[Wien] amorphous material EDOS calculation
Hi there, Would Wien2k be able to calculate EDOS of an amorphous material ? I'm thinking of generating a amorphous cluster using MD then input the coordinates using space group P. Has anyone try something similar? Thanks for the help. Jedo -- Jedo Kim, Ph.D Candidate Heat Transfer Physics Laboratory 2350 Hayward, 2186 GG Brown Bldg. University of Michigan, Ann Arbor, MI 48109-2143 Email: jedokim at umich.edu, jdzbox at hotmail.com Tel: 734-764-3487 (o); 734-276-8370 (cell) http://sitemaker.umich.edu/kaviany
[Wien] silicon structure
> You mean Wyckoff position 8a as (0, 0, 0) right? I tried that before, No, we mean the second setting and for this setting the coordinates of position 8a are (1/8,1/8,1/8). Alternatively, just use instead of the spacegroup the latrtice type "F" and specify the Si atoms at (0,0,0) and (.25,.25,.25) During initialization, sgroup should complain and generate a struct file compatible with WIEN2k. PS: I remember that I was quite confused myself as young researcher, that the common spacegroup-symbol + Wyckoff position is not necessarily sufficient to define a structure, but there are 2 different settings. > but the structure I see using Xcrysden was even more wrong. If I do > that, the file looks like > > Space group 227_Fd-3m > > a = 5.43 b = 5.43 c = 5.43 > 90 90 90 > > Atom 1 Si z = 14 RMT 1.8 > pos 1 x = 0.0 0.0 0.0 > pos 2 x = 0.0 0.25 0.25 > pos 3 x = 0.0 0.25 0.25 > pos 4 x = 0.0 0.25 0.25 > > It is a big change for me to work with space groups from lattice vectors. > > > For RMT sizes, I could not increase them because of the error I get from > the first step (x nn). I'm thinking that I am getting these errors > because my structure is not correct. Also, even though I increase them, > when I hit "set automatically RMT" it reduces it back to 1.8. > > > > On 6/14/2010 7:11 AM, Gerhard Fecher wrote: >> why are you giving two atoms for the basis of Si ? >> Set up 2 (see Peters remark) of spacegroup 229 should have only one on >> Wyckoff position 8a. >> >> did you recognize something from youre RMT sizes ? >> >> I usually use this example for my students to check if they know about >> crystal structures and >> to find out how they turn semiconductors into metals >> >> Ciao >> Gerhard >> >> >> Dr. Gerhard H. Fecher >> Institut of Inorganic and Analytical Chemistry >> Johannes Gutenberg - University >> 55099 Mainz >> >> Von: wien-bounces at zeus.theochem.tuwien.ac.at >> [wien-bounces at zeus.theochem.tuwien.ac.at]" im Auftrag >> von"Jedo [jedokim at umich.edu] >> Gesendet: Montag, 14. Juni 2010 12:35 >> An: wien at zeus.theochem.tuwien.ac.at >> Betreff: Re: [Wien] silicon structure >> >> Thanks for the answer. Still, I don't understand why WIEN2k is giving me >> a structure with this many atoms. I'm listing the Strucgen atoms when I >> save it. It adds 10 more atoms. The fractional coordinates look ok, but >> when I look at the structure using Xcrysden, it does not look right. I >> can send you the screen shot if you wish. >> Thanks for all the help. >> >> Space group 227_Fd-3m >> >> a = 5.43 b = 5.43 c = 5.43 >> 90 90 90 >> >> Atom 1 Si z = 14 RMT 1.21 >> pos 1 x = 0.0 0.0 0.0 >> pos 2 x = 0.0 0.25 0.25 >> pos 3 x = 0.0 0.25 0.25 >> pos 4 x = 0.0 0.25 0.25 >> >> Atom 2 Si x = 14 RMT 1.21 >> pos 1 0.25 0.25 0.25 >> pos 2 0.75 0.75 0.75 >> pos 3 0.75 0.5 0.5 >> pos 4 0.25 0.0 0.0 >> pos 5 0.0 0.0 0.25 >> pos 6 0.5 0.5 0.75 >> pos 7 0.5 0.75 0.5 >> pos 8 0.0 0.25 0.0 >> >> >> >> >> On 6/14/2010 12:59 AM, Peter Blaha wrote: >>> Nothing is wrong. >>> sgroup changes your input structure and shifts the origin to an >>> inversion center. This moves the Si atoms by (1/8,1/8,1/8). >>> >>> PS: The spacegroup 227 has 2 different "settings", i.e. origins with >>> tetrahedral symmetry or with inversion symmetry. Since all matrix >>> elements >>> can be kept as "real" numbers when inversion symmetry is present, WIEN2k >>> adopts automatically this setting. >>> >>> Jedo schrieb: Hi, I'm a newbie to wien2k. I have done some abinit calculation with silicon. So, I just wanted to start with Silicon again to test it. However, when I put the structure in, it gives me a very different structure. I'm not sure what I am doing wrong. My inputs for StructGen for Silicon is Spacegroup 227_Fd-3m Lattice parameters A 5.43 5.43 5.43 90 90 90 Si 0 0 0 Si 0.25 0.25 0.25 Is this correct? I'm used to inputing lattice vectors. Thanks for the help Jedo >> -- >> >> Jedo Kim, Ph.D Candidate >> Heat Transfer Physics Laboratory >> 2350 Hayward, 2186 GG Brown Bldg. >> University of Michigan, Ann Arbor, MI 48109-2143 >> Email: jedokim at umich.edu, jdzbox at hotmail.com >> Tel: 734-764-3487 (o); 734-276-8370 (cell) >> http://sitemaker.umich.edu/kaviany >> >> >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> ___ >> Wien mailing list >> Wien at zeus.theochem.tuwien.ac.at >> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien >> >> > -- Peter Blaha Inst.Materialchemie, TU Wien Getreidemarkt 9 A-1060 Vienna Austria
[Wien] Problem After Userconfig
FREADER to acroread (Y/n)
!!! The following lines will be added to your .bashrc file if you continue
!!!
A copy of your current .bashrc will be saved under .bashrc.savelapw!
# added by WIEN2k: BEGIN
#
alias lsi="ls -aslp *.in*"
alias lso="ls -aslp *.ou*"
alias lsd="ls -aslp *.def"
alias lsc="ls -aslp *.cl*"
alias lss="ls -aslp *.sc*"
alias lse="ls -aslp *.error"
alias pslapw="ps -ef |grep "lapw""
alias cdw="cd /home/wien/WIEN2k"
export OMP_NUM_THREADS=1
#export LD_LIBRARY_PATH=.
export EDITOR="emacs"
export SCRATCH=./
export WIENROOT=/home/wien/wien2k
export W2WEB_CASE_BASEDIR=/home/wien/WIEN2k
export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
export PDFREADER=acroread
export PATH=$PATH:$WIENROOT:$STRUCTEDIT_PATH:.
export OCTAVE_EXEC_PATH=${PATH}::
export OCTAVE_PATH=${STRUCTEDIT_PATH}::
ulimit -s unlimited
alias octave="octave -p $OCTAVE_PATH"
#
Do you want to continue (Y/n)?
*) adding aliases
*) adding environment variables
*) adding path to wien programs and set unlimited stacksize
done.
If you want to use k-point parallel execution on a non-shared memory
system, you must be able to login without specifying a password.
When using rsh you should modify your .rhosts file, if you are
using ssh you must generate (ssh-keygen) and transfer your "public keys".
Edit .rhosts file now? (y/N)
*
* WIEN 2k *
* user configuration *
*
Your user environment for WIEN users is now configured.
You have to restart your shell before the changes come
into effect (execute: . ~/.bashrc).
Start "w2web", define "user/password" and select a port. Then point
your web-browser to the proper address:PORT.
For proper usage of scfmonitor please add a line in ~/.Xdefaults :
gnuplot*raise: off
We wish you GOOD LUCK with your calculations.
Your WIEN2k Team
[wien at localhost wien2k]$ . ~/.bashrc
[wien at localhost wien2k]$
Sir, When I put w2web command for creating user name and password then
fllowing message shown
[wien at localhost wien2k]$ w2web
bash: /home/wien/wien2k/w2web: q: bad interpreter: No such file or directory
Sir, May I request you to guide me to resolve this problem.Sir I will be
very grateful to you.
With Kind Regards And Thanks
SANJAY KUMAR SINGH.
Research Scholar.
Condensed Matter Theory Group.
School Of Studies In Physics.
Jiwaji University.
Gwalior (M.P)? 474 011.
India.
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[Wien] Problem After Userconfig
7/6/2010)
>
>
> System: linuxifc
>
>
>
>
>
>
> S specify a system
>
>
> C specify compiler
>
>
> O specify compiler options, BLAS and LAPACK
>
>
> P configure Parallel execution
>
>
> D Dimension Parameters
>
>
> R Compile/Recompile
>
>
> U Update a package
>
>
> L Perl path (if not in /usr/bin/perl)
>
>
> Q Quit
>
>
>
>
> Selection: q
>
>
>
>
> site_config_lapw done.
>
>
> [wien at localhost wien2k]$ ./userconfig_lapw
>
>
> cp: cannot stat `/home/wien/.cshrc': No such file or directory
>
>
> cp: cannot stat `/home/wien/.cshrc': No such file or directory
>
>
> grep: /home/wien/.cshrc: No such file or directory
>
>
>
>
> *"
>
>
> * WIEN 2k *"
>
>
> * user configuration *"
>
>
> *"
>
>
> Last configuration: Mon Jun 14 12:18:27 IST 2010
>
>
> Wien Version: WIEN2k_10.1 (Release 7/6/2010)
>
>
> System: linuxifc
>
>
>
>
> Setting up user: wien
>
>
> Home directory: /home/wien
>
>
> Shell: bash
>
>
>
>
> Specify your prefered editor (default is emacs):
>
>
> editor shall be:
>
>
> Set editor to emacs (Y/n)
>
>
> Specify your prefered DATA directory, where your cases should be
>
>
> stored (for /home/wien/WIEN2k, just enter RETURN key):
>
>
> DATA directory:
>
>
>
>
> Set DATA directory to /home/wien/WIEN2k (Y/n)
>
>
> trying to create /home/wien/WIEN2k ...
>
>
>
>
> Specify your prefered scratch directory, where big case.vector files
>
>
> can be stored (Recommended is your working dir., just enter RETURN key):
>
>
> scratch directory:
>
>
> Set scratch directory to working directory (Y/n)
>
>
> Specify your program to read pdf files (default is acroread)
>
>
> (on some Linux systems use xpdf):
>
> Set PDFREADER to acroread (Y/n)
>
> !!! The following lines will be added to your .bashrc file if you continue
> !!!
>
>
> A copy of your current .bashrc will be saved under .bashrc.savelapw!
>
>
> # added by WIEN2k: BEGIN
>
>
> #
>
>
> alias lsi="ls -aslp *.in*"
>
>
> alias lso="ls -aslp *.ou*"
>
>
> alias lsd="ls -aslp *.def"
>
>
> alias lsc="ls -aslp *.cl*"
>
>
> alias lss="ls -aslp *.sc*"
>
>
> alias lse="ls -aslp *.error"
>
>
> alias pslapw="ps -ef |grep "lapw""
>
>
> alias cdw="cd /home/wien/WIEN2k"
>
>
> export OMP_NUM_THREADS=1
>
>
> #export LD_LIBRARY_PATH=.
>
>
> export EDITOR="emacs"
>
>
> export SCRATCH=./
>
>
> export WIENROOT=/home/wien/wien2k
>
>
> export W2WEB_CASE_BASEDIR=/home/wien/WIEN2k
>
>
> export STRUCTEDIT_PATH=$WIENROOT/SRC_structeditor/bin
>
>
> export PDFREADER=acroread
>
>
> export PATH=$PATH:$WIENROOT:$STRUCTEDIT_PATH:.
>
>
> export OCTAVE_EXEC_PATH=${PATH}::
>
>
> export OCTAVE_PATH=${STRUCTEDIT_PATH}::
>
>
> ulimit -s unlimited
>
>
> alias octave="octave -p $OCTAVE_PATH"
>
>
> #
>
>
>
> Do you want to continue (Y/n)?
>
>
> *) adding aliases
>
>
> *) adding environment variables
>
>
> *) adding path to wien programs and set unlimited stacksize
>
>
> done.
>
> If you want to use k-point parallel execution on a non-shared memory
>
>
> system, you must be able to login without specifying a password.
>
>
> When using rsh you should modify your .rhosts file, if you are
>
>
> using ssh you must generate (ssh-keygen) and transfer your "public keys".
>
>
> Edit .rhosts file now? (y/N)
>
>
> *
>
>
> * WIEN 2k *
>
>
> * user configuration *
>
>
> *
>
>
> Your user environment for WIEN users is now configured.
>
> You have to restart your shell before the changes come
>
> into effect (execute: . ~/.bashrc).
>
> Start "w2web", define "user/password" and select a port. Then point
>
>
> your web-browser to the proper address:PORT.
>
> For proper usage of scfmonitor please add a line in ~/.Xdefaults :
>
> gnuplot*raise: off
>
> We wish you GOOD LUCK with your calculations.
>
> Your WIEN2k Team
>
> [wien at localhost wien2k]$ . ~/.bashrc
>
>
> [wien at localhost wien2k]$
>
> Sir, When I put w2web command for creating user name and password then
> fllowing message shown
>
> [wien at localhost wien2k]$ w2web
>
> bash: /home/wien/wien2k/w2web: q: bad interpreter: No such file or
> directory
> Sir, May I request you to guide me to resolve this problem.Sir I will be
> very grateful to you.
>
> With Kind Regards And Thanks
>
> SANJAY KUMAR SINGH.
> Research Scholar.
> Condensed Matter Theory Group.
> School Of Studies In Physics.
> Jiwaji University.
> Gwalior (M.P)? 474 011.
> India.
>
> ___
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
>
>
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[Wien] Problem After Userconfig
This looks suspiciously as if you entered the "q" for "quit" after choosing "l" for the "Perl Path" option - so that the user configuration script recorded "q" as the name of your perl interpreter. Please run siteconfig_lapw again and check what is stored under the "L" menu. -- Dr. Martin Kroekermartin at ruby.chemie.uni-freiburg.de c/o Prof.Dr. Caroline Roehr Institut fuer Anorganische und Analytische Chemie der Universitaet Freiburg
[Wien] silicon structure
No, you are wrong you create only 4 positions (see below) but what is the meaning of 8 in the Wyckoff position ? go to http://www.cryst.ehu.es/ and check it. Ciao Gerhard Dr. Gerhard H. Fecher Institut of Inorganic and Analytical Chemistry Johannes Gutenberg - University 55099 Mainz Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at zeus.theochem.tuwien.ac.at]" im Auftrag von "Jedo [jedokim at umich.edu] Gesendet: Montag, 14. Juni 2010 13:46 An: A Mailing list for WIEN2k users Betreff: Re: [Wien] silicon structure Hi there, You mean Wyckoff position 8a as (0, 0, 0) right? I tried that before, but the structure I see using Xcrysden was even more wrong. If I do that, the file looks like Space group 227_Fd-3m a = 5.43 b = 5.43 c = 5.43 90 90 90 Atom 1 Si z = 14 RMT 1.8 pos 1 x = 0.0 0.0 0.0 pos 2 x = 0.0 0.25 0.25 pos 3 x = 0.0 0.25 0.25 pos 4 x = 0.0 0.25 0.25 It is a big change for me to work with space groups from lattice vectors. For RMT sizes, I could not increase them because of the error I get from the first step (x nn). I'm thinking that I am getting these errors because my structure is not correct. Also, even though I increase them, when I hit "set automatically RMT" it reduces it back to 1.8. On 6/14/2010 7:11 AM, Gerhard Fecher wrote: > why are you giving two atoms for the basis of Si ? > Set up 2 (see Peters remark) of spacegroup 229 should have only one on > Wyckoff position 8a. > > did you recognize something from youre RMT sizes ? > > I usually use this example for my students to check if they know about > crystal structures and > to find out how they turn semiconductors into metals > > Ciao > Gerhard > > > Dr. Gerhard H. Fecher > Institut of Inorganic and Analytical Chemistry > Johannes Gutenberg - University > 55099 Mainz > > Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at > zeus.theochem.tuwien.ac.at]" im Auftrag von"Jedo [jedokim at > umich.edu] > Gesendet: Montag, 14. Juni 2010 12:35 > An: wien at zeus.theochem.tuwien.ac.at > Betreff: Re: [Wien] silicon structure > > Thanks for the answer. Still, I don't understand why WIEN2k is giving me > a structure with this many atoms. I'm listing the Strucgen atoms when I > save it. It adds 10 more atoms. The fractional coordinates look ok, but > when I look at the structure using Xcrysden, it does not look right. I > can send you the screen shot if you wish. > Thanks for all the help. > > Space group 227_Fd-3m > > a = 5.43 b = 5.43 c = 5.43 > 90 90 90 > > Atom 1 Si z = 14 RMT 1.21 >pos 1 x = 0.0 0.0 0.0 >pos 2 x = 0.0 0.25 0.25 >pos 3 x = 0.0 0.25 0.25 >pos 4 x = 0.0 0.25 0.25 > > Atom 2 Si x = 14 RMT 1.21 >pos 1 0.25 0.25 0.25 >pos 2 0.75 0.75 0.75 >pos 3 0.75 0.50.5 >pos 4 0.25 0.00.0 >pos 5 0.0 0.00.25 >pos 6 0.5 0.50.75 >pos 7 0.5 0.75 0.5 >pos 8 0.0 0.25 0.0 > > > > > On 6/14/2010 12:59 AM, Peter Blaha wrote: > >> Nothing is wrong. >> sgroup changes your input structure and shifts the origin to an >> inversion center. This moves the Si atoms by (1/8,1/8,1/8). >> >> PS: The spacegroup 227 has 2 different "settings", i.e. origins with >> tetrahedral symmetry or with inversion symmetry. Since all matrix >> elements >> can be kept as "real" numbers when inversion symmetry is present, WIEN2k >> adopts automatically this setting. >> >> Jedo schrieb: >> >>> Hi, >>> >>> I'm a newbie to wien2k. I have done some abinit calculation with >>> silicon. So, I just wanted to start with Silicon again to test it. >>> However, when I put the structure in, it gives me a very different >>> structure. I'm not sure what I am doing wrong. My inputs for >>> StructGen for Silicon is >>> >>> Spacegroup 227_Fd-3m >>> Lattice parameters A 5.43 5.43 5.43 >>> 90 90 90 >>> >>> Si 0 0 0 >>> Si 0.25 0.25 0.25 >>> >>> Is this correct? I'm used to inputing lattice vectors. >>> Thanks for the help >>> >>> Jedo >>> >>> >> > -- > > Jedo Kim, Ph.D Candidate > Heat Transfer Physics Laboratory > 2350 Hayward, 2186 GG Brown Bldg. > University of Michigan, Ann Arbor, MI 48109-2143 > Email: jedokim at umich.edu, jdzbox at hotmail.com > Tel: 734-764-3487 (o); 734-276-8370 (cell) > http://sitemaker.umich.edu/kaviany > > > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > > -- Jedo Kim, Ph.D
[Wien] complex calculation
This is not so easy to fix, because the "complex" property can be set only after the initialization. However, after batch initialization the user can jump to any place (usually he is NOT going back to init). In any case, I made a few small modifications and it will set complex in SRC_w2web/htdocs/exec/initlapw.pl (as soon as you click on init and have a case.in1c file) SRC_w2web/htdocs/exec/rho.pl (Here it matters if you edit case.in5 or case.in5c) SRC_w2web/htdocs/util/initso.pl If you find other places where this is a problem, please let me know. Gerhard Fecher schrieb: > Just in case someone is wondering, that complex calculations do not run as > expected: > > I realised that the W2WEB Session Info is not changed to complex > if one uses batch initialisation but only during the step by step > initialization. > > Usually this seems not to be an issue as Wien (lapw etc) uses the correct -c > option > for such cases. > The proplem appears for example if one uses initso from w2web as > it does not find .in1c but asks to change .in1 if the info is not set to > complex. > > I did not find when this appeared the first time, at least it apperas in 9.2 > and 10.1 > > > Ciao > Gerhard > > > Dr. Gerhard H. Fecher > Institut of Inorganic and Analytical Chemistry > Johannes Gutenberg - University > 55099 Mainz > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ -- -- next part -- A non-text attachment was scrubbed... Name: initso.pl Type: application/x-perl Size: 6406 bytes Desc: not available URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100614/4449fa8a/attachment.pl> -- next part -- A non-text attachment was scrubbed... Name: rho.pl Type: application/x-perl Size: 8153 bytes Desc: not available URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100614/4449fa8a/attachment-0001.pl> -- next part -- A non-text attachment was scrubbed... Name: initlapw.pl Type: application/x-perl Size: 22015 bytes Desc: not available URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100614/4449fa8a/attachment-0002.pl>
[Wien] silicon structure
why are you giving two atoms for the basis of Si ? Set up 2 (see Peters remark) of spacegroup 229 should have only one on Wyckoff position 8a. did you recognize something from youre RMT sizes ? I usually use this example for my students to check if they know about crystal structures and to find out how they turn semiconductors into metals Ciao Gerhard Dr. Gerhard H. Fecher Institut of Inorganic and Analytical Chemistry Johannes Gutenberg - University 55099 Mainz Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at zeus.theochem.tuwien.ac.at]" im Auftrag von "Jedo [jedokim at umich.edu] Gesendet: Montag, 14. Juni 2010 12:35 An: wien at zeus.theochem.tuwien.ac.at Betreff: Re: [Wien] silicon structure Thanks for the answer. Still, I don't understand why WIEN2k is giving me a structure with this many atoms. I'm listing the Strucgen atoms when I save it. It adds 10 more atoms. The fractional coordinates look ok, but when I look at the structure using Xcrysden, it does not look right. I can send you the screen shot if you wish. Thanks for all the help. Space group 227_Fd-3m a = 5.43 b = 5.43 c = 5.43 90 90 90 Atom 1 Si z = 14 RMT 1.21 pos 1 x = 0.0 0.0 0.0 pos 2 x = 0.0 0.25 0.25 pos 3 x = 0.0 0.25 0.25 pos 4 x = 0.0 0.25 0.25 Atom 2 Si x = 14 RMT 1.21 pos 1 0.25 0.25 0.25 pos 2 0.75 0.75 0.75 pos 3 0.75 0.50.5 pos 4 0.25 0.00.0 pos 5 0.0 0.00.25 pos 6 0.5 0.50.75 pos 7 0.5 0.75 0.5 pos 8 0.0 0.25 0.0 On 6/14/2010 12:59 AM, Peter Blaha wrote: > Nothing is wrong. > sgroup changes your input structure and shifts the origin to an > inversion center. This moves the Si atoms by (1/8,1/8,1/8). > > PS: The spacegroup 227 has 2 different "settings", i.e. origins with > tetrahedral symmetry or with inversion symmetry. Since all matrix > elements > can be kept as "real" numbers when inversion symmetry is present, WIEN2k > adopts automatically this setting. > > Jedo schrieb: >> Hi, >> >> I'm a newbie to wien2k. I have done some abinit calculation with >> silicon. So, I just wanted to start with Silicon again to test it. >> However, when I put the structure in, it gives me a very different >> structure. I'm not sure what I am doing wrong. My inputs for >> StructGen for Silicon is >> >> Spacegroup 227_Fd-3m >> Lattice parameters A 5.43 5.43 5.43 >> 90 90 90 >> >> Si 0 0 0 >> Si 0.25 0.25 0.25 >> >> Is this correct? I'm used to inputing lattice vectors. >> Thanks for the help >> >> Jedo >> > -- Jedo Kim, Ph.D Candidate Heat Transfer Physics Laboratory 2350 Hayward, 2186 GG Brown Bldg. University of Michigan, Ann Arbor, MI 48109-2143 Email: jedokim at umich.edu, jdzbox at hotmail.com Tel: 734-764-3487 (o); 734-276-8370 (cell) http://sitemaker.umich.edu/kaviany ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] orbital moment and LDA+U
Dear wien2k users, I am running wien version 9.2 on a machine of type cluster with operating system Centos 5.4, fortran compiler ifort and math libraries intel mkl. The purpose of my calculations in to get the magnetic property of Fe doped Zn. I generate the structure of FeZn35 by using the lattice parameter of pure Zn and making a supercell of 2x2x2, then substitutes a Zn atom with Fe atom. I use the exchange correlation of PBE-GGA and klist 11x11x11. The DOS of d-electron of Zn atom shows that the peak is 7.5 eV below the fermi energy, but the experimental result is about 10 eV below fermi energy. So I use LDA+U and U = 0.5 Ry and the peak of d-electon move to -10 eV. Now I want to calculate the orbital moment of Fe atom and I have some problems: 1 Should I do the calculation with SOC if I want to calculate the orbital moment? Or just set the RINDEX=1LSINDEX=3 in the case.indm and add -dm in the runsp command. 2 Since I need use LDA+U and set RINDEX=0LSINDEX=0 in case.indm to get a correct result, how can I set the RINDEX=1LSINDEX=3 in the case.indm to get the orbital moment? 3 In the notes about spin-orbit, I found "s-o non-scf" and how can I achieve this? Any suggestions will be appriciate and thank you in advance! Best regards, -- Bin Shao College of Information Technical Science, Nankai University 94 Weijin Rd. Nankai Dist. Tianjin 300071, China Email: binshao1118 at gmail.com -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100614/0c14335b/attachment.htm>
[Wien] a parallel error of lapw0 with MBJLDA potential (updated)
> 1. I do not fully understand what you mean that "It is probably > completely uncritical for the gap,...". > After the temporary fixed in brj.f, can the code deal with correctly > the system which have very heavy elements? > and their bandgaps are reasonable? Yes. > 2. We doubt that there are still some bugs in lapw0_mpi, because the > bandgap is different, > > Ge: > 0.85eV (lapw0) > 0.71eV (lapw0_mpi) There was still a bug in the interstitial region in case you have more processors than atoms. It has been fixed and the new version is on the web. PS: This new version includes also improved W2kutil and W2kinit subroutines, which also compile under Sun Solaris. -- P.Blaha -- Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna Phone: +43-1-58801-15671 FAX: +43-1-58801-15698 Email: blaha at theochem.tuwien.ac.atWWW: http://info.tuwien.ac.at/theochem/ --
[Wien] Vresp mixing
A quick clarification about mixing vresp files, relevant to recent discussions of the modified Becke-Johnson exchange potential. In earlier versions of the mixer one had to change NORM to NO and use PRATT (with 1.0 Greed). The current version of the mixer does this automatically if the file on unit 5 ends in "vresp". -- Laurence Marks Department of Materials Science and Engineering MSE Rm 2036 Cook Hall 2220 N Campus Drive Northwestern University Evanston, IL 60208, USA Tel: (847) 491-3996 Fax: (847) 491-7820 email: L-marks at northwestern dot edu Web: www.numis.northwestern.edu Chair, Commission on Electron Crystallography of IUCR www.numis.northwestern.edu/ Electron crystallography is the branch of science that uses electron scattering and imaging to study the structure of matter.
[Wien] FW: Differences in the hcp and fcc stabilities of zirconium [Updated]
Dear Prof.Blaha,
Thank you for the reply. The change in total energy by spin orbit coupling
is only by a few rydbergs, but it shows a huge change in kJ/mol.
Thanks anyway.
I will come back to the mailing list after I have incorporated "so" in fcc
zirconium.
However, I still have the doubt.
In case, we do the total energy calculation for the stable state (ground
state) with sp, and so both,
Then for the lattice stability of the metastable state , do we have to do a
sp and so both.
In the paper I referred to my earlier mail, sp has been done for Zirconium
which sounds strange.
In your paper on hcp metals, you have not incorporated so for Zr.
That means for lattice stability
Ground state (sp, so) minus metastable state (sp,so) is right
ground state (sp,so) minus metastable state (so) is wrong
Am I right sir,
Suddhasattwa
-Original Message-
From: wien-boun...@zeus.theochem.tuwien.ac.at
[mailto:wien-bounces at zeus.theochem.tuwien.ac.at] On Behalf Of Peter Blaha
Sent: Sunday, June 13, 2010 9:40 PM
To: A Mailing list for WIEN2k users
Subject: Re: [Wien] FW: Differences in the hcp and fcc stabilities of
zirconium [Updated]
You cannot compare total energies of calculations with and without SO.
Ghosh SUDDHASATTWA schrieb:
>
>
> Dear Wien2k users,
>
> Initially, I did the total energy calculation of hcp Zirconium with c/a
> optimization.
>
> I had updated the command in the optimize.job
>
> Run_lapw -cc 0.0001 -ec 0.0001 -so
>
>
>
> I got a fairly good plot of energy vs c/a. The equilibrium energy with
> optimized c/a was -7198.44622432 Ry/atom
>
> I did the same job for fcc zirconium (metastable state)
>
> I did the volume optimization with the command in the optimize.job
>
> Run_lapw -cc 0.0001 -ec 0.0001
>
> Without spin orbit coupling
>
> The equilibrium energy was -7198.427610 Ry/atom
>
> If we take the difference, it comes out to be -0.01861432 Ry/atom.
>
> If we convert to kJ/mol, it comes out to be -24.435 kJ/mol (multiply
> Ry/atom by 13.6 eV and 96.48846 kJ/mol)
>
>
>
> The difference seems to be very large. The difference is reported to be*
> -3.69 kJ/mol *by VASP. (PAW-GGA) {CALPHAD, 28 (2004) 78-90}
>
> Can anybody tell me as to why I am getting such a high value of the
> lattice stability?
>
> Is it because of the incorporation of spin orbit coupling?
>
> I had initially used the in1new switch to get the best linearization
> energies for both the cases, still I am getting such a high value
>
> Any suggestions?
>
>
>
> Suddhasattwa
>
>
>
>
>
>
>
>
>
>
> ___
> Wien mailing list
> Wien at zeus.theochem.tuwien.ac.at
> http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
--
-
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pblaha at theochem.tuwien.ac.at
-
___
Wien mailing list
Wien at zeus.theochem.tuwien.ac.at
http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
[Wien] silicon structure
Hi there, You mean Wyckoff position 8a as (0, 0, 0) right? I tried that before, but the structure I see using Xcrysden was even more wrong. If I do that, the file looks like Space group 227_Fd-3m a = 5.43 b = 5.43 c = 5.43 90 90 90 Atom 1 Si z = 14 RMT 1.8 pos 1 x = 0.0 0.0 0.0 pos 2 x = 0.0 0.25 0.25 pos 3 x = 0.0 0.25 0.25 pos 4 x = 0.0 0.25 0.25 It is a big change for me to work with space groups from lattice vectors. For RMT sizes, I could not increase them because of the error I get from the first step (x nn). I'm thinking that I am getting these errors because my structure is not correct. Also, even though I increase them, when I hit "set automatically RMT" it reduces it back to 1.8. On 6/14/2010 7:11 AM, Gerhard Fecher wrote: > why are you giving two atoms for the basis of Si ? > Set up 2 (see Peters remark) of spacegroup 229 should have only one on > Wyckoff position 8a. > > did you recognize something from youre RMT sizes ? > > I usually use this example for my students to check if they know about > crystal structures and > to find out how they turn semiconductors into metals > > Ciao > Gerhard > > > Dr. Gerhard H. Fecher > Institut of Inorganic and Analytical Chemistry > Johannes Gutenberg - University > 55099 Mainz > > Von: wien-bounces at zeus.theochem.tuwien.ac.at [wien-bounces at > zeus.theochem.tuwien.ac.at]" im Auftrag von"Jedo [jedokim at > umich.edu] > Gesendet: Montag, 14. Juni 2010 12:35 > An: wien at zeus.theochem.tuwien.ac.at > Betreff: Re: [Wien] silicon structure > > Thanks for the answer. Still, I don't understand why WIEN2k is giving me > a structure with this many atoms. I'm listing the Strucgen atoms when I > save it. It adds 10 more atoms. The fractional coordinates look ok, but > when I look at the structure using Xcrysden, it does not look right. I > can send you the screen shot if you wish. > Thanks for all the help. > > Space group 227_Fd-3m > > a = 5.43 b = 5.43 c = 5.43 > 90 90 90 > > Atom 1 Si z = 14 RMT 1.21 >pos 1 x = 0.0 0.0 0.0 >pos 2 x = 0.0 0.25 0.25 >pos 3 x = 0.0 0.25 0.25 >pos 4 x = 0.0 0.25 0.25 > > Atom 2 Si x = 14 RMT 1.21 >pos 1 0.25 0.25 0.25 >pos 2 0.75 0.75 0.75 >pos 3 0.75 0.50.5 >pos 4 0.25 0.00.0 >pos 5 0.0 0.00.25 >pos 6 0.5 0.50.75 >pos 7 0.5 0.75 0.5 >pos 8 0.0 0.25 0.0 > > > > > On 6/14/2010 12:59 AM, Peter Blaha wrote: > >> Nothing is wrong. >> sgroup changes your input structure and shifts the origin to an >> inversion center. This moves the Si atoms by (1/8,1/8,1/8). >> >> PS: The spacegroup 227 has 2 different "settings", i.e. origins with >> tetrahedral symmetry or with inversion symmetry. Since all matrix >> elements >> can be kept as "real" numbers when inversion symmetry is present, WIEN2k >> adopts automatically this setting. >> >> Jedo schrieb: >> >>> Hi, >>> >>> I'm a newbie to wien2k. I have done some abinit calculation with >>> silicon. So, I just wanted to start with Silicon again to test it. >>> However, when I put the structure in, it gives me a very different >>> structure. I'm not sure what I am doing wrong. My inputs for >>> StructGen for Silicon is >>> >>> Spacegroup 227_Fd-3m >>> Lattice parameters A 5.43 5.43 5.43 >>> 90 90 90 >>> >>> Si 0 0 0 >>> Si 0.25 0.25 0.25 >>> >>> Is this correct? I'm used to inputing lattice vectors. >>> Thanks for the help >>> >>> Jedo >>> >>> >> > -- > > Jedo Kim, Ph.D Candidate > Heat Transfer Physics Laboratory > 2350 Hayward, 2186 GG Brown Bldg. > University of Michigan, Ann Arbor, MI 48109-2143 > Email: jedokim at umich.edu, jdzbox at hotmail.com > Tel: 734-764-3487 (o); 734-276-8370 (cell) > http://sitemaker.umich.edu/kaviany > > > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien > > > -- Jedo Kim, Ph.D Candidate Heat Transfer Physics Laboratory 2350 Hayward, 2186 GG Brown Bldg. University of Michigan, Ann Arbor, MI 48109-2143 Email: jedokim at umich.edu, jdzbox at hotmail.com Tel: 734-764-3487 (o); 734-276-8370 (cell) http://sitemaker.umich.edu/kaviany
[Wien] orbital moment and LDA+U
> Now I want to calculate the orbital moment of Fe atom and I have some > problems: Yes, you need to include SO to get the orbital moment. > > 1 Should I do the calculation with SOC if I want to calculate the > orbital moment? Or just set the RINDEX=1LSINDEX=3 in the case.indm and > add -dm in the runsp command. > 2 Since I need use LDA+U and set RINDEX=0LSINDEX=0 in case.indm to get a > correct result, how can I set the RINDEX=1LSINDEX=3 in the case.indm to > get the orbital moment? When using SO + LDA+U the orbital moment will be automatically printed (with the default RINDEX=0LSINDEX=0). > 3 In the notes about spin-orbit, I found "s-o non-scf" and how can I > achieve this? runsp -orb -so -i 1 -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pblaha at theochem.tuwien.ac.at -
[Wien] k-point parallelization in WIEN2K_09.1
I do NOT believe that k-point parallel with an older WIEN2k was possible (unless you set it up with "rsh" instead of "ssh" and defined a .rhosts file). Anyway, k-parallel does not use mpi at all and you have to read the requirements specified in the UG. Kakhaber Jandieri schrieb: > Dear Prof. Blaha, > > Thank you for your reply. > >> Can youssh node120 ps >> without supplying a password ? > > No, I can't ssh the nodes without password supply, but in my > parallel_options I have setenv MPI_REMOTE 0. I thought that our cluster > has a shared memory architecture, since the MPI-parallelization works > without any problem for 1 k-point. I cheeked the corresponding nodes. > All they were loaded. May be I misunderstood something. Are the > requirements for MPI-parallelization different from that for k-point > paralleization? > >> Try x lapw1 -p on the commandline. >> What exactly is the "error" ? > > Just now, to try your suggestions, I ran new task with k-point > parallelization. The .machines file is: > granularity:1 > 1:node120 > 1:node127 > 1:node121 > 1:node123 > > with node120 as a master node. > > The output of x lapw -p is: > starting parallel lapw1 at Sun Jun 13 22:44:08 CEST 2010 > -> starting parallel LAPW1 jobs at Sun Jun 13 22:44:08 CEST 2010 > running LAPW1 in parallel mode (using .machines) > 4 number_of_parallel_jobs > [1] 31314 > [2] 31341 > [3] 31357 > [4] 31373 > Permission denied, please try again. > Permission denied, please try again. > Received disconnect from 172.26.6.120: 2: Too many authentication > failures for kakhaber > [1]Done ( ( $remote $machine[$p] ... > Permission denied, please try again. > Permission denied, please try again. > Received disconnect from 172.26.6.127: 2: Too many authentication > failures for kakhaber > Permission denied, please try again. > Permission denied, please try again. > Received disconnect from 172.26.6.121: 2: Too many authentication > failures for kakhaber > [3] - Done ( ( $remote $machine[$p] ... > [2] - Done ( ( $remote $machine[$p] ... > Permission denied, please try again. > Permission denied, please try again. > Received disconnect from 172.26.6.123: 2: Too many authentication > failures for kakhaber > [4]Done ( ( $remote $machine[$p] ... > node120(1) node127(1) node121(1) node123(1) ** > LAPW1 crashed! > cat: No match. > 0.116u 0.324s 0:11.88 3.6%0+0k 0+864io 0pf+0w > error: command /home/kakhaber/WIEN2K_09/lapw1cpara -c lapw1.def failed > >> How many k-points do you have ? ( 4 ?) > > Yes, I have 4 k-points. > >> Content of .machine1 and .processes > > marc-hn:~/wien_work/GaAsB> cat .machine1 node120 > marc-hn:~/wien_work/GaAsB> cat .machine2 > node127 > marc-hn:~/wien_work/GaAsB> cat .machine3 > node121 > marc-hn:~/wien_work/GaAsB> cat .machine4 > node123 > > marc-hn:~/wien_work/GaAsB> cat .processes > init:node120 > init:node127 > init:node121 > init:node123 > 1 : node120 : 1 : 1 : 1 > 2 : node127 : 1 : 1 : 2 > 3 : node121 : 1 : 1 : 3 > 4 : node123 : 1 : 1 : 4 > >> While x lapw1 -p is running, do aps -ef |grep lapw > > I had not enough time to do it - the program crashed before. > >> Your .machines file is most likely a rather "useless" one. The mpi-lapw1 >> diagonalization (SCALAPACK) is almost a factor of 2 slower than the >> serial >> version, thus your speedup by using 2 processors in mpi-mode will be >> very small. > > Yes, I know, but I am simply trying to arrange the calculations using > Wien2K. For "real" calculations I will use much more processors. > > And finally, for additional information. As I wrote in my previous > letters, in > WIEN2k_08.1 k-point parallelization works, but all processes are running > on master node and all other reserved nodes are idle. I forgot to > mention: this is true for lapw1 only. Lapw2 is distributed among all > reserved nodes. > > Thank you one again. I am looking forward for your further advices. > > > Dr. Kakhaber Jandieri > Department of Physics > Philipps University Marburg > Tel:+49 6421 2824159 (2825704) > > > ___ > Wien mailing list > Wien at zeus.theochem.tuwien.ac.at > http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pblaha at theochem.tuwien.ac.at -
[Wien] silicon structure
Nothing is wrong. sgroup changes your input structure and shifts the origin to an inversion center. This moves the Si atoms by (1/8,1/8,1/8). PS: The spacegroup 227 has 2 different "settings", i.e. origins with tetrahedral symmetry or with inversion symmetry. Since all matrix elements can be kept as "real" numbers when inversion symmetry is present, WIEN2k adopts automatically this setting. Jedo schrieb: > Hi, > > I'm a newbie to wien2k. I have done some abinit calculation with > silicon. So, I just wanted to start with Silicon again to test it. > However, when I put the structure in, it gives me a very different > structure. I'm not sure what I am doing wrong. My inputs for StructGen > for Silicon is > > Spacegroup 227_Fd-3m > Lattice parameters A 5.43 5.43 5.43 > 90 90 90 > > Si 0 0 0 > Si 0.25 0.25 0.25 > > Is this correct? I'm used to inputing lattice vectors. > Thanks for the help > > Jedo > -- - Peter Blaha Inst. Materials Chemistry, TU Vienna Getreidemarkt 9, A-1060 Vienna, Austria Tel: +43-1-5880115671 Fax: +43-1-5880115698 email: pblaha at theochem.tuwien.ac.at -
[Wien] silicon structure
Thanks for the answer. Still, I don't understand why WIEN2k is giving me a structure with this many atoms. I'm listing the Strucgen atoms when I save it. It adds 10 more atoms. The fractional coordinates look ok, but when I look at the structure using Xcrysden, it does not look right. I can send you the screen shot if you wish. Thanks for all the help. Space group 227_Fd-3m a = 5.43 b = 5.43 c = 5.43 90 90 90 Atom 1 Si z = 14 RMT 1.21 pos 1 x = 0.0 0.0 0.0 pos 2 x = 0.0 0.25 0.25 pos 3 x = 0.0 0.25 0.25 pos 4 x = 0.0 0.25 0.25 Atom 2 Si x = 14 RMT 1.21 pos 1 0.25 0.25 0.25 pos 2 0.75 0.75 0.75 pos 3 0.75 0.50.5 pos 4 0.25 0.00.0 pos 5 0.0 0.00.25 pos 6 0.5 0.50.75 pos 7 0.5 0.75 0.5 pos 8 0.0 0.25 0.0 On 6/14/2010 12:59 AM, Peter Blaha wrote: > Nothing is wrong. > sgroup changes your input structure and shifts the origin to an > inversion center. This moves the Si atoms by (1/8,1/8,1/8). > > PS: The spacegroup 227 has 2 different "settings", i.e. origins with > tetrahedral symmetry or with inversion symmetry. Since all matrix > elements > can be kept as "real" numbers when inversion symmetry is present, WIEN2k > adopts automatically this setting. > > Jedo schrieb: >> Hi, >> >> I'm a newbie to wien2k. I have done some abinit calculation with >> silicon. So, I just wanted to start with Silicon again to test it. >> However, when I put the structure in, it gives me a very different >> structure. I'm not sure what I am doing wrong. My inputs for >> StructGen for Silicon is >> >> Spacegroup 227_Fd-3m >> Lattice parameters A 5.43 5.43 5.43 >> 90 90 90 >> >> Si 0 0 0 >> Si 0.25 0.25 0.25 >> >> Is this correct? I'm used to inputing lattice vectors. >> Thanks for the help >> >> Jedo >> > -- Jedo Kim, Ph.D Candidate Heat Transfer Physics Laboratory 2350 Hayward, 2186 GG Brown Bldg. University of Michigan, Ann Arbor, MI 48109-2143 Email: jedokim at umich.edu, jdzbox at hotmail.com Tel: 734-764-3487 (o); 734-276-8370 (cell) http://sitemaker.umich.edu/kaviany
[Wien] New exchange-correlation potential
Dear user, did you able to improve band gap of gaas with new Xc. kumar --- On Thu, 10/6/10, yhzhao wrote: From: yhzhao Subject: Re: [Wien] New exchange-correlation potential To: "A Mailing list for WIEN2k users" Date: Thursday, 10 June, 2010, 18:29 Hello, I have got a band gap of 0.8 eV, with lattice constant 5.6533 Angstrom and the space group No. is 216, with two atoms in (0.0 0.0 0.0) and (0.25 0.25 0.25). I have checked that: 1. In GaAs.inm_vresp, YES has been replaced by NO; 2. I have done the calculation as following steps: ??? For the first scf run, I have set NR2V and indxc=5 in GaAs.in0; ? ? Change NR2V to R2V and run one more scf cycle; ??? save lda; ??? Set indxc=28 in GaAs.in0; ??? cp GaAs.in0 GaAs.in0_grr and set index=50 in GaAs.in0_grr ??? run_lapw -p -cc 0.1 ??? plot bandstructure Anything wrong with my procedure? yonghong On 2010?06?10? 05:06, F. Tran wrote: Which value do you obtain? Did you use the correct structure? In Table 1 of the following paper: Tran et al., J. Phys.: Condens. Matter 19, 196208 (2007) it is indicated which structure and lattice constant were used. In case.inm_vresp, you have to replace YES by NO for the normalization. On Wed, 9 Jun 2010, yhzhao wrote: Hi, I have do all your suggested things, which given in the usersguide. However I cannot get the band gap, that is 1.64 eV for GaAs, as suggested by PRL 102, 226401 (2009). yonghong On 2010?06?09? 17:54, F. Tran wrote: Hello, In order to use the modified Becke-Johnson exchange potential you have to choose indxc=28 in case.in0 and indxc=50 in case.in0_grr. A few more things: In case.in0 you also need to replace NR2V by R2V such that the exchange-correlation potential is written in case.r2v, which will be used in the next iteration. You need case.inm_vresp such that case.vrespsum (which contains a part of the kinetic-energy density) is created. There is no adjustable parameters. The LDA correlation potential is added to the MBJ exchange potential. The LDA exchange-correlation functional is used for the energy. The MBJ exchange potential is not the derivative of an energy functional, which means that the method is not variational (i.e., the orbitals are not the ones which minimize the total energy, which is LDA). In particular, it means that you can not use forces to optimize internal parameters. On Wed, 9 Jun 2010, yhzhao wrote: Dear Prof. Pblaha, I have tried to calculate something using the new exchange potential with indxc=50 as suggested by the usersguide. At first I want to repeat some data given by PRL 102, 226401 (2009), for example, the band gap of GaAs. I can get a band gap of 0.7 eV for GaAs, which is much better than 0.3 eV of lda, but not much better than the value given by you in PRL 102, 226401 (2009). In the calculation, I use the experimental lattice constant. The k-grid have been increased as dense as 20x20x20 and RKmax as large as 9.0. Is there any adjustable parameter for the MBJ calculation? Thanks. Regards, yonghong ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -Inline Attachment Follows- ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: <http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20100614/4c80a155/attachment.htm>
[Wien] k-point parallelization in WIEN2K_09.1
Dear Prof. Blaha, Thank you for your reply. > Can youssh node120 ps > without supplying a password ? No, I can't ssh the nodes without password supply, but in my parallel_options I have setenv MPI_REMOTE 0. I thought that our cluster has a shared memory architecture, since the MPI-parallelization works without any problem for 1 k-point. I cheeked the corresponding nodes. All they were loaded. May be I misunderstood something. Are the requirements for MPI-parallelization different from that for k-point paralleization? > Try x lapw1 -p on the commandline. > What exactly is the "error" ? Just now, to try your suggestions, I ran new task with k-point parallelization. The .machines file is: granularity:1 1:node120 1:node127 1:node121 1:node123 with node120 as a master node. The output of x lapw -p is: starting parallel lapw1 at Sun Jun 13 22:44:08 CEST 2010 -> starting parallel LAPW1 jobs at Sun Jun 13 22:44:08 CEST 2010 running LAPW1 in parallel mode (using .machines) 4 number_of_parallel_jobs [1] 31314 [2] 31341 [3] 31357 [4] 31373 Permission denied, please try again. Permission denied, please try again. Received disconnect from 172.26.6.120: 2: Too many authentication failures for kakhaber [1]Done ( ( $remote $machine[$p] ... Permission denied, please try again. Permission denied, please try again. Received disconnect from 172.26.6.127: 2: Too many authentication failures for kakhaber Permission denied, please try again. Permission denied, please try again. Received disconnect from 172.26.6.121: 2: Too many authentication failures for kakhaber [3] - Done ( ( $remote $machine[$p] ... [2] - Done ( ( $remote $machine[$p] ... Permission denied, please try again. Permission denied, please try again. Received disconnect from 172.26.6.123: 2: Too many authentication failures for kakhaber [4]Done ( ( $remote $machine[$p] ... node120(1) node127(1) node121(1) node123(1) ** LAPW1 crashed! cat: No match. 0.116u 0.324s 0:11.88 3.6%0+0k 0+864io 0pf+0w error: command /home/kakhaber/WIEN2K_09/lapw1cpara -c lapw1.def failed > How many k-points do you have ? ( 4 ?) Yes, I have 4 k-points. > Content of .machine1 and .processes marc-hn:~/wien_work/GaAsB> cat .machine1 node120 marc-hn:~/wien_work/GaAsB> cat .machine2 node127 marc-hn:~/wien_work/GaAsB> cat .machine3 node121 marc-hn:~/wien_work/GaAsB> cat .machine4 node123 marc-hn:~/wien_work/GaAsB> cat .processes init:node120 init:node127 init:node121 init:node123 1 : node120 : 1 : 1 : 1 2 : node127 : 1 : 1 : 2 3 : node121 : 1 : 1 : 3 4 : node123 : 1 : 1 : 4 > While x lapw1 -p is running, do aps -ef |grep lapw I had not enough time to do it - the program crashed before. > Your .machines file is most likely a rather "useless" one. The mpi-lapw1 > diagonalization (SCALAPACK) is almost a factor of 2 slower than the serial > version, thus your speedup by using 2 processors in mpi-mode will be > very small. Yes, I know, but I am simply trying to arrange the calculations using Wien2K. For "real" calculations I will use much more processors. And finally, for additional information. As I wrote in my previous letters, in WIEN2k_08.1 k-point parallelization works, but all processes are running on master node and all other reserved nodes are idle. I forgot to mention: this is true for lapw1 only. Lapw2 is distributed among all reserved nodes. Thank you one again. I am looking forward for your further advices. Dr. Kakhaber Jandieri Department of Physics Philipps University Marburg Tel:+49 6421 2824159 (2825704)
