public class SimDimerLJadatom extends Simulation
Modifier and Type | Field and Description |
---|---|
ActivityIntegrate |
activityIntegrateDimer |
ActivityIntegrate |
activityIntegrateMD |
ActivityIntegrate |
activityIntegrateMin |
IVectorMutable |
adAtomPos |
IBox |
box |
CalcGradientDifferentiable |
calcGradientDifferentiable |
java.lang.Boolean |
calcModes |
CalcVibrationalModes |
calcVibrationalModes |
int[] |
d |
double[][] |
dForces |
SpeciesSpheresMono |
fixed |
double[] |
frequencies |
IntegratorDimerRT |
integratorDimer |
IntegratorDimerMin |
integratorDimerMin |
IntegratorVelocityVerlet |
integratorMD |
double[] |
lambdas |
java.lang.Boolean |
minSearch |
int[] |
modeSigns |
SpeciesSpheresMono |
movable |
IMoleculeList |
movableSet |
IVectorMutable[] |
normal |
java.lang.Boolean |
normalDir |
double[] |
positions |
PotentialMaster |
potentialMaster |
IVectorMutable[] |
saddle |
java.lang.Boolean |
saddleFine |
eventManager, random, seeds, space
Constructor and Description |
---|
SimDimerLJadatom() |
Modifier and Type | Method and Description |
---|---|
void |
enableDimerSearch(java.lang.String fileName,
long maxSteps,
java.lang.Boolean orthoSearch,
java.lang.Boolean fine) |
void |
enableMinimumSearch(java.lang.String fileName,
java.lang.Boolean normalDir) |
void |
enableMolecularDynamics(long maxSteps) |
void |
generateConfigs(java.lang.String fileName,
double percentd) |
void |
initializeConfiguration(java.lang.String fileName) |
static void |
main(java.lang.String[] args) |
void |
randomizePositions() |
void |
removeAtoms(double distance,
IVectorMutable center) |
void |
setMovableAtoms(double distance,
IVectorMutable center) |
addBox, addSpecies, atomTypeAddedNotify, atomTypeRemovedNotify, getBox, getBoxCount, getController, getEventManager, getIntegrator, getRandom, getRandomSeeds, getSpace, getSpecies, getSpeciesCount, makeUniqueElementSymbol, removeBox, removeSpecies, setRandom
public final PotentialMaster potentialMaster
public IntegratorVelocityVerlet integratorMD
public IntegratorDimerRT integratorDimer
public IntegratorDimerMin integratorDimerMin
public IBox box
public IVectorMutable[] saddle
public IVectorMutable[] normal
public SpeciesSpheresMono fixed
public SpeciesSpheresMono movable
public ActivityIntegrate activityIntegrateMD
public ActivityIntegrate activityIntegrateDimer
public ActivityIntegrate activityIntegrateMin
public CalcGradientDifferentiable calcGradientDifferentiable
public CalcVibrationalModes calcVibrationalModes
public double[][] dForces
public int[] d
public int[] modeSigns
public double[] positions
public double[] lambdas
public double[] frequencies
public IMoleculeList movableSet
public IVectorMutable adAtomPos
public java.lang.Boolean saddleFine
public java.lang.Boolean calcModes
public java.lang.Boolean minSearch
public java.lang.Boolean normalDir
public void setMovableAtoms(double distance, IVectorMutable center)
public void removeAtoms(double distance, IVectorMutable center)
public void initializeConfiguration(java.lang.String fileName)
public void generateConfigs(java.lang.String fileName, double percentd)
public void enableMolecularDynamics(long maxSteps)
public void enableDimerSearch(java.lang.String fileName, long maxSteps, java.lang.Boolean orthoSearch, java.lang.Boolean fine)
public void enableMinimumSearch(java.lang.String fileName, java.lang.Boolean normalDir)
public void randomizePositions()
public static void main(java.lang.String[] args)