core
Class SimSystem

java.lang.Object
  core.SimSystem

public class SimSystem

extends java.lang.Object

Contains the information for simulation system, such as number of dimensions, box dimension.

Since:

0.1

Version:

0.1, November 2002

Author:

Mika Kastenholz

See Also:

Particles

Field Summary

Angles	ang All Angles involving non-hydrogen atoms.
Angles	angh All Angles involving hydrogen atoms.
Bonds	bond All Bonds involving non-hydrogen atoms.
Bonds	bondh All Bonds involving hydrogen atoms.
double[]	box Box dimension.
Dihedrals	dih All Dihedrals involving non-hydrogen atoms.
Dihedrals	dihh All Dihedrals involving hydrogen atoms.
static int	DIM Number of dimensions used.
DenseExclusions	exclusionmap HashMap for Exclusions.
double	FPEPSI 1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) $\frac{1}{{4\pi \varepsilon _0 }}$
double	HBAR Planck's constant @f$\hbar @f$.
ImproperDihedrals	idih All ImproperDihedrals involving non-hydrogen atoms.
ImproperDihedrals	idihh All ImproperDihedrals involving hydrogen atoms.
LJ14HashMap	lj14map HashMap for LJ14.
LJTypeHashMap	ljmap HashMap for LJType look-up.
double	radP water probe radius; default 0.14 nm.

Constructor Summary

SimSystem()

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

ljmap

public LJTypeHashMap ljmap

HashMap for LJType look-up. Takes a LJType (int i, int j), returns the corresponding parameters.

exclusionmap

public DenseExclusions exclusionmap

HashMap for Exclusions. Takes 2 atoms (int i, int j), returns the corresponding boolean.

lj14map

public LJ14HashMap lj14map

HashMap for LJ14. Takes 2 atoms (int i, int j), returns the corresponding boolean.

box

public double[] box

Box dimension.

bondh

public Bonds bondh

All Bonds involving hydrogen atoms.

bond

public Bonds bond

All Bonds involving non-hydrogen atoms.

angh

public Angles angh

All Angles involving hydrogen atoms.

ang

public Angles ang

All Angles involving non-hydrogen atoms.

idihh

public ImproperDihedrals idihh

All ImproperDihedrals involving hydrogen atoms.

idih

public ImproperDihedrals idih

All ImproperDihedrals involving non-hydrogen atoms.

dihh

public Dihedrals dihh

All Dihedrals involving hydrogen atoms.

dih

public Dihedrals dih

All Dihedrals involving non-hydrogen atoms.

DIM

public static final int DIM

Number of dimensions used.

See Also:

Constant Field Values

HBAR

public double HBAR

Planck's constant @f$\hbar @f$.

FPEPSI

public double FPEPSI

1.0/(4.0*PI*EPS0) (EPS0 is the permittivity of vacuum) $\frac{1}{{4\pi \varepsilon _0 }}$

radP

public double radP

water probe radius; default 0.14 nm.

Constructor Detail

SimSystem

public SimSystem()