Domain Class Reference

#include <domain.h>

Collaboration diagram for Domain:

List of all members.

Public Member Functions

Domain (char *filename)

Domain constructor creates an instance of a domain.

~Domain ()

void BoundaryType (enum BoundaryTypes b, int idir, int inside)

enum BoundaryTypes BoundaryType (int idir, int inside)

void setMinBound (int i, REAL x)

void setMaxBound (int i, REAL x)

REAL minBound (int i)

REAL maxBound (int i)

int computeBounds (REAL x0[], REAL x1[])

Collection< Molecule > * Molecules ()

int run (int niter)

The Domain solver: running niter iterations.

void step (int iter)

int boundary (Molecule *molecule)

void injection ()

Inject cross-boundary species:.

void interaction ()

void interaction (int icounter)

Interaction interact (Molecule *a, Molecule *b)

void init ()

void load (char *filename)

Initializing molecules according to bulk properties (restart=0).

void save (char *taskname)

Private Attributes

int * distribution

molecule counts for all species

REAL bounds [2][DIM]

char boundaryName [maxBoundaryTypes][WORDLENGTH]

to be depricated

Bulk bulk

bulk of the domain: initialized only if Run::option.restart=0

Boundary boundaries [DIM][2]

six boundaries of a hexahedral domain

Collection< Molecule > molecules

Collection of molecules.

Pool< Molecule > * pool

Molecule pointer pool.

Detailed Description

Computational Domain.

Implements main data types inside a computational domain

Definition at line 83 of file domain.h.

Constructor & Destructor Documentation

Domain::Domain ( char * filename )

Domain constructor creates an instance of a domain.

get domain specs from XML configfile

read XML input file

Loop over file records

set xterm output mode:

Read the number of molecules:

Read species:

load reactions

Read domain specs:

Read domain bounds

Read initial bulk properties

Read boundary specs

Read boundary reactions:

< probability for the formation of these products as opposed to different products If only one pair of products exists the probability = 1

Definition at line 72 of file domain.cc.

References Species::Reaction::Add(), Boundary::adiabatic, List< Element >::append(), Boundary::area, Geom::area(), AtomicMassUnit, AvogadroNumber, BoltzmannConstant, boundaries, boundary(), boundaryName, bounds, bulk, GridContainer::cellsize, Run::configfile, Species::Specie::Cp(), Collection< Element >::Current(), Species::Gas::density, DIM, distribution, DOCTYPE, elasticBoundary, Species::Reaction::Outcome::Enthalpy(), Species::Reaction::First(), GasConstant, Boundary::gases, Bulk::gases, IO::getCharAttr(), Collection< Element >::goFirst(), Collection< Element >::goNext(), Species::Specie::Id(), init(), Bulk::init(), Boundary::init(), Collection< Element >::init(), insideBoundary, Collection< Element >::isFirst(), Potential::lengthscale(), load(), Species::Specie::Mass(), maxBound(), maxBoundaryTypes, MAXLINLEN, minBound(), molecules, Species::Reaction::Next(), Species::nspecies, Collection< Element >::number(), openBoundary, Run::option, IO::parseFloat(), IO::parseWord(), periodicBoundary, pool, Species::Reaction::Outcome::Probability(), Species::Reaction::Outcome::Product(), GridContainer::put(), Boundary::reactions, Species::reactions, REAL, setMaxBound(), setMinBound(), Species::Specie::Size(), Gui::size, Species::species, Potential::strength(), Boundary::temperature, Bulk::Temperature(), TINY, Boundary::type, VOIDSPECIE, WORDLENGTH, XMAX, Gui::xmax, XMIN, Gui::xmin, and Option::xterm.

Domain::~Domain ( )

Definition at line 617 of file domain.cc.

References Run::option.

Member Function Documentation

int Domain::boundary ( Molecule * molecule )

< do reaction: A + B =

< new molecule A type

< new molecule B type

Definition at line 1076 of file domain.cc.

References boundaries, bounds, Molecule::Coordinates(), Species::Specie::Cp(), DIM, DOF, DOFI, DOFK, Gui::dx, elasticBoundary, Species::Reaction::Outcome::Enthalpy(), Species::Reaction::First(), Collection< Element >::insertAfter(), insideBoundary, Molecule::InternalEnergy(), Molecule::KineticEnergy(), LENGTH, Species::Specie::Mass(), molecules, MULC, Species::Reaction::Next(), openBoundary, periodicBoundary, Species::Reaction::Outcome::Probability(), Species::Reaction::Outcome::Product(), Species::reacted, Boundary::reactions, REAL, RND, Species::Specie::Size(), SMALL, Species::species, Run::time, Species::Reaction::Outcome::Time(), Molecule::Type(), Boundary::type, Molecule::Velocity(), VOIDSPECIE, XMAX, and XMIN.

Referenced by Domain(), injection(), and run().

enum BoundaryTypes Domain::BoundaryType	(	int	idir,
		int	inside
	)			`[inline]`

Definition at line 101 of file domain.h.

References boundaries, DIM, and Boundary::type.

void Domain::BoundaryType	(	enum BoundaryTypes	b,
		int	idir,
		int	inside
	)			`[inline]`

Definition at line 94 of file domain.h.

References boundaries, DIM, and Boundary::type.

int Domain::computeBounds	(	REAL	x0[],
		REAL	x1[]
	)

Definition at line 829 of file domain.cc.

References Molecule::Coordinates(), Collection< Element >::Current(), DIM, Collection< Element >::goFirst(), Collection< Element >::goNext(), Collection< Element >::isFirst(), LARGE, molecules, and REAL.

void Domain::init ( )

create local gas-array

Go over all gases

point to current gas

select current gas-specie

Estimate the average velocity and the number of molecules of each specie to be injected into the bulk

get molecule's mass in atomic units

convert molecule's mass to kg

average velocity in one direction

get density in kg/m^3

get the number of molecules in the bulk

Inject all molecules:

Definition at line 621 of file domain.cc.

References AtomicMassUnit, BoltzmannConstant, bulk, List< Element >::Current(), Species::Gas::density, Bulk::gases, List< Element >::goFirst(), List< Element >::goNext(), Species::Specie::Id(), Bulk::inject(), List< Element >::isFirst(), Species::Specie::Mass(), molecules, List< Element >::number(), Run::option, Species::Gas::specie, Species::species, Molecule::Temperature(), Bulk::Temperature(), and Bulk::Volume().

Referenced by Domain().

void Domain::injection ( )

Inject cross-boundary species:.

Inject cross-boundary species. The algorithm uses the density and temperature to caclulate the frequency of injection of molecules of specie, $s$ at the boundary. The injection frequency, $f_s$ per unit area, $A$ is computed as

$f_s = \frac{N}{\Delta\,t}$

where $\Delta\,t_s$ is the time interval at which a molecule hits the boundary area $A$ , and $N$ is the number of molecules in a volume with the base $A$ and length $\Delta\,x$ as shown in the figure:

'

The time inteval, $\Delta\,t$ , between the collisions can be related to the component of velocity of the molecule of species $s$

, in direction $x$

, $v_{sx}$ , as follows:

$\Delta\,t = \frac{2\Delta\,x}{v_{sx}}$

The number of molecules, $N$ can be related to density, $\rho$ , as:

$N = \frac{\rho}{\mu}\Delta\,x\,A$

where $\mu$ is the mass of one molecule and $A = \Delta\,y\,\Delta\,z$ . Thus, the frequency is:

$f_s = \frac{\rho}{\mu}\Delta\,x\,A\frac{v_{sx}}{2\Delta\,x} = \frac{\rho\,v_{sx}}{2\mu}A$

get time-step in sec

Go over all 6 boundaries:

select a boundary

get boundry area in m^2

get boundary temperature in K

create local gas-array

Go over all gases

point to current gas

select current gas-specie

Use kinetic theory of gases to estimate collision frequency with the wall and the number of molecules injected. This number can be fractional, so split it into integer and fractional part and inject the fractional part using probability.

get molecule's mass in atomic units

convert molecule's mass to kg

get density in kg/m^3

estimate collision frequency per unit area

calculate the number of collisions with the boundary during the past time step

get the whole integer number of molecules injected

calculate the fractional part of a molecule injected

Inject all whole molecules:

Probabilistically inject the fractional molecules:

Definition at line 1260 of file domain.cc.

References Boundary::area, Geom::area(), AtomicMassUnit, BoltzmannConstant, boundaries, boundary(), Species::Gas::density, DIM, Boundary::gases, List< Element >::goFirst(), Boundary::Inject(), Species::Specie::Mass(), molecules, REAL, RND, Species::Gas::specie, Species::species, step(), Boundary::temperature, and Run::time.

Referenced by run().

Interaction Domain::interact	(	Molecule *	a,
		Molecule *	b
	)

Computes interaction between two molecules with the exchange of energy and momentum according to hard-ball collisions, and the possibility of chemical reactions. Also estimates time to the next collision. Initializing molecules according to bulk properties (restart=0) The velocity of each molecule is set from given temperature according to:

$\frac{3}{2}kT = \frac{mV_{av}^2}{2}$

Since the average velocity relates to the average velocity in one direction, x, as:

$V_{av}^2 = 3V_{x,av}^2$

we obtain for $V_{av,x} = kT$

Definition at line 1486 of file domain.cc.

References Species::Reaction::Outcome::ActivationEnergy(), Species::annihalated, Species::collided, Molecule::Coordinates(), Species::Specie::Cp(), DIM, DOF, DOFI, DOFK, Palette::dvi, Gui::dx, Species::Reaction::Outcome::Enthalpy(), Species::Reaction::First(), Species::Specie::Id(), Molecule::InternalEnergy(), Species::Specie::Mass(), Species::missed, Species::Reaction::Next(), Species::nspecies, Species::Reaction::Outcome::Probability(), Species::Reaction::Outcome::Product(), Species::reacted, Species::reactions, REAL, RND, SCLP, Species::Specie::Size(), SMALL, Species::species, Molecule::Type(), Molecule::Velocity(), and VOIDSPECIE.

Referenced by interaction().

void Domain::interaction ( int icounter )

DDD: dirty fix, should be as below, but did not work

DDD: end dirty fix

DDD: dirty fix, should be as below, but did not work

DDD

DDD: dirty fix: some interactions may go unaccounted

DDD

Definition at line 1383 of file domain.cc.

void Domain::interaction ( )

void Domain::load ( char * filename )

Initializing molecules according to bulk properties (restart=0).

Definition at line 687 of file domain.cc.

References Collection< Element >::append(), Molecule::Coordinate(), Potential::Cutoff(), DIM, Molecule::InternalEnergy(), IO::ioutput, LARGE, Potential::lengthscale(), MAXLINLEN, molecules, Species::nspecies, Collection< Element >::number(), Run::option, REAL, Species::Specie::Size(), Gui::size, Species::species, Run::time, Molecule::Type(), Molecule::Velocity(), and WORDLENGTH.

Referenced by Domain().

REAL Domain::maxBound ( int i ) [inline]

Definition at line 111 of file domain.h.

References bounds.

Referenced by Domain(), and Gui::readconf().

REAL Domain::minBound ( int i ) [inline]

Definition at line 110 of file domain.h.

References bounds.

Referenced by Domain(), and Gui::readconf().

Collection<Molecule>* Domain::Molecules ( ) [inline]

Definition at line 115 of file domain.h.

References molecules.

Referenced by Gui::display(), and Gui::initdisp().

int Domain::run ( int niter )

The Domain solver: running niter iterations.

The main loop over niter iterations or till the end of time:

Definition at line 849 of file domain.cc.

Referenced by Gui::animate(), Gui::keyboard(), main(), and Gui::runmany().

void Domain::save ( char * taskname )

Definition at line 1935 of file domain.cc.

References Molecule::Coordinate(), Collection< Element >::Current(), Run::elapsed(), Collection< Element >::goFirst(), Collection< Element >::goNext(), Species::Specie::Id(), Molecule::InternalEnergy(), IO::ioutput, Collection< Element >::isFirst(), MAXLINLEN, molecules, Collection< Element >::number(), Run::option, Species::species, Run::time, Molecule::Type(), Molecule::Velocity(), and VOIDSPECIE.

Referenced by Gui::keyboard(), main(), and run().

void Domain::setMaxBound	(	int	i,
		REAL	x
	)			`[inline]`

Definition at line 109 of file domain.h.

References bounds.

Referenced by Domain(), and Gui::initdisp().

void Domain::setMinBound	(	int	i,
		REAL	x
	)			`[inline]`

Definition at line 108 of file domain.h.

References bounds.

Referenced by Domain(), and Gui::initdisp().

void Domain::step ( int iter )

Referenced by injection(), and run().

Member Data Documentation

Boundary Domain::boundaries[DIM][2] [private]

six boundaries of a hexahedral domain

Definition at line 88 of file domain.h.

Referenced by boundary(), BoundaryType(), Domain(), and injection().

char Domain::boundaryName[maxBoundaryTypes][WORDLENGTH] [private]

to be depricated

Definition at line 86 of file domain.h.

Referenced by Domain().

REAL Domain::bounds[2][DIM] [private]

Definition at line 85 of file domain.h.

Referenced by boundary(), Domain(), maxBound(), minBound(), setMaxBound(), and setMinBound().

Bulk Domain::bulk [private]

bulk of the domain: initialized only if Run::option.restart=0

Definition at line 87 of file domain.h.

Referenced by Domain(), and init().

int* Domain::distribution [private]

molecule counts for all species

Definition at line 84 of file domain.h.

Referenced by Domain(), and run().

Collection<Molecule> Domain::molecules [private]

Collection of molecules.

Definition at line 89 of file domain.h.

Referenced by boundary(), computeBounds(), Domain(), init(), injection(), load(), Molecules(), run(), and save().

Pool<Molecule>* Domain::pool [private]

Molecule pointer pool.

Definition at line 90 of file domain.h.

Referenced by Domain().

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


Public Member Functions
	Domain (char *filename)
	Domain constructor creates an instance of a domain.
	~Domain ()
void	BoundaryType (enum BoundaryTypes b, int idir, int inside)
enum BoundaryTypes	BoundaryType (int idir, int inside)
void	setMinBound (int i, REAL x)
void	setMaxBound (int i, REAL x)
REAL	minBound (int i)
REAL	maxBound (int i)
int	computeBounds (REAL x0[], REAL x1[])
Collection< Molecule > *	Molecules ()
int	run (int niter)
	The Domain solver: running niter iterations.
void	step (int iter)
int	boundary (Molecule *molecule)
void	injection ()
	Inject cross-boundary species:.
void	interaction ()
void	interaction (int icounter)
Interaction	interact (Molecule a, Molecule b)
void	init ()
void	load (char *filename)
	Initializing molecules according to bulk properties (restart=0).
void	save (char *taskname)
Private Attributes
int *	distribution
	molecule counts for all species
REAL	bounds [2][DIM]
char	boundaryName [maxBoundaryTypes][WORDLENGTH]
	to be depricated
Bulk	bulk
	bulk of the domain: initialized only if Run::option.restart=0
Boundary	boundaries [DIM][2]
	six boundaries of a hexahedral domain
Collection< Molecule >	molecules
	Collection of molecules.
Pool< Molecule > *	pool
	Molecule pointer pool.