[Wien] charge density analysis

2013-06-04 Thread 王静
Hi! there,

   I am doing some calculations about Fe2+. The DOS plot indicates the spin 
down channel is full-filled by five d-electrons and the spin up channel is 
occupied by the sixth one. The charge density has been drawn by Xcrysden. In my 
opinion, the spin down channel should be a perfect ball since it has five 
d-electrons. In fact, as in the attached file(the unit cell is not give because 
the size is too large to be uploaded), it does not. In the calculation, the 
density flag is SCF density, spin flag is spin density, the Norm flag is 
valence density and Debug Flag is no debug. 
Did I misunderstand something? Any suggestions would be appreciated.

   Thanks very much!

WANG jing
wangjingj...@ciac.jl.cn
  2013-06-04
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[Wien] Segmentation fault error in LAPW0

2013-06-04 Thread Ushma Ahuja
Dear Wien2k users,

I have Wien2k 12.1 installed on i7 8-core with OS Red Hat Linux 5.0.
(ifort 12.1 compiler l_fcompxe_2011.10.319. For using Wien in parallel, I 
employed openmpi_1.4.5 along with fftw_3.3.3 and scalapack 2.0.2)
Potentials other than mBJ yield fine results without any problem. But with mBJ, 
I am getting the following error in the first cycle of scf:

LAPW0 END 
forrtl: severe (174): SIGSEGV, segmentation fault occurred 
ImagePCRoutineLine Source 
lapw0 0805558B c3fft_1_119 fftpack_helpers.f 
lapw008060D5D fftpack_mp_c3fft_ 397 fft_modules.F 
lapw0 080CE27C vresp_ 106 vresp.F 
lapw0 080E23FA xcpot3_ 147 xcpot3.F 
lapw0 080A136A MAIN__ 1935 lapw0.F 
lapw0 08053D94 Unknown Unknown Unknown
libc.so.00094FDEC Unknown Unknown Unknown
lapw0 08053CB1 Unknown Unknown Unknown

stop error

As suggested in an earlier Wien2k mail, I edited SRC_lapw0/fft_modules.f and 
SRC_lapw0/vresp.f files but got the same error again. (I used this patch 
http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-November/017911.html )

Help needed for this problem!

regards,
Ushma Ahuja
Faculty of Engineering
M .L. Sukhadia University, Udaipur
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[Wien] dstart error

2013-06-04 Thread vishal jain
Dear all,

I make a surface Fe(100) using Structgen, During the initilization its
shows following error

DSTART - Error
0.0u 0.0s 0:00.00 0.0% 0+0k 0+8io 0pf+0w


I also attached here structure file

Following comand I use to make surface

s=loadstruct(Fe.struct)

s1=makeprimitive (s);

n=[1 0 0];

s2=makesurface (s1,n,0,30,26);

savestruct (s2, Fe1.struct)


Thanks  Regards

Vishal Jain


dstart.error
Description: Binary data


Fe1.struct
Description: Binary data
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Re: [Wien] charge density analysis

2013-06-04 Thread Peter Blaha
In a spin-polarized calculation, both, the spin-up and the spin-dn
densities are used when runningx lapw5 -up/dn. Depending on the flag
 ADD or SUB it will then calculate:

up +/- dn-density  (or dn +/- up), and this is of course NOT spherical
symmetric for an Fe2+ ion.

You can  mv case.clmvaldn case.clmvaldn_saveand then
   x lapw5 -up
will plot solely the spin-up density.


On 06/04/2013 08:03 AM, 王静 wrote:
 Hi! there,
 
 I am doing some calculations about Fe2+. The DOS plot indicates the spin 
 down channel is full-filled by five d-electrons and the spin up channel is 
 occupied by the sixth one. The charge density has been drawn by Xcrysden. In 
 my opinion, the spin down channel should be a perfect ball since it has five 
 d-electrons. In fact, as in the attached file(the unit cell is not give 
 because the size is too large to be uploaded), it does not. In the 
 calculation, the density flag is SCF density, spin flag is spin density, the 
 Norm flag is valence density and Debug Flag is no debug.
 Did I misunderstand something? Any suggestions would be appreciated.
 
 Thanks very much!
 
  WANG jing
 wangjingj...@ciac.jl.cn
   2013-06-04
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Re: [Wien] dstart error

2013-06-04 Thread Peter Blaha

Instead of   makeprimitive, use makeconventional(s)

And please:   view  the resulting structure 

On 06/04/2013 08:25 AM, vishal jain wrote:

I make a surface Fe(100) using Structgen,



Following comand I use to make surface

s=loadstruct(Fe.struct)

s1=makeprimitive (s);

n=[1 0 0];

s2=makesurface (s1,n,0,30,26);

savestruct (s2, Fe1.struct)


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Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
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Re: [Wien] dstart error

2013-06-04 Thread vishal jain
Dear Sir,

As per your suggestion i use make conventional(s) but showing same error
I attached here  both error file and structure file

Thanks  Regards

Vishal Jain


On Tue, Jun 4, 2013 at 1:05 PM, Peter Blaha pbl...@theochem.tuwien.ac.atwrote:

 Instead of   makeprimitive, use makeconventional(s)

 And please:   view  the resulting structure 


 On 06/04/2013 08:25 AM, vishal jain wrote:

 I make a surface Fe(100) using Structgen,


  Following comand I use to make surface

 s=loadstruct(Fe.struct)

 s1=makeprimitive (s);

 n=[1 0 0];

 s2=makesurface (s1,n,0,30,26);

 savestruct (s2, Fe1.struct)


 --

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 --**--**
 --
 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.atWWW: http://info.tuwien.ac.at/**
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dstart.error
Description: Binary data


Fe1.struct
Description: Binary data
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Re: [Wien] dstart error

2013-06-04 Thread Peter Blaha

Ok. you have at least a Fe(100) surface.

Now you have to read what   init_lapw   tells you and have to act 
correspondingly. The problem is not in the dstart step, but previously!


sgroup writes a new struct file for you and you should accept it !

If not,  symmetry complains and you get big error/warning messages that 
you should shift the origin.


While one can sometimes neglect the changes from sgroup (but not this 
time), you can never neglect warnings/errors in symmetry !!


On 06/04/2013 10:15 AM, vishal jain wrote:

Dear Sir,

As per your suggestion i use make conventional(s) but showing same error
I attached here  both error file and structure file

Thanks  Regards

Vishal Jain


On Tue, Jun 4, 2013 at 1:05 PM, Peter Blaha
pbl...@theochem.tuwien.ac.at mailto:pbl...@theochem.tuwien.ac.at wrote:

Instead of   makeprimitive, use makeconventional(s)

And please:   view  the resulting structure 


On 06/04/2013 08:25 AM, vishal jain wrote:

I make a surface Fe(100) using Structgen,


Following comand I use to make surface

s=loadstruct(Fe.struct)

s1=makeprimitive (s);

n=[1 0 0];

s2=makesurface (s1,n,0,30,26);

savestruct (s2, Fe1.struct)


--

   P.Blaha

--__--__--
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[Wien] scp error

2013-06-04 Thread Yundi Quan
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] scp error

2013-06-04 Thread 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] scp error

2013-06-04 Thread Stefaan Cottenier


This looks like to be an issue with the SCRATCH variable. The 
case.vector* files are stored as $SCRATCH/case.vector*. Check on your 
system how you set this variable (echo $SCRATCH). If your .bashrc got 
messed up, it might even have a different value in an 
interactive/noninteractive session.


in lapw2*.def, you can see the full path of the vector files -- the 
string before case.vector* is the value of SCRATCH that was used during 
the scf cycle.


Stefaan


On 4/06/2013 11:19, Yundi Quan wrote:

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] dstart error

2013-06-04 Thread Lyudmila Dobysheva

04.06.2013 10:25, vishal jain wrote:

I make a surface Fe(100) using Structgen, During the initilization its
shows following error
DSTART - Error

  'DSTART' - can't open unit: 15
 'DSTART' -filename: Fe1.in2c

Dear Vishal Jain,

I see that both struct files attached have inversion symmetry but the 
error is about in2c file. Maybe there occasionally appeared the 
complex-calculation mark in w2web?

So, make the calculation with inversion: remove this mark if it exists
in w2web, and change session information

Best regards
  Lyudmila Dobysheva
--
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426001 Izhevsk, ul.Kirova 132
RUSSIA
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Re: [Wien] scp error

2013-06-04 Thread Yundi Quan
Thank Stefaan and Michael for your prompt replies.

My $SCRATCH file is set to ./ in the .bashrc file. I forgot to mention
that I used x lapw2 -qtl -p -it rather than x lapw2 -qtl -p. The
option -it tells WIEN2k to use iterative diagonalization, which should
not be a problem. In uplapw2_1.def, it says that
10,'./case.vectorup_1', 'unknown','unformatted',9000

I think this line tells lapw2 where to find the vector. But again, ./
seems to mean my home directory rather than my working directory.

I tried making a new scratch directory and set the $SCRATCH to that
directory as suggested by Michael. I hope it works.



Yundi



On Tue, Jun 4, 2013 at 2:34 AM, Yundi Quan yq...@ucdavis.edu wrote:


 -- Forwarded message --
 From: Yundi Quan quanyu...@gmail.com
 Date: Tue, Jun 4, 2013 at 2:19 AM
 Subject: [Wien] scp error
 To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at


 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] dstart error

2013-06-04 Thread vishal jain
Thank you Sir,




On Tue, Jun 4, 2013 at 2:40 PM, Lyudmila Dobysheva lyuk...@mail.ru wrote:

 04.06.2013 10:25, vishal jain wrote:

 I make a surface Fe(100) using Structgen, During the initilization its
 shows following error
 DSTART - Error

   'DSTART' - can't open unit: 15
  'DSTART' -filename: Fe1.in2c

 Dear Vishal Jain,

 I see that both struct files attached have inversion symmetry but the
 error is about in2c file. Maybe there occasionally appeared the
 complex-calculation mark in w2web?
 So, make the calculation with inversion: remove this mark if it exists
 in w2web, and change session information

 Best regards
   Lyudmila Dobysheva
 --**--**--
 Phys.-Techn. Institute of Ural Br. of Russian Ac. of Sci.
 426001 Izhevsk, ul.Kirova 132
 RUSSIA
 --**--**--
 Tel.:7(3412) 442118 (home), 218988(office), 722529(Fax)
 E-mail: l...@ftiudm.ru
 lyuk...@mail.ru (office) lyuk...@gmail.com (home)
 Skype:  lyuka17 (home), lyuka18 (office)
 http://fti.udm.ru/content/**view/25/103/lang,english/http://fti.udm.ru/content/view/25/103/lang,english/
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[Wien] Spin-polarization in ELNES calculations

2013-06-04 Thread David Holec
Dear Wien2k users,

Could anyone please explain to me the role of spin in ELNES
calculations? In particular, suppose I am trying to get ELNES of
ferromagnetic or antiferromagnetic compounds consisting of two
sublattices, one out of which is non-magnetic (CrN, in the
initialisation phase I set up/dn spins on Cr, and no magnetic moment
on N atoms). I am interested in both Cr L2,3 edge and N K edge.

Many thanks in advance for your help,
David
--
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Dept. of Physical Metallurgy and Materials Testing
Montanuniversität Leoben
Franz-Josef-Strasse 18
A-8700 Leoben
Austria
tel. +43-(0)3842-4024211
fax. +43-(0)3842-4024202
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Re: [Wien] scp error

2013-06-04 Thread Peter Blaha

-it does not have an effect for lapw2 since there is no diagonalization.

The problem is most likely that you need a proper .processes file to run 
x lapw2 -p. Most PBS-scripts create only   .machines and run_lapw 
will then generate later on .processes.


My suggestion:  First check if you have the vector files in case:

cd /home/my_username/wien2k/case
ls -alsrt *vector*

If they look ok (size and date !!!)

use   join_vectorfiles

to combine them to a single non-parallel vector and then
submit   x lapw2 -qtl   (without -p)

Note: in QTL-mode, lapw2 always runs only on a single core and the -p 
option is only used to let the code know about the parallel vector files.



On 06/04/2013 12:06 PM, Yundi Quan wrote:

Thank Stefaan and Michael for your prompt replies.

My $SCRATCH file is set to ./ in the .bashrc file. I forgot to mention
that I used x lapw2 -qtl -p -it rather than x lapw2 -qtl -p. The
option -it tells WIEN2k to use iterative diagonalization, which should
not be a problem. In uplapw2_1.def, it says that
10,'./case.vectorup_1', 'unknown','unformatted',9000

I think this line tells lapw2 where to find the vector. But again, ./
seems to mean my home directory rather than my working directory.

I tried making a new scratch directory and set the $SCRATCH to that
directory as suggested by Michael. I hope it works.



Yundi



On Tue, Jun 4, 2013 at 2:34 AM, Yundi Quan yq...@ucdavis.edu wrote:



-- Forwarded message --
From: Yundi Quan quanyu...@gmail.com
Date: Tue, Jun 4, 2013 at 2:19 AM
Subject: [Wien] scp error
To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at


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
 '. 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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--

  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.atWWW: 
http://info.tuwien.ac.at/theochem/

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Re: [Wien] Spin-polarization in ELNES calculations

2013-06-04 Thread Peter Blaha

You just have to run it for spin-up AND dn and sum up the results.

It has nothing to do whether you set N as non-magnetic or not, only 
the final scf-results are important and also the N-p DOS could be 
(slightly) different for spin-up and dn.


PS: ELNES does not know about spin-orbit coupling and L2 vs. L3.

On 06/04/2013 12:30 PM, David Holec wrote:

Dear Wien2k users,

Could anyone please explain to me the role of spin in ELNES
calculations? In particular, suppose I am trying to get ELNES of
ferromagnetic or antiferromagnetic compounds consisting of two
sublattices, one out of which is non-magnetic (CrN, in the
initialisation phase I set up/dn spins on Cr, and no magnetic moment
on N atoms). I am interested in both Cr L2,3 edge and N K edge.

Many thanks in advance for your help,
David
--
Dr. David Holec
Dept. of Physical Metallurgy and Materials Testing
Montanuniversität Leoben
Franz-Josef-Strasse 18
A-8700 Leoben
Austria
tel. +43-(0)3842-4024211
fax. +43-(0)3842-4024202
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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.atWWW: 
http://info.tuwien.ac.at/theochem/

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Re: [Wien] Spin-polarization in ELNES calculations

2013-06-04 Thread David Holec
Thanks Peter for your prompt response, this is very helpful and
clarifies my confusion ;-)

David
--
Dr. David Holec
Dept. of Physical Metallurgy and Materials Testing
Montanuniversität Leoben
Franz-Josef-Strasse 18
A-8700 Leoben
Austria
tel. +43-(0)3842-4024211
fax. +43-(0)3842-4024202


On 4 June 2013 14:16, Peter Blaha pbl...@theochem.tuwien.ac.at wrote:
 You just have to run it for spin-up AND dn and sum up the results.

 It has nothing to do whether you set N as non-magnetic or not, only the
 final scf-results are important and also the N-p DOS could be (slightly)
 different for spin-up and dn.

 PS: ELNES does not know about spin-orbit coupling and L2 vs. L3.


 On 06/04/2013 12:30 PM, David Holec wrote:

 Dear Wien2k users,

 Could anyone please explain to me the role of spin in ELNES
 calculations? In particular, suppose I am trying to get ELNES of
 ferromagnetic or antiferromagnetic compounds consisting of two
 sublattices, one out of which is non-magnetic (CrN, in the
 initialisation phase I set up/dn spins on Cr, and no magnetic moment
 on N atoms). I am interested in both Cr L2,3 edge and N K edge.

 Many thanks in advance for your help,
 David
 --
 Dr. David Holec
 Dept. of Physical Metallurgy and Materials Testing
 Montanuniversität Leoben
 Franz-Josef-Strasse 18
 A-8700 Leoben
 Austria
 tel. +43-(0)3842-4024211
 fax. +43-(0)3842-4024202
 ___
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 Wien@zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
 SEARCH the MAILING-LIST at:
 http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html


 --

   P.Blaha
 --
 Peter BLAHA, Inst.f. Materials Chemistry, TU Vienna, A-1060 Vienna
 Phone: +43-1-58801-165300 FAX: +43-1-58801-165982
 Email: bl...@theochem.tuwien.ac.atWWW:
 http://info.tuwien.ac.at/theochem/
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Re: [Wien] scp error

2013-06-04 Thread Laurence Marks
Let me add a couple of clarifications to what Peter suggested, since I
often get caught by the .process and .process2 files. I just did a
quick search of the UG and they do not appear to be described
(suggestion to Peter to add). Their format is somewhat self
explanatory (although they do not seem to be constructed to be very
human readable, i.e. no comments on the right.)

The shell scripts create these files during a -p run so, for instance,
lapw2 can run in parallel on the same nodes that lapw1 used and
therefore SCRATCH and other files which might only be in temporary
storage are consistent. When you run under PBS or several other
similar job control codes which nodes you use are dynamically
allocated and are then stored within these files. If you now run a
second job or interactive task to do some analysis you are likely to
have a different set of nodes allocated to you which can then create
problems.

If you are running interactively you can adjust these files for the
nodes that you have. Alternatively you can do a single -p pass
although unfortunately -it might switch to non-iterative because the
setup uses the .process file to cp the old vector file.

I suspect that it may be too hard to construct a shell script (or csh)
to set these up properly for a given .machines file by extracting the
relevant section from lapw1para, perhaps a good mini project for
someone.

On Tue, Jun 4, 2013 at 7:04 AM, Peter Blaha
pbl...@theochem.tuwien.ac.at wrote:
 -it does not have an effect for lapw2 since there is no diagonalization.

 The problem is most likely that you need a proper .processes file to run
  x lapw2 -p. Most PBS-scripts create only   .machines and run_lapw
 will then generate later on .processes.

 My suggestion:  First check if you have the vector files in case:

 cd /home/my_username/wien2k/case
 ls -alsrt *vector*

 If they look ok (size and date !!!)

 use   join_vectorfiles

 to combine them to a single non-parallel vector and then
 submit   x lapw2 -qtl   (without -p)

 Note: in QTL-mode, lapw2 always runs only on a single core and the -p
 option is only used to let the code know about the parallel vector files.


 On 06/04/2013 12:06 PM, Yundi Quan wrote:
 Thank Stefaan and Michael for your prompt replies.

 My $SCRATCH file is set to ./ in the .bashrc file. I forgot to mention
 that I used x lapw2 -qtl -p -it rather than x lapw2 -qtl -p. The
 option -it tells WIEN2k to use iterative diagonalization, which should
 not be a problem. In uplapw2_1.def, it says that
 10,'./case.vectorup_1', 'unknown','unformatted',9000

 I think this line tells lapw2 where to find the vector. But again, ./
 seems to mean my home directory rather than my working directory.

 I tried making a new scratch directory and set the $SCRATCH to that
 directory as suggested by Michael. I hope it works.



 Yundi



 On Tue, Jun 4, 2013 at 2:34 AM, Yundi Quan yq...@ucdavis.edu wrote:


 -- Forwarded message --
 From: Yundi Quan quanyu...@gmail.com
 Date: Tue, Jun 4, 2013 at 2:19 AM
 Subject: [Wien] scp error
 To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at


 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
  '. This works for scf calculations.
 However, when I use x lapw2 -qtl -band -p to calculate the band
 structure or x lapw2 -qtl -p to calculate the DOS, I always encounter
 the following error message:
 scp: .//case.vector_1 not found
 scp: .//case.vector_2 not found
 ...

 It seems scp is looking for case.vector_1 in my home directory rather
 than my working directory, even though I've added the line 'cd
 /home/my_username/case' in my bash file. This problem only occurs with
 using x lapw2 -qtl -p. I used to do scf calculation in serial and then
 use x lapw2 -qtl. But I'm wondering whether there is a workaround.


 Thanks.
 ___
 Wien mailing list
 Wien@zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
 SEARCH the MAILING-LIST at:
 http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html

 ___
 Wien mailing list
 Wien@zeus.theochem.tuwien.ac.at
 http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien
 SEARCH the MAILING-LIST at:  
 http://www.mail-archive.com/wien@zeus.theochem.tuwien.ac.at/index.html


 --

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.atWWW:
 http://info.tuwien.ac.at/theochem/
 --
 

Re: [Wien] scp error

2013-06-04 Thread Peter Blaha
I guess I also have to add some clarifications, because there is no 
.process or .process2 file, 



For parallel calculations the main file of interest is

.machines

And this file is used by lapw0para and lapw1para as input.

However, lapw1para produces

.processes

(because you may have more parallel jobs then specified in .machines 
(because of non-integer k-point/core ratio) and in particular because 
we allow explicitly to modify .machines during run_lapw (changing the 
parallelization by hand for the next iterations in case a machine is 
overloaded on a cluster).


The following parallel scripts (lapwso, lapw2) therefore read from 
.processes (and not from .machines). (Also vec2old and vec2pratt need 
.processes and this may cause eventually problems, although if you 
change the number of cores ot use a non-local $SCRATCH, it cannot do -it 
at the very beginning anyway).


This is (at least to some extend) documented in the UG (search eg. for 
processes).


These are usually the only 2 files of interest for a user.
There are no .process or .process2 files; and other .machineXX or 
.processesXX files are internal only.


I'm sometimes using PBS-scripts which do generate .processes, but the 
easiest thing would be to add a flag to lapw1para, so that it does not 
execute lapw1, but just generates the .processes file.




On 06/04/2013 02:42 PM, Laurence Marks wrote:

Let me add a couple of clarifications to what Peter suggested, since I
often get caught by the .process and .process2 files. I just did a
quick search of the UG and they do not appear to be described
(suggestion to Peter to add). Their format is somewhat self
explanatory (although they do not seem to be constructed to be very
human readable, i.e. no comments on the right.)

The shell scripts create these files during a -p run so, for instance,
lapw2 can run in parallel on the same nodes that lapw1 used and
therefore SCRATCH and other files which might only be in temporary
storage are consistent. When you run under PBS or several other
similar job control codes which nodes you use are dynamically
allocated and are then stored within these files. If you now run a
second job or interactive task to do some analysis you are likely to
have a different set of nodes allocated to you which can then create
problems.

If you are running interactively you can adjust these files for the
nodes that you have. Alternatively you can do a single -p pass
although unfortunately -it might switch to non-iterative because the
setup uses the .process file to cp the old vector file.

I suspect that it may be too hard to construct a shell script (or csh)
to set these up properly for a given .machines file by extracting the
relevant section from lapw1para, perhaps a good mini project for
someone.

On Tue, Jun 4, 2013 at 7:04 AM, Peter Blaha
pbl...@theochem.tuwien.ac.at wrote:

-it does not have an effect for lapw2 since there is no diagonalization.

The problem is most likely that you need a proper .processes file to run
  x lapw2 -p. Most PBS-scripts create only   .machines and run_lapw
will then generate later on .processes.

My suggestion:  First check if you have the vector files in case:

cd /home/my_username/wien2k/case
ls -alsrt *vector*

If they look ok (size and date !!!)

use   join_vectorfiles

to combine them to a single non-parallel vector and then
submit   x lapw2 -qtl   (without -p)

Note: in QTL-mode, lapw2 always runs only on a single core and the -p
option is only used to let the code know about the parallel vector files.


On 06/04/2013 12:06 PM, Yundi Quan wrote:

Thank Stefaan and Michael for your prompt replies.

My $SCRATCH file is set to ./ in the .bashrc file. I forgot to mention
that I used x lapw2 -qtl -p -it rather than x lapw2 -qtl -p. The
option -it tells WIEN2k to use iterative diagonalization, which should
not be a problem. In uplapw2_1.def, it says that
10,'./case.vectorup_1', 'unknown','unformatted',9000

I think this line tells lapw2 where to find the vector. But again, ./
seems to mean my home directory rather than my working directory.

I tried making a new scratch directory and set the $SCRATCH to that
directory as suggested by Michael. I hope it works.



Yundi



On Tue, Jun 4, 2013 at 2:34 AM, Yundi Quan yq...@ucdavis.edu wrote:



-- Forwarded message --
From: Yundi Quan quanyu...@gmail.com
Date: Tue, Jun 4, 2013 at 2:19 AM
Subject: [Wien] scp error
To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at


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
  '. 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: 

Re: [Wien] scp error

2013-06-04 Thread Laurence Marks
To err is human, to make slly name/spelling errors takes a Prof.

Yes, I should have written .processes etc, sorry.

On Tue, Jun 4, 2013 at 9:08 AM, Peter Blaha
pbl...@theochem.tuwien.ac.at wrote:
 I guess I also have to add some clarifications, because there is no
 .process or .process2 file, 


 For parallel calculations the main file of interest is

 .machines

 And this file is used by lapw0para and lapw1para as input.

 However, lapw1para produces

 .processes

 (because you may have more parallel jobs then specified in .machines
 (because of non-integer k-point/core ratio) and in particular because
 we allow explicitly to modify .machines during run_lapw (changing the
 parallelization by hand for the next iterations in case a machine is
 overloaded on a cluster).

 The following parallel scripts (lapwso, lapw2) therefore read from
 .processes (and not from .machines). (Also vec2old and vec2pratt need
 .processes and this may cause eventually problems, although if you
 change the number of cores ot use a non-local $SCRATCH, it cannot do -it
 at the very beginning anyway).

 This is (at least to some extend) documented in the UG (search eg. for
 processes).

 These are usually the only 2 files of interest for a user.
 There are no .process or .process2 files; and other .machineXX or
 .processesXX files are internal only.

 I'm sometimes using PBS-scripts which do generate .processes, but the
 easiest thing would be to add a flag to lapw1para, so that it does not
 execute lapw1, but just generates the .processes file.



 On 06/04/2013 02:42 PM, Laurence Marks wrote:
 Let me add a couple of clarifications to what Peter suggested, since I
 often get caught by the .process and .process2 files. I just did a
 quick search of the UG and they do not appear to be described
 (suggestion to Peter to add). Their format is somewhat self
 explanatory (although they do not seem to be constructed to be very
 human readable, i.e. no comments on the right.)

 The shell scripts create these files during a -p run so, for instance,
 lapw2 can run in parallel on the same nodes that lapw1 used and
 therefore SCRATCH and other files which might only be in temporary
 storage are consistent. When you run under PBS or several other
 similar job control codes which nodes you use are dynamically
 allocated and are then stored within these files. If you now run a
 second job or interactive task to do some analysis you are likely to
 have a different set of nodes allocated to you which can then create
 problems.

 If you are running interactively you can adjust these files for the
 nodes that you have. Alternatively you can do a single -p pass
 although unfortunately -it might switch to non-iterative because the
 setup uses the .process file to cp the old vector file.

 I suspect that it may be too hard to construct a shell script (or csh)
 to set these up properly for a given .machines file by extracting the
 relevant section from lapw1para, perhaps a good mini project for
 someone.

 On Tue, Jun 4, 2013 at 7:04 AM, Peter Blaha
 pbl...@theochem.tuwien.ac.at wrote:
 -it does not have an effect for lapw2 since there is no diagonalization.

 The problem is most likely that you need a proper .processes file to run
   x lapw2 -p. Most PBS-scripts create only   .machines and run_lapw
 will then generate later on .processes.

 My suggestion:  First check if you have the vector files in case:

 cd /home/my_username/wien2k/case
 ls -alsrt *vector*

 If they look ok (size and date !!!)

 use   join_vectorfiles

 to combine them to a single non-parallel vector and then
 submit   x lapw2 -qtl   (without -p)

 Note: in QTL-mode, lapw2 always runs only on a single core and the -p
 option is only used to let the code know about the parallel vector files.


 On 06/04/2013 12:06 PM, Yundi Quan wrote:
 Thank Stefaan and Michael for your prompt replies.

 My $SCRATCH file is set to ./ in the .bashrc file. I forgot to mention
 that I used x lapw2 -qtl -p -it rather than x lapw2 -qtl -p. The
 option -it tells WIEN2k to use iterative diagonalization, which should
 not be a problem. In uplapw2_1.def, it says that
 10,'./case.vectorup_1', 'unknown','unformatted',9000

 I think this line tells lapw2 where to find the vector. But again, ./
 seems to mean my home directory rather than my working directory.

 I tried making a new scratch directory and set the $SCRATCH to that
 directory as suggested by Michael. I hope it works.



 Yundi



 On Tue, Jun 4, 2013 at 2:34 AM, Yundi Quan yq...@ucdavis.edu wrote:


 -- Forwarded message --
 From: Yundi Quan quanyu...@gmail.com
 Date: Tue, Jun 4, 2013 at 2:19 AM
 Subject: [Wien] scp error
 To: A Mailing list for WIEN2k users wien@zeus.theochem.tuwien.ac.at


 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 

[Wien] wien2k help

2013-06-04 Thread qinfang zhang
Dear Sir,

I tried to install wien2k on my own cluster. My system is Debian wheezy,
amd64 and the version of Ifort is l_fcompxe_intel64_2013.4.183

I always have this problem when using the latest ifort 64 bit.

recpr.f(210): error #6285: There is no matching specific subroutine for
this generic subroutine call. [DOREALLOCATE]
call doreallocate(kzz, 3, nwav1)
-^
recpr.f(228): error #6285: There is no matching specific subroutine for
this generic subroutine call. [DOREALLOCATE]
call doreallocate(kzz, 3, nk)
-^
compilation aborted for recpr.f (code 1)

If I use the same version 32 bit ifort, it is OK.



The following is set as the guide from intel website.

Current settings:
O Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML
-traceback -i8 -I$(MKLROOT)/include/intel64/
ilp64 -I$(MKLROOT)/include
L Linker Flags: $(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread
P Preprocessor flags '-DParallel'
R R_LIB (LAPACK+BLAS): -L$(MKLROOT)/lib/intel64
$(MKLROOT)/lib/intel64/libmkl_blas95_ilp64.a
$(MKLROOT)/lib/intel64/libmkl_lapack95_ilp64.a -lmkl_intel_ilp64
-lmkl_sequential -lmkl_core -lpthread -lm


Best Regards,
qinfang

-- 
Qinfang Zhang ( 张勤芳 )
Key Laboratory for Advanced Technology in Enviromental Protection of
Jiangsu Province
Yancheng Institue of Technology
No. 9  Yingbin  Avenue, Yancheng, Jiangsu, P.R. China
Email: qfangzh...@gmail.com ;  q.zh...@riken.jp
Tel: 0086-515-88298920  Mobile: 0086-15161992601
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[Wien] OMP_NUM_THREAD

2013-06-04 Thread Jose Alfredo Camargo Martinez
Hi.
We install  Wien2k (serial mode) in a server with 64 processors  (Workstation 
AMD Opteron 6328 4X16 ). In  bashrc we defined OMP_NUM_THREAD=58.
When we run run_lapw (Kmax=7 and  N° of k-points=2000), only 33 processors 
running. 

Why it doesn't run in 58 processors? 

J. Camargo.
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Re: [Wien] wien2k help

2013-06-04 Thread Laurence Marks
For certain change -i8 and replace it by -r8.

---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 1-847-491-3996
Research is to see what everybody else has seen, and to think what nobody
else has thought
Albert Szent-Gyorgi
 On Jun 4, 2013 6:28 PM, qinfang zhang qfangzh...@gmail.com wrote:

   Dear Sir,

 I tried to install wien2k on my own cluster. My system is Debian wheezy,
 amd64 and the version of Ifort is l_fcompxe_intel64_2013.4.183

 I always have this problem when using the latest ifort 64 bit.

 recpr.f(210): error #6285: There is no matching specific subroutine for
 this generic subroutine call. [DOREALLOCATE]
 call doreallocate(kzz, 3, nwav1)
 -^
 recpr.f(228): error #6285: There is no matching specific subroutine for
 this generic subroutine call. [DOREALLOCATE]
 call doreallocate(kzz, 3, nk)
 -^
 compilation aborted for recpr.f (code 1)

 If I use the same version 32 bit ifort, it is OK.



 The following is set as the guide from intel website.

 Current settings:
 O Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML
 -traceback -i8 -I$(MKLROOT)/include/intel64/
 ilp64 -I$(MKLROOT)/include
 L Linker Flags: $(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread
 P Preprocessor flags '-DParallel'
 R R_LIB (LAPACK+BLAS): -L$(MKLROOT)/lib/intel64
 $(MKLROOT)/lib/intel64/libmkl_blas95_ilp64.a
 $(MKLROOT)/lib/intel64/libmkl_lapack95_ilp64.a -lmkl_intel_ilp64
 -lmkl_sequential -lmkl_core -lpthread -lm


  Best Regards,
  qinfang

 --
 Qinfang Zhang ( 张勤芳 )
 Key Laboratory for Advanced Technology in Enviromental Protection of
 Jiangsu Province
 Yancheng Institue of Technology
 No. 9  Yingbin  Avenue, Yancheng, Jiangsu, P.R. China
 Email: qfangzh...@gmail.com ;  q.zh...@riken.jp
 Tel: 0086-515-88298920  Mobile: 0086-15161992601

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Re: [Wien] OMP_NUM_THREAD

2013-06-04 Thread Laurence Marks
Read the mkl documentation, OMP_NUM_THREADS is advisory only.

In addition, read the Wien2k documentation to see how to do k-pt parallel
operation, it is not by this mechanism.

---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu 1-847-491-3996
Research is to see what everybody else has seen, and to think what nobody
else has thought
Albert Szent-Gyorgi
 On Jun 4, 2013 6:38 PM, Jose Alfredo Camargo Martinez sork8...@yahoo.es
wrote:

  Hi.
  We install  Wien2k (serial mode) in a server with 64 processors
  (Workstation AMD Opteron 6328 4X16 ). In  bashrc we defined
 OMP_NUM_THREAD=58.
  When we run run_lapw (Kmax=7 and  N° of k-points=2000), only 33
 processors running.

  Why it doesn't run in 58 processors?

  J. Camargo.


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[Wien] (no subject)

2013-06-04 Thread amit shankar
Dear Wien2k users,

I have Wien2k 12.1 installed on i7 8-core with OS  CENTOS6.3. I have installed 
Boltztrap 1.2.0 for calculating transport properties, in my system CeFe4Sb12, i 
have already done dos and band structure calculation after that wen i tried to 
run Boltztrap its giving me error  error in factorization .

please suggest me how to solve it.

With regards,
Amit, MZU___
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Re: [Wien] OMP_NUM_THREAD

2013-06-04 Thread Peter Blaha

You have to do some timing !

Check the time (eg. of the benchmark on the wien2k page) with OMP_NUM_THREAD 
=1,2,4 and maybe 8.
You will see, that the gain with 4 is already very small and thus more or less 
useless.

Many people think that using more cores makes a calculation automatically 
faster. This is not true.
Very often it can happen that more cores need LONGER time. (This is also true 
for k-parallel
wien2k calculations or mpi-runs, where you have to find out by timings (in the 
dayfile or stdout)
how far you can go).
At least at the beginning you have to find out what the optimal number of cores 
is for your specific case.
This number will vary from case to case (maybe only 2 cores for fcc Al using 
OMP_NUM_TREAD), to 2000 cores
(mpi) for a supercell with 1000 atoms ), and after some time you will have 
enough experience to select the proper
resources and method (OMP, k-parallel, mpi, often a combination of 2 of the 
methods (OMP+k-point or k-point+mpi)
for a new case.

PS: My experience with these huge shared memory machines (more than 16 cores) 
is NOT very good. Their
performance is usually quite lousy, probably because of memory-bus limitations. 
Maybe core-binding helps.


Am 05.06.2013 01:37, schrieb Jose Alfredo Camargo Martinez:

Hi.
We install  Wien2k (serial mode) in a server with 64 processors  (Workstation 
AMD Opteron 6328 4X16 ). In  bashrc we defined OMP_NUM_THREAD=58.
When we run run_lapw (Kmax=7 and  N° of k-points=2000), only 33 processors 
running.

Why it doesn't run in 58 processors?

J. Camargo.



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--
-
Peter Blaha
Inst. Materials Chemistry, TU Vienna
Getreidemarkt 9, A-1060 Vienna, Austria
Tel: +43-1-5880115671
Fax: +43-1-5880115698
email: pbl...@theochem.tuwien.ac.at
-
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Re: [Wien] wien2k help

2013-06-04 Thread Gavin Abo
For 64 bit, I think you have to compile Wien2k with interface layer 
without I (i.e., LP64).


On 6/4/2013 5:57 PM, Laurence Marks wrote:


For certain change -i8 and replace it by -r8.

---
Professor Laurence Marks
Department of Materials Science and Engineering
Northwestern University
www.numis.northwestern.edu http://www.numis.northwestern.edu 
1-847-491-3996
Research is to see what everybody else has seen, and to think what 
nobody else has thought

Albert Szent-Gyorgi

On Jun 4, 2013 6:28 PM, qinfang zhang qfangzh...@gmail.com 
mailto:qfangzh...@gmail.com wrote:


Dear Sir,

I tried to install wien2k on my own cluster. My system is Debian
wheezy, amd64 and the version of Ifort is l_fcompxe_intel64_2013.4.183

I always have this problem when using the latest ifort 64 bit.

recpr.f(210): error #6285: There is no matching specific
subroutine for
this generic subroutine call. [DOREALLOCATE]
call doreallocate(kzz, 3, nwav1)
-^
recpr.f(228): error #6285: There is no matching specific
subroutine for
this generic subroutine call. [DOREALLOCATE]
call doreallocate(kzz, 3, nk)
-^
compilation aborted for recpr.f (code 1)

If I use the same version 32 bit ifort, it is OK.



The following is set as the guide from intel website.

Current settings:
O Compiler options: -FR -mp1 -w -prec_div -pc80 -pad -ip -DINTEL_VML
-traceback -i8 -I$(MKLROOT)/include/intel64/
ilp64 -I$(MKLROOT)/include
L Linker Flags: $(FOPT) -L$(MKLROOT)/lib/$(MKL_TARGET_ARCH) -pthread
P Preprocessor flags '-DParallel'
R R_LIB (LAPACK+BLAS): -L$(MKLROOT)/lib/intel64
$(MKLROOT)/lib/intel64/libmkl_blas95_ilp64.a
$(MKLROOT)/lib/intel64/libmkl_lapack95_ilp64.a -lmkl_intel_ilp64
-lmkl_sequential -lmkl_core -lpthread -lm


Best Regards,
qinfang

-- 
Qinfang Zhang ( ??? )

Key Laboratory for Advanced Technology in Enviromental Protection
of Jiangsu Province
Yancheng Institue of Technology
No. 9  Yingbin  Avenue, Yancheng, Jiangsu, P.R. China
Email: qfangzh...@gmail.com mailto:qfangzh...@gmail.com ;
q.zh...@riken.jp mailto:q.zh...@riken.jp
Tel: 0086-515-88298920  Mobile: 0086-15161992601



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