21 June 2012

198. Nwchem -- freeze core and tddft on benzene

UPDATE: it's taken a while, but I've tested this on a large polyoxometalate cluster (>10 group 5/6 atoms and >30 oxygens) -- with a total of ca 700 alpha and beta orbitals, respectively, I froze 200 core orbs and used 3-21G/3-21G* w/ ub3lyp. The frozen core calculation took 44% of the time the full calculation took. The spectra look identical to within 3 nm (18 roots -- only 2 intermediate transitions have been shifted. All other transitions are identical). The full calc took 7 days and 4 hours, while the frozen calc took 3 days and 4 hours. 

Original post:
Benzene has 21 occupied α and 21 occupied β orbitals.

How many core orbitals can we freeze when looking at electronic transitions, how does freezing core orbitals affect the energies, and what are the performance gains, if any?

I used the following relevant statements
tddft
    cis
    freeze core X
    nroots 24
end
task tddft energy
Also, xc b3lyp and 6-31++g**.

Freeze core 10 means freeze 10 α and freeze 10 β orbitals.

Results:

Frozen Runtime    Transitions with f>0
0          1111 s     6.7835, 6.8038, 6.8042, 7.3479, 7.3496
5          1107 s     6.7835, 6.8038, 6.8042, 7.3480, 7.3498
10        1063 s     6.7838, 6.8040, 6.8045, 7.3761, 7.3862
15        1063 s     6.5878, 6.7840, 6.8042, 6.8046
20          719 s     6.8038, 6.8355, 7.1692, 7.5334, 8.1866

Evaluation:
We're not really looking at what's right or wrong -- the main goal is to understand how the results are affected (we might accidentally get 'right' answer doing something stupid). Freezing more than 10 α/β orbitals leads to significant differences in predicted transitions.

Taking oscillation strength into account and plotting it, we see that we really don't want to overdo it with the number of frozen cores -- 15 and 20 frozen cores yield results that are about as predictable as a coin toss. We also don't see any overwhelming performance gains, but that may well be due to the size and computational cost (or lack thereof) of the system.



Octave code:
spec1=load('bz631gppdd_cosmo.dat');
spec2=load('bz631gppdd_cosmo_f5.dat');
spec3=load('bz631gppdd_cosmo_f10.dat');
spec4=load('bz631gppdd_cosmo_f15.dat');
spec5=load('bz631gppdd_cosmo_f20.dat');

gau= @(x,c,w,i) i*(1/(w*sqrt(2*pi))).*exp(-0.5.*((x-c)./w).^2);
x=linspace(160,200,200);
y1=cumsum(gau(x,1241.25./spec1(:,2),4,spec1(:,3)));
y2=cumsum(gau(x,1241.25./spec2(:,2),4,spec2(:,3)));
y3=cumsum(gau(x,1241.25./spec3(:,2),4,spec3(:,3)));
y4=cumsum(gau(x,1241.25./spec4(:,2),4,spec4(:,3)));
y5=cumsum(gau(x,1241.25./spec5(:,2),4,spec5(:,3)));


subplot(3,2,1)
 plot(x,y1(rows(y1),:))
 axis([160 200 0 0.2]);
 title('0 frozen');
 subplot(3,2,3)
 plot(x,y2(rows(y2),:))
 axis([160 200 0 0.2]);
 title('5 frozen');
 subplot(3,2,5)
 plot(x,y3(rows(y3),:))
 axis([160 200 0 0.2]);
 title('10 frozen');
 subplot(3,2,2)
 plot(x,y4(rows(y4),:))
 axis([160 200 0 0.2]);
 title('15 frozen');
 subplot(3,2,4)
 plot(x,y5(rows(y5),:))
 axis([160 200 0 0.2]);
 title('20 frozen');
 subplot(3,2,6)
  plot(x,y1(rows(y1),:),x,y2(rows(y2),:), x, y3(rows(y3),:), x,y4(rows(y4),:),x,y5(rows(y5),:))
  axis([160 200 0 0.2]);
 title('');

197. Post-mortem of the Moe Quake

The news keep on reporting about a single injured person who was unlucky enough to be standing on a ladder close to the epicentre, but beyond that it seems like no-one else suffered any injuries serious enough to warrant medical attention.

Property damages are a different story though, but the news are having a field day with it, so no point in me repeating what they are saying. My only comment is that the Gippsland/La Trobe Valley area has been hit hard lately, first by floods, storms and now an earthquake -- in addition to recent job losses and uncertainties.

Anyway, science.

www.ga.gov.au has a nice page with technical information about the earthquake:
http://www.ga.gov.au/earthquakes/getQuakeDetails.do?quakeId=3226344

There are several seismograms available from different stations around the country (am I the only chemist who looks at them wanting to apply a FFT?)

Victoria


ACT

Northern QLD

The shape varies with the distance from the earthquake, which I guess tallies with different types of waves travelling at different speeds.

For those of us who are reasonably new to this area, the USGS has a historical earthquake map over Melbourne and the Gippsland/La Trobe valley area.

Here's seismicity in Australia as a whole, and it shows that SE Victoria is no stranger to phenomenon:

http://www.quakes.uq.edu.au/html/quake_info/OZ_QLD_info.html#6

Big earthquakes are a different matter though: http://earthquake.usgs.gov/earthquakes/world/australia/seismicity.php

Only a handful of earthquakes show up on this map, and they are  in WA and NT.

Here's a map with the number of large earthquakes per year (5 and above) -- and Melbourne is by no means the worst hit by the Top 5 cities in Australia
http://earthquake.usgs.gov/earthquakes/world/australia/density.php

Finally, here's a map with the 'earthquake hazard' estimates for different regions of Australia:
http://earthquake.usgs.gov/earthquakes/world/australia/gshap.php

It seems like SE Tassie is the safest, inhabited area. SW WA is the least safe one, but is still nothing compared to PNG and Indonesia and other countries on plate boundaries.

Here's a full paper on seismic hazards in Australia, which contains a nice map with past earthquakes indicated on it: http://www.sciencedirect.com/science/article/pii/S0040195104002185
I'm loading the picture from the publisher's website which is probably the lesser of two evils.

19 June 2012

196. M 5.5 Earthquake near Moe, Victoria. Felt in Melbourne, Australia, 19 June 2012

[20th of July 2012 earthquake here: http://verahill.blogspot.com.au/2012/07/another-earthquake-felt-in-melbourne.html ]

Just (ca 20:50/8.50 pm) experienced my first earthquake (South-eastern suburbs)  -- or rather earth tremor. Rattling doors, a bit of noise, a bit of shaking. Felt like about 10-15 s. More exciting than scary, although I would NOT have wanted to be any closer to the epicentre than we already were (100 km).

Funny it should happen in Australia after five years in California without the slightest tremor.

I like the possum comment below -- was my first thought too! The second one was wind.

If you felt it, you can report it here http://earthquake.usgs.gov/earthquakes/eventpage/usb000ajek#dyfi
There is a point in reporting your experience, since earthquakes aren't just reported in terms of the energy released, but also in terms of damage (or perception).

Update 22:02: http://www.seis.com.au/ is slowly coming back online, but there's no obvious information up yet.

http://www.seis.com.au/ and http://www.ga.gov.au/earthquakes/ went down immediately, and the ga.gov.au site is still down. www.seis.com.au is operating slowly.

Update 21:52. ABC 24 is covering it right now. Quake happened 7 minutes to 9 with the epicentre over by Trafalgar near Moe. No serious injuries. Upgraded to M 5.5.

Update 21:30
The news sites are catching up:
http://www.abc.net.au/news/2012-06-19/magnitude-52-quake-shakes-southern-vic/4080446

http://news.smh.com.au/breaking-news-national/melbourne-hit-by-earthquake-20120619-20m8d.html

http://www.heraldsun.com.au/news/more-news/strong-tremors-rock-victoria/story-fn7x8me2-1226401623358

http://www.theage.com.au/victoria/quake-shakes-melbourne-20120619-20m88.html

Update 21.27: ABC 24 just confirmed it. M 5.2. Moe was the epicentre.

Update 21.10: It's on the USGS website: http://earthquake.usgs.gov/earthquakes/eventpage/usb000ajek#summary




Apparently it was a Magnitude 5.2 centerd somewhere out in Gippsland. Best guess at time is 20:53:29.
The magnitude will likely be adjusted once local data is available.

Postscript:
I posted since the seismology sites were down and there was nothing on the news. Apparently I wasn't the only one who was looking for information: