runstruct_vasp errors

Alloy Theoretic Automated Toolkit (ATAT)
1

Hello all,

I’ve been tasked with setting ATAT up for our group and I feel like I have a pretty good grasp on everything (or at least a good grasp on how I can figure out things), yet there’s one thing that’s holding me up.

When I run runstruct_vasp I get the following errors:

tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
tail: n: invalid number of lines
awk: (FILENAME=- FNR=1) fatal: division by zero attempted
Segmentation fault

I’m assuming this has something to do with the numerous (and weird) invokations of "tail --n -n -n -n etc…" in the script, but I’m mostly guessing. I don’t have a ton of csh programming background so any help is appreciated and there no amount of dumbing down that could possibly insult my intelligence.

Thanks,
G

2

Please check the scripts ezvasp and str2ezvasp under <atat_dir>/glue/vasp.
The syntax should be tail -n +<num> instead of a string of -n’s. (Would you mind reproducing that line here?)
Also check if csh or tcsh exists under /bin.

3

Thanks for the reply,

I have looked, and csh is located in /bin (it’s actually redirecting to tcsh, but that should be fine, right?)
Here are two representative sequences of code that illustrate what I was referring to:

tail -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n +3 poscar.tmp | head -3 >! oldcell.tmp

echo set POTPATH=$POTgrep -i usepot $1 | tail -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n -n -1 | sed -e 's/ *[^ =]*[ =]//g' -e 's/ *$//g' > tmpez.sh

I have probably nine or so instances of this type of line in the ezvasp script and two instances in str2ezvasp.

Thanks again

4

That is very strange. A quick fix would be to manually delete all the extra -n’s. Each "tail" should be followed by one instance of -n only, so the two lines should look like:

tail -n +3 poscar.tmp | head -3 >! oldcell.tmp

echo set POTPATH=\$POT`grep -i usepot $1 | tail -n -1 | sed -e 's/ *[^ =]*[ =]//g' -e 's/ *$//g'` > tmpez.sh

Please let us know if you still have errors after that!

If you wish, you can download a fresh copy and see if you still get those extra -n’s in <atat_dir>/glue/vasp.

5

I had a great deal more of those weird continuous -n’s in other files, but after a tedious search-and-destroy, the program is now successfully running.

Thank you so much.

6

Sorry for the issue!
This may have occurred with old versions of ATAT were the installation script check if your system understood "tail " or "tail -n" and patched accordingly. It looks like the installation script incorrectly patched multiple times…

This issue should no longer occur on the latest version of ATAT:
All "tail" are invoked as "tail -n" (all systems seem to understand this syntax) and no patch is performed during install anymore.