluydts]

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
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Re: [Wien] Regarding electron density calculations

[Michael Sluydts]

That being said, one should be able to ask questions without fear of 
repercussions as to not unnecessarily reinvent the wheel.


In this case I belief searching for difference densities (and lapw5) in 
the user guide may provide the needed answers.


http://www.wien2k.at/reg_user/textbooks/usersguide.pdf

Best regards,

Michael

Víctor Luaña Cabal schreef op 1/05/2015 om 10:50:

On Fri, May 01, 2015 at 12:30:43PM +0530, Mamta Chauhan wrote:

I want to calculate the difference charge density. I can calculate the
valence charge density. but don't know to calculate the difference density.
Can anyone help me and suggest to calculate the difference density for
example TiC (Titanium Carbide) in Wien2k? Is there any tutorial available
for it?

Mamta,

1) Please, think a little ...

2) If you know how to obtain the electron density in a region (1D, 2D, 3D)
what impedes you to do two calculations modifying anything in your
system and obtain their difference?

3) Do you need that some slave provides you a script to do the difference?
Paint it in nice colors? Anything else, bwana?

Sorry if my words disturb you, but today it is the international day of
workers. Did you realise? Did you even know?

Good luck in your adventure of learning some physics and mathematics,

 Dr. Víctor Luaña
--
  .  ."Research is to see what everybody else has seen, and to
 / `' \   think what nobody else has thought"
/(o)(o)\  -- Albert Szent-Gyorgi
   /`. \/ .'\
  /   '`'`   \ "Lo mediocre es peor que lo bueno, pero también es peor
  |  \'`'`/  | que lo malo, porque la mediocridad no es un grado, es una
  |  |'`'`|  | actitud"
   \/`'`'`'\/  -- Jorge Wasenberg, 2015
===(((==)))==+=
! Dr.Víctor Luaña, in silico chemist & prof. ! Mediocre is worse than
! Departamento de Química Física y Analítica ! good, but it is also
! Universidad de Oviedo, 33006-Oviedo, Spain ! worse than bad, because
! e-mail:   vic...@fluor.quimica.uniovi.es   ! mediocrity is not a grade,
! phone: +34-985-103491  fax: +34-985-103125 ! it is an attitude
++
  GroupPage : http://azufre.quimica.uniovi.es/
  (being reworked)
 
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Re: [Wien] Problem when running MPI-parallel version of LAPW0

[Michael Sluydts]

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


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

[Michael Sluydts]

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] hi

[Michael Sluydts]

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
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Re: [Wien] octave problem, 2nd

[Michael Sluydts]

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] Xcrygen compilation

[Michael Sluydts]

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.


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Re: [Wien] Xcrygen compilation

[Michael Sluydts]

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 
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


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--
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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


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Re: [Wien] Xcrygen compilation

[Michael Sluydts]

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  
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


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Re: [Wien] Guidance require for structure generation

[Michael Sluydts]

Hello Naseem,

The problem you have is a lack of information. The spacegroup and 
stoichiometry still give you freedom through wyckoff positions to create 
a variety of structures.


There are multiple avenues you can take. The first is to search the 
literature and databases (COD: http://www.crystallography.net and ICSD 
if you have access to it http://www.fiz-karlsruhe.com/icsd_home.html), 
though I did not immediately find anything of interest in COD. If you 
cannot find the structure then it becomes a different problem, rather 
than determining materials properties you will have to do structure 
prediction.


Structure prediction is a discipline in itself (literature available) 
and can take a lot of time. If you know of similar compounds you may be 
able to base yourself on them as a starting point to reduce your search 
space, then try a few different configurations for the atoms, optimize 
your cells and see what is lowest in energy.


Other more advanced methods are things like genetic algorithms where you 
try different structures then combine them and gradually converge to a 
candidate for the optimal structure. Software like USPEX exists for this 
but I don't think it has been used with wien2k, though interfacing with 
it should not be entirely impossible.


Trying to get more details on what you might be looking for is going to 
be the first step either way.



Good luck,

Michael Sluydts



Naseem Hassan schreef op 4/07/2014 11:53:

Thank You All.

I benefited from all of you on mailing list. You are absolutely right 
I should learn instead of spoon feeding. I can understand fully that 
experts are already handling the burden of below average questions.


Inspite of all your recommendation I wish that someone should suggest 
a road map of topics that leads to solution of making new structure in 
WIEN2k. I see many emails on mailing list that suggest the similar 
kind of problem of making structure for a specific space group. I 
really wanted to learn this but always lost in multiple topics. Many 
of seniors to whom I know personally know can not solve this problem. 
Just suggesting, that it will beneficial for newcomers if someone can 
prepare a tutorial on this issue. We sometimes do not work on 
compounds just because we cannot make structure file in wien2k.


Best Regards
Naseem



On Fri, Jul 4, 2014 at 1:16 PM, Juan Manuel Perez Mato 
mailto:wmppe...@lg.ehu.es>> wrote:


Please, learn some elementary crystallography in the International
year of crystallography.

regards,

J. Manuel Perez-Mato
Fac. Ciencia y Tecnologia,
Universidad del Pais Vasco, UPV
48080 BILBAO,
Spain

tel. +34 946012473 
fax. +34 946013500 
***

El 04/07/2014, a las 02:37, Naseem Hassan escribió:


Dear Sir,

Every space group has some ideal positions. From little
experience in the past, I believe on selecting 3 atoms in the
start of structure generation and assigning positions for three
atoms will give the primitive cell for this space group. In this
primitive cell other positions appear automatically by Wien2k.
Does a space group has not ideal positions ?. I need ideal
positions for three atoms and then I will relax the structure to
actual positions for this compound. Modeling a material is
possible without experimental results. I am hopeful that you will
propose some kind of solution.

Thank you
Best Regards
Naseem Hassan




On Fri, Jul 4, 2014 at 1:22 AM, Peter Blaha
mailto:pbl...@theochem.tuwien.ac.at>> wrote:

Without atomic positions one cannot create a structure.

Am 03.07.2014 19:46, schrieb Naseem Hassan:

Dear Wien2k experts

I am reporting this difficulty after going through
mailing list and
literature review. Kindly guide how can I generate
structure file with
the following information.

Compound Formula:   V3S7Cl
Space Group: C mmm#65 Orthorhombic
lattice parameters:  a=20.6 b=3.8, c=3.9

I need *general structure file* for this compound I will
try to remove
error associated with RMTs and other initializing
parameters by my self.

Alternatively,

If I select 3 atoms in the structure generation and I
insert all the
parameters as stated above then I just miss the position
of three atoms
in the structure file. In order to fill the positions I
checked the
wycoff psoitions from the Bilbao Crystallographic server
but I am unable
to understand which position should I give. *If this
approach is
correct* then kindly just *provide the positions* which I
can fill at
  

Re: [Wien] Parallel compilation installation

[Michael Sluydts]

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 <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" 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



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Re: [Wien] [SPAM?]

[Michael Sluydts]

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


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Re: [Wien] request to Robert Laskowski

[Michael Sluydts]

While this is of course not the same as a global update of the files, it 
may be interesting to mention that these functions are all just matlab 
scripts in SRC_structeditor. So by using some simple matlab code you can 
quite quickly make your own functions to extend functionality.


In general you can just make a function file in an arbitrary path and 
then do addpath('~pathtoyourcustomfunctions~') to get access to them. I 
do this for quite a few system-specific operations, like adsorbing 
molecules to surfaces.



Kind regards,

Michael Sluydts





John Rundgren schreef op 4/06/2014 15:40:

Dear W2k team,

I should be much obliged if Robert Laskowski would introduce a new 
structeditor command

  so=orderallaintoconsecutivelayers(s,vec)
analogous to
  sm=movealla(s,vec).

For instance, I have successfully designed the supercell
  CORu0001-sqrt(3) x sqrt(3)R30deg
using structeditor. In the absence of a specific structeditor command 
I order the atoms by manual copying and pasting.


In low energy electron diffraction research atomic ordering after 
ascending coordinate normal to the surface is a rule. I like to hold 
out LEED as a motivation for a specific structeditor command.


Best,
John Rundgren, KTH

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

[Michael Sluydts]

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
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Re: [Wien] Errori in mini

[Michael Sluydts]

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" <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



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Re: [Wien] Regarding Bandstructure

[Michael Sluydts]

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

[Michael Sluydts]

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

=


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do not copy or use it for any purpose, or disclose its contents to any 
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[Wien] Problem with structeditor for slabs

[Michael Sluydts]

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);
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Re: [Wien] Configuring SCRATCH variable for parallel computation

[Michael Sluydts]

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).



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Re: [Wien] Problem with x symmetry

[Michael Sluydts]

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
 

[Wien] Problem with x symmetry

[Michael Sluydts]

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=0.99967

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

[Michael Sluydts]

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  
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

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Re: [Wien] XCrySDen error

[Michael Sluydts]

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


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Re: [Wien] (no subject)

[Michael Sluydts]

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*





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Re: [Wien] Wien2k data provenance

[Michael Sluydts]

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

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Re: [Wien] How to make more cpu participate in paralle processes

[Michael Sluydts]

Hello Lei,

Have you set up your .machines file properly? (it's described in the 
manual) Most likely you are just running on two threads and wien is not 
actually trying to parallellize properly.


If you have 12 k points then you can basically make 1 line per core with 
each line "1: hostname" possibly in your case 1:localhost if you're 
running the jobs only on the machine you're working on.


But try reading the manual and send us another mail if you get stuck.


Regards,

Michael Sluydts
??? schreef op 3/11/2013 14:34:

Dear all Wien2k users:
 I chosed paralle caculation in the SCF cycle , but only 2 cpus 
were running, while other 10 cpus  was free. Can anyone tell me why 
this is, how to solve this problem to Improve processing speed?

top - 17:54:11 up 5 days, 30 min,  1 user,  load average: 2.02, 2.02, 2.00
Tasks: 279 total,   3 running, 275 sleeping,   0 stopped,   1 zombie
Cpu(s): 16.7%us,  0.0%sy,  0.0%ni, 83.3%id,  0.0%wa,  0.0%hi,  0.0%si, 
0.0%st

Mem:  49448368k total,  6814276k used, 42634092k free,   316812k buffers
Swap: 51199144k total,0k used, 51199144k free,  3680536k cached
  PID USER  PR  NI VIRT  RES  SHR S %CPU %MEMTIME+ COMMAND
22849 student   25   0 1249m 1.1g 6448 R 100.0  2.4  32:43.95 lapw1
22834 student   25   0 1252m 1.1g 6440 R 99.8  2.4  32:43.43 lapw1
1 root  15   0 10312  728  616 S 0.0  0.0   0:02.25 init
2 root  RT  -5 0 00 S  0.0  0.0   0:00.04 migration/0
best regard

Lei Liu




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Re: [Wien] mbj probem gap

[Michael Sluydts]

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 
*À :* A Mailing list for WIEN2k users 
*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


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Re: [Wien] mbj probem gap

[Michael Sluydts]

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


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

[Michael Sluydts]

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 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 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.

   

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

[Michael Sluydts]

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 <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 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
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 &q

Re: [Wien] (no subject)

[Michael Sluydts]

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


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

[Michael Sluydts]

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



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Re: [Wien] l'approximation MBJ

[Michael Sluydts]

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



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Re: [Wien] L'approximation MBJ

[Michael Sluydts]

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


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Re: [Wien] structeditor for creating a surface

[Michael Sluydts]

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 
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


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-- 


  P.Blaha
--
Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
Phone: +43-1-58801-165300 
FAX: +43-1-58801-165982 

Email: bl...@theochem.tuwien.ac.at
<mailto:bl...@theochem.tuwien.ac.at>WWW:
http://info.tuwien.ac.at/theochem/
--
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Re: [Wien] Role of sgroup program

[Michael Sluydts]

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


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Re: [Wien] make struct

[Michael Sluydts]

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


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Re: [Wien] Problem in making antiferromagnetic structure

[Michael Sluydts]

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

*


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Re: [Wien] plane wave exhausted

[Michael Sluydts]

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.




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  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)

Re: [Wien] scp error

[Michael Sluydts]

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.
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Re: [Wien] RELATED TO STRUCTEDITOR

[Michael Sluydts]

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



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Re: [Wien] Need assistance

[Michael Sluydts]

Hello Mohammad,

For pure non-periodic clusters you may be able to try calculating 
optical properties in Gaussian. I'm not sure any kind of periodic code 
would be able to provide you with confinement, because confinement 
requires constrained dimensions which you are effectively removing by 
infinitely repeating your unit cell.


I am of course not sure whether you are studying colloidal quantum dots 
(nanocrystals) or the embedded kind in a semiconductor. I assume in 
theory you can represent some kind of quantum dot array in giant cells 
but once again it will become very heavy to calculate and I fear I'm not 
quite sure how you would get useful properties out of it. If you did 
that, maybe by studying the average potential variations throughout the 
cell you can study confinement, but I have no experience in this. If the 
confinement does not have to be 3-dimensional you can of course create 
an epitaxial structure in programs such as wien.


I myself use VASP and wien for my calculations but i only look at 
surface adsorption so I approximate them by infinite surfaces. Another 
program that may be useful for semi-periodic structures is Crystal09 
which seems to also be able to do 1D and 2D  structures, avoiding any 
artefacts you get from for instance repeating a surface slab in its 
surface direction.


You will most likely know best how your system looks like and what 
specific properties you need to extract useful data though.



Regards,

Michael Sluydts

Op 16/05/2013 10:38, Lawal Mohammed schreef:

Hello Michael and Co,
Can you please suggest any periodic code for quantum confinement 
effect? And how can confinement and surface effects be neglected, in 
such case what will be implication. please elaborate.

With kind regards
Mohammed
----
*From:* Michael Sluydts 
*To:* A Mailing list for WIEN2k users 
*Sent:* Wednesday, May 15, 2013 3:49 PM
*Subject:* Re: [Wien] Need assistance

Hello Mohammad,

It all depends what you want to do. Wien2k is optimal for calculating 
properties of periodic structures, so it is mostly recommended for bulk.


For confinement effects aperiodic code is recommended. However it is 
unlikely you will ever be able to calculate optical properties of 
anything larger than a small cluster aperiodically (extrapolation is 
of course a useful tool).


I myself do use periodic DFT to estimate surface adsorption on 
colloidal quantum dots, so you'll have to pick the right tool for 
whatever you are interested in.



Regards,

Michael Sluydts


Op 15/05/2013 9:37, Lawal Mohammed schreef:

Dear Wien2k Community,
I am a new user of Wien2k code. I want to know if it is possible to 
do simulation study of quantum dots using Wien2k. Actually, I am 
about to start a research on quantum dots based materials for 
intermediate band solar cells. Therefore, I really need to know the 
potential of Wien2k package. Could you please help me?

With kind regards
Mohammed Lawal



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Re: [Wien] Structeditor related

[Michael Sluydts]

Hello Vishal,

Does tcsh work in your normal commandline?

Also make sure all your paths are set properly. And keep in mind that 
showstruct will use xcrysden, so xcrysden will have to work too.


The paths are:

export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
export PATH=$PATH:$WIENROOT:$STRUCTEDIT_PATH:.
export OCTAVE_EXEC_PATH=$OCTAVE_EXEC_PATH:$PATH
export OCTAVE_PATH=$OCTAVE_PATH:$STRUCTEDIT_PATH
alias octave="octave -p $OCTAVE_PATH"

but since your structeditor itself works most of that should be right. 
Keep in mind that showstruct only visualizes so until you get it working 
you can use savestruct and view it in another window with xcrysden 
--wien_struct file.struct or other software of your choice.



Regards,

Michael Sluydts

Op 16/05/2013 8:49, vishal jain schreef:


Dear All

I try to test ag.struct file for learn use of structeditor tool
I found following error

octave:1> s=loadstruct("ag.struct")
octave:2> showstruct(s),
sh: 1: tcsh: not found
octave:3>

Thanks and Regards

Vishal Jain





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Re: [Wien] How to use structeditor

[Michael Sluydts]

Hello Vishal,

Everything should be possible in the structeditor, since in the end it 
just represents the structure by a matrix of positions. Some scripting 
may be needed though so be sure to look up some octave/matlab tutorials 
if you're not familiar with it.


You can either use the makesurface function to make slabs of each 
material and then combine them using mergestruct or just matrix 
operations (possibly after moving them with movealla). Alternatively you 
can just make a Si slab with makesurface and start adding to it with 
functions like addatom (and maybe make your own function to add an 
entire layer).


You'll have to use some geometry to make sure everything ends up in the 
right spot though and make sure that you are working in the right 
coordinate system (of the eventual cell, surface.lat2car is a useful 
property there).


Check the helpstruct command to get an idea of what all is possible (and 
after that you can always send another email with more specific questions).



Regards,

Michael Sluydts
Op 15/05/2013 17:28, vishal jain schreef:

Dear all,

I want to make Fe/Co/Al (5 trilayers) multilayer structure on Si(100) 
using structeditor, It's possible or not?


Thanks and Regards

Vishal Jain



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Re: [Wien] Need assistance

[Michael Sluydts]

Hello Mohammad,

It all depends what you want to do. Wien2k is optimal for calculating 
properties of periodic structures, so it is mostly recommended for bulk.


For confinement effects aperiodic code is recommended. However it is 
unlikely you will ever be able to calculate optical properties of 
anything larger than a small cluster aperiodically (extrapolation is of 
course a useful tool).


I myself do use periodic DFT to estimate surface adsorption on colloidal 
quantum dots, so you'll have to pick the right tool for whatever you are 
interested in.



Regards,

Michael Sluydts


Op 15/05/2013 9:37, Lawal Mohammed schreef:

Dear Wien2k Community,
I am a new user of Wien2k code. I want to know if it is possible to do 
simulation study of quantum dots using Wien2k. Actually, I am about to 
start a research on quantum dots based materials for intermediate band 
solar cells. Therefore, I really need to know the potential of Wien2k 
package. Could you please help me?

With kind regards
Mohammed Lawal



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Re: [Wien] installation problem

[Michael Sluydts]

Hello wasim,

Make sure the ports are open on the server and router. Ask your sysadmin 
to check the firewalls (and of course make sure that the ip is correct 
of course). If it's your own server maybe try 'service iptables stop'.



Regards,

Michael Sluydts


Op 10/04/2013 12:11, wasim raja Mondal schreef:


Dear wien2k users

I have installed wien2k in our cluster. After giving the port to 
browsers this error are coming.



Checking for Installation in 
/home/wasim/.w2web/viper5.intranet.jncasr.ac.in 
<http://viper5.intranet.jncasr.ac.in>


w2web server started, now point your web browser to
http://viper5.intranet.jncasr.ac.in:7436



erros are given below



The following error was encountered while trying to retrieve the URL: 
http://viper5.intranet.jncasr.ac.in:7436/


*Connection to 192.168.32.96 failed.*

The system returned: /(113) No route to host/

The remote host or network may be down. Please try the request again.

Your cache administrator is comp...@jncasr.ac.in 
<mailto:comp...@jncasr.ac.in?subject=CacheErrorInfo%20-%20ERR_CONNECT_FAIL&body=CacheHost%3A%20jncproxy.intranet.jncasr.ac.in%0D%0AErrPage%3A%20ERR_CONNECT_FAIL%0D%0AErr%3A%20%28113%29%20No%20route%20to%20host%0D%0ATimeStamp%3A%20Wed,%2010%20Apr%202013%2010%3A20%3A10%20GMT%0D%0A%0D%0AClientIP%3A%20192.168.33.78%0D%0AServerIP%3A%20192.168.32.96%0D%0A%0D%0AHTTP%20Request%3A%0D%0AGET%20%2F%20HTTP%2F1.1%0AHost%3A%20viper5.intranet.jncasr.ac.in%3A7436%0D%0AUser-Agent%3A%20Mozilla%2F5.0%20%28X11%3B%20Ubuntu%3B%20Linux%20x86_64%3B%20rv%3A13.0%29%20Gecko%2F20100101%20Firefox%2F13.0%0D%0AAccept%3A%20text%2Fhtml,application%2Fxhtml+xml,application%2Fxml%3Bq%3D0.9,*%2F*%3Bq%3D0.8%0D%0AAccept-Language%3A%20en-us,en%3Bq%3D0.5%0D%0AAccept-Encoding%3A%20gzip,%20deflate%0D%0AProxy-Connection%3A%20keep-alive%0D%0A%0D%0A%0D%0A>.







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Re: [Wien] (no subject)

[Michael Sluydts]

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






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Re: [Wien] "no space left on device?"

[Michael Sluydts]

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 found"no 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


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