BLJ60 example setup

In this example the objective was to link a crystal structure to a minimum from the amorphous region. OPTIM was first used to create min.data.info files using odata files such as:

DUMPDATA 
BFGSSTEPS 5000 
BFGSMIN 
ENDHESS 
MAXBFGS 0.2 2.0 
UPDATES 100 100 
BFGSCONV 0.000001 
BINARY 48 1.5 0.5 0.8 0.88 
PARAMS 3.587037905 3.587037905 3.587037905 1.79 
NORESET 
POINTS 
LS -11.46001238000000 5.188783135000000 10.47622879000000 
LS -2.955568051000000 1.530923988000000 8.223564292000001 
etc...

This produced min.data.info.finish and min.data.info.start, which were copied to a clean directory and read into min.data and points.min using READMIN with this pathdata file:

NATOMS 60 
COPYFILES perm.allow 
BULK 3.587037905 3.587037905 3.587037905 
PERMDIST 
SYSTEM LS 
TEMPERATURE 0.71 
CONNECTIONS 1 
SEED 1 
PERTURB 0.40 
ETOL 1.0D-7 
ITOL 0.01D0 
DIRECTION AB 
EXEC /home/wales/bin/OPTIM 
TRIPLES 
ADDTRIPLES 
STARTTRIPLES 
READMIN min.data.info.start 
CYCLES 0 
CPUS 1

A single OPTIM connect run was then started for DIJINITCONT. This initial cycle is necessary before trying multiple cycles, because there is only one possible connection attempt with only two minima. The relevant pathdata lines were:

DIJINITCONT EXP 
CYCLES 100 
COMMENT JOBSPERNODE 1 
PBS
PAIRLIST 1 

With a qsub file:

!/bin/csh
PBS -N BLJ60.1.3.37
PBS -q h8
PBS -j oe
PBS -l nodes=1:ppn=8
cd $PBS_O_WORKDIR cat $PBS_NODEFILE >& output wc output > nodes.info cat $PBS_NODEFILE >> nodes.info echo $USER >> nodes.info echo $PBS_O_WORKDIR >> nodes.info

/home/wales/bin/PATHSAMPLE >>& output

echo qstat -f ${PBS_JOBID}@volkhan echo

A subsequent run with CYCLES 100 on 8 cores found an initial path in five cycles, which took a few minutes wall clock time.