Appendix A: Exported Simulation State Data

  • Meta

    • Tissue Forge installation version

  • Simulator

    • Associated class(es): 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): 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): xBoundaryCondition, BoundaryConditions

    • Constituents (BoundaryConditions)

    • Kind (BoundaryCondition)

    • ID (BoundaryCondition)

    • Velocity (BoundaryCondition)

    • Restoration fraction (BoundaryCondition)

    • Name (BoundaryCondition)

    • Normal (BoundaryCondition)

    • Potential (BoundaryCondition)

    • Interaction cutoff (BoundaryCondition)

  • Particle

    • Associated class(es): Particle, Cluster

    • Total and initial forces

    • Number density

    • Velocity

    • Position

    • Creation time

    • Persistent force

    • Radius

    • Mass

    • Charge

    • ID [1]

    • Type ID

    • Cluster ID

    • Particle inventory

    • Style

    • State vector

  • Particle Type

    • Associated class(es): ParticleType, ClusterParticleType

    • ID [1]

    • Mass

    • Charge

    • Radius

    • Kinetic energy

    • Potential energy

    • Target energy

    • Minimum radius

    • Dynamics

    • Name

    • Particle inventory

    • Style

    • Species

  • Potential

    • Associated class(es): Potential, DPDPotential, CoulombRPotential

    • Minimum cutoff (all classes)

    • Maximum cutoff (all classes)

    • Name (all classes)

    • Type (all classes)

    • Interpolation coefficients (Potential)

    • Constituent potentials (Potential, CoulombRPotential)

    • Modes (CoulombRPotential)

    • Charge (Potential, CoulombRPotential)

    • Screening distance (CoulombRPotential)

    • Interaction strength coefficients (DPDPotential)

  • Force

    • Associated class(es): Force, Berendsen, Friction, Gaussian, CustomForce, ForceSum

    • Type (all classes)

    • Mean (Friction, Gaussian)

    • Standard deviation (Friction, Gaussian)

    • Magnitude (Friction)

    • Duration (Friction, Gaussian)

    • Time coefficient (Berendsen)

    • Constituent forces (ForceSum)

  • Bonds

    • Associated class(es): Bond, Angle, Dihedral

    • Particle IDs

    • Creation time

    • Half life

    • Dissociation energy

    • Potential energy

    • Potential

  • State and species

    • Associated class(es): state.StateVector, state.SpeciesList, state.SpeciesValue, state.Species

    • Species inventory(state.StateVector)

    • Species values(state.StateVector)

    • Species fluxes(state.StateVector)

    • SBML data (state.Species)

      • ID

      • Name

      • Type

      • Compartment

      • Initial amount / concentration

      • Substance units

      • Spatial size units

      • Units

      • Boundary condition

      • Charge

      • Conversion factor

  • Style

    • Associated class(es): rendering.Style, rendering.ColorMapper

    • Color (rendering.Style)

    • Color map (rendering.ColorMapper)