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<title>Re: [Wien] Problems in phonon calculations (3)</title>
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<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Dear <st2:PersonName w:st="on"><st1:title w:st="on">Prof.</st1:title> <st1:Sn
w:st="on">Blaha</st1:Sn></st2:PersonName>, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Thank you very much for the detailed reply <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>I had taken a 48 atom supercell with Pnma as space group in the phonon
calculations<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>I had used a about 1400 k–points in the IBZ with rkmax 7.00 <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>However, I had used rkmax of 8.00 when I optimized the lattice parameters.
<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>After it took more than 40 hours to complete lapw1, I used a 12 atom
supercell and completed case_1. I need some help here. I copy here the
case_1.scf<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> TOTAL FORCE IN mRy/a.u. = |F|
Fx
Fy Fz<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> with/without FOR in case.in2<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR001: 1.ATOM
7.217 -7.180
0.732 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR002: 2.ATOM
11.249 -7.074
-8.746 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR003: 3.ATOM
7.417 7.416
0.109 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR004: 4.ATOM
6.958 6.957
0.120 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR005: 5.ATOM
14.967 14.967
0.080 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR006: 6.ATOM
14.973 14.959
0.654 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR007: 7.ATOM
14.113 -14.028
1.543 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR008: 8.ATOM
15.810 -15.749
1.386 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR009: 9.ATOM
83.030 82.549
8.927 0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR010: 10.ATOM 95.213
94.803 8.826
0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR011: 11.ATOM 88.802
-88.782 1.906
0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FOR012: 12.ATOM 88.672
-88.672 -0.236
0.000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'> TOTAL FORCE WITH RESPECT TO THE
GLOBAL COORDINATE SYSTEM:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL001: 1.ATOM
0.732000000 0.000000000 -7.180000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL002: 2.ATOM
-8.746000000 0.000000000 -7.074000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL003: 3.ATOM
0.109000000 0.000000000 7.416000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL004: 4.ATOM
0.120000000 0.000000000 6.957000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL005: 5.ATOM
0.080000000 0.000000000 14.967000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL006: 6.ATOM
0.654000000 0.000000000 14.959000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL007: 7.ATOM
1.543000000 0.000000000 -14.028000000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL008: 8.ATOM
1.386000000 0.000000000 -15.749000000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL009: 9.ATOM
8.927000000 0.000000000 82.549000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL010: 10.ATOM
8.826000000 0.000000000 94.803000000
pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL011: 11.ATOM 1.906000000
0.000000000 -88.782000000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>:FGL012: 12.ATOM
-0.236000000 0.000000000 -88.672000000 pa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>rtial forces<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>May I kindly request you to suggest on the forces. Is it ok or do I
have to change –fc 0.1 to –fc 0.01? <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Thank you <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'>Suddhasattwa<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 face="Times New Roman"><span style='font-size:
11.0pt'><o:p> </o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'>
wien-bounces@zeus.theochem.tuwien.ac.at
[mailto:wien-bounces@zeus.theochem.tuwien.ac.at] <b><span style='font-weight:
bold'>On Behalf Of </span></b><st2:PersonName w:st="on"><st1:GivenName w:st="on">Peter</st1:GivenName>
<st1:Sn w:st="on">Blaha</st1:Sn></st2:PersonName><br>
<b><span style='font-weight:bold'>Sent:</span></b> Saturday, January 08, 2011
7:18 PM<br>
<b><span style='font-weight:bold'>To:</span></b> <st2:PersonName w:st="on"><st1:GivenName
w:st="on">A</st1:GivenName> <st1:middlename w:st="on">Mailing list</st1:middlename>
<st1:middlename w:st="on">for</st1:middlename> <st1:middlename w:st="on">WIEN2k</st1:middlename>
<st1:Sn w:st="on">users</st1:Sn></st2:PersonName><br>
<b><span style='font-weight:bold'>Subject:</span></b> Re: [<st1:Sn w:st="on">Wien</st1:Sn>]
Problems in phonon calculations (3)</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p><font size=2 face="Times New Roman"><span style='font-size:10.0pt'>You need
to understand what you are doing:<br>
<br>
I guess you submit your job in a directory AB2_phonon.<br>
<br>
The job creates a .machines file in THIS directory (look at it with some<br>
editor and verify that it looks as expected (with 24 lines)).<br>
<br>
Now understand the run_phonon job file.<br>
<br>
Inside the loop over all 18 cases it has a:<br>
<br>
cd case_$i and inside this directory it makes a run_lapw ...<br>
<br>
So change into case_1 and examine the .machines file.<br>
<br>
It will of course NOT show the 24 lines, but is some dummy-default .machines
file with just 2 lines.<br>
<br>
so before the cd case_$i insert
a line:<br>
<br>
cp .machines case_$i<br>
<br>
into the run_phonon job.<br>
<br>
<br>
PS: If your job is still running, you can also do this manually on the
commandline (for all case_1 ... case_18)<br>
and the proper .machines file will be used for all new iterations.<br>
<br>
PPS: If I look into your cpu-time (more than 40 h !! for lapw1) I doubt that
you want to wait<br>
until this job has finished (even on 24 cpus). How large is your supercell -
this determines how you can<br>
reduce the k-mesh!<br>
<br>
PPS: You should learn on small examples how to make meaningful calculations.
You must examine for<br>
YOUR system (nobody can help you here) and your properties, what a good RKMAX
or k-mesh is.<br>
In other words: caclculate phonons with a "low RKMAX and few
k-points", and increase the parameters<br>
until the frequencies did not change significantly anymore.<br>
<br>
<br>
<br>
Am 08.01.2011 07:42, schrieb <st2:PersonName w:st="on"><st1:GivenName w:st="on">Ghosh</st1:GivenName>
<st1:Sn w:st="on">SUDDHASATTWA</st1:Sn></st2:PersonName>:<br>
> Dear Wien2k users, and <st2:PersonName w:st="on"><st1:title w:st="on">Prof.</st1:title>
<st1:Sn w:st="on">Blaha</st1:Sn></st2:PersonName>,<br>
><br>
> Can you please help me out in the following querie. As suggested earlier,
I had initialized my phonon calculations with 48 atoms per lattice.<br>
><br>
> I created and initialized case_1<br>
><br>
> My phonon job file is<br>
><br>
> #!/bin/csh -f<br>
><br>
> #<br>
><br>
> set file=AB2_phonon<br>
><br>
> #<br>
><br>
> foreach i ( \<br>
><br>
> 1 \<br>
> 17 \<br>
><br>
> 18 \<br>
><br>
> )<br>
><br>
> cd case_$i<br>
><br>
> echo running case_$i<br>
><br>
> #<br>
><br>
> # select other options if necessary<br>
><br>
> run_lapw -I -i 200 -cc 0.0001 -in1ef -p -fc 0.1<br>
><br>
> #<br>
><br>
> # select other save-name if necessary<br>
><br>
> save_lapw case_${i}_gga_rkm7.00_3000k<br>
><br>
> cd ..<br>
><br>
> end<br>
><br>
> I submitted the job by qsub –pe kpoint 24 kpoint.sh<br>
><br>
> My machine file is<br>
><br>
> 1:ibnx70<br>
><br>
> 1:ibnx70<br>
><br>
> 1:ibnx70<br>
><br>
> 1:ibnx81<br>
><br>
> 1:ibnx81<br>
><br>
> 1:ibnx81<br>
><br>
> 1:ibnx81<br>
><br>
> 1:ibnx81<br>
><br>
> 1:ibnx79<br>
><br>
> 1:ibnx79<br>
><br>
> 1:ibnx79<br>
><br>
> 1:ibnx65<br>
><br>
> 1:ibnx65<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx60<br>
><br>
> 1:ibnx96<br>
><br>
> 1:ibnx96<br>
><br>
> 1:ibnx96<br>
><br>
> granularity:1<br>
><br>
> extrafine:1<br>
><br>
> For the last three days, the queuing shows the job is running<br>
><br>
> Surprisingly, there is no “running” mode in w2web.<br>
><br>
> I checked the case_1 directory<br>
><br>
> case_1.dayfile shows (surprisingly)<br>
><br>
> Calculating case_1 in
/group5/cg/sghosh/WIEN2k/lapw/phonon/UZr2_phonon/case_1<br>
><br>
> on nx70.igcar.gov.in with PID 10356<br>
><br>
> start (Thu Jan 6 19:11:06 IST 2011) with lapw0 (-in1ef/99 to go)<br>
><br>
> cycle 1 (Thu Jan 6 19:11:06 IST 2011) (-in1ef/99 to go)<br>
><br>
>> lapw0 -p (19:11:06) starting parallel lapw0 at Thu Jan 6
19:11:06 IST 20<br>
><br>
> 11<br>
><br>
> -------- .machine0 : processors<br>
><br>
> running lapw0 in single mode<br>
><br>
> 177.410u 5.691s 3:11.36 95.6% 0+0k 0+0io 17pf+0w<br>
><br>
>> lapw1 -c -p (19:14:17) starting parallel lapw1 at Thu Jan 6
19:14:1<br>
><br>
> 8 IST 2011<br>
><br>
> -> starting parallel LAPW1 jobs at Thu Jan 6 19:14:19 IST 2011<br>
><br>
> running LAPW1 in parallel mode (using .machines)<br>
><br>
> 2 number_of_parallel_jobs<br>
><br>
> localhost(672) 90833.210u 359.642s 1+01:28:03.65 99.46% 0+0k 0+0io 0pf<br>
><br>
> +0w<br>
><br>
> 105493.144u 437.929s 1+13:49:58.03 77.78% 0+0k 0+0io 0pf+0w<br>
><br>
> 120959.238u 433.725s 1+09:50:20.14 99.65% 0+0k 0+0io 0pf+0w<br>
><br>
> localhost(672) 90579.555u 334.655s 1+01:22:25.95 99.53% 0+0k 0+0io 0pf<br>
><br>
> +0w<br>
><br>
> 105170.999u 500.369s 1+13:44:24.32 77.78% 0+0k 0+0io 0pf+0w<br>
><br>
> 120363.259u 426.543s 1+09:40:41.44 99.63% 0+0k 0+0io 0pf+0w<br>
><br>
> Summary of lapw1para:<br>
><br>
> localhost k=1344 user=181413 wallclock=170<br>
><br>
> 73.491u 124.896s 33:50:25.33 0.1% 0+0k 0+0io 0pf+0w<br>
><br>
>> lapw2 -c -p (05:04:43) running LAPW2 in parallel mode<br>
><br>
> [1] 4250<br>
><br>
> [2] 4292<br>
><br>
> That is 2 number of parallel jobs. I thought it should be 24<br>
><br>
> Can you please why is this happening?<br>
><br>
> Thank you<br>
><br>
> Suddhasattwa<br>
><br>
> SUDDHASATTWAGHOSH<br>
><br>
> Scientific Officer (D)<br>
><br>
> Pyrochemical Process Studies Section<br>
><br>
> Fuel Chemistry Division<br>
><br>
> Chemistry Group<br>
><br>
> IndiraGandhi Centre for Atomic Research<br>
><br>
> Kalpakkam<br>
><br>
> Tamilnadu<br>
><br>
> 603102<br>
><br>
> <st2:country-region w:st="on"><st2:place w:st="on">India</st2:place></st2:country-region><br>
><br>
> Phone: 91-44-27480500 (Ext:24283)<br>
><br>
> Fax: 91-44-27480065<br>
><br>
><br>
><br>
> _______________________________________________<br>
> <st1:Sn w:st="on">Wien</st1:Sn> mailing list<br>
> Wien@zeus.theochem.tuwien.ac.at<br>
> <a href="http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien">http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien</a><br>
<br>
--<br>
-----------------------------------------<br>
<st2:PersonName w:st="on"><st1:GivenName w:st="on">Peter</st1:GivenName> <st1:Sn
w:st="on">Blaha</st1:Sn></st2:PersonName><br>
Inst. Materials Chemistry, TU Vienna<br>
Getreidemarkt 9, A-1060 <st2:place w:st="on"><st2:City w:st="on">Vienna</st2:City>,
<st2:country-region w:st="on">Austria</st2:country-region></st2:place><br>
Tel: +43-1-5880115671<br>
Fax: +43-1-5880115698<br>
email: pblaha@theochem.tuwien.ac.at<br>
-----------------------------------------<br>
_______________________________________________<br>
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