Difference between revisions of "PATHSAMPLE"
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import>Dw34 (New page: 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 fi...) |
import>Csw34 (Replacing page with '= Example input = * BLJ60 example input') |
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| − | Example |
+ | = Example input = |
| + | * [[BLJ60 example input]] |
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| − | In this example the objective was to link a crystal |
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| − | structure to a minimum from the amorphous region. OPTIM was first used to |
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| − | create min.data.info files using odata files such as: |
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| − | |||
| − | DUMPDATA |
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| − | BFGSSTEPS 5000 |
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| − | BFGSMIN |
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| − | ENDHESS |
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| − | MAXBFGS 0.2 2.0 |
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| − | UPDATES 100 100 |
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| − | BFGSCONV 0.000001 |
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| − | BINARY 48 1.5 0.5 0.8 0.88 |
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| − | PARAMS 3.587037905 3.587037905 3.587037905 1.79 |
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| − | NORESET |
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| − | POINTS |
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| − | LS -11.46001238000000 5.188783135000000 10.47622879000000 |
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| − | LS -2.955568051000000 1.530923988000000 8.223564292000001 |
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| − | etc. |
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| − | |||
| − | This produced min.data.info.finish and min.data.info.start, which were copied |
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| − | to a clean directory and read into min.data and points.min using READMIN with |
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| − | this pathdata file: |
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| − | |||
| − | NATOMS 60 |
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| − | COPYFILES perm.allow |
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| − | BULK 3.587037905 3.587037905 3.587037905 |
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| − | PERMDIST |
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| − | SYSTEM LS |
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| − | TEMPERATURE 0.71 |
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| − | CONNECTIONS 1 |
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| − | SEED 1 |
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| − | PERTURB 0.40 |
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| − | ETOL 1.0D-7 |
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| − | ITOL 0.01D0 |
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| − | DIRECTION AB |
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| − | EXEC /home/wales/bin/OPTIM |
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| − | TRIPLES |
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| − | ADDTRIPLES |
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| − | STARTTRIPLES |
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| − | READMIN min.data.info.start |
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| − | CYCLES 0 |
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| − | CPUS 1 |
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| − | |||
| − | A single OPTIM connect run was then started for DIJINITCONT. This initial |
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| − | cycle is necessary before tryin multiple cycles, because there is only one |
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| − | possible connection attempt with only two minima. The relevant pathdata lines were: |
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| − | DIJINITCONT EXP |
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| − | CYCLES 100 |
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| − | JOBSPERNODE 1 |
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| − | PAIRLIST 1 |
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| − | with a qsub file: |
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| − | #!/bin/csh |
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| − | #PBS -N BLJ60.1.3.37 |
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| − | #PBS -q h8 |
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| − | #PBS -j oe |
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| − | #PBS -l nodes=1:ppn=8 |
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| − | |||
| − | cd $PBS_O_WORKDIR |
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| − | cat $PBS_NODEFILE >& output |
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| − | wc output > nodes.info |
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| − | cat $PBS_NODEFILE >> nodes.info |
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| − | echo $USER >> nodes.info |
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| − | echo $PBS_O_WORKDIR >> nodes.info |
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| − | |||
| − | /home/wales/bin/PATHSAMPLE >>& output |
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| − | |||
| − | echo |
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| − | qstat -f ${PBS_JOBID}@volkhan |
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| − | echo |
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| − | |||
| − | A subsequent run with CYCLES 100 on 8 cores found an initial path in five cycles, |
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| − | which took a few minutes wall clock time. |
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