[Swift-commit] r5894 - in SwiftApps/CMTS/dimers: . bin conf input_files

[davidk at ci.uchicago.edu]

Author: davidk
Date: 2012-08-09 17:32:54 -0500 (Thu, 09 Aug 2012)
New Revision: 5894

Added:
   SwiftApps/CMTS/dimers/bin/restart2data.sh
Removed:
   SwiftApps/CMTS/dimers/input_files/end_20.restart
   SwiftApps/CMTS/dimers/input_files/end_25.restart
   SwiftApps/CMTS/dimers/input_files/end_30.restart
   SwiftApps/CMTS/dimers/input_files/end_35.restart
   SwiftApps/CMTS/dimers/input_files/end_40.restart
   SwiftApps/CMTS/dimers/input_files/end_45.restart
   SwiftApps/CMTS/dimers/input_files/end_50.restart
   SwiftApps/CMTS/dimers/input_files/end_55.restart
   SwiftApps/CMTS/dimers/input_files/end_60.restart
   SwiftApps/CMTS/dimers/input_files/end_65.restart
   SwiftApps/CMTS/dimers/input_files/end_70.restart
Modified:
   SwiftApps/CMTS/dimers/conf/local.cf
   SwiftApps/CMTS/dimers/dimers.swift
   SwiftApps/CMTS/dimers/rundimers.sh
Log:
Various updates to input files, swift script, and wrapper shell script


Added: SwiftApps/CMTS/dimers/bin/restart2data.sh
===================================================================
--- SwiftApps/CMTS/dimers/bin/restart2data.sh	                        (rev 0)
+++ SwiftApps/CMTS/dimers/bin/restart2data.sh	2012-08-09 22:32:54 UTC (rev 5894)
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+./restart2data $@
+for file in $( ls *.swift )
+do
+  mv $file $( basename $file .swift )
+done


Property changes on: SwiftApps/CMTS/dimers/bin/restart2data.sh
___________________________________________________________________
Added: svn:executable
   + *

Modified: SwiftApps/CMTS/dimers/conf/local.cf
===================================================================
--- SwiftApps/CMTS/dimers/conf/local.cf	2012-08-08 15:12:55 UTC (rev 5893)
+++ SwiftApps/CMTS/dimers/conf/local.cf	2012-08-09 22:32:54 UTC (rev 5894)
@@ -7,4 +7,5 @@
 provider.staging.pin.swiftfiles=false
 use.wrapper.staging=false
 
-#app rmsd=$PWD/../rmsd.sh
+#app insert_molecules=$PWD/../bin/insert_molecules
+#app restart2data=$PWD/../bin/restart2data.sh

Modified: SwiftApps/CMTS/dimers/dimers.swift
===================================================================
--- SwiftApps/CMTS/dimers/dimers.swift	2012-08-08 15:12:55 UTC (rev 5893)
+++ SwiftApps/CMTS/dimers/dimers.swift	2012-08-09 22:32:54 UTC (rev 5894)
@@ -1,13 +1,33 @@
 type file;
 
-app insert_molecules
+app (file lamps_config_output) insert_molecules (file lamps_config, file dimer, int delta, int v_radius)
+{
+  insert_molecules @lamps_config @dimer delta v_radius 0 25.0 @lamps_config_output;
+}
 
-app restart2data
+app (file output_file) restart2data (file restart_file, file config_file)
+{
+   restart2data @restart_file @config_file;
+}
 
-app lmp_john
-
 int start_ndimers=20;
-int max_ndimers=75;
+int max_ndimers=70;
 int delta_ndimers=5;
 int virion_radius=300;
 
+file dimer_file <"dimer_1232.lammps_config">;
+file initial_output <"empty.lammps_config">;
+file outputs[];
+outputs[start_ndimers-delta_ndimers] = initial_output;
+
+foreach i in [start_ndimers:max_ndimers:delta_ndimers] {
+
+   file molecule_output <single_file_mapper; file=@strcat("end_", i-delta_ndimers, ".lampps_config")>;
+   molecule_output = insert_molecules(outputs[i-delta_ndimers], dimer_file, delta_ndimers, virion_radius);
+
+   file restart_input <single_file_mapper; file=@strcat("end_", i, ".restart.swift")>;
+   file restart_output <single_file_mapper; file=@strcat("end_", i, ".restart")>;
+   restart_output = restart2data(restart_input, molecule_output);
+
+   outputs[i] = restart_output;
+}

Deleted: SwiftApps/CMTS/dimers/input_files/end_20.restart
===================================================================
(Binary files differ)

Deleted: SwiftApps/CMTS/dimers/input_files/end_25.restart
===================================================================
(Binary files differ)

Deleted: SwiftApps/CMTS/dimers/input_files/end_30.restart
===================================================================
(Binary files differ)

Deleted: SwiftApps/CMTS/dimers/input_files/end_35.restart
===================================================================
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Deleted: SwiftApps/CMTS/dimers/input_files/end_40.restart
===================================================================
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Deleted: SwiftApps/CMTS/dimers/input_files/end_45.restart
===================================================================
(Binary files differ)

Deleted: SwiftApps/CMTS/dimers/input_files/end_50.restart
===================================================================
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Deleted: SwiftApps/CMTS/dimers/input_files/end_55.restart
===================================================================
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Deleted: SwiftApps/CMTS/dimers/input_files/end_60.restart
===================================================================
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Deleted: SwiftApps/CMTS/dimers/input_files/end_65.restart
===================================================================
(Binary files differ)

Deleted: SwiftApps/CMTS/dimers/input_files/end_70.restart
===================================================================
(Binary files differ)

Modified: SwiftApps/CMTS/dimers/rundimers.sh
===================================================================
--- SwiftApps/CMTS/dimers/rundimers.sh	2012-08-08 15:12:55 UTC (rev 5893)
+++ SwiftApps/CMTS/dimers/rundimers.sh	2012-08-09 22:32:54 UTC (rev 5894)
@@ -58,7 +58,7 @@
 
 # Do the run
 cd $rundir
-cp ../rmsd.swift .
+cp ../dimers.swift .
 export WORK=$PWD/swiftwork
 mkdir -p $PWD/swiftwork/workers