PATHSAMPLE
Example setup for BLJ60 - DJW 1/2/11
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 tryin multiple cycles, because there is only one possible connection attempt with only two minima. The relevant pathdata lines were: DIJINITCONT EXP CYCLES 100 JOBSPERNODE 1 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.