This class performs the different steps to solve the equations of motion via molecular dynamics simulation, simple grancanonical simulation in Monte Carlo and solution of 1d differential equations. More...

#include <Forces.h>

Inheritance diagram for Forces:

List of all members.

Public Types
typedef void(Forces::*	CALC_THERM )()
	Pointer type to the potential function.
typedef double(Forces::*	TENS_REF )(double Pos1, double Pos2, double PosP1, double PosP2)
	Data type for distance/field functions.
Public Member Functions
	Forces (int argc, char *argv, int NPart, char ConfFile)
	Create an initial system and choose the simulation thecnique.
	Forces (int argc, char *argv, char ConfFileExt, char *Snapshot)
	Read an initial system and choose the simulation thecnique.
void	Shout (const char *s,...)
	Internal message.
void	AllocMethod ()
	Allocated the structures needed for the corresponding simulation method.
void	PrepareSys ()
	Calculate some initial quantities for the succesive calculations.
void	PrepareParallel (int argc, char **argv)
	Create the grid for the parallelisation.
	~Forces ()
	Frees the memory.
void	Info ()
	System's info.
int	ReadConfDinamica (char *File)
	Read the config file.
void	InitConst ()
	Read the config file.
int	ReSetNPart (int NewNPart)
	Realloc the number of particles.
int	ReSetNChain (int NewNChain)
	Realloc the number of chains.
void	ReSetNPCh (int NewNPCh)
	Set a new number of particle per chain.
void	ReOpen (char *FName, int Bf)
	Open a new file.
void	FillMatrix ()
	Fill the entries of the interaction matrix.
void	StudySys ()
	Obtain informations for a better performance in inserting the chains.
int	MinHelfrich ()
	Minimum of the Helfrich Hamiltonian.
int	DynIntegration ()
	Boh.
void	Dynamics ()
	Sum up all the forces and update the positions.
void	Solve ()
	Solve a system of four oder differential equation.
void	SolveLinks ()
	Solve a system of four oder differential equation of particles connected by links.
void	SolveLinksSparse ()
	Solve a system of four oder differential equation of particles connected by links.
void	SolveLinksIterative ()
	Solve a system of four oder differential equation of particles connected by links.
void	SolveRod ()
	Solve a system of four oder differential equation of particles connected by links.
void	SolveLeaves ()
	Solve a system of four oder differential equation of particles in a line.
int	Update ()
	Boh.
void	VelVerletRigid ()
	Velocity Verlet for a rigid body, first step.
void	VelVerletRigid2 ()
	Velocity Verlet for a rigid body, second step.
int	IfMetropolis (double ExpArg, double Weight)
	Metropolis acceptance criterium.
int	InsertBead (int p)
	Insert a particle in the box.
void	IgnoreCh (int c)
	Ignore a chain in the system (densities, pairlist)
void	RemChFromSys (int c)
	Delete a chain in the system.
void	SaveCh (int c)
	Save the chain configuration.
void	ReInsertCh (int c)
	Reinsert the chain in the previous position.
void	ConsiderCh (int c)
	Consider a chain in the system (densities, pairlist)
double	InsertCh (int c)
	Displace a chain in the box.
double	InsertRest (int pCurr, int StartPos)
	Build the rest of the chain.
double	RemoveChBias (int c)
	Remove a chain in the box.
double	InsertChBias (int c)
	Put a chain in the box.
double	WeightSetBond (int p, int t)
	Weight a set of bonds for the configurational bias.
double	CreateSetBond (int p, int t)
	Create a set of bonds for the configurational bias.
int	MoveBead (int p)
	Move a particle in the box.
int	TryInsert ()
	Trial insertion.
int	TryRemove ()
	Trial removal.
int	TryMove ()
	Trial movement.
int	TryMoveCh ()
	Trial desplacement of a chain.
int	TryInsertCh ()
	Trial insertion of a chain.
int	TryRemoveCh ()
	Trial removal of a chain.
int	TryInsertChBias ()
	Trial biased insertion of a chain.
int	TryRemoveChBias ()
	Trial biased removal of a chain.
void	WidomInsert (double *NrgDiff)
	Widom insertion.
void	WidomRemove (double *NrgDiff, int p)
	Widom removal.
void	WidomInsertCh (double *NrgDiff)
	Widom insertion.
void	WidomRemoveCh (double *NrgDiff, int c)
	Widom removal.
void	WidomBiasChIn (double *Weight)
	Widom with Rosenbluth weight.
void	WidomBiasChOut (double *Weight, int c)
	Widom with Rosenbluth weight.
void	VelVerlet1 ()
	First step of the velocity Verlet.
void	LangevinTherm ()
	Langevin thermostat.
void	AndersenTherm ()
	Andersen thermostat.
void	BerendsenTherm ()
	Berendsen thermostat.
void	NoTherm ()
	No thermostat.
void	VelVerlet2 ()
	Second step of the velocity Verlet.
void	ChooseThermostat (int Mode)
	Choose a calculation mode.
void	ApplyTherm ()
	Pointer to the energy function.
int	ForceFieldLine ()
	Helfrich Hamiltonian for a line.
int	SumSomeForces (int HowMany)
	Boh.
int	ForceFieldLeaves ()
	Helfrich Hamiltonian with an elastic coupling.
int	ForceFieldBulk ()
	Armonic potential on a lattice.
void	ForceFieldRod ()
	Bending potential on a rod.
void	ForceFieldRigid ()
	Interaction between rigid bodies.
void	CalcForcesDensFunc ()
	Calculate the forces for the density functional.
void	PrintForce ()
	Print the force and the potential.
void	GetForceField ()
	Calculate the force field summing every single contribution.
void	TabForceAlloc (int NTabExt)
	Tabulate the values of the force.
void	TabPot ()
	Tabulate the values of the potential.
void	NanoInteraction ()
	Calculate all the interaction with the nano.
double	NanoNrg (int p)
	Exchange energy with the nano.
double	NanoNrg (double *Pos, int t)
	Exchange energy with the nano.
void	DefForceParam ()
	Define the parameters for calculating the force.
void	DefNanoForceParam ()
	Define the parameters for calculating the force.
double	RigidLJ (int nNano, double Dist, double *Pot, double Sign)
	Force between to rigid bodies.
double	RigidHamaker (int n, double Dist, double *Pot, double Sign)
	Hamaker potential.
double	RigidCoulomb (int nNano, double Dist, double *Pot, double Sign)
	Force between to rigid bodies.
double	RigidDistanceRad (int n, int nn, double *dr)
	Distance between two bodies.
double	RigidDistanceAxis (int n, int nn, double *dr)
	Distance between two bodies.
void	PointShape (int iShape)
double	Harmonic (double Dist2, int t1, int t2, double *Pot)
	Harmonic potential.
double	StepPot (double Dist2, int t1, int t2, double *Pot)
	Step potential.
double	ElectroPot (double Dist2, int t1, int t2, double *Pot)
	Potential for the electrical lines.
double	LJ39 (double Dist2, int t1, int t2, double *Pot)
	Integrated Lennard Jones potential.
double	LJPot (double Dist2, int t1, int t2, double *Pot)
	Classical Lennard Jones potential.
double	Potential (double Dist, int t1, int t2, double *Pot)
	Pointer to a potential.
double	CalcTotNrgCh ()
	Calculate and sum up the energy of the chains.
double	CalcTotNrgBead ()
	Calculate and sum up the energy of the part.
double	CalcNrgBead (int p, double *Pot)
	Pointer to the energy function.
double	CalcNrgCh (int c, double *Pot)
	Pointer to the chain energy function.
double	NrgChBondDens (int c, double *Pot)
	Calculate the bond and the density functional energies.
double	NrgChDens (int c, double *Pot)
	Calculate the density functional energies.
double	CalcPairwise (int p, double *Pot)
	Calculate the non bonded interaction energy with the neighbouring particles.
double	CalcPairwiseCh (int c, double *Pot)
	Calculate the non bonded interaction energy with the neighbouring particles.
double	CalcBending (int p)
	Calculate the bonded interaction energy with the neighbouring particles.
double	CalcSpring (int p)
	Calculate the spring interaction energy with the neighbouring particles.
double	CalcBonded (int p, double *Pot)
	Calculate the spring and the bonded interactions with the other monomers in the chain.
double	CalcBendingGhost (double *Pos, int pExt)
	Calculate the bending energy for a ghost particle.
double	CalcBondedCh (int c, double *Pot)
	Calculate the bonded and spring interaction in a cell.
void	CalcNrgBeadDensFunc ()
	Calculate the spring, bending and non bonded interactions and write it in OldNrgPm.
double	CalcNrgBeadDensFunc (int p, double *Pot)
	Calculate the spring, bending and non bonded interactions.
double	CheckDomDec (int p)
	Check if all the particles are taken in account.
void	CheckPairList ()
	Check the pair list.
double	SumForcesMD ()
	Iterate all over the particles and calculate the forces.
double	Wei3 (const double r, const double a)
	Cubic weighting function.
double	DerWei3 (const double r, const double a)
	Derivative of the cubic weighting function.
double	Wei2 (const double r, const double b)
	Quadratic weighting function.
double	DerWei2 (const double r, const double b)
	Derivative of the quadratic weighting function.
double	DensFuncNrgGhost (double *Pos, int p1, int t1)
	Calculation of the energy from the density functional Hamiltonian for the ghost particle.
double	DensFuncNrgGhostInternal (double *Pos, int p1, int t1)
	Calculation of the energy from the density functional Hamiltonian for the ghost particle.
double	DensFuncNrgBead (int p1)
	Calculation of the energy from the density functional Hamiltonian for the particle p1.
double	DensFuncNrgCh (int c, double *Pot)
	Calculate the energy from the density functional Hamiltonian for the chain c.
double	DensFuncNrgChAv (int c)
	Calculate the average energy from the density functional Hamiltonian for the chain c.
double	DensFuncNrgChInternal (int c)
	Calculate the average energy from the density functional Hamiltonian for the chain c.
double	DensFuncNrgSys ()
	Calculation of the energy from the density functional Hamiltonian for the system.
void	CalcDens (int pInit, int pEnd)
	Calculate the local density for the particles between pInit and pEnd.
void	ClearDens ()
	Set the local densities to zero.
double	NrgStep (int p)
	The energy is constant within the cutoff.
double	NrgStepCh (int c, double *Pot)
	The energy per chain is constant within the cutoff.
double	NrgElectro (int p)
	Energy of an electric line.
int	AddDens (int pInit, int pEnd)
	Add the densities connected with the particles between pInit and pEnd.
int	RemDens (int pInit, int pEnd)
	Substract the densities connected with the particles between pInit and pEnd.
double	SumDens (int pInit, int pEnd)
	Sum the local density for the particles between pInit and pEnd and multiply the factors by the virial coefficients.
int	ListNeiCell (int p, double Pos, int NeiList)
	List of the cells close to the particle position.
void	PullBead ()
	Move a particle.
void	PushBead ()
	Move a particle.
void	SelectBead (int p)
	Select a particle.
void	Wave ()
	Sinusoidal surface wave.
void	AddCircle (int nNano)
	Add a circle as a boundary condition.
void	AddCylinder (int nNano)
	Add a cylinder as a boundary condition.
void	AddPore (int nNano)
	Add a pore as a boundary condition.
void	AddRigid ()
	Add all rigid bodies as a boundary condition.
double	HeightBoundary (double *Pos, int dir)
	Height of the boundary condition depending on the direction.
void	CreateInitial ()
	Create an initial configuration and an appropriate force field.
void	Create2d ()
	Create a plane of connected beads.
void	Create3d ()
	Create a lattice of connected beads.
void	CreateLeaves ()
	Create two connected sheets and add a protein.
void	CreateStalk ()
	Create the 1d representation of a stalk.
void	CreatePore ()
	Create the 1d representation of a pore.
void	Create1d ()
	Create single line of connected monomers.
void	CreateRigid ()
	Create rigid bodies.
void	CreateMC ()
	Create a initial disposition of particle for the MC sim.
void	CreateMD ()
	Create a initial disposition of particle for the MD sim.
void	CreateRod ()
	Create a initial disposition of particle for a stiff rod.
void	CreateElectro ()
	Create a initial disposition of houses to collect on a line.
void	AllocTens ()
	Alloc the pressure profile.
void	CalcTens ()
	Calculate the forces for the tension profile.
void	CalcDens ()
	Calculate the densities.
double	TensRefCart (double Pos1, double Pos2, double PosP1, double PosP2)
	Particle positions back folded on the tension reference point (Cartesian coordinates)
double	TensRefPol (double Pos1, double Pos2, double PosP1, double PosP2)
	Particle positions back folded on the tension reference point (polar coordinates)
double	TensRef (double Pos1, double Pos2, double PosP1, double PosP2)
	Particle positions back folded on the tension reference point.
void	SumTens (int p1, int p2, double Forces, double *DistRel)
	Sum the forces on the line joining the points p1 and p2.
void	SumTens (int p1, int p2, double *Pre)
	Sum the forces on the line joining the points p1 and p2.
void	SumTens (double Pos1, double Pos2, double *Pre)
	Sum the forces on the line joining the points p1 and p2.
void	WriteTens (char *TFile, int Comp, double InvNFile)
	Write the pressure and density profile.
void	WriteTens2d (FILE *FWrite, int Comp, double InvNFile)
	Write the 2d pressure profile.
void	ExplorePepSize ()
	Find the minimun bilayer thickness for different peptide sizes.
void	ExplorePepSize2d ()
	Find the minimun bilayer thickness for different peptide sizes.
void	ExploreDoubleMin ()
	Find the minimum for different interpeptide distances.
void	CalcTotNrg (char *FName, int nFile)
	Total energy of the system.
void	CalcNrgPep (char *File2Open, int f)
	Exchange energy of the protein.
void	RunDynamics ()
	Run a step further.
void	RunWidom (char *File2Read, int f)
	Build the widom histograms.
void	RunWidomChIn (char *File2Read, int f)
	Build the widom histograms.
void	RunWidomChOut (char *File2Read, int f)
	Build the widom histograms.
void	RosenIn (FILE *WidomIn)
	Rosenbluth weights for insertion.
void	RosenOut (FILE *WidomIn)
	Rosenbluth histograms for deletion.
void	RunWidomBiasChOut (FILE *WidomOut)
	Build the widom histograms with Rosenbluth weight.
void	ChooseSimMode ()
	Choose the simulation method.
void	Task ()
	Perform a operation every time step.
void	CalcTens (char *argv, int FilePos, int NFile)
	Calculate and sum up the pressure profile from the file list.
void	AvForces (char *argv, int FilePos, int NFile)
	Average of the forces.
void	Trial ()
	Trial loop.
void	MinimalMD ()
	Minmal md.
double	MinimalNrg ()
	Minmal nrg.
void	Sim1d ()
	Simulation loop for 1d.
void	Sim2d ()
	Simulation loop for 2d.
void	Sim3d ()
	Simulation loop for 1d.
void	SimLeaves ()
	Simulation loop for leaves.
void	SimRigid ()
	Simulation loop for rigid.
void	MinimizeSol ()
	Iterative process to approach to the solution.
int	Interp ()
	Show interpolating lines.
int	Graphics (int argc, char **argv)
	Initialize the scene.
void	keyboard (unsigned char key, int x, int y)
	Additional key bindings.
void	DrawSoil ()
	Two dimensional soil.
void	DrawCarpet ()
	Two dimensional surface.
void	DrawParticles ()
	Alternative drawing of the particle position.
void	DrBondLine (int p)
	Alternative drawing of the particle position.
void	DrawScene ()
	Draw the scene.
void	DrawNano ()
	Draws cylinder or spheres.
void	DynamicsView ()
	Idle function to run the dynamics.
void	Menu ()
	Menu.
Public Attributes
CALC_THERM	CalcTherm
	Pointer to the energy calculation function.
TENS_REF	Tens_Ref
	Pointer to a coordinate distance.
double	IncrDist
	Step to move a particle.
double	Deltat
	Time step.
double	NChemPotId
	Equilibrium number of particles/chains.
double	ChemPotId
	Chemical potential of the particles.
double	ChemPotEx
	Chemical potential of the particles.
double	GaussVar
	Standard deviation of the gaussian chain.
double	CutOff
	Cut off of the interactions.
double	Dx
	Spatial separation between particles.
double	Viscosity
	Viscosity of the medium.
double	Time
	Total time.
double	NrgPBead
	Average energy per particle.
int	Bead2Move
	Bead to move.
int	Old2Move
	Old part to move.
int	IntMax
	Boh.
int	nEdge [3]
	Number of particle per edge.
int	SysShape
	Shape of system.
int	CalcMode
	Calculation mode.
int	ThermMode
	Thermostat mode.
int	SimLimit
	Maximum number of time steps.
int	SysAlloc
	Which arrays are allocated.
int	IfInterp
	If interpolates with the splines.
int	IfLeaves
	Boh.
int	IfMove
	Boh.
int	IfNano
	Boh.
int	IfFillMatrix
	If the matrix has to be changed.
int	IfExit
	Exit from the loop.
int	NInsertion
	Count accepted moves.
int	NRemoval
	Count accepted moves.
int	NFile [2]
	First and last file of the list.
int	NUpdate
	How many timesteps before redrawing.
int	NWrite
	How many timesteps before write the snapshot.
int	NSpline
	Total number of points for drawing a spline.
KFORCES	Kf
	Prefactor of the forces.
FORCES *	Fm
	Array containing the forces for each particle.
TENS	Tens
	Structure for the pressure calculation.
DomDec *	Pc
	Pair list.
PART *	Pl
	Splines.
SingProc *	Proc
GLuint *	Cylinder
	List referring the cylinder.
GLuint	Particles
	List referring the particle.
int	NShow
	Boh.
int	IfMovie
	Produce the images for the video.
int	Frame
	Current number of frame.
int	IfExt
	Boh.
int	IfSpline
	Boh.
int	IfRot
	Boh.
int	IfSphere
	Visualize spheres or points.
int	BeadType
	Boundary condition for a single particle.
int	menu
	Menu identifier.
int	submenu
int	IfLine
	Boh.

Detailed Description

This class performs the different steps to solve the equations of motion via molecular dynamics simulation, simple grancanonical simulation in Monte Carlo and solution of 1d differential equations.

Definition at line 223 of file Forces.h.

Member Function Documentation

void StudySys ( )

Obtain informations for a better performance in inserting the chains.

a

Definition at line 488 of file ForcesIntegration.cpp.

References VarData::CNorm, VarData::InterBSpline1D(), VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, VarData::pNChain(), and VarData::pNPCh().

Referenced by ReadConfDinamica().

void Solve ( )

Solve a system of four oder differential equation.

Solve a differential equation.

Definition at line 9 of file ForcesLoop.cpp.

References SolveLeaves(), SolveLinksIterative(), SolveRod(), and SysShape.

Referenced by ExploreDoubleMin(), ExplorePepSize(), ExplorePepSize2d(), and keyboard().

void SolveLinks ( )

Solve a system of four oder differential equation of particles connected by links.

a

Definition at line 109 of file ForcesIntegration.cpp.

References AddRigid(), Matrice::Apply(), VarData::CNorm, FillMatrix(), VarData::Pm, VarData::pNPart(), and PART::Pos.

void SolveLinksIterative ( )

Solve a system of four oder differential equation of particles connected by links.

It uses Jacobi iterative method to converge to the solution.

Definition at line 47 of file ForcesIntegration.cpp.

References SPLINE::a0, SPLINE::a1, SPLINE::a2, SPLINE::a3, SPLINE::a4, AddRigid(), VarData::CLat1, VarData::CNorm, KFORCES::El, Kf, KFORCES::Lap, LINKS::Link, VarData::Ln, VarData::NEdge, VarData::pEdge(), VarData::Pm, VarData::pNPart(), PART::Pos, Matrice::Print(), KFORCES::SLap, and Matrice::Val().

Referenced by Solve().

void SolveRod ( )

Solve a system of four oder differential equation of particles connected by links.

a

Definition at line 29 of file ForcesIntegration.cpp.

References Matrice::Apply(), VarData::CNorm, VarData::pEdge(), VarData::Pm, VarData::pNPart(), and PART::Pos.

Referenced by Solve().

void SolveLeaves ( )

Solve a system of four oder differential equation of particles in a line.

a

Definition at line 5 of file ForcesIntegration.cpp.

References AddRigid(), Matrice::Apply(), VarData::CNorm, VarData::Pm, VarData::pNChain(), VarData::pNPCh(), and PART::Pos.

Referenced by Solve().

void VelVerletRigid ( )

Velocity Verlet for a rigid body, first step.

Update the position of a rotating cylinder.

Definition at line 321 of file ForcesIntegration.cpp.

References NANO::AMom, Vettore::Angle(), NANO::AVel, NANO::Axis, VarData::BackBone(), Matematica::Casuale(), Matrice::CopyOn(), Vettore::Export(), NANO::Force, NANO::Gamma, NANO::Height, NANO::Mass, VarData::Mat, Matrice::Mult(), VarData::Nano, Vettore::Normalize(), VarData::pDeltat(), VarData::pEdge(), VarData::pNNano(), NANO::Pos, NANO::Rad, Matrice::Set(), Matrice::Transpose(), NANO::Vel, Vettore::VetV(), Vettore::x, and NANO::Zeta.

Referenced by Dynamics(), and SimRigid().

void VelVerletRigid2 ( )

Velocity Verlet for a rigid body, second step.

a

Definition at line 382 of file ForcesIntegration.cpp.

References NANO::AMom, NANO::AVel, NANO::Force, NANO::Mass, VarData::Nano, VarData::pDeltat(), VarData::pNNano(), and NANO::Vel.

int IfMetropolis	(	double	ExpArg,
		double	Weight
	)

Metropolis acceptance criterium.

The general version of the Metropolis algorythm.

Definition at line 394 of file ForcesIntegration.cpp.

References Matematica::Casuale(), VarData::Mat, and VarData::pBeta().

Referenced by TryInsert(), TryInsertCh(), TryInsertChBias(), TryMove(), TryMoveCh(), TryRemove(), TryRemoveCh(), and TryRemoveChBias().

int InsertBead ( int p )

Insert a particle in the box.

Insert a particle in the system and in the cell list.

Definition at line 404 of file ForcesIntegration.cpp.

References DdLinkedList::AddPart(), Matematica::Casuale(), VarData::Mat, Pc, VarData::pEdge(), VarData::Pm, and PART::Pos.

Referenced by TryInsert(), and WidomInsert().

void IgnoreCh ( int c )

Ignore a chain in the system (densities, pairlist)

a

Definition at line 532 of file ForcesIntegration.cpp.

References Pc, VarData::Pm, VarData::pNPCh(), PART::Pos, RemDens(), and DdLinkedList::RemPart().

Referenced by ReInsertCh(), and TryMoveCh().

void RemChFromSys ( int c )

Delete a chain in the system.

a

Definition at line 540 of file ForcesIntegration.cpp.

References AddDens(), Pc, VarData::Pm, VarData::pNChain(), VarData::pNPart(), VarData::pNPCh(), PART::Pos, RemDens(), DdLinkedList::RemPart(), ReSetNChain(), ReSetNPart(), VarData::SwapChain(), and DdLinkedList::SwapPart().

Referenced by TryInsertCh(), TryInsertChBias(), TryRemoveCh(), TryRemoveChBias(), WidomBiasChIn(), and WidomInsertCh().

void SaveCh ( int c )

Save the chain configuration.

a

Definition at line 569 of file ForcesIntegration.cpp.

References VarData::Pm, VarData::pNPCh(), and PART::Pos.

Referenced by TryMoveCh().

void ReInsertCh ( int c )

Reinsert the chain in the previous position.

a

Definition at line 580 of file ForcesIntegration.cpp.

References ConsiderCh(), IgnoreCh(), VarData::Pm, VarData::pNPCh(), and PART::Pos.

Referenced by TryMoveCh().

void ConsiderCh ( int c )

Consider a chain in the system (densities, pairlist)

a

Definition at line 524 of file ForcesIntegration.cpp.

References AddDens(), DdLinkedList::AddPart(), Pc, VarData::Pm, VarData::pNPCh(), and PART::Pos.

Referenced by InsertCh(), and ReInsertCh().

double InsertCh ( int c )

Displace a chain in the box.

Insert a chain in the system and in the cell list.

Definition at line 592 of file ForcesIntegration.cpp.

References CalcMode, Matematica::Casuale(), VarData::CLat1, VarData::CLat2, VarData::CNorm, ConsiderCh(), InsertRest(), VarData::Mat, VarData::Nano, VarData::pEdge(), VarData::Pm, VarData::pNChain(), VarData::pNPart(), VarData::pNPCh(), PART::Pos, NANO::Pos, VarData::pVol(), NANO::Rad, ReSetNChain(), and ReSetNPart().

Referenced by TryInsertCh(), TryMoveCh(), and WidomInsertCh().

double InsertRest	(	int	pCurr,
		int	StartPos
	)

Build the rest of the chain.

Insert the remaining particles of the new created chain.

Definition at line 628 of file ForcesIntegration.cpp.

References Matematica::Gaussiano(), GaussVar, VarData::Mat, VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, VarData::pNPCh(), and PART::Pos.

Referenced by InsertCh().

double RemoveChBias ( int c )

Remove a chain in the box.

Remove a chain in the system calculating the weight of the super detailed balance.

Definition at line 724 of file ForcesIntegration.cpp.

References AddDens(), DdLinkedList::AddPart(), CalcBendingGhost(), DensFuncNrgGhost(), NanoNrg(), NrgPBead, Pc, VarData::Pm, VarData::pNPCh(), PART::Pos, RemDens(), DdLinkedList::RemPart(), and WeightSetBond().

Referenced by TryRemoveChBias(), and WidomBiasChOut().

double InsertChBias ( int c )

Put a chain in the box.

Create a chain choosing among a set of different bond vectors with a probability given by their Boltzmann factors.

Definition at line 766 of file ForcesIntegration.cpp.

References AddDens(), DdLinkedList::AddPart(), CalcBendingGhost(), CalcMode, Matematica::Casuale(), VarData::CLat1, VarData::CLat2, VarData::CNorm, CreateSetBond(), DensFuncNrgGhost(), VarData::Mat, VarData::Nano, NanoNrg(), NrgPBead, Pc, VarData::pEdge(), VarData::Pm, VarData::pNChain(), VarData::pNPart(), VarData::pNPCh(), PART::Pos, NANO::Pos, VarData::pVol(), NANO::Rad, ReSetNChain(), and ReSetNPart().

Referenced by TryInsertChBias(), and WidomBiasChIn().

double WeightSetBond	(	int	p,
		int	t
	)

Weight a set of bonds for the configurational bias.

Calculate the weights of a set of bonds created for the existing monomer of the chain to remove.

Definition at line 743 of file ForcesIntegration.cpp.

References CalcBendingGhost(), DensFuncNrgGhost(), Matematica::Gaussiano(), GaussVar, VarData::Mat, NanoNrg(), NrgPBead, VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, and PART::Pos.

Referenced by RemoveChBias().

double CreateSetBond	(	int	p,
		int	t
	)

Create a set of bonds for the configurational bias.

Create a set of bond vectors and choose among them one with a probability given by its Boltzmann weight.

Definition at line 816 of file ForcesIntegration.cpp.

References CalcBendingGhost(), Matematica::Casuale(), DensFuncNrgGhost(), Matematica::Gaussiano(), GaussVar, VarData::Mat, NanoNrg(), NrgPBead, VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, and PART::Pos.

Referenced by InsertChBias().

int MoveBead ( int p )

Move a particle in the box.

Give a new position for the particle p.

Definition at line 448 of file ForcesIntegration.cpp.

References Matematica::Gaussiano(), GaussVar, VarData::Mat, VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, and PART::Pos.

Referenced by TryMove().

int TryInsert ( )

Trial insertion.

a

Definition at line 413 of file ForcesIntegration.cpp.

References CalcNrgBead(), ChemPotEx, ChemPotId, IfMetropolis(), InsertBead(), Pc, VarData::Pm, VarData::pNPart(), VarData::pVol(), DdLinkedList::RemPart(), and ReSetNPart().

Referenced by Dynamics().

int TryRemove ( )

Trial removal.

a

Definition at line 432 of file ForcesIntegration.cpp.

References CalcNrgBead(), Matematica::Casuale(), ChemPotEx, ChemPotId, IfMetropolis(), VarData::Mat, Pc, VarData::Pm, VarData::pNPart(), VarData::pVol(), DdLinkedList::RemPart(), ReSetNPart(), DdLinkedList::SwapPart(), and VarData::SwapPart().

Referenced by Dynamics().

int TryMove ( )

Trial movement.

a

Definition at line 457 of file ForcesIntegration.cpp.

References CalcNrgBead(), Matematica::Casuale(), IfMetropolis(), VarData::Mat, MoveBead(), DdLinkedList::MovePart(), Pc, VarData::Pm, VarData::pNPart(), and PART::Pos.

Referenced by Dynamics().

int TryMoveCh ( )

Trial desplacement of a chain.

a

Definition at line 649 of file ForcesIntegration.cpp.

References CalcNrgCh(), Matematica::Casuale(), IfMetropolis(), IgnoreCh(), InsertCh(), VarData::Mat, VarData::pNChain(), VarData::pNPart(), VarData::pNPCh(), ReInsertCh(), ReSetNChain(), ReSetNPart(), and SaveCh().

Referenced by Dynamics().

int TryInsertCh ( )

Trial insertion of a chain.

a

Definition at line 697 of file ForcesIntegration.cpp.

References CalcNrgCh(), ChemPotEx, ChemPotId, IfMetropolis(), InsertCh(), VarData::pNChain(), VarData::pNPCh(), VarData::pVol(), and RemChFromSys().

Referenced by Dynamics().

int TryRemoveCh ( )

Trial removal of a chain.

a

Definition at line 675 of file ForcesIntegration.cpp.

References CalcNrgCh(), Matematica::Casuale(), ChemPotEx, ChemPotId, IfMetropolis(), VarData::Mat, VarData::pNChain(), VarData::pNPart(), VarData::pNPCh(), VarData::pVol(), and RemChFromSys().

Referenced by Dynamics().

int TryInsertChBias ( )

Trial biased insertion of a chain.

a

Definition at line 873 of file ForcesIntegration.cpp.

References ChemPotEx, ChemPotId, IfMetropolis(), InsertChBias(), VarData::pNChain(), VarData::pNPCh(), VarData::pVol(), and RemChFromSys().

Referenced by Dynamics().

int TryRemoveChBias ( )

Trial biased removal of a chain.

a

Definition at line 854 of file ForcesIntegration.cpp.

References Matematica::Casuale(), ChemPotEx, ChemPotId, IfMetropolis(), VarData::Mat, VarData::pNChain(), VarData::pNPart(), VarData::pNPCh(), VarData::pVol(), RemChFromSys(), and RemoveChBias().

Referenced by Dynamics().

void WidomInsert ( double * NrgDiff )

Widom insertion.

a

Definition at line 890 of file ForcesIntegration.cpp.

References CalcBendingGhost(), DensFuncNrgGhost(), InsertBead(), NanoNrg(), Pc, VarData::Pm, VarData::pNPart(), and DdLinkedList::RemPart().

Referenced by RunWidom().

void WidomRemove	(	double *	NrgDiff,
		int	p
	)

Widom removal.

a

Definition at line 901 of file ForcesIntegration.cpp.

References CalcNrgBead().

Referenced by RunWidom().

void WidomInsertCh ( double * NrgDiff )

Widom insertion.

a

Definition at line 908 of file ForcesIntegration.cpp.

References CalcNrgCh(), InsertCh(), VarData::pNChain(), VarData::pNPCh(), and RemChFromSys().

Referenced by RunWidomChIn().

void WidomRemoveCh	(	double *	NrgDiff,
		int	c
	)

Widom removal.

a

Definition at line 918 of file ForcesIntegration.cpp.

Referenced by RunWidomChOut().

void WidomBiasChIn ( double * Weight )

Widom with Rosenbluth weight.

a

Definition at line 926 of file ForcesIntegration.cpp.

References InsertChBias(), VarData::pNChain(), VarData::pNPCh(), and RemChFromSys().

Referenced by RosenIn().

void WidomBiasChOut	(	double *	Weight,
		int	c
	)

Widom with Rosenbluth weight.

a

Definition at line 935 of file ForcesIntegration.cpp.

References RemoveChBias().

Referenced by RosenOut().

void VelVerlet1 ( )

First step of the velocity Verlet.

a

Definition at line 942 of file ForcesIntegration.cpp.

References FORCES::Dir, FORCES::Ext, Fm, VarData::pDeltat(), VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, VarData::pNPart(), PART::Pos, and PART::Vel.

Referenced by Dynamics(), Sim1d(), Sim2d(), Sim3d(), SimLeaves(), and SimRigid().

void LangevinTherm ( )

Langevin thermostat.

a

Definition at line 957 of file ForcesIntegration.cpp.

References Matematica::Casuale(), FORCES::Dir, Fm, VarData::Mat, VarData::pDeltat(), VarData::Pm, VarData::pNPart(), PART::Vel, and Viscosity.

Referenced by ChooseThermostat().

void AndersenTherm ( )

Andersen thermostat.

a

Definition at line 971 of file ForcesIntegration.cpp.

References Matematica::Casuale(), Matematica::Gaussiano(), VarData::Mat, VarData::pDeltat(), VarData::Pm, VarData::pNPart(), VarData::pTemp(), and PART::Vel.

Referenced by ChooseThermostat().

void BerendsenTherm ( )

Berendsen thermostat.

a

Definition at line 984 of file ForcesIntegration.cpp.

References FORCES::Dir, Fm, VarData::pDeltat(), VarData::Pm, VarData::pNPart(), and PART::Vel.

Referenced by ChooseThermostat().

void VelVerlet2 ( )

Second step of the velocity Verlet.

a

Definition at line 1029 of file ForcesIntegration.cpp.

References FORCES::Dir, FORCES::Ext, Fm, VarData::pDeltat(), VarData::Pm, VarData::pNPart(), and PART::Vel.

Referenced by Dynamics(), Sim1d(), Sim2d(), Sim3d(), SimLeaves(), and SimRigid().

void ChooseThermostat ( int Mode )

Choose a calculation mode.

a

Definition at line 1003 of file ForcesIntegration.cpp.

References AndersenTherm(), BerendsenTherm(), CalcTherm, LangevinTherm(), and NoTherm().

Referenced by AllocMethod().

int ForceFieldLine ( )

Helfrich Hamiltonian for a line.

Use different types of splines to interpolate the points and calculate the second and forth derivative.

Definition at line 4 of file ForcesForceField.cpp.

References SPLINE::a2, SPLINE::a4, Matematica::Cubica(), FORCES::Dir, Dx, FORCES::Ext, Fm, Matematica::Forth(), IfInterp, Kf, KFORCES::Lap, VarData::Mat, Matematica::Parab(), Matematica::Parab2(), VarData::Pm, VarData::pNPart(), PART::Pos, KFORCES::SLap, Matematica::Spline3(), Matematica::Spline3Beg(), Matematica::Spline3End(), Matematica::Spline4(), and Matematica::Spline4Beg().

Referenced by Dynamics(), and Sim1d().

int ForceFieldLeaves ( )

Helfrich Hamiltonian with an elastic coupling.

Use different types of splines to interpolate the points and calculate the second and forth derivative, the two sheets have an elastic coupling.

Definition at line 130 of file ForcesForceField.cpp.

References SPLINE::a2, SPLINE::a4, FORCES::Dir, Dx, FORCES::Ext, Fm, Matematica::Forth(), Kf, KFORCES::Lap, KFORCES::LJ, VarData::Mat, VarData::Nano, VarData::NEdge, VarData::Pm, VarData::pNChain(), VarData::pNPart(), PART::Pos, NANO::Pos, NANO::Rad, KFORCES::SLap, Matematica::Spline3(), Matematica::Spline3End(), and Matematica::Spline4Beg().

Referenced by Dynamics(), and SimLeaves().

int ForceFieldBulk ( )

Armonic potential on a lattice.

Calculate the harmonic potential along the links.

Definition at line 187 of file ForcesForceField.cpp.

References FORCES::Dir, KFORCES::El, KFORCES::Elong, FORCES::Ext, Fm, Kf, LINKS::Link, VarData::Ln, LINKS::NLink, VarData::Pm, and VarData::pNPart().

Referenced by Dynamics(), and Sim3d().

void ForceFieldRod ( )

Bending potential on a rod.

Calculate the harmonic potential along the links.

Definition at line 210 of file ForcesForceField.cpp.

References FORCES::Dir, Fm, VarData::pkBen(), VarData::pkSpr(), VarData::pNBlock(), VarData::pNChain(), VarData::pNPCh(), VarData::pSprRest(), and VarData::TwoPartDist().

Referenced by Dynamics().

double RigidHamaker	(	int	n,
		double	Dist,
		double *	Pot,
		double	Sign
	)

Hamaker potential.

Hamker Physica IV 10 p 1058 (1937)

Definition at line 458 of file ForcesForceField.cpp.

References NANO::BaseLine, NANO::DistThr, NANO::ForThr, NANO::Hamaker, VarData::Nano, NANO::PotThr, and NANO::Rad.

Referenced by DefNanoForceParam(), and NanoNrg().

double CalcTotNrgCh ( )

Calculate and sum up the energy of the chains.

Fill the array OldNrgCh with the non bonded, spring and bending energy.

Definition at line 411 of file ForcesCalcEnergies.cpp.

References CalcNrgCh(), VarData::pNChain(), VarData::pNPCh(), and Shout().

Referenced by CalcTotNrg(), and RunWidomChOut().

double CalcTotNrgBead ( )

Calculate and sum up the energy of the part.

Fill the array OldNrgCh with the non bonded, spring and bending energy.

Definition at line 470 of file ForcesCalcEnergies.cpp.

References CalcNrgBead(), VarData::pNChain(), and Shout().

double NrgChBondDens	(	int	c,
		double *	Pot
	)

Calculate the bond and the density functional energies.

Calculate the bonded and non bonded energies for the chain c.

Definition at line 435 of file ForcesCalcEnergies.cpp.

References CalcBondedCh(), DensFuncNrgChInternal(), and VarData::pNPCh().

double CalcBonded	(	int	p,
		double *	Pot
	)

Calculate the spring and the bonded interactions with the other monomers in the chain.

Calculates the spring and bending force between B / \ A C.

Definition at line 29 of file ForcesCalcEnergies.cpp.

References VarData::pkBen(), VarData::pkSpr(), VarData::Pm, VarData::pNPart(), PART::Pos, and VarData::pSprRest().

Referenced by CalcNrgBeadDensFunc().

double CalcBendingGhost	(	double *	Pos,
		int	pExt
	)

Calculate the bending energy for a ghost particle.

Calculates the bending force between B / \ A C if the ghost particle C is at least the third in the chain.

Definition at line 80 of file ForcesCalcEnergies.cpp.

References VarData::pChain(), VarData::pEdge(), VarData::pInvEdge(), VarData::pkBen(), VarData::pNPCh(), and VarData::pPos().

Referenced by CreateSetBond(), InsertChBias(), RemoveChBias(), WeightSetBond(), and WidomInsert().

double CalcNrgBeadDensFunc	(	int	p,
		double *	Pot
	)

Calculate the spring, bending and non bonded interactions.

Calculate the bonded and non bonded energies for the chain c.

Definition at line 494 of file ForcesCalcEnergies.cpp.

References CalcBonded(), and DensFuncNrgBead().

double CheckDomDec ( int p )

Check if all the particles are taken in account.

Compare the pair found in the domain decomposition method with the ones found with the simple N^2 neighbours search.

Definition at line 658 of file ForcesCalcEnergies.cpp.

References DomDecBasics::cCurr, KFORCES::CutOff2, DdLinkedList::Dist2Curr(), DdLinkedList::IfCurr(), Kf, DdLinkedList::NextCurr(), DomDecBasics::p2Curr, Pc, VarData::pEdge(), VarData::pInvEdge(), VarData::pNPart(), VarData::pPos(), and DdLinkedList::SetCurr().

double DensFuncNrgCh	(	int	c,
		double *	Pot
	)

Calculate the energy from the density functional Hamiltonian for the chain c.

Calculate the bonded and non bonded energies for the chain c.

Definition at line 428 of file ForcesCalcEnergies.cpp.

References DensFuncNrgChInternal(), NanoNrg(), and VarData::pNPCh().

double NrgStep ( int p )

The energy is constant within the cutoff.

Step potential.

Definition at line 153 of file ForcesCalcEnergies.cpp.

References KFORCES::CutOff2, DdLinkedList::Dist2Curr(), DdLinkedList::IfCurr(), Kf, KFORCES::LJ, DdLinkedList::NextCurr(), DomDecBasics::p2Curr, Pc, VarData::Pm, VarData::pType(), and DdLinkedList::SetCurr().

double HeightBoundary	(	double *	Pos,
		int	dir
	)

Height of the boundary condition depending on the direction.

The boundary condition depends on the lateral distance from the border.

Definition at line 88 of file ForcesBoundary.cpp.

References NANO::Height, VarData::Nano, VarData::pNNano(), NANO::Pos, and NANO::Rad.

void ChooseSimMode ( )

Choose the simulation method.

main loop

Definition at line 3 of file ForcesLoop.cpp.

References SysShape.

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

src/Addyn/Forces.h
src/Addyn/Forces.cpp
src/Addyn/ForcesBoundary.cpp
src/Addyn/ForcesCalcEnergies.cpp
src/Addyn/ForcesCreate.cpp
src/Addyn/ForcesDraw.cpp
src/Addyn/ForcesForceField.cpp
src/Addyn/ForcesIntegration.cpp
src/Addyn/ForcesLoop.cpp
src/Addyn/ForcesTens.cpp

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