4.2.9 - Positioned Crystal Object - JdlPositionedCrystal

John W. Campbell

4.2.9.1 Introduction

This class stores details of a set crystal with one or two additional parameters directly relevant to the prediction of diffraction images.

Class, constructors and methods:

Class Details
Accessible Fields
Constructors
Set Values
Get Values
List Positioned Crystal Data

4.2.9.2 Class Details

Package:: Jdl.JdlPX;
Class name:: JdlPositionedCrystal
Class definition:: public class JdlPositionedCrystal
Extends:: Object
Implements:: Cloneable
Actions:: none

4.2.9.3 Accessible Fields

The following accessible fields have been defined:

JdlCell cell: JdlCell object defining the cell.
JdlSymmetry symm: JdlSymmetry object defining the symmetry.
boolean symmetry_set: Symmetry set flag: true if set, otherwise false.
boolean symmetry_complete: Symmetry complete flag: true if symmetry input complete, otherwise false.
double[][] umat: The U-Matrix.
double phi1: The first missetting angle in degrees.
double phi2: The second missetting angle in degrees.
double phi3: The second missetting angle in degrees.
double phi_orient: The start rotation angle of the goniometer.
double resolution: The resolution for a prediction in Angstroms.
int nwmax: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.
double eta: Mosaic spread in degrees.
double spot_size: The spot diameter in mm (for spot overlap calculations).

4.2.9.4 Constructors

4.2.9.4.1 Introduction

There are a series of constructors available specifying less or more parameter values explicitly and specifying full space group symmetry or only the crystal system and lattice type or both.

Constructors:

Constructor 1
Constructor 2
Constructor 3
Constructor 4
Constructor 5

Create a JdlPositionedCrystal object with default values for the spot size (0.5mm), eta (0.05), phi_orient (0.0) and the U-matrix ([1 0 0, 0 1 0, 0 0 1] with a full definition of the crystal symmetry.

Constructor Definition:

public JdlPositionedCrystal (JdlCell cell, JdlSymmetry symm, double resolution, int nwmax, double phi1, double phi2, double phi3)

Parameters List:

cell: The cell parameters in a JdlCell object (a, b, c, alpha, beta, gamma in Angstroms and degrees).
symm: A JdlSymmetry object defining the space group symmetry.
resolution: The resolution limit in Angstroms (for reflection prediction).
nwmax: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.
phi1: The first missetting angle in degrees.
phi2: The second missetting angle in degrees.
phi1: The third missetting angle in degrees.

4.2.9.4.3 Constructor 2

Create a JdlPositionedCrystal object with default values for the spot size (0.5mm), eta (0.05), phi_orient (0.0) and the U-matrix ([1 0 0, 0 1 0, 0 0 1] with only the crystal system and lattice type defining the symmetry.

Constructor Definition:

public JdlPositionedCrystal (JdlCell cell, int isys, int latt, double resolution, int nwmax, double phi1, double phi2, double phi3)

Parameters List:

cell: The cell parameters in a JdlCell object (a, b, c, alpha, beta, gamma in Angstroms and degrees).
isym: Crystal system (1-7) Tri, Mon, Ort, Tet, Hex, Rho, Cub.
latt: Lattice type (1-7) P, A, B, C, I, F, R.
resolution: The resolution limit in Angstroms (for reflection prediction).
nwmax: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.
phi1: The first missetting angle in degrees.
phi2: The second missetting angle in degrees.
phi1: The third missetting angle in degrees.

4.2.9.4.4 Constructor 3

Create a JdlPositionedCrystal object with a full definition of the crystal symmetry.

Constructor Definition:

public JdlPositionedCrystal (JdlCell cell, JdlSymmetry symm, double resolution, int nwmax, double [][] umat, double phi1, double phi2, double phi3, double phi_orient, double eta, double spot_size)

Parameters List:

cell: The cell parameters in a JdlCell object (a, b, c, alpha, beta, gamma in Angstroms and degrees).
symm: A JdlSymmetry object defining the space group symmetry.
resolution: The resolution limit in Angstroms (for reflection prediction).
nwmax: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.
umat: The U-Matrix
phi1: The first missetting angle in degrees.
phi2: The second missetting angle in degrees.
phi1: The third missetting angle in degrees.
phi_orient: Start rotation angle on goniometer.
eta: Mosaic spread in degrees.
spot_size: The spot diameter in mm (for spot overlap calculations).

4.2.9.4.5 Constructor 4

Create a JdlPositionedCrystal object with symmetry defined by crystal system and lattice type.

Constructor Definition:

public JdlPositionedCrystal (JdlCell cell, int isys, int latt, double resolution, int nwmax, double [][] umat, double phi1, double phi2, double phi3, double phi_orient, double eta, double spot_size)

Parameters List:

cell: The cell parameters in a JdlCell object (a, b, c, alpha, beta, gamma in Angstroms and degrees).
isym: Crystal system (1-7) Tri, Mon, Ort, Tet, Hex, Rho, Cub.
latt: Lattice type (1-7) P, A, B, C, I, F, R.
resolution: The resolution limit in Angstroms (for reflection prediction).
nwmax: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.
umat: The U-Matrix
phi1: The first missetting angle in degrees.
phi2: The second missetting angle in degrees.
phi1: The third missetting angle in degrees.
phi_orient: Start rotation angle on goniometer.
eta: Mosaic spread in degrees.
spot_size: The spot diameter in mm (for spot overlap calculations).

4.2.9.4.6 Constructor 5

Create a JdlPositionedCrystal object with a full definition of the crystal symmetry and with the crystal system and lattice type being set.

Constructor Definition:

public JdlPositionedCrystal (JdlCell cell, JdlSymmetry symm, int isys, int latt, double resolution, int nwmax, double [][] umat, double phi1, double phi2, double phi3, double phi_orient, double eta, double spot_size)

Parameters List:

cell: The cell parameters in a JdlCell object (a, b, c, alpha, beta, gamma in Angstroms and degrees).
symm: A JdlSymmetry object defining the space group symmetry.
isym: Crystal system (1-7) Tri, Mon, Ort, Tet, Hex, Rho, Cub.
latt: Lattice type (1-7) P, A, B, C, I, F, R.
resolution: The resolution limit in Angstroms (for reflection prediction).
nwmax: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.
umat: The U-Matrix
phi1: The first missetting angle in degrees.
phi2: The second missetting angle in degrees.
phi1: The third missetting angle in degrees.
phi_orient: Start rotation angle on goniometer.
eta: Mosaic spread in degrees.
spot_size: The spot diameter in mm (for spot overlap calculations).

4.2.9.5 Set Values

4.2.9.5.1 Introduction

This section has methods to set individual sets of values in the positioned crystal object. If the symmetry data (and/or crystal system and lattice type) need to be changed, a new JdlPositionedCrystal object should be constructed.

Methods:

Set cell - setCell
Set resolution - setResolution
Set nwmax - setNwMax
Set phi1 - setPhi1
Set phi2 - setPhi2
Set phi3 - setPhi3
Set phi_orient - setPhiOrient
Set mosaic spread - setEta
Set spot size - setSpotSize
Set U-Matrix - setUMatrix

4.2.9.5.2 Set cell - setCell

This method resets the cell parameters.

Method Definition:

public void setCell(JdlCell cell)

Parameters List:

cell: The cell parameters in a JdlCell object (a, b, c, alpha, beta, gamma in Angstroms and degrees).

4.2.9.5.3 Set resolution - setResolution

This method sets the prediction resolution.

Method Definition:

public void setResolution(double resolution)

Parameters List:

resolution: The resolution limit in Angstroms (for reflection prediction).

4.2.9.5.4 Set nwmax - setNwMax

This method sets the maximum acceptable number of images over which a spot may be spread.

Method Definition:

public void setNwMax(int nwmax)

Parameters List:

nwmax: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.

4.2.9.5.5 Set phi1 - setPhi1

This method sets the first missetting angle.

Method Definition:

public void setPhi1(double phi1)

Parameters List:

phi1: The first missetting angle in degrees.

4.2.9.5.6 Set phi2 - setPhi2

This method sets the second missetting angle.

Method Definition:

public void setPhi2(double phi2)

Parameters List:

phi2: The second missetting angle in degrees.

4.2.9.5.7 Set phi3 - setPhi3

This method sets the third missetting angle.

Method Definition:

public void setPhi3(double phi3)

Parameters List:

phi3: The third missetting angle in degrees.

4.2.9.5.8 Set phi_orient - setPhiOrient

This method sets the gonionmeter phi orientation start angle.

Method Definition:

public void setPhiOrient(double phi_orient)

Parameters List:

phi_orient: Start rotation angle on goniometer.

4.2.9.5.9 Set mosaic spread - setEta

This method sets the mosaic spread (eta) parameter.

Method Definition:

public void setEta(double eta)

Parameters List:

eta: Mosaic spread in degrees.

4.2.9.5.10 Set spot size - setSpotSize

This method sets the spot size for overlap calculations.

Method Definition:

public void setSpotSize(double spot_size)

Parameters List:

spot_size: The spot diameter in mm (for spot overlap calculations).

4.2.9.5.11 Set U-Matrix - setUMatrix

This method sets ther U-matrix.

Method Definition:

public void setUMatrix(Jdl3x3 umatr)

Parameters List:

umatr: The new U-matrix.

4.2.9.6 Get Values

4.2.9.6.1 Introduction

This section has methods to get individual sets of values from the positioned crystal object.

Methods:

Get symmetry - getSymmetry
Get symmetry status - getSymmetryStatus
Get crystal system - getSystem
Get lattice type - getLattice
Get cell - getCell
Get resolution - getResolution
Get nwmax - getNwMax
Get phi1 - getPhi1
Get phi2 - getPhi2
Get phi3 - getPhi3
Get phi_orient - getPhiOrient
Get mosaic spread - getEta
Get spot size - getSpotSize
Get U-Matrix - getUMatrix

4.2.9.6.2 Get symmetry - getSymmetry

Gets a reference to the crystal symmetry object if defined.

Method Definition:: public JdlSymmetry getSymmetry()
Parameters List:: none
Method Return:: A reference to the JdlSymmetry object (null if not defined).

4.2.9.6.3 Get symmetry status - getSymmetryStatus

Returns a status flag for the symmetry definition.

Method Definition:: public int getSymmetryStatus()
Parameters List:: none
Method Return:: Symmetry status flag:
= 0, Symmetry not defined
= 1, Symmetry defined and complete
= -1, Symmetry defined but incomplete

4.2.9.6.4 Get crystal system - getSystem

Returns the crystal system type (1-7) based on the full symmetry, if defined, or the input system type if the full symmetry was not defined.

Method Definition:: public int getSystem()
Parameters List:: none
Method Return:: The system number (1-7) Tri, Mon, Ort, Tet, Hex, Rho, Cub.

4.2.9.6.5 Get lattice type - getLattice

Returns the lattice type (1-7) based on the full symmetry, if defined, or the input lattice type if the full symmetry was not defined.

Method Definition:: public int getLattice()
Parameters List:: none
Method Return:: The lattice type (1-7) P, A, B, C, I, F, R.

4.2.9.6.6 Get cell - getCell

This method returns the cell parameters.

Method Definition:: public JdlCell getCell()
Parameters List:: none
Method Return:: The cell parameters in a new JdlCell object (a, b, c, alpha, beta, gamma in Angstroms and degrees).

4.2.9.6.7 Get resolution - getResolution

This method gets the prediction resolution.

Method Definition:: public double getResolution()
Parameters List:: none
Method Return:: The resolution limit in Angstroms (for reflection prediction).

4.2.9.6.8 Get nwmax - getNwMax

This method gets the maximum acceptable number of images over which a spot may be spread.

Method Definition:: public int getNwMax()
Parameters List:: none
Method Return:: The maximum number of images over which a reflection may be spread and not considered 'too wide' for processing.