[Swift-commit] r8309 - SwiftApps/ematter

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-11-25 09:42:32 -0600 (Tue, 25 Nov 2014)
New Revision: 8309

Modified:
   SwiftApps/ematter/genfdf
   SwiftApps/ematter/workflow.blues.swift
Log:
float index type

Modified: SwiftApps/ematter/genfdf
===================================================================
--- SwiftApps/ematter/genfdf	2014-11-25 02:34:48 UTC (rev 8308)
+++ SwiftApps/ematter/genfdf	2014-11-25 15:42:32 UTC (rev 8309)
@@ -3,5 +3,5 @@
 i=$1
 infdf=$2
 
-sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial                  $i.D0 eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal                    $i.D0 eV/" $infdf
+sed -e "s/VInitial[[:space:]]* 1.D0 eV/VInitial                  $i eV/" -e "s/VFinal[[:space:]]* 1.D0 eV/VFinal                    $i eV/" $infdf
 

Modified: SwiftApps/ematter/workflow.blues.swift
===================================================================
--- SwiftApps/ematter/workflow.blues.swift	2014-11-25 02:34:48 UTC (rev 8308)
+++ SwiftApps/ematter/workflow.blues.swift	2014-11-25 15:42:32 UTC (rev 8309)
@@ -1,5 +1,19 @@
+/* ==
+This is a Swift workflow script for the ematter application. The script contains the following parts:
+
+-- A one-line type declaration
+-- App function definitions
+-- Input files and variables definitions
+-- Output files definitions
+-- Invocation of app functions
+== */
+
+
 type file;
 
+
+/* == App function definitions == */
+
 /* == Lammps app definition == */
 app (file _dump) lammps_app (file _in, file _geo, file _eam)
 {
@@ -59,7 +73,6 @@
   genfdf _r @_infdf stdout=@_fdf;
 }
 
-
 /* == Smeagol transport Vn app definition == */
 app (file _out) smeagol_vn_app ( file _au3dm,
                    file _au3hst, file _aupsf,
@@ -71,32 +84,33 @@
   mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out; 
 }
 
-/* == Input and output files definition and mappings == */
+/* == Input files definitions == */
 file lammps_in <"in.lammps">;
 file lammps_geo <"AuTiO.geo">;
 file lammps_eam <"Au_u3.eam">;
 
-file lammps_dump <"lammps.dump">;
+file fdf_leads<"input_leads.fdf">;
+file fdf_v0<"input_t0.fdf">;
 
+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">;
+
 file pizza_src<"lastlammpsdump2xyz.py">;
 file pasta_src<"pasta">;
 
+
+/* == Output files definitions == */
 file xyz <"forsmeagol.xyz">;
+file lammps_dump <"lammps.dump">;
+file fdf_proc<"input_proc.fdf">;
 
-file fdf_in<"input_leads.fdf">;
-file fdf_v0<"input_t0.fdf">;
-file fdf_v1<"input_t1.fdf">;
-file fdf_proc_v1<"input_proc_t1.fdf">;
-
 file smeagol_lead_out <"out.smeagol.lead">;
 file au3dm <"Au3.DM">;
 file au3hst <"Au3.HST">;
-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">;
 file smeagol_transport_out<"out.smeagol_transport">;
 
 file bulklft <"bulklft.DAT">;
@@ -105,13 +119,14 @@
 file tio2auhm<"TiO2Au.HM">;
 file tio2audm<"TiO2Au.DM">;
 
-file smeagol_transport_outn[]<simple_mapper; location="smeagol_outn",
+file[float] smeagol_transport_outn<simple_mapper; location="smeagol_outn",
                               prefix="smeagol.", suffix=".out">;
 
-file fdf_proc_vn[];
+file[float] fdf_proc_vn;
 
-float Vstart=0.1;
-float Vend=1.0;
+float Vstart=0.1; /*== Change this value to change the starting voltage ==*/
+float Vend=1.0; /*== Change this value to change the ending voltage ==*/
+
 float Vstep=0.1;
 float Vs[]=[0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0];
 
@@ -127,7 +142,7 @@
 /* == Invoke smeagol lead == */
 (au3dm, au3hst, 
  bulklft, bulkrgt,
- smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_in,
+ smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_leads,
                                        opsf, osicpsf,
                                        tipsf, tisicpsf);
 
@@ -141,17 +156,17 @@
                                          tipsf, tisicpsf);
 
 /* == Invoke pasta == */
-(fdf_proc_v1) = pasta_app(pasta_src, xyz, fdf_v1);
+(fdf_proc) = pasta_app(pasta_src, xyz, fdf_v0);
 
 
 /* ==
 In a parallel 'foreach' loop, invoke gen_fdf and smeagol for the n V calculations
 == */
 
-foreach v,i in Vs
+foreach i in [Vstart:Vend:Vstep]
 {
 /* == generate fdfs for different voltages == */
-fdf_proc_vn[i]=gen_fdf(v,fdf_proc_v1);
+fdf_proc_vn[i]=gen_fdf(i,fdf_proc);
 
 (smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst,
                                           aupsf, ausicpsf,