root/samples/vasp-xtalopt.scheme
| Revision f7e7b950324126e33532e7e3119a797c492fbade, 40.6 kB (checked in by David C. Lonie <loniedavid@…>, 15 months ago) | |
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| 1 | [xtalopt] |
| 2 | edit\version=2 |
| 3 | edit\description= |
| 4 | edit\rempath= |
| 5 | edit\localpath= |
| 6 | edit\remote\host= |
| 7 | edit\remote\port=22 |
| 8 | edit\remote\username= |
| 9 | edit\remote\rempath= |
| 10 | edit\optimizer=vasp |
| 11 | edit\queueInterface=pbs |
| 12 | optimizer\VASP\KPOINTS_list=Automatic generation\n0\nAuto\n25\n, Automatic generation\n0\nAuto\n25\n, Automatic generation\n0\nAuto\n30\n, Automatic generation\n0\nAuto\n30\n, Automatic generation\n0\nAuto\n40\n\n, Automatic generation\n0\nAuto\n50\n\n |
| 13 | optimizer\VASP\user1= |
| 14 | optimizer\VASP\INCAR_list="%filename%\n\n# output options\nLWAVE = .FALSE. # write or don't write WAVECAR\nLCHARG = .FALSE. # write or don't write CHG and CHGCAR\nLELF = .FALSE. # write ELF\n\n# ionic relaxation\nNSW = 20 # number of ionic steps\nIBRION = 2 # 2=conjucate gradient, 1=Newton like\nISIF = 2 # 3=relax everything, 2=relax ions only, 4=keep volume fixed\n\n# precision parameters\nEDIFF = 1E-3 # 1E-3 very low precision for pre-relaxation, use 1E-5 next\nEDIFFG = 1E-2 # usually: 10 * EDIFF\nPREC = med # precision low, med, high, accurate\n\n# electronic relaxation\nISMEAR = -5 # -5 = tetraedon, 1..N = Methfessel\nENCUT = %user3% # cutoff energy\nPSTRESS = %user2%\nISYM=0\n", "%filename%\n\n# output options\nLWAVE = .FALSE. # write or don't write WAVECAR\nLCHARG = .FALSE. # write or don't write CHG and CHGCAR\nLELF = .FALSE. # write ELF\n\n# ionic relaxation\nNSW = 20 # number of ionic steps\nIBRION = 2 # 2=conjucate gradient, 1=Newton like\nISIF = 4 # 3=relax everything, 2=relax ions only, 4=keep volume fixed\n\n# precision parameters\nEDIFF = 1E-3 # 1E-3 very low precision for pre-relaxation, use 1E-5 next\nEDIFFG = 1E-2 # usually: 10 * EDIFF\nPREC = med # precision low, med, high, accurate\n\n# electronic relaxation\nISMEAR = -5 # -5 = tetraedon, 1..N = Methfessel\nENCUT = %user3% # cutoff energy\nPSTRESS = %user2%\nISYM=0\n", "%filename%\n \n# output options\nLWAVE = .FALSE. # write or don't write WAVECAR\nLCHARG = .FALSE. # write or don't write CHG and CHGCAR\nLELF = .FALSE. # write ELF\n\n# ionic relaxation\nNSW = 20 # number of ionic steps\nIBRION = 2 # 2=conjucate gradient, 1=Newton like\nISIF = 3 # 3=relax everything, 2=relax ions only, 4=keep volume fixed\n\n# precision parameters\nEDIFF = 1E-3 # 1E-3 very low precision for pre-relaxation, use 1E-5 next\nEDIFFG = 1E-2 # usually: 10 * EDIFF\nPREC = med # precision low, med, high, accurate\n\n# electronic relaxation\nISMEAR = -5 # -5 = tetraedon, 1..N = Methfessel\nENCUT = %user3% # cutoff energy\nPSTRESS = %user2%\nISYM=0\n", "%filename%\n\n# output options\nLWAVE = .FALSE. # write or don't write WAVECAR\nLCHARG = .FALSE. # write or don't write CHG and CHGCAR\nLELF = .FALSE. # write ELF\n\n# ionic relaxation\nNSW = 100 # number of ionic steps\nIBRION = 2 # 2=conjucate gradient, 1=Newton like\nISIF = 3 # 3=relax everything, 2=relax ions only, 4=keep volume fixed\n\n# precision parameters\nEDIFF = 1E-5 # 1E-3 very low precision for pre-relaxation, use 1E-5 next\nEDIFFG = 1E-4 # usually: 10 * EDIFF\nPREC = med # precision low, med, high, accurate\n\n# electronic relaxation\nISMEAR = -5 # -5 = tetraedon, 1..N = Methfessel\nENCUT = %user3% # cutoff energy\nPSTRESS = %user2%\n#ISYM=0\n", "%filename%\n\n# output options\nLWAVE = .FALSE. # write or don't write WAVECAR\nLCHARG = .FALSE. # write or don't write CHG and CHGCAR\nLELF = .FALSE. # write ELF\n\n# ionic relaxation\nNSW = 100 # number of ionic steps\nIBRION = 2 # 2=conjucate gradient, 1=Newton like\nISIF = 3 # 3=relax everything, 2=relax ions only, 4=keep volume fixed\n\n# precision parameters\nEDIFF = 1E-5 # 1E-3 very low precision for pre-relaxation, use 1E-5 next\nEDIFFG = 1E-4 # usually: 10 * EDIFF\nPREC = high # precision low, med, high, accurate\n\n# electronic relaxation\nISMEAR = -5 # -5 = tetraedon, 1..N = Methfessel\nENCUT = %user3% # cutoff energy\nPSTRESS = %user2%\n#ISYM=0\n", "%filename%\n\n# output options\nLWAVE = .FALSE. # write or don't write WAVECAR\nLCHARG = .FALSE. # write or don't write CHG and CHGCAR\nLELF = .FALSE. # write ELF\n\n# ionic relaxation\nNSW = 100 # number of ionic steps\nIBRION = 2 # 2=conjucate gradient, 1=Newton like\nISIF = 3 # 3=relax everything, 2=relax ions only, 4=keep volume fixed\n\n# precision parameters\nEDIFF = 1E-5 # 1E-3 very low precision for pre-relaxation, use 1E-5 next\nEDIFFG = 1E-4 # usually: 10 * EDIFF\nPREC = high # precision low, med, high, accurate\n\n# electronic relaxation\nISMEAR = -5 # -5 = tetraedon, 1..N = Methfessel\nENCUT = %user3% # cutoff energy\nPSTRESS = %user2%\n#ISYM=0\n" |
| 15 | optimizer\VASP\user2=0 |
| 16 | optimizer\VASP\QI\PBS\job.pbs_list="#/bin/bash \n#PBS -q parity \n#PBS -l nodes=1:ppn=8 \n#PBS -o ../%gen%x%id%-%incar%.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 /etc/profile.d/modules.sh\nmodule load vasp/4.6-impi-3.2-ib\nexport I_MPI_PIN=0\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 \nNPROCS=`cat $PBS_NODEFILE | wc -l` \nNNODES=`cat $PBS_NODEFILE | uniq | wc -l` \nUNIQ_HOSTS=tmp.hosts \ncat $PBS_NODEFILE | uniq > $UNIQ_HOSTS \nHOSTS_uniq=`cat $PBS_NODEFILE | uniq` \n \nmpdboot -n $NNODES -f $UNIQ_HOSTS -r /usr/bin/ssh -v \necho \"Running on $NPROCS processors across $NNODES nodes.\" \nmpiexec -machinefile $PBS_NODEFILE -np $NPROCS -envuser vasp \n \nmpdtrace \nmpdallexit \n \nfor node in `cat $PBS_NODEFILE | sort | uniq`; do \nssh $node \"ls -l $PBSTMPDIR\" \ndone \ncp $PBSTMPDIR/* $PBS_O_WORKDIR/ ", "#/bin/bash \n#PBS -q parity \n#PBS -l nodes=1:ppn=8 \n#PBS -o ../%gen%x%id%-%incar%.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 /etc/profile.d/modules.sh\nmodule load vasp/4.6-impi-3.2-ib\nexport I_MPI_PIN=0\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 \nNPROCS=`cat $PBS_NODEFILE | wc -l` \nNNODES=`cat $PBS_NODEFILE | uniq | wc -l` \nUNIQ_HOSTS=tmp.hosts \ncat $PBS_NODEFILE | uniq > $UNIQ_HOSTS \nHOSTS_uniq=`cat $PBS_NODEFILE | uniq` \n \nmpdboot -n $NNODES -f $UNIQ_HOSTS -r /usr/bin/ssh -v \necho \"Running on $NPROCS processors across $NNODES nodes.\" \nmpiexec -machinefile $PBS_NODEFILE -np $NPROCS -envuser vasp \n \nmpdtrace \nmpdallexit \n \nfor node in `cat $PBS_NODEFILE | sort | uniq`; do \nssh $node \"ls -l $PBSTMPDIR\" \ndone \ncp $PBSTMPDIR/* $PBS_O_WORKDIR/ ", "#/bin/bash \n#PBS -q parity \n#PBS -l nodes=1:ppn=8 \n#PBS -o ../%gen%x%id%-%incar%.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 /etc/profile.d/modules.sh\nmodule load vasp/4.6-impi-3.2-ib\nexport I_MPI_PIN=0\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 \nNPROCS=`cat $PBS_NODEFILE | wc -l` \nNNODES=`cat $PBS_NODEFILE | uniq | wc -l` \nUNIQ_HOSTS=tmp.hosts \ncat $PBS_NODEFILE | uniq > $UNIQ_HOSTS \nHOSTS_uniq=`cat $PBS_NODEFILE | uniq` \n \nmpdboot -n $NNODES -f $UNIQ_HOSTS -r /usr/bin/ssh -v \necho \"Running on $NPROCS processors across $NNODES nodes.\" \nmpiexec -machinefile $PBS_NODEFILE -np $NPROCS -envuser vasp \n \nmpdtrace \nmpdallexit \n \nfor node in `cat $PBS_NODEFILE | sort | uniq`; do \nssh $node \"ls -l $PBSTMPDIR\" \ndone \ncp $PBSTMPDIR/* $PBS_O_WORKDIR/ ", "#/bin/bash \n#PBS -q parity \n#PBS -l nodes=2:ppn=8 \n#PBS -o ../%gen%x%id%-%incar%.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 /etc/profile.d/modules.sh\nmodule load vasp/4.6-impi-3.2-ib\nexport I_MPI_PIN=0\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 \nNPROCS=`cat $PBS_NODEFILE | wc -l` \nNNODES=`cat $PBS_NODEFILE | uniq | wc -l` \nUNIQ_HOSTS=tmp.hosts \ncat $PBS_NODEFILE | uniq > $UNIQ_HOSTS \nHOSTS_uniq=`cat $PBS_NODEFILE | uniq` \n \nmpdboot -n $NNODES -f $UNIQ_HOSTS -r /usr/bin/ssh -v \necho \"Running on $NPROCS processors across $NNODES nodes.\" \nmpiexec -machinefile $PBS_NODEFILE -np $NPROCS -envuser vasp \n \nmpdtrace \nmpdallexit \n \nfor node in `cat $PBS_NODEFILE | sort | uniq`; do \nssh $node \"ls -l $PBSTMPDIR\" \ndone \ncp $PBSTMPDIR/* $PBS_O_WORKDIR/ ", "#/bin/bash \n#PBS -q parity \n#PBS -l nodes=2:ppn=8 \n#PBS -o ../%gen%x%id%-%incar%.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 /etc/profile.d/modules.sh\nmodule load vasp/4.6-impi-3.2-ib\nexport I_MPI_PIN=0\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 \nNPROCS=`cat $PBS_NODEFILE | wc -l` \nNNODES=`cat $PBS_NODEFILE | uniq | wc -l` \nUNIQ_HOSTS=tmp.hosts \ncat $PBS_NODEFILE | uniq > $UNIQ_HOSTS \nHOSTS_uniq=`cat $PBS_NODEFILE | uniq` \n \nmpdboot -n $NNODES -f $UNIQ_HOSTS -r /usr/bin/ssh -v \necho \"Running on $NPROCS processors across $NNODES nodes.\" \nmpiexec -machinefile $PBS_NODEFILE -np $NPROCS -envuser vasp \n \nmpdtrace \nmpdallexit \n \nfor node in `cat $PBS_NODEFILE | sort | uniq`; do \nssh $node \"ls -l $PBSTMPDIR\" \ndone \ncp $PBSTMPDIR/* $PBS_O_WORKDIR/ ", "#/bin/bash \n#PBS -q parity \n#PBS -l nodes=2:ppn=8 \n#PBS -o ../%gen%x%id%-%incar%.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 /etc/profile.d/modules.sh\nmodule load vasp/4.6-impi-3.2-ib\nexport I_MPI_PIN=0\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 \nNPROCS=`cat $PBS_NODEFILE | wc -l` \nNNODES=`cat $PBS_NODEFILE | uniq | wc -l` \nUNIQ_HOSTS=tmp.hosts \ncat $PBS_NODEFILE | uniq > $UNIQ_HOSTS \nHOSTS_uniq=`cat $PBS_NODEFILE | uniq` \n \nmpdboot -n $NNODES -f $UNIQ_HOSTS -r /usr/bin/ssh -v \necho \"Running on $NPROCS processors across $NNODES nodes.\" \nmpiexec -machinefile $PBS_NODEFILE -np $NPROCS -envuser vasp \n \nmpdtrace \nmpdallexit \n \nfor node in `cat $PBS_NODEFILE | sort | uniq`; do \nssh $node \"ls -l $PBSTMPDIR\" \ndone \ncp $PBSTMPDIR/* $PBS_O_WORKDIR/ " |
| 17 | optimizer\VASP\user3=400 |
| 18 | optimizer\VASP\user4= |
| 19 | queueinterface\pbsqueueinterface\version=1 |
| 20 | queueinterface\pbsqueueinterface\paths\qsub=qsub |
| 21 | queueinterface\pbsqueueinterface\paths\qstat=qstat |
| 22 | queueinterface\pbsqueueinterface\paths\qdel=qdel |
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