Class ForceField

java.lang.Object

org.episteme.natural.chemistry.computational.ForceField

public class ForceField
extends Object

Molecular mechanics force field calculations.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

Field Summary

Fields

Modifier and Type	Field	Description
static final Real	CC_BOND_LENGTH
static final Real	CC_DOUBLE_LENGTH
static final Real	CC_EPSILON
static final Real	CC_SIGMA
static final Real	CH_BOND_LENGTH
static final Real	OO_EPSILON
static final Real	OO_SIGMA

Constructor Summary

Constructors

Constructor	Description
ForceField()

Method Summary

Modifier and Type	Method	Description
static Real	angleBend(Real theta, Real theta0, Real k)	Harmonic angle bending: V(θ) = 0.5 * k * (θ - θ0)²
static Real	bondStretch(Real r, Real r0, Real k)	Harmonic bond stretching: V(r) = 0.5 * k * (r - r0)²
static Real	calculatePotentialEnergy(Molecule molecule)	Calculates total potential energy of a molecule.
static Real	coulomb(Real q1, Real q2, Real r)	Coulomb interaction (kcal/mol when q in e, r in Ã…)
static Real	lennardJones(Real r, Real epsilon, Real sigma)	Lennard-Jones 12-6 potential.
static Real	lennardJonesForce(Real r, Real epsilon, Real sigma)	Lennard-Jones force.
static Real	morse(Real r, Real re, Real De, Real a)	Morse potential: V(r) = D_e * [1 - exp(-a*(r-r_e))]²
static Real	torsion(Real phi, Real Vn, int n, Real gamma)	Torsional potential: V(φ) = V_n/2 * [1 + cos(n*φ- γ)]

Methods inherited from class Object

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

Field Details

CC_EPSILON

public static final Real CC_EPSILON

CC_SIGMA

public static final Real CC_SIGMA

OO_EPSILON

public static final Real OO_EPSILON

OO_SIGMA

public static final Real OO_SIGMA

CC_BOND_LENGTH

public static final Real CC_BOND_LENGTH

CC_DOUBLE_LENGTH

public static final Real CC_DOUBLE_LENGTH

CH_BOND_LENGTH

public static final Real CH_BOND_LENGTH

Constructor Details

ForceField

public ForceField()

Method Details

lennardJones

public static Real lennardJones(Real r,
 Real epsilon,
 Real sigma)

Lennard-Jones 12-6 potential. V(r) = ε * [(σ/r)^12 - 2*(σ/r)^6]

lennardJonesForce

public static Real lennardJonesForce(Real r,
 Real epsilon,
 Real sigma)

Lennard-Jones force. F(r) = 12ε/r * [(σ/r)^12 - (σ/r)^6]

bondStretch

public static Real bondStretch(Real r,
 Real r0,
 Real k)

Harmonic bond stretching: V(r) = 0.5 * k * (r - r0)²

angleBend

public static Real angleBend(Real theta,
 Real theta0,
 Real k)

Harmonic angle bending: V(θ) = 0.5 * k * (θ - θ0)²

torsion

public static Real torsion(Real phi,
 Real Vn,
 int n,
 Real gamma)

Torsional potential: V(φ) = V_n/2 * [1 + cos(n*φ- γ)]

coulomb

public static Real coulomb(Real q1,
 Real q2,
 Real r)

Coulomb interaction (kcal/mol when q in e, r in Ã…)

morse

public static Real morse(Real r,
 Real re,
 Real De,
 Real a)

Morse potential: V(r) = D_e * [1 - exp(-a*(r-r_e))]²

calculatePotentialEnergy

public static Real calculatePotentialEnergy(Molecule molecule)

Calculates total potential energy of a molecule.