[Swift-commit] r6099 - in SwiftTutorials/UofC_2012-11-27-fusion: . bin data scripts

davidk at ci.uchicago.edu davidk at ci.uchicago.edu
Wed Dec 5 14:21:36 CST 2012


Author: davidk
Date: 2012-12-05 14:21:35 -0600 (Wed, 05 Dec 2012)
New Revision: 6099

Added:
   SwiftTutorials/UofC_2012-11-27-fusion/README
   SwiftTutorials/UofC_2012-11-27-fusion/bin/
   SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
   SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
   SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
   SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
   SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
   SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
   SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
   SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c
   SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
   SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
   SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
   SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
   SwiftTutorials/UofC_2012-11-27-fusion/data/
   SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt
   SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp
   SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift
   SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx
Log:
Files needed to run tutorials on fusion, with the additional of two new mpi examples


Added: SwiftTutorials/UofC_2012-11-27-fusion/README
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/README	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/README	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,100 @@
+
+INTRODUCTION TO SWIFT
+
+SETUP
+
+Obtain the tutorial package
+
+Change directory into the created directory called "tutorial"
+
+This directory contains:
+
+bin:     script tools for the tutorial
+scripts: Swift scripts for the tutorial
+
+An output directory will be created by the Swift scripts
+
+
+Use bin/setup.sh to add tutorial programs to your PATH
+
+Run:
+
+source bin/setup.sh
+
+EXERCISE 1 - Run a simple command under Swift
+
+This script simply runs the getinfo command found in bin/getinfo.sh
+
+You can run this on the login node by typing:
+
+bin/getinfo.sh
+
+Inspect getinfo.sh to see what it does.
+
+The Swift syntax in scripts/script01.swift directs the output of
+getinfo.sh to file output/info.txt
+
+Run the Swift script by typing:
+
+runswift scripts/script01.swift
+
+Check that the output is created in the output directory
+
+EXERCISE 2 - Run parallel jobs
+
+The Swift syntax in scripts/script02.swift runs the getinfo
+script 25 times in parallel.  Each job produces an output
+file with a different name.
+
+runswift scripts/script02.swift
+
+Check that the output is created successfully
+
+EXERCISE 3 - Run parallel jobs with pipelines
+
+The Swift syntax in scripts/script02.swift runs the getinfo
+script 25 times in parallel.  Each job produces an output
+file with a different name.  Each output file is then read by the
+filterinfo task, which produces output in _concurrent
+
+Inspect bin/filterinfo.sh to see what it does to the output of getinfo.sh
+
+runswift scripts/script03.swift
+
+EXERCISE 4 - Name files in pipelines
+
+In Exercise 3, the final outputs were named by Swift.
+Exercise 4 is similar to 3 but allows you to name the final
+outputs.  Edit script04.swift to name the files in an appropriate
+way.
+
+EXERCISE 5 - Reduction
+
+Exercise 5 allows you to collect all of the filtered outputs
+and summarize them into one file.  This Swift script allows
+suminfo.sh to read all the files and collect a statistic.
+
+Inspect bin/suminfo.sh to see what it will do to the files it reads.
+
+EXERCISE 6 - Simple MPI test
+
+Exercise 6 is a simple MPI test. Each rank of the MPI job
+runs a "hostname" command and creates a file. The files
+get added to a tar file - output/results.tar. A wrapper
+script, bin/testmpi.sh runs mpiexec to launch the test 
+mpi program. This application uses the Fusion batch
+queue to request 2 nodes.
+
+View output/results.tar to see the results.
+
+EXERCISE 7 - NAMD MPI test
+
+Exercise 7 is a real application that runs NAMD
+using MPI. It is a simple parameter sweep that
+changes some values in the input files then does
+the run. Like exercise 6, this uses the batch queue
+with 2 nodes.
+
+CLEAN UP
+
+Simply run: bin/cleanup and enter y to confirm

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+echo Removing:
+echo
+ls -ltd script??-* swiftwork _concurrent output *.kml *.swiftx swift.log applist config sites.xml pathlist 2>/dev/null
+echo
+echo Enter y to proceed:
+read ok
+if [ _$ok = _y -o _$ok = _Y -o _$ok = _yes ]; then
+  echo
+  set -x
+  rm -rf script??-* swiftwork _concurrent output *.kml *.swiftx swift.log applist config sites.xml pathlist
+else
+  echo
+  echo No files removed.
+fi
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,2 @@
+#! /bin/sh
+grep getinfo.sh $1 | wc -l >$2


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,10 @@
+cat <<END
+cluster cat        /bin/cat               null null null
+cluster sh         /bin/sh                null null null
+cluster getinfo    $PWD/bin/getinfo.sh    null null null
+cluster filterinfo $PWD/bin/filterinfo.sh null null null
+cluster suminfo    $PWD/bin/suminfo.sh    null null null
+clustermpi rmsd    $PWD/bin/rmsd.sh       null null null
+clustermpi plot_pd $PWD/bin/plot_pd.pl    null null null
+clustermpi testmpi $PWD/bin/testmpi.sh    null null null
+END


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 2
+ps -u $USER -H


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 3
+ps -u $USER -H -f


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,70 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+# This code will run many short simulations in order to 
+# sweep the nonbonded parameter space
+
+# File names
+open (OFILE, ">", "output/rmsd_pd.dat");
+
+# Bead names
+my $b1name = "PX";
+my $b2name = "DT";
+
+# Bead ranges
+my $b1min=0.0;
+my $b1max=10.0;
+
+my $b2min=0.0;
+my $b2max=10.0;
+
+my $del=0.50;
+
+# Set large number to find RMSD min
+my $rmsdmin = 123456789.0;
+my $b1rmsdmin=0.0;
+my $b2rmsdmin=0.0;
+
+my $b1=$b1min;
+
+while ($b1<=$b1max) 
+{
+	my $b2=$b2min;
+
+	while ($b2<=$b2max)
+	{
+		if (-s "output/rmsd.$b1name${b1}_$b2name${b2}.dat")
+		{	
+			open(INPUT, "<", "output/rmsd.$b1name${b1}_$b2name${b2}.dat");
+			$_ = <INPUT>;
+
+			my @data = split(/ +/,$_);
+        		my $rmsd=$data[2]*1.0;
+			
+			# Find Minimum
+			if ($rmsd<$rmsdmin)
+			{
+				$rmsdmin=$rmsd;
+				$b1rmsdmin=$b1;
+				$b2rmsdmin=$b2;
+			}
+	
+			print OFILE "$b1 $b2 $rmsd\n";			
+			close(INPUT);
+		}		
+
+		$b2 = $b2+$del;
+	
+	}
+
+	print OFILE " \n";
+	$b1 = $b1+$del;
+
+}
+
+close(OFILE);
+
+print "Minimum Values\n";
+print "RMSD = $rmsdmin, eps_$b1name = $b1rmsdmin, eps_$b2name = $b2rmsdmin\n" ; 


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,47 @@
+#!/bin/bash 
+
+b1=$1
+b2=$2
+b1name=$3
+b2name=$4
+namd_input=$5
+namd_parameters=$6
+vmd_script=$7
+
+echo Command line arguments: $@
+echo
+
+echo Hostname: $( hostname )
+echo
+
+echo File listing
+echo ------------
+find
+echo
+
+echo Running the following sed commands
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+echo Done with sed
+echo
+
+namd2=$( which namd2 )
+echo Found namd2 at $namd2
+echo About to run mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input 
+mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input 
+
+echo
+echo About to run vmd -dispdev text -e $vmd_script 
+vmd -dispdev text -e $vmd_script 
+
+mv output/cg_clath_cage.dcd output/cg_clath_cage-$b1-$b2.dcd
+mv rmsd.dat output/rmsd.$b1name${b1}_$b2name${b2}.dat
+
+echo
+echo Files at end of run
+find
+echo


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,75 @@
+#! /bin/sh
+
+cat <<END >pathlist
+rule .*_concurrent/.* DIRECT $PWD/tmp
+rule .*               DIRECT /
+END
+
+cat <<END >config
+status.mode=provider
+use.provider.staging=false
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+file.gc.enabled=false
+tcp.port.range=50000,51000
+END
+
+reservationID=${reservationID:-swift}
+
+cat <<END >sites.xml
+
+<config>
+
+<pool handle="local">
+  <execution provider="local"/>
+  <profile namespace="karajan" key="jobThrottle">0.03</profile>
+  <profile namespace="karajan" key="initialScore">10000</profile>
+  <filesystem provider="local" url="none" />
+  <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+<pool handle="cluster">
+        <execution jobmanager="local:pbs" provider="coaster" url="none"/>
+        <filesystem provider="local" url="none" />
+        <profile namespace="globus" key="maxtime">3600</profile>
+        <profile namespace="globus" key="jobsPerNode">8</profile>
+        <profile namespace="globus" key="queue">shared</profile>
+        <profile namespace="globus" key="nodeGranularity">1</profile>
+        <profile namespace="globus" key="maxNodes">1</profile>
+        <profile namespace="karajan" key="jobThrottle">1.0</profile>
+        <profile namespace="karajan" key="initialScore">100</profile>
+        <profile namespace="globus" key="HighOverAllocation">100</profile>
+        <profile namespace="globus" key="LowOverAllocation">100</profile>
+        <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+<pool handle="clustermpi">
+  <execution jobmanager="local:pbs" provider="pbs" url="none"/>
+  <filesystem provider="local" url="none" />
+  <profile namespace="globus" key="maxtime">60</profile>
+  <profile namespace="globus" key="jobsPerNode">1</profile>
+  <profile namespace="globus" key="ppn">8</profile>
+  <profile namespace="karajan" key="jobThrottle">5.99</profile>
+  <profile namespace="karajan" key="initialScore">10000</profile>
+  <profile namespace="globus" key="count">2</profile>
+  <profile namespace="globus" key="jobType">single</profile>
+  <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+</config>
+
+END
+
+genapplist >applist
+
+set -x
+#swift -config config -tc.file applist -sites.file sites.xml -cdm.file pathlist $*
+swift -config config -tc.file applist -sites.file sites.xml $*
+
+
+
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1 @@
+PATH=/homes/davidk/swift-0.94/cog/modules/swift/dist/swift-svn/bin:/homes/davidk/namd_2.8-intel-openmpi:/homes/davidk/vmd:$PWD/bin:$PATH

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,2 @@
+#! /bin/sh
+awk '{ sum += $1 } END { print "Total processes observed: " sum }' $*


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
===================================================================
(Binary files differ)


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
___________________________________________________________________
Added: svn:executable
   + *
Added: svn:mime-type
   + application/octet-stream

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,51 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <mpi.h>
+#include <string.h>
+
+int main (argc, argv)
+     int argc;
+     char *argv[];
+{
+  int rank, size;
+
+  MPI_Init (&argc, &argv);			/* starts MPI */
+  MPI_Comm_rank (MPI_COMM_WORLD, &rank);	/* get current process id */
+  MPI_Comm_size (MPI_COMM_WORLD, &size);	/* get number of processes */
+
+  FILE *fp, *command;
+  char filename[100];
+  char hostname[1024];
+
+  sprintf(filename, "output.%d.txt", rank);
+  printf("Trying to write output to %s\n", filename);
+  fp = fopen(filename, "w");
+
+  if (fp == NULL) {
+     printf("Unable to write file\n");
+     exit(0);
+  } 
+
+  command = popen("/bin/hostname -f", "r");
+  if(command == NULL) {
+     printf("Failed to run command\n");
+     exit(1);
+  }
+
+  while (fgets(hostname, sizeof(hostname)-1, command) != NULL) {
+    hostname[(strlen(hostname)-1)] = '\0';
+    fprintf(fp, "Hostname: %s, rank: %d\n", hostname, rank);
+  }
+
+  fclose(fp);
+  printf("Done writing output file %s\n", filename);
+
+  MPI_Finalize();
+
+  // Create a tar file of results (only once)
+  if(rank == 0) {
+     system("mkdir output");
+     system("tar cvf output/results.tar output*.txt");
+  }
+  return 0;
+}

Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+mpiexec -machinefile $PBS_NODEFILE /homes/davidk/testmpi/testmpi


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,83 @@
+# NAMD Config file - autogenerated by NAMDgui plugin
+# Author: Jan Saam,  saam at charite.de
+
+# input
+coordinates             cg_clath_cage.pdb
+structure               cg_clath_cage.psf
+parameters              par_cg_clath.inp
+paratypecharmm          on
+
+# output
+set output              output/cg_clath_cage
+outputname              $output
+dcdfile                 ${output}.dcd
+xstFile                 ${output}.xst
+dcdfreq                 1000
+xstFreq                 1000
+
+binaryoutput            yes
+binaryrestart           yes
+outputEnergies          1000
+restartfreq             1000
+
+fixedAtoms              off
+
+# Basic dynamics
+exclude                 scaled1-4
+1-4scaling              1
+COMmotion               no
+dielectric              1.0
+
+
+# Simulation space partitioning
+cutoff			350
+switching               on
+switchdist              348                 
+pairlistdist            352
+
+# Multiple timestepping
+firsttimestep           0
+timestep                10
+stepspercycle           1
+nonbondedFreq           1
+fullElectFrequency      1
+rigidBonds              all
+
+# Temperature control
+
+set temperature         310
+temperature             $temperature;  # initial temperature
+
+# Langevin Dynamics
+langevin                on;            # do langevin dynamics
+langevinDamping         0.001             # damping coefficient (gamma) of 1/ps
+langevinTemp            $temperature;   # bath temperature
+langevinHydrogen        no;             # don't couple langevin bath to hydrogens
+
+
+
+# Scripting
+
+# Simulated Annealing
+#reassignFreq 10000
+#reassignTemp 310
+#minimize 10000
+#for { set TEMP 310 } { $TEMP <= 650 } { incr TEMP 5 } {
+#  run 10000
+#  reassignTemp $TEMP
+#  langevinTemp $TEMP
+#}
+#
+#run 1000000
+#
+#for { set TEMP 650 } { $TEMP >= 310 } { incr TEMP -5 } {
+#  reassignTemp $TEMP
+#  langevinTemp $TEMP
+#  run 10000
+#} 
+#run 1000000
+
+minimize            1000
+reinitvels          $temperature
+run                 2000
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,470 @@
+REMARK original generated coordinate pdb file
+ATOM      1  HB0 CLA X   1      92.981 164.025 331.473  1.00  0.00      A0    
+ATOM      2  PX1 CLA X   1     136.274 211.422 275.579  1.00  0.00      A0    
+ATOM      3  DT1 CLA X   1     200.662 208.148 159.192  1.00  0.00      A0    
+ATOM      4  AK1 CLA X   1     243.304 111.359  96.656  1.00  0.00      A0    
+ATOM      5  LT1 CLA X   1     223.763  18.662  85.497  1.00  0.00      A0    
+ATOM      6  PX2 CLA X   1     126.815  89.000 352.917  1.00  0.00      A0    
+ATOM      7  DT2 CLA X   1     128.673 -47.724 333.137  1.00  0.00      A0    
+ATOM      8  AK2 CLA X   1      49.929-132.718 287.973  1.00  0.00      A0    
+ATOM      9  LT2 CLA X   1     -24.828-143.462 235.435  1.00  0.00      A0    
+ATOM     10  PX3 CLA X   1      10.483 180.619 340.613  1.00  0.00      A0    
+ATOM     11  DT3 CLA X   1     -95.424 204.239 265.860  1.00  0.00      A0    
+ATOM     12  AK3 CLA X   1    -101.877 231.712 146.926  1.00  0.00      A0    
+ATOM     13  LT3 CLA X   1     -58.664 217.336  66.678  1.00  0.00      A0    
+ATOM     14  HB0 CLA X   1     152.597 263.250 182.367  1.00  0.00      B0    
+ATOM     15  PX1 CLA X   1     120.437 238.824 256.749  1.00  0.00      B0    
+ATOM     16  DT1 CLA X   1      18.642 174.399 313.695  1.00  0.00      B0    
+ATOM     17  AK1 CLA X   1     -88.420 151.452 262.690  1.00  0.00      B0    
+ATOM     18  LT1 CLA X   1    -128.527 143.156 177.443  1.00  0.00      B0    
+ATOM     19  PX2 CLA X   1      99.230 306.155 133.576  1.00  0.00      B0    
+ATOM     20  DT2 CLA X   1      21.433 316.316  21.125  1.00  0.00      B0    
+ATOM     21  AK2 CLA X   1      26.263 266.923 -95.151  1.00  0.00      B0    
+ATOM     22  LT2 CLA X   1      58.151 195.850-145.576  1.00  0.00      B0    
+ATOM     23  PX3 CLA X   1     223.451 225.604 155.002  1.00  0.00      B0    
+ATOM     24  DT3 CLA X   1     275.701 105.136 138.751  1.00  0.00      B0    
+ATOM     25  AK3 CLA X   1     235.267   1.374 186.863  1.00  0.00      B0    
+ATOM     26  LT3 CLA X   1     155.819 -36.632 217.712  1.00  0.00      B0    
+ATOM     27  HB0 CLA X   1     286.805 165.855  93.118  1.00  0.00      C0    
+ATOM     28  PX1 CLA X   1     303.935 101.204 144.420  1.00  0.00      C0    
+ATOM     29  DT1 CLA X   1     251.178  21.712 232.998  1.00  0.00      C0    
+ATOM     30  AK1 CLA X   1     142.263  28.038 287.691  1.00  0.00      C0    
+ATOM     31  LT1 CLA X   1      50.945  58.195 270.101  1.00  0.00      C0    
+ATOM     32  PX2 CLA X   1     234.620 227.534 121.486  1.00  0.00      C0    
+ATOM     33  DT2 CLA X   1     104.398 278.700 124.820  1.00  0.00      C0    
+ATOM     34  AK2 CLA X   1       0.965 276.330  50.135  1.00  0.00      C0    
+ATOM     35  LT2 CLA X   1     -42.600 228.187 -18.776  1.00  0.00      C0    
+ATOM     36  PX3 CLA X   1     303.934 158.846  11.493  1.00  0.00      C0    
+ATOM     37  DT3 CLA X   1     291.514  88.537-103.359  1.00  0.00      C0    
+ATOM     38  AK3 CLA X   1     250.991 -24.248-144.395  1.00  0.00      C0    
+ATOM     39  LT3 CLA X   1     191.706 -94.728-126.760  1.00  0.00      C0    
+ATOM     40  HB0 CLA X   1     -95.559 162.537 331.473  1.00  0.00      A1    
+ATOM     41  PX1 CLA X   1    -114.959 223.728 275.579  1.00  0.00      A1    
+ATOM     42  DT1 CLA X   1     -79.930 277.853 159.192  1.00  0.00      A1    
+ATOM     43  AK1 CLA X   1      25.213 266.386  96.656  1.00  0.00      A1    
+ATOM     44  LT1 CLA X   1      95.719 203.115  85.497  1.00  0.00      A1    
+ATOM     45  PX2 CLA X   1     -13.669 154.325 352.917  1.00  0.00      A1    
+ATOM     46  DT2 CLA X   1     105.666  87.572 333.137  1.00  0.00      A1    
+ATOM     47  AK2 CLA X   1     139.902 -23.120 287.973  1.00  0.00      A1    
+ATOM     48  LT2 CLA X   1     111.827 -93.233 235.435  1.00  0.00      A1    
+ATOM     49  PX3 CLA X   1    -151.180  99.388 340.613  1.00  0.00      A1    
+ATOM     50  DT3 CLA X   1    -224.588  19.480 265.860  1.00  0.00      A1    
+ATOM     51  AK3 CLA X   1    -251.607  27.627 146.926  1.00  0.00      A1    
+ATOM     52  LT3 CLA X   1    -217.550  57.864  66.678  1.00  0.00      A1    
+ATOM     53  HB0 CLA X   1    -151.683 263.777 182.367  1.00  0.00      B1    
+ATOM     54  PX1 CLA X   1    -146.609 223.714 256.749  1.00  0.00      B1    
+ATOM     55  DT1 CLA X   1    -141.713 103.344 313.695  1.00  0.00      B1    
+ATOM     56  AK1 CLA X   1    -175.371  -0.848 262.690  1.00  0.00      B1    
+ATOM     57  LT1 CLA X   1    -188.241 -39.730 177.443  1.00  0.00      B1    
+ATOM     58  PX2 CLA X   1    -215.523 239.014 133.576  1.00  0.00      B1    
+ATOM     59  DT2 CLA X   1    -263.221 176.720  21.125  1.00  0.00      B1    
+ATOM     60  AK2 CLA X   1    -218.030 156.206 -95.151  1.00  0.00      B1    
+ATOM     61  LT2 CLA X   1    -140.536 148.285-145.576  1.00  0.00      B1    
+ATOM     62  PX3 CLA X   1     -83.654 306.316 155.002  1.00  0.00      B1    
+ATOM     63  DT3 CLA X   1      46.800 291.332 138.751  1.00  0.00      B1    
+ATOM     64  AK3 CLA X   1     116.444 204.434 186.863  1.00  0.00      B1    
+ATOM     65  LT3 CLA X   1     109.634 116.627 217.712  1.00  0.00      B1    
+ATOM     66  HB0 CLA X   1      -0.232 331.308  93.118  1.00  0.00      C1    
+ATOM     67  PX1 CLA X   1      64.322 313.817 144.420  1.00  0.00      C1    
+ATOM     68  DT1 CLA X   1     106.786 228.382 232.998  1.00  0.00      C1    
+ATOM     69  AK1 CLA X   1      46.850 137.222 287.691  1.00  0.00      C1    
+ATOM     70  LT1 CLA X   1     -24.926  73.217 270.101  1.00  0.00      C1    
+ATOM     71  PX2 CLA X   1     -79.740 316.953 121.486  1.00  0.00      C1    
+ATOM     72  DT2 CLA X   1    -189.163 229.761 124.820  1.00  0.00      C1    
+ATOM     73  AK2 CLA X   1    -238.827 139.001  50.135  1.00  0.00      C1    
+ATOM     74  LT2 CLA X   1    -218.915  77.201 -18.776  1.00  0.00      C1    
+ATOM     75  PX3 CLA X   1      14.402 342.637  11.493  1.00  0.00      C1    
+ATOM     76  DT3 CLA X   1      69.082 296.727-103.359  1.00  0.00      C1    
+ATOM     77  AK3 CLA X   1     146.495 205.240-144.395  1.00  0.00      C1    
+ATOM     78  LT3 CLA X   1     177.890 118.659-126.760  1.00  0.00      C1    
+ATOM     79  HB0 CLA X   1    -188.541  -1.488 331.473  1.00  0.00      A2    
+ATOM     80  PX1 CLA X   1    -251.234  12.306 275.579  1.00  0.00      A2    
+ATOM     81  DT1 CLA X   1    -280.592  69.705 159.192  1.00  0.00      A2    
+ATOM     82  AK1 CLA X   1    -218.091 155.028  96.656  1.00  0.00      A2    
+ATOM     83  LT1 CLA X   1    -128.043 184.453  85.497  1.00  0.00      A2    
+ATOM     84  PX2 CLA X   1    -140.484  65.324 352.917  1.00  0.00      A2    
+ATOM     85  DT2 CLA X   1     -23.007 135.296 333.137  1.00  0.00      A2    
+ATOM     86  AK2 CLA X   1      89.973 109.599 287.973  1.00  0.00      A2    
+ATOM     87  LT2 CLA X   1     136.656  50.229 235.435  1.00  0.00      A2    
+ATOM     88  PX3 CLA X   1    -161.662 -81.231 340.613  1.00  0.00      A2    
+ATOM     89  DT3 CLA X   1    -129.164-184.759 265.860  1.00  0.00      A2    
+ATOM     90  AK3 CLA X   1    -149.729-204.084 146.926  1.00  0.00      A2    
+ATOM     91  LT3 CLA X   1    -158.887-159.472  66.678  1.00  0.00      A2    
+ATOM     92  HB0 CLA X   1    -304.279   0.528 182.367  1.00  0.00      B2    
+ATOM     93  PX1 CLA X   1    -267.047 -15.111 256.749  1.00  0.00      B2    
+ATOM     94  DT1 CLA X   1    -160.355 -71.055 313.695  1.00  0.00      B2    
+ATOM     95  AK1 CLA X   1     -86.951-152.300 262.690  1.00  0.00      B2    
+ATOM     96  LT1 CLA X   1     -59.713-182.886 177.443  1.00  0.00      B2    
+ATOM     97  PX2 CLA X   1    -314.754 -67.142 133.576  1.00  0.00      B2    
+ATOM     98  DT2 CLA X   1    -284.654-139.597  21.125  1.00  0.00      B2    
+ATOM     99  AK2 CLA X   1    -244.294-110.717 -95.151  1.00  0.00      B2    
+ATOM    100  LT2 CLA X   1    -198.687 -47.565-145.576  1.00  0.00      B2    
+ATOM    101  PX3 CLA X   1    -307.104  80.712 155.002  1.00  0.00      B2    
+ATOM    102  DT3 CLA X   1    -228.901 186.196 138.751  1.00  0.00      B2    
+ATOM    103  AK3 CLA X   1    -118.823 203.060 186.863  1.00  0.00      B2    
+ATOM    104  LT3 CLA X   1     -46.185 153.259 217.712  1.00  0.00      B2    
+ATOM    105  HB0 CLA X   1    -287.037 165.452  93.118  1.00  0.00      C2    
+ATOM    106  PX1 CLA X   1    -239.613 212.613 144.420  1.00  0.00      C2    
+ATOM    107  DT1 CLA X   1    -144.392 206.670 232.998  1.00  0.00      C2    
+ATOM    108  AK1 CLA X   1     -95.413 109.184 287.691  1.00  0.00      C2    
+ATOM    109  LT1 CLA X   1     -75.871  15.022 270.101  1.00  0.00      C2    
+ATOM    110  PX2 CLA X   1    -314.360  89.420 121.486  1.00  0.00      C2    
+ATOM    111  DT2 CLA X   1    -293.560 -48.939 124.820  1.00  0.00      C2    
+ATOM    112  AK2 CLA X   1    -239.791-137.330  50.135  1.00  0.00      C2    
+ATOM    113  LT2 CLA X   1    -176.315-150.986 -18.776  1.00  0.00      C2    
+ATOM    114  PX3 CLA X   1    -289.532 183.791  11.493  1.00  0.00      C2    
+ATOM    115  DT3 CLA X   1    -222.432 208.190-103.359  1.00  0.00      C2    
+ATOM    116  AK3 CLA X   1    -104.496 229.489-144.395  1.00  0.00      C2    
+ATOM    117  LT3 CLA X   1     -13.817 213.386-126.760  1.00  0.00      C2    
+ATOM    118  HB0 CLA X   1     -92.981-164.025 331.473  1.00  0.00      A3    
+ATOM    119  PX1 CLA X   1    -136.274-211.422 275.579  1.00  0.00      A3    
+ATOM    120  DT1 CLA X   1    -200.662-208.148 159.192  1.00  0.00      A3    
+ATOM    121  AK1 CLA X   1    -243.304-111.359  96.656  1.00  0.00      A3    
+ATOM    122  LT1 CLA X   1    -223.763 -18.662  85.497  1.00  0.00      A3    
+ATOM    123  PX2 CLA X   1    -126.815 -89.000 352.917  1.00  0.00      A3    
+ATOM    124  DT2 CLA X   1    -128.673  47.724 333.137  1.00  0.00      A3    
+ATOM    125  AK2 CLA X   1     -49.929 132.718 287.973  1.00  0.00      A3    
+ATOM    126  LT2 CLA X   1      24.828 143.462 235.435  1.00  0.00      A3    
+ATOM    127  PX3 CLA X   1     -10.483-180.619 340.613  1.00  0.00      A3    
+ATOM    128  DT3 CLA X   1      95.424-204.239 265.860  1.00  0.00      A3    
+ATOM    129  AK3 CLA X   1     101.877-231.712 146.926  1.00  0.00      A3    
+ATOM    130  LT3 CLA X   1      58.664-217.336  66.678  1.00  0.00      A3    
+ATOM    131  HB0 CLA X   1    -152.597-263.250 182.367  1.00  0.00      B3    
+ATOM    132  PX1 CLA X   1    -120.437-238.824 256.749  1.00  0.00      B3    
+ATOM    133  DT1 CLA X   1     -18.642-174.399 313.695  1.00  0.00      B3    
+ATOM    134  AK1 CLA X   1      88.420-151.452 262.690  1.00  0.00      B3    
+ATOM    135  LT1 CLA X   1     128.527-143.156 177.443  1.00  0.00      B3    
+ATOM    136  PX2 CLA X   1     -99.230-306.155 133.576  1.00  0.00      B3    
+ATOM    137  DT2 CLA X   1     -21.433-316.316  21.125  1.00  0.00      B3    
+ATOM    138  AK2 CLA X   1     -26.263-266.923 -95.151  1.00  0.00      B3    
+ATOM    139  LT2 CLA X   1     -58.151-195.850-145.576  1.00  0.00      B3    
+ATOM    140  PX3 CLA X   1    -223.451-225.604 155.002  1.00  0.00      B3    
+ATOM    141  DT3 CLA X   1    -275.701-105.136 138.751  1.00  0.00      B3    
+ATOM    142  AK3 CLA X   1    -235.267  -1.374 186.863  1.00  0.00      B3    
+ATOM    143  LT3 CLA X   1    -155.819  36.632 217.712  1.00  0.00      B3    
+ATOM    144  HB0 CLA X   1    -286.805-165.855  93.118  1.00  0.00      C3    
+ATOM    145  PX1 CLA X   1    -303.935-101.204 144.420  1.00  0.00      C3    
+ATOM    146  DT1 CLA X   1    -251.178 -21.712 232.998  1.00  0.00      C3    
+ATOM    147  AK1 CLA X   1    -142.263 -28.038 287.691  1.00  0.00      C3    
+ATOM    148  LT1 CLA X   1     -50.945 -58.195 270.101  1.00  0.00      C3    
+ATOM    149  PX2 CLA X   1    -234.620-227.534 121.486  1.00  0.00      C3    
+ATOM    150  DT2 CLA X   1    -104.398-278.700 124.820  1.00  0.00      C3    
+ATOM    151  AK2 CLA X   1      -0.965-276.330  50.135  1.00  0.00      C3    
+ATOM    152  LT2 CLA X   1      42.600-228.187 -18.776  1.00  0.00      C3    
+ATOM    153  PX3 CLA X   1    -303.934-158.846  11.493  1.00  0.00      C3    
+ATOM    154  DT3 CLA X   1    -291.514 -88.537-103.359  1.00  0.00      C3    
+ATOM    155  AK3 CLA X   1    -250.991  24.248-144.395  1.00  0.00      C3    
+ATOM    156  LT3 CLA X   1    -191.706  94.728-126.760  1.00  0.00      C3    
+ATOM    157  HB0 CLA X   1      95.559-162.537 331.473  1.00  0.00      A4    
+ATOM    158  PX1 CLA X   1     114.959-223.728 275.579  1.00  0.00      A4    
+ATOM    159  DT1 CLA X   1      79.930-277.853 159.192  1.00  0.00      A4    
+ATOM    160  AK1 CLA X   1     -25.213-266.386  96.656  1.00  0.00      A4    
+ATOM    161  LT1 CLA X   1     -95.719-203.115  85.497  1.00  0.00      A4    
+ATOM    162  PX2 CLA X   1      13.669-154.325 352.917  1.00  0.00      A4    
+ATOM    163  DT2 CLA X   1    -105.666 -87.572 333.137  1.00  0.00      A4    
+ATOM    164  AK2 CLA X   1    -139.902  23.120 287.973  1.00  0.00      A4    
+ATOM    165  LT2 CLA X   1    -111.827  93.233 235.435  1.00  0.00      A4    
+ATOM    166  PX3 CLA X   1     151.180 -99.388 340.613  1.00  0.00      A4    
+ATOM    167  DT3 CLA X   1     224.588 -19.480 265.860  1.00  0.00      A4    
+ATOM    168  AK3 CLA X   1     251.607 -27.627 146.926  1.00  0.00      A4    
+ATOM    169  LT3 CLA X   1     217.550 -57.864  66.678  1.00  0.00      A4    
+ATOM    170  HB0 CLA X   1     151.683-263.777 182.367  1.00  0.00      B4    
+ATOM    171  PX1 CLA X   1     146.609-223.714 256.749  1.00  0.00      B4    
+ATOM    172  DT1 CLA X   1     141.713-103.344 313.695  1.00  0.00      B4    
+ATOM    173  AK1 CLA X   1     175.371   0.848 262.690  1.00  0.00      B4    
+ATOM    174  LT1 CLA X   1     188.241  39.730 177.443  1.00  0.00      B4    
+ATOM    175  PX2 CLA X   1     215.523-239.014 133.576  1.00  0.00      B4    
+ATOM    176  DT2 CLA X   1     263.221-176.720  21.125  1.00  0.00      B4    
+ATOM    177  AK2 CLA X   1     218.030-156.206 -95.151  1.00  0.00      B4    
+ATOM    178  LT2 CLA X   1     140.536-148.285-145.576  1.00  0.00      B4    
+ATOM    179  PX3 CLA X   1      83.654-306.316 155.002  1.00  0.00      B4    
+ATOM    180  DT3 CLA X   1     -46.800-291.332 138.751  1.00  0.00      B4    
+ATOM    181  AK3 CLA X   1    -116.444-204.434 186.863  1.00  0.00      B4    
+ATOM    182  LT3 CLA X   1    -109.634-116.627 217.712  1.00  0.00      B4    
+ATOM    183  HB0 CLA X   1       0.232-331.308  93.118  1.00  0.00      C4    
+ATOM    184  PX1 CLA X   1     -64.322-313.817 144.420  1.00  0.00      C4    
+ATOM    185  DT1 CLA X   1    -106.786-228.382 232.998  1.00  0.00      C4    
+ATOM    186  AK1 CLA X   1     -46.850-137.222 287.691  1.00  0.00      C4    
+ATOM    187  LT1 CLA X   1      24.926 -73.217 270.101  1.00  0.00      C4    
+ATOM    188  PX2 CLA X   1      79.740-316.953 121.486  1.00  0.00      C4    
+ATOM    189  DT2 CLA X   1     189.163-229.761 124.820  1.00  0.00      C4    
+ATOM    190  AK2 CLA X   1     238.827-139.001  50.135  1.00  0.00      C4    
+ATOM    191  LT2 CLA X   1     218.915 -77.201 -18.776  1.00  0.00      C4    
+ATOM    192  PX3 CLA X   1     -14.402-342.637  11.493  1.00  0.00      C4    
+ATOM    193  DT3 CLA X   1     -69.082-296.727-103.359  1.00  0.00      C4    
+ATOM    194  AK3 CLA X   1    -146.495-205.240-144.395  1.00  0.00      C4    
+ATOM    195  LT3 CLA X   1    -177.890-118.659-126.760  1.00  0.00      C4    
+ATOM    196  HB0 CLA X   1     188.541   1.488 331.473  1.00  0.00      A5    
+ATOM    197  PX1 CLA X   1     251.234 -12.306 275.579  1.00  0.00      A5    
+ATOM    198  DT1 CLA X   1     280.592 -69.705 159.192  1.00  0.00      A5    
+ATOM    199  AK1 CLA X   1     218.091-155.028  96.656  1.00  0.00      A5    
+ATOM    200  LT1 CLA X   1     128.043-184.453  85.497  1.00  0.00      A5    
+ATOM    201  PX2 CLA X   1     140.484 -65.324 352.917  1.00  0.00      A5    
+ATOM    202  DT2 CLA X   1      23.007-135.296 333.137  1.00  0.00      A5    
+ATOM    203  AK2 CLA X   1     -89.973-109.599 287.973  1.00  0.00      A5    
+ATOM    204  LT2 CLA X   1    -136.656 -50.229 235.435  1.00  0.00      A5    
+ATOM    205  PX3 CLA X   1     161.662  81.231 340.613  1.00  0.00      A5    
+ATOM    206  DT3 CLA X   1     129.164 184.759 265.860  1.00  0.00      A5    
+ATOM    207  AK3 CLA X   1     149.729 204.084 146.926  1.00  0.00      A5    
+ATOM    208  LT3 CLA X   1     158.887 159.472  66.678  1.00  0.00      A5    
+ATOM    209  HB0 CLA X   1     304.279  -0.528 182.367  1.00  0.00      B5    
+ATOM    210  PX1 CLA X   1     267.047  15.111 256.749  1.00  0.00      B5    
+ATOM    211  DT1 CLA X   1     160.355  71.055 313.695  1.00  0.00      B5    
+ATOM    212  AK1 CLA X   1      86.951 152.300 262.690  1.00  0.00      B5    
+ATOM    213  LT1 CLA X   1      59.713 182.886 177.443  1.00  0.00      B5    
+ATOM    214  PX2 CLA X   1     314.754  67.142 133.576  1.00  0.00      B5    
+ATOM    215  DT2 CLA X   1     284.654 139.597  21.125  1.00  0.00      B5    
+ATOM    216  AK2 CLA X   1     244.294 110.717 -95.151  1.00  0.00      B5    
+ATOM    217  LT2 CLA X   1     198.687  47.565-145.576  1.00  0.00      B5    
+ATOM    218  PX3 CLA X   1     307.104 -80.712 155.002  1.00  0.00      B5    
+ATOM    219  DT3 CLA X   1     228.901-186.196 138.751  1.00  0.00      B5    
+ATOM    220  AK3 CLA X   1     118.823-203.060 186.863  1.00  0.00      B5    
+ATOM    221  LT3 CLA X   1      46.185-153.259 217.712  1.00  0.00      B5    
+ATOM    222  HB0 CLA X   1     287.037-165.452  93.118  1.00  0.00      C5    
+ATOM    223  PX1 CLA X   1     239.613-212.613 144.420  1.00  0.00      C5    
+ATOM    224  DT1 CLA X   1     144.392-206.670 232.998  1.00  0.00      C5    
+ATOM    225  AK1 CLA X   1      95.413-109.184 287.691  1.00  0.00      C5    
+ATOM    226  LT1 CLA X   1      75.871 -15.022 270.101  1.00  0.00      C5    
+ATOM    227  PX2 CLA X   1     314.360 -89.420 121.486  1.00  0.00      C5    
+ATOM    228  DT2 CLA X   1     293.560  48.939 124.820  1.00  0.00      C5    
+ATOM    229  AK2 CLA X   1     239.791 137.330  50.135  1.00  0.00      C5    
+ATOM    230  LT2 CLA X   1     176.315 150.986 -18.776  1.00  0.00      C5    
+ATOM    231  PX3 CLA X   1     289.532-183.791  11.493  1.00  0.00      C5    
+ATOM    232  DT3 CLA X   1     222.432-208.190-103.359  1.00  0.00      C5    
+ATOM    233  AK3 CLA X   1     104.496-229.489-144.395  1.00  0.00      C5    
+ATOM    234  LT3 CLA X   1      13.817-213.386-126.760  1.00  0.00      C5    
+ATOM    235  HB0 CLA X   1      95.559 162.537-331.473  1.00  0.00      A6    
+ATOM    236  PX1 CLA X   1     114.959 223.728-275.579  1.00  0.00      A6    
+ATOM    237  DT1 CLA X   1      79.930 277.853-159.192  1.00  0.00      A6    
+ATOM    238  AK1 CLA X   1     -25.213 266.386 -96.656  1.00  0.00      A6    
+ATOM    239  LT1 CLA X   1     -95.719 203.115 -85.497  1.00  0.00      A6    
+ATOM    240  PX2 CLA X   1      13.669 154.325-352.917  1.00  0.00      A6    
+ATOM    241  DT2 CLA X   1    -105.666  87.572-333.137  1.00  0.00      A6    
+ATOM    242  AK2 CLA X   1    -139.902 -23.120-287.973  1.00  0.00      A6    
+ATOM    243  LT2 CLA X   1    -111.827 -93.233-235.435  1.00  0.00      A6    
+ATOM    244  PX3 CLA X   1     151.180  99.388-340.613  1.00  0.00      A6    
+ATOM    245  DT3 CLA X   1     224.588  19.480-265.860  1.00  0.00      A6    
+ATOM    246  AK3 CLA X   1     251.607  27.627-146.926  1.00  0.00      A6    
+ATOM    247  LT3 CLA X   1     217.550  57.864 -66.678  1.00  0.00      A6    
+ATOM    248  HB0 CLA X   1     151.683 263.777-182.367  1.00  0.00      B6    
+ATOM    249  PX1 CLA X   1     146.609 223.714-256.749  1.00  0.00      B6    
+ATOM    250  DT1 CLA X   1     141.713 103.344-313.695  1.00  0.00      B6    
+ATOM    251  AK1 CLA X   1     175.371  -0.848-262.690  1.00  0.00      B6    
+ATOM    252  LT1 CLA X   1     188.241 -39.730-177.443  1.00  0.00      B6    
+ATOM    253  PX2 CLA X   1     215.523 239.014-133.576  1.00  0.00      B6    
+ATOM    254  DT2 CLA X   1     263.221 176.720 -21.125  1.00  0.00      B6    
+ATOM    255  AK2 CLA X   1     218.030 156.206  95.151  1.00  0.00      B6    
+ATOM    256  LT2 CLA X   1     140.536 148.285 145.576  1.00  0.00      B6    
+ATOM    257  PX3 CLA X   1      83.654 306.316-155.002  1.00  0.00      B6    
+ATOM    258  DT3 CLA X   1     -46.800 291.332-138.751  1.00  0.00      B6    
+ATOM    259  AK3 CLA X   1    -116.444 204.434-186.863  1.00  0.00      B6    
+ATOM    260  LT3 CLA X   1    -109.634 116.627-217.712  1.00  0.00      B6    
+ATOM    261  HB0 CLA X   1       0.232 331.308 -93.118  1.00  0.00      C6    
+ATOM    262  PX1 CLA X   1     -64.322 313.817-144.420  1.00  0.00      C6    
+ATOM    263  DT1 CLA X   1    -106.786 228.382-232.998  1.00  0.00      C6    
+ATOM    264  AK1 CLA X   1     -46.850 137.222-287.691  1.00  0.00      C6    
+ATOM    265  LT1 CLA X   1      24.926  73.217-270.101  1.00  0.00      C6    
+ATOM    266  PX2 CLA X   1      79.740 316.953-121.486  1.00  0.00      C6    
+ATOM    267  DT2 CLA X   1     189.163 229.761-124.820  1.00  0.00      C6    
+ATOM    268  AK2 CLA X   1     238.827 139.001 -50.135  1.00  0.00      C6    
+ATOM    269  LT2 CLA X   1     218.915  77.201  18.776  1.00  0.00      C6    
+ATOM    270  PX3 CLA X   1     -14.402 342.637 -11.493  1.00  0.00      C6    
+ATOM    271  DT3 CLA X   1     -69.082 296.727 103.359  1.00  0.00      C6    
+ATOM    272  AK3 CLA X   1    -146.495 205.240 144.395  1.00  0.00      C6    
+ATOM    273  LT3 CLA X   1    -177.890 118.659 126.760  1.00  0.00      C6    
+ATOM    274  HB0 CLA X   1     188.541  -1.488-331.473  1.00  0.00      A7    
+ATOM    275  PX1 CLA X   1     251.234  12.306-275.579  1.00  0.00      A7    
+ATOM    276  DT1 CLA X   1     280.592  69.705-159.192  1.00  0.00      A7    
+ATOM    277  AK1 CLA X   1     218.091 155.028 -96.656  1.00  0.00      A7    
+ATOM    278  LT1 CLA X   1     128.043 184.453 -85.497  1.00  0.00      A7    
+ATOM    279  PX2 CLA X   1     140.484  65.324-352.917  1.00  0.00      A7    
+ATOM    280  DT2 CLA X   1      23.007 135.296-333.137  1.00  0.00      A7    
+ATOM    281  AK2 CLA X   1     -89.973 109.599-287.973  1.00  0.00      A7    
+ATOM    282  LT2 CLA X   1    -136.656  50.229-235.435  1.00  0.00      A7    
+ATOM    283  PX3 CLA X   1     161.662 -81.231-340.613  1.00  0.00      A7    
+ATOM    284  DT3 CLA X   1     129.164-184.759-265.860  1.00  0.00      A7    
+ATOM    285  AK3 CLA X   1     149.729-204.084-146.926  1.00  0.00      A7    
+ATOM    286  LT3 CLA X   1     158.887-159.472 -66.678  1.00  0.00      A7    
+ATOM    287  HB0 CLA X   1     304.279   0.528-182.367  1.00  0.00      B7    
+ATOM    288  PX1 CLA X   1     267.047 -15.111-256.749  1.00  0.00      B7    
+ATOM    289  DT1 CLA X   1     160.355 -71.055-313.695  1.00  0.00      B7    
+ATOM    290  AK1 CLA X   1      86.951-152.300-262.690  1.00  0.00      B7    
+ATOM    291  LT1 CLA X   1      59.713-182.886-177.443  1.00  0.00      B7    
+ATOM    292  PX2 CLA X   1     314.754 -67.142-133.576  1.00  0.00      B7    
+ATOM    293  DT2 CLA X   1     284.654-139.597 -21.125  1.00  0.00      B7    
+ATOM    294  AK2 CLA X   1     244.294-110.717  95.151  1.00  0.00      B7    
+ATOM    295  LT2 CLA X   1     198.687 -47.565 145.576  1.00  0.00      B7    
+ATOM    296  PX3 CLA X   1     307.104  80.712-155.002  1.00  0.00      B7    
+ATOM    297  DT3 CLA X   1     228.901 186.196-138.751  1.00  0.00      B7    
+ATOM    298  AK3 CLA X   1     118.823 203.060-186.863  1.00  0.00      B7    
+ATOM    299  LT3 CLA X   1      46.185 153.259-217.712  1.00  0.00      B7    
+ATOM    300  HB0 CLA X   1     287.037 165.452 -93.118  1.00  0.00      C7    
+ATOM    301  PX1 CLA X   1     239.613 212.613-144.420  1.00  0.00      C7    
+ATOM    302  DT1 CLA X   1     144.392 206.670-232.998  1.00  0.00      C7    
+ATOM    303  AK1 CLA X   1      95.413 109.184-287.691  1.00  0.00      C7    
+ATOM    304  LT1 CLA X   1      75.871  15.022-270.101  1.00  0.00      C7    
+ATOM    305  PX2 CLA X   1     314.360  89.420-121.486  1.00  0.00      C7    
+ATOM    306  DT2 CLA X   1     293.560 -48.939-124.820  1.00  0.00      C7    
+ATOM    307  AK2 CLA X   1     239.791-137.330 -50.135  1.00  0.00      C7    
+ATOM    308  LT2 CLA X   1     176.315-150.986  18.776  1.00  0.00      C7    
+ATOM    309  PX3 CLA X   1     289.532 183.791 -11.493  1.00  0.00      C7    
+ATOM    310  DT3 CLA X   1     222.432 208.190 103.359  1.00  0.00      C7    
+ATOM    311  AK3 CLA X   1     104.496 229.489 144.395  1.00  0.00      C7    
+ATOM    312  LT3 CLA X   1      13.817 213.386 126.760  1.00  0.00      C7    
+ATOM    313  HB0 CLA X   1      92.981-164.025-331.473  1.00  0.00      A8    
+ATOM    314  PX1 CLA X   1     136.274-211.422-275.579  1.00  0.00      A8    
+ATOM    315  DT1 CLA X   1     200.662-208.148-159.192  1.00  0.00      A8    
+ATOM    316  AK1 CLA X   1     243.304-111.359 -96.656  1.00  0.00      A8    
+ATOM    317  LT1 CLA X   1     223.763 -18.662 -85.497  1.00  0.00      A8    
+ATOM    318  PX2 CLA X   1     126.815 -89.000-352.917  1.00  0.00      A8    
+ATOM    319  DT2 CLA X   1     128.673  47.724-333.137  1.00  0.00      A8    
+ATOM    320  AK2 CLA X   1      49.929 132.718-287.973  1.00  0.00      A8    
+ATOM    321  LT2 CLA X   1     -24.828 143.462-235.435  1.00  0.00      A8    
+ATOM    322  PX3 CLA X   1      10.483-180.619-340.613  1.00  0.00      A8    
+ATOM    323  DT3 CLA X   1     -95.424-204.239-265.860  1.00  0.00      A8    
+ATOM    324  AK3 CLA X   1    -101.877-231.712-146.926  1.00  0.00      A8    
+ATOM    325  LT3 CLA X   1     -58.664-217.336 -66.678  1.00  0.00      A8    
+ATOM    326  HB0 CLA X   1     152.597-263.250-182.367  1.00  0.00      B8    
+ATOM    327  PX1 CLA X   1     120.437-238.824-256.749  1.00  0.00      B8    
+ATOM    328  DT1 CLA X   1      18.642-174.399-313.695  1.00  0.00      B8    
+ATOM    329  AK1 CLA X   1     -88.420-151.452-262.690  1.00  0.00      B8    
+ATOM    330  LT1 CLA X   1    -128.527-143.156-177.443  1.00  0.00      B8    
+ATOM    331  PX2 CLA X   1      99.230-306.155-133.576  1.00  0.00      B8    
+ATOM    332  DT2 CLA X   1      21.433-316.316 -21.125  1.00  0.00      B8    
+ATOM    333  AK2 CLA X   1      26.263-266.923  95.151  1.00  0.00      B8    
+ATOM    334  LT2 CLA X   1      58.151-195.850 145.576  1.00  0.00      B8    
+ATOM    335  PX3 CLA X   1     223.451-225.604-155.002  1.00  0.00      B8    
+ATOM    336  DT3 CLA X   1     275.701-105.136-138.751  1.00  0.00      B8    
+ATOM    337  AK3 CLA X   1     235.267  -1.374-186.863  1.00  0.00      B8    
+ATOM    338  LT3 CLA X   1     155.819  36.632-217.712  1.00  0.00      B8    
+ATOM    339  HB0 CLA X   1     286.805-165.855 -93.118  1.00  0.00      C8    
+ATOM    340  PX1 CLA X   1     303.935-101.204-144.420  1.00  0.00      C8    
+ATOM    341  DT1 CLA X   1     251.178 -21.712-232.998  1.00  0.00      C8    
+ATOM    342  AK1 CLA X   1     142.263 -28.038-287.691  1.00  0.00      C8    
+ATOM    343  LT1 CLA X   1      50.945 -58.195-270.101  1.00  0.00      C8    
+ATOM    344  PX2 CLA X   1     234.620-227.534-121.486  1.00  0.00      C8    
+ATOM    345  DT2 CLA X   1     104.398-278.700-124.820  1.00  0.00      C8    
+ATOM    346  AK2 CLA X   1       0.965-276.330 -50.135  1.00  0.00      C8    
+ATOM    347  LT2 CLA X   1     -42.600-228.187  18.776  1.00  0.00      C8    
+ATOM    348  PX3 CLA X   1     303.934-158.846 -11.493  1.00  0.00      C8    
+ATOM    349  DT3 CLA X   1     291.514 -88.537 103.359  1.00  0.00      C8    
+ATOM    350  AK3 CLA X   1     250.991  24.248 144.395  1.00  0.00      C8    
+ATOM    351  LT3 CLA X   1     191.706  94.728 126.760  1.00  0.00      C8    
+ATOM    352  HB0 CLA X   1     -95.559-162.537-331.473  1.00  0.00      A9    
+ATOM    353  PX1 CLA X   1    -114.959-223.728-275.579  1.00  0.00      A9    
+ATOM    354  DT1 CLA X   1     -79.930-277.853-159.192  1.00  0.00      A9    
+ATOM    355  AK1 CLA X   1      25.213-266.386 -96.656  1.00  0.00      A9    
+ATOM    356  LT1 CLA X   1      95.719-203.115 -85.497  1.00  0.00      A9    
+ATOM    357  PX2 CLA X   1     -13.669-154.325-352.917  1.00  0.00      A9    
+ATOM    358  DT2 CLA X   1     105.666 -87.572-333.137  1.00  0.00      A9    
+ATOM    359  AK2 CLA X   1     139.902  23.120-287.973  1.00  0.00      A9    
+ATOM    360  LT2 CLA X   1     111.827  93.233-235.435  1.00  0.00      A9    
+ATOM    361  PX3 CLA X   1    -151.180 -99.388-340.613  1.00  0.00      A9    
+ATOM    362  DT3 CLA X   1    -224.588 -19.480-265.860  1.00  0.00      A9    
+ATOM    363  AK3 CLA X   1    -251.607 -27.627-146.926  1.00  0.00      A9    
+ATOM    364  LT3 CLA X   1    -217.550 -57.864 -66.678  1.00  0.00      A9    
+ATOM    365  HB0 CLA X   1    -151.683-263.777-182.367  1.00  0.00      B9    
+ATOM    366  PX1 CLA X   1    -146.609-223.714-256.749  1.00  0.00      B9    
+ATOM    367  DT1 CLA X   1    -141.713-103.344-313.695  1.00  0.00      B9    
+ATOM    368  AK1 CLA X   1    -175.371   0.848-262.690  1.00  0.00      B9    
+ATOM    369  LT1 CLA X   1    -188.241  39.730-177.443  1.00  0.00      B9    
+ATOM    370  PX2 CLA X   1    -215.523-239.014-133.576  1.00  0.00      B9    
+ATOM    371  DT2 CLA X   1    -263.221-176.720 -21.125  1.00  0.00      B9    
+ATOM    372  AK2 CLA X   1    -218.030-156.206  95.151  1.00  0.00      B9    
+ATOM    373  LT2 CLA X   1    -140.536-148.285 145.576  1.00  0.00      B9    
+ATOM    374  PX3 CLA X   1     -83.654-306.316-155.002  1.00  0.00      B9    
+ATOM    375  DT3 CLA X   1      46.800-291.332-138.751  1.00  0.00      B9    
+ATOM    376  AK3 CLA X   1     116.444-204.434-186.863  1.00  0.00      B9    
+ATOM    377  LT3 CLA X   1     109.634-116.627-217.712  1.00  0.00      B9    
+ATOM    378  HB0 CLA X   1      -0.232-331.308 -93.118  1.00  0.00      C9    
+ATOM    379  PX1 CLA X   1      64.322-313.817-144.420  1.00  0.00      C9    
+ATOM    380  DT1 CLA X   1     106.786-228.382-232.998  1.00  0.00      C9    
+ATOM    381  AK1 CLA X   1      46.850-137.222-287.691  1.00  0.00      C9    
+ATOM    382  LT1 CLA X   1     -24.926 -73.217-270.101  1.00  0.00      C9    
+ATOM    383  PX2 CLA X   1     -79.740-316.953-121.486  1.00  0.00      C9    
+ATOM    384  DT2 CLA X   1    -189.163-229.761-124.820  1.00  0.00      C9    
+ATOM    385  AK2 CLA X   1    -238.827-139.001 -50.135  1.00  0.00      C9    
+ATOM    386  LT2 CLA X   1    -218.915 -77.201  18.776  1.00  0.00      C9    
+ATOM    387  PX3 CLA X   1      14.402-342.637 -11.493  1.00  0.00      C9    
+ATOM    388  DT3 CLA X   1      69.082-296.727 103.359  1.00  0.00      C9    
+ATOM    389  AK3 CLA X   1     146.495-205.240 144.395  1.00  0.00      C9    
+ATOM    390  LT3 CLA X   1     177.890-118.659 126.760  1.00  0.00      C9    
+ATOM    391  HB0 CLA X   1    -188.541   1.488-331.473  1.00  0.00      A10   
+ATOM    392  PX1 CLA X   1    -251.234 -12.306-275.579  1.00  0.00      A10   
+ATOM    393  DT1 CLA X   1    -280.592 -69.705-159.192  1.00  0.00      A10   
+ATOM    394  AK1 CLA X   1    -218.091-155.028 -96.656  1.00  0.00      A10   
+ATOM    395  LT1 CLA X   1    -128.043-184.453 -85.497  1.00  0.00      A10   
+ATOM    396  PX2 CLA X   1    -140.484 -65.324-352.917  1.00  0.00      A10   
+ATOM    397  DT2 CLA X   1     -23.007-135.296-333.137  1.00  0.00      A10   
+ATOM    398  AK2 CLA X   1      89.973-109.599-287.973  1.00  0.00      A10   
+ATOM    399  LT2 CLA X   1     136.656 -50.229-235.435  1.00  0.00      A10   
+ATOM    400  PX3 CLA X   1    -161.662  81.231-340.613  1.00  0.00      A10   
+ATOM    401  DT3 CLA X   1    -129.164 184.759-265.860  1.00  0.00      A10   
+ATOM    402  AK3 CLA X   1    -149.729 204.084-146.926  1.00  0.00      A10   
+ATOM    403  LT3 CLA X   1    -158.887 159.472 -66.678  1.00  0.00      A10   
+ATOM    404  HB0 CLA X   1    -304.279  -0.528-182.367  1.00  0.00      B10   
+ATOM    405  PX1 CLA X   1    -267.047  15.111-256.749  1.00  0.00      B10   
+ATOM    406  DT1 CLA X   1    -160.355  71.055-313.695  1.00  0.00      B10   
+ATOM    407  AK1 CLA X   1     -86.951 152.300-262.690  1.00  0.00      B10   
+ATOM    408  LT1 CLA X   1     -59.713 182.886-177.443  1.00  0.00      B10   
+ATOM    409  PX2 CLA X   1    -314.754  67.142-133.576  1.00  0.00      B10   
+ATOM    410  DT2 CLA X   1    -284.654 139.597 -21.125  1.00  0.00      B10   
+ATOM    411  AK2 CLA X   1    -244.294 110.717  95.151  1.00  0.00      B10   
+ATOM    412  LT2 CLA X   1    -198.687  47.565 145.576  1.00  0.00      B10   
+ATOM    413  PX3 CLA X   1    -307.104 -80.712-155.002  1.00  0.00      B10   
+ATOM    414  DT3 CLA X   1    -228.901-186.196-138.751  1.00  0.00      B10   
+ATOM    415  AK3 CLA X   1    -118.823-203.060-186.863  1.00  0.00      B10   
+ATOM    416  LT3 CLA X   1     -46.185-153.259-217.712  1.00  0.00      B10   
+ATOM    417  HB0 CLA X   1    -287.037-165.452 -93.118  1.00  0.00      C10   
+ATOM    418  PX1 CLA X   1    -239.613-212.613-144.420  1.00  0.00      C10   
+ATOM    419  DT1 CLA X   1    -144.392-206.670-232.998  1.00  0.00      C10   
+ATOM    420  AK1 CLA X   1     -95.413-109.184-287.691  1.00  0.00      C10   
+ATOM    421  LT1 CLA X   1     -75.871 -15.022-270.101  1.00  0.00      C10   
+ATOM    422  PX2 CLA X   1    -314.360 -89.420-121.486  1.00  0.00      C10   
+ATOM    423  DT2 CLA X   1    -293.560  48.939-124.820  1.00  0.00      C10   
+ATOM    424  AK2 CLA X   1    -239.791 137.330 -50.135  1.00  0.00      C10   
+ATOM    425  LT2 CLA X   1    -176.315 150.986  18.776  1.00  0.00      C10   
+ATOM    426  PX3 CLA X   1    -289.532-183.791 -11.493  1.00  0.00      C10   
+ATOM    427  DT3 CLA X   1    -222.432-208.190 103.359  1.00  0.00      C10   
+ATOM    428  AK3 CLA X   1    -104.496-229.489 144.395  1.00  0.00      C10   
+ATOM    429  LT3 CLA X   1     -13.817-213.386 126.760  1.00  0.00      C10   
+ATOM    430  HB0 CLA X   1     -92.981 164.025-331.473  1.00  0.00      A11   
+ATOM    431  PX1 CLA X   1    -136.274 211.422-275.579  1.00  0.00      A11   
+ATOM    432  DT1 CLA X   1    -200.662 208.148-159.192  1.00  0.00      A11   
+ATOM    433  AK1 CLA X   1    -243.304 111.359 -96.656  1.00  0.00      A11   
+ATOM    434  LT1 CLA X   1    -223.763  18.662 -85.497  1.00  0.00      A11   
+ATOM    435  PX2 CLA X   1    -126.815  89.000-352.917  1.00  0.00      A11   
+ATOM    436  DT2 CLA X   1    -128.673 -47.724-333.137  1.00  0.00      A11   
+ATOM    437  AK2 CLA X   1     -49.929-132.718-287.973  1.00  0.00      A11   
+ATOM    438  LT2 CLA X   1      24.828-143.462-235.435  1.00  0.00      A11   
+ATOM    439  PX3 CLA X   1     -10.483 180.619-340.613  1.00  0.00      A11   
+ATOM    440  DT3 CLA X   1      95.424 204.239-265.860  1.00  0.00      A11   
+ATOM    441  AK3 CLA X   1     101.877 231.712-146.926  1.00  0.00      A11   
+ATOM    442  LT3 CLA X   1      58.664 217.336 -66.678  1.00  0.00      A11   
+ATOM    443  HB0 CLA X   1    -152.597 263.250-182.367  1.00  0.00      B11   
+ATOM    444  PX1 CLA X   1    -120.437 238.824-256.749  1.00  0.00      B11   
+ATOM    445  DT1 CLA X   1     -18.642 174.399-313.695  1.00  0.00      B11   
+ATOM    446  AK1 CLA X   1      88.420 151.452-262.690  1.00  0.00      B11   
+ATOM    447  LT1 CLA X   1     128.527 143.156-177.443  1.00  0.00      B11   
+ATOM    448  PX2 CLA X   1     -99.230 306.155-133.576  1.00  0.00      B11   
+ATOM    449  DT2 CLA X   1     -21.433 316.316 -21.125  1.00  0.00      B11   
+ATOM    450  AK2 CLA X   1     -26.263 266.923  95.151  1.00  0.00      B11   
+ATOM    451  LT2 CLA X   1     -58.151 195.850 145.576  1.00  0.00      B11   
+ATOM    452  PX3 CLA X   1    -223.451 225.604-155.002  1.00  0.00      B11   
+ATOM    453  DT3 CLA X   1    -275.701 105.136-138.751  1.00  0.00      B11   
+ATOM    454  AK3 CLA X   1    -235.267   1.374-186.863  1.00  0.00      B11   
+ATOM    455  LT3 CLA X   1    -155.819 -36.632-217.712  1.00  0.00      B11   
+ATOM    456  HB0 CLA X   1    -286.805 165.855 -93.118  1.00  0.00      C11   
+ATOM    457  PX1 CLA X   1    -303.935 101.204-144.420  1.00  0.00      C11   
+ATOM    458  DT1 CLA X   1    -251.178  21.712-232.998  1.00  0.00      C11   
+ATOM    459  AK1 CLA X   1    -142.263  28.038-287.691  1.00  0.00      C11   
+ATOM    460  LT1 CLA X   1     -50.945  58.195-270.101  1.00  0.00      C11   
+ATOM    461  PX2 CLA X   1    -234.620 227.534-121.486  1.00  0.00      C11   
+ATOM    462  DT2 CLA X   1    -104.398 278.700-124.820  1.00  0.00      C11   
+ATOM    463  AK2 CLA X   1      -0.965 276.330 -50.135  1.00  0.00      C11   
+ATOM    464  LT2 CLA X   1      42.600 228.187  18.776  1.00  0.00      C11   
+ATOM    465  PX3 CLA X   1    -303.934 158.846 -11.493  1.00  0.00      C11   
+ATOM    466  DT3 CLA X   1    -291.514  88.537 103.359  1.00  0.00      C11   
+ATOM    467  AK3 CLA X   1    -250.991 -24.248 144.395  1.00  0.00      C11   
+ATOM    468  LT3 CLA X   1    -191.706 -94.728 126.760  1.00  0.00      C11   
+END


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,1078 @@
+PSF
+
+      38 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS topology top_cg_clath.impr.inp 
+ REMARKS segment A0 { first NONE; last NONE; auto angles  }
+ REMARKS segment B0 { first NONE; last NONE; auto angles  }
+ REMARKS segment C0 { first NONE; last NONE; auto angles  }
+ REMARKS segment A1 { first NONE; last NONE; auto angles  }
+ REMARKS segment B1 { first NONE; last NONE; auto angles  }
+ REMARKS segment C1 { first NONE; last NONE; auto angles  }
+ REMARKS segment A2 { first NONE; last NONE; auto angles  }
+ REMARKS segment B2 { first NONE; last NONE; auto angles  }
+ REMARKS segment C2 { first NONE; last NONE; auto angles  }
+ REMARKS segment A3 { first NONE; last NONE; auto angles  }
+ REMARKS segment B3 { first NONE; last NONE; auto angles  }
+ REMARKS segment C3 { first NONE; last NONE; auto angles  }
+ REMARKS segment A4 { first NONE; last NONE; auto angles  }
+ REMARKS segment B4 { first NONE; last NONE; auto angles  }
+ REMARKS segment C4 { first NONE; last NONE; auto angles  }
+ REMARKS segment A5 { first NONE; last NONE; auto angles  }
+ REMARKS segment B5 { first NONE; last NONE; auto angles  }
+ REMARKS segment C5 { first NONE; last NONE; auto angles  }
+ REMARKS segment A6 { first NONE; last NONE; auto angles  }
+ REMARKS segment B6 { first NONE; last NONE; auto angles  }
+ REMARKS segment C6 { first NONE; last NONE; auto angles  }
+ REMARKS segment A7 { first NONE; last NONE; auto angles  }
+ REMARKS segment B7 { first NONE; last NONE; auto angles  }
+ REMARKS segment C7 { first NONE; last NONE; auto angles  }
+ REMARKS segment A8 { first NONE; last NONE; auto angles  }
+ REMARKS segment B8 { first NONE; last NONE; auto angles  }
+ REMARKS segment C8 { first NONE; last NONE; auto angles  }
+ REMARKS segment A9 { first NONE; last NONE; auto angles  }
+ REMARKS segment B9 { first NONE; last NONE; auto angles  }
+ REMARKS segment C9 { first NONE; last NONE; auto angles  }
+ REMARKS segment A10 { first NONE; last NONE; auto angles  }
+ REMARKS segment B10 { first NONE; last NONE; auto angles  }
+ REMARKS segment C10 { first NONE; last NONE; auto angles  }
+ REMARKS segment A11 { first NONE; last NONE; auto angles  }
+ REMARKS segment B11 { first NONE; last NONE; auto angles  }
+ REMARKS segment C11 { first NONE; last NONE; auto angles  }
+
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+       8 A0   1    CLA  AK2  AK     0.000000     34620.7800           0
+       9 A0   1    CLA  LT2  LT     0.000000     55013.7800           0
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+      12 A0   1    CLA  AK3  AK     0.000000     34620.7800           0
+      13 A0   1    CLA  LT3  LT     0.000000     55013.7800           0
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+      15 B0   1    CLA  PX1  PX     0.000000     46422.2000           0
+      16 B0   1    CLA  DT1  DT     0.000000     49195.2000           0
+      17 B0   1    CLA  AK1  AK     0.000000     34620.7800           0
+      18 B0   1    CLA  LT1  LT     0.000000     55013.7800           0
+      19 B0   1    CLA  PX2  PX     0.000000     46422.2000           0
+      20 B0   1    CLA  DT2  DT     0.000000     49195.2000           0
+      21 B0   1    CLA  AK2  AK     0.000000     34620.7800           0
+      22 B0   1    CLA  LT2  LT     0.000000     55013.7800           0
+      23 B0   1    CLA  PX3  PX     0.000000     46422.2000           0
+      24 B0   1    CLA  DT3  DT     0.000000     49195.2000           0
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+      26 B0   1    CLA  LT3  LT     0.000000     55013.7800           0
+      27 C0   1    CLA  HB0  HB     0.000000     30478.0300           0
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+      29 C0   1    CLA  DT1  DT     0.000000     49195.2000           0
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+      33 C0   1    CLA  DT2  DT     0.000000     49195.2000           0
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+      36 C0   1    CLA  PX3  PX     0.000000     46422.2000           0
+      37 C0   1    CLA  DT3  DT     0.000000     49195.2000           0
+      38 C0   1    CLA  AK3  AK     0.000000     34620.7800           0
+      39 C0   1    CLA  LT3  LT     0.000000     55013.7800           0
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+      41 A1   1    CLA  PX1  PX     0.000000     46422.2000           0
+      42 A1   1    CLA  DT1  DT     0.000000     49195.2000           0
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+      54 B1   1    CLA  PX1  PX     0.000000     46422.2000           0
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+      56 B1   1    CLA  AK1  AK     0.000000     34620.7800           0
+      57 B1   1    CLA  LT1  LT     0.000000     55013.7800           0
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+      63 B1   1    CLA  DT3  DT     0.000000     49195.2000           0
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+      65 B1   1    CLA  LT3  LT     0.000000     55013.7800           0
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+      67 C1   1    CLA  PX1  PX     0.000000     46422.2000           0
+      68 C1   1    CLA  DT1  DT     0.000000     49195.2000           0
+      69 C1   1    CLA  AK1  AK     0.000000     34620.7800           0
+      70 C1   1    CLA  LT1  LT     0.000000     55013.7800           0
+      71 C1   1    CLA  PX2  PX     0.000000     46422.2000           0
+      72 C1   1    CLA  DT2  DT     0.000000     49195.2000           0
+      73 C1   1    CLA  AK2  AK     0.000000     34620.7800           0
+      74 C1   1    CLA  LT2  LT     0.000000     55013.7800           0
+      75 C1   1    CLA  PX3  PX     0.000000     46422.2000           0
+      76 C1   1    CLA  DT3  DT     0.000000     49195.2000           0
+      77 C1   1    CLA  AK3  AK     0.000000     34620.7800           0
+      78 C1   1    CLA  LT3  LT     0.000000     55013.7800           0
+      79 A2   1    CLA  HB0  HB     0.000000     30478.0300           0
+      80 A2   1    CLA  PX1  PX     0.000000     46422.2000           0
+      81 A2   1    CLA  DT1  DT     0.000000     49195.2000           0
+      82 A2   1    CLA  AK1  AK     0.000000     34620.7800           0
+      83 A2   1    CLA  LT1  LT     0.000000     55013.7800           0
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+      89 A2   1    CLA  DT3  DT     0.000000     49195.2000           0
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+     154 C3   1    CLA  DT3  DT     0.000000     49195.2000           0
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+     159 A4   1    CLA  DT1  DT     0.000000     49195.2000           0
+     160 A4   1    CLA  AK1  AK     0.000000     34620.7800           0
+     161 A4   1    CLA  LT1  LT     0.000000     55013.7800           0
+     162 A4   1    CLA  PX2  PX     0.000000     46422.2000           0
+     163 A4   1    CLA  DT2  DT     0.000000     49195.2000           0
+     164 A4   1    CLA  AK2  AK     0.000000     34620.7800           0
+     165 A4   1    CLA  LT2  LT     0.000000     55013.7800           0
+     166 A4   1    CLA  PX3  PX     0.000000     46422.2000           0
+     167 A4   1    CLA  DT3  DT     0.000000     49195.2000           0
+     168 A4   1    CLA  AK3  AK     0.000000     34620.7800           0
+     169 A4   1    CLA  LT3  LT     0.000000     55013.7800           0
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+     172 B4   1    CLA  DT1  DT     0.000000     49195.2000           0
+     173 B4   1    CLA  AK1  AK     0.000000     34620.7800           0
+     174 B4   1    CLA  LT1  LT     0.000000     55013.7800           0
+     175 B4   1    CLA  PX2  PX     0.000000     46422.2000           0
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+     177 B4   1    CLA  AK2  AK     0.000000     34620.7800           0
+     178 B4   1    CLA  LT2  LT     0.000000     55013.7800           0
+     179 B4   1    CLA  PX3  PX     0.000000     46422.2000           0
+     180 B4   1    CLA  DT3  DT     0.000000     49195.2000           0
+     181 B4   1    CLA  AK3  AK     0.000000     34620.7800           0
+     182 B4   1    CLA  LT3  LT     0.000000     55013.7800           0
+     183 C4   1    CLA  HB0  HB     0.000000     30478.0300           0
+     184 C4   1    CLA  PX1  PX     0.000000     46422.2000           0
+     185 C4   1    CLA  DT1  DT     0.000000     49195.2000           0
+     186 C4   1    CLA  AK1  AK     0.000000     34620.7800           0
+     187 C4   1    CLA  LT1  LT     0.000000     55013.7800           0
+     188 C4   1    CLA  PX2  PX     0.000000     46422.2000           0
+     189 C4   1    CLA  DT2  DT     0.000000     49195.2000           0
+     190 C4   1    CLA  AK2  AK     0.000000     34620.7800           0
+     191 C4   1    CLA  LT2  LT     0.000000     55013.7800           0
+     192 C4   1    CLA  PX3  PX     0.000000     46422.2000           0
+     193 C4   1    CLA  DT3  DT     0.000000     49195.2000           0
+     194 C4   1    CLA  AK3  AK     0.000000     34620.7800           0
+     195 C4   1    CLA  LT3  LT     0.000000     55013.7800           0
+     196 A5   1    CLA  HB0  HB     0.000000     30478.0300           0
+     197 A5   1    CLA  PX1  PX     0.000000     46422.2000           0
+     198 A5   1    CLA  DT1  DT     0.000000     49195.2000           0
+     199 A5   1    CLA  AK1  AK     0.000000     34620.7800           0
+     200 A5   1    CLA  LT1  LT     0.000000     55013.7800           0
+     201 A5   1    CLA  PX2  PX     0.000000     46422.2000           0
+     202 A5   1    CLA  DT2  DT     0.000000     49195.2000           0
+     203 A5   1    CLA  AK2  AK     0.000000     34620.7800           0
+     204 A5   1    CLA  LT2  LT     0.000000     55013.7800           0
+     205 A5   1    CLA  PX3  PX     0.000000     46422.2000           0
+     206 A5   1    CLA  DT3  DT     0.000000     49195.2000           0
+     207 A5   1    CLA  AK3  AK     0.000000     34620.7800           0
+     208 A5   1    CLA  LT3  LT     0.000000     55013.7800           0
+     209 B5   1    CLA  HB0  HB     0.000000     30478.0300           0
+     210 B5   1    CLA  PX1  PX     0.000000     46422.2000           0
+     211 B5   1    CLA  DT1  DT     0.000000     49195.2000           0
+     212 B5   1    CLA  AK1  AK     0.000000     34620.7800           0
+     213 B5   1    CLA  LT1  LT     0.000000     55013.7800           0
+     214 B5   1    CLA  PX2  PX     0.000000     46422.2000           0
+     215 B5   1    CLA  DT2  DT     0.000000     49195.2000           0
+     216 B5   1    CLA  AK2  AK     0.000000     34620.7800           0
+     217 B5   1    CLA  LT2  LT     0.000000     55013.7800           0
+     218 B5   1    CLA  PX3  PX     0.000000     46422.2000           0
+     219 B5   1    CLA  DT3  DT     0.000000     49195.2000           0
+     220 B5   1    CLA  AK3  AK     0.000000     34620.7800           0
+     221 B5   1    CLA  LT3  LT     0.000000     55013.7800           0
+     222 C5   1    CLA  HB0  HB     0.000000     30478.0300           0
+     223 C5   1    CLA  PX1  PX     0.000000     46422.2000           0
+     224 C5   1    CLA  DT1  DT     0.000000     49195.2000           0
+     225 C5   1    CLA  AK1  AK     0.000000     34620.7800           0
+     226 C5   1    CLA  LT1  LT     0.000000     55013.7800           0
+     227 C5   1    CLA  PX2  PX     0.000000     46422.2000           0
+     228 C5   1    CLA  DT2  DT     0.000000     49195.2000           0
+     229 C5   1    CLA  AK2  AK     0.000000     34620.7800           0
+     230 C5   1    CLA  LT2  LT     0.000000     55013.7800           0
+     231 C5   1    CLA  PX3  PX     0.000000     46422.2000           0
+     232 C5   1    CLA  DT3  DT     0.000000     49195.2000           0
+     233 C5   1    CLA  AK3  AK     0.000000     34620.7800           0
+     234 C5   1    CLA  LT3  LT     0.000000     55013.7800           0
+     235 A6   1    CLA  HB0  HB     0.000000     30478.0300           0
+     236 A6   1    CLA  PX1  PX     0.000000     46422.2000           0
+     237 A6   1    CLA  DT1  DT     0.000000     49195.2000           0
+     238 A6   1    CLA  AK1  AK     0.000000     34620.7800           0
+     239 A6   1    CLA  LT1  LT     0.000000     55013.7800           0
+     240 A6   1    CLA  PX2  PX     0.000000     46422.2000           0
+     241 A6   1    CLA  DT2  DT     0.000000     49195.2000           0
+     242 A6   1    CLA  AK2  AK     0.000000     34620.7800           0
+     243 A6   1    CLA  LT2  LT     0.000000     55013.7800           0
+     244 A6   1    CLA  PX3  PX     0.000000     46422.2000           0
+     245 A6   1    CLA  DT3  DT     0.000000     49195.2000           0
+     246 A6   1    CLA  AK3  AK     0.000000     34620.7800           0
+     247 A6   1    CLA  LT3  LT     0.000000     55013.7800           0
+     248 B6   1    CLA  HB0  HB     0.000000     30478.0300           0
+     249 B6   1    CLA  PX1  PX     0.000000     46422.2000           0
+     250 B6   1    CLA  DT1  DT     0.000000     49195.2000           0
+     251 B6   1    CLA  AK1  AK     0.000000     34620.7800           0
+     252 B6   1    CLA  LT1  LT     0.000000     55013.7800           0
+     253 B6   1    CLA  PX2  PX     0.000000     46422.2000           0
+     254 B6   1    CLA  DT2  DT     0.000000     49195.2000           0
+     255 B6   1    CLA  AK2  AK     0.000000     34620.7800           0
+     256 B6   1    CLA  LT2  LT     0.000000     55013.7800           0
+     257 B6   1    CLA  PX3  PX     0.000000     46422.2000           0
+     258 B6   1    CLA  DT3  DT     0.000000     49195.2000           0
+     259 B6   1    CLA  AK3  AK     0.000000     34620.7800           0
+     260 B6   1    CLA  LT3  LT     0.000000     55013.7800           0
+     261 C6   1    CLA  HB0  HB     0.000000     30478.0300           0
+     262 C6   1    CLA  PX1  PX     0.000000     46422.2000           0
+     263 C6   1    CLA  DT1  DT     0.000000     49195.2000           0
+     264 C6   1    CLA  AK1  AK     0.000000     34620.7800           0
+     265 C6   1    CLA  LT1  LT     0.000000     55013.7800           0
+     266 C6   1    CLA  PX2  PX     0.000000     46422.2000           0
+     267 C6   1    CLA  DT2  DT     0.000000     49195.2000           0
+     268 C6   1    CLA  AK2  AK     0.000000     34620.7800           0
+     269 C6   1    CLA  LT2  LT     0.000000     55013.7800           0
+     270 C6   1    CLA  PX3  PX     0.000000     46422.2000           0
+     271 C6   1    CLA  DT3  DT     0.000000     49195.2000           0
+     272 C6   1    CLA  AK3  AK     0.000000     34620.7800           0
+     273 C6   1    CLA  LT3  LT     0.000000     55013.7800           0
+     274 A7   1    CLA  HB0  HB     0.000000     30478.0300           0
+     275 A7   1    CLA  PX1  PX     0.000000     46422.2000           0
+     276 A7   1    CLA  DT1  DT     0.000000     49195.2000           0
+     277 A7   1    CLA  AK1  AK     0.000000     34620.7800           0
+     278 A7   1    CLA  LT1  LT     0.000000     55013.7800           0
+     279 A7   1    CLA  PX2  PX     0.000000     46422.2000           0
+     280 A7   1    CLA  DT2  DT     0.000000     49195.2000           0
+     281 A7   1    CLA  AK2  AK     0.000000     34620.7800           0
+     282 A7   1    CLA  LT2  LT     0.000000     55013.7800           0
+     283 A7   1    CLA  PX3  PX     0.000000     46422.2000           0
+     284 A7   1    CLA  DT3  DT     0.000000     49195.2000           0
+     285 A7   1    CLA  AK3  AK     0.000000     34620.7800           0
+     286 A7   1    CLA  LT3  LT     0.000000     55013.7800           0
+     287 B7   1    CLA  HB0  HB     0.000000     30478.0300           0
+     288 B7   1    CLA  PX1  PX     0.000000     46422.2000           0
+     289 B7   1    CLA  DT1  DT     0.000000     49195.2000           0
+     290 B7   1    CLA  AK1  AK     0.000000     34620.7800           0
+     291 B7   1    CLA  LT1  LT     0.000000     55013.7800           0
+     292 B7   1    CLA  PX2  PX     0.000000     46422.2000           0
+     293 B7   1    CLA  DT2  DT     0.000000     49195.2000           0
+     294 B7   1    CLA  AK2  AK     0.000000     34620.7800           0
+     295 B7   1    CLA  LT2  LT     0.000000     55013.7800           0
+     296 B7   1    CLA  PX3  PX     0.000000     46422.2000           0
+     297 B7   1    CLA  DT3  DT     0.000000     49195.2000           0
+     298 B7   1    CLA  AK3  AK     0.000000     34620.7800           0
+     299 B7   1    CLA  LT3  LT     0.000000     55013.7800           0
+     300 C7   1    CLA  HB0  HB     0.000000     30478.0300           0
+     301 C7   1    CLA  PX1  PX     0.000000     46422.2000           0
+     302 C7   1    CLA  DT1  DT     0.000000     49195.2000           0
+     303 C7   1    CLA  AK1  AK     0.000000     34620.7800           0
+     304 C7   1    CLA  LT1  LT     0.000000     55013.7800           0
+     305 C7   1    CLA  PX2  PX     0.000000     46422.2000           0
+     306 C7   1    CLA  DT2  DT     0.000000     49195.2000           0
+     307 C7   1    CLA  AK2  AK     0.000000     34620.7800           0
+     308 C7   1    CLA  LT2  LT     0.000000     55013.7800           0
+     309 C7   1    CLA  PX3  PX     0.000000     46422.2000           0
+     310 C7   1    CLA  DT3  DT     0.000000     49195.2000           0
+     311 C7   1    CLA  AK3  AK     0.000000     34620.7800           0
+     312 C7   1    CLA  LT3  LT     0.000000     55013.7800           0
+     313 A8   1    CLA  HB0  HB     0.000000     30478.0300           0
+     314 A8   1    CLA  PX1  PX     0.000000     46422.2000           0
+     315 A8   1    CLA  DT1  DT     0.000000     49195.2000           0
+     316 A8   1    CLA  AK1  AK     0.000000     34620.7800           0
+     317 A8   1    CLA  LT1  LT     0.000000     55013.7800           0
+     318 A8   1    CLA  PX2  PX     0.000000     46422.2000           0
+     319 A8   1    CLA  DT2  DT     0.000000     49195.2000           0
+     320 A8   1    CLA  AK2  AK     0.000000     34620.7800           0
+     321 A8   1    CLA  LT2  LT     0.000000     55013.7800           0
+     322 A8   1    CLA  PX3  PX     0.000000     46422.2000           0
+     323 A8   1    CLA  DT3  DT     0.000000     49195.2000           0
+     324 A8   1    CLA  AK3  AK     0.000000     34620.7800           0
+     325 A8   1    CLA  LT3  LT     0.000000     55013.7800           0
+     326 B8   1    CLA  HB0  HB     0.000000     30478.0300           0
+     327 B8   1    CLA  PX1  PX     0.000000     46422.2000           0
+     328 B8   1    CLA  DT1  DT     0.000000     49195.2000           0
+     329 B8   1    CLA  AK1  AK     0.000000     34620.7800           0
+     330 B8   1    CLA  LT1  LT     0.000000     55013.7800           0
+     331 B8   1    CLA  PX2  PX     0.000000     46422.2000           0
+     332 B8   1    CLA  DT2  DT     0.000000     49195.2000           0
+     333 B8   1    CLA  AK2  AK     0.000000     34620.7800           0
+     334 B8   1    CLA  LT2  LT     0.000000     55013.7800           0
+     335 B8   1    CLA  PX3  PX     0.000000     46422.2000           0
+     336 B8   1    CLA  DT3  DT     0.000000     49195.2000           0
+     337 B8   1    CLA  AK3  AK     0.000000     34620.7800           0
+     338 B8   1    CLA  LT3  LT     0.000000     55013.7800           0
+     339 C8   1    CLA  HB0  HB     0.000000     30478.0300           0
+     340 C8   1    CLA  PX1  PX     0.000000     46422.2000           0
+     341 C8   1    CLA  DT1  DT     0.000000     49195.2000           0
+     342 C8   1    CLA  AK1  AK     0.000000     34620.7800           0
+     343 C8   1    CLA  LT1  LT     0.000000     55013.7800           0
+     344 C8   1    CLA  PX2  PX     0.000000     46422.2000           0
+     345 C8   1    CLA  DT2  DT     0.000000     49195.2000           0
+     346 C8   1    CLA  AK2  AK     0.000000     34620.7800           0
+     347 C8   1    CLA  LT2  LT     0.000000     55013.7800           0
+     348 C8   1    CLA  PX3  PX     0.000000     46422.2000           0
+     349 C8   1    CLA  DT3  DT     0.000000     49195.2000           0
+     350 C8   1    CLA  AK3  AK     0.000000     34620.7800           0
+     351 C8   1    CLA  LT3  LT     0.000000     55013.7800           0
+     352 A9   1    CLA  HB0  HB     0.000000     30478.0300           0
+     353 A9   1    CLA  PX1  PX     0.000000     46422.2000           0
+     354 A9   1    CLA  DT1  DT     0.000000     49195.2000           0
+     355 A9   1    CLA  AK1  AK     0.000000     34620.7800           0
+     356 A9   1    CLA  LT1  LT     0.000000     55013.7800           0
+     357 A9   1    CLA  PX2  PX     0.000000     46422.2000           0
+     358 A9   1    CLA  DT2  DT     0.000000     49195.2000           0
+     359 A9   1    CLA  AK2  AK     0.000000     34620.7800           0
+     360 A9   1    CLA  LT2  LT     0.000000     55013.7800           0
+     361 A9   1    CLA  PX3  PX     0.000000     46422.2000           0
+     362 A9   1    CLA  DT3  DT     0.000000     49195.2000           0
+     363 A9   1    CLA  AK3  AK     0.000000     34620.7800           0
+     364 A9   1    CLA  LT3  LT     0.000000     55013.7800           0
+     365 B9   1    CLA  HB0  HB     0.000000     30478.0300           0
+     366 B9   1    CLA  PX1  PX     0.000000     46422.2000           0
+     367 B9   1    CLA  DT1  DT     0.000000     49195.2000           0
+     368 B9   1    CLA  AK1  AK     0.000000     34620.7800           0
+     369 B9   1    CLA  LT1  LT     0.000000     55013.7800           0
+     370 B9   1    CLA  PX2  PX     0.000000     46422.2000           0
+     371 B9   1    CLA  DT2  DT     0.000000     49195.2000           0
+     372 B9   1    CLA  AK2  AK     0.000000     34620.7800           0
+     373 B9   1    CLA  LT2  LT     0.000000     55013.7800           0
+     374 B9   1    CLA  PX3  PX     0.000000     46422.2000           0
+     375 B9   1    CLA  DT3  DT     0.000000     49195.2000           0
+     376 B9   1    CLA  AK3  AK     0.000000     34620.7800           0
+     377 B9   1    CLA  LT3  LT     0.000000     55013.7800           0
+     378 C9   1    CLA  HB0  HB     0.000000     30478.0300           0
+     379 C9   1    CLA  PX1  PX     0.000000     46422.2000           0
+     380 C9   1    CLA  DT1  DT     0.000000     49195.2000           0
+     381 C9   1    CLA  AK1  AK     0.000000     34620.7800           0
+     382 C9   1    CLA  LT1  LT     0.000000     55013.7800           0
+     383 C9   1    CLA  PX2  PX     0.000000     46422.2000           0
+     384 C9   1    CLA  DT2  DT     0.000000     49195.2000           0
+     385 C9   1    CLA  AK2  AK     0.000000     34620.7800           0
+     386 C9   1    CLA  LT2  LT     0.000000     55013.7800           0
+     387 C9   1    CLA  PX3  PX     0.000000     46422.2000           0
+     388 C9   1    CLA  DT3  DT     0.000000     49195.2000           0
+     389 C9   1    CLA  AK3  AK     0.000000     34620.7800           0
+     390 C9   1    CLA  LT3  LT     0.000000     55013.7800           0
+     391 A10  1    CLA  HB0  HB     0.000000     30478.0300           0
+     392 A10  1    CLA  PX1  PX     0.000000     46422.2000           0
+     393 A10  1    CLA  DT1  DT     0.000000     49195.2000           0
+     394 A10  1    CLA  AK1  AK     0.000000     34620.7800           0
+     395 A10  1    CLA  LT1  LT     0.000000     55013.7800           0
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+     397 A10  1    CLA  DT2  DT     0.000000     49195.2000           0
+     398 A10  1    CLA  AK2  AK     0.000000     34620.7800           0
+     399 A10  1    CLA  LT2  LT     0.000000     55013.7800           0
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+     401 A10  1    CLA  DT3  DT     0.000000     49195.2000           0
+     402 A10  1    CLA  AK3  AK     0.000000     34620.7800           0
+     403 A10  1    CLA  LT3  LT     0.000000     55013.7800           0
+     404 B10  1    CLA  HB0  HB     0.000000     30478.0300           0
+     405 B10  1    CLA  PX1  PX     0.000000     46422.2000           0
+     406 B10  1    CLA  DT1  DT     0.000000     49195.2000           0
+     407 B10  1    CLA  AK1  AK     0.000000     34620.7800           0
+     408 B10  1    CLA  LT1  LT     0.000000     55013.7800           0
+     409 B10  1    CLA  PX2  PX     0.000000     46422.2000           0
+     410 B10  1    CLA  DT2  DT     0.000000     49195.2000           0
+     411 B10  1    CLA  AK2  AK     0.000000     34620.7800           0
+     412 B10  1    CLA  LT2  LT     0.000000     55013.7800           0
+     413 B10  1    CLA  PX3  PX     0.000000     46422.2000           0
+     414 B10  1    CLA  DT3  DT     0.000000     49195.2000           0
+     415 B10  1    CLA  AK3  AK     0.000000     34620.7800           0
+     416 B10  1    CLA  LT3  LT     0.000000     55013.7800           0
+     417 C10  1    CLA  HB0  HB     0.000000     30478.0300           0
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+     419 C10  1    CLA  DT1  DT     0.000000     49195.2000           0
+     420 C10  1    CLA  AK1  AK     0.000000     34620.7800           0
+     421 C10  1    CLA  LT1  LT     0.000000     55013.7800           0
+     422 C10  1    CLA  PX2  PX     0.000000     46422.2000           0
+     423 C10  1    CLA  DT2  DT     0.000000     49195.2000           0
+     424 C10  1    CLA  AK2  AK     0.000000     34620.7800           0
+     425 C10  1    CLA  LT2  LT     0.000000     55013.7800           0
+     426 C10  1    CLA  PX3  PX     0.000000     46422.2000           0
+     427 C10  1    CLA  DT3  DT     0.000000     49195.2000           0
+     428 C10  1    CLA  AK3  AK     0.000000     34620.7800           0
+     429 C10  1    CLA  LT3  LT     0.000000     55013.7800           0
+     430 A11  1    CLA  HB0  HB     0.000000     30478.0300           0
+     431 A11  1    CLA  PX1  PX     0.000000     46422.2000           0
+     432 A11  1    CLA  DT1  DT     0.000000     49195.2000           0
+     433 A11  1    CLA  AK1  AK     0.000000     34620.7800           0
+     434 A11  1    CLA  LT1  LT     0.000000     55013.7800           0
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+     436 A11  1    CLA  DT2  DT     0.000000     49195.2000           0
+     437 A11  1    CLA  AK2  AK     0.000000     34620.7800           0
+     438 A11  1    CLA  LT2  LT     0.000000     55013.7800           0
+     439 A11  1    CLA  PX3  PX     0.000000     46422.2000           0
+     440 A11  1    CLA  DT3  DT     0.000000     49195.2000           0
+     441 A11  1    CLA  AK3  AK     0.000000     34620.7800           0
+     442 A11  1    CLA  LT3  LT     0.000000     55013.7800           0
+     443 B11  1    CLA  HB0  HB     0.000000     30478.0300           0
+     444 B11  1    CLA  PX1  PX     0.000000     46422.2000           0
+     445 B11  1    CLA  DT1  DT     0.000000     49195.2000           0
+     446 B11  1    CLA  AK1  AK     0.000000     34620.7800           0
+     447 B11  1    CLA  LT1  LT     0.000000     55013.7800           0
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+     449 B11  1    CLA  DT2  DT     0.000000     49195.2000           0
+     450 B11  1    CLA  AK2  AK     0.000000     34620.7800           0
+     451 B11  1    CLA  LT2  LT     0.000000     55013.7800           0
+     452 B11  1    CLA  PX3  PX     0.000000     46422.2000           0
+     453 B11  1    CLA  DT3  DT     0.000000     49195.2000           0
+     454 B11  1    CLA  AK3  AK     0.000000     34620.7800           0
+     455 B11  1    CLA  LT3  LT     0.000000     55013.7800           0
+     456 C11  1    CLA  HB0  HB     0.000000     30478.0300           0
+     457 C11  1    CLA  PX1  PX     0.000000     46422.2000           0
+     458 C11  1    CLA  DT1  DT     0.000000     49195.2000           0
+     459 C11  1    CLA  AK1  AK     0.000000     34620.7800           0
+     460 C11  1    CLA  LT1  LT     0.000000     55013.7800           0
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+     462 C11  1    CLA  DT2  DT     0.000000     49195.2000           0
+     463 C11  1    CLA  AK2  AK     0.000000     34620.7800           0
+     464 C11  1    CLA  LT2  LT     0.000000     55013.7800           0
+     465 C11  1    CLA  PX3  PX     0.000000     46422.2000           0
+     466 C11  1    CLA  DT3  DT     0.000000     49195.2000           0
+     467 C11  1    CLA  AK3  AK     0.000000     34620.7800           0
+     468 C11  1    CLA  LT3  LT     0.000000     55013.7800           0
+
+     432 !NBOND: bonds
+       1       2       1       6       1      10       2       3
+       3       4       4       5       6       7       7       8
+       8       9      10      11      11      12      12      13
+      14      15      14      19      14      23      15      16
+      16      17      17      18      19      20      20      21
+      21      22      23      24      24      25      25      26
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+
+     432 !NTHETA: angles
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+       2       3       4       2       1      10       2       1       6
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+     158     159     160     158     157     166     158     157     162
+     159     160     161     162     163     164     162     157     166
+     163     164     165     166     167     168     167     168     169
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+     315     316     317     318     319     320     318     313     322
+     319     320     321     322     323     324     323     324     325
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+     332     333     334     335     336     337     336     337     338
+     339     348     349     339     344     345     339     340     341
+     340     341     342     340     339     348     340     339     344
+     341     342     343     344     345     346     344     339     348
+     345     346     347     348     349     350     349     350     351
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+     353     354     355     353     352     361     353     352     357
+     354     355     356     357     358     359     357     352     361
+     358     359     360     361     362     363     362     363     364
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+     392     393     394     392     391     400     392     391     396
+     393     394     395     396     397     398     396     391     400
+     397     398     399     400     401     402     401     402     403
+     404     413     414     404     409     410     404     405     406
+     405     406     407     405     404     413     405     404     409
+     406     407     408     409     410     411     409     404     413
+     410     411     412     413     414     415     414     415     416
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+     419     420     421     422     423     424     422     417     426
+     423     424     425     426     427     428     427     428     429
+     430     439     440     430     435     436     430     431     432
+     431     432     433     431     430     439     431     430     435
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+     458     459     460     461     462     463     461     456     465
+     462     463     464     465     466     467     466     467     468
+
+       0 !NPHI: dihedrals
+
+
+     468 !NIMPHI: impropers
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+       1      10      11      12       2       6       1      10
+       2       1       6       7       2       1      10      11
+       2       3       4       5       6       1       2       3
+       6       1      10      11       6       7       8       9
+      10       1       2       3      10       1       6       7
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+      15      19      14      23      15      14      19      20
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+      19      20      21      22      23      14      15      16
+      23      14      19      20      23      24      25      26
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+      32      27      36      37      32      33      34      35
+      36      27      28      29      36      27      32      33
+      36      37      38      39      40      41      42      43
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+     249     248     257     258     249     250     251     252
+     253     248     249     250     253     248     257     258
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+     262     263     264     265     266     261     262     263
+     266     261     270     271     266     267     268     269
+     270     261     262     263     270     261     266     267
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+     275     279     274     283     275     274     279     280
+     275     274     283     284     275     276     277     278
+     279     274     275     276     279     274     283     284
+     279     280     281     282     283     274     275     276
+     283     274     279     280     283     284     285     286
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+     287     296     297     298     288     292     287     296
+     288     287     292     293     288     287     296     297
+     288     289     290     291     292     287     288     289
+     292     287     296     297     292     293     294     295
+     296     287     288     289     296     287     292     293
+     296     297     298     299     300     301     302     303
+     300     305     306     307     300     309     310     311
+     301     305     300     309     301     300     305     306
+     301     300     309     310     301     302     303     304
+     305     300     301     302     305     300     309     310
+     305     306     307     308     309     300     301     302
+     309     300     305     306     309     310     311     312
+     313     314     315     316     313     318     319     320
+     313     322     323     324     314     318     313     322
+     314     313     318     319     314     313     322     323
+     314     315     316     317     318     313     314     315
+     318     313     322     323     318     319     320     321
+     322     313     314     315     322     313     318     319
+     322     323     324     325     326     327     328     329
+     326     331     332     333     326     335     336     337
+     327     331     326     335     327     326     331     332
+     327     326     335     336     327     328     329     330
+     331     326     327     328     331     326     335     336
+     331     332     333     334     335     326     327     328
+     335     326     331     332     335     336     337     338
+     339     340     341     342     339     344     345     346
+     339     348     349     350     340     344     339     348
+     340     339     344     345     340     339     348     349
+     340     341     342     343     344     339     340     341
+     344     339     348     349     344     345     346     347
+     348     339     340     341     348     339     344     345
+     348     349     350     351     352     353     354     355
+     352     357     358     359     352     361     362     363
+     353     357     352     361     353     352     357     358
+     353     352     361     362     353     354     355     356
+     357     352     353     354     357     352     361     362
+     357     358     359     360     361     352     353     354
+     361     352     357     358     361     362     363     364
+     365     366     367     368     365     370     371     372
+     365     374     375     376     366     370     365     374
+     366     365     370     371     366     365     374     375
+     366     367     368     369     370     365     366     367
+     370     365     374     375     370     371     372     373
+     374     365     366     367     374     365     370     371
+     374     375     376     377     378     379     380     381
+     378     383     384     385     378     387     388     389
+     379     383     378     387     379     378     383     384
+     379     378     387     388     379     380     381     382
+     383     378     379     380     383     378     387     388
+     383     384     385     386     387     378     379     380
+     387     378     383     384     387     388     389     390
+     391     392     393     394     391     396     397     398
+     391     400     401     402     392     396     391     400
+     392     391     396     397     392     391     400     401
+     392     393     394     395     396     391     392     393
+     396     391     400     401     396     397     398     399
+     400     391     392     393     400     391     396     397
+     400     401     402     403     404     405     406     407
+     404     409     410     411     404     413     414     415
+     405     409     404     413     405     404     409     410
+     405     404     413     414     405     406     407     408
+     409     404     405     406     409     404     413     414
+     409     410     411     412     413     404     405     406
+     413     404     409     410     413     414     415     416
+     417     418     419     420     417     422     423     424
+     417     426     427     428     418     422     417     426
+     418     417     422     423     418     417     426     427
+     418     419     420     421     422     417     418     419
+     422     417     426     427     422     423     424     425
+     426     417     418     419     426     417     422     423
+     426     427     428     429     430     431     432     433
+     430     435     436     437     430     439     440     441
+     431     435     430     439     431     430     435     436
+     431     430     439     440     431     432     433     434
+     435     430     431     432     435     430     439     440
+     435     436     437     438     439     430     431     432
+     439     430     435     436     439     440     441     442
+     443     444     445     446     443     448     449     450
+     443     452     453     454     444     448     443     452
+     444     443     448     449     444     443     452     453
+     444     445     446     447     448     443     444     445
+     448     443     452     453     448     449     450     451
+     452     443     444     445     452     443     448     449
+     452     453     454     455     456     457     458     459
+     456     461     462     463     456     465     466     467
+     457     461     456     465     457     456     461     462
+     457     456     465     466     457     458     459     460
+     461     456     457     458     461     456     465     466
+     461     462     463     464     465     456     457     458
+     465     456     461     462     465     466     467     468
+
+       0 !NDON: donors
+
+
+       0 !NACC: acceptors
+
+
+       0 !NNB
+
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0       0       0       0       0
+       0       0       0       0
+
+       1       0 !NGRP
+       0       0       0
+


Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
___________________________________________________________________
Added: svn:executable
   + *

Added: SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1 @@
+Hi Swift!

Added: SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,80 @@
+* Charmm Parameter file
+* For 13 bead CG clathrin model
+* Handmade by FXV - 7-21-11
+* Initial guess (very rough)
+
+BONDS
+!
+
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb          b0
+!
+
+HB PX   0.5              85.5
+PX DT   0.018           135.2
+DT AK   0.045	        124.2
+AK LT   0.08	         94.1
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!
+!atom types     Ktheta    Theta0
+!
+PX HB PX	70.0		120.00
+DT PX HB	50.0		144.3
+AK DT PX	35.0		132.6
+LT AK DT	150.0		141.5
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types             Kchi    n   delta
+!
+X    X    X    X    0.0        1     0.0 ! No dihedrals
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types           Kpsi                   psi0
+!
+PX PX HB PX	200.00			0	161.17
+PX HB PX DT	 10.0			0	-30.4
+HB PX DT AK	 9.5			0	-16.1
+PX DT AK LT	 45.0			0	 26.1
+
+NONBONDED
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom  ignored    epsilon      Rmin/2
+!
+HB    0.000000         HBEPS          43.075000
+PX    0.000000         PXEPS          18.425000
+DT    0.000000         DTEPS          10.455000
+AK    0.000000         AKEPS          25.975000
+LT    0.000000         LTEPS          36.905000
+
+
+END
+					  	

Added: SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,56 @@
+#====================================
+# THis script will measure the 
+# the average angles, bond lengths
+# and dihedral angles.
+#
+# -FXV Oct, 2011
+#===================================
+
+mol delete all
+
+# set atom selection
+set seltext "type HB AK" 
+
+# Set the initial frame
+set inifrm 200
+
+set psf cg_clath_cage.psf
+set pdb cg_clath_cage.pdb
+set dcd cg_clath_cage.dcd
+
+# Load input files
+mol load psf $psf
+# Load trajectory
+mol addfile $pdb type pdb
+mol addfile $dcd type dcd first $inifrm last -1 waitfor all
+
+# Get molecule information
+set mol [molinfo top]
+
+# Get the number of frames
+set nmfrm [molinfo $mol get numframes]
+puts "number of frames $nmfrm"
+
+# open rmsd file
+set frmsd [open rmsd.dat w]
+
+# Select atoms
+set ref [atomselect top $seltext frame 0] 
+	
+# Loop over the number of frames
+for {set ifrm 0} {$ifrm <= $nmfrm} {incr ifrm} {
+	
+	set sel [atomselect top $seltext frame $ifrm]
+	
+	set irmsd [measure rmsd $ref $sel]
+	
+	lappend rmsdlist $irmsd
+
+
+}
+
+# Analysis
+puts $frmsd "B1 B2 [vecmean $rmsdlist]"
+
+exit
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,12 @@
+type file;
+
+app (file o) cat (file i)
+{
+  cat @i stdout=@o;
+}
+
+file out[]<simple_mapper; location="outdir", prefix="f.",suffix=".out">;
+foreach j in [1:@toint(@arg("n","1"))] {
+  file data<"data.txt">;
+  out[j] = cat(data);
+}

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,9 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+file info <"output/info.txt">;
+info = getinfo();

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,13 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+}
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,19 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+app (file o) filterinfo (file i)
+{
+  filterinfo @i @o;
+}
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+  file filtered = filterinfo(info);
+}
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,25 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+app (file o) filter (file i)
+{
+  filterinfo @i @o;
+}
+
+file filtered[];
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+  // replace: filtered[i] = filter(info);
+  // with:
+  string filfname = ???
+  filfname = 
+  filtered[i] = 
+}
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,30 @@
+type file;
+
+app (file o) getinfo ()
+{
+  getinfo stdout=@o;
+}
+
+app (file o) filter (file i)
+{
+  filterinfo @i @o;
+}
+
+app (file o) reduce (file i[])
+{
+  suminfo @filenames(i) stdout=@o;
+}
+
+file filtered[];
+
+foreach i in [0:24] {
+  string fname = @strcat("output/info.",i,".txt");
+  file info <single_file_mapper; file=fname>;
+  info = getinfo();
+  filtered[i] = filter(info);
+}
+
+file sum<"output/sum.data">;
+
+sum = reduce(filtered);
+

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,9 @@
+type file;
+
+app (file r) testmpi ()
+{
+  testmpi;
+}
+
+file results <"output/results.tar">;
+results = testmpi();

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,451 @@
+<project><!-- CACHE ID fde29c67-b524-4558-b5f9-1228186b92ec-no-provenance -->
+  <import file="sys.xml"/>
+  <import file="scheduler.xml"/>
+  <import file="rlog.xml"/>
+  <import file="vdl.k"/>
+  <types>
+     <xs:schema targetNamespace="http://ci.uchicago.edu/swift/2009/02/swiftscript" xmlns="http://ci.uchicago.edu/swift/2009/02/swiftscript" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+      	   <xs:simpleType name="file">
+      	   <xs:restriction base="string"/>
+      	   </xs:simpleType>
+     </xs:schema>
+  </types>
+  <global name="swift#string#17013">
+    <vdl:new type="string" value=".dcd" />
+  </global>
+  <global name="swift#string#17006">
+    <vdl:new type="string" value="logs/rmsd-" />
+  </global>
+  <global name="swift#string#17012">
+    <vdl:new type="string" value="output/cg_clath_cage-" />
+  </global>
+  <global name="swift#string#17010">
+    <vdl:new type="string" value=".err.txt" />
+  </global>
+  <global name="swift#string#17001">
+    <vdl:new type="string" value="DT" />
+  </global>
+  <global name="swift#string#17017">
+    <vdl:new type="string" value=".dat" />
+  </global>
+  <global name="swift#string#17016">
+    <vdl:new type="string" value="_" />
+  </global>
+  <global name="swift#string#17000">
+    <vdl:new type="string" value="PX" />
+  </global>
+  <global name="swift#string#17015">
+    <vdl:new type="string" value="output/rmsd." />
+  </global>
+  <global name="swift#string#17008">
+    <vdl:new type="string" value=".out.txt" />
+  </global>
+  <global name="swift#string#17007">
+    <vdl:new type="string" value="-" />
+  </global>
+  <global name="swift#float#17003">
+    <vdl:new type="float" value="1.0" />
+  </global>
+  <global name="swift#float#17002">
+    <vdl:new type="float" value="0.0" />
+  </global>
+  <global name="swift#float#17004">
+    <vdl:new type="float" value="0.5" />
+  </global>
+  <element name="rmsd" arguments="o,e,dcdf,datf,b1_val,b2_val,b1_name,b2_name,namd_input_file,namd_params_file,vmd_script_file,psf_file,pdb_file" _defline="3">
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+     
+    <unitStart name="rmsd" line="3" type="PROCEDURE" outputs="o,e,dcdf,datf"/>
+    <vdl:execute>
+      <vdl:tr>rmsd</vdl:tr>
+      <vdl:stagein var="{b1_val}"/>
+      <vdl:stagein var="{b2_val}"/>
+      <vdl:stagein var="{b1_name}"/>
+      <vdl:stagein var="{b2_name}"/>
+      <vdl:stagein var="{namd_input_file}"/>
+      <vdl:stagein var="{namd_params_file}"/>
+      <vdl:stagein var="{vmd_script_file}"/>
+      <vdl:stagein var="{psf_file}"/>
+      <vdl:stagein var="{pdb_file}"/>
+      <vdl:stageout var="{o}"/>
+      <vdl:stageout var="{e}"/>
+      <vdl:stageout var="{dcdf}"/>
+      <vdl:stageout var="{datf}"/>
+
+      <vdl:arguments>
+        <variable>b1_val</variable>
+        <variable>b2_val</variable>
+        <variable>b1_name</variable>
+        <variable>b2_name</variable>
+        <swiftscript:filename _traceline="5">
+         <variable>namd_input_file</variable> 
+        </swiftscript:filename>
+        <swiftscript:filename _traceline="5">
+         <variable>namd_params_file</variable> 
+        </swiftscript:filename>
+        <swiftscript:filename _traceline="5">
+         <variable>vmd_script_file</variable> 
+        </swiftscript:filename>
+      </vdl:arguments>
+      <vdl:stdout>
+        <swiftscript:filename _traceline="5">
+         <variable>o</variable> 
+        </swiftscript:filename>
+      </vdl:stdout><vdl:stderr>
+        <swiftscript:filename _traceline="5">
+         <variable>e</variable> 
+        </swiftscript:filename>
+      </vdl:stderr>
+    </vdl:execute>
+    <vdl:closedataset var="{o}"/>
+    <vdl:closedataset var="{e}"/>
+    <vdl:closedataset var="{dcdf}"/>
+    <vdl:closedataset var="{datf}"/>
+    <unitEnd name="rmsd" line="3" type="PROCEDURE"/></element>
+
+  <set name="b1name">
+        <vdl:new type="string" dbgname="b1name" waitfor="88000" _defline="9"/>
+  </set>
+   
+  <set name="b2name">
+        <vdl:new type="string" dbgname="b2name" waitfor="88001" _defline="10"/>
+  </set>
+   
+  <set name="b1min">
+        <vdl:new type="float" dbgname="b1min" waitfor="88002" _defline="13"/>
+  </set>
+   
+  <set name="b1max">
+        <vdl:new type="float" dbgname="b1max" waitfor="88003" _defline="14"/>
+  </set>
+   
+  <set name="b2min">
+        <vdl:new type="float" dbgname="b2min" waitfor="88004" _defline="15"/>
+  </set>
+   
+  <set name="b2max">
+        <vdl:new type="float" dbgname="b2max" waitfor="88005" _defline="16"/>
+  </set>
+   
+  <set name="delta">
+        <vdl:new type="float" dbgname="delta" waitfor="88006" _defline="19"/>
+  </set>
+   
+  <set name="namd_params">
+        <vdl:new type="file" dbgname="namd_params" _defline="22">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="par_cg_clath.inp"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="namd_input">
+        <vdl:new type="file" dbgname="namd_input" _defline="23">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="cg_clath_cage.conf"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="vmd_script">
+        <vdl:new type="file" dbgname="vmd_script" _defline="24">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="rmsd.temp.tcl"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="psf">
+        <vdl:new type="file" dbgname="psf" _defline="25">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="cg_clath_cage.psf"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="pdb">
+        <vdl:new type="file" dbgname="pdb" _defline="26">
+          <vdl:mapping descriptor="single_file_mapper">
+            <vdl:parameter name="file" value="cg_clath_cage.pdb"/>
+            <vdl:parameter name="swift#input" value="true" />
+          </vdl:mapping>
+        </vdl:new>
+  </set>
+   
+  <set name="dats">
+    <vdl:new type="file[float][float]" dbgname="dats" waitfor="88013" _defline="27">
+      <vdl:mapping descriptor="concurrent_mapper">
+        <vdl:parameter name="prefix">dats-345532ce-25ec-45f9-933b-4d188d42079b</vdl:parameter>
+      </vdl:mapping>
+    </vdl:new>
+  </set>
+   
+  <restartLog>
+  	<vdl:mains>
+		<vdl:startprogressticker />
+		<vdl:mainp>
+		    <uparallel>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b1name"/>
+		             <vdl:setfieldvalue _traceline="10">
+		                 <variable>b1name</variable>
+		                 <variable>swift#string#17000</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b1name}" closeID="88000" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b2name"/>
+		             <vdl:setfieldvalue _traceline="13">
+		                 <variable>b2name</variable>
+		                 <variable>swift#string#17001</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b2name}" closeID="88001" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b1min"/>
+		             <vdl:setfieldvalue _traceline="14">
+		                 <variable>b1min</variable>
+		                 <variable>swift#float#17002</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b1min}" closeID="88002" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b1max"/>
+		             <vdl:setfieldvalue _traceline="15">
+		                 <variable>b1max</variable>
+		                 <variable>swift#float#17003</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b1max}" closeID="88003" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b2min"/>
+		             <vdl:setfieldvalue _traceline="16">
+		                 <variable>b2min</variable>
+		                 <variable>swift#float#17002</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b2min}" closeID="88004" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="b2max"/>
+		             <vdl:setfieldvalue _traceline="19">
+		                 <variable>b2max</variable>
+		                 <variable>swift#float#17003</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{b2max}" closeID="88005" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="delta"/>
+		             <vdl:setfieldvalue _traceline="22">
+		                 <variable>delta</variable>
+		                 <variable>swift#float#17004</variable>
+		             </vdl:setfieldvalue>
+		            <partialCloseDataset var="{delta}" closeID="88006" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		        <sequential>
+		            <unitStart type="SCOPE" outputs="dats"/>
+		          <vdl:tparallelFor name="$"  _traceline="29" 
+		           _vvar="b1">
+		            <getarrayiterator><sequential>
+		           <set name="swift#from"><variable>b1min</variable></set>
+		           <set name="swift#to"><variable>b1max</variable></set>
+		           <set name="swift#step"><variable>delta</variable></set>
+		           <set name="swift#rangeout">
+		            <vdl:range>
+		              <argument name="from"><variable>swift#from</variable></argument>
+		              <argument name="to"><variable>swift#to</variable></argument>
+		              <argument name="step"><variable>swift#step</variable></argument>
+		            </vdl:range>
+		           </set>
+		            
+		           <variable>swift#rangeout</variable>
+		          </sequential></getarrayiterator>
+		            <set names="$$, b1">
+		              <each items="{$}"/>
+		            </set>
+		          	<unitStart line="29" type="FOREACH_IT"/>
+
+		                <sequentialWithID>
+		                    <sequential>
+		                      <vdl:tparallelFor name="$"  
+		                       _vvar="b2">
+		                        <getarrayiterator><sequential>
+		                       <set name="swift#from"><variable>b2min</variable></set>
+		                       <set name="swift#to"><variable>b2max</variable></set>
+		                       <set name="swift#step"><variable>delta</variable></set>
+		                       <set name="swift#rangeout">
+		                        <vdl:range>
+		                          <argument name="from"><variable>swift#from</variable></argument>
+		                          <argument name="to"><variable>swift#to</variable></argument>
+		                          <argument name="step"><variable>swift#step</variable></argument>
+		                        </vdl:range>
+		                       </set>
+		                        
+		                       <variable>swift#rangeout</variable>
+		                      </sequential></getarrayiterator>
+		                        <set names="$$, b2">
+		                          <each items="{$}"/>
+		                        </set>
+		                      	<unitStart line="30" type="FOREACH_IT"/>
+
+		                          <set name="swift#mapper#17005">
+		                                <vdl:new type="string" dbgname="swift#mapper#17005" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="output">
+		                            <vdl:new type="file" dbgname="output" waitfor="88008" _defline="31">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17005</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                          <set name="swift#mapper#17009">
+		                                <vdl:new type="string" dbgname="swift#mapper#17009" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="error">
+		                            <vdl:new type="file" dbgname="error" waitfor="88009" _defline="32">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17009</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                          <set name="swift#mapper#17011">
+		                                <vdl:new type="string" dbgname="swift#mapper#17011" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="dcd">
+		                            <vdl:new type="file" dbgname="dcd" waitfor="88010" _defline="33">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17011</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                          <set name="swift#mapper#17014">
+		                                <vdl:new type="string" dbgname="swift#mapper#17014" waitfor="" _defline=""/>
+		                          </set>
+		                           
+		                          <set name="dat">
+		                            <vdl:new type="file" dbgname="dat" waitfor="88011" _defline="34">
+		                              <vdl:mapping descriptor="single_file_mapper">
+		                                <vdl:parameter name="file"><variable>swift#mapper#17014</variable></vdl:parameter>
+		                              </vdl:mapping>
+		                            </vdl:new>
+		                          </set>
+		                           
+		                            <uparallel>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17005</variable>
+		                                         <swiftscript:strcat _traceline="31">
+		                                          <variable>swift#string#17006</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17008</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17009</variable>
+		                                         <swiftscript:strcat _traceline="32">
+		                                          <variable>swift#string#17006</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17010</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17011</variable>
+		                                         <swiftscript:strcat _traceline="33">
+		                                          <variable>swift#string#17012</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17013</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="-1">
+		                                         <variable>swift#mapper#17014</variable>
+		                                         <swiftscript:strcat _traceline="34">
+		                                          <variable>swift#string#17015</variable><variable>b1name</variable><variable>b1</variable><variable>swift#string#17016</variable><variable>b2name</variable><variable>b2</variable><variable>swift#string#17017</variable> 
+		                                         </swiftscript:strcat>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                     <vdl:setfieldvalue _traceline="36">
+		                                         <vdl:getfieldsubscript>
+		                                           <argument name="var"><vdl:getfieldsubscript>
+		                                           <argument name="var"><variable>dats</variable></argument>
+		                                           <argument name="subscript"><variable>b1</variable></argument>
+		                                         </vdl:getfieldsubscript></argument>
+		                                           <argument name="subscript"><variable>b2</variable></argument>
+		                                         </vdl:getfieldsubscript>
+		                                         <variable>dat</variable>
+		                                     </vdl:setfieldvalue>
+		                                </sequential>
+		                                <sequential>
+		                                    <unitStart type="SCOPE" outputs="output,error,dcd,dat"/>
+		                                  <rmsd _traceline="36">
+		                                      <variable>output</variable>
+		                                      <variable>error</variable>
+		                                      <variable>dcd</variable>
+		                                      <variable>dat</variable>
+		                                      <variable>b1</variable>
+		                                      <variable>b2</variable>
+		                                      <variable>b1name</variable>
+		                                      <variable>b2name</variable>
+		                                      <variable>namd_input</variable>
+		                                      <variable>namd_params</variable>
+		                                      <variable>vmd_script</variable>
+		                                      <variable>psf</variable>
+		                                      <variable>pdb</variable>
+		                                  </rmsd>
+		                                    <unitEnd type="SCOPE"/>
+		                                </sequential>
+		                            </uparallel>
+		                            <vdl:cleandataset var="{dat}"/>
+		                            <vdl:cleandataset var="{error}"/>
+		                            <vdl:cleandataset var="{dcd}"/>
+		                            <vdl:cleandataset var="{output}"/>
+		                          <unitEnd line="30" type="FOREACH_IT"/>
+		                      </vdl:tparallelFor>
+		                    </sequential>
+		                </sequentialWithID>
+
+		              <unitEnd line="29" type="FOREACH_IT"/>
+		          </vdl:tparallelFor>
+		            <partialCloseDataset var="{dats}" closeID="88013" />
+		            <unitEnd type="SCOPE"/>
+		        </sequential>
+		    </uparallel>
+		</vdl:mainp>
+		<vdl:stopprogressticker />
+	</vdl:mains>
+  </restartLog>
+  <vdl:cleandataset var="{namd_params}"/>
+  <vdl:cleandataset var="{vmd_script}"/>
+  <vdl:cleandataset var="{psf}"/>
+  <vdl:cleandataset var="{namd_input}"/>
+  <vdl:cleandataset var="{pdb}"/>
+  <vdl:cleandataset var="{dats}"/>
+  <vdl:cleandataset shutdown="true"/>
+</project>

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,38 @@
+type file;
+
+app (file o, file e, file dcdf, file datf) rmsd (float b1_val, float b2_val, string b1_name, string b2_name, file namd_input_file, file namd_params_file, file vmd_script_file, file psf_file, file pdb_file)
+{
+  rmsd b1_val b2_val b1_name b2_name @namd_input_file @namd_params_file @vmd_script_file stdout=@o stderr=@e;
+}
+
+# Bead names
+string b1name = "PX";
+string b2name = "DT";
+
+# Bead ranges
+float b1min=0.0;
+float b1max=1.0;
+float b2min=0.0;
+float b2max=1.0;
+
+# Delta
+float delta=0.5;
+
+# Files
+file namd_params <"par_cg_clath.inp">;
+file namd_input <"cg_clath_cage.conf">;
+file vmd_script <"rmsd.temp.tcl">;
+file psf <"cg_clath_cage.psf">;
+file pdb <"cg_clath_cage.pdb">;
+file[float][float] dats;
+
+foreach b1 in [b1min:b1max:delta] {
+   foreach b2 in [b2min:b2max:delta] {
+      file output <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".out.txt")>;
+      file error <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".err.txt")>;
+      file dcd <single_file_mapper; file=@strcat("output/cg_clath_cage-", b1, "-", b2, ".dcd")>;
+      file dat <single_file_mapper; file=@strcat("output/rmsd.", b1name, b1, "_", b2name, b2, ".dat")>;
+      dats[b1][b2] = dat;
+      (output, error, dcd, dat) = rmsd(b1, b2, b1name, b2name, namd_input, namd_params, vmd_script, psf, pdb);
+   }
+}

Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx	                        (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx	2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,157 @@
+<program xmlns="http://ci.uchicago.edu/swift/2009/02/swiftscript"
+         xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+         xmlns:xs="http://www.w3.org/2001/XMLSchema">
+  <types>
+     	<type>
+     		<typename>file</typename>
+     		<typealias>string</typealias>
+     		<typestructure></typestructure>
+     	</type>
+  </types>
+  <procedure name="rmsd" src="line 3">
+
+    <output name="o" type="file"  xsi:nil="true"/>
+
+    <output name="e" type="file"  xsi:nil="true"/>
+
+    <output name="dcdf" type="file"  xsi:nil="true"/>
+
+    <output name="datf" type="file"  xsi:nil="true"/>
+
+    <input name="b1_val" type="float"  xsi:nil="true"/>
+
+    <input name="b2_val" type="float"  xsi:nil="true"/>
+
+    <input name="b1_name" type="string"  xsi:nil="true"/>
+
+    <input name="b2_name" type="string"  xsi:nil="true"/>
+
+    <input name="namd_input_file" type="file"  xsi:nil="true"/>
+
+    <input name="namd_params_file" type="file"  xsi:nil="true"/>
+
+    <input name="vmd_script_file" type="file"  xsi:nil="true"/>
+
+    <input name="psf_file" type="file"  xsi:nil="true"/>
+
+    <input name="pdb_file" type="file"  xsi:nil="true"/>
+    <binding>
+      <application src="line 3">
+        <executable>rmsd</executable>
+        <stdout><function name="filename" src="line 5">
+          <variableReference>o</variableReference></function></stdout><stderr><function name="filename" src="line 5">
+          <variableReference>e</variableReference></function></stderr><variableReference>b1_val</variableReference><variableReference>b2_val</variableReference><variableReference>b1_name</variableReference><variableReference>b2_name</variableReference><function name="filename" src="line 5">
+          <variableReference>namd_input_file</variableReference></function><function name="filename" src="line 5">
+          <variableReference>namd_params_file</variableReference></function><function name="filename" src="line 5">
+          <variableReference>vmd_script_file</variableReference></function>  </application>
+    </binding>
+  </procedure>
+  <variable name="b1name" type="string" isGlobal="false" xsi:nil="true" src="line 9"/>
+  <assign src="line 10">
+   <variableReference>b1name</variableReference>
+   <stringConstant>PX</stringConstant>
+  </assign>
+  <variable name="b2name" type="string" isGlobal="false" xsi:nil="true" src="line 10"/>
+  <assign src="line 13">
+   <variableReference>b2name</variableReference>
+   <stringConstant>DT</stringConstant>
+  </assign>
+  <variable name="b1min" type="float" isGlobal="false" xsi:nil="true" src="line 13"/>
+  <assign src="line 14">
+   <variableReference>b1min</variableReference>
+   <floatConstant>0.0</floatConstant>
+  </assign>
+  <variable name="b1max" type="float" isGlobal="false" xsi:nil="true" src="line 14"/>
+  <assign src="line 15">
+   <variableReference>b1max</variableReference>
+   <floatConstant>1.0</floatConstant>
+  </assign>
+  <variable name="b2min" type="float" isGlobal="false" xsi:nil="true" src="line 15"/>
+  <assign src="line 16">
+   <variableReference>b2min</variableReference>
+   <floatConstant>0.0</floatConstant>
+  </assign>
+  <variable name="b2max" type="float" isGlobal="false" xsi:nil="true" src="line 16"/>
+  <assign src="line 19">
+   <variableReference>b2max</variableReference>
+   <floatConstant>1.0</floatConstant>
+  </assign>
+  <variable name="delta" type="float" isGlobal="false" xsi:nil="true" src="line 19"/>
+  <assign src="line 22">
+   <variableReference>delta</variableReference>
+   <floatConstant>0.5</floatConstant>
+  </assign>
+  <variable name="namd_params" type="file" isGlobal="false" src="line 22"><file name="par_cg_clath.inp"/></variable>
+  <variable name="namd_input" type="file" isGlobal="false" src="line 23"><file name="cg_clath_cage.conf"/></variable>
+  <variable name="vmd_script" type="file" isGlobal="false" src="line 24"><file name="rmsd.temp.tcl"/></variable>
+  <variable name="psf" type="file" isGlobal="false" src="line 25"><file name="cg_clath_cage.psf"/></variable>
+  <variable name="pdb" type="file" isGlobal="false" src="line 26"><file name="cg_clath_cage.pdb"/></variable>
+  <variable name="dats" type="file[float][float]" isGlobal="false" xsi:nil="true" src="line 27"/>
+  <foreach var="b1"  src="line 29">
+  <in>
+    <range>
+      <variableReference>b1min</variableReference>
+      <variableReference>b1max</variableReference>
+      <variableReference>delta</variableReference>
+    </range>
+  </in>
+  <body><foreach var="b2"  src="line 30">
+    <in>
+      <range>
+        <variableReference>b2min</variableReference>
+        <variableReference>b2max</variableReference>
+        <variableReference>delta</variableReference>
+      </range>
+    </in>
+    <body><variable name="output" type="file" isGlobal="false" src="line 31">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 31">
+            <stringConstant>logs/rmsd-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.out.txt</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <variable name="error" type="file" isGlobal="false" src="line 32">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 32">
+            <stringConstant>logs/rmsd-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.err.txt</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <variable name="dcd" type="file" isGlobal="false" src="line 33">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 33">
+            <stringConstant>output/cg_clath_cage-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.dcd</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <variable name="dat" type="file" isGlobal="false" src="line 34">
+        <mapping descriptor="single_file_mapper">
+          <param name="file"><function name="strcat" src="line 34">
+            <stringConstant>output/rmsd.</stringConstant><variableReference>b1name</variableReference><variableReference>b1</variableReference><stringConstant>_</stringConstant><variableReference>b2name</variableReference><variableReference>b2</variableReference><stringConstant>.dat</stringConstant></function></param>
+        </mapping>
+      </variable>
+      <assign src="line 36">
+       <arraySubscript>
+        <arraySubscript>
+         <variableReference>dats</variableReference>
+         <variableReference>b1</variableReference>
+        </arraySubscript>
+        <variableReference>b2</variableReference>
+       </arraySubscript>
+       <variableReference>dat</variableReference>
+      </assign>
+      <call proc="rmsd" src="line 36">
+        <output><variableReference>output</variableReference></output>
+        <output><variableReference>error</variableReference></output>
+        <output><variableReference>dcd</variableReference></output>
+        <output><variableReference>dat</variableReference></output>
+        <input><variableReference>b1</variableReference></input>
+        <input><variableReference>b2</variableReference></input>
+        <input><variableReference>b1name</variableReference></input>
+        <input><variableReference>b2name</variableReference></input>
+        <input><variableReference>namd_input</variableReference></input>
+        <input><variableReference>namd_params</variableReference></input>
+        <input><variableReference>vmd_script</variableReference></input>
+        <input><variableReference>psf</variableReference></input>
+        <input><variableReference>pdb</variableReference></input>
+      </call></body>
+    </foreach></body>
+  </foreach>
+</program>




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