It's important to always check your XDATCAR. You can check how your atoms are moving during this optimization/relaxation with xyz XDATCAR. The total energy of the last step (last line) can be used for later analysis. Look at the force of the last step, if it's smaller than your convergence criteria (EDIFFG parameter in your INCAR), your job is converged. Vef.pl will read your OUTCAR and output (step number, force, total energy, energy change from step 0). If your job finished, check if it is converged with vef.pl in your job directory. If qstat shows no job for you, that means your jobs are finished or dead. Įmail the error message to Ray, then delete your job with qdel jobid Post submission analysis JobID being the first number shown in the line of the job entry, followed by job name, use this command to get the error message: qstat -j jobid | grep error. Įqw means that there is an error in the job. In most cases, jobs listed above yours will run before yours do if their job status is qw. To see where you stand in the line, use xqstat to show jobs of all users. Wait for 10 seconds, then use qstat to check the status of your job. There is more information about this file on our Queuing system page. Look for the line "#$ -N JobName", change "JobName" to "Pt32" Go to your job directory: cd ~/lab2/pt32/ Go to your pt32 directory and edit the sub file and chage the jobname to something informative. Your model looks like this: (this image is interactive!) To see what elements are contained in it, use command grep PAW POTCAR DO NOT EDIT THIS FILE YOURSELF! ONLY USE THE SCRIPT GIVEN TO YOU FOR MAKING AN CORRECT POTCAR! In this case, the only element is Pt. A more detailed description of each line's significance can be found here POTCAR: It has parameters for how to simulating each element. You can view the coordinates directly with vim or you can use a molecular viewer ag POSCAR or xyz POSCAR. POSCAR: It has the initial coordinates of the atoms in your system. The 'more file ' command allows you to look at a file's contents. In this case, a maximum of 200 iterations are requested (NSW tag) to minimize (IBRION tag) a particle until the force on any atom is less than 0.005 eV/Ang (EDIFFG tag). INCAR: It has a list of tags which indicates the calculations details. Trying to read about it may cost you more time you can afford so handle your curiosity with caution! To understand what it does requires some knowledge of solid state physics. KPOINTS: Don't change this file and try to ignore it. You can find them in the directory you just copied over.Ĭlick here to read more about what each of the files are for. You need 5 files (KIPPs) to run a VASP job: KPOINTS INCAR POSCAR POTCAR. In your home directory create a directory titled "lab2".Ĭreate a the lab2 directory with mkdir lab2Ĭopy over the directory which contains all prepared files for you to your lab2 directory.Ĭp -r /home/fri/lab_files_2022/lab2/pt32 ~/lab2/ Job set up and submission VASP tutorial through calculation of Pt32 Click here to go back to Lab 2 Directory set up
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