This is file README. you should have the following files: 1. Makefile 2. shaker.h 3. shaker.c 4. gly.vib 5. water.vib 6. vib.net 7. README (The file you are reading now) The files are separated by double hash lines "-----------------------" "-----------------------" Data. ----- gly.vib and water.vib are two data files that shaker can read. If you would like a better description of the data file, let me know. I wasn't sure what to send. Both data sets were calculated with the Gaussian90 program, appropriate data was extracted with Jim Jensen's program (see below). Note that we have since fixed a bug in the mover program, that we found after trying to make mode assignments on a larger molecule. The mover program I just sent to Terry is the fixed version, but the data files here are not corrected. If you'd like a corrected data set, let me know. The format for the data file is straight forward. The first number is the number of atoms. The next set of integers are the atomic numbers of the respective atom centers. The next set of numbers are float and represent the x,y,z, coordinates of the atom centers for the ground state geometry. Then next float number is by itself and is the value of the first frequency. The next set of x, y, z floats are the displacement vectors for the frequency. and so on. Network ------- vib.net is the pre-made network for shaker. A nice demo should come up for you with gly.vib as the data being visualized. Move the dial labeled MODE to change what vibrational mode you are seeing. The frequency will be displayed in the box under the two dials. sleep is turned on when you first start. About A Companion Command Line Filter, "mover". -------------------------------------- We have a companion command line filter called mover. It was written by Jim Jensen. It has been sent separately to the center. It reads a Gaussian90 checkpoint file(binary), computes, and writes the ascii data shaker needs. Originally, we were going to incorporate it into shaker, but there would be portability problems. Jim's program uses calls to the Gaussain library util.a, so if a machine were not a gaussian machine the module wouldn't work. We checked with Gaussian and they had no problems with us using util.a as long as we didn't distribute util.a and we noted credit for Gaussian where appropriate. QUESTIONS --------- So if I left something out: Janet L. Jensen phone: (410) 671-5836/5665 fax: (410) 671-3160 e-mail: jljensen@crdec6.apgea.army.mil address: SMCCR-DDT CRDEC APG-EA Edgewood, MD 21010-5423 ***************************************** ******* MODULE UPDATE - 05/19/92 ****** ***************************************** Data. ----- gly.vib and water.vib are two data files that shaker can read. If you would like a better description of the data file, let me know. I wasn't sure what to send. Both data sets were calculated with the Gaussian90 program, appropriate data was extracted with Jim Jensen's program (see below). Network ------- vib.net is a pre-made network for shaker. A nice demo should come up for you with gly.vib as the data being visualized. Move the dial labeled MODE to change what vibrational mode you are seeing. The frequency will be displayed in the box under the two dials. sleep is turned on. About A Companion Command Line Filter. -------------------------------------- We have a companion command line filter written by Jim Jensen, but is not included here. It reads a Gaussian90 checkpoint file(binary), computes, and writes the ascii data shaker needs. Originally, we were going to incorporate it into shaker, but there would be portability problems. Jim's program uses calls to the Gaussain library util.a, so if a machine were not a gaussian machine the module wouldn't work. We checked with Gaussian and they had no problems with us using util.a as long as we didn't distribute util.a and we noted credit for Gaussian where appropriate. We'll be happy to send Jim's program to you if you like and include it with the shaker module as a separate command line filter. FUTURE STUFF ------------ We got some improvements to shaker that will be coming soon. A better makebonds will be the first thing. Also, I probably got to clean it up a bit. QUESTIONS --------- I wasn't exactly sure what to put, so if I left something out: Janet L. Jensen phone: (410) 671-5836/5665 fax: (410) 671-3160 e-mail: jljensen@crdec6.apgea.army.mil address: SMCCR-DDT CRDEC APG-EA Edgewood, MD 21010-5423