P2WaterPotentialsJankowski

java.lang.Object
- etomica.potential.P2WaterPotentialsJankowski

All Implemented Interfaces:: IPotential, IPotentialAtomic

public class P2WaterPotentialsJankowski
extends java.lang.Object
implements IPotentialAtomic

Field Summary

Fields
Modifier and Type	Field	Description
`protected static double`	`a0`
`protected static double`	`alfst`
`protected static Vector[]`	`alignedV1`
`protected static Vector[]`	`alignedV2`
`protected static double[]`	`angles`
`protected static double`	`anoise`
`protected Box`	`b`
`protected static Vector[]`	`bisectorVec`
`protected static double[]`	`bl`
`protected Boundary`	`boundary`
`protected static double[]`	`c`
`protected static Vector[]`	`cartA`
`protected static Vector[]`	`cartB`
`protected static double[]`	`ccpol2Angles`
`protected static double[]`	`ccpol2BL`
`protected static double`	`cmtoau`
`protected static boolean`	`comHack`
`protected static double`	`comHackDist`
`protected double`	`eMon`
`protected static boolean`	`flag`
`protected static boolean`	`flip`
`protected static double`	`har2kcal`
`protected static int`	`iasdone`
`protected int`	`icc`
`protected static int`	`idonl`
`protected int`	`iEmbed`
`protected int`	`iMonomer`
`protected static int`	`iopt`
`protected static int`	`iPotParts`
`protected static int`	`ipr`
`protected int`	`iSurf`
`protected static int`	`isyst`
`protected static int[][][]`	`itypus`
`protected static int`	`iweight`
`protected static int`	`linp`
`protected static int`	`lout`
`protected static int`	`maxpar1`
`protected static int`	`maxpar2`
`protected static double`	`mH`
`protected static double`	`mH2O`
`protected static double`	`mO`
`protected static int`	`naamax`
`protected static int`	`nbbmax`
`protected static int`	`npowers`
`protected static int`	`nsitea`
`protected static int`	`nsiteb`
`protected static int`	`nsitemax`
`protected static int`	`ntpot`
`protected static int`	`ntypemax`
`protected static int[]`	`numtm`
`protected static double[][][]`	`parab`
`protected static double[][]`	`param`
`protected static Vector[]`	`posVec`
`protected IPotentialAtomic`	`pRigid`
`protected static double`	`r0`
`protected static double`	`rcond`
`protected static double`	`rHSCore`
`protected static Vector[]`	`sa`
`protected static double`	`safetl`
`protected static Vector[]`	`sb`
`protected static int[]`	`set_sites_itypea`
`protected static Vector`	`set_sites_sa`
`protected static Vector[]`	`set_sites_sitea`
`protected static Vector[][]`	`siteat`
`protected static Vector[][]`	`sitebt`
`protected Space`	`space`
`protected static double`	`timlim`
`protected double`	`tKelvin`
`protected static double`	`tolf`
`protected static double`	`tolr`
`protected static Vector`	`tttprod`
`protected static double[]`	`values`

Constructor Summary

Constructors
Constructor	Description
`P2WaterPotentialsJankowski(Space space, int iSurface, int iMon, double tSim, IPotentialAtomic pRigid)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`static double`	`align_on_z_axis(Vector[] carta, Vector[] cartb)`
`static void`	`atomToPosVec(IAtom atomi)`
`static double`	`d(int n, double beta, double r)`
`static double`	`dipind(int iaa, int ibb, int[] itypea, int[] itypeb)`
`void`	`eck_rad_tst(Vector[] rPos)`
`double`	`energy(IAtomList atoms)`	Returns the interaction energy between the given atoms.
`double[]`	`getAngles()`
`double[]`	`getBondLengths()`
`double`	`getEnergy(Vector[] carta, Vector[] cartb)`
`double`	`getRange()`	Returns the range over which the potential applies.
`static void`	`main(java.lang.String[] args)`
`int`	`nBody()`	The number of atoms on which the potential depends.
`static IAtomList`	`posVecToAtoms(Vector[] a1, Vector[] b1)`
`static double`	`poten()`
`static int`	`potparts(int iaa, int ibb, double rij, int ia, int ib, int[] itypea, int[] itypeb)`
`static int`	`potparts_old(int iaa, int ibb, double rij, int ia, int ib, int[] itypea, int[] itypeb)`
`static double`	`pots(double q1, double q2, double theta)`
`static void`	`processAtoms(IAtomList atomL)`
`void`	`put_rigid()`
`void`	`radau_f1_tst(Vector[] rPos)`
`static void`	`set_sites(Vector[] cartX)`
`static void`	`setAngles(double[] angleRadians)`
`static void`	`setBondLengths(double[] blAngstroms)`
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts so that it can properly consider the boundaries.
`static Vector`	`TTTprod(Vector Ri, Vector Rj, Vector u, double rij)`

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

Field Detail

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

Constant Field Values

naamax
```
protected static final int naamax
```
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Constant Field Values

nbbmax
```
protected static final int nbbmax
```
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Constant Field Values

ntypemax
```
protected static final int ntypemax
```
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Constant Field Values

maxpar1
```
protected static final int maxpar1
```
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Constant Field Values

maxpar2
```
protected static final int maxpar2
```
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Constant Field Values

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

values
```
protected static final double[] values
```

param

protected static final double[][] param

parab

protected static final double[][][] parab

nsitea
```
protected static final int nsitea
```
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Constant Field Values

nsiteb
```
protected static final int nsiteb
```
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Constant Field Values

ntpot
```
protected static final int ntpot
```
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Constant Field Values

idonl
```
protected static final int idonl
```
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Constant Field Values

iopt
```
protected static final int iopt
```
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Constant Field Values

iweight
```
protected static final int iweight
```
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Constant Field Values

iasdone
```
protected static final int iasdone
```
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Constant Field Values

linp
```
protected static final int linp
```
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Constant Field Values

lout
```
protected static final int lout
```
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Constant Field Values

ipr
```
protected static final int ipr
```
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Constant Field Values

isyst
```
protected static final int isyst
```
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Constant Field Values

npowers
```
protected static final int npowers
```
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Constant Field Values

tolf
```
protected static final double tolf
```
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Constant Field Values

tolr
```
protected static final double tolr
```
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Constant Field Values

anoise
```
protected static final double anoise
```
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Constant Field Values

timlim
```
protected static final double timlim
```
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Constant Field Values

alfst
```
protected static final double alfst
```
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Constant Field Values

safetl
```
protected static final double safetl
```
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Constant Field Values

r0
```
protected static final double r0
```
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Constant Field Values

rcond
```
protected static final double rcond
```
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Constant Field Values

a0
```
protected static final double a0
```
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Constant Field Values

har2kcal
```
protected static final double har2kcal
```
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Constant Field Values

cmtoau
```
protected static final double cmtoau
```
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Constant Field Values

mH
```
protected static final double mH
```
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Constant Field Values

mO
```
protected static final double mO
```
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Constant Field Values

mH2O
```
protected static final double mH2O
```
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Constant Field Values

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

Constant Field Values

iPotParts
```
protected static int iPotParts
```

bl
```
protected static double[] bl
```

angles
```
protected static double[] angles
```

ccpol2BL
```
protected static double[] ccpol2BL
```

ccpol2Angles
```
protected static double[] ccpol2Angles
```

set_sites_sitea

protected static Vector[] set_sites_sitea

sa
```
protected static Vector[] sa
```

sb
```
protected static Vector[] sb
```

alignedV1
```
protected static Vector[] alignedV1
```

alignedV2
```
protected static Vector[] alignedV2
```

bisectorVec
```
protected static Vector[] bisectorVec
```

posVec
```
protected static Vector[] posVec
```

siteat
```
protected static Vector[][] siteat
```

sitebt
```
protected static Vector[][] sitebt
```

set_sites_sa
```
protected static Vector set_sites_sa
```

cartA
```
protected static Vector[] cartA
```

cartB
```
protected static Vector[] cartB
```

set_sites_itypea

protected static int[] set_sites_itypea

numtm
```
protected static int[] numtm
```

tttprod
```
protected static Vector tttprod
```

itypus
```
protected static int[][][] itypus
```

comHackDist
```
protected static double comHackDist
```

flag
```
protected static boolean flag
```

comHack
```
protected static boolean comHack
```

flip
```
protected static boolean flip
```

boundary
```
protected Boundary boundary
```

space
```
protected Space space
```

iSurf
```
protected int iSurf
```

iEmbed
```
protected int iEmbed
```

icc
```
protected int icc
```

iMonomer
```
protected int iMonomer
```

pRigid
```
protected IPotentialAtomic pRigid
```

b
```
protected Box b
```

tKelvin
```
protected double tKelvin
```

eMon
```
protected double eMon
```

Constructor Detail

P2WaterPotentialsJankowski

public P2WaterPotentialsJankowski(Space space,
                                  int iSurface,
                                  int iMon,
                                  double tSim,
                                  IPotentialAtomic pRigid)

Method Detail

pots

public static double pots(double q1,
                          double q2,
                          double theta)

set_sites

public static void set_sites(Vector[] cartX)

TTTprod

public static Vector TTTprod(Vector Ri,
                             Vector Rj,
                             Vector u,
                             double rij)

dipind

public static double dipind(int iaa,
                            int ibb,
                            int[] itypea,
                            int[] itypeb)

d

public static double d(int n,
                       double beta,
                       double r)

potparts_old

public static int potparts_old(int iaa,
                               int ibb,
                               double rij,
                               int ia,
                               int ib,
                               int[] itypea,
                               int[] itypeb)

potparts

public static int potparts(int iaa,
                           int ibb,
                           double rij,
                           int ia,
                           int ib,
                           int[] itypea,
                           int[] itypeb)

poten
```
public static double poten()
```

align_on_z_axis

public static double align_on_z_axis(Vector[] carta,
                                     Vector[] cartb)

posVecToAtoms

public static IAtomList posVecToAtoms(Vector[] a1,
                                      Vector[] b1)

atomToPosVec

public static void atomToPosVec(IAtom atomi)

processAtoms

public static void processAtoms(IAtomList atomL)

main

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

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

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

radau_f1_tst

public void radau_f1_tst(Vector[] rPos)

eck_rad_tst

public void eck_rad_tst(Vector[] rPos)

put_rigid
```
public void put_rigid()
```

getBondLengths
```
public double[] getBondLengths()
```

setBondLengths

public static void setBondLengths(double[] blAngstroms)

getAngles
```
public double[] getAngles()
```

setAngles

public static void setAngles(double[] angleRadians)

getEnergy

public double getEnergy(Vector[] carta,
                        Vector[] cartb)

Class P2WaterPotentialsJankowski

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

nsitemax

naamax

nbbmax

ntypemax

maxpar1

maxpar2

c

values

param

parab

nsitea

nsiteb

ntpot

idonl

iopt

iweight

iasdone

linp

lout

ipr

isyst

npowers

tolf

tolr

anoise

timlim

alfst

safetl

r0

rcond

a0

har2kcal

cmtoau

mH

mO

mH2O

rHSCore

iPotParts

bl

angles

ccpol2BL

ccpol2Angles

set_sites_sitea

sa

sb

alignedV1

alignedV2

bisectorVec

posVec

siteat

sitebt

set_sites_sa

cartA

cartB

set_sites_itypea

numtm

tttprod

itypus

comHackDist

flag

comHack

flip

boundary

space

iSurf

iEmbed

icc

iMonomer

pRigid

b

tKelvin

eMon

Constructor Detail

P2WaterPotentialsJankowski