RenderableSimulationBox

Inherits Renderable

Renders a molecular dynamics simulation with multiple molecule types in a periodic boundary box. This can for example be used to show the distribution of different molecules or atoms in a specific spatial region, such as a planet’s atmosphere.

Multiple molecules can be provided and for each the path containing the structural data and the count of molecules has to be provided. Specifying the trajectory file that describes the movement of each individual molecule in its own relative frame, is optional.

Members

Name	Documentation	Type	Description	Optional
AngularVelocity	Average angular velocity at the start of the simulation (radians/s).	Double	Value of type ‘Double’	No
CollisionRadius	Radius of the collision sphere around molecules.	Double	Value of type ‘Double’	No
LinearVelocity	Average linear velocity at the start of the simulation (m/s).	Double	Value of type ‘Double’	No
Molecules	The list of files that are used to initiate this simulation box.	Table	Table parameters	No
SimulationBox	Size of the periodic simulation box.	Vector3<double>	Value of type ‘Vector3’	No
AnimationSpeed	Playback speed of the animation (in frames per second).	Double	Value of type ‘Double’	Yes
CircleColor	Color of the circle outlining the simulation.	Vector4<double>	Value of type ‘Vector4’	Yes
CircleFalloff	Falloff exponent of the circle outlining the simulation.	Double	Value of type ‘Double’	Yes
CircleWidth	Width of the circle outlining the simulation.	Double	Value of type ‘Double’	Yes
Coloring	Uniform, The color mapping for the atoms.	String	In list { Cpk, AtomIndex, ResId, ResIndex, ChainId, ChainIndex, SecondaryStructure }	Yes
DimInAtmosphere	Decides if the object should be dimmed (i.e. faded out) when the camera is in the sunny part of an atmosphere.	Boolean	Value of type ‘Boolean’	Yes
Enabled	Determines whether this object will be visible or not.	Boolean	Value of type ‘Boolean’	Yes
Filter	The filter used to remove parts of the dataset.	String	Value of type ‘String’	Yes
Opacity	This value determines the opacity of this renderable. A value of 0 means completely transparent.	Double	In range: ( 0, 1)	Yes
RenderBinMode	A value that specifies if the renderable should be rendered in the Background, Opaque, Pre-/PostDeferredTransparency, Overlay, or Sticker rendering step.	String	In list { Background, Opaque, PreDeferredTransparent, Overlay, PostDeferredTransparent, Sticker }	Yes
Representation	The visual representation type to use for the molecule.	String	In list { SpaceFill, Licorice, Ribbons, Cartoon }	Yes
RepScale	Thickness of the atoms when using the Space Fill or Licorice representations.	Double	Value of type ‘Double’	Yes
SimulationSpeed	Adjust the speed of the simulation (seconds per second).	Double	Value of type ‘Double’	Yes
Tag	A single tag or a list of tags that this renderable will respond to when setting properties.	Table, or String	Value of type ‘Table’, or Value of type ‘String’	Yes
Type	The type of the renderable.	String	Value of type ‘String’	Yes

Inherited members from Renderable

Name	Documentation	Type	Description	Optional
DimInAtmosphere	Decides if the object should be dimmed (i.e. faded out) when the camera is in the sunny part of an atmosphere.	Boolean	Value of type ‘Boolean’	Yes
Enabled	Determines whether this object will be visible or not.	Boolean	Value of type ‘Boolean’	Yes
Opacity	This value determines the opacity of this renderable. A value of 0 means completely transparent.	Double	In range: ( 0, 1)	Yes
RenderBinMode	A value that specifies if the renderable should be rendered in the Background, Opaque, Pre-/PostDeferredTransparency, Overlay, or Sticker rendering step.	String	In list { Background, Opaque, PreDeferredTransparent, Overlay, PostDeferredTransparent, Sticker }	Yes
Tag	A single tag or a list of tags that this renderable will respond to when setting properties.	Table, or String	Value of type ‘Table’, or Value of type ‘String’	Yes
Type	The type of the renderable.	String	Value of type ‘String’	Yes

Table parameters for Molecules

The list of files that are used to initiate this simulation box.

• Optional: No

Name	Documentation	Type	Description	Optional
*		Table	Table parameters	Yes

Table parameters for *

• Optional: Yes

Name	Documentation	Type	Description	Optional
Count	How many of this type of molecule should be rendered in the simulation box.	Integer	Greater or equal to: 0	No
MoleculeFile	The path to a molecule file that contains the structural information for the molecule.	String	Value of type ‘String’	No
TrajectoryFile	If provided, this trajectory file is used to move the individual atoms of the molecule. In addition, each molecule as a whole will be moving through the simulation box on a straight path, even if no trajectory file is provided.	String	Value of type ‘String’	Yes

Asset Examples

local marsAsset = asset.require("scene/solarsystem/planets/mars/globe")



local moleculeCO2 = asset.resource({
  Name = "Molecule CO2",
  Type = "HttpSynchronization",
  Identifier = "molecule_dynamics_co2",
  Version = 1
})


local Latitude = 58.5877
local Longitude = 16.1924

local MarsMolecules1km = {
  Identifier = "MarsMolecules1km",
  Parent = marsAsset.Mars.Identifier,
  Transform = {
    Translation = {
      Type = "GlobeTranslation",
      Globe = marsAsset.Mars.Identifier,
      Latitude = Latitude,
      Longitude = Longitude,
      Altitude = 1000.0
    }
  },
  Renderable = {
    Type = "RenderableSimulationBox",
    Molecules = {
      {
        MoleculeFile = moleculeCO2 .. "co2.arc",
        TrajectoryFile = moleculeCO2 .. "co2.arc",
        Count = 1
      }
    },
    LinearVelocity = 10.0,
    AngularVelocity = math.rad(60.0),
    SimulationBox = { 100.0, 100.0, 100.0 },
    CollisionRadius = 2.0,
    AnimationSpeed = 100
  },
  Tag = { "molecule_visualization", "molecule_atmosphere" },
  GUI = {
    Name = "Mars 1km",
    Path = "/Microcosmos/Atmosphere",
    Description = [[Visualizes Mars' atmosphere at a height of approximately 1km above the
      surface. As Mars' atmosphere almost exclusively consists of carbon dioxide, only
      that molecule is shown in the simulation box at an approximate density.]]
  }
}


asset.onInitialize(function()
  openspace.addSceneGraphNode(MarsMolecules1km)
end)

asset.onDeinitialize(function()
  openspace.removeSceneGraphNode(MarsMolecules1km)
end)

asset.export(MarsMolecules1km)



asset.meta = {
  Name = "Mars Atmosphere",
  Description = [[Visualizes Mars' atmosphere at the molecular scale.]],
  Author = "OpenSpace Team",
  URL = "https://openspaceproject.com",
  License = "MIT license"
}