## Install on Linux

### Prequisites

##### Python

As a prerequisite, Python must be installed. For the recommended installation under pyenv, see Python on Linux.

##### glibc

Our BornAgain binaries (pip package and installer) are built on Debian 11 and require glibc version 2.31 or higher.

To see which glibc version is available on your system, run

    $ ldd --version

Versions for other Linux distributions can be seen at https://repology.org/project/glibc/versions

### Installation methods

##### as Python-only package

If the BornAgain GUI is not required as only Python scripting mode is to be used, then BornAgain can be installed as a Python package from the `pip` repository:

    $ python -m pip install bornagain

##### as a Debian package

A BornAgain Debian/Ubuntu package (Python and GUI) is provided by external maintainers at https://tracker.debian.org/pkg/bornagain.

The only drawback is that versions may be lagging behind, in unstable by a couple of months, in stable by several years.

##### using our installer

A Linux installer for BornAgain (GUI and Python scripting) can be downloaded from https://bornagainproject.org/ext/files/23.0/linux_x64. Choose the installer that fits your version of Python.

The installer is self-extracting and does not need root permission.

We recommend installation to a dedicated directory (here `~/ba`):

    $ chmod u+x BornAgain-23.0-python3.12-linux_x64.sh # permit execution
    $ BornAgain-23.0-python3.12-linux_x64.sh --help # show options
    $ ba_path='~/ba'
    $ mkdir $ba_path
    $ ./BornAgain-23.0-python3.12-linux_x64.sh --exclude-subdir --skip-license --prefix=$ba_path

Then the GUI can be executed:

    $ cd $ba_path
    $ ./bin/bornagain

The corresponding Python wheel is included in the folder `$ba_path/share/BornAgain/wheel/` and can be installed via a the following command:

    $ python -m pip install $ba_path/share/BornAgain/wheel/*.whl

The GUI package was tested with the standard X11 window system. If you are using the alternative Wayland window system, please let us know about your experience.

- Introduction
  - Functionality overview
  - Architectural overview

- Install or build
  - Install Python
    - Python on Linux
    - Python on Windows
    - Python on Mac
    - Python modules
  - Install BornAgain
    - Linux
    - Windows
    - MacOS
    - Development snapshot
  - Build BornAgain
    - Unix
      - Install third-party software
      - Get the source
      - Build and install BornAgain
      - Run a first simulation
    - Windows

- Graphical user interface
  - Quick Start
  - GUI overview
  - Fitting in the GUI

- Python scripting
  - Run a script
  - Understand the syntax
  - Fitting
  - Upgrading

- Reference
  - Simulation model
    - Simulation classes
      - Specular
        - Example
      - Scattering
        - Examples
          - GISAS
          - without DWBA terms
          - with specular peak
          - SAS
          - Polarized SANS
          - Monte-Carlo
      - Off-specular
        - Off-specular
      - Depth probe
        - Examples
          - Thin film
          - Transmitted modulus
          - Resonator
    - Common settings
      - Background
      - Options
        - Monte-Carlo
        - # threads
        - Average materials
        - Include specular
      - Progress monitor
  - Instrument model
    - Beam
      - Footprint
      - Beam divergence
    - Scan
      - TOF reflectometry
      - TOF resolution
      - Beam Angular Spread
      - Beam Wavelength Spread
    - Detectors
      - SphericalDetector
      - 2d detector resolution
      - Offspec detector
    - Neutron polarization
      - Spin asymmetry example
    - Examples
      - 2D detector resolution
      - Neutron polarization
        - Magnetic layer
        - Ditto, realistic instrument
        - Polarized scattering
  - Sample model
    - Materials
      - Magnetization
    - Sample
      - Layer
      - LayerStack
      - Layout
    - Roughness
      - Interface model
      - Transient
      - Cross-correlation
      - Examples
        - GISAS
        - Reflectivity
    - Particles
      - Form factor
        - Hard particles
          - Bipyramid4
          - Box
          - CantellatedCube
          - Cone
          - Cylinder
          - Dodecahedron
          - EllipsoidalCylinder
          - HemiEllipsoid
          - HorizontalCylinder
          - Icosahedron
          - PlatonicOctahedron
          - PlatonicTetrahedron
          - Prism3
          - Prism6
          - Pyramid2
          - Pyramid3
          - Pyramid4
          - Pyramid6
          - Sphere
          - SphericalSegment
          - Spheroid
          - SpheroidalSegment
          - TruncatedCube
        - Ripples
          - Bar ripple
          - Cosine ripple
          - Sawtooth ripple
        - Soft particles
          - FuzzySphere
          - Gauss
        - Custom formfactor
      - Composite particles
        - Core and shell
        - Compound particle
        - Mesocrystal
      - Examples
        - Compound particle
        - Core and shell
        - Crossing an interface
        - Mesocrystal
        - Rotation example
        - Dense cylinders
        - Dense hemispheres
        - Uncorrelated mixture
        - Polydispersity
    - Particle assemblies
      - Grating
        - 1D lattice
        - Cosine ripples in a lattice
        - Triangular ripples in a lattice
      - 2D lattice
        - Square lattice
        - Lattice orientation distribution
        - Finite square lattice
        - Lattice with basis
        - Multi-layer lattice
        - Position variance
      - Radial paracrystal
      - 2D paracrystal
      - Others
        - Size-distribution model: decoupling approximation
        - Size-distribution model: local monodisperse approximation
        - Size-distribution model: size-spacing coupling approximation
  - Model modifiers
    - Rotation
    - Distributions
  - Data types
    - Class Datafield
      - Export
      - Find intensity peaks
    - SLD profile
      - SLD profile with rough interfaces
      - SLD profile with a sliced particle layer
  - Plotting
    - Functions
    - Configuration
    - Heat map
    - LaTeX markup
    - Export
    - Plot axes in different units
  - Fitting
    - Data import
      - TIFF
    - Minimizer settings
    - Multiple datasets
    - Examples
      - Fitting with masks
      - Custom objective function
      - Fitting along slices
      - GISAS 2D fits
      - Experiment at GALAXI
      - Find background
      - Minimizer settings
      - Bayesian Sampling
      - Consecutive fitting
      - Considering uncertainties
      - External minimizer
      - External minimizer: plotting
      - Simultaneous fit of two datasets
      - Spin asymmetry fit example
      - Reflectometry: Fit Pt layer
      - Reflectometry: Fit honeycomb

- Literature
  - Babonneau2010
  - Babonneau2013
  - Croset2021
  - Lazzari2002
  - Lazzari2006
  - Pospelov2020
  - Renaud2009
  - Sears1992
  - Wuttke2021

- How to
  - Get announcements
  - Solve known problems
    - Set Python environmental variables under Windows
  - Request help or report bugs
  - Cite BornAgain

- Developers' corner
  - Configure
    - Build
    - Pyenv
  - Develop
    - Manual checks
    - Debug
    - Webdoc
    - Code analyses
  - Release
    - Manual GUI test