the generated MODCAR is zero bit

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hakuna
Posts: 49
Joined: Sat Oct 29, 2005 12:52 am

the generated MODCAR is zero bit

Post by hakuna » Mon Jul 09, 2018 8:46 am

Hi, Dear all
i run a CINEB and it roughly converges, then i use neb2dim.pl to generate the MODCAR for a fine TS search using dimmer merhod.
i cp the CONTCARs to the POSCARs in 0x folders , run neb2dim.pl, it generate a dim folder
the strange thing is that the MODECAR is empty, what is wrong with my operations?
i added the related files below
Attachments
test.tar.gz
(558.78 KiB) Downloaded 28 times

graeme
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Location: University of Texas at Austin
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Re: the generated MODCAR is zero bit

Post by graeme » Tue Jul 10, 2018 2:12 am

I can't see what is going on with this calculation. There are no OUTCARs in the 0? directories and the exts.dat file has energies of over 70 eV, which makes no sense.

The way this should work is to run an NEB calculation and then simply run the neb2dim.pl script to set up a dimer calculation. There is no need to copy any POSCAR or CONTCAR files.

hakuna
Posts: 49
Joined: Sat Oct 29, 2005 12:52 am

Re: the generated MODCAR is zero bit

Post by hakuna » Wed Jul 11, 2018 3:16 am

thank you Graeme!

after a NEB calculation, runing neb2dim.pl, it says "NO EXTS.DAT IN THIS DIRECTORY; RUN nebresults.pl"

when running nebresults.pl, there appears the info:

Unziping the OUTCARs ... done
Do nebbarrier.pl ; nebspline.pl
sh: gnuplot: command not found
Do nebef.pl
Do nebmovie.pl
Do nebjmovie.pl
Do nebconverge.pl
mv: cannot stat 'vaspout1.eps': No such file or directory
mv: cannot stat 'vaspout2.eps': No such file or directory
mv: cannot stat 'vaspout3.eps': No such file or directory
mv: cannot stat 'vaspout4.eps': No such file or directory
mv: cannot stat 'vaspout5.eps': No such file or directory
Zipping the OUTCARs again ... done

......

is it nessary to have gunplot installed when generating MODCAR using neb2dimer.pl?

hakuna
Posts: 49
Joined: Sat Oct 29, 2005 12:52 am

Re: the generated MODCAR is zero bit

Post by hakuna » Wed Jul 11, 2018 11:12 am

in neb2dim.pl usage/description "Sets up a dimer run from a NEB run. It is assumed that the configuration is contained in POSCARs, i.e. vfin.pl has been run. If no input argument is given then the dimer is formed by interpolation around the highest point in the exts.dat file. Otherwise it is formed around the input image.......", does this mean we should run vfin.pl after NEB run ? vfin.pl will cp CONTCARs to POSCAEs in 0x, is it so?
i think it is, so i cp CONTCARs to POSCAEs in 0x and the POSCARs are remained in 0x, then run neb2dim.pl without input argument, it says "NO EXTS.DAT IN THIS DIRECTORY; RUN nebresults.pl", nebresults.pl seems needing gmuplot to generate MEP which is needed in generting MODCAR, right?

then i have two tests to generate the MODCAR based on NEB, in 0x directories, only POSCAR(copied from CONTCAR) remain, and then runing neb2dim.pl with argument, say 3,it realy generate MODCAR in a new dim directory, the strange is the MODCAR is 0 bit in test1[this deals with a bond rotation], but it seems ok in test2[dealing with a bond brocken] , why they are so different?
i added here the test1 and test2
Attachments
test2.zip
(429.36 KiB) Downloaded 28 times
test1.zip
(477.87 KiB) Downloaded 29 times

graeme
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Re: the generated MODCAR is zero bit

Post by graeme » Wed Jul 11, 2018 2:14 pm

Neither of these are correct.

1. Run the neb calculation.
2. Run "vfin.pl subdir" where dir is the name of the directory to store the calculation.
3. Go into that directory "cd subdir" and make sure the calculation is sensible; you can run nebresults.pl and check the output
4. From that subdir (which now contains a exts.dat file) run neb2dim.pl

You do not need to have gnuplot installed - you can just ignore the messages about plots that are not generated.

hakuna
Posts: 49
Joined: Sat Oct 29, 2005 12:52 am

Re: the generated MODCAR is zero bit

Post by hakuna » Thu Jul 12, 2018 7:56 am

thank you for the nicely reply!
i'll fight it

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