Create a set of PBS scripts to run a simulation on a cluster. Each script starts with something like:
#PBS -S /bin/bash #PBS -lnodes=1:cores12:ppn=11 #PBS -lwalltime=12:00:00
If these commands are not correct or complete for the cluster you use, edit createPBS().
For each job in joblist a single line command is added to the script:
python command jobid > log/jobid.out 2> log/jobid.err &
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Create a new pbs script and add initial commands and settings.
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Add single line command to existing PBS script:
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Finish pbs file
Parameters: | filename (str) – filename of the new pbs script |
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Make images for a single simulation simulation
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Calculate compactness for one simulation, the compactness is in a file: outpath/id_compactness.data
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Calculate orderparameters for one simulation. All order parameters are collected and saved in a file outpath/id_orderparameter.data
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Calculate clusters and mean squared displacement and rotation for each cell in a simulation. For more details on clustering see the documentation of getCellClusters().
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