Utilities/Scripts
All utilities/scripts are provided without charge by Lisa M. Pérez at the Laboratory for Molecular Simulation (LMS)
at Texas A&M University and are provided on an "as is" basis. The utilities/scripts are designed for use on the computers
at Texas A&M University and would need small modifications to run elsewhere.
PBS, LSF, or LoadLeveler (Queueing system) related commands and scripts
To use PBS or LSF, I have an easy to use c-shell script for Gaussian 03/Gaussian98 calculations that will prepare job files for you and submit
them to the queue of choice. You will need to have already prepared the Gaussian03/Gaussian98 input file to use the script. The script is setup in such a
way that your input files have to end with the extention .com and your output files will be named with the extention .log. I strongly suggest
that you look in the script file and the job file that it creates to determine how they work, because you will probably want to modify them
to fit your needs in the future. You may name them anything you wish. qprep files have also been prepared for the labmol machines in the LMS lab,
titan, k2, agave, and cosmos (TAMU supercomputing center machines). For more information on titan, k2, agave, and cosmos, please visit the supercomputer center at
http://sc.tamu.edu/ , and for information on PBS please visit
http://www.openpbs.org/about.html.
The qprep script can be modified to use with programs other than G03/G98.
Description of qprep: qprep generates and submits G03/G98 job files to the queue (PBS, LSF, or LoadLeveler)
Download qprep for:
chmsgi
labmol
hydra
cosmos
agave
k2
Installation Instructions for qprep:
- Download the appropriate file for your unix based machine. You may name it anything you wish,but most people use qprep. You may need to right click on the
appropriate link (ie chmsgi) above and choose "Save Link As..."
- To run this script, you will need to type: chmod u+x qprep (substitute qprep for whatever you called it)
- You will also want to make an alias that points to the script such that you can run it from any directory. ( alias qprep ~/qprep or alias qprep="~/qprep" )
- and then type ./qprep for help on how to use the script
Description of bjobs.awk: bjobs.awk takes the information from the command bjobs -l -uall and prints information about all jobs in
the queueing system in column format.
Download bjobs.awk for:
agave
Installation Instructions for bjobs.awk:
- Download bjobs.awk (You may have to right clicking on the link below and choose "Save Link As...")
- To run this script, you will need to type: chmod u+x bjobs.awk (substitute bjobs.awk for whatever you called it)
- and then open the file with your favorite editor and follow the instructions in the header of the file.
Description of qstat_fs.bash: qstat_fs.bash will take the results from a qstat command on cosmos and print it back out
with an additional column listing the users fair share value. The higher your fair share value, the lower the priority you have in the queue. This script will only work with the following qstat
flags: -u username, -r, -G, -a, -s, and -M. For information on these flags and others available for the qstat command type man qstat or info qstat at the prompt on cosmos.
Download qstat_fs.bash for:
cosmos
Installation Instructions for qstat_fs.bash:
- Download qstat_fs.bash (You may have to right clicking on the link below and choose "Save Link As...")
- To run this script, you will need to type: chmod u+x qstat_fs.bash (substitute qstat_fs.bash for whatever you called it)
- and then open the file with your favorite editor and follow the instructions in the header of the file.
Gaussian (98/03) related commands and scripts
Description of cc1.awk: cc1.awk will take the cartesian coordinates from a g03 archive and make a cc1 file suitable for the mac version of chem3d without
connectivity (cc1_dos.awk creates a dos formatted file for the pc version of chem3d). If there are results from a frequency calculations (freq or opt+freq) it will pull the coordinates from
the frequency calculation. If it is only an optimization it will pull the optimized coordinates from the archive. (cc1_dos.awk also appears to work on mac OS X but the ^M's may cause
some problems)
Download cc1.awk for:
unix/macDOS
Installation Instructions for cc1.awk:
- Download cc1.awk (cc1_dos.awk). You may name it anything you wish, but most people use cc1.awk (cc1_dos.awk). You may need to right click on the link below and choose "Save Link As...")
- Open the file with your favorite editor and follow the instructions in the header of the file.
Description of cubeprep: cubeprep will use Guassian (98 or 03) to generate a low resolution molecular orbital, potential, or density cube file.
Download cubeprep for:
chmsgi, k2, or agave
Installation Instructions for cubeprep:
- Download cubeprep. You may name it anything you wish,but most people use cubeprep. You may need to right click on the link below and choose "Save Link As..."
- To run this script, you will need to type: chmod u+x cubeprep (substitute cubeprep for whatever you called it)
- and then type ./cubeprep for instructions.
You can also use the Gaussian 03 utility cubegen to generate one molecular orbitals per cube file. First you must make an fchk file:
syntax: cubegen 0 mo=value filename.fchk filename.cube npts h
where value is the molecular orbital number of interest or the word homo or lumo and npts is the resolution (40 low to 100 very high).
Description of log_to_pdb.awk: This awk script will take the cartesian coordinates from the last standard orientation in a g03 log file and make a pdb file.
Download log_to_pdb.awk for:
All Platforms
Installation Instructions for log_to_pdb.awk:
- Download log_to_pdb.awk. You may name it anything you wish,but most people use log_to_pdb.awk You may need to right click on the link below and choose "Save Link As..."
Description of uv: The uv script will take the output from a gaussian td or cis calculation and use the program synspec to create a simulated uv/vis spectra and plot it using gnuplot.
Download uv for:
chmsgi, hydra, cosmos, agave, or k2.
Installation Instructions for uv:
- Download uv. You may name it anything you wish,but most people use uv. You may need to right click on the link below and choose "Save Link As..."
- To run this script, you will need to type: chmod u+x uv (substitute uv for whatever you called it)
- and then type ./uv for instructions.
- I would suggest that you make a subdirectory to run the uv script since it will create quite a few new files.
ADF scripts
Description of adf_to_molden.awk: adf_to_molden.awk is an awk script that will take the optimization information from a ADF output file
and make a file suitable for Molden (visualization program).
Download adf_to_molden.awk for:
cosmos
Installation Instructions for adf_to_molden.awk:
- Download the adf_to_molden.awk file to your unix based machine (you may need to right click on the adf_to_molden.awk link above and choose "Save Link As...")
- and then open the file with your favorite editor and follow the instructions in the header of the file.
Description of adf_to_car.awk: adf_to_car.awk is an awk script that will take the final geometry from an ADF optimization and make a car file.
Download adf_to_car.awk for:
cosmos
Installation Instructions for adf_to_car.awk:
- Download the adf_to_car.awk file to your unix based machine (you may need to right click on the adf_to_car.awk link above and choose "Save Link As...")
- and then open the file with your favorite editor and follow the instructions in the header of the file.
Labmol scripts
Download openlab for:
labmol machines
Description of openlab: openlab will query the labmol machines and determine which machines are currently being used. A usage value of 0.5 or
higher indicates that the machine is running a calculation.
Installation Instructions for openlab:
- Download the openlab file to your unix based machine. You may need to right click on the openlab link above and choose "Save Link As..."
- To run this script, you will need to type: chmod u+x openlab
- and then type ./openlab
