In press, available from the Journal of Physical Chemistry A. The INS experiment was carried out using the TOSCA instrument across the pond at the ISIS facility of the Rutherford Appleton Laboratory. The solid-state calculations were performed, as usual, with DMol3 from Accelrys. The paper was presented originally at the 2005 ACS DC meeting, available in the posters page on this site. Another example of theory and vibrational spectroscopy generating a far more complete picture than crystallography alone.

D. G. Allis and B. S. Hudson

Abstract: The inelastic neutron scattering (INS) spectrum of polycrystalline Cs2[B12H12] is assigned through 1200 cm-1 based on aqueous and solid-state Raman/IR measurements and normal mode analyses from solid-state density functional theory. The Cs+ cations are responsible for frequency shifts of the internal cage vibrational modes and Ih cage mode splittings due to the crystal Th site symmetry. These changes to the [B12H12]-2 molecular modes make isolated molecule calculations inadequate for use in complete assignments. Solid-state calculations reveal that 30/40 cm-1 shifts of Tg/Hg molecular modes are responsible for structure in the INS spectrum unobserved by optical methods or in aqueous solutions.

www.isis.rl.ac.uk/molecularspectroscopy/tosca
www.isis.rl.ac.uk
www.accelrys.com

Yes, yes, I know. After all, I do work for the company. Why WOULDN’T I use the program?! The development of nanoENGINEER-1 is going tremendously well. Now on the verge of another alpha release, I decided, in the interest of seeing what kind of imagery functionality the package might benefit from, to see if I could make the old Nanotech Gallery happen with the new software.

I could not be happier with the results.

The problems to date are all with Povray. That is, my amateur understanding of it. As an order of alignment, I was doing all of my graphic work with VMD, which is still the method of choice for biomolecular images (mostly because I’m still using NAMD/Charmm for my occasional forays into drug development). It’s a tall order to replicate the quality of graphics VMD is capable of, but it’s clear (to me, anyway) that nE-1 is more than up to the challenge.

Welcoming 2006 with a bang. Or the molecular foundations for a bang, anyway. In the Journal of Physical Chemistry A (J. Phys. Chem. A 2006, 110, 1951). The experimental results were provided by TeraView, Ltd., solid-state calculations with DMol3 from Accelrys.

D. G. Allis, D. A. Prokhorova, and T. M. Korter

Abstract: The experimental solid-state terahertz (THz) spectrum (3-120 cm-1) of the beta-crystal form of the high explosive octahydro – 1,3,5,7 – tetranitro – 1,3,5,7 – tetrazocine (HMX) has been analyzed using solid-state density functional theory calculations. Various density functionals (both generalized gradient approximation and local density approximation) are compared in terms of their abilities to reproduce the experimentally observed solid-state structure and low-frequency vibrational motions. Good-to-excellent agreement between solid-state theory and experiment can be achieved in the THz region where isolated-molecule calculations fail to reproduce the observed spectral features, demonstrating a clear limitation of using isolated-molecule calculations for the assignment of THz frequency motions in molecular solids. The deficiency of isolated-molecule calculations is traced to modification of the molecular structure in the solid state through crystal packing effects and the formation of weak C-H…O hydrogen bonds.

West coast architect Mark Burginger (www.burginger.com) is a brother-in-spatial-learning, having peaked my curiosity almost a year ago with a great design for a unique building block (dare I say “toy?”). The design clicked very quickly once I saw what he was capable of building with it. I suspect formal images and designs will be made available soon on the new website for what are now known as Qubits (the artist formerly known as building block)! I’ll let him do the formal introduction, though. I expect to have some of my own designs up once the Qubits hit the market. I’m drawn to anything related to building blocks because one of the many possible pathways in advanced nanoscale engineering or intermediate molecular manufacturing is found in the design and manipulation of simple rigid subunits (which supramolecular chemistry and certain branches of materials science are currently addressing). Towards that end, anything anyone can do to improve other’s understanding of spatial relationships is excellent in my book. Molecular models in a student’s hands do far more to explain a concept like steric interactions than any diagram could.

One short year later, Mark’s won some significant awards and accolades (one notable award being from the Elwood & Stephanie Norris Foundation. In case you missed it, Woody had a pretty good run last year as well). Better still, he managed to wrap the whole Burginger clan (that’s Lisa, Garrett, Lyndsay, Hayley) into Team Qubits (“Or else!” he says…). I, of course, wish them all the best. They’ve got my vote. With luck, they’ll soon have my money, too. And don’t get me started on that “Geometric Construction Toy for Children” thing.

http://www.qubits.com

The following is a step-by-step guide to getting PC-GAMESS 6.4 (perhaps prior. I’m not inclined to check, but would appreciate a confirmation) running on a(n) SMP (that’s Symmetric MultiProcessing (useless trivia), a single motherboard with multiple processors) system. All of the websites describing what’s below are less… obvious than I would like, especially concerning the infamous .pg file for SMP machines. What’s below is specifically geared for a dual-core/dual-board (four processor) system, but is easily changed to other SMP cases.

1. Obtain the most recent (6.4 as of this posting) version of PC-GAMESS from the good Dr. Alex Granovsky.

2. After extracting the contents of the downloaded .exe file, you’ll notice the wmpi1_3.exe file. Double click to install this program, blindly saying yes to everything it asks.

3. In your c:\ directory (dig into My Computer), create the sub-directories pg1, pg2, pg3, and pg4 (note: the names are completely arbitrary). When that’s done, your folders should look like the following (PEXECUTE.BAT and PRUNGAMESS.BAT are separate batch files you can download below):

4. Into c:\pg1, place all of the extracted PC-GAMESS files (whatever came out of the .exe run). The folder should look like this (with three input files added by myself for testing):

5. Into the folders c:\pg2, c:\pg3, and c:\pg4, copy and paste (from c:\pg1) the files FASTDIAG.DLL, PCGP2P.DLL, and PGAMESS.EXE. These directories will look like the following:

6. Back in c:\pg1, create or place pgamess.pg, the wmpi config file you can download HERE (if you download, remove the .txt extension before use). The file is, simply,

local 0
localhost 1 c:\pg2\pgamess.exe
localhost 1 c:\pg3\pgamess.exe
localhost 1 c:\pg4\pgamess.exe

No surprises, but I’ve never found the SMP .pg file listed anywhere. This file is just for SMP runs. local 0 refers to the “base” copy of PGAMESS (in c:\pg1, the PC-GAMESS home directory). The localhost 1 lines call each of the other three directories and PGAMESS.EXE for the three remaining processors (in the quad box). For a dual core or dual CPU box, you’d remove c:\pg3 and c:\pg4 and delete the third and fourth lines in pgamess.pg.

7. The command line will look like the following (note: the input file must be named “input“):

c:\pg1> PGAMESS.EXE c:\pg1 c:\pg2 c:\pg3 c:\pg4 -p4local > filename.out

All should, in theory, work without hitch. For a batch-type system (you can’t add new files, but you can run existing jobs in the same directory automatically and sequentially), download the files PEXECUTE.BAT and PRUNGAMESS.BAT and place them into c:\pg1 (make sure to remove the .txt extension before use if you download these). To run this script, simply double-click on PRUNGAMESS.BAT.

NOTE1: Of course, what’s shown is not the most efficient way to run PC-GAMESS. For maximum speed-up, you’ll want a single hard drive dedicated to EACH processor (so each temp file is being written to a different disk). Your folders c:\pg1, c:\pg2, c:\pg3, and c:\pg4 would then be c:\pg1, d:\pg2, e:\pg3, and f:\pg4.

NOTE2: A number of my calculations fail randomly with MPI memory allocation/write errors on dual core/dual cpu AMD Opteron machines running Windows XP. These errors are actually hard drive write problems and not RAM problems. You can get around this problem (errors and OK buttons will pop up) by running the calculations in-RAM (DIRSCF=.TRUE.) and ramping up the amount of used RAM (with the MEMORY= keyword).