Sam

java.lang.Object
- etomica.simulation.Simulation
- - etomica.modules.sam.Sam

```
public class Sam
extends Simulation
```
Self-assembled monolayer module.

Field Summary

Fields
Modifier and Type	Field	Description
`double`	`bondL_CC`
`double`	`bondTheta`
`Box`	`box`
`int`	`chainLength`
`double[]`	`chainPhi`
`double`	`chainPsi`
`double`	`chainTheta`
`ConfigurationSAM`	`config`
`CriterionTether3`	`criterion3`
`PotentialCalculationForceSumWall`	`forceSum`
`double`	`harmonicStrength`
`IntegratorVelocityVerletSAM`	`integrator`
`int`	`numXCells`
`int`	`numZCells`
`PotentialGroup`	`p1Intra`
`P1Sinusoidal`	`p1SurfaceBond`
`P2Harmonic`	`p2BondCC`
`P2Harmonic`	`p2BondCS`
`P2LennardJones`	`p2CH2`
`P2LennardJones`	`p2CH2CH3`
`P2SoftSphericalTruncatedSwitched`	`p2CH2CH3t`
`P2SoftSphericalTruncatedSwitched`	`p2CH2Surface`
`P2SoftSphericalTruncatedSwitched`	`p2CH2t`
`P2LennardJones`	`p2CH3`
`P2SoftSphericalTruncatedSwitched`	`p2CH3t`
`P2LennardJones`	`p2S`
`P2LennardJones`	`p2SCH2`
`P2SoftSphericalTruncatedSwitched`	`p2SCH2t`
`P2SoftSphericalTruncatedSwitched`	`p2St`
`P2SoftSphericalTruncatedSwitched`	`p2SulfurSurfaceLJ`
`P2Harmonic`	`p2SurfaceBond`
`P3BondAngle`	`p3Bond`
`P4BondTorsion`	`p4BondCCCC`
`P4BondTorsion`	`p4BondCCCS`
`IMoleculePositionDefinition`	`positionDefinition`
`PotentialMasterList`	`potentialMaster`
`double`	`sigmaCH2`
`double`	`sinusoidalB`
`double`	`sizeCellX`
`double`	`sizeCellZ`
`SpeciesGeneral`	`species`
`SpeciesGeneral`	`speciesSurface`
`P1WCAWall`	`wallPotential`

Fields inherited from class etomica.simulation.Simulation
eventManager, random, seeds, space

Constructor Summary

Constructors
Constructor Description

Sam()

Constructors
Constructor	Description
`Sam()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`void`	`findTetherBonds()`
`double`	`getChainPhi(int iChain)`
`double`	`getChainPsi()`
`double`	`getChainTheta()`
`int`	`getNumXCells()`
`int`	`getNumZCells()`
`static void`	`main(java.lang.String[] args)`
`void`	`setChainLength(int newChainLength)`
`void`	`setChainPhi(int iChain, double newPhi)`
`void`	`setChainPsi(double newPsi)`
`void`	`setChainTheta(double newTheta)`
`void`	`setNumXCells(int newNumXCells)`
`void`	`setNumZCells(int newNumZCells)`
`protected void`	`updateConformation(int iChain)`
`protected void`	`updateRCut()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from class etomica.simulation.Simulation
addBox, addSpecies, box, getBox, getBoxCount, getBoxes, getController, getEventManager, getIntegrator, getRandom, getRandomSeeds, getSpace, getSpecies, getSpeciesCount, getSpeciesList, makeBox, makeBox, makeUniqueElementSymbol, removeBox, setRandom, species

Field Detail

p1SurfaceBond

public final P1Sinusoidal p1SurfaceBond

sinusoidalB
```
public final double sinusoidalB
```

p2SurfaceBond
```
public final P2Harmonic p2SurfaceBond
```

harmonicStrength
```
public final double harmonicStrength
```

species
```
public SpeciesGeneral species
```

speciesSurface
```
public SpeciesGeneral speciesSurface
```

box
```
public Box box
```

integrator

public IntegratorVelocityVerletSAM integrator

positionDefinition

public IMoleculePositionDefinition positionDefinition

wallPotential
```
public P1WCAWall wallPotential
```

config
```
public ConfigurationSAM config
```

p2CH2
```
public P2LennardJones p2CH2
```

p2CH3
```
public P2LennardJones p2CH3
```

p2CH2CH3
```
public P2LennardJones p2CH2CH3
```

p2S
```
public P2LennardJones p2S
```

p2SCH2
```
public P2LennardJones p2SCH2
```

p2CH2t

public P2SoftSphericalTruncatedSwitched p2CH2t

p2CH3t

public P2SoftSphericalTruncatedSwitched p2CH3t

p2CH2CH3t

public P2SoftSphericalTruncatedSwitched p2CH2CH3t

p2St

public P2SoftSphericalTruncatedSwitched p2St

p2SCH2t

public P2SoftSphericalTruncatedSwitched p2SCH2t

p2BondCC
```
public P2Harmonic p2BondCC
```

p2BondCS
```
public P2Harmonic p2BondCS
```

p3Bond
```
public P3BondAngle p3Bond
```

p4BondCCCC
```
public P4BondTorsion p4BondCCCC
```

p4BondCCCS
```
public P4BondTorsion p4BondCCCS
```

p1Intra
```
public PotentialGroup p1Intra
```

p2SulfurSurfaceLJ

public P2SoftSphericalTruncatedSwitched p2SulfurSurfaceLJ

p2CH2Surface

public P2SoftSphericalTruncatedSwitched p2CH2Surface

criterion3
```
public CriterionTether3 criterion3
```

chainLength
```
public int chainLength
```

chainTheta
```
public double chainTheta
```

chainPsi
```
public double chainPsi
```

chainPhi
```
public double[] chainPhi
```

bondL_CC
```
public double bondL_CC
```

bondTheta
```
public double bondTheta
```

forceSum

public PotentialCalculationForceSumWall forceSum

potentialMaster

public PotentialMasterList potentialMaster

numZCells
```
public int numZCells
```

numXCells
```
public int numXCells
```

sizeCellZ
```
public double sizeCellZ
```

sizeCellX
```
public double sizeCellX
```

sigmaCH2
```
public double sigmaCH2
```

Constructor Detail
- Sam
```
public Sam()
```

Method Detail

main

public static void main(java.lang.String[] args)

updateConformation

protected void updateConformation(int iChain)

getChainTheta
```
public double getChainTheta()
```

setChainTheta

public void setChainTheta(double newTheta)

getChainPsi
```
public double getChainPsi()
```

setChainPsi

public void setChainPsi(double newPsi)

setChainPhi

public void setChainPhi(int iChain,
                        double newPhi)

getChainPhi

public double getChainPhi(int iChain)

findTetherBonds
```
public void findTetherBonds()
```

getNumZCells
```
public int getNumZCells()
```

setNumZCells

public void setNumZCells(int newNumZCells)

getNumXCells
```
public int getNumXCells()
```

setNumXCells

public void setNumXCells(int newNumXCells)

updateRCut
```
protected void updateRCut()
```

setChainLength

public void setChainLength(int newChainLength)

Class Sam

Field Summary

Fields inherited from class etomica.simulation.Simulation

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from class etomica.simulation.Simulation

Field Detail

p1SurfaceBond

sinusoidalB

p2SurfaceBond

harmonicStrength

species

speciesSurface

box

integrator

positionDefinition

wallPotential

config

p2CH2

p2CH3

p2CH2CH3

p2S

p2SCH2

p2CH2t

p2CH3t

p2CH2CH3t

p2St

p2SCH2t

p2BondCC

p2BondCS

p3Bond

p4BondCCCC

p4BondCCCS

p1Intra

p2SulfurSurfaceLJ

p2CH2Surface

criterion3

chainLength

chainTheta

chainPsi

chainPhi

bondL_CC

bondTheta

forceSum

potentialMaster

numZCells

numXCells

sizeCellZ

sizeCellX

sigmaCH2

Constructor Detail

Sam

Method Detail

main

updateConformation

getChainTheta

setChainTheta

getChainPsi

setChainPsi

setChainPhi

getChainPhi

findTetherBonds

getNumZCells

setNumZCells

getNumXCells

setNumXCells

updateRCut

setChainLength