SubSystem Class Reference

Public Member Functions
	SubSystem ()
void	InitNeighborNode (std::array< int, 3 > vproc)
void	Update (double DeltaT)
void	Kick (double DeltaT)
void	AtomCopy ()
std::vector< int >	AtomMove (bool)
void	ShiftAtoms ()
void	WrapAtoms ()
int	bbd (Atom atom, int ku)
int	bmv (Atom atom, int ku)
void	EvalProps (int stepCount)
void	WriteXYZ (int step)

Static Public Member Functions
static double	Dmod (double a, double b)
static double	RandR (double *seed)
static void	RandVec3 (double *p, double *seed)

Public Attributes
int	pid
	sequential processor ID of this cell
int	n
	Number of resident atoms in this processor.
int	nglob
	Total number of atoms summed over processors.
double	comt
	elapsed wall clock time & Communication time in second
std::array< double, 3 >	al
	Box length per processor.
std::array< int, 3 >	vid
	Vector index of this processor.
std::array< int, 3 >	myparity
	Parity of this processor.
std::array< int, 6 >	nn
	Neighbor node list of this processor.
std::vector< std::vector< double > >	sv
	Shift vector to the 6 neighbors.
std::array< double, 3 >	vSum
std::array< double, 3 >	gvSum
std::vector< Atom >	atoms
	resident and moved in atoms
std::array< int, 3 >	vproc {}
	Vector processor decomposition of subsystems arranged in a 3D array.
std::array< int, 3 >	InitUcell {}
	Unit cell system properties.
double	Density
	Density of fcc.
double	InitTemp
	Inital temperature of system.
double	DeltaT
	Time scale of single step in simulation.
int	StepLimit
	Total number of steps to carry out the simulation.
int	StepAvg
	Average of simulation steps before reporting system information.
double	kinEnergy
	Calculated kinetic energy while simulation.
double	potEnergy
	Calculated potential energy while simulation.
double	totEnergy
	Calculated total energy energy while simulation.
double	temperature
	Calculated temperature of the system at the end of the time-step.

Constructor & Destructor Documentation

SubSystem()

SubSystem::SubSystem

(

)

Constructor - Creates subsystem with with the specified atoms in the input file and assigns random velocities

Subsystem refers to the group of atoms and their properties when the atoms reside in a processor/rank

Member Function Documentation

AtomCopy()

void SubSystem::AtomCopy

(

)

Exchange boundary-atom co-ordinates among neighbor nodes

AtomMove()

vector< int > SubSystem::AtomMove

(

bool

shouldTrack

)

Send moved-out atoms to neighbor nodes and receive moved-in atoms from neighbor nodes returns the indexes of the atoms that have moved

bbd()

int SubSystem::bbd	(	Atom	atom,
		int	ku
	)

Returns true if an Atom lies in them boundary to a neighbor ID

Parameters

atom	atom id in the system
ku	the neighboring direction w.r.t the subsystem

Returns

1 true, 0 false

bmv()

int SubSystem::bmv	(	Atom	atom,
		int	ku
	)

Return true if an Atom lies in them boundary to a neighbor ID

Parameters

atom	atom id in the system
ku	the neighboring direction w.r.t the subsystem

Returns

1 true, 0 false

Dmod()

static double SubSystem::Dmod ( double  a, double  b  )

inlinestatic

Method to return modulus

Parameters

a
b

Returns

EvalProps()

void SubSystem::EvalProps

(

int

stepCount

)

Evaluates physical properties: kinetic, potential & total energies

Parameters

stepCount

Time step corresponding to the which the evaluation takes place

InitNeighborNode()

void SubSystem::InitNeighborNode

(

std::array< int, 3 >

vproc

)

Initiates the neighbor node table for the Subsystem decomposed in X,Y & Z as a 3D matrix as defined by vproc

Parameters

vproc

Vector processor decomposition of subsystems arranged in a 3D array

Kick()

void SubSystem::Kick

(

double

DeltaT

)

Update the velocities after a time-step DeltaT

Parameters

DeltaT

RandR()

static double SubSystem::RandR ( double *  seed )

inlinestatic

Method to generat erandom double value from a seed

Parameters

seed

Returns

RandVec3()

static void SubSystem::RandVec3 ( double *  p, double *  seed  )

inlinestatic

Fills up a double pointer of length 3 with random values

Parameters

p
seed

ShiftAtoms()

void SubSystem::ShiftAtoms

(

)

Obtain the final position of the atoms by shifting the atom co-ordinates of the moved in-atoms to the position of the atoms they replace for the time step

Update()

void SubSystem::Update

(

double

DeltaT

)

Update Atomic co-ordinates to r(t+Dt)

Parameters

DeltaT

duration for which the state must be updated

WrapAtoms()

void SubSystem::WrapAtoms

(

)

Take atom co-ordinated from global co-ordinates and translate them to wrapped box co-ordinates

WriteXYZ()

void SubSystem::WriteXYZ

(

int

step

)

Write out XYZ co-ordinates from each frame into separate files

Parameters

step

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

• MD_Engine/pmd.hpp
• MD_Engine/pmd.cpp