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 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.
void	DensProfNormalSlab (int NBin, int NSample, int Coord)
	Calculate the density profile projecting the particles on the normal density.
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.
void	PrintDens (FILE FileToWrite, double Plot, double LatDim, int NBin)
	Print the density profile in the surfaces representation.
void	RadDens2Thick (int NBin)
	Calculate the thickness from the radial density profile.
void	RadDens2Thick2d (int NBin)
	Calculate the thickness from the radial density profile.
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
void	RadDistrF (int NBin, int How, int nNano)
	3d (rad,norma,dens) density profile with respect to a initial position radNano radCm radCmN
void	BondDistr (int NSample)
	Distribution of the bond lengths.
void	E2EDistr (int NSample)
	Distribution of end to end distances.
void	SplayDistr (int NSample)
	Distribution of end to end distances.
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.
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.
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.
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.
void	ElasticCouplingNVT ()
	Measure the elastic coupling between the two sheets.
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.
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.
void	FetchPore ()
	Write the position of the pore for every snapshot.
void	StalkArea ()
	Area of hydrophobic in the torus.
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.
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.
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.
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 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.
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.
double	Vicinanze
	Boh.
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

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, Matrice::ConvoluteMatrix(), BLOCK::EndIdx, Matrice::FillGaussian(), 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(), Matrice::Print(), 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.