P2WaterSzalewicz

java.lang.Object
- etomica.models.water.P2WaterSzalewicz

All Implemented Interfaces:

IPotential, IPotentialAtomic, IPotentialTorque, PotentialSoft
```
public class P2WaterSzalewicz
extends java.lang.Object
implements IPotentialTorque
```
Water potential as described by http://dx.doi.org/10.1063/1.4875097 This class handles 2-body, 3-body and induction terms. The behavior can be set to compute all(ALL), induction only (INDUCTION), only 2-body (TWO_BODY) or only non-additive (NON_PAIR) via the setComponent() method.

Nested Class Summary

Nested Classes
Modifier and Type Class Description

static class P2WaterSzalewicz.Component

class P2WaterSzalewicz.P2H2OSC

Nested Classes
Modifier and Type	Class	Description
`static class`	`P2WaterSzalewicz.Component`
`class`	`P2WaterSzalewicz.P2H2OSC`

Field Summary

Fields
Modifier and Type	Field	Description
`protected double[]`	`aj`
`protected double[]`	`aj3`
`protected Vector[]`	`allOr`
`protected double`	`bohrConv`
`static boolean`	`broken3body`
`protected static double[]`	`c`
`protected static double[]`	`c3`
`protected static double[]`	`chrg3`
`protected static double`	`cmzFix`
`protected Vector[]`	`com0`
`protected Vector[]`	`com3`
`protected P2WaterSzalewicz.Component`	`component`
`protected static double`	`core`
`static boolean`	`debug`
`protected double[][]`	`distPol`
`protected double[][]`	`dmptab`
`protected Vector[][]`	`E0`
`protected Vector`	`E1`
`protected Vector`	`epom`
`protected static double`	`gamma`
`protected Vector[]`	`Gpol`
`protected Vector`	`H1O`
`protected static double[]`	`H1pol`
`protected Vector`	`H2O`
`protected static double[]`	`H2pol`
`protected int[]`	`ijk`
`protected static int[][]`	`ind_beta`
`protected static int[][]`	`ind_C10`
`protected static int[][]`	`ind_C6`
`protected static int[][]`	`ind_C8`
`protected static int[]`	`ind_charge`
`protected static int[][]`	`ind_d1`
`protected static int[][]`	`ind_d10`
`protected static int[][]`	`ind_d6`
`protected static int[][]`	`ind_d8`
`protected int[][][][][][]`	`ind_lin`
`protected static int[][]`	`ind3_beta`
`protected static int[][]`	`ind3_gamma`
`protected static int[][]`	`ind3_R0`
`protected static double`	`mass`
`protected static int`	`nlin`
`protected int`	`nlin3`
`protected static int`	`npol`
`protected static int`	`nsite3`
`protected Vector`	`or2`
`protected static double[]`	`params`
`protected static double[]`	`params3`
`protected static double[]`	`pol`
`protected Vector`	`polE1`
`protected static double`	`R0`
`protected Vector[]`	`Rpol`
`protected Vector`	`rTmp`
`protected Vector`	`S2`
`protected Vector`	`S3`
`protected Vector`	`sep`
`protected static double[][]`	`siteDoubles`
`protected Vector[][]`	`sitePos`
`protected Vector[][]`	`sitePos3`
`protected static Vector[]`	`sites`
`protected Space`	`space`

Constructor Summary

Constructors
Constructor Description

P2WaterSzalewicz(Space space, int nBody)

Constructors
Constructor	Description
`P2WaterSzalewicz(Space space, int nBody)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`protected double`	`damp(int n, double beta, double r)`
`protected void`	`efieldBohrDamped(Vector veci, Vector[] sitebt, double delta)`	Calculate the contribution of molecule b to the field on a Use the CC-pol site charges.
`double`	`energy(IAtomList atoms)`	Returns the interaction energy between the given atoms.
`protected double[]`	`eulerFromOrientation(OrientationFull3D or)`
`protected void`	`fill(int iat, int jat, int kat, int ip, int jp, int kp, int nr)`
`protected double`	`fit3b()`
`static double[]`	`getQ()`
`double`	`getRange()`	Returns the range over which the potential applies.
`static Vector[]`	`getSites(Space space)`
`Vector[]`	`gradient(IAtomList atoms)`	Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied.
`Vector[]`	`gradient(IAtomList atoms, Tensor pressureTensor)`	Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor.
`Vector[][]`	`gradientAndTorque(IAtomList atoms)`
`double`	`indN_iter()`	Compute the iterative induction between N water molecules using several polarization centers in the molecular plane
`static void`	`main(java.lang.String[] args)`
`static void`	`main1(java.lang.String[] args)`
`static void`	`main2(java.lang.String[] args)`
`static void`	`main3(java.lang.String[] args)`
`P2WaterSzalewicz.P2H2OSC`	`makeSemiclassical(double temperature)`
`int`	`nBody()`	The number of atoms on which the potential depends.
`void`	`printFortranInput(IAtomList atoms)`	Prints atom coordinates and euler angles in a format compatible with the CCpol fortran program The orientations are taken from the given atoms.
`protected double`	`S2fit(double AOOex, double AHHex, double AOHex, double betaOO, double betaHH, double betaOH, double exqpos)`
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts so that it can properly consider the boundaries.
`void`	`setComponent(P2WaterSzalewicz.Component newComponent)`
`protected void`	`Tprod(Vector Ri, Vector Rj, Vector u, double rij)`	Calculate the vector V resulting from the action of the dipole propagator tensor T_ij on U Ri, Rj - position vectors of molecules i and j, respectively rij = \|Ri - Rj\|^(-3)
`double`	`virial(IAtomList atoms)`

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

Field Detail

broken3body
```
public static final boolean broken3body
```
See Also:

Constant Field Values

siteDoubles

protected static final double[][] siteDoubles

mass
```
protected static final double mass
```

cmzFix
```
protected static final double cmzFix
```

sites
```
protected static final Vector[] sites
```

params
```
protected static final double[] params
```

c
```
protected static final double[] c
```

ind_charge

protected static final int[] ind_charge

ind_beta

protected static final int[][] ind_beta

params3

protected static final double[] params3

c3
```
protected static final double[] c3
```

ind3_beta

protected static final int[][] ind3_beta

ind3_gamma

protected static final int[][] ind3_gamma

ind3_R0
```
protected static final int[][] ind3_R0
```

ind_d1
```
protected static final int[][] ind_d1
```

ind_d6
```
protected static final int[][] ind_d6
```

ind_d8
```
protected static final int[][] ind_d8
```

ind_d10
```
protected static final int[][] ind_d10
```

ind_C6
```
protected static final int[][] ind_C6
```

ind_C8
```
protected static final int[][] ind_C8
```

ind_C10
```
protected static final int[][] ind_C10
```

gamma
```
protected static final double gamma
```
See Also:

Constant Field Values

R0
```
protected static final double R0
```
See Also:

Constant Field Values

sitePos
```
protected final Vector[][] sitePos
```

com0
```
protected final Vector[] com0
```

rTmp
```
protected final Vector rTmp
```

or2
```
protected final Vector or2
```

allOr
```
protected final Vector[] allOr
```

npol
```
protected static final int npol
```
See Also:

Constant Field Values

E0
```
protected final Vector[][] E0
```

E1
```
protected final Vector E1
```

polE1
```
protected final Vector polE1
```

ind_lin

protected final int[][][][][][] ind_lin

component

protected P2WaterSzalewicz.Component component

aj3
```
protected final double[] aj3
```

bohrConv
```
protected final double bohrConv
```

space
```
protected final Space space
```

nlin
```
protected static final int nlin
```
See Also:

Constant Field Values

nlin3
```
protected final int nlin3
```

aj
```
protected final double[] aj
```

core
```
protected static final double core
```
See Also:

Constant Field Values

debug
```
public static boolean debug
```

Rpol
```
protected final Vector[] Rpol
```

Gpol
```
protected final Vector[] Gpol
```

epom
```
protected final Vector epom
```

distPol
```
protected final double[][] distPol
```

dmptab
```
protected final double[][] dmptab
```

pol
```
protected static final double[] pol
```

H1pol
```
protected static final double[] H1pol
```

H2pol
```
protected static final double[] H2pol
```

H1O
```
protected final Vector H1O
```

H2O
```
protected final Vector H2O
```

com3
```
protected final Vector[] com3
```

sitePos3
```
protected final Vector[][] sitePos3
```

sep
```
protected final Vector sep
```

nsite3
```
protected static final int nsite3
```
See Also:

Constant Field Values

ijk
```
protected final int[] ijk
```

chrg3
```
protected static final double[] chrg3
```

S2
```
protected final Vector S2
```

S3
```
protected final Vector S3
```

Constructor Detail

P2WaterSzalewicz

public P2WaterSzalewicz(Space space,
                        int nBody)

Method Detail
- getSites
```
public static Vector[] getSites(Space space)
```
- getQ
```
public static double[] getQ()
```
- fill
```
protected void fill(int iat,
                    int jat,
                    int kat,
                    int ip,
                    int jp,
                    int kp,
                    int nr)
```
- setComponent
```
public void setComponent(P2WaterSzalewicz.Component newComponent)
```
- virial
```
public double virial(IAtomList atoms)
```
  Specified by:
  
  virial in interface PotentialSoft
- gradient
```
public Vector[] gradient(IAtomList atoms)
```
  Description copied from interface: PotentialSoft
  
  Returns the gradient of the potential as it applies to each atom in the given AtomSet, indicating how the energy would change as the position of the first atom is varied. The method is allowed to return an array of Vectors with fewer elements than the number of atoms in the AtomSet.
  
  Specified by:
  
  gradient in interface PotentialSoft
  
  Returns:
- gradient
```
public Vector[] gradient(IAtomList atoms,
                         Tensor pressureTensor)
```
  Description copied from interface: PotentialSoft
  
  Returns the same gradient as gradient(AtomSet) and also adds in the contribution of the AtomSet to the pressureTensor. Their contribution is added to the given Tensor. This combined method exists for computational efficiency. Calculating the pressureTensor is generally trivial once the gradient is known but often requires intermediate information.
  
  Specified by:
  
  gradient in interface PotentialSoft
- energy
```
public double energy(IAtomList atoms)
```
  Description copied from interface: IPotentialAtomic
  
  Returns the interaction energy between the given atoms. There might be 0, 1, 2 or more atoms in the AtomSet.
  
  Specified by:
  
  energy in interface IPotentialAtomic
- printFortranInput
```
public void printFortranInput(IAtomList atoms)
```
  Prints atom coordinates and euler angles in a format compatible with the CCpol fortran program The orientations are taken from the given atoms. The com0 array is assumed to be set up. Call this method after calling energy or from within the energy method itself.
- eulerFromOrientation
```
protected double[] eulerFromOrientation(OrientationFull3D or)
```
- damp
```
protected double damp(int n,
                      double beta,
                      double r)
```
- indN_iter
```
public double indN_iter()
```
  Compute the iterative induction between N water molecules using several polarization centers in the molecular plane
- efieldBohrDamped
```
protected void efieldBohrDamped(Vector veci,
                                Vector[] sitebt,
                                double delta)
```
  Calculate the contribution of molecule b to the field on a Use the CC-pol site charges. Units: input positions of bohr, output fields in au
- Tprod
```
protected void Tprod(Vector Ri,
                     Vector Rj,
                     Vector u,
                     double rij)
```
  Calculate the vector V resulting from the action of the dipole propagator tensor T_ij on U Ri, Rj - position vectors of molecules i and j, respectively rij = |Ri - Rj|^(-3)
- fit3b
```
protected double fit3b()
```
- S2fit
```
protected double S2fit(double AOOex,
                       double AHHex,
                       double AOHex,
                       double betaOO,
                       double betaHH,
                       double betaOH,
                       double exqpos)
```
- getRange
```
public double getRange()
```
  Description copied from interface: IPotential
  
  Returns the range over which the potential applies. IAtoms with a greater separation do not interact.
  
  Specified by:
  
  getRange in interface IPotential
- setBox
```
public void setBox(Box box)
```
  Description copied from interface: IPotential
  
  Informs the potential of the box on which it acts so that it can properly consider the boundaries.
  
  Specified by:
  
  setBox in interface IPotential
- nBody
```
public int nBody()
```
  Description copied from interface: IPotential
  
  The number of atoms on which the potential depends.
  
  Specified by:
  
  nBody in interface IPotential
- gradientAndTorque
```
public Vector[][] gradientAndTorque(IAtomList atoms)
```
  Specified by:
  
  gradientAndTorque in interface IPotentialTorque
- makeSemiclassical
```
public P2WaterSzalewicz.P2H2OSC makeSemiclassical(double temperature)
```
- main1
```
public static void main1(java.lang.String[] args)
```
- main3
```
public static void main3(java.lang.String[] args)
```
- main2
```
public static void main2(java.lang.String[] args)
```
- main
```
public static void main(java.lang.String[] args)
```

Class P2WaterSzalewicz

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

broken3body

siteDoubles

mass

cmzFix

sites

params

c

ind_charge

ind_beta

params3

c3

ind3_beta

ind3_gamma

ind3_R0

ind_d1

ind_d6

ind_d8

ind_d10

ind_C6

ind_C8

ind_C10

gamma

R0

sitePos

com0

rTmp

or2

allOr

npol

E0

E1

polE1

ind_lin

component

aj3

bohrConv

space

nlin

nlin3

aj

core

debug

Rpol

Gpol

epom

distPol

dmptab

pol

H1pol

H2pol

H1O

H2O

com3

sitePos3

sep

nsite3

ijk

chrg3

S2

S3

Constructor Detail

P2WaterSzalewicz

Method Detail

getSites

getQ

fill

setComponent

virial

gradient

gradient

energy

printFortranInput

eulerFromOrientation