C2M2.MolecularDynamics.Simulation.ExampleMDSimulation Class Reference

Inheritance diagram for C2M2.MolecularDynamics.Simulation.ExampleMDSimulation:

Collaboration diagram for C2M2.MolecularDynamics.Simulation.ExampleMDSimulation:

Public Member Functions
override float	GetSimulationTime ()
override Vector3[]	GetValues ()
	Require derived classes to make simulation values available More...
override void	SetValues (RaycastHit hit)
	Receive an interaction request, and translate it onto the proper sphere More...
Vector3[]	Force (Vector3[] pos, int[][] bond_topo)
	Evaluates the forces. First will try doing for system of oscillators. Then will extend to non-bonded interactions More...
Vector3[]	angle_Force (Vector3[] pos)
	Compute angle forces More...
Public Member Functions inherited from C2M2.Simulation.Simulation< Vector3[], Transform[], VRRaycastableColliders, VRGrabbableColliders >
void	Initialize ()
void	Update ()
void	StartSimulation ()
	Launch Solve thread More...
void	StopSimulation ()
	Stop current Solve thread More...

Public Attributes
float	kb = 0.001987f
float	T = 100.0f
float	kappa = 6f
float	r0 = 3.65f
Public Attributes inherited from C2M2.MolecularDynamics.Simulation.MDSimulation
string	pdbPath = "PE/pe_cg.pdb"
string	psfPath = "PE/octatetracontane_128.cg.psf"
float	radius = 1f
string	shaderName = "Standard"
Color[]	atomColors = new Color[] { Color.cyan, Color.gray }
Material	bondMaterial
float	maxBondLength = 10f
MethodType	methodType = MethodType.gjI
int	timestepCount = 50000
float	timestepSize = .1f
float	gamma = 0.1f
float	boxLengthX = 58.065f
float	boxLengthY = 58.065f
float	boxLengthZ = 58.065f
Public Attributes inherited from C2M2.Simulation.Simulation< Vector3[], Transform[], VRRaycastableColliders, VRGrabbableColliders >
bool	dryRun
	Run solve code without visualization or interaction More...
bool	startOnAwake
	Should the simulation start itself in Awake? More...

Protected Member Functions
override void	Solve ()
	Molecular dynamics simulation code More...
Protected Member Functions inherited from C2M2.MolecularDynamics.Simulation.MDSimulation
override Transform[]	BuildVisualization ()
	Reads and stores PDB and PSF data, uses the data to build the system visualization More...
override void	UpdateVisChild (in Vector3[] simulationValues)
	Used here to update bond visualization. More...
Protected Member Functions inherited from C2M2.Simulation.PositionFieldSimulation
override void	OnAwakePost (Transform[] viz)
override void	UpdateVisualization (in Vector3[] simulationValues)
Protected Member Functions inherited from C2M2.Simulation.Simulation< Vector3[], Transform[], VRRaycastableColliders, VRGrabbableColliders >
abstract void	UpdateVisualization (in ValueType newValues)
	Update the visualization. This will be called once per Update() call More...
virtual void	PreSolve ()
	Called on the main thread before the Solve thread is launched More...
virtual void	OnAwakePre ()
virtual void	OnAwakePost (VizType viz)
virtual void	OnStart ()
virtual void	OnUpdate ()
virtual void	OnPause ()
virtual void	OnQuit ()

Private Member Functions
void	ResolvePBC ()

Private Attributes
Vector3[]	force = null
float	dt
int	t

Additional Inherited Members
Public Types inherited from C2M2.MolecularDynamics.Simulation.MDSimulation
enum class	MethodType { gjI , gjII , gjIII }
Protected Attributes inherited from C2M2.MolecularDynamics.Simulation.MDSimulation
float	c = -1
Dictionary< Transform, int >	particleLookup
Vector3[]	coord = null
Vector3[]	vel = null
	Velocity of each particle More...
Vector3[]	r = null
Vector3Int[]	pbcFlag = null
int[]	bonds = null
	Each two indices represents one bond. More...
int[]	angles = null
float[]	mass = null
string[]	types = null
int[][]	bond_topo = null
Protected Attributes inherited from C2M2.Simulation.Simulation< Vector3[], Transform[], VRRaycastableColliders, VRGrabbableColliders >
Mutex	mutex
	Provide mutual exclusion to derived classes More...
Properties inherited from C2M2.Simulation.Simulation< Vector3[], Transform[], VRRaycastableColliders, VRGrabbableColliders >
VizType	viz [get, protected set]

Member Function Documentation

angle_Force()

Vector3 [] C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.angle_Force

(

Vector3[]

pos

)

Compute angle forces

Force()

Vector3 [] C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.Force	(	Vector3[]	pos,
		int	bond_topo[][]
	)

Evaluates the forces. First will try doing for system of oscillators. Then will extend to non-bonded interactions

GetSimulationTime()

override float C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.GetSimulationTime

(

)

GetValues()

override Vector3 [] C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.GetValues ( )

virtual

Require derived classes to make simulation values available

Implements C2M2.Simulation.Simulation< Vector3[], Transform[], VRRaycastableColliders, VRGrabbableColliders >.

ResolvePBC()

void C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.ResolvePBC ( )

private

SetValues()

override void C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.SetValues

(

RaycastHit

hit

)

Receive an interaction request, and translate it onto the proper sphere

Solve()

override void C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.Solve ( )

protectedvirtual

Molecular dynamics simulation code

Implements C2M2.Simulation.Simulation< Vector3[], Transform[], VRRaycastableColliders, VRGrabbableColliders >.

Member Data Documentation

dt

float C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.dt

private

force

Vector3 [] C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.force = null

private

kappa

float C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.kappa = 6f

kb

float C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.kb = 0.001987f

r0

float C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.r0 = 3.65f

T

float C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.T = 100.0f

t

int C2M2.MolecularDynamics.Simulation.ExampleMDSimulation.t

private

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The documentation for this class was generated from the following file:

• C:/Users/jaros/Desktop/tempvr/virtual-reality/Assets/Scripts/C2M2/MolecularDynamics/Simulation/ExampleMDSimulation.cs