Package ffx.xray

Class NeutronFormFactor

java.lang.Object

ffx.xray.NeutronFormFactor

All Implemented Interfaces:

FormFactor

public final class NeutronFormFactor
extends Object
implements FormFactor

This implementation uses the coefficients from International Tables, Vol. C, chapter 4.4.4.

Since:

1.0

Author:

Timothy D. Fenn

See Also:

• V. F. Sears, Int. Tables Vol. C (2006). Table 4.4.4.1
• B. T. M. Willis, Int. Tables Vol. C (2006). Chapter 6.1.3
• M. J. Schnieders, T. D. Fenn, V. S. Pande and A. T. Brunger, Acta Cryst. (2009). D65 952-965.

Constructor Summary

Constructors

Constructor	Description
NeutronFormFactor(Atom atom)	Constructor for NeutronFormFactor.
NeutronFormFactor(Atom atom, double badd)	Constructor for NeutronFormFactor.
NeutronFormFactor(Atom atom, double badd, double[] xyz)	Constructor for NeutronFormFactor.

Method Summary

Modifier and Type	Method	Description
double	f(HKL hkl)	f
static double[]	getFormFactorA(String atom)	getFormFactorA
static int	getFormFactorIndex(String atom)	getFormFactorIndex
double	rho(double f, double lambda, double[] xyz)	Compute the real space density rho
void	rhoGrad(double[] xyz, double dfc, RefinementMinimize.RefinementMode refinementmode)	Compute the real space gradient
void	update(double[] xyz)	update the coordinates to the current position
void	update(double[] xyz, double badd)	update the coordinates to the current position and Badd

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

NeutronFormFactor

public NeutronFormFactor(Atom atom)

Constructor for NeutronFormFactor.

Parameters:

atom - a Atom object.

NeutronFormFactor

public NeutronFormFactor(Atom atom,
 double badd)

Constructor for NeutronFormFactor.

Parameters:

atom - a Atom object.

badd - a double.

NeutronFormFactor

public NeutronFormFactor(Atom atom,
 double badd,
 double[] xyz)

Constructor for NeutronFormFactor.

Parameters:

atom - a Atom object.

badd - a double.

xyz - an array of double.

Method Details

getFormFactorA

public static double[] getFormFactorA(String atom)

getFormFactorA

Parameters:

atom - a String object.

Returns:

an array of double.

getFormFactorIndex

public static int getFormFactorIndex(String atom)

getFormFactorIndex

Parameters:

atom - a String object.

Returns:

a int.

f

public double f(HKL hkl)

f

Parameters:

hkl - a HKL object.

Returns:

a double.

rho

public double rho(double f,
 double lambda,
 double[] xyz)

Compute the real space density rho

Specified by:

rho in interface FormFactor

Parameters:

f - the current density to modify

lambda - the state variable

xyz - the requested point for evaluating density

Returns:

the real space density value at xyz

rhoGrad

public void rhoGrad(double[] xyz,
 double dfc,
 RefinementMinimize.RefinementMode refinementmode)

Compute the real space gradient

Specified by:

rhoGrad in interface FormFactor

Parameters:

xyz - the requested point for evaluating gradient

dfc - the multiplier to apply to the gradient

refinementmode - RefinementMinimize.RefinementMode determines which gradients will be computed

update

public void update(double[] xyz)

update the coordinates to the current position

Specified by:

update in interface FormFactor

Parameters:

xyz - an array of double.

update

public void update(double[] xyz,
 double badd)

update the coordinates to the current position and Badd

Specified by:

update in interface FormFactor

Parameters:

xyz - an array of double.

badd - a double.