Adk44: Created page with "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'..."

2019-05-10T17:27:48Z

Created page with "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'..."

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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:

<pre>
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...
</pre>

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:

<pre>
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
</pre>

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:

<pre>
DIJINITCONT EXP
CYCLES 100
COMMENT JOBSPERNODE 1
PBS
PAIRLIST 1
</pre>

With a qsub file:

<pre>
!/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
</pre>

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

BLJ60 example setup - Revision history

Adk44: Created page with "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'..."