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| 1 | [xtalopt] |
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| 2 | edit\version=2 |
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| 3 | edit\description= |
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| 4 | edit\rempath= |
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| 5 | edit\localpath= |
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| 6 | edit\remote\host= |
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| 7 | edit\remote\port=22 |
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| 8 | edit\remote\username= |
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| 9 | edit\remote\rempath= |
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| 10 | edit\optimizer=castep |
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| 11 | edit\queueInterface=pbs |
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| 12 | optimizer\CASTEP\xtal.cell_list=%percent%BLOCK LATTICE_CART\n%cellVector1Angstrom%\n%cellVector2Angstrom%\n%cellVector3Angstrom%\n%percent%ENDBLOCK LATTICE_CART\n\n%percent%BLOCK POSITIONS_FRAC\n%coordsFrac%\n%percent%ENDBLOCK POSITIONS_FRAC\n |
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| 13 | optimizer\CASTEP\xtal.param_list=task : geometryoptimization\n\n |
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| 14 | optimizer\CASTEP\QI\PBS\job.pbs_list="#/bin/bash\n#PBS -q parity\n#PBS -l nodes=2:ppn=8\n#PBS -o ../%gen%x%id%-%incar%-%description%.out\n#PBS -N %description%-%gen%x%id%-%optStep%\n#PBS -j oe\n#PBS -m e\n##PBS -W umask=022\n\n###Include this for xtalopt scripts!###\nexport PBS_O_WORKDIR=%rempath%\necho $PBS_O_WORKDIR\n# -----------------------------------------------------------------------\n# start: prepare script to clean up scratch directories\n# ----------------------------------------------------------------------- \nCLEANUPSCRIPT=~/pbscleanup_$PBS_JOBID.sh \necho \"# clean up job $PBS_JOBID\" >$CLEANUPSCRIPT\nfor i in `cat $PBS_NODEFILE | sort | uniq`; do\necho \"ssh $i \\\"rm -r $PBSTMPDIR\\\" \" >> $CLEANUPSCRIPT\ndone\nchmod +x $CLEANUPSCRIPT\n# -----------------------------------------------------------------------\n# end: prepare script to clean up scratch directories\n# -----------------------------------------------------------------------\n\nsource /san/projects3/ezurek/software/src/Castep_170206.ifc/tag.sh\n\ncd $PBS_O_WORKDIR\nfor node in `cat $PBS_NODEFILE | sort | uniq`; do\nssh $node \"cp $PBS_O_WORKDIR/* $PBSTMPDIR/;\";\ndone\ncd $PBSTMPDIR\necho \"running in directory $PBSTMPDIR\"\n\n###########\n# End PBS setup. User comands start below.\n# Do NOT redirect standard output. It will all be collected in\n# the PBS output file specified in the header above.\n###########\n\nmpiexec castep xtal\n\nfor node in `cat $PBS_NODEFILE | sort | uniq`; do\nssh $node \"ls -l $PBSTMPDIR\"\ndone\ncp $PBSTMPDIR/* $PBS_O_WORKDIR/\n" |
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| 15 | optimizer\CASTEP\user1= |
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| 16 | optimizer\CASTEP\user2= |
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| 17 | optimizer\CASTEP\user3= |
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| 18 | optimizer\CASTEP\user4= |
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| 19 | queueinterface\pbsqueueinterface\version=1 |
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| 20 | queueinterface\pbsqueueinterface\paths\qsub=qsub |
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| 21 | queueinterface\pbsqueueinterface\paths\qstat=qstat |
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| 22 | queueinterface\pbsqueueinterface\paths\qdel=qdel |
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