.. _appendix_a:

Appendix A: Exported Simulation State Data
-------------------------------------------

- Meta
    - Tissue Forge installation version
- Simulator
    - Associated class(es): :class:`Simulator`
    - Dimension
    - Cell layout
    - Global cutoff
    - Integrator
    - Timestep
    - Pseudo-random number generator seed
    - Simulation time at export
    - Boundary conditions
    - Maximum distance
    - Clip planes
- Universe
    - Associated class(es): :class:`Universe`
    - Simulation name
    - Particles and clusters
    - Particle types
    - Bonds, angles and dihedrals
    - Temperature
    - Kinetic energy
    - Built-in potentials
    - Built-in forces
- Boundary
    - Associated class(es): :class:`xBoundaryCondition`, :class:`BoundaryConditions`
    - Constituents (:class:`BoundaryConditions`)
    - Kind (:class:`BoundaryCondition`)
    - ID (:class:`BoundaryCondition`)
    - Velocity (:class:`BoundaryCondition`)
    - Restoration fraction (:class:`BoundaryCondition`)
    - Name (:class:`BoundaryCondition`)
    - Normal (:class:`BoundaryCondition`)
    - Potential (:class:`BoundaryCondition`)
    - Interaction cutoff (:class:`BoundaryCondition`)
- Particle
    - Associated class(es): :class:`Particle`, :class:`Cluster`
    - Total and initial forces
    - Number density
    - Velocity
    - Position
    - Creation time
    - Persistent force
    - Radius
    - Mass
    - Charge
    - ID [#f1]_
    - Type ID
    - Cluster ID
    - Particle inventory
    - Style
    - State vector
- Particle Type
    - Associated class(es): :class:`ParticleType`, :class:`ClusterParticleType`
    - ID [#f1]_
    - Mass
    - Charge
    - Radius
    - Kinetic energy
    - Potential energy
    - Target energy
    - Minimum radius
    - Dynamics
    - Name
    - Particle inventory
    - Style
    - Species
- Potential
    - Associated class(es): :class:`Potential`, :class:`DPDPotential`, :class:`CoulombRPotential`
    - Minimum cutoff (all classes)
    - Maximum cutoff (all classes)
    - Name (all classes)
    - Type (all classes)
    - Interpolation coefficients (:class:`Potential`)
    - Constituent potentials (:class:`Potential`, :class:`CoulombRPotential`)
    - Modes (:class:`CoulombRPotential`)
    - Charge (:class:`Potential`, :class:`CoulombRPotential`)
    - Screening distance (:class:`CoulombRPotential`)
    - Interaction strength coefficients (:class:`DPDPotential`)
- Force
    - Associated class(es): :class:`Force`, :class:`Berendsen`, :class:`Friction`, :class:`Gaussian`,
      :class:`CustomForce`, :class:`ForceSum`
    - Type (all classes)
    - Mean (:class:`Friction`, :class:`Gaussian`)
    - Standard deviation (:class:`Friction`, :class:`Gaussian`)
    - Magnitude (:class:`Friction`)
    - Duration (:class:`Friction`, :class:`Gaussian`)
    - Time coefficient (:class:`Berendsen`)
    - Constituent forces (:class:`ForceSum`)
- Bonds
    - Associated class(es): :class:`Bond`, :class:`Angle`, :class:`Dihedral`
    - Particle IDs
    - Creation time
    - Half life
    - Dissociation energy
    - Potential energy
    - Potential
- State and species
    - Associated class(es): :class:`state.StateVector`, :class:`state.SpeciesList`, :class:`state.SpeciesValue`, :class:`state.Species`
    - Species inventory(:class:`state.StateVector`)
    - Species values(:class:`state.StateVector`)
    - Species fluxes(:class:`state.StateVector`)
    - SBML data (:class:`state.Species`)
        - ID
        - Name
        - Type
        - Compartment
        - Initial amount / concentration
        - Substance units
        - Spatial size units
        - Units
        - Boundary condition
        - Charge
        - Conversion factor
- Style
    - Associated class(es): :class:`rendering.Style`, :class:`rendering.ColorMapper`
    - Color (:class:`rendering.Style`)
    - Color map (:class:`rendering.ColorMapper`)

.. footnotes::
.. [#f1] Not conserved on import