[Swift-commit] r8310 - SwiftApps/ematter

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-11-25 10:06:54 -0600 (Tue, 25 Nov 2014)
New Revision: 8310

Added:
   SwiftApps/ematter/runlocal
Modified:
   SwiftApps/ematter/sites.local.xml
   SwiftApps/ematter/workflow.blues.swift
Log:
more comments in code

Added: SwiftApps/ematter/runlocal
===================================================================
--- SwiftApps/ematter/runlocal	                        (rev 0)
+++ SwiftApps/ematter/runlocal	2014-11-25 16:06:54 UTC (rev 8310)
@@ -0,0 +1,3 @@
+#! /bin/sh
+
+/home/ketan/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift -sites.file sites.local.xml -config cf -tc.file apps workflow.blues.swift


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

Modified: SwiftApps/ematter/sites.local.xml
===================================================================
--- SwiftApps/ematter/sites.local.xml	2014-11-25 15:42:32 UTC (rev 8309)
+++ SwiftApps/ematter/sites.local.xml	2014-11-25 16:06:54 UTC (rev 8310)
@@ -1,4 +1,8 @@
 <?xml version="1.0" encoding="UTF-8"?>
+<!--
+  This is a sites file. This file defines
+  the properties of an execution site used by Swift
+-->
 <config xmlns="http://www.ci.uchicago.edu/swift/SwiftSites">
 <pool handle="localblues">
 <execution provider="coaster" url="none" jobmanager="local:local" />

Modified: SwiftApps/ematter/workflow.blues.swift
===================================================================
--- SwiftApps/ematter/workflow.blues.swift	2014-11-25 15:42:32 UTC (rev 8309)
+++ SwiftApps/ematter/workflow.blues.swift	2014-11-25 16:06:54 UTC (rev 8310)
@@ -68,9 +68,9 @@
 }
 
 /* == Generate fdfs app definition == */
-app (file _fdf) gen_fdf(float _r, file _infdf)
+app (file _fdf) gen_fdf(file _genfdf_src, float _r, file _infdf)
 {
-  genfdf _r @_infdf stdout=@_fdf;
+  bash @_genfdf_src _r @_infdf stdout=@_fdf;
 }
 
 /* == Smeagol transport Vn app definition == */
@@ -84,7 +84,7 @@
   mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out; 
 }
 
-/* == Input files definitions == */
+/* == Input files definitions: Make sure these files are available in the current directory == */
 file lammps_in <"in.lammps">;
 file lammps_geo <"AuTiO.geo">;
 file lammps_eam <"Au_u3.eam">;
@@ -101,17 +101,17 @@
 
 file pizza_src<"lastlammpsdump2xyz.py">;
 file pasta_src<"pasta">;
+file genfdf_src<"genfdf">;
 
-
 /* == Output files definitions == */
 file xyz <"forsmeagol.xyz">;
 file lammps_dump <"lammps.dump">;
 file fdf_proc<"input_proc.fdf">;
 
-file smeagol_lead_out <"out.smeagol.lead">;
+file smeagol_lead_out <"smeagol_out/out.smeagol.lead">;
+file smeagol_transport_out<"smeagol_out/out.smeagol_transport">;
 file au3dm <"Au3.DM">;
 file au3hst <"Au3.HST">;
-file smeagol_transport_out<"out.smeagol_transport">;
 
 file bulklft <"bulklft.DAT">;
 file bulkrgt <"bulkrgt.DAT">;
@@ -119,7 +119,7 @@
 file tio2auhm<"TiO2Au.HM">;
 file tio2audm<"TiO2Au.DM">;
 
-file[float] smeagol_transport_outn<simple_mapper; location="smeagol_outn",
+file[float] smeagol_transport_outn<simple_mapper; location="smeagol_out",
                               prefix="smeagol.", suffix=".out">;
 
 file[float] fdf_proc_vn;
@@ -132,6 +132,9 @@
 
 /* == End files and variable declaration == */
 
+
+/* == Invocation of apps == */
+
 /* == Invoke lammps == */
 (lammps_dump) = lammps_app (lammps_in, lammps_geo, lammps_eam);
 
@@ -166,7 +169,7 @@
 foreach i in [Vstart:Vend:Vstep]
 {
 /* == generate fdfs for different voltages == */
-fdf_proc_vn[i]=gen_fdf(i,fdf_proc);
+fdf_proc_vn[i]=gen_fdf(genfdf_src, i,fdf_proc);
 
 (smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst,
                                           aupsf, ausicpsf,