Operates and visualizes the information in the VarData class. More...

#include <ElPoly.h>

Inheritance diagram for ElPoly:

Public Types
typedef void(ElPoly::*	DRAW_PART) (int p)
	Data type for distance/field functions.

typedef void(ElPoly::*	DRAW_BOND) (double Pos1, double Pos2, float *Color)
	Data type for distance/field functions.

Public Types inherited from VarData
typedef double(VarData::*	NANO_DIST) (double *Pos, int n)
	Data type for distance/field functions.

Public Member Functions
	ElPoly (int argc, char *argv, int FilePos)
	Constructor.

	~ElPoly ()
	Desctructor.

int	DensProf (int NBin, int NSample, int Coord)
	Calculate the density profile dens. More...

void	DensProfNormalSlab (int NBin, int NSample, int Coord)
	Calculate the density profile projecting the particles on the normal density. More...

int	Diff2Files (int NBin, int How)
	Density and thickness profile arond the nanoparticle.

void	RestPress (int NBin)
	Pressure difference between the virial and the ideal gas term.

void	SlabProf (int NBin, int nNano, int Coord1)
	Thickness and density profile along Coord1. More...

void	PrintDens (FILE FileToWrite, double Plot, double LatDim, int NBin)
	Print the density profile in the surfaces representation. More...

void	RadDens2Thick (int NBin)
	Calculate the thickness from the radial density profile. More...

void	RadDens2Thick2d (int NBin)
	Calculate the thickness from the radial density profile. More...

int	Temperature (int NBin, int Coord)
	Spatial distribution of the temperature.

void	CartDens (int NBin, int nNano)
	3d (rad,norma,dens) density profile in cartesian coordinates More...

void	RadDistrF (int NBin, int How, int nNano)
	3d (rad,norma,dens) density profile with respect to a initial position radNano radCm radCmN More...

void	BondDistr (int NSample)
	Distribution of the bond lengths. More...

void	E2EDistr (int NSample)
	Distribution of end to end distances.

void	SplayDistr (int NSample)
	Distribution of end to end distances. More...

int	RadialShell (int NBin)
	Outer shell of a projected (rad,normal) graph.

int	NanoParticle (int NBin)
	Diffusion and density profile around the nanoparticle nano.

int	WormF (int Partition, int NBin)
	Density profile of a non straight worm shape membrane worm.

void	StalkF (int NSample)
	Separate the leaflets.

void	ThickFromDens (int NBin)
	Calculate the thickness profile from the density plot. More...

void	AreaDistrF (int NBin)
	Distribution of the areas around the protein.

void	RadNormPos (int NBin, int NGrid)
	Radial profile of the normal position of the particles.

int	SurfTens (int NBin)
	Radial summation of the 3d tension profile.

void	SumTens ()
	Sum more tension profile files.

int	PressTrace ()
	Trace of the pressure profile.

int	PressRadial ()
	Contour plot around the inclusion.

int	Tens2dCartRad ()
	Change the pressure profile from cartesian to radial.

void	StalkLineProfF (int NBin)
	Write the line describing a linear stalk. More...

void	Prova ()
	Dummy function to operate on a sequence of files.

void	PairCorr (int NBin, int NDim)
	1d pair correlation

int	PairCorrelationF (int NBin, int How)
	1d, 2d pair correlation of the chains pairRound pairSquare (obsolete)

int	Diffusivity ()
	Diffusivity coefficient of the chains diff.

void	DiffSlab (int NSlab)
	Diffusivity of particles starting from an initial slab.

int	ScatteringF (int NBin, int How)
	2d Scattering scatt scatt2

int	NChainPSquareF ()
	Calculates the number of chain per area area.

void	AreaCompr (int NSample)
	Calculates the number of chain per area area. More...

int	SpectrumF (int NBin)
	Calculates the 1d, 2d spectrum spe.

void	Midplane (int NBin)
	Midplanes for a sequence of snapshots.

void	SpectrumMidplane (int NBin)
	Calculates the 1d, 2d spectrum spe.

void	HeaderAverage (int nNano)
	Read the header and average the information.

void	WidomOut (char *InFile, int NBin)
	Create a system file with a chain less and the information about the missing chain.

void	WidomOut ()
	Create NCh systems with a chain less.

void	WidomIn (char *InFile, int NBin)
	Create the histogram of the energy of adding lipids.

void	WidomIn ()
	Create a set of files with a chain more.

void	End2EndDistr (char *OutFile)
	Write the end to end distance of the chains.

void	BondDistr (char *OutFile, int NBin)
	Write the bond distance between the monomers.

void	Decoupling (int What)
	Decoupling of the direction/end to end distance of the chains.

void	ElasticCoupling (int NSample)
	Measure the elastic coupling between the two sheets. More...

void	ElasticCouplingNVT ()
	Measure the elastic coupling between the two sheets. More...

void	BilayerDistance (char *OutFile, int NBin)
	Measure the elastic coupling between the two sheets.

void	EndToEndDist ()
	Distribution of the end to end distances.

int	ProjectionF (int NBin, int Coord)
	Projection of the system against one direction pro.

int	CoreF (int NBin, int How)
	Sampling of the three dimentional space. More...

int	Surface (int NBin, int Coord)
	Area of a surfuce projected on the coordinate Coord surf.

int	From3To2d (int Coord, double Param)
	Project the velocities of a 3d system on a 2d system wrt a coordinate.

int	From2To1d (int Coord)
	Projet a 2d system on one of the two coordinates.

int	From3To1d (int Coord)
	Project a 3d system on one coordinate.

void	IsoSurf (int NSample, double *IsoValue, int NIso)
	Density plot all over different snapshots and calculation of the isolevel surface.

void	IsoLine (int NSample, double *IsoValue, int NIso, int How)
	Calculate the discrete density of the system and the correspondent isolines.

void	IsoLine (FILE F2Write, double Plot, int NSample, double *IsoLevel, int NIso)
	Perform the marching cubes on a density plot and print the isolines.

void	FetchStalk ()
	Write the position of the stalk for every snapshot. More...

void	FetchPore ()
	Write the position of the pore for every snapshot.

void	StalkArea ()
	Area of hydrophobic in the torus. More...

void	AvSnap ()
	Average the postion of the lipids over many snapshots.

void	SlabAngleProfs (int NBin, int NAngle, int Coord)
	Radial profiles of the slab density between 0⁰ and 90⁰ subdivided in NAngle angles. More...

void	Sample (int NSample)
	Sample the space in NSample lattice points.

void	Conv2Tecplot (int NBin, int How)
	Prepare a countor plot for tecplot.

void	Conv2Vmd ()
	esport the data in vmd file format

void	Conv2Povray ()
	esport the data in pov file format for rendering

void	Conv2rzd (int NSample)
	esport the data in radius depth density file format

void	Conv2xyzd (int NSample)
	esport the data in radius depth density file format

void	DrField (int NGrid, double IsoLevel, int nNano, FILE *FWrite)
	Draw a scalar field.

void	DrBondPovRay (double Pos1, double Pos2, float *Color)
	Draw the bonds.

void	HeaderPovRay ()
	Print the header for povray.

void	DrNanoPovRay (int n)
	PovRay draw function.

void	DrPartPovRay (int p)
	PovRay draw function.

void	ConvLattice (int NSample, char *FName)
	Convert into a square lattice.

void	RemoveChains ()
	Remove chains satisfying a condition.

int	Angle (int NBin)
	Calculation of the contact angle angle Boh?

double	ContactAngle (double x)
	Definition of the contact angle function Boh.

int	CenterOfMass (int Coord)
	Averaged center of mass Boh.

int	ChangeFile ()
	Defines the first and the last file to be elaborated file.

int	SpecifyCoord ()
	Defines the normal coordinate coord.

int	OpenFile (int f)
	Opens the f file of the list open.

int	OpenFile (char *FileName)
	Opens a file.

int	PropertiesF ()
	Calculates some properties of the system prop.

char *	ChooseDraw (int ExtWhat2Draw)
	Convert the internal definition for the menu of ElPoly in string.

void	ChooseDraw (char *String)
	Assing the correct value of What2Draw from. More...

void	DivideLayers (int How)
	Reorder the LIPID block in four different layers.

void	SetBoundFile (int InitFile, int EndFile)
	Set the initial and final number of files.

void	Processing (int f)
	Information on the current file elaborated.

void	Shift2Center ()
	Shift the system to the center.

void	SetBackFold (int Bf)
	Set backfold type.

void	SetNVisSkip (int NSkip)
	Set backfold type.

void	RenderPart (void)
	Choose the visualisation (obsolete)

void	DrRunTime ()
	Draws in run time (expensive)

void	DrColor ()
	Visualisation of the particle system with velocity color scheme.

void	DrPartList ()
	Create a list of all the particles.

void	DrVector (Vettore v, Vettore Origin)
	Draw a vector.

void	DrVectors ()
	Draw the chains as vectors.

int	DrIntorno (int p, double Blue)
	Visualize only particles within a certain distance.

void	DrCrossLinks ()
	Visualize the cross links.

int	Graphics (int argc, char **argv)
	Boh.

void	ESlide ()
	Sequence of pictures.

void	ESlide1 ()
	Sequence of pictures.

void	DrProtein (const char *FileName, int nBlock)
	Load and draw the linking of a protein.

void	DrNano ()
	Draw the nanoparticle structure.

void	DrCrossLinks (char *FileName)
	Draw the cross linked particles.

void	DrawPart (int p)
	Pointer to a generic function.

void	DrPartOpenGl (int p)
	OpenGl draw function.

void	DrawNano (int n)
	Pointer to a generic function.

void	DrNanoOpenGl (int n)
	OpenGl draw function.

void	DrawFuncHeader ()
	Assign the pointer to the corrispondent draw function, intilize the visualization.

void	DrawFuncFooter ()
	Dnd the visualization.

void	DrBond (int p)
	Finde the neighbour of the particle p and draw the bond.

void	DrawBond (double Pos1, double Pos2, float *Color)
	Pointer to a generic function.

void	DrBondNo (double Pos1, double Pos2, float *Color)
	Null function.

void	DrBondOpenGl (double Pos1, double Pos2, float *Color)
	Draw the bonds.

void	keyboard (unsigned char key, int x, int y)
	Draws all the particles and bonds.

void	ElDrawMouse (int button, int state, int x, int y)
	Scaling.

void	CompileList ()
	Compile the list with some useful primitives.

void	DrPosCol ()
	Boh.

void	Menu ()
	Creates the menu.

void	ElMenuChoise (int option)
	Choose what to visualize.

void	ElMenuVisual (int option)
	Choose what to visualize.

void	CreateMenu ()
	Creates the menu.

void	DrIsoipse (int NBin, int NIsoipse, int CoordN)
	Draws all the same quotes surfaces.

void	DrSurface ()
	Draws the surface like a sheet using the chains position.

void	DrSmooth (double *Plot, int NSample, double Min, double Max)
	Draw the surface in triangles.

void	DrSample (int NSample)
	Samples the surface and draws it in triangles.

void	DrSpectrum ()
	Calculate the spectrum of the surface and draws it in triangles.

void	DrDerivative ()
	Samples the surface, applies a 2d matrix derivative and draws the surface in triangles.

void	DrChains ()
	Position of every chain in hexagons.

void	DrPolygon ()
	Every particle is traeted as a vertex.

void	DrQuad ()
	Call a square in every particle position.

void	DrDensity ()
	(rad,norm,dens) visualisation

void	DrQuad1 ()
	Intensity scheme.

void	DrPotential ()
	Potential function.

void	DrShell ()
	Draw the outer shell.

void	DrVoronoi ()
	Voronoi tassellation.

void	DrInterpSurface ()
	Boh.

void	DrIsolevel (int NSample, double IsoLevel)
	Defines the triangles at the boundaries of the density close to the IsoLevel value. More...

void	DrField (int NGrid, double IsoLevel, int nNano)
	Draw a scalar field.

void	DrSquareMesh ()
	Draw the polygons for a square mesh.

void	DrNormalPoint (int p, int NEdge)
	Draw the normal to a point.

void	DrTria (Vettore v00, Vettore v01, Vettore v11, Vettore vN)
	single triangle defined by three vectors

void	DrTriaContour (Vettore v00, Vettore v01, Vettore *v11)
	Draw the contour of three vectors.

void	DrDoubleTria (Vettore v00, Vettore v01, Vettore v11, Vettore v10, Vettore *vN)
	Double triangle defined by four vectors.

void	DrCreateStalk ()
	Visualize the surface calculated in Stalk()

void	DrStalk ()
	Visualize the surface from Stalk.xvl.

void	Tile ()
	Cover a regular square grid of points with tiles.

void	DrTriangulate ()
	Triangulate a surface.

void	DrMesh ()
	Build a mesh from the lipid positions.

void	DrGenMesh ()
	Generate a mesh from a function.

void	DrCells ()
	Construct cells from the lipid positions.

void	DefineSkin (int NSample)
	Find the covering surface for given points.

void	DefineSurf ()
	Find the covering surface for given points.

Public Member Functions inherited from VarData
	VarData ()
	Set the constants.

	~VarData ()
	Destructor.

void	VarMessage (const char *s,...)
	If enabled call the function position.

bool	Open (char *InFile, int BF)
	Open the. More...

bool	OpenRisk (char *InFile, int BF)
	Opens a file without reallocationg.

bool	OpenTrust (char *InFile, int BF)
	Opens a file checking if the information are correct.

void	AllocPart ()
	Alloc the structures.

void	AllocChain ()
	Alloc the structures.

Properties	SysProperties ()
	Calculate some basis properties.

void	SysInfo (char *cSystem)
	Print a string with the system information.

void	SysDef (char *cSystem)
	Print a string with the system definitions.

char *	SysState ()
	Calculates fundamental quantities.

void	SetCoeff ()
	Set the virial coefficients from the known values of density coex...

void	SetCoeff (double v2, double v3)
	Set and normalize the virial coefficients from the arrays v2 and v3.

double	TwoPartDist (int p1, int p2, double *RelDist)
	Return the relative distance between two particles (wrapped)

double	TwoPartDist (double Pos, int p2, double RelDist)
	Return the relative distance between two particles (wrapped)

double	TwoPartDist2 (int p1, int p2, double *RelDist)
	Return the relative distance between two particles (wrapped)

double	TwoPartDist2 (double Pos, int p2, double RelDist)
	Return the relative distance between two particles (wrapped)

int	TwoPartDist (int p1, int p2, double *RelDist, double CutOff)
	Return the relative distance between two particles (wrapped) if the particles are within the cut off.

int	TwoPartDist (double Pos, int p2, double RelDist, double CutOff)
	Return the relative distance between two particles (wrapped) if the particles are within the cut off.

bool	Write (char *OutFile)
	Writes a "system-file" or a "x y z" file".

bool	WriteTxvl (char *OutFile)
	Writes a "system-file" or a "x y z" file".

bool	WriteXvt (char *OutFile)
	Writes a "system-file" or a "x y z" file".

bool	WriteXyz (char *OutFile)
	Writes a "system-file" or a "x y z" file".

void	HeaderInteraction (FILE *FileToWrite)
	Header interactions.

void	StringNano (char *NString, int n)
	String for the rigid inclusion in the header file.

int	HeaderNano (FILE *FileToWrite)
	Write the nano section of the header to the file.

int	HeaderSoft (char *Line)
	Header soft.

void	WriteLinkedSurf (FILE FWrite, double Plot, int NSample, int NType, double Bound, int PId)
	Write the positions of the egdes of the rectangles.

void	WriteSurf (FILE F2Write, double *Plot, int NSample, int OffSet)
	Write the particle position as linked edges of squares.

void	ShapeId (int iShape, char *Shape)
	Identifier of the shape.

bool	BackFold (int How)
	Backfold the particle position.

int	BfDefChain ()
	Definition of the chain.

int	BfEdge ()
	Find the box size if missing.

void	DistFromNp ()
	Define the distance form the nanoparticle.

void	ShiftRef (int BackFold)
	Backfold the system wrt the reference position.

int	StalkPos (double *OldPos)
	Find the position of the stalk.

void	BfPep ()
	Backfold the nano described as a cluster of monomers.

void	BackBone (double *Line, int NBin)
	Describe the backbone of a filament.

void	StalkLineProf (double *Line, int NBin)
	Describe the line for a linear stalk.

void	StalkPos2 (double OldPos, double CmStalk)
	Find the position of the stalk second method.

void	StalkPos3 (double OldPos, double CmStalk)
	Find the position of the stalk third method.

int	StalkPos4 (double OldPos, double CmStalk)
	Find the position of the stalk forth method.

double	NormalWeight (VAR_TRIANGLE Triang, double Weight, int NGrid, int NTri)
	Weight of the neighblorung normal on a vertex.

void	ConnectLineChain (VAR_LINE *Triang, int NGrid, int NTri)
	Connect the lines in a chain. More...

void	ConnectLineChain2 (VAR_LINE *Triang, int NGrid, int NTri)
	Connect the lines in a chain. More...

void	ConnectLineChain3 (VAR_LINE *Triang, int NGrid, int NTri)
	Connect the lines in a chain. More...

double	PorePos ()
	Find the position of the pore.

int	Fetch (char str, char mask, char *fmt,...)
	Retrive from a string the information concerning the mask.

int	BraketPos (char str, char mask, int sPos, int sLen)
	Retrive from a string the position of the brakets.

int	Fetch (char str, char mask, int NArg, double *Val)
	Retrive from a string the information concerning the mask.

bool	ReadString (const char String, char cLine, double *Value)
	Copy the value in the. More...

bool	ReadString (const char String, double Value, char *line)
	Copy the value in the. More...

bool	ReadString (const char String, char cLine, int *Value)
	Copy the value in the. More...

int	ReadVal (char pLine, double Value)
	Copy the value in the String to the Value referring to the position of pLine.

int	ReadLineXvt (char cLine, double Pos, int *Type)
	Read a single line in format Xvt.

bool	ReadConf (char *InFile)
	Reads a "configuration file".

void	ReadHeader (FILE *FileToRead)
	Reads a header.

void	ReadHeaderTxvl (FILE *FileToRead)
	Reads a header for a txvl file format.

void	ReadHeaderXvt (FILE *FileToRead)
	Reads a header of xvl file format.

int	ReadPart (FILE *FileToRead)
	Reads particle type and position.

int	ReadPartTxvl (FILE *FileToRead)
	Reads a type-position-velocity-link file.

int	ReadPartXvt (FILE *FileToRead)
	Reads a position-velocity-type file.

int	ReadPartXyz (FILE *FileToRead)
	Reads a x y z file.

int	ReadPartXyzt (FILE *FileToRead)
	Reads a x y z t file.

int	ReadPassThru (FILE *FileToRead)
	Reads the information to alloc the structure.

int	ReadSoft (FILE *ConfFile)
	Reads the specifications about the nano.

void	ReadNano (FILE *ConfFile, int NCircle, int NHeight)
	Reads the specifications about the hard object.

int	NanoString (char *cLine, int n)
	Reads and set the specifics of the nano.

void	SubNanoHeader (char *cFile)
	Substitue the nano header.

int	ShapeId (char *Shape)
	Identifier of the shape.

int	DefSoft (char nome2, char ConfF)
	Define and write the system as described in the conf file.

int	TrialSys ()
	Creates a trial system.

bool	CreateSoft (int *arch, double Thickness, int s)
	Creates an initial system.

void	CreateTube (int *arch, double Thickness, int s)
	Soft in a tube shape.

void	CreatePlanar (int *arch, double Thickness, int s)
	planar membrane

void	CreateVesicle (int *arch, double Thickness, int s)
	vesicle

void	CreateCoating (int *arch, double Thickness, int s)
	coating around a cylindrical nanoparticle

void	CreateObstacle (int *arch, double Thickness, int s)
	Creates obstacles.

int	CheckNano (double *Pos, int s)
	No particle inside the nano.

void	AddProtein (int NCircle, int NHeight, int nNano, char *filename)
	Defines the nanoparticle as a net of monomers.

void	CreateProtein (int nNano, int nStart)
	Defines the nanoparticle as a net of monomers.

void	AddStuffing (char *filename, int nStuffing, int nNano)
	Fill the protein with water.

void	AddSolvent (char *filename, int nWater)
	Add phantom solvent at the bottom.

void	AddChains (char *filename, double Thickness)
	Add homopolymer chains in the bilayer.

void	AddCholesterol (char *filename, double Thickness, int s)
	Add cholesterol chains in the bilayer.

void	DefBlock (int *NChStep, int How)
	Define four different blocks.

void	DefRest (int *arch, int s)
	set the remaining information

int	PutPart (int j, int p, int HalfLim, double sigma)
	return the number in the chain of the next particle put

void	FindNeighbours (char *FileName)
	Find the couples of most neighbouring chains.

void	SwapChain (int c1, int c2, int b)
	Swap two chains.

void	SwapChain (int c1, int c2)
	Swap two cahins.

void	SwapPart (int p1, int p2)
	Swap two particle.

void	ChangeNChain (int NChain, int b)
	Update the new number of chains.

bool	ShiftSys (int How)
	Shift the system accordin to the SHIFT_ definitions.

void	SampleSurface (double *Plot, int NSample, int Type)
	Define a normal coordinate for every patch.

MOMENTI	SampleSurfacePart (double *Plot, int NSample, int Type)
	Define a normal coordinate for every patch.

MOMENTI	SampleSurface (Matrice *Plot, int NSample, int Type)
	Define a normal coordinate for every patch.

MOMENTI	SampleSurfaceMem (int NSample)
	Allocate and fill PlotMem with the particle average position.

void	LoadDensFile (double **Plot, int NBin)
	Load in the array Plot the density of the system.

int	SpatialDerivative (Matrice Surface, Matrice Resp, SPLINE Weight, int NSample)
	Perform a spatial derivative on a surface.

void	ShiftBlock (Vettore *Shift, int b)
	Shift a block wrt to Shift.

void	RotateBlock (Vettore Axis, Vettore Origin, int b)
	Rotate a block wrt to the Axis from the Origin.

void	MirrorBlock (Vettore Px1, Vettore Px2, Vettore *Px3, int b)
	Mirror the position wrt to a plane.

void	Transform (int block)
	Transform a block.

void	Point2Shape (int iShape)
	Point to the shape function.

double	NanoDist2 (double *Pos, int n)
	Pointer to a generic function.

double	NanoDist2 (double x, double y, double z, int n)
	Distance from the nanoparticle.

double	FieldNo (double *Pos, int n)
	No field.

double	FieldSphere (double *Pos, int n)
	Scalar field of a sphere.

double	FieldElips (double *Pos, int n)
	Scalar field of a elipsoid.

double	FieldParab (double *Pos, int n)
	Scalar field of a elipsoid.

double	FieldCyl (double *Pos, int n)
	Scalar field of a cylinder.

double	FieldTransMem (double *Pos, int n)
	Scalar field of a transmembrane protein.

double	FieldJanus (double *Pos, int n)
	Scalar field of a janus peptide.

double	FieldTorus (double *Pos, int n)
	Scalar field of a janus peptide.

double	FieldTilt (double *Pos, int n)
	Scalar field of a tilted cylinder.

double	FieldBound (double *Pos, int n)
	Scalar field of a hard wall at the box edges.

double	FieldTiltWall (double *Pos, int n)
	Scalar field of a tilted cylinder.

int	PairCorrelation (double *Point, int NSample, int How, int Type)
	1-d pair correlation

int	PairCorrelationRound (double **Point, int NSample, int Type)
	Circular 2-d pair correlation.

int	PairCorrelationSquare (double **Point, int NSample, int Type)
	2-d pair correlation on a square

int	PairCorrelationPep (double **Point, int NSample, int Type)
	2-d pair correlation on a square fererring to the pep position

int	Scattering2d (double **Point, int NSample, int Type)
	2-d Scattering

int	Scattering2D (double **Point, int NSample, int Type)
	2-d scattering

void	Spettro2d (double *Points, int NSample, int Type)
	1-d spectrum of a surface

void	Spettro2d (double *Plot, int NSample)
	2-d spectrum of a sirface

int	DensityProfile (int coord, int NSample, int NType, double *dDensity)
	Calculate the density profile for the x, y, z, r coordinate. More...

int	Core (double ***Plot, int NSample, double Border[3][2])
	Sampled three dimentional weighted shape of the system.

int	RadDistr (int NSample, double *Plot, double Border[2], int How)
	rzd representation of the system referring to More...

int	Worm (int Partition, int NSample, double Border, double dPoint)
	Density profile along a worm like micelle.

void	VolumeCircSlab (double *VolContr, int NSample)
	Fill an array of. More...

void	Stalk (int NSample, int NLevel, double **Plot, double Threshold)
	Following the contour of a stalk.

int	Arrange (int **Triangle, int Vertex)
	The naerest. More...

int	Folding ()
	Boh...

int	OrderPos ()
	A cell list to be fixed.

int	CalcnPos (double *Pos)
	return a univocal index of the chain position

int	Neighbour (double *Pos)
	Boh.

int	NChainPSquare (double *Plot)
	Distribution of number of chain per patch.

int	LateralFluctuation (double *Plot, int LatValue)
	Boh.

int	Voronoi ()
	Voronoi tassellation.

int	PosVectInt (double *Pos)
	Return the integer index with respect to the partition NSquare.

int	InterParab (PART PmIn, PART PmOut, int NIn, int nOut)
	Discontinous parabolas.

int	InterParab2 (PART PmIn, PART PmOut, int NIn, int NOut)
	Discontinous parabolas.

int	InterCubica (PART PmIn, PART PmOut, int NIn, int NOut)
	Discontinous cubic.

int	InterForth (PART PmIn, PART PmOut, int NIn, int NOut)
	Discontinous forth degree.

int	InterSpline3 (PART PmIn, PART PmOut, int NIn, int NOut)
	third order spline

int	InterSpline4 (PART PmIn, PART PmOut, int NIn, int NOut)
	forth order spline

int	InterBSpline (PART PmIn, PART PmOut, int NIn, int NOut)
	BSpline.

int	InterBSpline2D (double PlIn, double PmOut, int NIn, int NOut)
	2-d BSpline

int	InterBSpline2D (double PlIn, double PmOut, int NIn, int NOut)
	2-d BSpline More...

int	InterBSpline1D (double PlIn, double PmOut, int NIn, int NOut)
	1-d BSpline

int	InterPoly (PART PmIn, PART PmOut, int NIn, int nOut)
	NIn-polynomian.

int	InterDerMatrix (PART *Pm, int NMass, SPLINE Weight, double Offset)
	Boh.

void	SmoothGrid (int NSample, char *FWrite)
	Smooth a grid with BSplines.

void	SmoothGrid (int NSample)
	Smooth a grid with BSplines and update the particle positions. More...

void	ConvoluteMatrix (double Plot, int NGrid, Matrice Mask, int NDim)
	Convolute a matrix.

void	ConvoluteMatrix1 (double Plot, int NGrid, Matrice Mask)
	Convolute a matrix 1d.

void	ConvoluteMatrix2 (double Plot, int NGrid, Matrice Mask)
	Convolute a matrix 2d.

void	ConvoluteMatrix3 (double Plot, int NGrid, Matrice Mask)
	Convolute a matrix 3d.

int	SetNPart (int NewNPart)
	Set and reallocate the number of particles.

int	SetNChain (int NewNCh)
	Set and reallocate the number of chains.

int	SetNLink (int NewNCh)
	Set and reallocate the number of links.

void	SetNPCh (int NewNCh)
	Set and reallocate the number of particles per chains.

void	SetNType (int NewNType)
	Set the number of species.

int	AllocLinks (int NewNCh)
	(re)allocate the links

int	SetNBlock (int Val)
	Set NBlock.

int	SetNNano (int Val)
	Set NNano.

void	Copy (PART P1, PART P2, int NPartOld)
	Copy the part P2 on part P1.

void	Copy (CHAIN C1, CHAIN C2, int NChainOld)
	Copy the chain C2 on chain C1.

VAR_TRIANGLE *	MarchingCubes (double Plot, int NSample, double IsoLevel, int NTri)
	Defines the triangles close to the IsoLevel of the 3d density Plot.

VAR_LINE *	MarchingSquares (double Plot, int NSample, double IsoLevel, int NTri)
	Defines the triangles close to the IsoLevel of the 3d density Plot.

void	AreaDistr (double Distr, double RadDistr, int NSample)
	Calculate the (temporal/radial) area distribution.

double	pTime ()
	Total time.

double	pDeltat ()
	Delta t.

double	pTemp ()
	Temperature.

double	pBeta ()
	Beta factor 1/kTB.

double	pEnergy (int d)
	Pot, kinetik, free.

double	pEdge (int d)
	xyzr edges of the simulation box

double	pInvEdge (int d)
	Inverted xyzr edges of the simulation box.

double	pVol ()
	xyzr edges of the simulation box

double	pCm (int d)
	Center of mass of the system.

double	pVelMax (int d)
	Maximum velocity.

double	pchiN ()
	Incompatibility.

double	pkappaN ()
	Incompressibility.

double	pkBen ()
	Bending coupling.

double	pkSpr ()
	Spring coupling.

void	SetkBen (double Val)
	Bending coupling.

void	SetkSpr (double Val)
	Spring coupling.

void	SetSprRest (double Val)
	Rest distance of the harmonic potential.

double	pSprRest ()
	Rest distance of the harmonic potential.

double	prho ()
	Density coexistence.

double	pReOverCutOff ()
	Re/CutOff.

double	pWei2Par ()
	Parameter of the second order weighting function.

double	pWei3Par ()
	Parameter of the third order weighting function.

int	pStep ()
	Number of steps.

int	pNPart ()
	Number of particle.

int	pNChain ()
	Number of chain.

int	pNChain (int b)
	Number of chain.

int	pNPCh ()
	Number of particle per chain.

int	pNPCh (int c)
	Number of particle per chain.

int	pNType ()
	of types of the particle

int	pNLink ()
	Maximum number of bonds.

int	pNNano ()
	Number of nanoparticles.

int	pNBlock ()
	Number of blocks.

int	pNAllocP ()
	Allocated number of particles.

int	pNAllocC ()
	Allocated number of chains.

void	SetEdge (double Val, int d)
	Set Edge.

void	SetCNorm (int d)
	Set Edge.

void	SetScaleF (double *Scale)
	Set scale factor.

void	SetShiftPos (double *RefPos)
	Set reference pos.

void	SetIfNormalize (int If)

void	SetDeltat (double Val)
	Set DeltaT.

void	SetStep (int Val)
	Set Step.

void	SetTemp (double Val)
	Set Temperature.

void	SetTime (double Val)
	Set Time.

void	IncrStep ()
	Increment Step.

double	pPos (int p, int d)
	Return back folded position.

double	pChPos (int p, int d)
	Return back folded position.

void	pPos (int p, double *Pos)
	Return back folded position.

double *	pPos (int p)
	Print the particle position.

double	pPosNoBkf (int p, int d)
	Return the velocity.

double	pVel (int p, int d)
	Return the velocity.

void	SetPos (int p, double *Pos)
	Set the particle position.

void	SetPos (int p, int d, double Pos)
	Set the particle position.

void	SetVel (int p, double *Vel)
	Set the particle velocity.

void	SetType (int p, int t)
	Set the particle type.

int	pType (int p)
	Return the type.

int	pChain (int p)
	Return the chain.

double	pNanoPos (int n, int d)
	Return back folded nano position.

void	SetBkf (int p)
	Set the back folded array for the particle p.

void	SetNanoBkf (int n)
	Set the back folded array for the nano n.

void	pPos (double *Pos)
	Print a position.

Public Attributes
DRAW_PART	Draw_Part
	Pointer to a distance/field function.

DRAW_PART	Draw_Nano
	Pointer to a distance.

DRAW_BOND	Draw_Bond
	Pointer to a distance/field function.

GLuint	Quad

GLuint	Point

GLuint *	Cylinder

GLuint	MetalCylinder

GLuint	Hexagon

GLuint	Cube

GLuint	Arrow

GLuint	GlWall

double	Saturation
	Saturation of the color (increase intensity)

char	Block2Draw [20]
	Name of the block to draw.

int	NFile [2]
	First and last file of the list.

int	NFileTot
	Total number of file.

int	NPro
	Boh.

int	quando
	Current number of the file list.

int	LineSize
	Line size of the gl.

int	IfIntorno
	If it visualizes only the particles/chains within a certain distance.

int	IfLine
	Boh. More...

int	IfChType
	Type of the chains to be visualized.

int	NBackFold
	Type of backfold.

int	What2Draw
	Draw the content in the appropriate visulization.

int	NVisSkip
	How many lipids are skipped in the visualization.

int	DrawOutput
	Boh. More...

double	Vicinanze
	Boh. More...

double	InvScaleUn
	Define the shrink factor between the box edges.

double	ExtParam
	External parameter (e.g. for MarchingCubes)

double	ScaleFact
	Normal scaling factor (z zooming)

FILE *	DrawOutFile
	Output file for drawing.

SingProc *	Proc

Public Attributes inherited from VarData
Matematica *	Mat
	Implementation of all usefull algorythms.

MatInt *	MInt
	Matrix of the prefactor of the interactions.

NANO_DIST	Nano_Dist
	Pointer to a distance/field function.

char	cWhat2Draw [STRSIZE]
	What to draw.

NANO *	Nano
	Extra particle.

PART *	Pm
	Particle information of all particle.

LINKS *	Ln
	Array of linking between the particles.

CHAIN *	Ch
	Information on all chains.

SOFT *	Soft
	Soft bodies.

BLOCK *	Block
	Information for every block.

double *	PlotMem
	Particle position/density on the square lattice.

double	ShiftPos [3]
	Reference position.

double	ScaleF [3]
	Scale factor.

int	NSoft
	Number of soft bodies.

int	NPartNearSphere
	Number of particle to be considered in the radial density profile.

int	NAddChain
	Additional homopolymer chains into the membrane.

int	NAddChol
	Additional cholesterol chains into the membrane.

int	NSolvent
	Solvent molecules.

int	NStuffing
	Stuffing for the cylinder.

int	CNorm
	Normal coordinate.

int	CLat1
	lateral coordinate

int	CLat2
	lateral coordinate

int	NChType
	Type of chain selected.

int	NPType
	Type of particle selected.

int	NEdge
	Number of particles per edge.

int	SysType
	Contains the definition of the system.

int	SysFormat
	Contains the definition of the file format.

int	SysCreate
	Contains the information for the creation.

int	IfNormalize
	If normalize the lateral dimensions to one.

int	IfPlotMem
	If PlotMem is allocated and filled.

Detailed Description

Operates and visualizes the information in the VarData class.

Definition at line 61 of file ElPoly.h.

Member Function Documentation

int DensProf	(	int	NBin,
		int	NSample,
		int	Coord
	)

Calculate the density profile dens.

a

sum on small patches and shift wrt the weighted average

Definition at line 24 of file ElPolyProfDens.cpp.

References VarData::BfDefChain(), VarData::Block, VarData::Ch, VarData::CLat1, VarData::CLat2, VarData::CNorm, BLOCK::EndIdx, VarData::Nano, NFile, VarData::OpenRisk(), VarData::pChain(), VarData::pchiN(), VarData::pCm(), VarData::pEdge(), Vettore::PerpTo3(), VarData::pInvEdge(), VarData::pkappaN(), VarData::pNanoPos(), VarData::pNBlock(), VarData::pNChain(), VarData::pNNano(), VarData::pNPart(), VarData::pPos(), VarData::prho(), Processing(), VarData::pType(), Vettore::Set(), VarData::SetEdge(), VarData::SysDef(), CHAIN::Type, and VarData::VolumeCircSlab().

void DensProfNormalSlab	(	int	NBin,
		int	NSample,
		int	Coord
	)

Calculate the density profile projecting the particles on the normal density.

a to be completed

sum on small patches and shift wrt the weighted average

Definition at line 157 of file ElPolyProfDens.cpp.

References VarData::BfDefChain(), VarData::Block, VarData::Ch, VarData::CLat1, VarData::CLat2, VarData::CNorm, BLOCK::EndIdx, VarData::Nano, NFile, VarData::OpenRisk(), VarData::pChain(), VarData::pchiN(), VarData::pCm(), VarData::pEdge(), Vettore::PerpTo3(), VarData::pInvEdge(), VarData::pkappaN(), VarData::pNanoPos(), VarData::pNBlock(), VarData::pNChain(), VarData::pNNano(), VarData::pNPart(), VarData::pPos(), VarData::prho(), Processing(), VarData::pType(), Vettore::Set(), VarData::SetEdge(), VarData::SysDef(), CHAIN::Type, and VarData::VolumeCircSlab().

void SlabProf	(	int	NBin,
		int	nNano,
		int	Coord1
	)

Thickness and density profile along Coord1.

a

Definition at line 292 of file ElPolyProfDens.cpp.

References VarData::Block, VarData::CLat1, VarData::CLat2, VarData::CNorm, Matrice::ConvoluteMatrix(), BLOCK::EndIdx, Matrice::FillGaussian(), VarData::Nano, NFile, Vettore::Normalize(), VarData::OpenRisk(), VarData::pCm(), VarData::pEdge(), Vettore::PerpTo(), VarData::pInvEdge(), VarData::Pm, VarData::pNanoPos(), VarData::pNBlock(), VarData::pNNano(), PART::Pos, NANO::Pos, VarData::pPos(), Matrice::Print(), PrintDens(), Processing(), Vettore::ProjOnAxis(), VarData::pType(), Vettore::Set(), VarData::SetNNano(), and Vettore::Val().

void PrintDens	(	FILE *	FileToWrite,
		double **	Plot,
		double *	LatDim,
		int	NBin
	)

Print the density profile in the surfaces representation.

a

Definition at line 414 of file ElPolyProfDens.cpp.

References ChooseDraw().

Referenced by BondDistr(), CartDens(), Diff2Files(), RadDistrF(), SlabProf(), and SplayDistr().

void RadDens2Thick ( int NBin )

Calculate the thickness from the radial density profile.

a

Definition at line 1031 of file ElPolyProfDens.cpp.

References VarData::LoadDensFile(), NFile, and VarData::pEdge().

void RadDens2Thick2d ( int NBin )

Calculate the thickness from the radial density profile.

a

Definition at line 1090 of file ElPolyProfDens.cpp.

References NFile, VarData::pEdge(), VarData::pInvEdge(), VarData::pNPart(), VarData::pPos(), and VarData::pType().

void CartDens	(	int	NBin,
		int	nNano
	)

3d (rad,norma,dens) density profile in cartesian coordinates

a

Definition at line 456 of file ElPolyProfDens.cpp.

References VarData::CLat1, VarData::CLat2, VarData::CNorm, Matrice::ConvoluteMatrix(), Matrice::FillGaussian(), NBackFold, NFile, VarData::OpenRisk(), VarData::pCm(), VarData::pEdge(), VarData::pInvEdge(), VarData::pNPart(), VarData::pPos(), Matrice::Print(), PrintDens(), Processing(), and VarData::pType().

void RadDistrF	(	int	NBin,
		int	How,
		int	nNano
	)

3d (rad,norma,dens) density profile with respect to a initial position radNano radCm radCmN

a

Definition at line 557 of file ElPolyProfDens.cpp.

References Vettore::Angle(), Angle(), NANO::Axis, VarData::BfDefChain(), VarData::Block, VarData::CLat1, VarData::CLat2, VarData::CNorm, BLOCK::EndIdx, Matrice::Mult(), VarData::Nano, NBackFold, NFile, VarData::OpenRisk(), VarData::pChain(), VarData::pCm(), VarData::pEdge(), Vettore::PerpTo3(), VarData::pInvEdge(), VarData::Pm, VarData::pNanoPos(), VarData::pNBlock(), VarData::pNNano(), VarData::pNPCh(), VarData::PorePos(), VarData::pPos(), PrintDens(), Processing(), Vettore::ProjOnAxis(), VarData::pType(), Vettore::Set(), VarData::SetEdge(), Vettore::Val(), Vettore::VetV(), VarData::VolumeCircSlab(), and Vettore::x.

void BondDistr ( int NSample )

Distribution of the bond lengths.

Calculate the (r,z) profile of the bond length distribution.

Definition at line 783 of file ElPolyProfDens.cpp.

References VarData::Block, VarData::CLat1, VarData::CLat2, VarData::CNorm, Matrice::ConvoluteMatrix(), BLOCK::EndIdx, Matrice::FillGaussian(), VarData::Nano, NFile, VarData::OpenRisk(), VarData::pChain(), VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, VarData::pNBlock(), PART::Pos, NANO::Pos, VarData::pPos(), Matrice::Print(), PrintDens(), Processing(), VarData::pType(), VarData::SetEdge(), and VarData::VolumeCircSlab().

void SplayDistr ( int NSample )

Distribution of end to end distances.

Calculate the (r,z) profile of the splay angle distribution.

Definition at line 870 of file ElPolyProfDens.cpp.

References Vettore::Angle(), Angle(), VarData::Block, VarData::CLat1, VarData::CLat2, VarData::CNorm, Matrice::ConvoluteMatrix(), Matrice::FillGaussian(), BLOCK::InitIdx, Matematica::InterRett(), RETTA::m, VarData::Mat, VarData::Nano, BLOCK::NChain, NFile, BLOCK::NPCh, VarData::OpenRisk(), VarData::pEdge(), VarData::pInvEdge(), VarData::Pm, VarData::pNBlock(), VarData::pNPCh(), PART::Pos, NANO::Pos, Matrice::Print(), PrintDens(), Processing(), RETTA::q, VarData::SetEdge(), and VarData::VolumeCircSlab().

void ThickFromDens ( int NBin )

Calculate the thickness profile from the density plot.

a

Definition at line 1128 of file ElPolyProfDens.cpp.

References VarData::CLat1, VarData::CLat2, VarData::pCm(), VarData::pEdge(), VarData::pInvEdge(), VarData::pNPart(), VarData::pPos(), and VarData::pVel().

void StalkLineProfF ( int NBin )

Write the line describing a linear stalk.

Call the function StalkLineProf to reconstruct the linear shape of the stalk and calculate the power spectrum.

Definition at line 388 of file ElPolyProfile.cpp.

References VarData::CLat1, VarData::CLat2, NFile, VarData::Open(), VarData::pEdge(), VarData::pInvEdge(), Processing(), and VarData::StalkLineProf().

void AreaCompr ( int NSample )

Calculates the number of chain per area area.

Subdivide the simulation box in SubDiv[CLat1]xSubDiv[CLat2] squares and calculate the average number of chains and its stadard deviation.

The compressibility is in the limit lim_l = l^2<N_c^2>/<N_c>^2 where l is the dimension of the patch and NTimes different patches size are taken in account. It works in NVT.

Definition at line 1146 of file ElPolyMeasure.cpp.

References VarData::CLat1, VarData::CLat2, VarData::NEdge, NFile, VarData::OpenRisk(), VarData::pchiN(), VarData::pChPos(), VarData::pEdge(), VarData::pInvEdge(), VarData::pkappaN(), VarData::pNChain(), VarData::prho(), Processing(), and VarData::SysDef().

void ElasticCoupling ( int NSample )

Measure the elastic coupling between the two sheets.

Divides the box size in small patches and calculate the thinning for every patch.

For every patch size are stored the mean values and variance of the thickness. As output it is printed the area per patch, the correspondent thickness, the standard deviation and the elastic coupling modulus.

Definition at line 1248 of file ElPolyMeasure.cpp.

References VarData::Ch, VarData::CLat1, VarData::CLat2, VarData::CNorm, NFile, VarData::OpenRisk(), VarData::pChain(), VarData::pchiN(), VarData::pEdge(), VarData::pInvEdge(), VarData::pkappaN(), VarData::pNPart(), VarData::pPos(), VarData::prho(), Processing(), VarData::pType(), VarData::SysDef(), and CHAIN::Type.