runstruct_vasp hangs with Debian 7 replacing Debian 6

Alloy Theoretic Automated Toolkit (ATAT)
1

Since "The distribution [on the NIST CTCMS cluster] was upgraded from Debian 6.0 to Debian 7.0," runstruct_vasp does not work. Instead it hangs for as long as one waits. :frowning:

2

To debug this, Iā€™d need you to try this:

csh -v "runstruct_vasp [your options]"

so I can see where it hangs.

3

I tried:

20 (alfred) 291 >csh -v ~/bin/runstruct_vasp

and got:

set wrapfile="vasp.wrap"

while ( $#argv != 0 )

if ( ! $?extractonly ) then

if ( ! -e ~/.ezvasp.rc ) then

source ~/.ezvasp.rc

set VASPCMD="vasp"

set POTGGA="/usr/local/lib/pot_gga"
set POTLDA="/usr/local/lib/pot_lda"
endif

if ( ! $?notgenvaspin ) then
str2ezvasp $wrapfile

Where it seems to hang again

Thanks,
Ben

4

Also:

20 (alfred) 292 >ps
PID TTY TIME CMD
2401 pts/15 00:00:00 tcsh
9045 pts/15 00:00:00 csh
9049 pts/15 00:00:00 str2ezvasp
9059 pts/15 00:02:56 cellcvrt
9060 pts/15 00:01:51 tail
9274 pts/15 00:00:00 ps
28932 pts/15 00:09:21 maps
2

5

Apparently cellcvrt is generating an infinite loop:

13 (ruth) 169 >cellcvrt -c < POSCAR
1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
-nan -nan -nan
-nan -nan -nan
-nan -nan -nan
end

1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
-nan -nan -nan
-nan -nan -nan
-nan -nan -nan
end

1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
-nan -nan -nan
-nan -nan -nan
-nan -nan -nan
end

1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
0.595446 0.744462 0.803922
0.368373 0.750989 0.413670
0.441689 0.918591 0.570800
0.671725 0.918791 0.967204
end

1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
0.726071 0.769667 0.730027
0.914388 0.958669 0.919188
0.000000 0.000000 0.000000
0.000000 0.000000 0.000000
end

1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
0.000000 0.000000 0.000000
0.000000 0.000000 0.000000
0.000000 0.000000 0.000000
0.000000 0.000000 0.000000
end

1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
0.000000 0.000000 0.000000
0.000000 0.000000 0.000000
0.000000 0.000000 0.000000
end

1.000000 0.000000 0.000000
0.000000 1.000000 0.000000
0.000000 0.000000 1.000000
-nan -nan -nan
-nan -nan -nan
-nan -nan -nan
end
:
:
:
and more of the same

6

OK, problem solved.

It seems that when I installed a new version of atat,
cellcvrt did not update in my bin directory, and after
updating by hand runstruct_vasp seems to work perfectly.

SOrry for the inconvenience.

Ben

7

ok good! I was scratching my head on this one!