Installing SCONE

# Install required dependencies (Ubuntu/Debian)
sudo apt update
sudo apt install -y build-essential gfortran cmake git

# Required libraries
sudo apt install -y liblapack-dev libblas-dev libhdf5-dev

# Optional: Intel Math Kernel Library for better performance
# sudo apt install intel-mkl-full

# Clone SCONE repository (verify URL with official documentation)
git clone https://github.com/CambridgeNuclear/SCONE.git
cd SCONE

# Create build directory
mkdir build && cd build

# Configure with CMake
cmake -DCMAKE_BUILD_TYPE=Release \
      -DCMAKE_Fortran_COMPILER=gfortran \
      -DSCONE_ENABLE_HDF5=ON \
      ..

# Build using multiple cores
make -j$(nproc)

# Verify build (if tests are available)
if [ -f CTest ]; then
    ctest --output-on-failure
fi

# Set up environment (add to ~/.bashrc for persistence)
echo 'export SCONE_DIR="$HOME/SCONE"' >> ~/.bashrc
echo 'export PATH="$PATH:$SCONE_DIR/build/bin"' >> ~/.bashrc
source ~/.bashrc

# Install Homebrew if not already installed
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install required dependencies
brew install gcc cmake libomp hdf5 lapack

# Clone SCONE repository
git clone https://github.com/CambridgeNuclear/SCONE.git
cd SCONE

# Create build directory and configure with CMake
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release -DSCONE_ENABLE_HDF5=ON -DCMAKE_Fortran_COMPILER=gfortran ..

# Build using multiple cores
make -j4

# Run tests to verify installation
ctest -j4

# Add SCONE to your PATH (add to ~/.zshrc for persistence)
echo 'export PATH="$PATH:$HOME/SCONE/build/bin"' >> ~/.zshrc
source ~/.zshrc

# Install Windows Subsystem for Linux (WSL) first
# Open PowerShell as Administrator and run:
wsl --install

# After WSL is installed, launch Ubuntu and follow these steps:
sudo apt update
sudo apt install -y build-essential gfortran cmake liblapack-dev libhdf5-dev

# Clone SCONE repository
git clone https://github.com/CambridgeNuclear/SCONE.git
cd SCONE

# Create build directory and configure with CMake
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release -DSCONE_ENABLE_HDF5=ON ..

# Build using multiple cores
make -j4

# Run tests to verify installation
ctest -j4

cmake -DCMAKE_BUILD_TYPE=Debug -DSCONE_ENABLE_HDF5=ON -DSCONE_ENABLE_MPI=OFF ..

# Create a directory for nuclear data
mkdir -p ~/nuclear_data

# Download ENDF/B-VII.1 ACE-format data (or JEF-3.1.1, etc.)
cd ~/nuclear_data
curl -O https://www.nndc.bnl.gov/endf/b7.1/acefiles/ENDF-B-VII.1-neutron-293.6K.tar.gz
tar -xzf ENDF-B-VII.1-neutron-293.6K.tar.gz

# SCONE reads ACE libraries via the aceLibrary path inside the nuclearData block
# of your input file. No separate config file or environment variable is required.

git clone https://github.com/CambridgeNuclear/SCONE.git
cd SCONE
mkdir build && cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make -j4
ctest -j4

cd build
ctest -j4  # Run tests using 4 cores
ctest -R geometry  # Run only geometry-related tests
ctest -V  # Verbose output for debugging test failures

# If ctest fails, the executable may still exist - check build/ or build/bin/

# Create a minimal test input (from SCONE root directory)
cat > test_case.inp << 'EOL'
type eigenPhysicsPackage;
pop 1000; active 10; inactive 5; XSdata ce; dataType ce;
collisionOperator { neutronCE { type neutronCEstd; } }
transportOperator { type transportOperatorDT; }
geometry {
  type geometryStd; boundary (0 0 0 0 0 0); graph { type shrunk; }
  surfaces {
    cellR { id 3; type zCylinder; radius 0.63; origin (0.0 0.0 0.0); }
  }
  cells {}
  universes {
    root { id 1; type rootUniverse; border 3; fill u<999>; }
    pin { id 999; type pinUniverse; radii (0.39218 0.40005 0.45720 0.0); fills (UO2-31 Helium Zircaloy Water); }
  }
}
nuclearData {
  handles { ce { type aceNeutronDatabase; aceLibrary $SCONE_ACE; } }
  materials {
    UO2-31 { temp 600; composition { 92235.06 7.2175E-04; 92238.06 2.2253E-02; 8016.06 4.5853E-02; } }
    Water { temp 600; composition { 1001.06 6.6667E-02; 8016.06 3.3333E-02; } }
    Zircaloy { temp 600; composition { 40090.06 5.0E-03; 40091.06 1.1E-03; 40092.06 1.7E-03; 40094.06 1.7E-03; 40096.06 2.8E-04; 26000.06 1.3E-04; 14000.06 1.0E-04; } }
    Helium { temp 600; composition { 2004.06 2.4044E-04; } }
  }
}
inactiveTally {}
activeTally { fissionRate { type collisionClerk; response (fission); fission { type macroResponse; MT -6; } } }
EOL

# Set ACE path, then run:
export SCONE_ACE=/path/to/your/JEF311.aceXS   # or IntegrationTestFiles/testLib for minimal tests
./build/scone.out test_case.inp

# Create a .vscode directory in your project
mkdir -p .vscode

# Create a settings.json file for Fortran configuration
cat > .vscode/settings.json << EOL
{
  "fortran.linter.includePaths": [
    "${workspaceFolder}/src/**"
  ],
  "fortran.fortls.path": "fortls",
  "fortran.fortls.launchWith": ["fortls", "--enable_code_actions"],
  "fortran.fortls.nthreads": 4,
  "editor.formatOnSave": true,
  "editor.rulers": [100],
  "files.associations": {
    "*.inp": "fortran"
  }
}
EOL

# Create a launch.json file for debugging
cat > .vscode/launch.json << EOL
{
  "version": "0.2.0",
  "configurations": [
    {
      "type": "cppdbg",
      "request": "launch",
      "name": "Debug SCONE",
      "program": "${workspaceFolder}/build/bin/scone",
      "args": ["${file}"],
      "cwd": "${workspaceFolder}",
      "MIMode": "gdb",
      "setupCommands": [
        {
          "description": "Enable pretty-printing for gdb",
          "text": "-enable-pretty-printing",
          "ignoreFailures": true
        }
      ]
    }
  ]
}
EOL

# Install fortran-language-server
pip install fortran-language-server

# Add to your .vimrc or init.vim
# For vim-plug users
call plug#begin()
Plug 'dense-analysis/ale'  " Linting
Plug 'prabirshrestha/vim-lsp'  " Language Server Protocol
Plug 'autozimu/LanguageClient-neovim'  " For Neovim
call plug#end()

" Configure LSP
let g:ale_linters = {'fortran': ['fortls']}
let g:ale_fixers = {'fortran': ['fprettify']}
let g:ale_fix_on_save = 1

" Optional: Install fprettify for code formatting
pip install fprettify