Package ffx.potential.parameters

Class PolarizeType

java.lang.Object

ffx.potential.parameters.BaseType

ffx.potential.parameters.PolarizeType

All Implemented Interfaces:

Comparator<String>

@FFXProperty(name="polarize",
             clazz=java.lang.String.class,
             propertyGroup=PotentialFunctionParameter,
             description="[1 integer, up to 3 reals and up to 8 integers]\nProvides the values for a single atomic dipole polarizability parameter.\nThe initial integer modifier, if positive, gives the atom type number for which a polarizability parameter is to be defined.\nIf the first integer modifier is negative, then the parameter value to follow applies only to the specific atom whose atom number is the negative of the modifier.\nThe first real number modifier gives the value of the dipole polarizability in Ang^3.\nThe second real number modifier, if present, gives the Thole damping value.\nA Thole value of zero implies undamped polarization.\nThe third real modifier, if present, gives a direct field damping value only used with the AMOEBA+ polarization model.\nThe remaining integer modifiers list the atom type numbers of atoms directly bonded to the current atom and which will be considered to be part of the current atom\u2019s polarization group.\nIf the parameter is for a specific atom, then the integers defining the polarization group are ignored.\n")
public final class PolarizeType
extends BaseType
implements Comparator<String>

The PolarizeType class defines an isotropic atomic polarizability.

If this modifier is not present, then charge penetration values will be used for polarization damping, as in the HIPPO polarization model.

Since:

1.0

Author:

Michael J. Schnieders

Field Summary

Fields

Modifier and Type	Field	Description
final double	ddp	Direct polarization damping.
static final double	DEFAULT_DIRECT_11_SCALE
static final double	DEFAULT_DIRECT_12_SCALE
static final double	DEFAULT_DIRECT_13_SCALE
static final double	DEFAULT_DIRECT_14_SCALE
static final double	DEFAULT_POLAR_12_INTRA
static final double	DEFAULT_POLAR_12_SCALE
static final double	DEFAULT_POLAR_13_INTRA
static final double	DEFAULT_POLAR_13_SCALE
static final double	DEFAULT_POLAR_14_INTRA
static final double	DEFAULT_POLAR_14_SCALE
static final double	DEFAULT_POLAR_15_INTRA
static final double	DEFAULT_POLAR_15_SCALE
double	pdamp	Value of polarizability scale factor.
final double	polarizability	Isotropic polarizability in units of Angstroms^3.
int[]	polarizationGroup	Connected types in the polarization group of each atom (can be null).
final double	thole	Thole damping factor.
int	type	Atom type number.

Fields inherited from class ffx.potential.parameters.BaseType

key

Constructor Summary

Constructors

Constructor	Description
PolarizeType(int atomType, double polarizability, double thole, double ddp, int[] polarizationGroup)	PolarizeType Constructor.
PolarizeType(PolarizeType polarizeType, double polarizability)	Construct a PolarizeType from a reference type and updated polarizability.

Method Summary

Modifier and Type	Method	Description
void	add(int atomType)	Add an atom type to the polarization group.
static void	addXMLAttributes(Element node, ForceField forceField)	Add constant attributes to the AmoebaMultipoleForce
static void	assignPolarizationGroups(Atom[] atoms, int[][] ip11, int[][] ip12, int[][] ip13)	assignPolarizationGroups.
static PolarizeType	average(PolarizeType polarizeType1, PolarizeType polarizeType2, int atomType, int[] polarizationGroup)	Average two PolarizeType instances.
int	compare(String s1, String s2)
boolean	equals(Object o)
static void	growGroup(List<Integer> group, Atom seed)	A recursive method that checks all atoms bonded to the seed atom for inclusion in the polarization group.
int	hashCode()
static PolarizeType	parse(String input, String[] tokens)	Construct a PolarizeType from an input string.
String	toString()
Element	toXML(Document doc)	Write PolarizeType to OpenMM XML format.

Methods inherited from class ffx.potential.parameters.BaseType

getKey, log, print, setKey, setKey

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Comparator

reversed, thenComparing, thenComparing, thenComparing, thenComparingDouble, thenComparingInt, thenComparingLong

Field Details

DEFAULT_DIRECT_11_SCALE

public static final double DEFAULT_DIRECT_11_SCALE

See Also:

• Constant Field Values

DEFAULT_DIRECT_12_SCALE

public static final double DEFAULT_DIRECT_12_SCALE

See Also:

• Constant Field Values

DEFAULT_DIRECT_13_SCALE

public static final double DEFAULT_DIRECT_13_SCALE

See Also:

• Constant Field Values

DEFAULT_DIRECT_14_SCALE

public static final double DEFAULT_DIRECT_14_SCALE

See Also:

• Constant Field Values

DEFAULT_POLAR_12_SCALE

public static final double DEFAULT_POLAR_12_SCALE

See Also:

• Constant Field Values

DEFAULT_POLAR_13_SCALE

public static final double DEFAULT_POLAR_13_SCALE

See Also:

• Constant Field Values

DEFAULT_POLAR_14_SCALE

public static final double DEFAULT_POLAR_14_SCALE

See Also:

• Constant Field Values

DEFAULT_POLAR_15_SCALE

public static final double DEFAULT_POLAR_15_SCALE

See Also:

• Constant Field Values

DEFAULT_POLAR_12_INTRA

public static final double DEFAULT_POLAR_12_INTRA

See Also:

• Constant Field Values

DEFAULT_POLAR_13_INTRA

public static final double DEFAULT_POLAR_13_INTRA

See Also:

• Constant Field Values

DEFAULT_POLAR_14_INTRA

public static final double DEFAULT_POLAR_14_INTRA

See Also:

• Constant Field Values

DEFAULT_POLAR_15_INTRA

public static final double DEFAULT_POLAR_15_INTRA

See Also:

• Constant Field Values

thole

public final double thole

Thole damping factor.

pdamp

public double pdamp

Value of polarizability scale factor.

ddp

public final double ddp

Direct polarization damping.

polarizability

public final double polarizability

Isotropic polarizability in units of Angstroms^3.

type

public int type

Atom type number.

polarizationGroup

public int[] polarizationGroup

Connected types in the polarization group of each atom (can be null).

Constructor Details

PolarizeType

public PolarizeType(int atomType,
 double polarizability,
 double thole,
 double ddp,
 int[] polarizationGroup)

PolarizeType Constructor.

Parameters:

atomType - The atom type.

polarizability - The polarizability.

thole - The Thole damping constant.

polarizationGroup - The atom types in the polarization group.

PolarizeType

public PolarizeType(PolarizeType polarizeType,
 double polarizability)

Construct a PolarizeType from a reference type and updated polarizability.

Parameters:

polarizeType - The reference PolarizeType.

polarizability - The updated polarizability.

Method Details

assignPolarizationGroups

public static void assignPolarizationGroups(Atom[] atoms,
 int[][] ip11,
 int[][] ip12,
 int[][] ip13)

assignPolarizationGroups.

Parameters:

atoms - an array of Atom objects.

ip11 - an array of

invalid reference

int

objects.

ip12 - an array of

invalid reference

int

objects.

ip13 - an array of

invalid reference

int

objects.

average

public static PolarizeType average(PolarizeType polarizeType1,
 PolarizeType polarizeType2,
 int atomType,
 int[] polarizationGroup)

Average two PolarizeType instances. The atom types to include in the new polarizationGroup must be supplied.

Parameters:

polarizeType1 - The first PolarizeType.

polarizeType2 - The second PolarizeType.

atomType - The atom type to use for the new PolarizeType.

polarizationGroup - The atom types to include in the new polarizationGroup.

Returns:

The averaged PolarizeType.

parse

public static PolarizeType parse(String input,
 String[] tokens)

Construct a PolarizeType from an input string.

Parameters:

input - The overall input String.

tokens - The input String tokenized.

Returns:

a PolarizeType instance.

growGroup

public static void growGroup(List<Integer> group,
 Atom seed)

A recursive method that checks all atoms bonded to the seed atom for inclusion in the polarization group. The method is called on each newly found group member.

Parameters:

group - XYZ indices of current group members.

seed - The bonds of the seed atom are queried for inclusion in the group.

add

public void add(int atomType)

Add an atom type to the polarization group.

Parameters:

atomType - The atom type to add.

compare

public int compare(String s1,
 String s2)

Specified by:

compare in interface Comparator<String>

equals

public boolean equals(Object o)

Specified by:

equals in interface Comparator<String>

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

toString

public String toString()

Basic toString method.

Nicely formatted polarization type.

Overrides:

toString in class BaseType

addXMLAttributes

public static void addXMLAttributes(Element node,
 ForceField forceField)

Add constant attributes to the AmoebaMultipoleForce

Parameters:

node - the AmoebaMultipoleForce element.

forceField - the ForceField for collecting constants.

toXML

public Element toXML(Document doc)

Write PolarizeType to OpenMM XML format.