P2CO2H2OWheatley

java.lang.Object
- etomica.models.co2.P2CO2H2OWheatley

All Implemented Interfaces:

IPotential, IPotentialAtomic, IPotentialTorque, PotentialSoft
```
public class P2CO2H2OWheatley
extends java.lang.Object
implements IPotentialTorque
```
Ab initio potential for CO2-H2O by Wheatley and Harvey http://dx.doi.org/10.1063/1.3574345 The CO2 molecule is expected first

Nested Class Summary

Nested Classes
Modifier and Type Class Description

class P2CO2H2OWheatley.P2CO2H2OSC

class P2CO2H2OWheatley.P2CO2H2OSCTI

Nested Classes
Modifier and Type	Class	Description
`class`	`P2CO2H2OWheatley.P2CO2H2OSC`
`class`	`P2CO2H2OWheatley.P2CO2H2OSCTI`

Field Summary

Fields
Modifier and Type	Field	Description
`protected Vector[]`	`allOr0`
`protected Vector[]`	`allOr1`
`protected static double`	`checkCore`
`protected static double`	`checkCoreCO`
`protected double`	`CO`
`protected static double`	`core`
`protected static double`	`coreCO`
`protected boolean`	`debugging`
`protected Vector`	`drij`
`protected static double[]`	`fparams`
`protected Vector[][]`	`gradientAndTorque`
`protected static int[][]`	`iparams`
`protected double`	`mass1`
`protected double`	`minR`
`protected Vector`	`or01`
`protected Vector`	`or02`
`protected Vector`	`orH2O3`
`protected Tensor`	`rot0`
`protected Tensor`	`rot1`
`protected Vector[][]`	`sitePos`
`protected static double`	`sitesCO2L`
`protected static double`	`sitesHH`
`protected static double`	`sitesOH`
`protected Space`	`space`
`protected Vector`	`torque`

Constructor Summary

Constructors
Constructor Description

P2CO2H2OWheatley(Space space)

Constructors
Constructor	Description
`P2CO2H2OWheatley(Space space)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`energy(IAtomList atoms)`	Returns the interaction energy between the given atoms.
`protected void`	`getPerp(Vector or, Vector perp1, Vector perp2)`
`double`	`getRange()`	Returns the range over which the potential applies.
`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)`
`static void`	`main(java.lang.String[] args)`	Randomly moves molcules all over, computing and checking 2nd derivative
`static void`	`main2(java.lang.String[] args)`
`static void`	`main2DGrid(java.lang.String[] args)`	Writes x-y grid of energies
`static void`	`mainQ(java.lang.String[] args)`	Check charges (all sums should be 0 for neutral molecules)
`static void`	`mainTestU(java.lang.String[] args)`	Reads geometry.txt file and computes energy for each configuration
`P2CO2H2OWheatley.P2CO2H2OSC`	`makeSemiclassical(double temperature)`	Creates a Feynman-Hibbs implementation of a semi-classical potential based on this model for the given temperature.
`P2CO2H2OWheatley.P2CO2H2OSCTI`	`makeSemiclassicalTI(double temperature)`	Creates a Takahashi-Imada implementation of a semi-classical potential based on this model for the given temperature.
`int`	`nBody()`	The number of atoms on which the potential depends.
`void`	`setBox(Box box)`	Informs the potential of the box on which it acts so that it can properly consider the boundaries.
`double`	`virial(IAtomList atoms)`

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

- Field Detail
  - iparams
```
protected static final int[][] iparams
```
  - fparams
```
protected static final double[] fparams
```
  - sitesCO2L
```
protected static final double sitesCO2L
```
    See Also:
    
    Constant Field Values
  - sitesOH
```
protected static final double sitesOH
```
    See Also:
    
    Constant Field Values
  - sitesHH
```
protected static final double sitesHH
```
    See Also:
    
    Constant Field Values
  - sitePos
```
protected final Vector[][] sitePos
```
  - space
```
protected final Space space
```
  - rot0
```
protected final Tensor rot0
```
  - rot1
```
protected final Tensor rot1
```
  - or01
```
protected final Vector or01
```
  - or02
```
protected final Vector or02
```
  - orH2O3
```
protected final Vector orH2O3
```
  - allOr0
```
protected final Vector[] allOr0
```
  - allOr1
```
protected final Vector[] allOr1
```
  - gradientAndTorque
```
protected final Vector[][] gradientAndTorque
```
  - drij
```
protected final Vector drij
```
  - torque
```
protected final Vector torque
```
  - mass1
```
protected final double mass1
```
  - minR
```
protected double minR
```
  - CO
```
protected double CO
```
  - core
```
protected static final double core
```
    See Also:
    
    Constant Field Values
  - coreCO
```
protected static final double coreCO
```
    See Also:
    
    Constant Field Values
  - checkCore
```
protected static final double checkCore
```
    See Also:
    
    Constant Field Values
  - checkCoreCO
```
protected static final double checkCoreCO
```
    See Also:
    
    Constant Field Values
  - debugging
```
protected boolean debugging
```
- Constructor Detail
  - P2CO2H2OWheatley
```
public P2CO2H2OWheatley(Space space)
```
- Method Detail
  - getPerp
```
protected void getPerp(Vector or,
                       Vector perp1,
                       Vector perp2)
```
  - 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
  - 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 P2CO2H2OWheatley.P2CO2H2OSC makeSemiclassical(double temperature)
```
    Creates a Feynman-Hibbs implementation of a semi-classical potential based on this model for the given temperature.
  - makeSemiclassicalTI
```
public P2CO2H2OWheatley.P2CO2H2OSCTI makeSemiclassicalTI(double temperature)
```
    Creates a Takahashi-Imada implementation of a semi-classical potential based on this model for the given temperature.
  - 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
  - mainTestU
```
public static void mainTestU(java.lang.String[] args)
                      throws java.io.IOException
```
    Reads geometry.txt file and computes energy for each configuration
    
    Throws:
    
    java.io.IOException
  - mainQ
```
public static void mainQ(java.lang.String[] args)
```
    Check charges (all sums should be 0 for neutral molecules)
  - main
```
public static void main(java.lang.String[] args)
```
    Randomly moves molcules all over, computing and checking 2nd derivative
  - main2
```
public static void main2(java.lang.String[] args)
```
  - main2DGrid
```
public static void main2DGrid(java.lang.String[] args)
                       throws java.io.IOException
```
    Writes x-y grid of energies
    
    Throws:
    
    java.io.IOException

Class P2CO2H2OWheatley

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

iparams

fparams

sitesCO2L

sitesOH

sitesHH

sitePos

space

rot0

rot1

or01

or02

orH2O3

allOr0

allOr1

gradientAndTorque

drij

torque

mass1

minR

CO

core

coreCO

checkCore

checkCoreCO

debugging

Constructor Detail

P2CO2H2OWheatley

Method Detail

getPerp

energy

getRange

setBox

nBody

gradientAndTorque

makeSemiclassical

makeSemiclassicalTI

virial

gradient

gradient

mainTestU

mainQ

main

main2

main2DGrid