[Swift-commit] r8308 - SwiftApps/ematter

[ketan at ci.uchicago.edu]

Author: ketan
Date: 2014-11-24 20:34:48 -0600 (Mon, 24 Nov 2014)
New Revision: 8308

Modified:
   SwiftApps/ematter/pasta
   SwiftApps/ematter/workflow.blues.swift
Log:
_

Modified: SwiftApps/ematter/pasta
===================================================================
--- SwiftApps/ematter/pasta	2014-11-24 19:37:55 UTC (rev 8307)
+++ SwiftApps/ematter/pasta	2014-11-25 02:34:48 UTC (rev 8308)
@@ -4,8 +4,11 @@
 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
+tac $filexyz | sed -n '0,/^Atoms/p' | sed  '$d' | tac | awk '{print $2, $3, $4, $1}' > 1.tmp
 
+grep "0.0 0.0 0.0\|0.0 0.0 2.5\|0.0 0.0 5.0\|0.0 0.0 7.5" 1.tmp > tmp.extract
+grep -v "0.0 0.0 0.0\|0.0 0.0 2.5\|0.0 0.0 5.0\|0.0 0.0 7.5" 1.tmp >> tmp.extract
+
 #delete everything between the coordinates block
 sed -i '/\%block AtomicCoordinatesAndAtomicSpecies/,/%endblock AtomicCoordinatesAndAtomicSpecies/{//!d}' $filefdf
 

Modified: SwiftApps/ematter/workflow.blues.swift
===================================================================
--- SwiftApps/ematter/workflow.blues.swift	2014-11-24 19:37:55 UTC (rev 8307)
+++ SwiftApps/ematter/workflow.blues.swift	2014-11-25 02:34:48 UTC (rev 8308)
@@ -54,7 +54,7 @@
 }
 
 /* == Generate fdfs app definition == */
-app (file _fdf) gen_fdf(int _r, file _infdf)
+app (file _fdf) gen_fdf(float _r, file _infdf)
 {
   genfdf _r @_infdf stdout=@_fdf;
 }
@@ -75,6 +75,7 @@
 file lammps_in <"in.lammps">;
 file lammps_geo <"AuTiO.geo">;
 file lammps_eam <"Au_u3.eam">;
+
 file lammps_dump <"lammps.dump">;
 
 file pizza_src<"lastlammpsdump2xyz.py">;
@@ -109,8 +110,10 @@
 
 file fdf_proc_vn[];
 
-int Vstart=1;
-int Vend=2;
+float Vstart=0.1;
+float Vend=1.0;
+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];
 
 /* == End files and variable declaration == */
 
@@ -145,10 +148,10 @@
 In a parallel 'foreach' loop, invoke gen_fdf and smeagol for the n V calculations
 == */
 
-foreach i in [Vstart:Vend]
+foreach v,i in Vs
 {
 /* == generate fdfs for different voltages == */
-fdf_proc_vn[i]=gen_fdf(i,fdf_proc_v1);
+fdf_proc_vn[i]=gen_fdf(v,fdf_proc_v1);
 
 (smeagol_transport_outn[i]) = smeagol_vn_app(au3dm, au3hst,
                                           aupsf, ausicpsf,