UT theoretical chemistry code forum

hello,

I tried to run the test example of aKMC, however it fails each time, I use the following script for akmc_dynmat.sub, etc
Do you think there is a problem with my script.
Thanks in advance,

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#!/bin/csh
#PBS -k eo
#PBS -A lc_swh
#PBS -N akmc-test
#PBS -o my.out
#PBS -e my.err
#PBS -l walltime=02:00:00,nodes=0006:myri:ppn=2

# The following should contain your program and any arguments
set mycommand = "/home/ali/akmc/vasp"

if ($?PBS_JOBID) then # if this is a PBS job
echo "Starting" $PBS_JOBID `date`
echo "Initiated on `hostname`"
echo ""
cd $PBS_O_WORKDIR # connect to working directory of qsub
else
echo "This script must be run as a PBS jobs"
exit 1
endif


if ($?PBS_NODEFILE) then
# count the number of processors assigned by PBS
set NP = `wc -l $PBS_NODEFILE | awk '{print $1}'`
echo Running on $NP processors: `cat $PBS_NODEFILE`
else
echo "This job did not have the number of nodes specified with"
echo "the node= resource"
exit 1
endif

cd /home/ali/akmc
# run the program

module swap pnnl_env pnnl_env/i4
mpiexec $mycommand

echo "Done " `date`

exit

I suggest you try to run an independent job with your submission script to see if the script is correct. If not, check with the guy in charge of VASP maintenance on PNNL.

Hello,
Thank you for your help.
Now using the sample test files at least first step i.e. the min directory can be run by command akmc.pl,
however, I do not know why it stops after the structural minimization is stopped.

And when I tried to run, e.g., akmc_sp.sub separately in the min directory to check
if there is any problem with the script itself,
It complains for files 02/CHAGCAR, etc ...
which I think that it can NOT be the a correct message since we use dimer method and NOT NEB.

Any suggestions?

thanks in advance,
cheers

it seems that you are using the old akmc script. Try to update your vtstscripts.
you also need to check if you have compiled the Vasp with the most recent vtstcodes.

with the lastest version akmc.pl, I also meet the same problem, after minimization, the perl script seems to be finished. I think that there are some problems in akmc.pl, and it can not write the jobs.dat after the minimization. The status is always "submited", maybe this is the reason that the scripts is interrupted. Am I right ? Give me some advice, thanks.