[Wien] Re: Wien digest, Vol 1 #82 - 65 msgs
Belkadi Amina
amina_belkadi2003 at yahoo.fr
Sat Dec 4 15:10:57 CET 2004
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Today's Topics:
1. Re: incorrect distribution over parallel nodes (Peter Blaha)
2. optic under parallel (WANG Yuan Xu)
3. Optical properties (Chukwuemeka Okoye)
4. RE: Partial charges inside atomic spheres (stargmoon)
5. Re: Optical properties (Fred Nastos)
6. incorrect distribution over parallel nodes - Resolved (Igor Mazin)
7. question about sgroup (Fred Nastos)
8. Re: question about sgroup (georg at chem.au.dk)
9. Re: Optical properties (Chukwuemeka Okoye)
10. Re: Optical properties (Fred Nastos)
11. Re: Optical properties (Chukwuemeka Okoye)
12. Re: Optical properties (Fred Nastos)
13. (no subject) (SENAPATI, Laxmidhar)
14. Re: (no subject) (Javad Hashemifar)
15. EV GGA and property calculation (Dr. Sharat Chandra)
16. The calculated-error of the magnetic moment (ccmp at nju.edu.cn)
17. Re: The calculated-error of the magnetic moment (Stefaan Cottenier)
18. The calculated-error of the magnetic moment (ccmp at nju.edu.cn)
19. small bug in sgroup (Stefano Rubino)
20. Re: The calculated-error of the magnetic moment (fecher)
21. Re: The calculated-error of the magnetic moment (Peter Blaha)
22. Re: The calculated-error of the magnetic moment (Torsten Andersen)
23. How to install on IBM p650 (kongshi)
24. Re: EV GGA and property calculation (Fred Nastos)
25. Re: small bug in sgroup (Peter Blaha)
26. Energy, forces and muffin tin radii (Leonardo Pisani)
27. Re: Energy, forces and muffin tin radii (Stefaan Cottenier)
28. Re: How to install on IBM p650 (Torsten Andersen)
29. Re: Energy, forces and muffin tin radii (L. D. Marks)
30. To LO or not to LO ? (L. D. Marks)
31. Re: Energy, forces and muffin tin radii (Stefaan Cottenier)
32. Re: Energy, forces and muffin tin radii (Leonardo Pisani)
33. RE:how to install on IBM p650 (to Torsten Andersen) (kongshi)
34. Re: RE:how to install on IBM p650 (to Torsten Andersen) (Torsten Andersen)
35. Re: Energy, forces and muffin tin radii (Stefaan Cottenier)
36. How to prevent parallel runs ? (fecher)
37. Re: How to prevent parallel runs ? (Torsten Andersen)
38. Re: How to prevent parallel runs ? (Peter Blaha)
39. Re: To LO or not to LO ? (Peter Blaha)
40. Re: How to prevent parallel runs ? (fecher)
41. Re: Energy, forces and muffin tin radii (Leonardo Pisani)
42. Re: Energy, forces and muffin tin radii (Stefaan Cottenier)
43. Re: How to prevent parallel runs ? (buero at luitz.at)
44. Problems on running wien2k (chahra mef)
45. RE: Problems on running wien2k (Jorissen Kevin)
46. Re:how to install wien2k on IBM p650 (kongshi)
47. Re:how to install wien2k on IBM p650 (kongshi)
48. Re: Re:how to install wien2k on IBM p650 (Torsten Andersen)
49. How to generate struct with StructGen (SENAPATI, Laxmidhar)
50. Re: How to generate struct with StructGen (Antoine Villesuzanne)
51. RE: How to generate struct with StructGen (Rashid ahmed)
52. Warning msg in lstart (Hongming Weng)
53. Re: Warning msg in lstart (Fred Nastos)
54. wien2k_4 installation (Bohdan Andriyevsky)
55. (no subject) (Belkadi Amina)
56. Re: wien2k_4 installation (L. D. Marks)
57. Problem in running Joint (Kalobaran Maiti)
58. [Fwd: question concerning joint] (Florent Boucher)
59. Minimization NAN (Leonardo Pisani)
60. Re: Minimization NAN (L. D. Marks)
61. super unit cell (Bing Zhou)
62. Re: wien2k_4 installation (Peter Blaha)
63. A difficulty on installing WIEN2k code ! (zhgh at theory.issp.ac.cn)
64. Re: XCrysDen does not open (Torsten Andersen)
65. supercell (Bing Zhou)
--__--__--
Message: 1
Date: Wed, 24 Nov 2004 23:04:29 +0100 (CET)
From: Peter Blaha
To: WIEN mailing-list
Subject: Re: [Wien] incorrect distribution over parallel nodes
Reply-To: wien at zeus.theochem.tuwien.ac.at
This is probably due to an attempted load balencing, which is fine and
desirable without scratch disks.
Include granularity:1 in .machines
This should fix the distribution 1+2 k to node 1; 3+4 to node 2,....
> I found that with a relatively large number of nodes
> in simple parallelization sometimes the script
> incorrectly distrubutes the k-points over the nodes,
> which later results in a crash. Here is an example.
> 50 k-point were excuted on 25 machines. This is the
> .machines file:
> 1:compute-3-35.local
> 1:compute-3-34.local
> 1:compute-3-33.local
> 1:compute-3-32.local
>
> 1:compute-3-11.local
> 1:compute-3-10.local
>
> Now see the result of running the following command:
> >foreach f ( `sed 's/1://' .machines` )
> > echo $f
> > ssh $f "ls -trs /scratch/mazin/RUN5*"
> > echo ""
> >end
>
> Note below that
>
> 1680 /scratch/mazin/RUN5.vectorup_1
> 1780 /scratch/mazin/RUN5.vectorup_26
> 1680 /scratch/mazin/RUN5.vectordn_1
> 1780 /scratch/mazin/RUN5.vectordn_26
> 6608 /scratch/mazin/RUN5.vectorsoup_1
> 6608 /scratch/mazin/RUN5.vectorsodn_1
> 7012 /scratch/mazin/RUN5.vectorsoup_26
> 7012 /scratch/mazin/RUN5.vectorsodn_26
>
> compute-3-34.local
> 1716 /scratch/mazin/RUN5.vectorup_2
> 1800 /scratch/mazin/RUN5.vectorup_27
> 1716 /scratch/mazin/RUN5.vectordn_2
> 1800 /scratch/mazin/RUN5.vectordn_27
> 6748 /scratch/mazin/RUN5.vectorsoup_2
> 6748 /scratch/mazin/RUN5.vectorsodn_2
> 7092 /scratch/mazin/RUN5.vectorsoup_27
> 7092 /scratch/mazin/RUN5.vectorsodn_27
>
>
>
> compute-3-32.local
> 1768 /scratch/mazin/RUN5.vectorup_4
> 1744 /scratch/mazin/RUN5.vectorup_35
> 1768 /scratch/mazin/RUN5.vectordn_4
> 1800 /scratch/mazin/RUN5.vectordn_29
> 6960 /scratch/mazin/RUN5.vectorsoup_4
> 6960 /scratch/mazin/RUN5.vectorsodn_4
> 0 /scratch/mazin/RUN5.vectorup_29
> 0 /scratch/mazin/RUN5.vectorsoup_29
> 0 /scratch/mazin/RUN5.vectorsodn_29
>
>
>
> compute-3-25.local
> 1792 /scratch/mazin/RUN5.vectorup_11
> 1744 /scratch/mazin/RUN5.vectorup_36
> 1792 /scratch/mazin/RUN5.vectordn_11
> 1744 /scratch/mazin/RUN5.vectordn_36
> 7056 /scratch/mazin/RUN5.vectorsoup_11
> 7056 /scratch/mazin/RUN5.vectorsodn_11
> 6860 /scratch/mazin/RUN5.vectorsoup_36
> 6860 /scratch/mazin/RUN5.vectorsodn_36
>
>
>
>
>
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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.at WWW: http://info.tuwien.ac.at/theochem/
--------------------------------------------------------------------------
--__--__--
Message: 2
Date: Thu, 25 Nov 2004 14:54:03 +0900
From: "WANG Yuan Xu"
To: "wien"
Subject: [Wien] optic under parallel
Reply-To: wien at zeus.theochem.tuwien.ac.at
Dear all,
When i exec "x optic -p", the error informaion is "host: name hello not found", while other command such as "x lapw1 -p" is OK.
Who can tell me reason?
Best
WANG Yuan Xu
National Institute for Materials Science
Computational Materials Science Center
Namiki 1-1, Tsukuba 305-0044, Japan
Phone +81-29-8513354-8092; Fax +81-29-8541207
wang.yuanxu at nims.go.jp
2004-11-25
--__--__--
Message: 3
Date: Thu, 25 Nov 2004 01:19:37 -0800 (PST)
From: Chukwuemeka Okoye
To: wien at zeus.theochem.tuwien.ac.at
Subject: [Wien] Optical properties
Reply-To: wien at zeus.theochem.tuwien.ac.at
--0-1177979422-1101374377=:77683
Content-Type: text/plain; charset=us-ascii
Dear wien users,
I am calculating the optical conductivity of bcc iron and found that the absorptive part is not always positive. This means that a plot of Re_sigma_xx Re_sigma_yy Re_sigma_zz using file fe.absorpup has a negative part between 2.7eV and about 14.0eV. I think this is strange. This is because the mathematical _expression (per spin) for Re_sigma_xx etc. makes it impossible for it to be negative.
Thanks.
C M I Okoye
Chukwuemeka M I Okoye
Department of Physics and Astronomy,
University of Nigeria,Nsukka,
Enugu State, Nigeria.
+2348045257257
+234 42 771611
--0-1177979422-1101374377=:77683
Content-Type: text/html; charset=us-ascii
Dear wien users,
I am calculating the optical conductivity of bcc iron and found that the absorptive part is not always positive. This means that a plot of Re_sigma_xx Re_sigma_yy Re_sigma_zz using file fe.absorpup has a negative part between 2.7eV and about 14.0eV. I think this is strange. This is because the mathematical _expression (per spin) for Re_sigma_xx etc. makes it impossible for it to be negative.
Thanks.
C M I Okoye
Chukwuemeka M I Okoye
Department of Physics and Astronomy,
University of Nigeria,Nsukka,
Enugu State, Nigeria.
+2348045257257
+234 42 771611
--0-1177979422-1101374377=:77683--
--__--__--
Message: 4
Date: Thu, 25 Nov 2004 06:28:19 -0800 (PST)
From: stargmoon
Subject: RE: [Wien] Partial charges inside atomic spheres
To: wien at zeus.theochem.tuwien.ac.at
Reply-To: wien at zeus.theochem.tuwien.ac.at
--0-8406118-1101392899=:53811
Content-Type: text/plain; charset=us-ascii
Thanks a lot, Kevin.
Best,
Stargmoon
Jorissen Kevin wrote:
To your second question :
charge transfer observed in calculations is always a lot smaller (easily a factor of 10, say) than the formal valence would suggest.
Also, there are many ways to define the charge of an atom (and none of them is 'right', since atoms don't exist anyway ...), so one must be very careful when interpreting the numbers.
I would do the calculation not only for the particular compound that interests me, but also for similar compounds of which the valence is 'well established' (ie, something with CU2+ and something with Cu4+), and then compare the numbers - it is safer to interpret tendencies than numbers.
It is then still up to you to decide in what way you are going to measure charges - muffin tin integration? Bader? Mulliken? RA? Stockholder? ...
I personally like the concept of Bader charges, but not everyone agrees.
Kevin Jorissen
EMAT - Electron Microscopy for Materials Science (http://webhost.ua.ac.be/emat/)
Dept. of Physics
UA - Universiteit Antwerpen
Groenenborgerlaan 171
B-2020 Antwerpen
Belgium
tel +32 3 2653249
fax + 32 3 2653257
e-mail kevin.jorissen at ua.ac.be
________________________________
Van: wien-admin at zeus.theochem.tuwien.ac.at namens stargmoon
Verzonden: wo 24-11-2004 17:56
Aan: wien at zeus.theochem.tuwien.ac.at
Onderwerp: [Wien] Partial charges inside atomic spheres
Dear Prof. Blaha and wien community,
To Prof. Blaha: In your paper Phys. Rev. B vol 67, p075102 (2003), table 1 shows the partial charges for one spin direction calculated inside the atomic spheres. I don't understand why the Cu s charges are larger than 1, and Cu p charges are larger than 3. Is this contradictive to Pauli repulsion principle? If not, what do the partial charges inside the atomic spheres stand for?
To wien community: Can we estimate the valence state of each atom in an ionic compound from first-principles calculations? For example, in the case of La2CuO4, if we just consider the neutral condition, we have two possible choices assuming oxygen takes its normal ionic state O2-:
1, La takes its 2+ valence state, Cu takes its 4+
2, La takes its 3+ valence state, Cu takes its 2+
Can we determine which one is the most possible choice from our ab inito calculations?
Looking forward to your reply.
Thanks in advance!
Best,
Stargmoon
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Thanks a lot, Kevin.
Best,
Stargmoon
Jorissen Kevin <Kevin.Jorissen at ua.ac.be> wrote:
To your second question :
charge transfer observed in calculations is always a lot smaller (easily a factor of 10, say) than the formal valence would suggest.
Also, there are many ways to define the charge of an atom (and none of them is 'right', since atoms don't exist anyway ...), so one must be very careful when interpreting the numbers.
I would do the calculation not only for the particular compound that interests me, but also for similar compounds of which the valence is 'well established' (ie, something with CU2+ and something with Cu4+), and then compare the numbers - it is safer to interpret tendencies than numbers.
It is then still up to you to decide in what way you are going to measure charges - muffin tin integration? Bader? Mulliken? RA? Stockholder? ...
I personally like the concept of Bader charges, but not everyone agrees.
>Kevin
Jorissen
EMAT - Electron Microscopy for Materials Science (http://webhost.ua.ac.be/emat/)
Dept. of Physics
UA - Universiteit Antwerpen
Groenenborgerlaan 171
B-2020 Antwerpen
Belgium
tel +32 3 2653249
fax + 32 3 2653257
e-mail kevin.jorissen at ua.ac.be
________________________________
Van: wien-admin at zeus.theochem.tuwien.ac.at namens stargmoon
Verzonden: wo 24-11-2004 17:56
Aan: wien at zeus.theochem.tuwien.ac.at
Onderwerp: [Wien] Partial charges inside atomic spheres
Dear Prof. Blaha and wien community,
To Prof. Blaha: In your paper Phys. Rev. B vol 67, p075102 (2003), table 1 shows the partial charges for one spin direction calculated inside the atomic spheres. I don't understand why the Cu s charges are larger than 1, and Cu p charges are larger than 3. Is this contradictive to Pauli repulsion principle? If not, what do the partial charges inside the atomic spheres stand for?
To wien com!
munity:
Can we estimate the valence state of each atom in an ionic compound from first-principles calculations? For example, in the case of La2CuO4, if we just consider the neutral condition, we have two possible choices assuming oxygen takes its normal ionic state O2-:
1, La takes its 2+ valence state, Cu takes its 4+
2, La takes its 3+ valence state, Cu takes its 2+
Can we determine which one is the most possible choice from our ab inito calculations?
Looking forward to your reply.
Thanks in advance!
Best,
Stargmoon
________________________________
Do you Yahoo!?
The all-new My Yahoo! - Get yours free!
> ATTACHMENT part 2 application/ms-tnef name=winmail.dat
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From: Fred Nastos
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