[Swift-commit] r8305 - in SwiftApps: . ematter
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Sun Nov 23 18:50:37 CST 2014
Author: ketan
Date: 2014-11-23 18:50:37 -0600 (Sun, 23 Nov 2014)
New Revision: 8305
Added:
SwiftApps/ematter/
SwiftApps/ematter/apps
SwiftApps/ematter/cf
SwiftApps/ematter/genfdf
SwiftApps/ematter/lastlammpsdump2xyz.py
SwiftApps/ematter/pasta
SwiftApps/ematter/runbgq
SwiftApps/ematter/runblues
SwiftApps/ematter/sites.blues.xml
SwiftApps/ematter/sites.cobalt-local.xml
SwiftApps/ematter/sites.cobalt.xml
SwiftApps/ematter/sites.local.xml
SwiftApps/ematter/workflow.bgq.swift
SwiftApps/ematter/workflow.blues.swift
Log:
adding ematter
Added: SwiftApps/ematter/apps
===================================================================
--- SwiftApps/ematter/apps (rev 0)
+++ SwiftApps/ematter/apps 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,17 @@
+localhost cat /bin/cat null null null
+localhost python /usr/bin/python null null null
+localhost bash /bin/bash null null null
+#
+cluster bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null
+cluster2 bgsh /home/ketan/SwiftApps/subjobs/bg.sh null null null
+#
+blues lammps lmp_linux null null null
+blues smeagol /home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg null null null
+blues bash /bin/bash null null null
+blues python /soft/python/2.7.6/bin/python null null null
+#
+localblues lammps lmp_blues null null null
+localblues smeagol /home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg null null null
+localblues mpiexec mpiexec null null null
+localblues bash /bin/bash null null null
+localblues python /soft/python/2.7.6/bin/python null null null
Added: SwiftApps/ematter/cf
===================================================================
--- SwiftApps/ematter/cf (rev 0)
+++ SwiftApps/ematter/cf 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,7 @@
+use.provider.staging=true
+wrapperlog.always.transfer=false
+execution.retries=0
+provider.staging.pin.swiftfiles=false
+sitedir.keep=false
+use.wrapper.staging=false
+
Added: SwiftApps/ematter/genfdf
===================================================================
--- SwiftApps/ematter/genfdf (rev 0)
+++ SwiftApps/ematter/genfdf 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,11 @@
+#!/bin/bash
+
+startrng=$1
+endrng=$2
+infdf=$3
+
+for i in $(seq $startrng $endrng)
+do
+sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial $i.D0 eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal $i.D0 eV/" $infdf > $i.fdf
+done
+
Property changes on: SwiftApps/ematter/genfdf
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/ematter/lastlammpsdump2xyz.py
===================================================================
--- SwiftApps/ematter/lastlammpsdump2xyz.py (rev 0)
+++ SwiftApps/ematter/lastlammpsdump2xyz.py 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,22 @@
+#!/usr/bin/env python
+
+# Set the import path to find the Pizza tools.
+# Warning! Nonportable.
+
+import sys
+sys.path.append('/home/ketan/pizza-2Jul14/src')
+import dump, xyz
+
+if __name__ == '__main__':
+ # read the dump file (the first cl arg)
+ d = dump.dump(sys.argv[1])
+ # Get array of times
+ t = d.time()
+ # Convert the list of dumped states to xyz (in memory)
+ x = xyz.xyz(d)
+ # Dump just the last time instance to a file (the second cl arg)
+ # This can be easily changed to use any other time slice between 0
+ # and len(t)-1 inclusive. This will require additional validation
+ # of the additional input parameter, though.
+ x.single(t[-1],sys.argv[2])
+
Property changes on: SwiftApps/ematter/lastlammpsdump2xyz.py
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/ematter/pasta
===================================================================
--- SwiftApps/ematter/pasta (rev 0)
+++ SwiftApps/ematter/pasta 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,17 @@
+#!/bin/bash
+
+filexyz=$1
+filefdf=$2
+fileresfdf=$3
+#extract after the last occurrence of Atom and move first column to last
+tac $filexyz | sed -n '0,/^Atoms/p' | sed '$d' | tac | awk '{print $2, $3, $4, $1}' > tmp.extract
+
+#delete everything between the coordinates block
+sed -i '/\%block AtomicCoordinatesAndAtomicSpecies/,/%endblock AtomicCoordinatesAndAtomicSpecies/{//!d}' $filefdf
+
+cp $filefdf $fileresfdf
+
+#insert the tmp.extract between the above patterns
+sed -i '/\%block AtomicCoordinatesAndAtomicSpecies/ r tmp.extract' $fileresfdf
+
+echo "Pasta served"
Property changes on: SwiftApps/ematter/pasta
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/ematter/runbgq
===================================================================
--- SwiftApps/ematter/runbgq (rev 0)
+++ SwiftApps/ematter/runbgq 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,4 @@
+#! /bin/sh
+
+/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.cobalt-local.xml -config cf -tc.file apps workflow.swift
+#$HOME/swift-0.95-main/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt-local.xml -config cf -tc.file apps workflow.swift
Property changes on: SwiftApps/ematter/runbgq
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/ematter/runblues
===================================================================
--- SwiftApps/ematter/runblues (rev 0)
+++ SwiftApps/ematter/runblues 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,4 @@
+#! /bin/sh
+
+/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.blues.xml -config cf -tc.file apps workflow.blues.swift
+#$HOME/swift-0.95-main/cog/modules/swift/dist/swift-svn/bin/swift -sites.file cobalt-local.xml -config cf -tc.file apps workflow.swift
Property changes on: SwiftApps/ematter/runblues
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/ematter/sites.blues.xml
===================================================================
--- SwiftApps/ematter/sites.blues.xml (rev 0)
+++ SwiftApps/ematter/sites.blues.xml 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,18 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
+<pool handle="blues">
+ <execution provider="coaster" jobmanager="local:pbs"/>
+ <filesystem provider="local" url="none" />
+ <profile namespace="globus" key="maxtime">2300</profile>
+ <profile namespace="globus" key="maxWalltime">00:20:00</profile>
+ <profile namespace="globus" key="jobsPerNode">16</profile>
+ <profile namespace="globus" key="slots">1</profile>
+ <profile namespace="globus" key="ppn">16</profile>
+ <profile namespace="globus" key="nodeGranularity">1</profile>
+ <profile namespace="globus" key="maxnodes">1</profile>
+ <profile namespace="karajan" key="jobThrottle">0.20</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <workdirectory>/tmp/swift.workdir</workdirectory>
+</pool>
+</config>
+
Added: SwiftApps/ematter/sites.cobalt-local.xml
===================================================================
--- SwiftApps/ematter/sites.cobalt-local.xml (rev 0)
+++ SwiftApps/ematter/sites.cobalt-local.xml 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,38 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
+
+<pool handle="cluster">
+<execution provider="coaster" jobmanager="local:cobalt" />
+
+<profile namespace="globus" key="slots">1</profile>
+<profile namespace="globus" key="mode">script</profile>
+
+<profile namespace="karajan" key="jobThrottle">0.99</profile>
+<profile namespace="karajan" key="initialScore">10000</profile>
+<profile namespace="globus" key="maxwalltime">00:55:00</profile>
+<profile namespace="globus" key="walltime">3500</profile>
+<profile namespace="globus" key="maxTime">3500</profile>
+
+<profile namespace="globus" key="maxnodes">32</profile>
+<profile namespace="globus" key="nodegranularity">32</profile>
+<profile key="SUBBLOCK_SIZE" namespace="env">8</profile>
+<profile key="WORKER_LOGGING_LEVEL" namespace="env">DEBUG</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">TRUE</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">ON</profile>
+<profile key="WORKER_LOG_DIR" namespace="env">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+<profile namespace="globus" key="workerLoggingDirectory">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="jobsPerNode">4</profile>
+
+<workdirectory>/home/ketan/swiftwork</workdirectory>
+<filesystem provider="local"/>
+
+</pool>
+<pool handle="localhost">
+<execution provider="coaster" url="none" jobmanager="local:local" />
+<workdirectory>/home/ketan/swiftwork</workdirectory>
+<profile namespace="karajan" key="jobThrottle">0.09</profile>
+<filesystem provider="local"/>
+</pool>
+</config>
+
Added: SwiftApps/ematter/sites.cobalt.xml
===================================================================
--- SwiftApps/ematter/sites.cobalt.xml (rev 0)
+++ SwiftApps/ematter/sites.cobalt.xml 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,57 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
+
+<pool handle="cluster">
+<execution provider="coaster" jobmanager="local:cobalt" />
+
+<profile namespace="globus" key="slots">2</profile>
+<profile namespace="globus" key="mode">script</profile>
+
+<profile namespace="karajan" key="jobThrottle">2.99</profile>
+<profile namespace="karajan" key="initialScore">10000</profile>
+<profile namespace="globus" key="maxwalltime">00:40:00</profile>
+<profile namespace="globus" key="walltime">2050</profile>
+
+<profile namespace="globus" key="maxnodes">64</profile>
+<profile namespace="globus" key="nodegranularity">64</profile>
+<profile key="SUBBLOCK_SIZE" namespace="env">8</profile>
+<profile key="WORKER_LOGGING_LEVEL" namespace="env">DEBUG</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">TRUE</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">ON</profile>
+<profile key="WORKER_LOG_DIR" namespace="env">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+<profile namespace="globus" key="workerLoggingDirectory">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="jobsPerNode">8</profile>
+
+<workdirectory>/home/ketan/swiftwork</workdirectory>
+<filesystem provider="local"/>
+
+</pool>
+
+<pool handle="cluster2">
+<execution provider="coaster" jobmanager="local:cobalt" />
+
+<profile namespace="globus" key="slots">2</profile>
+<profile namespace="globus" key="mode">script</profile>
+
+<profile namespace="karajan" key="jobThrottle">2.99</profile>
+<profile namespace="karajan" key="initialScore">10000</profile>
+<profile namespace="globus" key="maxwalltime">00:40:00</profile>
+<profile namespace="globus" key="walltime">2050</profile>
+
+<profile namespace="globus" key="maxnodes">64</profile>
+<profile namespace="globus" key="nodegranularity">64</profile>
+<profile key="SUBBLOCK_SIZE" namespace="env">8</profile>
+<profile key="WORKER_LOGGING_LEVEL" namespace="env">DEBUG</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">TRUE</profile>
+<profile key="ENABLE_WORKER_LOGGING" namespace="env">ON</profile>
+<profile key="WORKER_LOG_DIR" namespace="env">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="workerLoggingLevel">DEBUG</profile>
+<profile namespace="globus" key="workerLoggingDirectory">/home/ketan/workerlogs</profile>
+<profile namespace="globus" key="jobsPerNode">8</profile>
+
+<workdirectory>/home/ketan/swiftwork</workdirectory>
+<filesystem provider="local"/>
+
+</pool>
+</config>
Added: SwiftApps/ematter/sites.local.xml
===================================================================
--- SwiftApps/ematter/sites.local.xml (rev 0)
+++ SwiftApps/ematter/sites.local.xml 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
+<pool handle="localblues">
+<execution provider="coaster" url="none" jobmanager="local:local" />
+<profile namespace="globus" key="maxwalltime">09:55:00</profile>
+<profile namespace="globus" key="walltime">35000</profile>
+<profile namespace="globus" key="maxTime">36000</profile>
+<workdirectory>/home/ketan/swiftwork</workdirectory>
+<profile namespace="karajan" key="jobThrottle">0.09</profile>
+<filesystem provider="local"/>
+</pool>
+</config>
+
Added: SwiftApps/ematter/workflow.bgq.swift
===================================================================
--- SwiftApps/ematter/workflow.bgq.swift (rev 0)
+++ SwiftApps/ematter/workflow.bgq.swift 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,131 @@
+type file;
+
+// Lammps app definition
+app (file _dump, file _out,
+ file _err) lammps_app (string _lammps_exe, file _in,
+ file _geo, file _eam)
+{
+ bgsh _lammps_exe "-in" @_in stdout=@_out stderr=@_err;
+}
+
+// Pizza app definition
+app (file _xyz, file _out, file _err) pizza_app (file _pizza_src, file _dump)
+{
+ python @_pizza_src @_dump @_xyz stdout=@_out stderr=@_err;
+}
+
+// Pasta app definition
+app (file _fdf, file _out, file _err) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp)
+{
+ bash @_pasta_src @_xyz @_fdf_tmp @_fdf stdout=@_out stderr=@_err;
+}
+
+/* smeagol lead inputs
+Au.psf Au.sic.psf input.fdf
+O.psf O.sic.psf Ti.psf Ti.sic.psf */
+
+//Smeagol lead app definition
+app (file _au3dm, file _au3hst,
+ file _bulklft, file _bulkrgt,
+ file _out, file _err) smeagol_lead_app (string _smeagol_exe, file _aupsf,
+ file _ausicpsf, file _inputfdf,
+ file _opsf, file _osicpsf,
+ file _tipsf, file _tisicpsf)
+{
+ bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out stderr=@_err;
+}
+
+/* smeagol transport V0 inputs
+Au3.DM Au3.HST Au.psf
+Au.sic.psf bulklft.DAT bulkrgt.DAT
+input.fdf O.psf O.sic.psf
+Ti.psf Ti.sic.psf */
+
+//Smeagol transport V0 app definition
+app (file _tio2auhm, file _tio2audm,
+ file _out, file _err) smeagol_v0_app ( string _smeagol_exe, file _au3dm,
+ file _au3hst, file _aupsf,
+ file _ausicpsf, file _bulklft,
+ file _bulkrgt, file _inputfdf,
+ file _opsf, file _osicpsf,
+ file _tipsf, file _tisicpsf )
+{
+ bgsh _smeagol_exe stdin=@_inputfdf stdout=@_out stderr=@_err;
+}
+
+//Smeagol transport Vn app definition
+//app () smeagol_vn_app (){}
+
+// Files
+file lammps_in <"in.lammps">;
+file lammps_geo <"AuTiO.geo">;
+file lammps_eam <"Au_u3.eam">;
+
+file lammps_out <"out.lammps">;
+file lammps_err <"err.lammps">;
+file lammps_dump <"lammps.dump">;
+
+string lammps_exe="/soft/applications/lammps/24Apr13/lmp_bgq_xlomp";
+
+//Invoke lammps
+(lammps_dump, lammps_out, lammps_err) = lammps_app (lammps_exe, lammps_in,
+ lammps_geo, lammps_eam);
+
+file pizza_src<"lastlammpsdump2xyz.py">;
+
+file pizza_out <"out.pizza">;
+file pizza_err <"err.pizza">;
+file xyz <"forsmeagol.xyz">;
+
+//Invoke pizza
+(xyz, pizza_out, pizza_err) = pizza_app(pizza_src, lammps_dump);
+
+file fdf_in<"input_leads.fdf">;
+
+file pasta_src<"pasta">;
+
+file smeagol_lead_out <"out.smeagol.lead">;
+file smeagol_lead_err <"err.smeagol.lead">;
+file au3dm <"Au3.DM">;
+file au3hst <"Au3.HST">;
+file bulklft <"bulklft.DAT">;
+file bulkrgt <"bulkrgt.DAT">;
+
+file aupsf <"Au.psf">;
+file ausicpsf <"Au.sic.psf">;
+file opsf <"O.psf">;
+file osicpsf <"O.sic.psf">;
+file tipsf <"Ti.psf">;
+file tisicpsf <"Ti.sic.psf">;
+
+string smeagol_exe="/gpfs/mira-fs1/projects/Oxygen_defects_ALCC/share/bin/smeagol-1.2_csg";
+
+//Invoke smeagol lead
+(au3dm, au3hst,
+ bulklft, bulkrgt,
+ smeagol_lead_out,
+ smeagol_lead_err) = smeagol_lead_app (smeagol_exe, aupsf,
+ ausicpsf, fdf_in,
+ opsf, osicpsf,
+ tipsf, tisicpsf);
+
+file fdf_v0<"input_t0.fdf">;
+file fdf_proc<"input_proc_t0.fdf">;
+file pasta_out<"out.pasta">;
+file pasta_err<"err.pasta">;
+
+//Invoke pasta
+(fdf_proc, pasta_out, pasta_err) = pasta_app(pasta_src, xyz, fdf_v0);
+
+file smeagol_transport_out<"out.smeagol_transport">;
+file smeagol_transport_err<"err.smeagol_transport">;
+file tio2auhm<"TiO2Au.HM">;
+file tio2audm<"TiO2Au.DM">;
+//Invoke smeagol transport V0
+(tio2auhm, tio2audm,
+ smeagol_transport_out, smeagol_transport_err) = smeagol_v0_app(smeagol_exe, au3dm,
+ au3hst, aupsf, ausicpsf,
+ bulklft, bulkrgt,
+ fdf_proc, opsf, osicpsf,
+ tipsf, tisicpsf);
+
Added: SwiftApps/ematter/workflow.blues.swift
===================================================================
--- SwiftApps/ematter/workflow.blues.swift (rev 0)
+++ SwiftApps/ematter/workflow.blues.swift 2014-11-24 00:50:37 UTC (rev 8305)
@@ -0,0 +1,147 @@
+type file;
+
+// Lammps app definition
+app (file _dump) lammps_app (file _in,
+ file _geo, file _eam)
+{
+ lammps "-in" @_in stdout=@_out stderr=@_err;
+}
+
+// Pizza app definition
+app (file _xyz) pizza_app (file _pizza_src, file _dump)
+{
+ python @_pizza_src @_dump @_xyz stdout=@_out stderr=@_err;
+}
+
+// Pasta app definition
+app (file _fdf) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp)
+{
+ bash @_pasta_src @_xyz @_fdf_tmp @_fdf;
+}
+
+/* smeagol lead inputs
+Au.psf Au.sic.psf input.fdf
+O.psf O.sic.psf Ti.psf Ti.sic.psf */
+
+//Smeagol lead app definition
+app (file _au3dm, file _au3hst,
+ file _bulklft, file _bulkrgt,
+ file _out) smeagol_lead_app (file _aupsf,
+ file _ausicpsf, file _inputfdf,
+ file _opsf, file _osicpsf,
+ file _tipsf, file _tisicpsf)
+{
+ //smeagol stdin=@_inputfdf stdout=@_out stderr=@_err;
+ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err;
+}
+
+/* smeagol transport V0 inputs
+Au3.DM Au3.HST Au.psf
+Au.sic.psf bulklft.DAT bulkrgt.DAT
+input.fdf O.psf O.sic.psf
+Ti.psf Ti.sic.psf */
+
+//Smeagol transport V0 app definition
+app (file _tio2auhm, file _tio2audm,
+ file _out) smeagol_v0_app ( file _au3dm,
+ file _au3hst, file _aupsf,
+ file _ausicpsf, file _bulklft,
+ file _bulkrgt, file _inputfdf,
+ file _opsf, file _osicpsf,
+ file _tipsf, file _tisicpsf )
+{
+ //smeagol stdin=@_inputfdf stdout=@_out stderr=@_err;
+ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err;
+}
+
+app (file[] _fdf) gen_fdf(file _infdf, int _rstart, int _rend){
+ genfdf _rstart _rend @_infdf;
+}
+
+
+//Smeagol transport Vn app definition
+app (file _out) smeagol_vn_app ( file _au3dm,
+ file _au3hst, file _aupsf,
+ file _ausicpsf, file _bulklft,
+ file _bulkrgt, file _inputfdf,
+ file _opsf, file _osicpsf,
+ file _tipsf, file _tisicpsf ){
+
+ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out stderr=@_err;
+}
+
+// Files
+file lammps_in <"in.lammps">;
+file lammps_geo <"AuTiO.geo">;
+file lammps_eam <"Au_u3.eam">;
+
+file lammps_dump <"lammps.dump">;
+
+//Invoke lammps
+(lammps_dump) = lammps_app (lammps_in,
+ lammps_geo, lammps_eam);
+
+file pizza_src<"lastlammpsdump2xyz.py">;
+
+file xyz <"forsmeagol.xyz">;
+
+//Invoke pizza
+(xyz) = pizza_app(pizza_src, lammps_dump);
+
+file fdf_in<"input_leads.fdf">;
+
+file pasta_src<"pasta">;
+
+file smeagol_lead_out <"out.smeagol.lead">;
+file au3dm <"Au3.DM">;
+file au3hst <"Au3.HST">;
+file bulklft <"bulklft.DAT">;
+file bulkrgt <"bulkrgt.DAT">;
+
+file aupsf <"Au.psf">;
+file ausicpsf <"Au.sic.psf">;
+file opsf <"O.psf">;
+file osicpsf <"O.sic.psf">;
+file tipsf <"Ti.psf">;
+file tisicpsf <"Ti.sic.psf">;
+
+//Invoke smeagol lead
+(au3dm, au3hst,
+ bulklft, bulkrgt,
+ smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_in,
+ opsf, osicpsf,
+ tipsf, tisicpsf);
+
+file fdf_v0<"input_t0.fdf">;
+file smeagol_transport_out<"out.smeagol_transport">;
+file tio2auhm<"TiO2Au.HM">;
+file tio2audm<"TiO2Au.DM">;
+
+//Invoke smeagol transport V0
+(tio2auhm, tio2audm,
+ smeagol_transport_out) = smeagol_v0_app(au3dm, au3hst,
+ aupsf, ausicpsf,
+ bulklft, bulkrgt,
+ fdf_v0, opsf, osicpsf,
+ tipsf, tisicpsf);
+
+
+file fdf_v1<"input_t1.fdf">;
+file fdf_proc_v1<"input_proc_t1.fdf">;
+
+//Invoke pasta
+(fdf_proc_v1) = pasta_app(pasta_src, xyz, fdf_v1);
+
+file smeagol_transport_out2<"out.smeagol_transport2">;
+
+int rstart=1;
+int rend=2;
+foreach i in [rstart:rend]
+{
+
+(smeagol_transport_out2) = smeagol_vn_app(au3dm, au3hst,
+ aupsf, ausicpsf,
+ bulklft, bulkrgt,
+ fdf_proc_v1, opsf, osicpsf,
+ tipsf, tisicpsf);
+}
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