The parameterization of the new nanoENGINEER-1 simulator is being performed for molecules containing H through Cl at the B3LYP/6-31+G(d,p) level of theory. Unfortunately, the 6-31+G(d,p) basis set is not available for the 4th row elements (Ga,Ge,As,Se,Br), meaning an alternate basis set is required (for the 4th row, that is). In GAMESS-US, this is simple if the input files are in Cartesian format. This same approach cannot be used in Z-matrix input formats. A (maybe THE only) way to call mixed basis sets for Z-matrices in GAMESS-US is provided here. The procedure involves making an external basis set file with the required basis sets, changing the $BASIS control to read the external file, and modifying rungms to read the external basis set file.
Below is a sample input file. The only noteworthy differences between it and any other input file are (a) the $BASIS line, which tells GAMESS-US to use the external file (EXTFIL=.TRUE.) and (b) the call to use external basis sets named STO2GBAS. In this external file, you can have multiple groups of elements and basis sets, but not multiple basis set types for the SAME ELEMENT in the same group (so far as I know at the moment). This means that the external basis set example file I have available here has Hydrogen (H) and F (Fluorine) STO-2G (STO2GBAS) and 3-21G (321GBASI) basis set groups, but that you CANNOT call the STO2GBAS Hydrogen basis set and 321GBASI Fluorine basis set.
Continue reading “Using External Basis Sets In GAMESS-US, Running Mixed Basis Set Calculations With Z-Matrix Inputs”
And I’m posting this from my PowerBook G4 running OSX, so I’ve got all the major players covered.
There are (in the vicinity of) one-half-million things that can go wrong between buying a bunch of computer parts and Accelrys licenses and having the Client-Server License system set up and working flawlessly. If everything goes correctly, the biggest problem one might experience is figuring out what the installation instructions have to do with the installation of the software.
In an ideal world, what follows is all you should need to do in order to get (I suspect) most any Accelrys product working correctly in a (Linux) Client-Server (MS Windows) system (my own interest is DMol3, which I will refer to throughout). The system I’m working with has the DMol3 license(s) set up on a Windows XP machine. The Windows box, besides being the license server, is the only platform the Materials Studio GUI will run on (makes that decision easy). What we want to have happen over the course of a DMol3 run is:
Continue reading “Setting Up Linux Machines To Obtain Accelrys Licenses From A Windows License Server”
Another little pointer for those searching madly for Linux installation help. Working on OpenSuse installations on a number of ASUS K8N-DL motherboards. On these boards, Suse installation goes just fine for all of 30 seconds, then freezes cold. After much searching, it was discovered that the BIOS requires updating. The fix is as follows (it’s a good idea to update the board BIOS anyway when you first buy it. No telling how long the board sat on a shelf somewhere before you got to it).
1. Go to www.asus.com.
2. Click on DOWNLOADS (or just click HERE as long as the link works).
3. Type K8N-DL in the “Input Model to Searc” (sic) search box (or whatever board you have).
4. Click on the available K8N-DL link and download the first file (should be K8NDL1007.zip, version 1007, 2005/10/26 update or whatever the latest one is).
5. Put the unzipped file D8003a00.700 on a floppy.
6. Reboot the machine in question.
7. Hit Alt-F2 to get to the FlashBIOS update.
8. Let the update go and wait patiently.
After this, OpenSuse 10.0 will/should install just fine.
“He faced the ultimate test…Whether or not you can survive death- that’s the ultimate test for your ass, ain’t it?”
I was half-way through “Richard Pryor: Live in Concert” when the news passed the wires. My iPod is never without Lenny Bruce, George Carlin, and Richard Pryor. What Lenny Bruce broke open, Richard Pryor broke through. Never before, none since. “That’s the politics, baby.”
In the process of setting up the CIA cluster for DMol3 (Accelrys) and Gaussian calculations. The use of a batch queuing system is recommended by Accelrys to take advantage of available resources (as they become available). The only open-source package they put their name to is OpenPBS (at openpbs.org). Compilation on a 64bit dual core AMD Opteron box (or any 64bit Linux system) gives the following error message.
a] [../OpenPBS ]# ./configure
creating cache ./config.cache
checking host system type... Invalid configuration `ia64-pc-linux-gnuoldld': machine `ia64-pc' not recognized
Invalid configuration `ia64-pc-linux': machine `ia64-pc' not recognized
configure: error: config.sub failed on ia64-pc-linux
Continue reading “OpenPBS config.guess File (Force Mod) For An AMD64 (IA64) Installation”
Sander Olson was kind enough to offer me a chance to speak… er… type my peace in an interview at nanotech.biz. The link to the interview is HERE. I’m the new interviewee in a list that includes such heavy hitters (and friends/collabs) as Robert Freitas, Tihamer Toth-Fejel, Chris Phoenix, and none other than the good Dr. Hall.
From a prior version of the site…
This batch script acts similar to GQueue for MacGamess, with the exception that you can’t add files after the .bat file has been implemented (run). This new version automatically goes through a directory containing PC-GAMESS input (.inp) files and runs them without having to specify each name in a long batch file. all one has to do is double-click on the rungamess.bat file from a window and it will automatically start the command prompt and program.
There is a limit to the use of the FOR command in DOS that I’ve not yet found a way to overcome, so the actual batch script is divided into two files. The first, rungamess.bat, contains the code that collects the .inp files and passes each name sequentially to execute.bat, the file that actually starts PC-GAMESS and runs the calculation. While an annoyance to have two files, once they are placed you never have to touch them again (unless you want to pass parallel calculation parameters to the executable, which are done in the execute.bat file).
Continue reading “An (Old) Automatic PC-GAMESS Batch Script”
The OpenSuse 10.0 CD set, still the only distro to install cleanly on my Precision M70, DOESN’T contain lots of useful developmental software and libraries some of ye olde quantum chemical codes need to run. This is painfully apparent to those who have downloaded the pre-compiled GAMESS-US code and found it not to do run (and what’s with the OSX in the README?) because of missing libg2c files. Yes, even real tech geeks are too lazy to make some days. That may have come out wrong.
If your goal is just to get the program running, the quick fix is to feed your machine just the libraries (a proper compilation or, uh, more complete Linux installation would also work, but that’s beyond the scope of this blog). This involves the following:
Continue reading “(Why Did) OpenSuse (Do That?), GAMESS-US, And libg2c”
The site’s in a bit of a transition.