Contains simulation parameters and physical constants. More...

#include <Parameters.hpp>

Public Attributes
bool	VERBOSE_MODE = true
	Whether to print verbose output during simulation.

int	maxIterations = 1E5
	Max number of iteration.

std::string	restartInputFile = ""
	Optional checkpoint file to restart from.

std::string	checkpointOutputFile = "slimed_restart.chk"
	Checkpoint file written during minimization.

int	checkpointOutputInterval = 1000
	Iteration interval for checkpoint writes; <=0 disables checkpointing.

double	kCurv = 83.4
	Bending modulus i.e. curvature constant (kc)

double	uSurf = 250.0
	Surface area constraint i.e. surface constant (us)

double	uVol = 0.0
	Volume constraint i.e. volume constant (uv)

double	kReg = 83.4
	Coefficient of the regularization constraint (k)

double	kSpring
	Spring constant for insertion zones (K)

bool	setRelaxAreaToDefault = false
	true to set area0 equal to area of starting config

double	area0
	Target area for membrane (S0)

double	area
	Total area of the membrane (S)

double	vol0
	Target volume for membrane (V0)

double	vol
	Total volume of the membrane (V)

double	insertCurv
	Spontaneous curvature of insertions (C0)

double	spontCurv
	Spontaneous curvature of membrane (c0)

double	sideX = 100.0
	X-axis length for flat membrane.

double	sideY = 100.0
	Y-axis length for flat membrane.

double	radius = 25.0
	Radius for spherical membrane.

double	lFace = 5.0
	lFace

int	nFaceX = -1
	Number of faces (edges) along X axis for flat membrane.

int	nFaceY = -1
	Number of faces (edges) along Y axis for flat membrane.

double	dFaceX
	Initial actual face side length along X axis for flat membrane.

double	dFaceY
	Initial actual face side length along Y axis for flat membrane.

double	meanL
	Mean length of edges after subdivision.

double	sigma = 0.0
	Noise level for vertex positions.

int	subDivideTimes
	Number of times to subdivide each edge.

bool	isInsertionAreaConstraint = false
	Whether to apply area constraint to insertions.

bool	isAdditiveScheme = false
	Whether to use additive scheme for constraints.

bool	isGlobalConstraint = true
	Whether to apply global constraint across entire membrane.

double	elementTriangleArea0
	Target area for individual triangles.

int	gaussQuadratureN = 2
	Number of Gaussian quadrature points to use.

Matrix	VWU
	(N,3) matrix of vertex coordinates and weights

Matrix	gaussQuadratureCoeff
	(N,1) matrix of Gaussian quadrature coefficients

std::vector< Matrix >	shapeFunctions
	List of shape functions for each triangle.

SubdivisionMatrix	subMatrix
	Subdivision matrix for irregular patches.

BoundaryType	boundaryCondition = BoundaryType::Periodic
	Type of boundary condition ("Fixed", "Periodic", "Free")

bool	usingNCG = true
	Whether to use nonlinear conjugate gradient method.

bool	isNCGstuck = false
	Whether NCG method has gotten stuck.

double	deltaEnergyConverge = 1e-5
	Convergence criteria for total energy.

double	deltaForceScaleConverge = 1e-5
	Convergence criteria for max force scale.

double	gamaShape = 0.2
	Shape deformation coefficient.

double	gamaArea = 0.2
	Area deformation coefficient.

bool	usingRpi = true
	Whether to use R-pi adaptive method for regularization energy;.

bool	xyzOutput = true
	Whether to output XYZ coordinates of vertices.

bool	meshpointOutput = true
	Whether to output meshpoints.

bool	isEnergyHarmonicBondIncluded = false
	Whether to include energy of spline points.

std::vector< Matrix >	scaffoldingPoints
	List of spline points.

std::vector< int >	scaffoldingPoints_correspondingVertexIndex
	Corresponding vertex indices for spline points.

double	scaffoldingSphereRaidus = 50.0
	spherical radius of the scaffolding lattice cap

double	springConst = 4.5
	Spring constant for harmonic bond potential.

double	springConstScaler = 1.31607401
	Spring constant scaler per iteration interval.

int	springConstScalingInterv = 200
	Iteration interval for spring constant scaling.

int	springConstUpperBound = 1000.0
	Max spring constant to stop scaling of spring constant.

int	propagateScaffoldingInterv = 7
	Iteration interval for repositioning scaffolding based on energy and force.

int	propagateScaffoldingNstep = 100
	Number of steps every time propagating scaffolding.

double	splinePointsZcoordScaling = 0.0

double	lbond = 9.0
	Harminc bond length in nm.

double	relaxLengthRatioApproximation = 1.0
	ratio of relax length to cap length approximation

double	scaffoldingZeroPlaneZ = 0.0
	Height of the flat membrane plane around the Gag cap.

std::string	scaffoldingFileName = ""

bool	isGagScaffoldingEnergyIncluded = false
	Whether to include Gag-specific internal scaffold energy.

std::string	gagReferenceStateFileName = ""
	Extracted selected/json/*.dat file used as Gag reference geometry.

std::string	gagReactionFileName = ""
	NERDSS .inp file used to identify Gag reaction blocks.

bool	isIdealizedProteinLatticeEnergyIncluded = false
	Whether to include idealized per-instance protein lattice energy.

std::string	idealizedProteinLatticeFileName = ""
	JSON / .dat file containing the initialized idealized lattice state.

double	gagKsigma = 0.0
	Spring constant for COM-COM bond length term.

double	gagKtheta = 0.0
	Spring constant for COM-COM bond angle term.

double	gagKphi = 0.0
	Spring constant for COM-graph torsion term mapped from phi.

double	gagKomega = 0.0
	Spring constant for COM-graph torsion term mapped from omega.

double	gagFiniteDifferenceStep = 1.0e-4
	Step size used for scaffold finite-difference gradients.

double	gagPropagationStepSize = 1.0e-6
	Step size used when propagating the scaffold with Gag forces.

int	gagPreRelaxSteps = 200
	Number of Gag-only pre-relaxation steps before membrane coupling.

double	timeStep = 0.1

double	diffConst = 0.01

double	KBT = 4.17

unsigned int	randomSeed = 42
	random seed used in normal distribution

bool	surfacepointOutput = true
	whether to output surface point file

bool	thermalFluctuationEnabled = false
	Enable Metropolis thermal trial moves during minimization.

bool	thermalFluctuationPureMMC = false
	Run pure Metropolis Monte Carlo trial moves without NCG.

int	thermalFluctuationInterval = 50
	Iteration interval between thermal trial moves.

double	thermalFluctuationTemperatureKelvin = 298.0
	Effective thermodynamic temperature in Kelvin.

double	thermalFluctuationMinTemperatureKelvin = 298.0
	Lower bound for annealed temperature in Kelvin.

double	thermalFluctuationCoolingRate = 1.0
	Multiplicative cooling rate after each thermal trial.

double	thermalFluctuationStepScale = 0.02
	Gaussian displacement std. dev. as a fraction of lFace.

bool	isInsertionIncluded = false

std::vector< std::vector< int > >	insertionPatch

Energy	energy

Energy	energyPrev

DeformationCount	deformationCount

Detailed Description

Contains simulation parameters and physical constants.

The Param struct stores a variety of parameters and physical constants that are used to initialize and run a membrane simulation. This includes properties like the membrane size, shape, and subdivision, as well as boundary conditions, time step, and diffusion constant. Many of these variables have default values but can be customized by changing the corresponding member variables in a Param object.

Note that some variables in this struct are deprecated or unused and should not be relied upon for correct behavior of the simulation. These variables may be removed or modified in future versions of the code.

Member Data Documentation

◆ area

double Param::area

Total area of the membrane (S)

◆ area0

double Param::area0

Target area for membrane (S0)

◆ boundaryCondition

BoundaryType Param::boundaryCondition = BoundaryType::Periodic

Type of boundary condition ("Fixed", "Periodic", "Free")

◆ checkpointOutputFile

std::string Param::checkpointOutputFile = "slimed_restart.chk"

Checkpoint file written during minimization.

◆ checkpointOutputInterval

int Param::checkpointOutputInterval = 1000

Iteration interval for checkpoint writes; <=0 disables checkpointing.

◆ deformationCount

DeformationCount Param::deformationCount

◆ deltaEnergyConverge

double Param::deltaEnergyConverge = 1e-5

Convergence criteria for total energy.

◆ deltaForceScaleConverge

double Param::deltaForceScaleConverge = 1e-5

Convergence criteria for max force scale.

◆ dFaceX

double Param::dFaceX

Initial actual face side length along X axis for flat membrane.

◆ dFaceY

double Param::dFaceY

Initial actual face side length along Y axis for flat membrane.

◆ diffConst

double Param::diffConst = 0.01

◆ elementTriangleArea0

double Param::elementTriangleArea0

Target area for individual triangles.

◆ energy

Energy Param::energy

◆ energyPrev

Energy Param::energyPrev

◆ gagFiniteDifferenceStep

double Param::gagFiniteDifferenceStep = 1.0e-4

Step size used for scaffold finite-difference gradients.

◆ gagKomega

double Param::gagKomega = 0.0

Spring constant for COM-graph torsion term mapped from omega.

◆ gagKphi

double Param::gagKphi = 0.0

Spring constant for COM-graph torsion term mapped from phi.

◆ gagKsigma

double Param::gagKsigma = 0.0

Spring constant for COM-COM bond length term.

◆ gagKtheta

double Param::gagKtheta = 0.0

Spring constant for COM-COM bond angle term.

◆ gagPreRelaxSteps

int Param::gagPreRelaxSteps = 200

Number of Gag-only pre-relaxation steps before membrane coupling.

◆ gagPropagationStepSize

double Param::gagPropagationStepSize = 1.0e-6

Step size used when propagating the scaffold with Gag forces.

◆ gagReactionFileName

std::string Param::gagReactionFileName = ""

NERDSS .inp file used to identify Gag reaction blocks.

◆ gagReferenceStateFileName

std::string Param::gagReferenceStateFileName = ""

Extracted selected/json/*.dat file used as Gag reference geometry.

◆ gamaArea

double Param::gamaArea = 0.2

Area deformation coefficient.

◆ gamaShape

double Param::gamaShape = 0.2

Shape deformation coefficient.

◆ gaussQuadratureCoeff

Matrix Param::gaussQuadratureCoeff

(N,1) matrix of Gaussian quadrature coefficients

◆ gaussQuadratureN

int Param::gaussQuadratureN = 2

Number of Gaussian quadrature points to use.

◆ idealizedProteinLatticeFileName

std::string Param::idealizedProteinLatticeFileName = ""

JSON / .dat file containing the initialized idealized lattice state.

◆ insertCurv

double Param::insertCurv

Spontaneous curvature of insertions (C0)

◆ insertionPatch

std::vector<std::vector<int> > Param::insertionPatch

◆ isAdditiveScheme

bool Param::isAdditiveScheme = false

Whether to use additive scheme for constraints.

◆ isEnergyHarmonicBondIncluded

bool Param::isEnergyHarmonicBondIncluded = false

Whether to include energy of spline points.

◆ isGagScaffoldingEnergyIncluded

bool Param::isGagScaffoldingEnergyIncluded = false

Whether to include Gag-specific internal scaffold energy.

◆ isGlobalConstraint

bool Param::isGlobalConstraint = true

Whether to apply global constraint across entire membrane.

◆ isIdealizedProteinLatticeEnergyIncluded

bool Param::isIdealizedProteinLatticeEnergyIncluded = false

Whether to include idealized per-instance protein lattice energy.

◆ isInsertionAreaConstraint

bool Param::isInsertionAreaConstraint = false

Whether to apply area constraint to insertions.

◆ isInsertionIncluded

bool Param::isInsertionIncluded = false

◆ isNCGstuck

bool Param::isNCGstuck = false

Whether NCG method has gotten stuck.

◆ KBT

double Param::KBT = 4.17

◆ kCurv

double Param::kCurv = 83.4

Bending modulus i.e. curvature constant (kc)

◆ kReg

double Param::kReg = 83.4

Coefficient of the regularization constraint (k)

◆ kSpring

double Param::kSpring

Spring constant for insertion zones (K)

◆ lbond

double Param::lbond = 9.0

Harminc bond length in nm.

◆ lFace

double Param::lFace = 5.0

lFace

◆ maxIterations

int Param::maxIterations = 1E5

Max number of iteration.

◆ meanL

double Param::meanL

Mean length of edges after subdivision.

◆ meshpointOutput

bool Param::meshpointOutput = true

Whether to output meshpoints.

◆ nFaceX

int Param::nFaceX = -1

Number of faces (edges) along X axis for flat membrane.

◆ nFaceY

int Param::nFaceY = -1

Number of faces (edges) along Y axis for flat membrane.

◆ propagateScaffoldingInterv

int Param::propagateScaffoldingInterv = 7

Iteration interval for repositioning scaffolding based on energy and force.

◆ propagateScaffoldingNstep

int Param::propagateScaffoldingNstep = 100

Number of steps every time propagating scaffolding.

◆ radius

double Param::radius = 25.0

Radius for spherical membrane.

◆ randomSeed

unsigned int Param::randomSeed = 42

random seed used in normal distribution

◆ relaxLengthRatioApproximation

double Param::relaxLengthRatioApproximation = 1.0

ratio of relax length to cap length approximation

◆ restartInputFile

std::string Param::restartInputFile = ""

Optional checkpoint file to restart from.

◆ scaffoldingFileName

std::string Param::scaffoldingFileName = ""

◆ scaffoldingPoints

std::vector<Matrix> Param::scaffoldingPoints

List of spline points.

◆ scaffoldingPoints_correspondingVertexIndex

std::vector<int> Param::scaffoldingPoints_correspondingVertexIndex

Corresponding vertex indices for spline points.

◆ scaffoldingSphereRaidus

double Param::scaffoldingSphereRaidus = 50.0

spherical radius of the scaffolding lattice cap

◆ scaffoldingZeroPlaneZ

double Param::scaffoldingZeroPlaneZ = 0.0

Height of the flat membrane plane around the Gag cap.

◆ setRelaxAreaToDefault

bool Param::setRelaxAreaToDefault = false

true to set area0 equal to area of starting config

◆ shapeFunctions

std::vector<Matrix> Param::shapeFunctions

List of shape functions for each triangle.

◆ sideX

double Param::sideX = 100.0

X-axis length for flat membrane.

◆ sideY

double Param::sideY = 100.0

Y-axis length for flat membrane.

◆ sigma

double Param::sigma = 0.0

Noise level for vertex positions.

◆ splinePointsZcoordScaling

double Param::splinePointsZcoordScaling = 0.0

◆ spontCurv

double Param::spontCurv

Spontaneous curvature of membrane (c0)

◆ springConst

double Param::springConst = 4.5

Spring constant for harmonic bond potential.

◆ springConstScaler

double Param::springConstScaler = 1.31607401

Spring constant scaler per iteration interval.

◆ springConstScalingInterv

int Param::springConstScalingInterv = 200

Iteration interval for spring constant scaling.

◆ springConstUpperBound

int Param::springConstUpperBound = 1000.0

Max spring constant to stop scaling of spring constant.

◆ subDivideTimes

int Param::subDivideTimes

Number of times to subdivide each edge.

◆ subMatrix

SubdivisionMatrix Param::subMatrix

Subdivision matrix for irregular patches.

◆ surfacepointOutput

bool Param::surfacepointOutput = true

whether to output surface point file

◆ thermalFluctuationCoolingRate

double Param::thermalFluctuationCoolingRate = 1.0

Multiplicative cooling rate after each thermal trial.

◆ thermalFluctuationEnabled

bool Param::thermalFluctuationEnabled = false

Enable Metropolis thermal trial moves during minimization.

◆ thermalFluctuationInterval

int Param::thermalFluctuationInterval = 50

Iteration interval between thermal trial moves.

◆ thermalFluctuationMinTemperatureKelvin

double Param::thermalFluctuationMinTemperatureKelvin = 298.0

Lower bound for annealed temperature in Kelvin.

◆ thermalFluctuationPureMMC

bool Param::thermalFluctuationPureMMC = false

Run pure Metropolis Monte Carlo trial moves without NCG.

◆ thermalFluctuationStepScale

double Param::thermalFluctuationStepScale = 0.02

Gaussian displacement std. dev. as a fraction of lFace.

◆ thermalFluctuationTemperatureKelvin

double Param::thermalFluctuationTemperatureKelvin = 298.0

Effective thermodynamic temperature in Kelvin.

◆ timeStep

double Param::timeStep = 0.1

◆ usingNCG

bool Param::usingNCG = true

Whether to use nonlinear conjugate gradient method.

◆ usingRpi

bool Param::usingRpi = true

Whether to use R-pi adaptive method for regularization energy;.

◆ uSurf

double Param::uSurf = 250.0

Surface area constraint i.e. surface constant (us)

◆ uVol

double Param::uVol = 0.0

Volume constraint i.e. volume constant (uv)

◆ VERBOSE_MODE

bool Param::VERBOSE_MODE = true

Whether to print verbose output during simulation.

◆ vol

double Param::vol

Total volume of the membrane (V)

◆ vol0

double Param::vol0

Target volume for membrane (V0)

◆ VWU

Matrix Param::VWU

(N,3) matrix of vertex coordinates and weights

◆ xyzOutput

bool Param::xyzOutput = true

Whether to output XYZ coordinates of vertices.

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

include/Parameters.hpp

Public Attributes