[Swift-commit] r8422 - in SwiftApps/subjobs: . simanalyze/part05 vasp
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Sat Apr 4 12:21:19 CDT 2015
Author: ketan
Date: 2015-04-04 12:21:19 -0500 (Sat, 04 Apr 2015)
New Revision: 8422
Added:
SwiftApps/subjobs/simanalyze/part05/mira.conf
SwiftApps/subjobs/vasp/
SwiftApps/subjobs/vasp/INCAR
SwiftApps/subjobs/vasp/KPOINTS
SwiftApps/subjobs/vasp/POSCAR
SwiftApps/subjobs/vasp/POTCAR
SwiftApps/subjobs/vasp/cetus.conf
SwiftApps/subjobs/vasp/cobaltvasp.sh
SwiftApps/subjobs/vasp/job.sh
SwiftApps/subjobs/vasp/runcetus.sh
SwiftApps/subjobs/vasp/runvasp.sh
SwiftApps/subjobs/vasp/vasp.swift
SwiftApps/subjobs/vasp/vaspostproc.sh
SwiftApps/subjobs/vasp/vaspreproc.sh
Modified:
SwiftApps/subjobs/bg.sh
Log:
add vasp app
Modified: SwiftApps/subjobs/bg.sh
===================================================================
--- SwiftApps/subjobs/bg.sh 2015-04-01 00:01:17 UTC (rev 8421)
+++ SwiftApps/subjobs/bg.sh 2015-04-04 17:21:19 UTC (rev 8422)
@@ -19,7 +19,7 @@
fi
#Run the preprocessing script
-./$preproc
+/bin/bash $preproc "$@"
#export SUBBLOCK_SIZE=16
@@ -86,13 +86,14 @@
CORNER=${SWIFT_SUBBLOCK_ARRAY[$SWIFT_JOB_SLOT]}
#Some logging
+ processedargs=$(echo "$@" | cut -d" " -f 1)
echo "$0": running BLOCK="$COBALT_PARTNAME" SLOT="$SWIFT_JOB_SLOT"
echo "$0": running cmd: "$0" args: "$@"
- echo "$0": running runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+ echo "$0": runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 : "$processedargs"
#without timeout
#runjob --strace none --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
- runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 16 --np "$((16*$SUBBLOCK_SIZE))" : "$@"
+ runjob --block "$COBALT_PARTNAME" --corner "$CORNER" --shape "$SHAPE" -p 1 : "$processedargs"
echo "Runjob finished."
fi
@@ -108,7 +109,7 @@
fi
#Run the postprocessing script
-./$postproc
+/bin/bash $postproc "$@"
exit 0
Added: SwiftApps/subjobs/simanalyze/part05/mira.conf
===================================================================
--- SwiftApps/subjobs/simanalyze/part05/mira.conf (rev 0)
+++ SwiftApps/subjobs/simanalyze/part05/mira.conf 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1 @@
+link ../../conf/mira.conf
\ No newline at end of file
Property changes on: SwiftApps/subjobs/simanalyze/part05/mira.conf
___________________________________________________________________
Added: svn:special
+ *
Added: SwiftApps/subjobs/vasp/INCAR
===================================================================
--- SwiftApps/subjobs/vasp/INCAR (rev 0)
+++ SwiftApps/subjobs/vasp/INCAR 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,18 @@
+ SYSTEM = Fe4N 5 atoms Pm-3m
+
+ Electronic Relaxation 1
+ ENCUT = 3200 eV
+ NELM = 50
+ EDIFF = 5E-05 stopping-criterion for ELM
+
+ Ionic Relaxation
+ NSW = 400 number of steps for ionic relaxation
+ IBRION = 1 quasi-Newtonian
+ ISIF = 4 forces, relax ions, compute forces
+ EDIFFG = 5E-04 convergence criterion for ir
+
+
+ Magnetic stuff
+ ISPIN = 3
+ MAGMOM = 4*5 1*0
+ RWIGS = 4*1.35 1*1.0
Added: SwiftApps/subjobs/vasp/KPOINTS
===================================================================
--- SwiftApps/subjobs/vasp/KPOINTS (rev 0)
+++ SwiftApps/subjobs/vasp/KPOINTS 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,6 @@
+Automatic mesh
+0
+Monkhorst Pack
+ 1 1 1
+ 0. 0. 0.
+
Added: SwiftApps/subjobs/vasp/POSCAR
===================================================================
--- SwiftApps/subjobs/vasp/POSCAR (rev 0)
+++ SwiftApps/subjobs/vasp/POSCAR 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,13 @@
+ gamma-Fe4N Cubic
+ 0.997298612
+ 3.7900000000000000 0.0000000000000000 0.0000000000000000
+ 0.0000000000000000 3.7900000000000000 0.0000000000000000
+ 0.0000000000000000 0.0000000000000000 3.7900000000000000
+ Fe N
+ 4 1
+Direct
+ 0.0 0.0 0.0
+ 0.0 0.5 0.5
+ 0.5 0.5 0.0
+ 0.5 0.0 0.5
+ 0.5 0.5 0.5
Added: SwiftApps/subjobs/vasp/POTCAR
===================================================================
--- SwiftApps/subjobs/vasp/POTCAR (rev 0)
+++ SwiftApps/subjobs/vasp/POTCAR 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,3678 @@
+ PAW_PBE Fe_pv 06Sep2000
+ 14.0000000000000000
+ parameters from PSCTR are:
+ VRHFIN =Fe: 3pd7s1
+ LEXCH = PE
+ EATOM = 2456.8974 eV, 180.5769 Ry
+
+ TITEL = PAW_PBE Fe_pv 06Sep2000
+ LULTRA = F use ultrasoft PP ?
+ IUNSCR = 1 unscreen: 0-lin 1-nonlin 2-no
+ RPACOR = 1.750 partial core radius
+ POMASS = 55.847; ZVAL = 14.000 mass and valenz
+ RCORE = 2.200 outmost cutoff radius
+ RWIGS = 2.200; RWIGS = 1.164 wigner-seitz radius (au A)
+ ENMAX = 293.238; ENMIN = 219.929 eV
+ RCLOC = 1.701 cutoff for local pot
+ LCOR = T correct aug charges
+ LPAW = T paw PP
+ EAUG = 578.342
+ DEXC = -.002
+ RMAX = 2.693 core radius for proj-oper
+ RAUG = 1.300 factor for augmentation sphere
+ RDEP = 2.296 radius for radial grids
+ QCUT = -4.642; QGAM = 9.285 optimization parameters
+
+ Description
+ l E TYP RCUT TYP RCUT
+ 1 .000 23 2.000
+ 1 -.400 23 2.000
+ 2 .000 23 2.200
+ 2 .000 23 2.200
+ 0 .000 23 2.000
+ 0 2.000 23 2.000
+ 3 .000 7 .000
+ Error from kinetic energy argument (eV)
+ NDATA = 100
+ STEP = 20.000 1.050
+ 199. 197. 196. 193. 192. 189. 187. 185.
+ 182. 179. 177. 173. 170. 166. 162. 157.
+ 153. 148. 144. 137. 132. 127. 120. 115.
+ 110. 103. 95.3 90.5 83.4 76.6 70.0 63.6
+ 57.6 51.8 46.4 41.3 35.1 30.8 25.7 22.3
+ 18.2 14.7 11.7 9.21 7.12 5.42 4.06 2.74
+ 1.96 1.25 .765 .504 .292 .170 .975E-01 .731E-01
+ .649E-01 .632E-01 .619E-01 .576E-01 .500E-01 .404E-01 .306E-01 .205E-01
+ .141E-01 .927E-02 .689E-02 .608E-02 .597E-02 .588E-02 .539E-02 .448E-02
+ .339E-02 .239E-02 .161E-02 .125E-02 .113E-02 .112E-02 .107E-02 .928E-03
+ .710E-03 .503E-03 .369E-03 .311E-03 .302E-03 .288E-03 .247E-03 .185E-03
+ .134E-03 .110E-03 .103E-03 .974E-04 .809E-04 .618E-04 .477E-04 .423E-04
+ .392E-04 .339E-04 .262E-04 .213E-04
+END of PSCTR-controll parameters
+ local part
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+ pseudo wavefunction
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+ ae wavefunction
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+ -.291923580824E-01 -.284000952307E-01 -.274373978241E-01 -.263023460098E-01 -.249939657333E-01
+ -.235122729198E-01 -.218583090782E-01 -.200341671656E-01 -.180430066110E-01 -.158890565087E-01
+ -.135776061524E-01 -.111149822919E-01 -.850851273348E-02 -.576647613306E-02 -.289803799079E-02
+ .868271008447E-04 .317742698748E-02 .636245733779E-02 .963012050375E-02 .129682556736E-01
+ .163644740595E-01 .198062866325E-01 .232812064380E-01 .267768090194E-01 .302807492650E-01
+ .337807596243E-01 .372646755965E-01 .407205212938E-01 .441366371868E-01 .475017902611E-01
+ .508052161010E-01 .540365814686E-01 .571858810087E-01 .602432831776E-01 .631989321856E-01
+ .660427052515E-01 .687639202596E-01 .713509877236E-01 .737910018668E-01 .760692678938E-01
+ .781687651807E-01 .800695486385E-01 .817480926280E-01 .831765835639E-01 .843221689026E-01
+ .851461715846E-01 .856032805383E-01 .856407293072E-01 .851974765745E-01 .842034041498E-01
+ .825785499752E-01 .802323959449E-01 .770632327454E-01 .729576267103E-01 .677900167541E-01
+ .614224728949E-01 .537046517788E-01 .444739889225E-01 .335561720662E-01 .207659451252E-01
+ .590829718095E-02 -.112199070159E-01 -.308277630007E-01 -.531276210327E-01 -.783316948937E-01
+ -.106647977832E+00 -.138275362190E+00 -.173397902213E+00 -.212178158210E+00 -.254749569528E+00
+ -.301207818949E+00 -.351601173439E+00 -.405919818242E+00 -.464084251523E+00 -.525932864509E+00
+ -.591208917696E+00 -.659547216885E+00 -.730460902614E+00
+ End of Dataset
+ PAW_PBE N_h 13Feb2001
+ 5.00000000000000000
+ parameters from PSCTR are:
+ VRHFIN =N: s2p3
+ LEXCH = PE
+ EATOM = 264.5486 eV, 19.4438 Ry
+
+ TITEL = PAW_PBE N_h 13Feb2001
+ LULTRA = F use ultrasoft PP ?
+ IUNSCR = 0 unscreen: 0-lin 1-nonlin 2-no
+ RPACOR = .000 partial core radius
+ POMASS = 14.001; ZVAL = 5.000 mass and valenz
+ RCORE = 1.100 outmost cutoff radius
+ RWIGS = 1.480; RWIGS = .783 wigner-seitz radius (au A)
+ ENMAX = 755.582; ENMIN = 566.687 eV
+ ICORE = 2 local potential
+ LCOR = T correct aug charges
+ LPAW = T paw PP
+ EAUG = 904.640
+ DEXC = .000
+ RMAX = 1.677 core radius for proj-oper
+ RAUG = 1.300 factor for augmentation sphere
+ RDEP = 1.115 radius for radial grids
+ QCUT = -7.452; QGAM = 14.904 optimization parameters
+
+ Description
+ l E TYP RCUT TYP RCUT
+ 0 .000 23 1.100
+ 0 .000 23 1.100
+ 1 .000 23 1.100
+ 1 .000 23 1.100
+ 2 .000 7 1.100
+ Error from kinetic energy argument (eV)
+ NDATA = 100
+ STEP = 20.000 1.050
+ 133. 130. 129. 126. 125. 122. 119. 118.
+ 115. 112. 111. 108. 105. 103. 99.9 97.2
+ 94.5 91.8 89.2 85.3 82.8 80.3 76.7 74.3
+ 72.0 68.6 65.4 63.3 60.2 57.3 54.4 51.7
+ 49.1 46.6 44.2 41.9 39.0 36.9 34.2 32.4
+ 30.0 27.8 25.7 23.7 21.9 20.2 18.6 16.7
+ 15.3 13.7 12.3 11.2 9.96 8.84 7.64 6.74
+ 5.93 5.06 4.30 3.64 3.06 2.56 2.13 1.71
+ 1.40 1.10 .859 .662 .484 .363 .257 .178
+ .121 .800E-01 .493E-01 .317E-01 .197E-01 .130E-01 .957E-02 .842E-02
+ .812E-02 .811E-02 .795E-02 .744E-02 .658E-02 .551E-02 .437E-02 .323E-02
+ .231E-02 .165E-02 .122E-02 .103E-02 .961E-03 .952E-03 .933E-03 .867E-03
+ .745E-03 .605E-03 .452E-03 .343E-03
+END of PSCTR-controll parameters
+ local part
+ 170.075338972103111
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+ -.568653713563E-01 -.643833519108E-01
+ pseudo wavefunction
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+ .469691947805E+00 .492397306341E+00 .515766206280E+00 .539763957058E+00 .564347774484E+00
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+ .720596339034E+00 .747288909493E+00 .773873775956E+00 .800217651740E+00 .826178197315E+00
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+ .965181540373E+00 .984082427784E+00 .100137672298E+01 .101694961907E+01 .103070881580E+01
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+ .106513667140E+01 .105951590919E+01
+ ae wavefunction
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+ .733341181578E-02 .777429781760E-02 .824108215208E-02 .873522808145E-02 .925827612928E-02
+ .981184765789E-02 .103976485641E-01 .110174730928E-01 .116732077659E-01 .123668354262E-01
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+ .306777119238E-01 .324337430530E-01 .342849628725E-01 .362360527272E-01 .382918816234E-01
+ .404575098967E-01 .427381925586E-01 .451393822735E-01 .476667319122E-01 .503260966243E-01
+ .531235353679E-01 .560653118313E-01 .591578946758E-01 .624079570260E-01 .658223751276E-01
+ .694082260906E-01 .731727846277E-01 .771235186983E-01 .812680839588E-01 .856143169185E-01
+ .901702266971E-01 .949439852730E-01 .999439161104E-01 .105178481049E+00 .110656265340E+00
+ .116385960702E+00 .122376346281E+00 .128636267393E+00 .135174611916E+00 .142000284232E+00
+ .149122176577E+00 .156549137709E+00 .164289938775E+00 .172353236286E+00 .180747532104E+00
+ .189481130385E+00 .198562091398E+00 .207998182192E+00 .217796824093E+00 .227965037026E+00
+ .238509380698E+00 .249435892702E+00 .260750023621E+00 .272456569271E+00 .284559600216E+00
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+ .365621686691E+00 .380537300641E+00 .395846667028E+00 .411543816721E+00 .427621250673E+00
+ .444069854932E+00 .460878815830E+00 .478035535801E+00 .495525550466E+00 .513332448110E+00
+ .531437793276E+00 .549821057247E+00 .568459559656E+00 .587328427601E+00 .606400581552E+00
+ .625646761242E+00 .645035609268E+00 .664533834316E+00 .684106476974E+00 .703717293083E+00
+ .723329243608E+00 .742905026222E+00 .762407502025E+00 .781799786725E+00 .801044752505E+00
+ .820103803160E+00 .838935065448E+00 .857491485850E+00 .875719528735E+00 .893559046860E+00
+ .910944422795E+00 .927806518361E+00 .944074703498E+00 .959678416184E+00 .974548104615E+00
+ .988615703182E+00 .100181487992E+01 .101408123971E+01 .102535257998E+01 .103556922786E+01
+ .104467444950E+01 .105261490576E+01 .105934112503E+01 .106480796684E+01 .106897505609E+01
+ .107180717351E+01 .107327459381E+01 .107335336666E+01 .107202553894E+01 .106927931812E+01
+ .106510917804E+01 .105951590919E+01
+ pseudo wavefunction
+ .239377382215E-09 .254451440250E-09 .270474740944E-09 .287507059946E-09 .305611937093E-09
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+ ae wavefunction
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+ -.101715379233E+00 -.112792147163E+00
+ End of Dataset
Added: SwiftApps/subjobs/vasp/cetus.conf
===================================================================
--- SwiftApps/subjobs/vasp/cetus.conf (rev 0)
+++ SwiftApps/subjobs/vasp/cetus.conf 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,34 @@
+sites : cluster
+site.cluster {
+ execution {
+ type: "coaster"
+ URL: "localhost"
+ jobManager: "local:cobalt"
+ options {
+ maxNodesPerJob: 512
+ maxJobs: 1
+ tasksPerNode: 64
+ nodeGranularity: 512
+ maxJobTime = "00:60:00"
+ }
+ }
+ filesystem {
+ type: "local"
+ URL: "localhost"
+ }
+ staging : swift
+ workDirectory: "/home/"${env.USER}"/swift.work"
+ maxParallelTasks: 64
+ initialParallelTasks: 63
+ app.bgsh {
+ executable: "/home/ketan/SwiftApps/subjobs/bg.sh"
+ maxWallTime: "00:15:00"
+ env.SUBBLOCK_SIZE="8"
+ }
+}
+
+executionRetries: 0
+keepSiteDir: true
+providerStagingPinSwiftFiles: false
+alwaysTransferWrapperLog: true
+
Added: SwiftApps/subjobs/vasp/cobaltvasp.sh
===================================================================
--- SwiftApps/subjobs/vasp/cobaltvasp.sh (rev 0)
+++ SwiftApps/subjobs/vasp/cobaltvasp.sh 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+runjob -p 1 --block $COBALT_PARTNAME : /home/naromero/vasp.5.3.3.bgq.power_elpa_sep2013/vasp.bgq.ibm.real
Property changes on: SwiftApps/subjobs/vasp/cobaltvasp.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/subjobs/vasp/job.sh
===================================================================
--- SwiftApps/subjobs/vasp/job.sh (rev 0)
+++ SwiftApps/subjobs/vasp/job.sh 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+qsub -A ExM -t 10 -n 1 --mode script cobaltvasp.sh
Property changes on: SwiftApps/subjobs/vasp/job.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/subjobs/vasp/runcetus.sh
===================================================================
--- SwiftApps/subjobs/vasp/runcetus.sh (rev 0)
+++ SwiftApps/subjobs/vasp/runcetus.sh 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,4 @@
+#! /bin/sh
+
+/home/ketan/swift-k/dist/swift-svn/bin/swift -config cetus.conf -reducedLogging -minimalLogging vasp.swift
+
Property changes on: SwiftApps/subjobs/vasp/runcetus.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/subjobs/vasp/runvasp.sh
===================================================================
--- SwiftApps/subjobs/vasp/runvasp.sh (rev 0)
+++ SwiftApps/subjobs/vasp/runvasp.sh 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,18 @@
+#!/bin/bash
+
+incar=$1
+poscar=$2
+potcar=$3
+kpoints=$4
+latt_factor=$5
+
+echo Command line arguments: $@
+echo
+
+sed -i "2s/.*/$latt_factor/" $poscar
+
+/home/naromero/vasp.5.3.3.bgq.power_elpa_sep2013/vasp.bgq.ibm
+
+cp OUTCAR output/vasp-outcar-${latt_factor}
+cp CONTCAR output/vasp-contcar-${latt_factor}
+
Property changes on: SwiftApps/subjobs/vasp/runvasp.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/subjobs/vasp/vasp.swift
===================================================================
--- SwiftApps/subjobs/vasp/vasp.swift (rev 0)
+++ SwiftApps/subjobs/vasp/vasp.swift 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,23 @@
+type file;
+
+app (file _o, file _e, file _outcar, file _contcar) runvasp (file _vaspreproc, file _vaspostproc, file _vasp_incar, file _vasp_poscar, file _vasp_potcar, file _vasp_kpoints, int _latt_factor) {
+ #bgsh @_vasprun @_vasp_incar @_vasp_poscar @_vasp_potcar @_vasp_kpoints _latt_factor stdout=@_o stderr=@_e;
+ bgsh "/home/naromero/vasp.5.3.3.bgq.power_elpa_sep2013/vasp.bgq.ibm.real" @_vaspreproc @_vaspostproc _latt_factor stdout=@_o stderr=@_e;
+}
+
+# Files
+file vaspreproc <"vaspreproc.sh">;
+file vaspostproc <"vaspostproc.sh">;
+
+file incar <"INCAR">;
+file poscar <"POSCAR">;
+file potcar <"POTCAR">;
+file kpoints <"KPOINTS">;
+
+foreach fact in [1:300]{
+ file output <single_file_mapper; file=strcat("logs/vasp-", fact, ".out.txt")>;
+ file error <single_file_mapper; file=strcat("logs/vasp-", fact, ".err.txt")>;
+ file outcar <single_file_mapper; file=strcat("output/vasp-outcar-", fact)>;
+ file contcar <single_file_mapper; file=strcat("output/vasp-contcar-", fact)>;
+ (output, error, outcar, contcar) = runvasp(vaspreproc, vaspostproc, incar, poscar, potcar, kpoints, fact);
+}
Added: SwiftApps/subjobs/vasp/vaspostproc.sh
===================================================================
--- SwiftApps/subjobs/vasp/vaspostproc.sh (rev 0)
+++ SwiftApps/subjobs/vasp/vaspostproc.sh 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+latt_factor=$4
+
+echo Command line arguments: $@
+
+cp OUTCAR output/vasp-outcar-${latt_factor}
+cp CONTCAR output/vasp-contcar-${latt_factor}
+
Property changes on: SwiftApps/subjobs/vasp/vaspostproc.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/subjobs/vasp/vaspreproc.sh
===================================================================
--- SwiftApps/subjobs/vasp/vaspreproc.sh (rev 0)
+++ SwiftApps/subjobs/vasp/vaspreproc.sh 2015-04-04 17:21:19 UTC (rev 8422)
@@ -0,0 +1,9 @@
+#!/bin/bash
+
+latt_factor=$4
+
+echo Command line arguments: $@
+echo
+
+#sed -i "2s/.*/$latt_factor/" POSCAR
+
Property changes on: SwiftApps/subjobs/vasp/vaspreproc.sh
___________________________________________________________________
Added: svn:executable
+ *
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