Back to lab 4

Part 2: Step1 band

To ask a question, email Ray the path to your job. This process is almost identical to how you made your bands for step1.
The only way to maximize your chance of success is to make better initial and final images.

1. Go to your step2 directory and create the "band" directory.
2. Create the band with nebmake.pl ../ini/CONTCAR ../fin/CONTCAR 5 .

   The script nebmake.pl arg1 arg2 arg3 takes in 3 arguments. arg1 is the path to the initial state geometry. arg2 is the path to the final image geometry.
   The geometries doesn't need to be CONTCAR files but they must be converged geometries. So, you can use POSCARs here as long as the geometry contained within is converged.
   arg1 and arg2 must be of the same format. A file editted by ase gui and saved is in VASP-4 format while a file produced by VASP is in VASP-5 format. If you have a format difference between files of converged geometry, you can open the VASP-5 one, edit nothing but save as itself again. This will rewrite the file in VASP-4 format.
   arg3 is the number of images between initial and final state. 5 is a reasonable initial guess that is not too expensive. We always want an odd number of images. In the ideal case where the middle image is the transition state, we will have equal number of images before and after the transition state.

3. Run the script nebavoid.pl 0.5 . This will keep your atoms from overlapping with each other.
4. Visually examine the the movement made by the band with nebmovie.pl and xyz movie . With some experience, you will detect motions that makes no sence to chemistry.
5. Copy over the KPOINTS and POTCAR from your ini or fin directory.
6. Copy over the INCAR and slurm_fri.sub from /home/fri/lab_files_2022/lab4

   Notice that the INCAR contains a line "IMAGES". It must equal to the arg3 of nebmake.pl script, i.e. the number of images in the band.
   In slurm_fri.sub, the line "-pe" now has "mpi24 120". This means that you are using 24-core-nodes and you are requesting 120 cores, meaning that this calculation requires 5 nodes. The number of nodes requested must equal to the number of images in the band!

7. Edit the jobname accordingly and submit the job. After every run, you need to wrap up the job with vfin.pl first before any analysis.
8. After vfin.pl has created the run# directory, go to run# and run the script nebmresults.pl to analyze the run.

   nebresult.pl creates the following important file: nebef.dat, movie, mep.eps.
   The movie shows the band after the first round of optimization. Look at it with xyz. With experience you'll know if the band is getting better or worse.
   nebef.dat contains the forces and energies of each image. When the force on every image is below the convergence criteria (in some cases, getting very close is OK as well), your band is converged.
   mep.eps shows the energy landscape of the reaction. Looking at the mep (minimum energy pathway) and how it changes over runs tell you if your band is getting better or worse. Some problematic cases are displayed in the mep gallery.
   

9. Keep running the band until it converges. When it does, the file exts.dat contains the saddle point (transition state). It should be very close to one of the images. You can use the energy and geometry of that image as the energy and geometry of the transition state.

Back to lab 4