PATHSAMPLE: Difference between revisions
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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 = |
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* [[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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