## Python scripting

#### About

The Python application programming interface (API) enables users to run simulations and fits from the high-level programming language Python. This can be done in interactive sessions or by executing a script, using the command line, a Jupyter notebook, or an integrated development environment (IDE) like PyCharm.

Scripting is more versatile than the GUI and provides functionality that is not yet available in the GUI, or never will be. For instance, one can

- set up arbitrarily complicated combined and constrained fits;
- batch process huge data sets;
- react to a simulation or fit outcome through control clauses;
- extend the functionality of the BornAgain core, for instance by adding particle form factors or correlation functions.

##### Install

Install Python and the BornAgain Python module as explained in the installation instructions.

##### Check installation

Launch a Python shell, notebook or IDE. At the Python command prompt, enter the command

    import bornagain

If the BornAgain module is found, Python will just print the next command prompt. Otherwise it will raise a `ModuleNotFoundError`.

##### Run first example script

Run a first example script. Then read the explanation.

##### Modify some example

Finally, to start productive work, choose an example script that somehow ressembles your application problem, and modify it step by step.

Examples can be found

- in these web docs in section Script examples;
- in the BornAgain sources in directory auto/Examples.

Most examples are covered by nightly tests. If nonetheless an example does not work as expected, then please report this as a bug.

##### Further tutorials

- Fitting
- Upgrading

- 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