(7) Get the total energy from the output (1 Hartree = kcal/mol) and label the structure with the energy.

Transcription

1 RUNNING GAUSSIAN ON THE RedHawk cluster computers: General Procedure: The general procedure is to prepare the input file on a PC using GausView, then transfer this file via WinSCP to the RedHawk cluster computer at Miami University, which has Gaussian03 and 09 programs. You will need to use four different programs to prepare for a Gaussian calculation. These programs are GausView, GEdit, WinSCP, and Putty or Cygwin. Specific steps are as following: (1) Use GausView to draw a structure and specify the basis set and method to be used. Save the file in Gaussian input format, myfile.com or myfile.gif. (2) Use GEdit to open the above file and edit it so it is ready for running Gaussian 03 or 09 on the RedHawk cluster computer. You will need two files to run a Gaussian job on the RedHawk: a.scr (script) file and a.com file. Save the edited files in unix/linux format. (3) Use WinSCP (an encrypted FTP tool) to put the files on the cluster computer. You need a user name and a password. RedHawk address is redhawk.hpc.muohio.edu. (4) On the PC using Putty and Xming to connect to and login to the cluster computer. To start a job, type: qsub myfile.scr This will put your job in the que and wait for your turn to run the Gaussian job. The myfile.scr should be replaced by your input file name. To check the job status, type: qstat -a at the prompt. To delete a job, type: qdel job id (look up job id from the que). (5) After the computation is complete, you should have four files in your directory: they are myfile.com, myfile.scr, myfile.chk, and myfile.log. Use WinSCP to retrieve the.log file and save on the PC. Word. (6) Use GausView to open the.log file and get the optimized structure and paste into (7) Get the total energy from the output (1 Hartree = kcal/mol) and label the structure with the energy. Other useful Commands in Unix: man "command" - prints a description of what the "command" does. As an example type man man the output will explain the function of the man command.

2 vi or view - used to view and edit a file. For viewing only: Ctrl D goes down. Ctrl B back. Shift g goes to the end of output. :q! quits the vi program and dumps you back to command line. If you need to edit a few words in unix, you may use vi also: x deletes one character, r or s switches to input mode. In input mode, you can type in characters. To get out of input mode, type ESC. To save changes: use :wq! chmod -used to change file permissions. Unix files have strict file ownership. If you get the message " You don't have permissions to this file", you may type: chmod 666 filename to give permission to access the filename. cp filename1 /filename2. Copies a file from one directory to another. Full path name can be used and it is possible to rename a file while keeping copy of old one for future reference. Example: cp imanidiot /imanidiot2 mv - moves a file from one dir to another. Can also be used to rename a file without having two copies on the system, which would occur with the cp command. kill - don't do this unless you know exactly what you are doing. If you manage to kill an essential process on the computer it may crash. Type kill "PID" where the PID is the process ID #. This number can be located by ps -ef command and looking for the job that you want to kill ps - process status. top gives a process status, which is regularly updated. Use Ctrl C to get back to command line. clear clears the screen and places cursor at top of screen. ls provides a listing of the current directory. If you want to see a listing of another directory without changing the directory type in the full path name of the directory that you wish to see after the ls commmand. rm this command will delete files. The rmdir command will remove an empty dir. Examples of input files:

3 For the Origin at OSC, two files are needed to run in the batch mode. The first one is the.com file, which is named CH3CHO.MPL.com in this particular case and has the following format. # MP2/LanL2DZ SP CH3CHO-MP2/LanL2DZ Single point calculation 0 1 C O C H H H H The second file is the.job file, which is named CH3CHO.MPL.job in this case and has the following lines. # This script converted on Mon Jun 24 13:56:13 EDT 2002 #PBS -N CH3CHO.MPL #QSUB -r CH3CHO.MPL #PBS -e CH3CHO.MPL.err #QSUB -e CH3CHO.MPL.err #PBS -o CH3CHO.MPL.out #QSUB -o CH3CHO.MPL.out

4 #PBS #QSUB -J m #PBS -me #QSUB -me #PBS -M your_ @muohio.edu #QSUB -mu your_ @muohio.edu #PBS -S /bin/sh #QSUB -s /bin/sh #PBS -l cput=10:51:00 #QSUB -lt 10:51:00 #PBS -l vmem=64mw #QSUB -lm 64Mw #PBS -l "ncpus=2" #QSUB -l mpp_p=2 set -x set echo $PBS_O_WORKDIR cd $TMPDIR pwd df INPUT=CH3CHO.MPL.com cp $PBS_O_WORKDIR/$INPUT. g98a.9./$input ls -al cp * $PBS_O_WORKDIR

5 These are the basics. For more in-depth explanations read the Gaussian98 users manual, the "red book" by Foresman and Frisch.