Purely for keeping track of the content I generate on the internet, I’m reproducing the contents of a photo submission to spaceweather.com taken at Darling Hill Observatory during our November 2009 Public Viewing Session (as announced at the Syracuse Astronomical Society website HERE). The original can be found at the Spaceweather Spotter page HERE.

Image taken: Nov. 13, 2009

Location: Vesper, NY, USA

Details: The ISS made an early evening fly-by during the last official Public Viewing session for 2009 of the Syracuse Astronomical Society in Vesper, NY. The 6:36 p.m. EST fly-by made it as far as Alcor and Mizar before passing into Earth’s shadow (the Big Dipper is just entering the tree line to our North). Details: Canon SD780 IS, 15″ exposure, 400 ISO.

The original post can be found at spaceweather.com/submissions/…Damian-Allis-ISS_BigDipper_1258219906.jpg. A PDF’ed version of the page from the spaceweather.com site is stored locally for posterity HERE.

Now enjoying the benefits of dispersion-corrected solid-state density functional theory (and a proper MPICH2 implementation for infrared intensity calculations, although this now a problem for reasons to be addressed in an upcoming post) in Crystal09, three issues in recent calculations caused me to think hard enough about keyword formats and job runs that I have opted to post briefly about what to do in case google and bing are your preferred methods of manual searching.

1. How To Run Only A Single-Point Energy Calculation In Crystal06/Crystal09

This had never come up before and, by the time I needed to find an input file to see what do to, the first google search provided Civalleri’s Total Energy Calculation page that currently has broken links to .zip files. There is quite a bit about the different geometry optimization approaches in the manual, but a search for “single-point” provides no information about what to do for only single-point energy calculations.

The solution, it should be obvious after, is simply to not include the geometry optimization section in the input file. What would otherwise be the following (with arbitrary geometry optimization-like info between [COORDINATES] and [BASIS SETS]…

[COORDINATES]
OPTGEOM
TOLDEG
0.000005
TOLDEX
0.000020
END
END
[BASIS SETS]

becomes…

[COORDINATES]
[BASIS SETS]

One problem solved by simply not having any optimization parameters (again, makes sense and is now google-able).

2. Proper GRIMME Input Format For Long-Range Dispersion Contributions In Crystal09

This is another example where one’s first efforts in translating the manual into calculations may lead to considerable confusion until the proper format is finally identified (by which time you’ve run many pruned-down input tests).

GRIMME
1.05 20. 25.
1.05 20. 25. s6 (scaling factor) d (steepness) Rcut (cutoff radius)
5
1  0.14 1.001 Hydrogen Conventional Atomic number , C6 , Rvdw
6  1.75 1.452 Carbon Conventional Atomic number , C6 , Rvdw
7  1.23 1.397 Nitrogen Conventional Atomic number , C6 , Rvdw
8  0.70 1.342 Oxygen Conventional Atomic number , C6 , Rvdw
17 5.07 1.639 Chlorine Conventional Atomic number , C6 ,'Rvdw

I’m not even sure where the final ,’Rvdw comes from. Your .out file may terminate with the following error (or something similar)…

rank 7 in job 8  korterquad_51438   caused collective abort of all ranks
  exit status of rank 7: killed by signal 9

And the ERROR.peN file with any content will show the following, clearly pointing to a GRIMME-specific error…

 ERROR **** GRIMME_INPUT **** ELEMENT NOT DEFINED:           1

The problem is the additional content within the manual pages for the GRIMME keyword that require pruning (or, at least, some identifier to show what is and what is not needed). The proper GRIMME section above is properly provided in the INPUT file as…

GRIMME
1.05 20. 25.
5
1  0.14 1.001
6  1.75 1.452
7  1.23 1.397
8  0.70 1.342
17 5.07 1.639

Where (see page 88 of the Crystal09 manual)…

GRIMME <- keyword is called
1.05 20. 25. <- scaling factor, steepness, cutoff distance
5 <- number of elements in the list (not the total number of atoms)
1  0.14 1.001 <- atomic number, dispersion coefficient, van der Waals radius
...

When all is properly run, the bottom of your output file will look something like the following:

 CYC  43 ETOT(AU) -5.784662098123E+03 DETOT  1.18E-11 tst  8.17E-15 PX  6.73E-08

 == SCF ENDED - CONVERGENCE ON ENERGY      E(AU) -5.7846620981229E+03 CYCLES  43

 ENERGY EXPRESSION=HARTREE+FOCK EXCH*0.20000+(BECKE  EXCH)*0.80000+LYP    CORR

 TOTAL ENERGY(DFT)(AU)( 43) -5.7846620981229E+03 DE 1.2E-11 tester 8.2E-15
 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT EDFT        TELAPSE     4705.82 TCPU     4651.41

 *******************************************************************************

 GRIMME DISPERSION ENERGY CORRECTION

 SCALE FACTOR (S6):     1.0500

 GRIMME DISPERSION ENERGY (AU) -1.9723347118951E-01
 TOTAL ENERGY + DISP (AU) -5.7848593315941E+03

 *******************************************************************************

The Crystal09 manual refers you to Table 1 of the Stefan Grimme paper, “Semiempirical GGA-type density functional constructed with a long-range dispersion correction” (Journal of Computational Chemistry, Volume 27, Issue 15, Pages 1787 – 1799), which I’ve put together into the proper format below. Be sure to (1) delete the elements in parentheses ( -> get rid of the (H) <- ), (2) remove those atoms you do not need, (3) be sure to change the “number of elements” number for your structure, and (4) get and reference the Grimme paper so you have the proper C6 parameters and van der Waals radii accounted for (you’ll be the right nitwit if I mis-copied something and you ran with it (although I trust my input), and you should have the reference regardless).

( H)   1   0.14 1.001
(Li)   3   1.61 0.825
(Na)  11   5.71 1.144
( K)  19  10.80 1.485
(Rb)  37  24.67 1.628

(Be)   4   1.61 1.408
(Mg)  12   5.71 1.364
(Ca)  20  10.80 1.474
(Sr)  38  24.67 1.606

( B)   5   3.13 1.485
(Al)  13  10.79 1.639
(Ga)  31  16.99 1.650
(In)  49  37.32 1.672

( C)   6   1.75 1.452
(Si)  14   9.23 1.716
(Ge)  32  17.10 1.727
(Sn)  50  38.71 1.804

( N)   7   1.23 1.397
( P)  15   7.84 1.705
(As)  33  16.37 1.760
(Sb)  51  38.44 1.881

( O)   8   0.70 1.342
( S)  16   5.57 1.683
(Se)  34  12.64 1.771
(Te)  52  31.74 1.892

( F)   9   0.75 1.287
(Cl)  17   5.07 1.639
(Br)  35  12.47 1.749
( I)  53  31.50 1.892

(He)   2   0.08 1.012
(Ne)  10   0.63 1.243
(Ar)  18   4.61 1.595
(Kr)  36  12.01 1.727
(Xe)  54  29.99 1.881
Y-Cd      24.67 1.639
Sc-Zn     10.80 1.562

Note that the d-block is identical for each row (so no atom numbers provided).

3. Removing The MPICH2 Content From The Output File In Pcrystal(/09)

This final issue does not occur in Pcrystal(/06) but does in Pcrystal(/09), with the reason being (I assume) the new use of MPICH2 in Pcrystal(/09) instead of MPICH in Pcrystal(/06).  The problem comes from running the following set of commands at the terminal window in MPICH2:

mpiexec -machinefile machine -np N /path/to/Pcrystal &>FILENAME.out &

Embedded within the FILENAME.out file will be all flavors of MPI-specific output, perhaps such as the following (in this case errors, but it happens in proper output as well):

application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
application called MPI_Abort(MPI_COMM_WORLD, 1) - process 7
rank 7 in job 9  korterquad_51438   caused collective abort of all ranks
 exit status of rank 7: return code 1
rank 4 in job 9  korterquad_51438   caused collective abort of all ranks
 exit status of rank 4: killed by signal 9

or…

mpiexec_machine (handle_stdin_input 1089): stdin problem; if pgm is run in background...
mpiexec_machine (handle_stdin_input 1090):     e.g.: mpiexec -n 4 a.out < /dev/null &

The solution is to break up the mpiexec output from the Pcrystal output, performed by directing the mpiexec-specific content to, in this case, /dev/null (because it is not necessary except for diagnostic purposes).

mpiexec -machinefile machine -np N /path/to/Pcrystal < /dev/null &>FILENAME.out &

Which removes all traces of mpi-specific output from FILENAME.out.

As first appeared in the May 2010 edition of the Syracuse Astronomical Society newsletter The Astronomical Chronicle (PDF).

Constellation Map generated with Starry Night Pro 6.

It is only fitting that, as we approach Summer and the unbelievable wealth of binocular and telescope objects that reside within the central region of the Milky Way, we spend at least one article on an otherwise mundane (to the amateur astronomer, anyway) Constellation. We endeavor this act of balance in the presentation of night sky viewing (and in the interest of accounting for all of the sky by the time these articles are done) by featuring Libra, The Scales.

The history of Libra in Western culture is one of science, religion, theft, imminent domain, here-say, and whatever existed as copyright in the Roman days (it is tough to make a Constellation associated with the Law interesting enough for prime time TV, as the only thing there is to murder is the presentation of any historical interpretation attributed to it). The reference to this collection of stars as a balance is reported to go as far back as the Sumerians (approximately 2000 B.C.), where this collection was known as “ZIBBA AN-NA”, or the “balance of heaven.” It is of particularly humorous irony this month that the Greeks were responsible for the disappearance of “the balance” from the night sky in favor of over-inflating the magnitude of the already important constellation Scorpius (for historical perspective, this article is being written as Greek economic infrastructure is falling apart faster than the Parthenon during the Siege of Athens in 1687 by Francesco Morosini, the Doge of Venice [as a good Greek, I shake my fist at the Gods in anger]).

The Romans saw fit to either return to the Sumerian tradition or simply declaw Scorpius, as Libra once again became a set of Scales. It is fate that the pinchers of an arthropod would be returned to the type of covering for reptiles. With the first publications of Libra-friendly star groupings and names upon the demotion of the now more diminutive Scorpius, one might even argue that the pen is mightier than the claws.

When not being visually accosted by rock n’ roll advertisements for lawyers behind cheap bookcase backdrops offering beaucoup bucks for your injury settlements, the legal profession often seems quite dull and arcane in its own right (sorry, Ray). Libra is equally subdued in its presentation, offering no Messier Objects within its official borders and no other really “interesting” things observable through binoculars or small telescopes. Perhaps the most interesting aspect about the constellation itself is its identification as the only inanimate object of the Zodiac, the ring of Constellations that encompass the ecliptic, or the apparent path of the Sun throughout the year.

That is not, however, to say that there isn’t anything worth its weight in hydrogen residing within the Libra boundaries. If we perform a considerable zooming in just above Zubeneschamali (phew! That translates to the “northern claw,” just as its counterpart Zubenelgenubi translates to the “southern claw.” These names would indicate that Arab astronomers opted to use both Greek and Roman sources despite the obvious conflict in the star groupings), we can see (with very good scopes) the star Gliese 581 (shown below), home of one of the most populated planetary systems yet discovered (although it is important to remember that this number is only of those planets we can detect, which means those with significant gravitational influence on their stellar anchor). This is marked “1” in the opening image. To date, there are four detected stars around Gliese 581 (note that the star name is always first, followed by a letter designation), including Gliese 581 b, a Neptune-sized object with a 5.4 day orbit, c, a rocky Earth-like planet within the Gliese 581 Habitable Zone 1.5 times wider and 5 times more dense than our own, d, a planet 1/2 as massive as Uranus and still within in the Habitable Zone, and e, a planet 1.6 times as massive as Earth and the smallest yet identified. the star Gliese 581 not only represents a feat of mathematical prowess on the part of Terran researchers, but is also of specific interest because of the number of planets within its Habitable Zone, the region within which conditions are believed to be similar to our own (specifically, liquid water on the surface). Some even refer to this as the “Goldilocks Zone,” where it’s not too cold and not too hot. One might say that this region is where a proper balance of hot and cold is reached…

Gliese 581

Of all of the asterisms (groups of stars that are not designated as Constellations but that still have specific meaning. For instance, the Big Dipper is an asterism within the Constellation Ursa Major) that have jumped out at me during my binocular viewing adventures, the one marked by the “2″ is perhaps the one that most stood out to my eyes. It is one of the most perfect isosceles triangles in the nighttime sky and is reasonably clear around it such that only this shape stands out in low-power optics. When it’s out, I always look for this small golden nugget residing within the Zubeneschamali-side of the scales, tipping the balance towards the arrival of the Summer constellations Scorpius and Sagittarius, the pair that mark the inside of our own galaxy and where a disproportionate number of Messier riches abound.

As first appeared in the April 2010 edition of the Syracuse Astronomical Society newsletter The Astronomical Chronicle (PDF).

Constellation Map generated with Starry Night Pro 6.

I continue to groom the Eastern sky in this month’s Constellation presentation by spending some time conditioning you to appreciate the subtle shapeliness and glowing highlights just a short clip from last month’s subject, Canes Venatici (I will endeavor to refrain from additional dry hair humor in the rest of the article). Coma Berenices, or “Berenice’s Hair,” is an unusual constellation in many respects. It is one of the few constellations that owes its name (and history) to an actual person, is one of the constellations that was promoted from a lowly asterism, it marks the location of the North Galactic Pole, and, as one of the edge-sharing constellations with Virgo, Coma Berenices contains a plethora of Messier Objects (and is an excellent constellation to have memorized if binocular viewing is in your future and you just don’t wanna wait to find something). As has been a general theme with many of these past articles, even the most simple constellations have weaved into them a wealth of astronomical treasures.

“The lives of the priests were almost cut as short as Queen Berenice’s hair.” I have to assume this line has been told in one form or another over the course of the last few millennia as part of the discussion of this simple right angle. Queen Berenice II was the wife of King Ptolemy III Euergetes of Egypt, perhaps best known as the monarch under whom the great port city of Alexandria, home to such notable Greek mathematicians as Euclid and Pappus (you did know what I meant by a “right angle,” didn’t you?) rose to prominence. As history tells us, Ptolemy rode off to seek revenge for the death of his sister, Berenice promised the goddess Aphrodite her hair upon Ptolemy’s safe return, Aphrodite saw fit to collect on said offering, and Berenice offered her golden locks to Afro, er, pardon, Aphrodite’s temple. As if her bad hair day were not enough, the next morning found her offering gone from the temple. The court astronomer Conon of Samos offered the most logical explanation (much to the relief of the temple priests, who were close to getting a far-too-close shave of their own), one which was so convincing that it remains with us today. Aphrodite, well, washed that hair right away from those men, and sent it on its way… skyward. What we now know as Coma Berenices had, at one time (and likely for some amount of time after), been the furry end of the tail of Leo the Lion, Berenice’s close and equally blonde companion. It is believed that Come Berenices graduated from asterism (simply any collection of stars that are NOT official constellations) to constellation with the help of Tycho Brahe in his 1602 star catalogue (reinforced by Johann Bayer in his 1603 work, Uranometria).

The dwarf planet Makemake.

It is a testament to the changing times that I can mention the presence of a planetary neighbor tangled in Coma Berenices that I would not have known to mention when the new SAS newsletter began its membership cycle only two years ago. The dwarf planet Makemake (shown above from a Hubble image and provided to wikipedia by Mike Brown, its discoverer) is currently veryvery close to the south-most bright star, gamma-Com. While helping to provide a marker for one of the smallest catalogued objects in the Night Sky, Coma Berenices also marks an important location for our most important source of observables in the same Sky. The North Galactic Pole (position shown below), is the point 90 degrees above us with respect to the galactic plane (the discussion of the Galactic Coordinate System is far too, well, large to include here, so I refer you to its wikipedia entry HERE).

The North Galactic Pole

Coma Berenices hosts a single Messier Object that is not a galaxy, although, like hair, detail is based on proximity. M53 is a bino-visible (7.7 magnitude) globular cluster approximately 65,000 light years away. As is often the case, our terran view (especially in CNY) does not do this object the justice provided by our tax dollars in the form of Hubble images (shown below). Looking at the constellation image at the top of this article, you may notice a bit of a knot just to the right of Makemake. As it happens, the density of stars in this region of Coma Berenices is high enough that is does have a designation as the very open cluster Melotte 111 in the less well known “other-M” Melotte catalogue. We are far too close to it for the cluster to appear to us as something like the densely-packed Pleiades, but there may be a close-by planet to the Pleiades saying the same thing about the region around our gamma-Com!

M53

The rest of the Messier Objects in Coma Berenices are galaxies, with all but one of them bright (close-by) members of the Virgo Cluster, the gigantic collection of up-to 2000 galaxies discussed briefly in last month’s newsletter. Coma Berenices and its border with Virgo are regions that all Messier Marathoners cannot wait to have appear prominently in their early-morning March skies, as finding and checking-off these objects in your race-to-the-finish search as fast as two-in-one shampooing. The six Virgo members are (listed top-down) M85, M100, M98, M99, M88, and M91. You will note that M86, M84, M90, M89, M87, M58, M59, and M60 (phew!) are also in very close proximity in Virgo. Your problem is not finding smudge patches in your binoculars. You’re problem is finding out which one you’re looking at!

The lenticular (a morphological hybrid between elliptical and spiral galaxy shapes) galaxy M85 (NGC 4382) marks the northernmost edge of the Virgo cluster. Admittedly, the detail in the Hubble image is a bit lacking (shown below), one of the signs of an old elliptical galaxy where star formation is no longer ongoing in any significant amount). This galaxy lies 60 million light years away and is the 94th MOST distant Messier Object. With M85 centered in your Telrad, you’ll find M100 just at the edge of your outer ring.

M85

M100 (NGC 4321, shown at below-left from ESO) has a shape to it that all likely think of when they picture a galaxy in their mind’s eye. One of the most prominent members of the Virgo cluster, this “grand design spiral” galaxy is 55 million light years away and has been observed intensely enough for us to know that it hosts the satellite galaxy NGC 4323. As galaxies go, M100 is jumpin’ with supernovae, with five catalogued since 1901. Centering your Telrad on M100, M99 approaches your outer ring by about the amount that M98 and M88 sits beyond it.

M100

We see the spiral galaxy M98 (NGC 4192, shown below, from Astrofotografia) almost edge-on, making for a view similar to, but less interesting that, the Andromeda Galaxy (M31). If you’re keeping excellent track of your Doppler shifting, you’ll note that M98 is racing towards us at 125 km/sec which, at 60 million light years away, gives us plenty of time to hit the salon before its arrival.

The image of the pinwheel-looking (a name that already has the galaxy M33 associated with it) M99 (below), was taken by amateur astronomer Hunter Wilson and is currently the choice image at wikipedia for this galaxy (no small feat considering the telescope competition both on the ground AND in orbit). The slight unwinding (well, slight to our eyes, but tens of thousands of light years fit into that gap) of the right-most arm is attributed to VIRGOHI21, a region of hydrogen gas and a massive amount of presumed dark matter.

M99

The spiral galaxy M88 (NGC 4501, shown below and also by Hunter Wilson) is racing towards the center of the Virgo cluster (in the direction of M87). This galaxy is noteworthy for its very tight and very regular spiraling that falls smoothly all the way to the galaxy core, home of a supermassive black hole 80 million times the mass of the Sun.

M88

The last Messier member of the Virgo cluster in Coma Berenices is M91 (NGC 4548, shown below). Messier (in 1781) and Herschel (in 1784) both lay claim to its discovery despite the gap in timing. The linked picture for this image is as noteworthy for the soft blending of nebulosity and starry regions as for the multitude of small galaxies also contained in the field of view. Well worth a look.

M91

Finally, the outlier Messier galaxy in this region is M64 (NGC 4826, shown below), known to amateur astronomers as the Black Eye Galaxy. This view is obvious even in our telescopes! Not only is the galaxy interesting for the dark band pointed towards us, but it has become doubly-interesting recently with the discovery that the black band is spinning in the opposite direction of the rest of the galaxy, with the current hypothesis being that the black band is the remains of a companion galaxy that may have collided with the central galaxy one billion years ago. when you next see it, think of the astronomer Conon and the priests he saved from a similar fate.

M64

The cover art for the 7 May 2010 issue of the Journal of Organic Chemistry accompanies the article by (2nd semester organic chemistry professor, co-author, and 2010 American Chemical Society James Flack Norris Award in Physical Organic Chemistry recipient) John E. Baldwin and Alexey P. Kostikov entitled “On the Stereochemical Characteristic of the Thermal Reactions of Vinylcyclobutane.”

This Perspective outlines the stereochemical and mechanistic complexities inherent in the thermal reactions converting vinylcyclobutane to cyclohexene, butadiene, and ethylene. The structural isomerization and the fragmentation processes seem, at first sight, to be obvious and simple. When considered more carefully and investigated with the aid of deuterium-labeled stereochemically well-defined vinylcyclobutane derivatives there emerges a complex kinetic situation traced by 56 structure-to-structure transformations and 12 independent kinetic parameters. Experimental determinations of stereochemical details of stereomutations and [1,3] carbon sigmatropic shifts are now being pursued and will in time contribute to gaining relevant evidence casting light on the reaction dynamics involved as flexible short-lived diradical intermediates trace the paths leading from one d2-labeled vinylcyclobutane starting material to a mixture of 16 structures.

The cover image is meant to convey as much useful information as possible without any verbiage, although this is clearly not a concept meant to be crystal clear to a non-chemist (but kudos if you got the idea without my having to address it).

Included below are the four iterations involved in the cover draft, between which a considerable amount of verbal back-and-forth occurred (that is discussed briefly) to get what was intended to be presented. The iterations are provided both to show how different visions of what might be seen as the most-key of the key points change as content is presented to the client/researcher and, frankly, these all involved quite a bit of busy work and it seems a shame to not have them floating around somewhere accessible.

The original cover idea (above) was quite mundane but provided a bit more information (cryptic as it may appear to the non-mechanistic organic chemist) about what might be occurring in the absence of a brief read of the introduction of the article. This image emphasizes that a constant rearrangement occurs of the vinylcyclobutane (by the many, many arrows and the four different arrangements of deuteriums in the rearrangement) but does not address that the other 12 structures are products of reactions that are generated as the vinylcyclobutane rearranges and undergoes other but simultaneous intramolecular reactions. The absence of the connection between the rearrangement and the formation of products (which include the vinylcyclobutanes) removed this first iteration from the final running.

The second iteration (above) is a significant (well, I think so) improvement in the getting-across of the business end of the research. The vinylcyclobutane rearrangement is still central to the preferred emphasis of the cover (soon to go away) and the connection between the rearrangement and the formation of products is now hinted at directly by the use of the faded arrows. The second-tier information passed along in this image is that the vinylcyclobutane is one of the products, which is not stressed in the image (by the inclusion of four additional arrows from the central graphic (and, with that addition, the inclusion of arrows feeding the vinylcyclobutanes back into the center). If this had been an Angew. Chemie article, the circular design would have been a perfect fit.

It was at this point that a new piece of content was provided in the form of a medium-resolution digital photo of a piece of artwork by Anne Baldwin. The artwork was chosen as much for the colors as for the chaotic quality of the swirls, which was the one aspect of the entire process that the previous two images did not address and which Dr. Baldwin saw as the more significant point to convey. Some Gaussian blurring and a Gaussian basis set later, the new reactant/product combination as scrambled to complement the background and to make clear that one molecule (that at the arrow) lead to everything else in the image, including itself. The slight red halo around the deuterium (dark blue) is a result of an overlay of the blue spheres and red spheres rendered with slightly larger radii.

The arrow color and shading was stolen from Jean-Michel Folon. Example (The Cry) below. If you’ve one of the copies of La morte di un albero (mine is #630), see Comme un aimant (1971).

I admittedly prefer this (that is, the above cover idea) to the final version as the arrow indicates the forward direction of reactions and adds a hint of symmetry to an otherwise jumbled image.

As for the selected cover image (and final iteration, above), the considerable real estate taken up by the vinylcyclobutane in the previous image is recovered, which highlights the starting molecule differently and has the arrow simply angled into a less-busy space.

The final selection may make more sense in light of the image Baldwin chose to use for the graphical abstract.

A word to the perspective cover artist – This is a point that should be obvious but is often not until it is made obvious by an editor when it is much too late. Your images should be as LARGE as possible. Each of the images above is a 200 MB Photoshop file that would print without pixilation or granularity at 600 dpi on a 24” x 36” poster.