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add uncompressed FFE source to the repo
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source/ffe/0README

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#####################################
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FFE Setup on Linux, MacOS and Windows
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#####################################
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On Linux and MacOS, either FFESetup*.sh or FFESetup*.csh must
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be invoked in order to set environment variables needed to run
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Force Field Explorer from the command line. Note the scripts
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can be sourced or run directly. On Windows, the FFESetupWin.bat
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script must be invoked prior to running FFE by double-clicking
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the app to achieve the same effect.
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source/ffe/FFESetupLinux.csh

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#!/bin/csh
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#
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# #########################################################
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# ## ##
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# ## Initialization Script for Tinker-FFE on Linux/csh ##
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# ## ##
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# #########################################################
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#
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# This is a csh/tcsh script to set environment variables
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# needed to run Force Field Explorer at the command line
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#
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# Note FFE_HOME and TINKER_HOME are special directory names
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# needed by the Force Field Explorer application
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#
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#
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# Set Tinker-FFE installation directory
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#
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setenv INSTALLDIR "$HOME/Tinker-FFE"
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#
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# Set location of FFE, Tinker, JRE and FFE libraries
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#
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setenv FFE_HOME "$INSTALLDIR/ffe"
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setenv TINKER_HOME "$INSTALLDIR/tinker"
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setenv JRE_HOME "$INSTALLDIR/jre"
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setenv FFE_LIB "$FFE_HOME/lib"
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setenv FFE_NATIVE "$FFE_HOME/native"
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#
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# Set location of system-dependent Linux library
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#
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setenv OS_LIB "$FFE_NATIVE/linux/libffe.so"
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#
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# Append the Tinker binaries to default PATH
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#
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if !($?PATH) then
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setenv PATH "$TINKER_HOME/bin"
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else
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setenv PATH "$TINKER_HOME/bin:$PATH"
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endif
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#
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# Set LD_LIBRARY_PATH environment variable
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#
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if !($?LD_LIBRARY_PATH) then
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setenv LD_LIBRARY_PATH "$JRE_HOME/lib/server:$JRE_HOME/lib"
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else
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setenv LD_LIBRARY_PATH "$JRE_HOME/lib/server:$JRE_HOME/lib:LD_LIBRARY_PATH"
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endif
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#
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# Add required JAR files to CLASSPATH variable
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#
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if !($?CLASSPATH) then
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setenv CLASSPATH "$FFE_LIB/AppleJavaExtensions-1.6.jar:$FFE_LIB/commons-io-2.6.jar:$FFE_LIB/commons-lang-2.7.jar:$FFE_LIB/commons-logging-1.3.jar:$FFE_LIB/ffe-8.8.jar:$FFE_LIB/gluegen-rt-android-natives-macosx-universal.jar:$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar:$FFE_LIB/groovy-all-2.4.4.jar:$FFE_LIB/j3dcore-1.7.jar:$FFE_LIB/j3dutils-1.7.jar:$FFE_LIB/jh-2.0.5.jar:$FFE_LIB/joal-natives-macosx-universal.jar:$FFE_LIB/joal.jar:$FFE_LIB/jogl-all-noawt-natives-macosx-universal.jar:$FFE_LIB/jogl-all.jar:$FFE_LIB/sunjce_provider.jar:$FFE_LIB/vecmath-1.7.jar:$OS_LIB"
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else
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setenv CLASSPATH "$FFE_LIB/AppleJavaExtensions-1.6.jar:$FFE_LIB/commons-io-2.6.jar:$FFE_LIB/commons-lang-2.7.jar:$FFE_LIB/commons-logging-1.3.jar:$FFE_LIB/ffe-8.8.jar:$FFE_LIB/gluegen-rt-android-natives-linux-amd64.jar:$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar:$FFE_LIB/groovy-all-2.4.4.jar:$FFE_LIB/j3dcore-1.7.jar:$FFE_LIB/j3dutils-1.7.jar:$FFE_LIB/jh-2.0.5.jar:$FFE_LIB/joal-natives-linux-amd64.jar:$FFE_LIB/joal.jar:$FFE_LIB/jogl-all-noawt-natives-linux-amd64.jar:$FFE_LIB/jogl-all.jar:$FFE_LIB/sunjce_provider.jar:$FFE_LIB/vecmath-1.7.jar:$OS_LIB:$CLASSPATH"
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endif
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#
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# Create an alias to execute Force Field Explorer
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#
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#alias ffe "java -server -ms2048M -mx4096M -Djava.library.path=$FFE_LIB -Dtinker.dir=$TINKER_HOME -jar $FFE_LIB/ffe-8.8.jar"
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alias ffe "$FFE_HOME/Force*Field*Explorer"

source/ffe/FFESetupLinux.sh

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#!/bin/sh
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shopt -s expand_aliases
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#
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# ########################################################
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# ## ##
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# ## sh Initialization Script for Tinker-FFE on Linux ##
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# ## ##
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# ########################################################
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#
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# This is an sh/bash script to set environment variables
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# needed to run Force Field Explorer at the command line
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#
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# Note FFE_HOME and TINKER_HOME are special directory names
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# needed by the Force Field Explorer application
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#
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#
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# Set Tinker-FFE installation directory
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#
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INSTALLDIR="$HOME/Tinker-FFE"
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export INSTALLDIR
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#
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# Set location of JRE, Tinker and Force Field Explorer
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#
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FFE_HOME="$INSTALLDIR/ffe"
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export FFE_HOME
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TINKER_HOME="$INSTALLDIR/tinker"
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export TINKER_HOME
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JRE_HOME="$INSTALLDIR/jre"
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export JRE_HOME
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FFE_LIB="$FFE_HOME/lib"
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export FFE_LIB
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FFE_NATIVE="$FFE_HOME/native"
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export FFE_NATIVE
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#
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# Set location of system-dependent Linux library
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#
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OS_LIB="$FFE_NATIVE/linux/libffe.so"
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export OS_LIB
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#
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# Append the Tinker binaries to default PATH
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#
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if [ -z "${PATH}" ]
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then
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PATH="$TINKER_HOME/bin"
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else
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PATH="$TINKER_HOME/bin:$PATH"
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fi
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export PATH
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#
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# Add required JAR files to CLASSPATH variable
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#
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if [ -z "${CLASSPATH}" ]
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then
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CLASSPATH="$FFE_LIB/AppleJavaExtensions-1.6.jar;$FFE_LIB/commons-io-2.6.jar;$FFE_LIB/commons-lang-2.7.jar;$FFE_LIB/commons-logging-1.3.jar;$FFE_LIB/ffe-8.8.jar;$FFE_LIB/gluegen-rt-android-natives-linux-amd64.jar;$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar;$FFE_LIB/groovy-all-2.4.4.jar;$FFE_LIB/j3dcore-1.7.jar;$FFE_LIB/j3dutils-1.7.jar;$FFE_LIB/jh-2.0.5.jar;$FFE_LIB/joal-natives-linux-amd64.jar;$FFE_LIB/joal.jar;$FFE_LIB/jogl-all-noawt-natives-linux-amd64.jar;$FFE_LIB/jogl-all.jar;$FFE_LIB/sunjce_provider.jar;$FFE_LIB/vecmath-1.7.jar;$OS_LIB"
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else
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CLASSPATH="$FFE_LIB/AppleJavaExtensions-1.6.jar;$FFE_LIB/commons-io-2.6.jar;$FFE_LIB/commons-lang-2.7.jar;$FFE_LIB/commons-logging-1.3.jar;$FFE_LIB/ffe-8.8.jar;$FFE_LIB/gluegen-rt-android-natives-linux-amd64.jar;$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar;$FFE_LIB/groovy-all-2.4.4.jar;$FFE_LIB/j3dcore-1.7.jar;$FFE_LIB/j3dutils-1.7.jar;$FFE_LIB/jh-2.0.5.jar;$FFE_LIB/joal-natives-linux-amd64.jar;$FFE_LIB/joal.jar;$FFE_LIB/jogl-all-noawt-natives-linux-amd64.jar;$FFE_LIB/jogl-all.jar;$FFE_LIB/sunjce_provider.jar;$FFE_LIB/vecmath-1.7.jar;$OS_LIB;$CLASSPATH"
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fi
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export CLASSPATH
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#
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# Create an alias to execute Force Field Explorer
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#
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#alias ffe="java -server -ms2048M -mx4096M -Djava.library.path=$FFE_LIB -Dtinker.dir=$TINKER_HOME -jar $FFE_LIB/ffe-8.8.jar"
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alias ffe="$FFE_HOME/Force*Field*Explorer"

source/ffe/FFESetupMac.csh

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#!/bin/csh
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#
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# #########################################################
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# ## ##
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# ## csh Initialization Script for Tinker-FFE on MacOS ##
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# ## ##
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# #########################################################
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#
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# This is a csh/tcsh script to set environment variables
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# needed to run Force Field Explorer at the command line
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#
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# Note FFE_HOME and TINKER_HOME are special directory names
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# needed by the Force Field Explorer application
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#
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#
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# Set Tinker-FFE installation directory
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#
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setenv INSTALLDIR "$HOME/Tinker-FFE"
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#
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# Set location of FFE, Tinker, JRE and FFE libraries
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#
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setenv FFE_HOME "$INSTALLDIR/ffe"
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setenv TINKER_HOME "$INSTALLDIR/tinker"
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setenv JRE_HOME "$INSTALLDIR/.install4j/jre.bundle/Contents/Home/jre"
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setenv FFE_LIB "$FFE_HOME/lib"
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setenv FFE_NATIVE "$FFE_HOME/native"
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#
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# Set location of system-dependent MacOS library
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#
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setenv OS_LIB "$FFE_NATIVE/macos/libffe.jnilib"
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#
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# Append the Tinker binaries to default PATH
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#
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if !($?PATH) then
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setenv PATH "$TINKER_HOME/bin"
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else
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setenv PATH "$TINKER_HOME/bin:$PATH"
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endif
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#
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# Set LD_LIBRARY_PATH environment variable
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#
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if !($?LD_LIBRARY_PATH) then
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setenv LD_LIBRARY_PATH "$JRE_HOME/lib/server:$JRE_HOME/lib"
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else
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setenv LD_LIBRARY_PATH "$JRE_HOME/lib/server:$JRE_HOME/lib:LD_LIBRARY_PATH"
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endif
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#
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# Add required JAR files to CLASSPATH variable
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#
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if !($?CLASSPATH) then
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setenv CLASSPATH "$FFE_LIB/AppleJavaExtensions-1.6.jar:$FFE_LIB/commons-io-2.6.jar:$FFE_LIB/commons-lang-2.7.jar:$FFE_LIB/commons-logging-1.3.jar:$FFE_LIB/ffe-8.8.jar:$FFE_LIB/gluegen-rt-android-natives-macosx-universal.jar:$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar:$FFE_LIB/groovy-all-2.4.4.jar:$FFE_LIB/j3dcore-1.7.jar:$FFE_LIB/j3dutils-1.7.jar:$FFE_LIB/jh-2.0.5.jar:$FFE_LIB/joal-natives-macosx-universal.jar:$FFE_LIB/joal.jar:$FFE_LIB/jogl-all-noawt-natives-macosx-universal.jar:$FFE_LIB/jogl-all.jar:$FFE_LIB/sunjce_provider.jar:$FFE_LIB/vecmath-1.7.jar:$OS_LIB"
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else
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setenv CLASSPATH "$FFE_LIB/AppleJavaExtensions-1.6.jar:$FFE_LIB/commons-io-2.6.jar:$FFE_LIB/commons-lang-2.7.jar:$FFE_LIB/commons-logging-1.3.jar:$FFE_LIB/ffe-8.8.jar:$FFE_LIB/gluegen-rt-android-natives-macosx-universal.jar:$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar:$FFE_LIB/groovy-all-2.4.4.jar:$FFE_LIB/j3dcore-1.7.jar:$FFE_LIB/j3dutils-1.7.jar:$FFE_LIB/jh-2.0.5.jar:$FFE_LIB/joal-natives-macosx-universal.jar:$FFE_LIB/joal.jar:$FFE_LIB/jogl-all-noawt-natives-macosx-universal.jar:$FFE_LIB/jogl-all.jar:$FFE_LIB/sunjce_provider.jar:$FFE_LIB/vecmath-1.7.jar:$OS_LIB:$CLASSPATH"
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endif
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#
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# Create an alias to execute Force Field Explorer
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#
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#alias ffe "java -server -ms2048M -mx4096M -Djava.library.path=$FFE_LIB -Dtinker.dir=$TINKER_HOME -jar $FFE_LIB/ffe-8.8.jar"
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alias ffe "$FFE_HOME/Force*Field*Explorer.app/Contents/MacOS/JavaApplicationStub"

source/ffe/FFESetupMac.sh

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#!/bin/sh
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shopt -s expand_aliases
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#
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# ########################################################
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# ## ##
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# ## sh Initialization Script for Tinker-FFE on MacOS ##
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# ## ##
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# ########################################################
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#
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# This is an sh/bash script to set environment variables
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# needed to run Force Field Explorer at the command line
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#
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# Note FFE_HOME and TINKER_HOME are special directory names
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# needed by the Force Field Explorer application
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#
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#
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# Set Tinker-FFE installation directory
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#
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INSTALLDIR="$HOME/Tinker-FFE"
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export INSTALLDIR
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#
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# Set location of JRE, Tinker and Force Field Explorer
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#
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FFE_HOME="$INSTALLDIR/ffe"
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export FFE_HOME
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TINKER_HOME="$INSTALLDIR/tinker"
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export TINKER_HOME
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JRE_HOME="$INSTALLDIR/.install4j/jre.bundle/Contents/Home/jre"
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export JRE_HOME
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FFE_LIB="$FFE_HOME/lib"
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export FFE_LIB
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FFE_NATIVE="$FFE_HOME/native"
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export FFE_NATIVE
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#
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# Set location of system-dependent MacOS library
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#
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OS_LIB="$FFE_NATIVE/macos/libffe.jnilib"
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export OS_LIB
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#
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# Append the Tinker binaries to default PATH
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#
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if [ -z "${PATH}" ]
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then
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PATH="$TINKER_HOME/bin"
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else
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PATH="$TINKER_HOME/bin:$PATH"
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fi
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export PATH
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#
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# Add required JAR files to CLASSPATH variable
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#
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if [ -z "${CLASSPATH}" ]
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then
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CLASSPATH="$FFE_LIB/AppleJavaExtensions-1.6.jar;$FFE_LIB/commons-io-2.6.jar;$FFE_LIB/commons-lang-2.7.jar;$FFE_LIB/commons-logging-1.3.jar;$FFE_LIB/ffe-8.8.jar;$FFE_LIB/gluegen-rt-android-natives-macosx-universal.jar;$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar;$FFE_LIB/groovy-all-2.4.4.jar;$FFE_LIB/j3dcore-1.7.jar;$FFE_LIB/j3dutils-1.7.jar;$FFE_LIB/jh-2.0.5.jar;$FFE_LIB/joal-natives-macosx-universal.jar;$FFE_LIB/joal.jar;$FFE_LIB/jogl-all-noawt-natives-macosx-universal.jar;$FFE_LIB/jogl-all.jar;$FFE_LIB/sunjce_provider.jar;$FFE_LIB/vecmath-1.7.jar;$OS_LIB"
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else
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CLASSPATH="$FFE_LIB/AppleJavaExtensions-1.6.jar;$FFE_LIB/commons-io-2.6.jar;$FFE_LIB/commons-lang-2.7.jar;$FFE_LIB/commons-logging-1.3.jar;$FFE_LIB/ffe-8.8.jar;$FFE_LIB/gluegen-rt-android-natives-macosx-universal.jar;$FFE_LIB/gluegen-rt.jar:$FFE_LIB/gluegen.jar;$FFE_LIB/groovy-all-2.4.4.jar;$FFE_LIB/j3dcore-1.7.jar;$FFE_LIB/j3dutils-1.7.jar;$FFE_LIB/jh-2.0.5.jar;$FFE_LIB/joal-natives-macosx-universal.jar;$FFE_LIB/joal.jar;$FFE_LIB/jogl-all-noawt-natives-macosx-universal.jar;$FFE_LIB/jogl-all.jar;$FFE_LIB/sunjce_provider.jar;$FFE_LIB/vecmath-1.7.jar;$OS_LIB;$CLASSPATH"
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fi
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export CLASSPATH
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#
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# Create an alias to execute Force Field Explorer
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#
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#alias ffe="java -server -ms2048M -mx4096M -Djava.library.path=$FFE_LIB -Dtinker.dir=$TINKER_HOME -jar $FFE_LIB/ffe-8.8.jar"
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alias ffe="$FFE_HOME/Force*Field*Explorer.app/Contents/MacOS/JavaApplicationStub"

source/ffe/FFESetupWin.bat

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@echo off
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set location=%~dp0
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set tinkerdir=%location%tinker
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set ffedir=%location%ffe
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set ffejardir=%ffedir%\lib\ffe-8.8.jar
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set ffedlldir=%ffedir%\native\windows\ffe.dll
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set tclasspath=%ffejardir%;%ffedlldir%;
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setx TINKER "%tinkerdir%"
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setx FFEHOME "%ffedir%"
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set "blankspace="
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call set CLASSPATH=%%CLASSPATH:%tclasspath%=%blankspace%%%
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setx CLASSPATH "%tclasspath%%CLASSPATH%"
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mklink /J bin jre\bin
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mklink /J lib jre\lib

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