care and feeding of graduate students (life as a professor)

As the next images demonstrate, used effectively the in-camera HDR of the Nikon D5100 works quite well.

Normal:

and HDR:

These show a high-contrast image of the Tyndale monument taken shortly before sundown. Without HDR almost no details are visible for the foreground.

A couple more fun strolls in the Cotswalds.

First the “Rock of Ages”. Apparently the rocks in Burrington Coombe (coombe is an Anglo-Saxon word for a valley) were the inspiration for a famous hymn. Pity that they’re clearly sedimentary and preserve fossils which sort of, maybe, make it clear that Adam and Eve are allegorical (at best). None the less there is a fun stroll there. We parked at the Burrington pub (a favourite for cavers) and walked up the down, then down the down.

England has, this year, been rather wet. So it was mucky.

That said, there are lots of caves, foxgloves, and a set of tumulus’s on the top.

Another longer hike is around Castle Coombe.

This path uses more roads than ideal, and even follows the old coach road for a bit. It also passes the site of a Roman Villa. Not much is visible, but we did see a couple of tile fragments – so the villa was there.

Linux KVM (kernel virtual machine) is now part of the current kernel – including Ubuntu. One of the classes I teach involves computer security and it is always hard for the students to have their own “root” or “administrator” machine. There is no way on this earth that I will let them use mine – because I want the machine to still work.

So I’m investigating QEMU/KVM. I followed the instructions from http://qemu-buch.de/cgi-bin/moin.cgi/QuickStartGuide, which seem to be quite good. On a quad core AMD machine, I’ve been able to create images for windows XP sp2, and windows 2000. I’ll shortly try windows XP sp4. I have a copy of Red Hat 2.0 – wonder if that’ll work too?

You have to create a boot disk with qemu-img and install the operating system into that. (qemu -cdrom /dev/dvd ….). The reason for this is that the QEMU virtual hardware isn’t the same as the real hardware so the drivers on disk may not work. You also can run into complications if the file system is being accessed by two operating systems at the same time without a locking mechanism. Once done you have a disk image that can be examined and modified from the Linux partition. It is a regular file so it can be created once and then copied for each new experiment. So we could move beyond simple virus-like constructions to real viruses in a controlled environment. (windows viruses do not, in general, infect linux). I could even demonstrate the killer double fork script on a linux machine with some chance of not actually harming the original hardware.

It seems to fit the bill on a single machine. Our computer lab is already somewhat virtual in that the individual workstations are virtual images so there may be complications. I doubt they are insoluble. In any case it will work on the instructor’s workstation which is not virtual

A couple more notes:

1. Create the disk images with the raw mode if you want to examine them. Qcow2 is QEMU specific. Qcow2 is better for general use as you can resize it.
2. Make sure virtualization is enabled on your hardware. (kvm-ok, run as system will tell you)
3. Big raw images can be difficult to move. There are ways to mount qcow2 images in loopback mode.
4. windows 95 seems difficult. I’ve installed Dos622 from a boot image (copy the files to c:, then use sys c: to make it bootable). Windows gets about half-way through starting up then crashes. ARGH!

I left my GPS at my brother in laws. Hence the hand drawn maps.

1. Day 1
   
   

   Walk up Kinder Scout

   Approximately 12-13 miles (shoelace estimate). We started in the morning, ate lunch at Kinder falls and then dinner at the Sportsman’s pub. (Either it or the George are probably the best in town). Exhausted the teenagers.

2. Day 2
   

   Lantern Pike

   
   It rained most of the day – so we only had time for a short walk, 3-4 miles. Out the Seth Vally walk and up the hill. There is an unmarked stub that takes you up to the top. There is a monument to one of the founders of open trail access on the top.
3. Day 3
   

   Seth Valley Trail

   
   This is a good one for a rainy day. Walked to New Mills, then along the millennium bridge, up past the train station to the visitors centre. The millennium bridge is along the train embankment and quite impressive. There is an Archimedes Screw used to generate power nearby, which generates about 60KW of power as well as allows the trout and salmon to migrate. The visitor’s centre is well worth the visit (toilets, information and food – as well as friendly directions). Walked up to the post office which is next to a Sainsbury express. Picked up some cider and beer (to slow me down). About 6 miles total.
4. Day 4
   
   

   Hill to the south

   
   8 miles. Good practice walk for the next day. Beautiful views. We had hoped to find a pub/sit down place for food in New Mills for a snack, but missed them.
5. Day 5
   

   Walk to Edale

   
   12-13 miles. Walked up over the Edale pass then along by the southern edge of Kinder scout. This trail is a bit harder than it looks. It took about an hour to get to the pass, then 2 hours to do the same distance on the flat and downhill. The downhill was cute, a nice trail goes to the edge of what appears to be a cliff and then the trail goes down it. Stopped for lunch at the “Old Nags Head Pub”. Then headed to the train station. Unfortunately the trains are every 2 hours. (We’d planned to travel by train to New Mills and walk back from that). So we decided to follow the Pennine way back to Edale pass and then Hayfield. Jacob’s ladder was on the way and turned out to be a non-event. (steep but easy). Picked up fish and chips at the Village Chippy on the way back and a passable bottle of English wine across the street at the village store.

Visiting family in the UK. Had a nice 1.92 mile after dinner stroll on part of the Cotswald way.

The rainy weather has broken for the last two days so the paths are merely muddy. We drove up to Nibley after dinner and strolled up to the Tyndale monument. Tyndale is an important figure in the reformation – he risked his life to translate the bible into English (something even the Roman Catholics now (reluctantly) accept). The path from the road is a steep but short climb up some rather slippery mud and wood steps. After climbing the tower – and getting a bit dizzy on its spiral staircase – we wandered off through the woods to find Bracken Hill fort. The loop at the end of the trail follows one of its walls. (you can just see it in the picture). It is rather overgrown and would be hard to recognize, except it is being cleared and restored.

There are two approaches to English muck in summer. 1) wear wellies and try to keep your feet dry and 2) wear sandals and just get wet. I tend to like the second of these approaches – you cannot keep the feet dry because they will sweat if nothing else, but the feet dry quickly in sandals. It is the same idea as trail runners and works well as long as you have sandals that fit and give enough support (keens work for me but your mileage may be different)

Digital SLR bodies have reached that magic point where the quality of the image is limited by the lenses and where the price, although high, is not out of reach for a non-professional. This re-opens the option of using filters and lenses in a much more controlled manner – something that even with kits like the CHDK is very difficult. It is always better to optimise and control the signal rather than to try to reconstruct from flawed data.

The next few photos show some preliminary experiments and comparisons using the in-camera HDR on a Nikon D5100 with polariser and various coloured filters.

Polariser vs. Polariser with HDR on Landscapes

The polariser on its own brings out the clouds, but compared with polariser/HDR the level of detail and drama is weak.

Using both the polariser and HDR give the best results for landscapes.

Polariser vs. Polariser with HDR when there is less contrast

This photo of a Buddleia flower shows (in the original) good detail and contrast.

HDR tends to wash out the image when it doesn’t have a lot of contrast to start with.

Getting Good Black and White Images.

Back in the day one trick to get high quality black and white images was to use a coloured filter with the film and emphasise the red/yellow colours with respect to the blues.

Something similar can be done. The D5100 will convert from colour to “monochrome” and thus produce reasonable images.

The red filter produces a bizarre image.

Converting to black and white brings out the clouds but loses the details.

The details are still lost, even when correcting for the highlights with the Gimp. (the correction is simply to adjust the histogram of density values so that it fills the whole range, the black and white generated by the camera from this image does not produce white for the brightest pixels)

Yellow preserves more colour information.

However converting from yellow to black and white leaves a lot to be desired as well. (This looks a bit like old-fashioned Infrared film)

Using HDR with a yellow filter recovers features in the sky.

These features are preserved in the black and white image.

The yellow/b&w is not quite as contrasty as the red/b&w so this is a matter of taste.

HDR with the red filter is interesting.

The HDR/Red gives good results. Especially after correcting the highlights with the Gimp

We broke out the light weight motor boat today. A riverhawk with a 5HP motor, runs all day on a couple of gallons of petrol.

I’m using this as an example to show what the paths from an etrex 20 look like with google earth:

and with FoxtrotGPS:

FoxtrotGPS is more than a little less stable than Google Earth, but shows what is available from sources other than the “sage of mountainview”.

The maps show an afternoon trip. The difficult thing on this lake is dodging the buried logs. The engine is a tohatsu 5hp, and we’ve found it runs better with 10w-40 formulated for older engines.

I’ve posted the occasional trail map on this blog. The paths were determined with a Garmin GP60csx, which is a fairly nice unit. However, it doesn’t come – in the US – with baseline maps for Europe or the UK. The maps are available, for a price, but the price is comparable to buying a new unit.

So it was time to retire the venerable old GPS and try a new one. The Etrex 20 is about 1/2 the weight (a significant savings) and uses the new Russian Glonass system as well as the US GPS satellites. This dramatically improves the accuracy as the errors in the two systems are uncorrelated – thus allowing accuracies of about 10 ft. To put this in context, the 10 year old etrex units could put you on one side of a football field or soccer pitch, the 5 year old 60csx could place you to about 15-20 meters, and this does about 3 meter precision. Not bad. The sensitivity is much improved as is the accuracy of the estimated track distances. (GPS units tend to creep up in distance due to shifts in estimated positions – so even standing still – you can add mileage).

That’s fine, but what is really exciting is that the Etrex actually can be used with linux! Not using Garmin software, mind you, and not directly, but in a really useful way none the less. When plugged into a USB port the unit acts like a mass storage device and the garmin/gpx directory contains the tracks you’ve saved. I suspect, but haven’t yet tried it, that you can put a track there as well. There are some files that contain the current position, but I’m not sure that it will update in real time.

The tracks can be read from the unit, and then displayed in a mapping program like Google Earth or FoxtrotGPS. This is amazing – now I don’t need a windows machine with my GPS!

I had a chance to look at little rock city park near Leesburg Alabama. It is a popular rock-climbing venue that is readily available from the Atlanta area.

We visited on a typical spring weekend, and had to cut short our explorations due to a thunderstorm (it is an exposed ridge after all, and I had no interest in practical electroshock).

The rocks are decidedly spectacular and it is easy to see why they are attractive for climbing. Hightower trail troop 266 has even had a few eagle projects there.

There is even a good view of Lake Weiss.

The county is “upgrading” the park. This has it’s good parts and bad parts.

They are building defined campsites, with a defined ranger station. Currently people simply camp among the rocks, which is OK sort of, but they haven’t exactly been following good leave no trace guidelines. The sites are away from the rocks and more sheltered in the event of a storm.
There will be water, toilets, and services.
There will be parking.
It will be available to more people

It also will have it’s bad sides:

There will be defined campsites and you will have to use them.
The campsites are set up for trailers.
There will be a charge to use the site.
There will be more “just campers”

I think, on average it will be a good thing. The current users, by camping among the rocks, and being less than good stewards are endangering the park. While I wouldn’t be concerned with a scout troop – since it is big enough – I might feel a little out of place with a family or small group.

There is also some hiking in the area and we followed a woods road down to a spring house foundation about 1/4 mile from the rocks. Unfortunately, we didn’t have a chance to do too much more exploring as the weather was problematic.

One of the harder things to do in computational chemistry is to model phase changes. Theoretically it is almost impossible as one needs very large scale (infinite) calculations to account for putative large-scale fluctuations. None the less it is a fun problem.

I took 1000 waters, using molecular dynamics constant volume and temperature in the AMMP program, and the tuna potential set (”tuna” refers to the name of the program used to adjust parameters to fit independent data, the potential is similar to the SPC water potential and reproduces radial distributions etc quite well). The goal is to look at pair correlation times as a function of temperature. The pair correlation time (how long two different molecules are close together) should be very long for ice and rather shorter for water.

As a start, though, I looked at the energy of the system. There were no surprises with the total energy which increased more or less linearly with temperature. However, the standard deviations were different, Since Cv, the constant volume heat capacity, is related to the standard deviation of the energy (Cv = c (sigma/T)^2 ) I rescaled the data by the absolute temperature squared and plotted that.

There is a dip around 250-275K! which is just the right place.
Estimated Cv

More detailed, with more time and more temperature values, simulations around the putative phase change are shown below.
Cv calcualted on a longer run and with more temperatures

Cv calcualted on a longer run and with more temperatures

So it looks like it might work.