Initialize the atom configuration. More...

#include "initAtoms.h"
#include <math.h>
#include <assert.h>
#include "constants.h"
#include "decomposition.h"
#include "parallel.h"
#include "random.h"
#include "linkCells.h"
#include "timestep.h"
#include "memUtils.h"
#include "performanceTimers.h"

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Functions
static void	computeVcm (SimFlat *s, real_t vcm[3])
	Computes the center of mass velocity of the system. More...

Atoms *	initAtoms (LinkCell *boxes)
	Allocates memory to store atom data. More...

void	destroyAtoms (Atoms *atoms)

void	createFccLattice (int nx, int ny, int nz, real_t lat, SimFlat *s)
	Creates atom positions on a face centered cubic (FCC) lattice with nx * ny * nz unit cells and lattice constant lat. More...

void	setVcm (SimFlat *s, real_t newVcm[3])
	Sets the center of mass velocity of the system. More...

void	setTemperature (SimFlat *s, real_t temperature)
	Sets the temperature of system. More...

void	randomDisplacements (SimFlat *s, real_t delta)
	Add a random displacement to the atom positions. More...

Detailed Description

Initialize the atom configuration.

Definition in file initAtoms.c.

Function Documentation

void computeVcm	(	SimFlat *	s,
		real_t	vcm[3]
	)

static

Computes the center of mass velocity of the system.

Definition at line 202 of file initAtoms.c.

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void createFccLattice	(	int	nx,
		int	ny,
		int	nz,
		real_t	lat,
		SimFlat *	s
	)

Creates atom positions on a face centered cubic (FCC) lattice with nx * ny * nz unit cells and lattice constant lat.

Set momenta to zero.

Definition at line 64 of file initAtoms.c.

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void destroyAtoms ( Atoms * atoms )

Definition at line 52 of file initAtoms.c.

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Atoms* initAtoms ( LinkCell * boxes )

Allocates memory to store atom data.

Call functions such as createFccLattice and setTemperature to set up initial atom positions and momenta.

Definition at line 23 of file initAtoms.c.

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void randomDisplacements	(	SimFlat *	s,
		real_t	delta
	)

Add a random displacement to the atom positions.

Atoms are displaced by a random distance in the range [-delta, +delta] along each axis.

Parameters

[in] delta The maximum displacement (along each axis).

Definition at line 187 of file initAtoms.c.

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void setTemperature	(	SimFlat *	s,
		real_t	temperature
	)

Sets the temperature of system.

Selects atom velocities randomly from a boltzmann (equilibrium) distribution that corresponds to the specified temperature. This random process will typically result in a small, but non zero center of mass velocity and a small difference from the specified temperature. For typical MD runs these small differences are unimportant, However, to avoid possible confusion, we set the center of mass velocity to zero and scale the velocities to exactly match the input temperature.

Definition at line 145 of file initAtoms.c.

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void setVcm	(	SimFlat *	s,
		real_t	newVcm[3]
	)

Sets the center of mass velocity of the system.

Parameters

[in] newVcm The desired center of mass velocity.

Definition at line 111 of file initAtoms.c.

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Functions

Detailed Description

Function Documentation