Cylinder Class Reference

A three dimensional cylinder with fixed boundary conditions in the x and y directions and periodic boundary conditions in the z direction. More...

#include <container.h>

Inheritance diagram for Cylinder:

Collaboration diagram for Cylinder:

Public Member Functions
	Cylinder (const double, const double, const int)
	Create a cylinder given density, radius and number of particles. More...
	Cylinder (const double, const double)
	Create a cylinder given its radius and length. More...
	~Cylinder ()
	Destructor.
void	putInside (dVec &r) const
	Make sure that a suplied vector is put inside the cylinder.
dVec	randPosition (MTRand &) const
	Return a random position inside the cylinder. More...
dVec	randUpdate (MTRand &, const dVec &) const
	Return a random position close to the supplied one.
dVec	randUpdateJumpShell (MTRand &, const dVec &) const
	Return a random position close to the supplied one. More...
dVec	randUpdateSmall (MTRand &, const dVec &) const
	Return a random position close to the supplied one. More...
int	gridIndex (const dVec &) const
	Given a particle position, return a single integer which maps to a unique grid position. More...
double	gridBoxVolume (const int) const
	Given a grid index, return the hyper volume of the associated grid box. More...
Public Member Functions inherited from Container
	Container ()
	Initialize all variables.
virtual	~Container ()
	Empty destructor.
void	putInBC (dVec &r) const
	Place a vector in boundary conditions. More...
void	putInBC1 (dVec &r) const
double	gridRadius2 (const int) const
	The radius of a grid box. More...

Additional Inherited Members
Data Fields inherited from Container
TinyVector< unsigned int, NDIM >	periodic
	Determines which dimensions have periodic bc.
dVec	side
	The linear dimensions of the box.
dVec	sideInv
	The inverse box dimensions.
dVec	sideInv2
	2 times the inverse box dimensions
double	volume
	The volume of the container in A^3.
double	rcut2
	The smallest separation squared.
double	maxSep
	The maximum possible separation for 2 beads on the same timeslice.
string	name
	The name of the container.
int	numGrid
	The number of grid boxes for the position grid.
bool	fullyPeriodic
	Is the prism fully periodic?
dVec	gridSize
	The grid size in each dimension.
Protected Attributes inherited from Container
dVec	pSide
	Periodic * side.

Detailed Description

A three dimensional cylinder with fixed boundary conditions in the x and y directions and periodic boundary conditions in the z direction.

Definition at line 143 of file container.h.

Constructor & Destructor Documentation

Cylinder() [1/2]

Cylinder::Cylinder	(	const double	_rho,
		const double	radius,
		const int	numParticles
	)

Create a cylinder given density, radius and number of particles.

We create a 3d cylinder (otherwise exit) with periodic boundary conditions only in the z-direction. The radius is fixed, and the length is determined by the density in atoms/A^3.

Definition at line 229 of file container.cpp.

                                                                                 {
 
    /* We can only make a cylinder in 3 dimensions */
    if (NDIM != 3) {
        cerr << "You can only create a cylinder in 3 dimensions, change NDIM!" 
            << endl;
        exit(EXIT_FAILURE);
    }
    else {
        /* We can compute the linear length from the density, number of particles
         * and radius */
        double L = (1.0*numParticles)/(_rho * M_PI * radius * radius);
 
        /* We check to make sure that our aspect ratio is at least 2:1 */
        if (L < 2.0*radius) 
            cerr << "L:r is smaller than 2:1!" << endl;
 
        /* Setup the prism size in each of the three dimensions which the 
         * cylinder will be inscribed insde of.  We make it 2R X 2R X L  */
        side[0] = side[1] = 2.0 * radius;
        side[2] = L;
 
        rcut2 = 0.25*side[2]*side[2];
 
        sideInv = 1.0/side;
        sideInv2 = 2.0*sideInv;
 
        /* setup which dimensions have periodic boundary conditions, 1.0 for yes 
         * and 0.0 for no. */
        periodic[0] = periodic[1] = 0;
        periodic[2] = 1;
 
        pSide = periodic*side;
 
        /* Compute the maximum possible separation possible inside the box */
        maxSep = sqrt(dot(side/(periodic + 1.0),side/(periodic + 1.0)));
 
        /* Compute the cylinder volume. We use the radius here instead of the actual
         * side.  This is the 'active' volume */
        volume = M_PI*radius*radius*L;
 
        name = "Cylinder";
 
        /* The grid size for the lookup table */
        gridSize = side/NGRIDSEP;
 
    } // end else
}

Cylinder() [2/2]

Cylinder::Cylinder	(	const double	radius,
		const double	L
	)

Create a cylinder given its radius and length.

We create a 3d cylinder (otherwise exit) with periodic boundary conditions only in the z-direction. The radius and length are given in angstroms.

Parameters

L	The length of the cylinder
radius	The radius of the cylinder

Definition at line 286 of file container.cpp.

                                                      {
 
    /* We can only make a cylinder in 3 dimensions */
    if (NDIM != 3) {
        cerr << "You can only create a cylinder in 3 dimensions, change NDIM!" 
            << endl;
        exit(EXIT_FAILURE);
    }
    else {
        /* We check to make sure that our aspect ratio is at least 2:1 */
        if (L < 2.0*radius)
            cerr << "L:r is smaller than 2:1!" << endl;
 
        /* Setup the prism size in each of the three dimensions which the 
         * cylinder will be inscribed insde of.  We make it 2R X 2R X L 
         * to account for */
        side[0] = side[1] = 2.0 * radius;
        side[2] = L;
 
        rcut2 = 0.25*side[2]*side[2];
 
        sideInv = 1.0/side;
        sideInv2 = 2.0*sideInv;
 
        /* setup which dimensions have periodic boundary conditions, 1 for yes 
         * and 0 for no. */
        periodic[0] = periodic[1] = 0;
        periodic[2] = 1;
 
        /* Compute the maximum possible separation possible inside the box */
        maxSep = sqrt(dot(side/(periodic + 1.0),side/(periodic + 1.0)));
 
        pSide = periodic*side;
 
        /* Compute the cylinder volume. We use the radius here instead of the actual
         * side.  This is the 'active' volume */
        volume = M_PI*radius*radius*L;
 
        name = "Cylinder";
 
        /* The grid size for the lookup table */
        gridSize = side/NGRIDSEP;
 
    } // end else
}

Member Function Documentation

gridBoxVolume()

double Cylinder::gridBoxVolume ( const int  n ) const

virtual

Given a grid index, return the hyper volume of the associated grid box.

Parameters

n	The grid index

Returns

The hyper volume of the grid box

Implements Container.

Definition at line 470 of file container.cpp.

                                                {
 
    /* Get the first grid box index */
    return blitz::product(gridSize);
}

gridIndex()

int Cylinder::gridIndex ( const dVec &  pos ) const

virtual

Given a particle position, return a single integer which maps to a unique grid position.

Used for correlating estimators with individual particle positions.

Parameters

pos	The particle position

Returns

An integer representing a grid box number

Implements Container.

Definition at line 432 of file container.cpp.

                                             {
 
    // /* Get the r and theta components */
    // double r = sqrt(pos[0]*pos[0]+ pos[1]*pos[1]);
    // double theta = atan2(pos[1],pos[0]);
    // theta += (theta < 0.0)*2.0*M_PI;
 
    // /* Get the 3d vector index */
    // iVec grid;
    // grid[0] = static_cast<int>(abs(r-EPS)/(gridSize[0]+EPS));
    // grid[1] = static_cast<int>(abs(theta-EPS)/(gridSize[1]+EPS));
    // grid[2] = static_cast<int>(abs(pos[2] + 0.5*side[2] - EPS )/(gridSize[2] + EPS));
 
    // /* return the flattened index */
    // int gNumber = grid[0]*NGRIDSEP*NGRIDSEP + grid[1]*NGRIDSEP + grid[2];
 
    // PIMC_ASSERT(gNumber<numGrid);
    // return gNumber;
 
    int gNumber = 0;
    for (int i = 0; i < NDIM; i++) {  
        int scale = 1;
        for (int j = i+1; j < NDIM; j++) 
            scale *= NGRIDSEP;
        gNumber += scale * 
            static_cast<int>(abs( pos[i] + 0.5*side[i] - EPS ) / (gridSize[i] + EPS));
    }
    PIMC_ASSERT(gNumber<numGrid);
 
    return gNumber;
}

randPosition()

dVec Cylinder::randPosition ( MTRand &  random ) const

virtual

Return a random position inside the cylinder.

See also

http://extremelearning.com.au/how-to-generate-uniformly-random-points-on-n-spheres-and-n-balls/

Implements Container.

Definition at line 342 of file container.cpp.

                                                {
 
    dVec randPos;
    double r = 0.5*side[0]*sqrt(random.randExc());
    double phi = random.randExc(2.0*M_PI);
    randPos[0] = r * cos(phi);
    randPos[1] = r * sin(phi);
    randPos[2] = side[2]*(-0.5 + random.randExc());
 
    return randPos;
}

randUpdateJumpShell()

dVec Cylinder::randUpdateJumpShell	(	MTRand &	random,
		const dVec &	pos
	)		const

Return a random position close to the supplied one.

Shell Jump

Definition at line 369 of file container.cpp.

                                                                         {
    dVec randPos;
    randPos = pos;
    double theta = atan2(pos[1],pos[0]);
    double oldr = sqrt(pos[0]*pos[0] + pos[1]*pos[1]);
    double newr;
 
    if (random.rand() > 0.5)
        newr = oldr + (1.00 + 2.50*random.rand());
    else
        newr = oldr - (1.00 + 2.50*random.rand());
 
    if (newr < 0.0)
        newr *= -1.0;
 
    double ranTheta = M_PI*(-0.05 + 0.1*random.rand());
    randPos[0] = newr*cos(theta + ranTheta);
    randPos[1] = newr*sin(theta + ranTheta);
    randPos[2] += constants()->displaceDelta()*(-0.5 + random.rand());
 
    putInside(randPos);
    return randPos;
}

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randUpdateSmall()

dVec Cylinder::randUpdateSmall	(	MTRand &	random,
		const dVec &	pos
	)		const

Return a random position close to the supplied one.

Same Shell.

Definition at line 397 of file container.cpp.

                                                                     {
    dVec randPos;
    randPos = pos;
    for (int i = 0; i < NDIM; i++) 
        randPos[i] += constants()->displaceDelta()*(-0.5 + random.rand());
    putInside(randPos);
    return randPos;
}

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

• include/container.h
• src/container.cpp