[Swift-commit] r8370 - SwiftApps/ematter/galaxy

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2015-01-21 14:28:56 -0600 (Wed, 21 Jan 2015)
New Revision: 8370

Added:
   SwiftApps/ematter/galaxy/pastawrap
   SwiftApps/ematter/galaxy/smeagol0wrap
   SwiftApps/ematter/galaxy/smeagol_leadwrap
Log:
wrappers

Added: SwiftApps/ematter/galaxy/pastawrap
===================================================================
--- SwiftApps/ematter/galaxy/pastawrap	                        (rev 0)
+++ SwiftApps/ematter/galaxy/pastawrap	2015-01-21 20:28:56 UTC (rev 8370)
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+src=$1
+dump=$2
+xyz=$3
+
+ln -s $src pizzasrc.py
+ln -s $dump dump.lammps 
+
+python pizzasrc.py dump.lammps xyz.xyz
+
+mv xyz.xyz $xyz
+


Property changes on: SwiftApps/ematter/galaxy/pastawrap
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftApps/ematter/galaxy/smeagol0wrap
===================================================================
--- SwiftApps/ematter/galaxy/smeagol0wrap	                        (rev 0)
+++ SwiftApps/ematter/galaxy/smeagol0wrap	2015-01-21 20:28:56 UTC (rev 8370)
@@ -0,0 +1,79 @@
+#!/bin/bash
+
+
+#  swiftsmeagol0.py
+#   "${_au3dm}"
+#   "${_au3hst}"
+#   "${_aupsf}"
+#   "${_ausicpsf}" 
+#   "${_bulklft}"
+#   "${_bulkrgt}"
+#   "${_inputfdf}"
+#   "${_opsf}"
+#   "${_osicpsf}"
+#   "${_tipsf}"
+#   "${_tisicpsf}"
+#   "${_tio2auhm}"
+#   "${_tio2audm}"
+#   "${_out}"
+#   "${local_or_compute}"
+
+au3dm=$1
+shift
+
+au3hst=$1
+shift
+
+aupsf=$1
+shift
+
+ausicpsf=$1
+shift
+
+bulklft=$1
+shift
+
+bulkrgt=$1
+shift
+
+inputfdf=$1
+shift
+
+opsf=$1
+shift
+
+osicpsf=$1
+shift
+
+tipsf=$1
+shift
+
+tisicpsf=$1
+shift
+
+tio2auhm=$1
+shift
+
+tio2audm=$1
+shift
+
+out=$1
+
+ln -s $au3dm Au3.DM
+ln -s $au3hst Au3.HST
+ln -s $aupsf Au.psf
+ln -s $ausicpsf Au.sic.psf
+ln -s $bulklft bulklft.DAT 
+ln -s $bulkrgt bulkrgt.DAT
+ln -s $inputfdf input.fdf
+ln -s $opsf O.psf
+ln -s $osicpsf O.sic.psf
+ln -s $tipsf Ti.psf
+ln -s $tisicpsf Ti.sic.psf
+
+mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" < input.fdf > out0.txt;
+
+mv out0.txt $out
+mv TiO2Au.HM $tio2auhm
+mv TiO2Au.DM $tio2audm
+


Property changes on: SwiftApps/ematter/galaxy/smeagol0wrap
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftApps/ematter/galaxy/smeagol_leadwrap
===================================================================
--- SwiftApps/ematter/galaxy/smeagol_leadwrap	                        (rev 0)
+++ SwiftApps/ematter/galaxy/smeagol_leadwrap	2015-01-21 20:28:56 UTC (rev 8370)
@@ -0,0 +1,71 @@
+#!/bin/bash
+
+#swiftsmeagol_lead.py
+#  "${_aupsf}"
+#  "${_ausicpsf}" 
+#  "${_inputfdf}"
+#  "${_opsf}"
+#  "${_osicpsf}"
+#  "${_tipsf}"
+#  "${_tisicpsf}"
+#  "${_au3dm}"
+#  "${_au3hst}"
+#  "${_bulklft}"
+#  "${_bulkrgt}"
+#  "${_out}"
+#  "${local_or_compute}"
+#
+
+aupsf=$1
+shift
+
+ausicpsf=$1
+shift
+
+inputfdf=$1
+shift
+
+opsf=$1
+shift
+
+osicpsf=$1
+shift
+
+tipsf=$1
+shift
+
+tisicpsf=$1
+shift
+
+au3dm=$1
+shift
+
+au3hst=$1
+shift
+
+bulklft=$1
+shift
+
+bulkrgt=$1
+shift
+
+out=$1
+
+
+ln -s $aupsf Au.psf
+ln -s $ausicpsf Au.sic.psf
+ln -s $inputfdf input.fdf
+ln -s $opsf O.psf
+ln -s $osicpsf O.sic.psf
+ln -s $tipsf Ti.psf
+ln -s $tisicpsf Ti.sic.psf
+
+mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" < input.fdf > out_lead.txt;
+
+mv out_lead.txt $out
+mv Au3.DM $au3dm 
+mv Au3.HST $au3hst
+mv bulklft.DAT $bulklft 
+mv bulkrgt.DAT $bulkrgt 
+
+


Property changes on: SwiftApps/ematter/galaxy/smeagol_leadwrap
___________________________________________________________________
Added: svn:executable
   + *