####### VARIABLES: LINES TO CHECK OVER WHEN STARTING A NEW RUN ###############################################################################################
RunName='2023_02_20_Symmetric_Run'      ## This is the name of the run. You need to make a unique name each time you run.
TotalGens=100                   ## number of generations (after initial) to run through
NPOP=50                         ## number of individuals per generation; please keep this value below 99
Seeds=10                        ## This is how many AraSim jobs will run for each individual## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
FREQ=60                         ## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
NNT=30000                       ## Number of Neutrinos Thrown in AraSim
exp=18                          ## exponent of the energy for the neutrinos in AraSim
ScaleFactor=1.0                 ## ScaleFactor used when punishing fitness scores of antennae larger than the drilling holes
GeoFactor=1                     ## This is the number by which we are scaling DOWN our antennas. This is passed to many files
num_keys=4                      ## how many XF keys we are letting this run use
database_flag=0                 ## 0 if not using the database, 1 if using the database
                                ## These next 3 define the symmetry of the cones.
RADIUS=0                        ## If 1, radius is asymmetric. If 0, radius is symmetric
LENGTH=0                        ## If 1, length is asymmetric. If 0, length is symmetric
ANGLE=0                         ## If 1, angle is asymmetric. If 0, angle is symmetric
CURVED=0                        ## If 1, evolve curved sides. If 0, sides are straight
A=0                             ## If 1, A is asymmetric
B=0                             ## If 1, B is asymmetric
SEPARATION=0                    ## If 1, separation evolves. If 0, separation is constant
NSECTIONS=1                     ## The number of chromosomes
DEBUG_MODE=0                    ## 1 for testing (ex: send specific seeds), 0 for real runs
                                ## These next variables are the values passed to the GA
REPRODUCTION=3                  ## Number (not fraction!) of individuals formed through reproduction
CROSSOVER=36                    ## Number (not fraction!) of individuals formed through crossover
MUTATION=25                     ## Probability of mutation (divided by 100)
SIGMA=6                         ## Standard deviation for the mutation operation (divided by 100)
ROULETTE=8                      ## Percent of individuals selected through roulette (divided by 10)
TOURNAMENT=2                    ## Percent of individuals selected through tournament (divided by 10)
RANK=0                          ## Percent of individuals selected through rank (divided by 10)
ELITE=0                         ## Elite function on/off (1/0)

#####################################################################################################################################################

#pueoBuilder Installation Tutorial

This tutorial will guide you through the process of building the tools included in pueoBuilder from scratch, including the prerequisites and any environment variables that you will need to set. This sort of thing is always a bit of a nightmare process for me, so hopefully this guide can help you skip some of the frustration that I ran into. I did not have root acces on the system I was building on, so the instructions below are what I had to do to get things working with local installations. If you have root access, then things might be a bit easier. For reference I'm working on CentOS 7, other operating systems might have different problems that arise. 

##Prerequisites
As far as I can tell, the prerequisites that need to be built first are:

-cmake 3.21.2 (I had problems with 3.11.4)
-gcc 11.1.0 (9.X will not work)
-fftw 3.3.9
-gsl 2.7.1 (for ROOT)
-ROOT 6.24.00

###CMake
You can download the source files for CMake here: https://cmake.org/download/. Untar the source files with:

    tar -xzvf cmake-3.22.1.tar.gz

Compiling CMake is as easy as following the directions on the website: https://cmake.org/install/, but since we're doing a local build, we'll use the `configure` script instead of the listed `bootstrap` script. As an example, suppose that I downloaded the above tar file to `/scratch/wluszczak/cmake`: 

    mkdir install
    cd cmake-3.22.1
    ./configure --prefix=/scratch/wluszczak/cmake/install
    make
    make install

You should additionally add this directory to your `$PATH` variable:

    export PATH=/scratch/wluszczak/cmake/install/bin:$PATH

To check to make sure that you are using the correct version of CMake, run:

    cmake --version

and you should get:

    cmake version 3.22.1

    CMake suite maintained and supported by Kitware (kitware.com/cmake).

### gcc 11.1.0

Download the gcc source from github here: https://github.com/gcc-mirror/gcc/tags. I used the 11.1.0 release, though there is a more recent 11.2.0 release that I have not tried. Once you have downloaded the source files, untar the directory:

    tar -xzvf gcc-releases-gcc-11.1.0.tar.gz

Then install the prerequisites for gcc:
    
    cd gcc-releases-gcc-11.1.0
    contrib/download_prerequisites

One of the guides I looked at also recommended installing flex separately, but I didn't seem to need to do this, and I'm not sure how you would go about it without root priviledges, though I imagine it's similar to the process for all the other packages here (download the source and then build by providing an installation prefix somewhere)

After you have installed the prerequisites, create a build directory:

    cd ../
    mkdir build
    cd build

Then configure GCC for compilation like so:

    ../gcc-releases-gcc-11.1.0/configure -v --prefix=/home/wluszczak/gcc-11.1.0 --enable-checking=release --enable-languages=c,c++,fortran --disable-multilib --program-suffix=-11.1

I don't remember why I installed to my home directory instead of the /scratch/ directories used above. In principle the installation prefix can go wherever you have write access. Once things have configured, compile gcc with:

    make -j $(nproc)
    make install

Where `$(nproc)` is the number of processing threads you want to devote to compilation. More threads will run faster, but be more taxing on your computer. For reference, I used 8 threads and it took ~15 min to finish. 

Once gcc is built, we need to set a few environment variables:

    export PATH=/home/wluszczak/gcc-11.1.0/bin:$PATH
    export LD_LIBRARY_PATH=/home/wluszczak/gcc-11.1.0/lib64:$LD_LIBRARY_PATH

We also need to make sure cmake uses this compiler:

    export CC=/home/wluszczak/gcc-11.1.0/bin/gcc-11.1
    export CXX=/home/wluszczak/gcc-11.1.0/bin/g++-11.1
    export FC=/home/wluszczak/gcc-11.1.0/bin/gfortran-11.1

If your installation prefix in the configure command above was different, substitute that directory in place of `/home/wluszczak/gcc-11.1.0` for all the above export commands. To easily set these variables whenever you want to use gcc-11.1.0, you can stick these commands into a single shell script:

    #load_gcc11.1.sh
    export PATH=/home/wluszczak/gcc-11.1.0/bin:$PATH
    export LD_LIBRARY_PATH=/home/wluszczak/gcc-11.1.0/lib64:$LD_LIBRARY_PATH

    export CC=/home/wluszczak/gcc-11.1.0/bin/gcc-11.1
    export CXX=/home/wluszczak/gcc-11.1.0/bin/g++-11.1
    export FC=/home/wluszczak/gcc-11.1.0/gfortran-11.1

(again substituting your installation prefix in place of mine). You can then set all these environment variables by simply running:
    
    source load_gcc11.1.sh

Once this is done, you can check that gcc-11.1.0 is properly installed by running:

    gcc-11.1 --version

Note that plain old

    gcc --version

might still point to an older version of gcc. This is fine though. 

###FFTW 3.3.9
Grab the source code for the appropriate versino of FFTW from here: http://www.fftw.org/download.html

However, do NOT follow the installation instructions on the webpage. Those instructions might work if you have root privileges, but I personally couldn't seem to to get things to work that way. Instead, we're going to build fftw with cmake. Untar the fftw source files:

    tar -xzvf fftw-3.3.9.tar.gz

Make a build directory and cd into it:
    
    mkdir build
    cd build

Now build using cmake, using the flags shown below. For reference, I downloaded and untarred the source file in `/scratch/wluszczak/fftw/build`, so adjust your install prefix accordingly to point to your own build directory that you created in the previous step.

    cmake -DCMAKE_INSTALL_PREFIX=/scratch/wluszczak/fftw/build/ -DBUILD_SHARED_LIBS=ON -DENABLE_OPENMP=ON -DENABLE_THREADS=ON ../fftw-3.3.9
    make install -j $(nproc)

Now comes the weird part. Remove everything except the `include` and `lib64` directories in your build directory (if you installed to a different `CMAKE_INSTALL_PREFIX`, the include and lib64 directories might be located there instead. The important thing is that you want to remove everything, but leave the `include` and `lib64` directories untouched):

    rm *
    rm -r CMakeFiles

Now rebuild fftw, but with an additional flag:

    cmake -DCMAKE_INSTALL_PREFIX=/scratch/wluszczak/fftw/build/ -DBUILD_SHARED_LIBS=ON -DENABLE_OPENMP=ON -DENABLE_THREADS=ON -DENABLE_FLOAT=ON ../fftw-3.3.9
    make install -j $(nproc)

At the end of the day, your fftw install directory should have the following files:

    include/fftw3.f  
    include/fftw3.f03
    include/fftw3.h  
    include/fftw3l.f03  
    include/fftw3q.f03 
    lib64/libfftw3f.so          
    lib64/libfftw3f_threads.so.3      
    lib64/libfftw3_omp.so.3.6.9  
    lib64/libfftw3_threads.so
    lib64/libfftw3f_omp.so        
    lib64/libfftw3f.so.3        
    lib64/libfftw3f_threads.so.3.6.9  
    lib64/libfftw3.so            
    lib64/libfftw3_threads.so.3
    lib64/libfftw3f_omp.so.3      
    lib64/libfftw3f.so.3.6.9    
    lib64/libfftw3_omp.so             
    lib64/libfftw3.so.3          
    lib64/libfftw3_threads.so.3.6.9
    lib64/libfftw3f_omp.so.3.6.9  
    lib64/libfftw3f_threads.so  
    lib64/libfftw3_omp.so.3           
    lib64/libfftw3.so.3.6.9

Why do we have to do things this way? I don't know, I'm bad at computers. Maybe someone more knowledgeable knows. I found that when I didn't do this step, I'd run into errors that pueoBuilder could not find some subset of the required files (either the ones added by building with `-DENABLE_FLOAT`, or the ones added by building without `-DENABLE_FLOAT`). 

Once fftw has been installed, export your install directory (the one with the include and lib64 folders) to the following environment variable:

    export FFTWDIR=/scratch/wluszczak/fftw/build

Again, substituting your own fftw install prefix that you used above in place of `/scratch/wluszczak/fftw/build`

###gsl 2.7.1
gsl 2.7.1 is needed for the `mathmore` option in ROOT. If you have an outdated version of gsl, ROOT will still compile, but it will skip installing `mathmore` and `root-config --has-mathmore` will return `no`. To fix this, grab the latest source code for gsl from here: https://www.gnu.org/software/gsl/. Untar the files to a directory of your choosing:

    tar -xzvf gsl-latest.tar.gz

For some reason I also installed gsl to my home directory, but in principle you can put it wherever you want. 

    mkdir /home/wluszczak/gsl
    ./configure --prefix=/home/wluszczak/gsl
    make
    make check
    make install

To make sure ROOT can find this installation of gsl, you'll again need to set an environment variable prior to building ROOT:

    export GSL_ROOT_DIR=/home/wluszczak/gsl/
    
I also added this to my $PATH variable, though I don't remember if that was required to get things working or not:

    export PATH=/home/wluszczak/gsl/bin/:$PATH 
    export LD_LIBRARY_PATH=/home/wluszczak/gsl/lib:$LD_LIBRARY_PATH

###ROOT 6.24.00
Download the specific version of ROOT that you need from here: https://root.cern/install/all_releases/

You might need to additionally install some of the dependencies (https://root.cern/install/dependencies/), but it seems like everything I needed was already installed on my system. 

Untar the source you downloaded:
    
    tar -xzvf root_v6.24.00.source.tar.gz

Make some build and install directories:

    mkdir build install
    cd build

Run CMake, but be sure to enable the fortan, mathmore and minuit2 options. For reference, I had downloaded and untarred the source files to `/scratch/wluszczak/root`. Your installation and source paths will be different.

    cmake -DCMAKE_INSTALL_PREFIX=/scratch/wluszczak/root/install/ /scratch/wluszczak/root/root-6.24.00/ -Dfortran=ON -Dminuit2=ON -Dmathmore=ON

Note: if you end up with an error related to compiling XROOTD, then add -Dxrootd=OFF to the original cmake command above.

Then proceed to start the build:

    cmake --build . --target install -j $(nproc)
    

If everything has worked then after the above command finishes running, you should be able to run the following file to finish setting up ROOT:

    source ../install/bin/thisroot.sh

##pueoBuilder
By this point, you should have working installations of CMake 3.21.2, gcc-11.1.0, fftw 3.3.9, and ROOT 6.24.00. Additionally, the following environment variables should have been set:

    export PATH=/scratch/wluszczak/cmake/install/bin:$PATH

    export PATH=/home/wluszczak/gcc-11.1.0/bin:$PATH
    export LD_LIBRARY_PATH=/home/wluszczak/gcc-11.1.0/lib64:$LD_LIBRARY_PATH

    export CC=/home/wluszczak/gcc-11.1.0/bin/gcc-11.1
    export CXX=/home/wluszczak/gcc-11.1.0/bin/g++-11.1
    export FC=/home/wluszczak/gcc-11.1.0/gfortran-11.1

    export FFTWDIR=/scratch/wluszczak/fftw/build

At this point, the hard work is mostly done. Check out pueoBuilder with:

    git clone git@github.com:PUEOCollaboration/pueoBuilder 

set the following environment variables:

    export PUEO_BUILD_DIR=/scratch/wluszczak/PUEO/pueoBuilder
    export PUEO_UTIL_INSTALL_DIR=/scratch/wluszczak/PUEO/pueoBuilder
    export NICEMC_SRC=${PUEO_BUILD_DIR}/components/nicemc
    export NICEMC_BUILD=${PUEO_BUILD_DIR}/build/components/nicemc
    export PUEOSIM_SRC=${PUEO_BUILD_DIR}/components/pueoSim
    export LD_LIBRARY_PATH=${PUEO_UTIL_INSTALL_DIR}/lib:$LD_LIBRARY_PATH

Where $PUEO_BUILD_DIR and $PUEO_UTIL_INSTALL_DIR point to where you cloned pueoBuilder to (in my case, `/scratch/wluszczak/PUEO/pueoBuilder`. Now you should be able to just run:

    ./pueoBuilder.sh

Perform a prayer to the C++ gods while you're waiting for it to compile, and hopefully at the end of the day you'll have a working set of PUEO software. 

##Issues I Ran Into
If you already have an existing installation of ROOT, you may still need to recompile to make sure you're using the same c++ standard that the PUEO software is using. I believe the pre-compiled ROOT binaries available through their website are insufficient, though maybe someone else has been able to get those working. 

If you're running into errors about c++ standard or compiler version even after you have installed gcc-11.1.0, then for some reason your system isn't recognizing your local installation of gcc-11.1.0. Check the path variables ($PATH and $LD_LIBRARY_PATH) to make sure the gcc-11.1.0 `bin` directory is being searched.

If you're running into an error that looks like:
        
    CMake Error: The following variables are used in this project, but they are set to NOTFOUND.
    Please set them or make sure they are set and tested correctly in the CMake files:
    FFTWF_LIB (ADVANCED)

then pueoBuilder can't seem to find your fftw installation (or files that are supposed to be included in that installation), try rebuilding with different flags according to which files it seems to think are missing.

If it seems like pueoBuilder can't seem to find your fftw installation at all (i.e. you're getting some error that looks like `missing: FFTW_LIBRARIES` or `missing: FFTW_INCLUDES`), check the environment variables that are supposed to point to your fftw installation (`$FFTWDIR`) and make sure there are the correct files in the `lib` and `include` subdirectories. 

App.getActiveProject().getGeometryAssembly().clear();
var freq = [83.33, 100.00, 116.67, 133.33, 150.00, 166.67, 183.34, 200.00, 216.67, 233.34, 250.00, 266.67, 283.34, 300.00, 316.67, 333.34, 350.00, 366.67, 383.34, 400.01, 416.67, 433.34, 450.01, 466.67, 483.34, 500.01, 516.68, 533.34, 550.01, 566.68, 583.34, 600.01, 616.68, 633.34, 650.01, 666.68, 683.35, 700.01, 716.68, 733.35, 750.01, 766.68, 783.35, 800.01, 816.68, 833.35, 850.02, 866.68, 883.35, 900.02, 916.68, 933.35, 950.02, 966.68, 983.35, 1000.00, 1016.70, 1033.40, 1050.00, 1066.70] 
CreatePEC();
var units = " cm";
num_ridges = 4; // either 2 or 4
// Make the walls and a ridge
build_walls(10,1,30);
// Note that to avoid overlap, we need x0 >= y0
x0=0.04001; // previously 0.04
y0=0.04; // previously 0.04
build_ridges(x0, y0, 0.0, 0.1, 0.06, 0.3, 0.26, 0.1, 0.1, 1); 
CreateAntennaSource();
CreateGrid();
CreateSensors();
CreateAntennaSimulationData();
QueueSimulation();

// Try making copies of the ridge
var new_ridges = new EllipticalPattern();
Output.println(new_ridges.getInstances());
new_ridges.setInstances(7);
//new_ridges.clone();
//Output.println(new_ridges);

// Makes the outer walls of the horn antenna
// S is the side length of the bottom of the wall
// a is the coefficient for the linear function the walls extrude according to
function build_walls(S,m,H) 
{
	// Make the edges to define the square
	var edge1 = Line( new Cartesian3D(-S + units,-S + units, 0), new Cartesian3D(-S + units, S + units, 0));
	var edge2 = Line( new Cartesian3D(-S + units, S + units, 0), new Cartesian3D(S + units, S + units, 0));
	var edge3 = Line( new Cartesian3D(S + units,S + units, 0), new Cartesian3D(S + units, -S + units, 0));
	var edge4 = Line( new Cartesian3D(S + units,-S + units, 0), new Cartesian3D(-S + units, -S + units, 0));
	
	// Declare sketches to be made from the edges
	var wallSegment = new Sketch();
	var bottomSegment = new Sketch();
	wallSegment.addEdge(edge1);
	wallSegment.addEdge(edge2);
	wallSegment.addEdge(edge3);
	wallSegment.addEdge(edge4);
	bottomSegment.addEdge(edge1);
	bottomSegment.addEdge(edge2);
	bottomSegment.addEdge(edge3);
	bottomSegment.addEdge(edge4);

	// Let's start by making the bottom
	var bottomCover = new Cover(bottomSegment);
	var bottomRecipe = new Recipe();
	bottomRecipe.append( bottomCover );
	var bottomModel = new Model();
	bottomModel.setRecipe( bottomRecipe );
	// Add the surface
	//var bottom = App.getActiveProject().getGeometryAssembly().append(bottomModel);
	//bottom.name = "Bottom square";

	// Now we need to extrude the edges to get height
	var walls = new Extrude( wallSegment, H + units);				// Makes an Extrude
	var wallOptions = walls.getOptions();						// Gives the possible options for 
	// We will use the draft law option to extrude linearly
	wallOptions.draftOption = SweepOptions.DraftLaw;			// allows for draftlaw
	wallOptions.draftLaw = "("+m+"*x)";							// Set the expression for the extrude
	wallOptions.draftOption = 4;								// 4 indicates we use draftlaw
    //Walter - Change the gap type to Extended to get the desired shape
	wallOptions.gapType = SweepOptions.Extended; 				// I actually don't like this when we have x^2, but it doesn't do much for just x
    //Walter - Create a shell instead of a solid part
	wallOptions.createSolid = false;							// This way the shape isn't filled in
	walls.setOptions ( wallOptions );							// Sets the settings we assigned above

	// Make a recipe for a model
	var wallRecipe = new Recipe();
	wallRecipe.append(walls);
	var wallModel = new Model();
	wallModel.setRecipe(wallRecipe);
	wallModel.name = "Outer Walls";
	wallModel.getCoordinateSystem().translate(new Cartesian3D(0,0,0));	// Makes the model start at the origin

	// Set the material for these parts
	var wallProject = App.getActiveProject().getGeometryAssembly().append(wallModel);	// Adds the model to the project
	var pecMaterial = App.getActiveProject().getMaterialList().getMaterial( "PEC" );	// Makes the material available
	App.getActiveProject().setMaterial( wallProject, pecMaterial );						// Sets the material
	//App.getActiveProject().setMaterial( bottom, pecMaterial );						// Sets the material

}

// A function to build the inner ridges
// Here are the arguments, which are primarily used when making the LawEdges
// Bottom x distance from center
// Bottom y distance from center
// Top x distance from center
// Top y distance from center
// Full x
// Full y
// Full height
function build_ridges(x_0, y_0, z_0, x_f, y_f, z_f, tau, beta, S, m)
{

//	build_ridges(0.04, 0.04, 0.0, 0.1, 0.06, 0.3, 0.26, 0.1, 0.1, 1);

	// Logarithmic slopes
	//var Log1 = new LawEdge( "0.04 + u", "0.04 + 0.02/0.26*u", "1/10*ln((exp(3)-1.0)/0.26*u+1.0)", 0, 0.26); // alpha = z_max/beta
	//var Log2 = new LawEdge( "0.04 + u", "-0.04 - 0.02/0.26*u", "1/10*ln((exp(3)-1.0)/0.26*u+1.0)", 0, 0.26);

	var Log1 = new LawEdge( ""+x_0+" + ("+z_f+"-"+x_0+")/"+tau+"*u", ""+y_0+" + ("+y_f+"-"+y_0+")/"+tau+"*u", ""+beta+"*ln((exp("+z_f+"/"+beta+")-1.0)/"+tau+"*u+1.0)", 0, tau); // alpha = z_max/beta
	var Log2 = new LawEdge( ""+x_0+" + ("+z_f+"-"+x_0+")/"+tau+"*u", "-"+y_0+" - ("+y_f+"-"+y_0+")/"+tau+"*u", ""+beta+"*ln((exp("+z_f+"/"+beta+")-1.0)/"+tau+"*u+1.0)", 0, tau);


	// Inner straight slopes 
	var IS1 = new LawEdge( ""+x_0+" + ("+z_f+"-"+x_0+")/"+tau+"*u", ""+y_0+" + ("+y_f+"-"+y_0+")/"+tau+"*u", "("+z_f+"-"+z_0+")/"+tau+"*u", 0, tau); // a_0 + at, b_0 + bt, c_0 + ct
	var IS2 = new LawEdge( ""+x_0+" + ("+z_f+"-"+x_0+")/"+tau+"*u", "-"+y_0+" - ("+y_f+"-"+y_0+")/"+tau+"*u", "("+z_f+"-"+z_0+")/"+tau+"*u", 0, tau);

	// Bottom line
	var BL1 = new LawEdge(""+x_0+" + ("+x_f+"-"+x_0+")/"+tau+"*u", ""+y_0+"", ""+z_0+"", 0, tau);
	var BL2 = new LawEdge(""+x_0+" + ("+x_f+"-"+x_0+")/"+tau+"*u", "-"+y_0+"", ""+z_0+"", 0, tau);

	// Top line
	var TL1 = new LawEdge(""+z_f+" + "+x_f+"/"+tau+"*u", ""+y_f+"", ""+z_f+"", 0, tau);
	var TL2 = new LawEdge(""+z_f+" + "+x_f+"/"+tau+"*u", "-"+y_f+"", ""+z_f+"", 0, tau);

	// Outer Straight slopes
	var OS1 = new LawEdge( ""+x_f+" + "+z_f+"/"+tau+"*u", ""+y_0+" + ("+y_f+" - "+y_0+")/"+tau+"*u", ""+z_f+"/"+tau+"*u", 0, tau);
	var OS2 = new LawEdge( ""+x_f+" + "+z_f+"/"+tau+"*u", "-"+y_0+" - ("+y_f+" - "+y_0+")/"+tau+"*u", ""+z_f+"/"+tau+"*u", 0, tau);

	// Inner top line
	var ITL = new LawEdge( ""+z_f+"", "-"+y_f+" + 2*"+y_f+"/"+tau+"*u", ""+z_f+"", 0, tau);

	// Outer top line
	var OTL = new LawEdge( ""+x_f+" + "+z_f+"", "-"+y_f+" + 2*"+y_f+"/"+tau+"*u", ""+z_f+"", 0, tau);

	// Inner bottom line
	var IBL = new LawEdge( ""+x_0+"", "-"+y_0+" + 2*"+y_0+"/"+tau+"*u", ""+z_0+"", 0, tau);

	// Outer bottom line
	var OBL = new LawEdge( ""+x_f+"", "-"+y_0+" + 2*"+y_0+"/"+tau+"*u", ""+z_0+"", 0, tau);

	// Make the sketches
	var straightEdge1 = new Sketch(); 	// All straight edges (IS1, BL1, TL1, OS1)
	var straightEdge2 = new Sketch(); 	// All straight edges (IS2, BL2, TL2, OS2)	
	var curvedLog1 = new Sketch(); 		// Logarithmic edge (IS1 and Log1)
	var curvedLog2 = new Sketch(); 		// Logarithmic edge (IS2 and Log2)
	var topRectangle = new Sketch(); 	// Top rectangle
	var bottomRectangle = new Sketch(); // Bottom rectangle

	// Add the edges to the sketches
	straightEdge1.addEdges( [IS1, BL1, TL1, OS1] );	// Inner straight slope
	curvedLog1.addEdges( [IS1, Log1] );				// Right logarithm part
	straightEdge2.addEdges( [IS2, BL2, TL2, OS2] ); 	// Inner straight slope
	curvedLog2.addEdges( [IS2, Log2] );			 	// Left logarithm part
	topRectangle.addEdges( [ITL, OTL, TL1, TL2] );		// Top rectangle
	bottomRectangle.addEdges( [IBL, OBL, BL1, BL2] );	// Bottom Rectangle

	//WALTER - The Elliptical pattern is added as a recipe to the parts
	//In this case the location of the center and direction of the normal are simple, but for more complex scenarios, may need to use mroe functionality to find them.
	var ePattern = new EllipticalPattern();
	ePattern.setCenter(new CoordinateSystemPosition(0,0,0));
	ePattern.setNormal(new CoordinateSystemDirection(0,0,1));
	ePattern.setInstances(num_ridges);
	ePattern.setRotated(true);

	var cov = new Array();
	cov.push(new Cover(straightEdge1));
	cov.push(new Cover(straightEdge2));
	cov.push(new Cover(curvedLog1));
	cov.push(new Cover(curvedLog2));
	cov.push(new Cover(topRectangle));
	cov.push(new Cover(bottomRectangle));

	var pecMaterial = App.getActiveProject().getMaterialList().getMaterial( "PEC" );

	//WALTER - We can loop over all our parts and add them to the project as follows.  You can use similar concepts above.
	models = new Assembly();
	for(var w = 0; w < cov.length; w++)
	{
		var r = new Recipe();
		r.append(cov[w]);
		r.append(ePattern);
		var m = new Model();
		m.setRecipe(r);
		m.name = "Test Surface " + (w+1);
		//WALTER - Seperate array for the models, though we could just get them from the GemoetryAssembly again
		models.append(m);
		App.getActiveProject().setMaterial( m, pecMaterial );

	}

	// Work on the loft
	var vertex_position1 = curvedLog1.getPosition(curvedLog1.getVertexIds()[0]);	
	var vertex_position2 = curvedLog2.getPosition(curvedLog2.getVertexIds()[0]);

	var loft = new Loft(models.at(2).pickFace(new Cartesian3D (0, 0, 0), vertex_position1, 0.5), "0.0", models.at(3).pickFace(new Cartesian3D(0,0,0), vertex_position2, 0.5), "0.0");
	loft.setPart1(models.at(2));
	loft.setPart2(models.at(3));
		
	var r12 = new Recipe();
	r12.append( loft );
	r12.append(ePattern);
	var m12 = new Model();
	m12.setRecipe( r12 );
	m12.name = "Loft 1";
	models.append(m12);

	//WALTER - append the assembly to the project, then loop over it to assign the material
	var assembly = App.getActiveProject().getGeometryAssembly().append(models);
	for(x = 0; x < assembly.size(); x++)
	{
		Output.println(assembly.at(x));
		App.getActiveProject().setMaterial( assembly.at(x), pecMaterial );
	}

}



// CreatPEC Function
function CreatePEC() //borrowed from XF demo
{
    //Make the material.  We will use PEC, or Perfect Electrical Conductor:
    var pec = new Material();
    pec.name = "PEC";
    var pecProperties = new PEC();      // This is the electric properties that defines PEC
    var pecMagneticFreespace = new MagneticFreespace();     // We could make a material that acts as PEC and PMC, but in this case we just care about electrical components.
    var pecPhysicalMaterial = new PhysicalMaterial();
    pecPhysicalMaterial.setElectricProperties( pecProperties );
    pecPhysicalMaterial.setMagneticProperties( pecMagneticFreespace );
    pec.setDetails( pecPhysicalMaterial );
    // PEC is historically a "white" material, so we can easily change its appearance:
    var pecBodyAppearance = pec.getAppearance();
    var pecFaceAppearance = pecBodyAppearance.getFaceAppearance();  // The "face" appearance is the color/style associated with the surface of geometry objects
        pecFaceAppearance.setColor( new Color( 255, 255, 255, 255 ) );  // Set the surface color to white. (255 is the maximum intensity, these are in order R,G,B,A).
    // Check for an existing material
    if( null != App.getActiveProject().getMaterialList().getMaterial( pec.name ) )
    {
            App.getActiveProject().getMaterialList().removeMaterial( pec.name );
    }
	    App.getActiveProject().getMaterialList().addMaterial( pec );
}

function CreateAntennaSource()
{
    // Here we will create our waveform, create our circuit component definition for the feed, and create
    // a CircuitComponent that will attach those to our current geometry.
    var waveformList = App.getActiveProject().getWaveformList();
        // clear the waveform list
	    waveformList.clear();

    // Create a gaussian derivative input wave
    var waveform = new Waveform();
    var GDer = new GaussianDerivativeWaveformShape ();
    GDer.pulseWidth = 2e-9;
    waveform.setWaveformShape( GDer );
    waveform.name ="Gaussian Derivative";
    var waveformInList = waveformList.addWaveform( waveform );

    // Now to create the circuit component definition:
    var componentDefinitionList = App.getActiveProject().getCircuitComponentDefinitionList();
    // clear the list
    componentDefinitionList.clear();

    // Create our Feed
    var feed1 = new Feed();
    var feed2 = new Feed();

    feed1.feedType = Feed.Voltage; // Set its type enumeration to be Voltage.
    //feed2.feedType = Feed.Voltage; // Set its type enumeration to be Voltage.

    // Define a 50-ohm resistance for this feed
    var rlc = new RLCSpecification();
    rlc.setResistance( "50 ohm" );
    rlc.setCapacitance( "0" );
    rlc.setInductance( "0" );
    feed1.setImpedanceSpecification( rlc );
    feed1.setWaveform( waveformInList );  // Make sure to use the reference that was returned by the list, or query the list directly
    feed1.name = "50-Ohm Voltage Source";
    var feedInList = componentDefinitionList.addCircuitComponentDefinition( feed1 );


	feed2.setImpedanceSpecification( rlc );
    feed2.setWaveform( waveformInList );  // Make sure to use the reference that was returned by the list, or query the list directly
    feed2.name = "50-Ohm Voltage Source 2";
    var feedInList = componentDefinitionList.addCircuitComponentDefinition( feed2 );

    // Now create a circuit component that will be the feed point for our simulation
    var componentList = App.getActiveProject().getCircuitComponentList();
    componentList.clear();

    var component1 = new CircuitComponent();
	var component2 = new CircuitComponent();

	component1.name = "Source";
	component2.name = "Source";

    component1.setAsPort( true );
    component2.setAsPort( true );
    // Define the endpoints of this feed - these are defined in world position, but you can also attach them to edges, faces, etc.
    var coordinate1 = new CoordinateSystemPosition( -x0, 0, 0);
    var coordinate2 = new CoordinateSystemPosition( x0, 0, 0);
	var coordinate3 = new CoordinateSystemPosition( 0, -x0, 0);
    var coordinate4 = new CoordinateSystemPosition( 0, x0, 0);
    component1.setCircuitComponentDefinition( feed1 );

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Hm4+ysiEz6lldlmBy8g5Yy8WB3j3O4orYpWR4FlwbNkpazhTokktreFA1vDx
/NiHyqghpzXoB50Dcfnj7SecbGBcUcc+tlsZSe6tzrHKOaD/Sb2u8Y0NXE5V
T8yRw5GAWayQ6WoDPKbqso63LUSsnw7TZOFoSf+G5eNJGxh7GOqr2mMLxX8p
KVR64khcsNQ/c9UWTocsZ0ce5kJ7satj/EUcBTluBVtNLoRz3be3jHLBzz94

####### VARIABLES: LINES TO CHECK OVER WHEN STARTING A NEW RUN ###############################################################################################
RunName='2023_04_29_Test_10'	## This is the name of the run. You need to make a unique name each time you run.
TotalGens=100			## number of generations (after initial) to run through
NPOP=24			## number of individuals per generation; please keep this value below 99
Seeds=2			## This is how many AraSim jobs will run for each individual## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
FREQ=60				## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
NNT=1000			## Number of Neutrinos Thrown in AraSim   
exp=18				## exponent of the energy for the neutrinos in AraSim
ScaleFactor=1.0			## ScaleFactor used when punishing fitness scores of antennae larger than the drilling holes
GeoFactor=1			## This is the number by which we are scaling DOWN our antennas. This is passed to many files
num_keys=4			## how many XF keys we are letting this run use
database_flag=0			## 0 if not using the database, 1 if using the database
				## These next 3 define the symmetry of the cones.
PUEO=1				## IF 1, we evolve the PUEO quad-ridged horn antenna, if 0, we evolve the Bicone
RADIUS=1			## If 1, radius is asymmetric. If 0, radius is symmetric		
LENGTH=1			## If 1, length is asymmetric. If 0, length is symmetric
ANGLE=1				## If 1, angle is asymmetric. If 0, angle is symmetric
CURVED=1			## If 1, evolve curved sides. If 0, sides are straight
A=1				## If 1, A is asymmetric
B=1				## If 1, B is asymmetric
SEPARATION=0    		## If 1, separation evolves. If 0, separation is constant
NSECTIONS=2 			## The number of chromosomes
DEBUG_MODE=0			## 1 for testing (ex: send specific seeds), 0 for real runs
				## These next variables are the values passed to the GA
REPRODUCTION=6			## Number (not fraction!) of individuals formed through reproduction
CROSSOVER=10			## Number (not fraction!) of individuals formed through crossover
MUTATION=1			## Probability of mutation (divided by 100)
SIGMA=5				## Standard deviation for the mutation operation (divided by 100)
ROULETTE=2			## Percent of individuals selected through roulette (divided by 10)
TOURNAMENT=2			## Percent of individuals selected through tournament (divided by 10)
RANK=6				## Percent of individuals selected through rank (divided by 10)
ELITE=0				## Elite function on/off (1/0)

####### VARIABLES: LINES TO CHECK OVER WHEN STARTING A NEW RUN ###############################################################################################
RunName='2023_05_01_Test_5'	## This is the name of the run. You need to make a unique name each time you run.
TotalGens=10			## number of generations (after initial) to run through
NPOP=24			## number of individuals per generation; please keep this value below 99
Seeds=10			## This is how many AraSim jobs will run for each individual## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
FREQ=60				## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
NNT=40000			## Number of Neutrinos Thrown in AraSim   
exp=19				## exponent of the energy for the neutrinos in AraSim
ScaleFactor=1.0			## ScaleFactor used when punishing fitness scores of antennae larger than the drilling holes
GeoFactor=1			## This is the number by which we are scaling DOWN our antennas. This is passed to many files
num_keys=6			## how many XF keys we are letting this run use
database_flag=0			## 0 if not using the database, 1 if using the database
				## These next 3 define the symmetry of the cones.
PUEO=1				## IF 1, we evolve the PUEO quad-ridged horn antenna, if 0, we evolve the Bicone
RADIUS=1			## If 1, radius is asymmetric. If 0, radius is symmetric		
LENGTH=1			## If 1, length is asymmetric. If 0, length is symmetric
ANGLE=1				## If 1, angle is asymmetric. If 0, angle is symmetric
CURVED=1			## If 1, evolve curved sides. If 0, sides are straight
A=1				## If 1, A is asymmetric
B=1				## If 1, B is asymmetric
SEPARATION=0    		## If 1, separation evolves. If 0, separation is constant
NSECTIONS=2 			## The number of chromosomes
DEBUG_MODE=0			## 1 for testing (ex: send specific seeds), 0 for real runs
				## These next variables are the values passed to the GA
REPRODUCTION=6			## Number (not fraction!) of individuals formed through reproduction
CROSSOVER=10			## Number (not fraction!) of individuals formed through crossover
MUTATION=1			## Probability of mutation (divided by 100)
SIGMA=5				## Standard deviation for the mutation operation (divided by 100)
ROULETTE=2			## Percent of individuals selected through roulette (divided by 10)
TOURNAMENT=2			## Percent of individuals selected through tournament (divided by 10)
RANK=6				## Percent of individuals selected through rank (divided by 10)
ELITE=0				## Elite function on/off (1/0)

####### VARIABLES: LINES TO CHECK OVER WHEN STARTING A NEW RUN ###############################################################################################
RunName='2023_05_08'	## This is the name of the run. You need to make a unique name each time you run.
TotalGens=10			## number of generations (after initial) to run through
NPOP=50			## number of individuals per generation; please keep this value below 99
Seeds=10			## This is how many AraSim jobs will run for each individual## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
FREQ=60				## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
NNT=40000			## Number of Neutrinos Thrown in AraSim   
exp=19				## exponent of the energy for the neutrinos in AraSim
ScaleFactor=1.0			## ScaleFactor used when punishing fitness scores of antennae larger than the drilling holes
GeoFactor=1			## This is the number by which we are scaling DOWN our antennas. This is passed to many files
num_keys=6			## how many XF keys we are letting this run use
database_flag=0			## 0 if not using the database, 1 if using the database
				## These next 3 define the symmetry of the cones.
PUEO=1				## IF 1, we evolve the PUEO quad-ridged horn antenna, if 0, we evolve the Bicone
RADIUS=1			## If 1, radius is asymmetric. If 0, radius is symmetric		
LENGTH=1			## If 1, length is asymmetric. If 0, length is symmetric
ANGLE=1				## If 1, angle is asymmetric. If 0, angle is symmetric
CURVED=1			## If 1, evolve curved sides. If 0, sides are straight
A=1				## If 1, A is asymmetric
B=1				## If 1, B is asymmetric
SEPARATION=0    		## If 1, separation evolves. If 0, separation is constant
NSECTIONS=2 			## The number of chromosomes
DEBUG_MODE=0			## 1 for testing (ex: send specific seeds), 0 for real runs
				## These next variables are the values passed to the GA
REPRODUCTION=3			## Number (not fraction!) of individuals formed through reproduction
CROSSOVER=36			## Number (not fraction!) of individuals formed through crossover
MUTATION=1			## Probability of mutation (divided by 100)
SIGMA=5				## Standard deviation for the mutation operation (divided by 100)
ROULETTE=20			## Percent of individuals selected through roulette (divided by 10)
TOURNAMENT=20			## Percent of individuals selected through tournament (divided by 10)
RANK=60				## Percent of individuals selected through rank (divided by 10)
ELITE=0				## Elite function on/off (1/0)

####### VARIABLES: LINES TO CHECK OVER WHEN STARTING A NEW RUN ###############################################################################################
RunName='2023_08_30_realized_curved'	## This is the name of the run. You need to make a unique name each time you run.
TotalGens=100			## number of generations (after initial) to run through
NPOP=50				## number of individuals per generation; please keep this value below 99
Seeds=5			## This is how many AraSim jobs will run for each individual## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
FREQ=60				## the number frequencies being iterated over in XF (Currectly only affects the output.xmacro loop)
NNT=1500			## Number of Neutrinos Thrown in AraSim   
exp=18				## exponent of the energy for the neutrinos in AraSim
ScaleFactor=1.0			## ScaleFactor used when punishing fitness scores of antennae larger than the drilling holes
GeoFactor=1			## This is the number by which we are scaling DOWN our antennas. This is passed to many files
num_keys=4			## how many XF keys we are letting this run use
database_flag=0			## 0 if not using the database, 1 if using the database
				## These next 3 define the symmetry of the cones.
RADIUS=0			## If 1, radius is asymmetric. If 0, radius is symmetric		
LENGTH=0			## If 1, length is asymmetric. If 0, length is symmetric
ANGLE=0				## If 1, angle is asymmetric. If 0, angle is symmetric
CURVED=1			## If 1, evolve curved sides. If 0, sides are straight
A=0				## If 1, A is asymmetric
B=1				## If 1, B is asymmetric
SEPARATION=0    		## If 1, separation evolves. If 0, separation is constant
NSECTIONS=1 			## The number of chromosomes
DEBUG_MODE=0			## 1 for testing (ex: send specific seeds), 0 for real runs
				## These next variables are the values passed to the GA
REPRODUCTION=6			## Number (not fraction!) of individuals formed through reproduction
CROSSOVER=36			## Number (not fraction!) of individuals formed through crossover
MUTATION=2			## Probability of mutation (divided by 100)
SIGMA=5				## Standard deviation for the mutation operation (divided by 100)
ROULETTE=10			## Percent of individuals selected through roulette (divided by 10)
TOURNAMENT=10			## Percent of individuals selected through tournament (divided by 10)
RANK=30				## Percent of individuals selected through rank (divided by 10)
ELITE=0				## Elite function on/off (1/0)
ParallelAra=1 ## Sets whether AraSim is being run on multiple threads or not