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...) |
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| + | A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis. PATHSAMPLE is documented [http://www-wales.ch.cam.ac.uk/PATHSAMPLE.2.1.doc/ here]. |
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| − | Example setup for BLJ60 - DJW 1/2/11 |
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| + | == Tutorials == |
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| − | In this example the objective was to link a crystal |
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| + | These tutorials are under development. Please correct any mistakes you find and, of course, feel free to add more! |
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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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| + | * [[Adding a model for PATHSAMPLE]] |
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| − | DUMPDATA |
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| + | * [[List of output files for PATHSAMPLE]] |
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| − | BFGSSTEPS 5000 |
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| + | * [[Loading OPTIM's min.data.info files into PATHSAMPLE]] |
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| − | BFGSMIN |
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| + | * [[Using BHINTERP to find minima between two end points]] |
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| − | ENDHESS |
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| + | * [[Finding an initial path between two end points (minima)]] |
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| − | MAXBFGS 0.2 2.0 |
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| + | * [[Adding partially finished OPTIM stationary points to a PATHSAMPLE database]] |
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| − | UPDATES 100 100 |
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| + | * [[Optimising a path]] -- SHORTCUT, UNTRAP and FREEPAIRS |
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| − | BFGSCONV 0.000001 |
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| + | * [[Calculating rate constants (GT and fastest path)]] |
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| − | BINARY 48 1.5 0.5 0.8 0.88 |
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| + | * [[Calculating rate constants (SGT, DGT, and SDGT)]] |
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| − | PARAMS 3.587037905 3.587037905 3.587037905 1.79 |
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| + | * [[Removing minima and transition states from the database]] |
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| − | NORESET |
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| + | * [[Relaxing existing minima with new potential and creating new database]] |
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| − | POINTS |
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| + | * [[Relaxing existing transition states with new potential and creating new database]] |
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| − | LS -11.46001238000000 5.188783135000000 10.47622879000000 |
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| + | * [[If things go wrong...]] |
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| − | LS -2.955568051000000 1.530923988000000 8.223564292000001 |
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| + | * [[If you lost file min.data, but still you have points.min]] |
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| − | etc. |
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| + | * [[path.info file is not read, causes PATHSAMPLE to die]] |
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| − | |||
| + | * [[BLJ60 example input]] |
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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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Latest revision as of 11:33, 14 May 2019
A driver for OPTIM to create stationary point databases using discrete path sampling and perform kinetic analysis. PATHSAMPLE is documented here.
Tutorials
These tutorials are under development. Please correct any mistakes you find and, of course, feel free to add more!
- Adding a model for PATHSAMPLE
- List of output files for PATHSAMPLE
- Loading OPTIM's min.data.info files into PATHSAMPLE
- Using BHINTERP to find minima between two end points
- Finding an initial path between two end points (minima)
- Adding partially finished OPTIM stationary points to a PATHSAMPLE database
- Optimising a path -- SHORTCUT, UNTRAP and FREEPAIRS
- Calculating rate constants (GT and fastest path)
- Calculating rate constants (SGT, DGT, and SDGT)
- Removing minima and transition states from the database
- Relaxing existing minima with new potential and creating new database
- Relaxing existing transition states with new potential and creating new database
- If things go wrong...
- If you lost file min.data, but still you have points.min
- path.info file is not read, causes PATHSAMPLE to die
- BLJ60 example input