Hi everyone,
Thanks to Prof. Henkelman for your kind help and patience.
I have already ran two cases of the Cl-NEB successfully.
In order to analyze the simulation data carefully, I have few questions related to the post-analysis.
1. According to the suggestions of "nebmake.pl", "For later analysis, put OUTCARs in folders 00 and 09!", I have eight images. Do I need to copy all the OUTCARs into the folder 00 and folder 09? If it is ture, How do I name the OUTCARs in the folder? Are those OUTCAR01,.., and OUTCAR08? Why do we need to copy all the OUTCARs into folder 00 and folder 09 at the same time?
2. Do I need to copy the vtstscripts into the folder which contains the vasp output files? For example, I have a folder "o4-1" which is the working folder for vasp, contained all the calculation results of vtst-vasp. Do I need to copy all the perl scripts into the folder o4-1?
Any suggestions and comments are grateful.
Thank you very much.
James
Post-analysis of a NEB calculation
Moderator: moderators
1. The way we intended our analysis scripts to work is to run: 'vfin.pl dirname' after a vasp run is complete (from the directory containing the INCAR, POTCAR ...) . It should detect what kind of run it is. For a NEB calculation, all OUTCAR, POSCAR, and CONTCAR files will be transferred to the directory name specified, and be ready for analysis. To get the barrier height and information about the forces along the band, run 'nebresults.pl' in the directory dirname.
2. The vtstscripts do not have to be in the location of the data. The directory containing the scripts just needs to be in your path.
2. The vtstscripts do not have to be in the location of the data. The directory containing the scripts just needs to be in your path.
Thank you very much. But I met a problem in "vfin.pl&am
My OS environment is WinXP with Cygwin.
I copied the vtstscripts into the folder vtstscripts of Drive D and I set up the path correctly into the .bash_profile. It is okay to run "vfin.pl dirname" directly.
I saved all the neb i/o files into the folder "o4-1" in Drive D.
I also created an empty folder named "test".
I changed my current directory into the folder o4-1.
I typed "vfin.pl /cygdrive/d/test", and I got an error message. It seems that the directory setting in "nebclean.sh" might have a problem.
I have sent the snapshot of my screen to you, Prof. Henkelman.
I appreciate your kind help.
I copied the vtstscripts into the folder vtstscripts of Drive D and I set up the path correctly into the .bash_profile. It is okay to run "vfin.pl dirname" directly.
I saved all the neb i/o files into the folder "o4-1" in Drive D.
I also created an empty folder named "test".
I changed my current directory into the folder o4-1.
I typed "vfin.pl /cygdrive/d/test", and I got an error message. It seems that the directory setting in "nebclean.sh" might have a problem.
I have sent the snapshot of my screen to you, Prof. Henkelman.
I appreciate your kind help.
You are a brave person running this on windows; but in principle it should work. If you do come across anything that breaks, and see a way to fix it, we'll update the scripts. I think there are so few people running on windows, however, that we won't do any cygwin testing ourselves. As a side issue, do you have vasp running on windows?
Looking at your screen snapshot, this might be a simple problem. First, go to the directory with your vasp files:
cd /cygdrive/d/test
now try typing:
vfin.pl myrun
and the files should get moved and compressed in the subdirectory myrun. The problem I see is that the directory name should be a subdirectory that will be created, not the location of your files (that is assumed to be the current directory).
Looking at your screen snapshot, this might be a simple problem. First, go to the directory with your vasp files:
cd /cygdrive/d/test
now try typing:
vfin.pl myrun
and the files should get moved and compressed in the subdirectory myrun. The problem I see is that the directory name should be a subdirectory that will be created, not the location of your files (that is assumed to be the current directory).