BLJ60 example input - Revision history

import>Jmc49 at 17:54, 1 February 2016

2016-02-01T17:54:00Z

← Older revision		Revision as of 17:54, 1 February 2016
Line 47:		Line 47:
	DIJINITCONT EXP		DIJINITCONT EXP
	CYCLES 100		CYCLES 100
	JOBSPERNODE 1		COMMENT JOBSPERNODE 1
			PBS
	PAIRLIST 1		PAIRLIST 1
	</pre>		</pre>

import>Dw34 at 16:13, 1 February 2011

2011-02-01T16:13:53Z

← Older revision		Revision as of 16:13, 1 February 2011
Line 12:		Line 12:
	PARAMS 3.587037905 3.587037905 3.587037905 1.79		PARAMS 3.587037905 3.587037905 3.587037905 1.79
	NORESET		NORESET
			POINTS
	~~POINTS~~ LS -11.46001238000000 5.188783135000000 10.47622879000000 ~~LS -2.955568051000000 1.530923988000000 8.223564292000001 etc...~~		LS -11.46001238000000 5.188783135000000 10.47622879000000
			LS -2.955568051000000 1.530923988000000 8.223564292000001
			etc...
	</pre>		</pre>

Line 56:		Line 59:
	PBS -j oe		PBS -j oe
	PBS -l nodes=1:ppn=8		PBS -l nodes=1:ppn=8
			cd $PBS_O_WORKDIR
	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
			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		/home/wales/bin/PATHSAMPLE >>& output

import>Csw34: New page: 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 ...

2011-02-01T15:43:09Z

New page: 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 ...

New page

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
JOBSPERNODE 1
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.