Saturday, March 20, 2010

Point Reyes

I will be headed to Point Reyes tomorrow.  There is an incredible assortment of geology there.  I'll be sure to look for as many sedimentary structures as I can find.  I will have my G11, which should allow for some excellent photographic detail.

The annotated Kolob Canyon photo will have to wait a little longer...

In other news, I am taking Basin Analysis this Spring quarter.  In addition to that, I'll be learning about environmental applications in GIS, Non-Renewable Resources (lecture-based inorganic chemistry in disguise), and paleoclimatology.  Should be a very nice multidisciplinary quarter.

Saturday, March 13, 2010

Useful Software for Geology Majors

If you're studying geology and are a computer geek, I have some ideas that you may not have thought of. But knowing how resourceful most computer geeks are, I am sure you have found similar things.

OSXStereonet can take input planes and lines (e.g., strike/dip, trend/plunge) and take care of important calculations often made on a stereonet.  It can do a cylindrical and conical best-fit, find poles to all planes, generate Kamb contours, and much more.  This software is a must for all geology majors and professionals.  OS X only.


Mendeley is not open source, but it does use a few open sourced libraries such as QT.  But that isn't important.  What is important is that it helps you manage journal articles for writing research papers in a very natural way. It automatically extracts metadata from downloaded PDFs and fills in the bibliographic details.  If the software thinks it doesn't have everything, it'll prompt you.  But best of all, it has a built in PDF reader that allows for highlighting and note taking... plus those same PDFs can be uploaded to Mendeley servers for syncing with other computers!  Or, share your bibliography using the Mendeley website.  It can also create a customizable organized directory tree of all the papers you have loaded into it.  I use it to categorize articles, take notes,  and export references to BibTex.  Others may want to use it to cite while you write in documents.  What is key with this software is that it does not get in my way!  With software like this, who needs Dark Age software like EndNote or an amazingly cluttered desktop? For OSX, Windows, and Linux.


Anki replace Mnemosyne as my favored flashcard software.  Mnemosyne has not seen a release in over a year.

Anki is open source software  and is flash card program that uses algorithms that prevents wasting time on cards you know. It schedules cards based your rankings.  It allows you to use LaTeX and paste in arbitrary raster images from the clipboard.  Must have for those that need to memorize material.  It is cross-platform.


Mnemosyne lets you modify the LaTeX preamble. So you can add packages which can make inputing cards much faster. I use the package mhchem. It typesets chemical equations or formulas using input that is very natural for most people familiar with chemistry. It aligns numbers in equations very nicely. Get it and typeset your flashcards using that package. Its documentation is a very easy read.


LaTeXiT is for MacOSX. What better way to put your favorite TeX formulas into most any other OSX software. It is really fantastic. Double joy when you find that Grapher that comes with OSX can give LaTeX formatting for formulas that you used to generate graphs! Of course GNUPlot is probably necessary for your research papers. If you have OSX Snow Leopard, follow these instructions to compile GNUPlot.

The Periodic Table

The Periodic Table is a OSX Dashboard widget. It isn't a must have but damn is it convenient to find out very quickly ion charges and atomic mass! Now where is a good isotopes widget? ;-)

PDF-XChange Viewer

PDF-XChange Viewer is for Windows but free. Unlike Adobe Acrobat Reader (for the vast majority of PDFs I have used), but like OSX's Preview, it can do annotations. For slideshow heavy courses where the professor posts before lecture, this is a must have. It also has drawing tools and a highlighter. Be careful though as some PDF readers might get confused with abundant annotations and stack them atop each other and refuse to let you rearrange them.


Inkscape is the de-facto open source software for creating vector-based graphics.  It's for MacOS X, Windows, and Linux.  However, you need the latest XQuartz environment for MacOS X for it to run.  If you need to redraft infinitely scalable sketches from your field book, look no further.  But if you can afford Adobe Illustrated, or your department has it on their lab computers, I suppose you might be better off.  But at least, with this, you can work on diagram-based assignments at home.  Inkscape can also be a terrific way to create forms for use in the field.  It export to PDF.

Adobe Illustrator
This software needs no introduction.  If you're having problems with Inkscape, picking up an academic license of Illustrator might be a worthwhile solution.  Illustrator is great for finishing off maps exported from ArcGIS.  It can also help you draw various things handy to structural geology such as balanced cross sections and strain ellipses.


On OSX v10.4 and greater, use rsync -aE /Volume/thumbdrive /Users/username/somebackuplocation regularly to backup your thumbdrives without copying data that has not changed. -E might not be useful copying off a FAT32 thumbdrive but it is there in case OSX can actually use those file attribute data on the HFS+ side. Definitely use it if you're backing up to a HFS+ external drive or vice versa. -a is archive mode which sets a bunch of flags that ensures you get a quality backup.  But, timemachine is rather nice, too.  It's really an overglorified, but awesome, rsync :-)


Synctoy is software for Windows.  It is an easy to use method to sync files between disks, flash drives, networks, and so on.  If you operate Windows, and maintain files on a fallible flash drive, you better keep backups on your other computers.  Synctoy makes backups faster by only copying files that are new or have been updated.

Friday, March 5, 2010

Zions National Park, Part 1

In June of 2004, I visited Zions National Park in southern Utah.  I took an incredible number of photographs, but at the time I did not know much about geology.  Thus features that now look obvious to me were not features at all.

As I look through my photos, I can spot faint sedimentary structures.  My camera at the time was 3.1 megapixels.  It certainly could not resolve fine details from afar; and that's all I have!

This first image has what appears to be planar laminations at the base of the formation.  I believe that I can discern some cross stratification above that.  If I had more time, I would trace them so that they are evident.  In my original photos they can be seen pretty easily but for personal reasons I prefer not distributing my master copies.

In the second image, I can barely make out more obvious signs of cross stratification at center left by the dark linear feature.  They're dipping to the right, so one might say that water was flowing in that direction.

In the next post, I'll actually annotate the features on a really nice photo!  It is a closer view of photo two on this post.

Monday, March 1, 2010

Trough Cross-Stratification

This photograph was taken about a mile east of Butte Community College on the Durham-Pentz Highway.

I am the person in the photo.  Unfortunately, I am awful for  a scale due to perspective.

This is a roadcut and it clearly shows trough cross-stratification, perhaps from a stream.  The structures that clues us in are the abundance of smiley faces.  These are created as subaqueous dunes migrate and their troughs cuts off previously deposited dune peaks.

Streams have these kinds of structures at the thalweg or just above it.  The thalweg is the deepest, and often the fastest, part of a stream.  It is what develops cut banks. The fastest, outside portion of a stream's meander cuts into terraces creating a cut bank.  The interior portion of the meander develops a point bar.  If sediment were deposited above the trough cross-stratification, we might see fining upwards and current ripples.  That would indicate a pointbar.  If we could see sediment below this structure, we might see mud from overbank deposits.  That is Walther's Law: vertical succession of beds shows differences in lateral environments (providing unconformities do not exist!).

If you click on the photo, you should notice that the grain sizes are pretty apparent.  They are medium to coarse, though I lean towards coarse.  That would be an additional line of evidence that this was deposited by a stream.

I cannot say for certain which direction this stream flowed.  From this perspective it is either in or out of the photograph.  But I would hazard to guess water flows in to the photograph since the troughs seem to be dipping that way.

In summary, this is a cut-and-fill structure which represents the bottom of a stream!  Cool!

USC's SedPak

SedPak is software written by the geology department at the University of South Carolina.  So University of North Carolina has the wonderful rock and mineral texture library, and USC has SedPak.

SedPak is freely available and uses the motif graphical user interface in X11/XOrg.  It works very well on Ubuntu 9.10.  This is in stark contrast to FUZZIM, which is only available as a PowerPC binary for Mac OS9.  To my knowledge, there is no source code available for it and there is only one place to get the binary (all those GOPHER links? Very much dead).  It may forever be locked up in the confines of Mac Classic environments running within OSX (or in SheepShaver PowerPC emulator software).

At first glance, its interface is more confusing than FUZZIM.  SedPak uses a server-client interface (common in the *nix world), which can break if a database file has incorrect data.  Despite that, it looks pretty powerful and has many ways to visualize data.  For example, you can create a facies file to help describe the facies deposited in a basin.  A chronostratigraphic log can be generated, as well as sand-silt ratios.  In addition, wells can be defined, and specific portions of basin sediments can be isolated by using the sea level curve.  Carbonates can be included in models and hydrocarbon development can be tracked.

It has a GUI with many tools to *visually* design surfaces, sea level curves, temperature curves, and more.  For those that know spreadsheet-fu, data can be manually entered to create more precise environment models.  From what I understand, SedPak it uses a geometric model rather than the "fuzzy" model employed in FUZZIM.  It is blazingly fast yet seems to take into account most things that FUZZIM does.

I have much to learn about this software and the concepts that drive it.