ffx.crystal.Crystal

Direct Known Subclasses:: NCSCrystal, ReplicatesCrystal

public class Crystal extends Object

The Crystal class encapsulates the lattice parameters and space group that describe the geometry and symmetry of a crystal. Methods are available to apply the minimum image convention and space group symmetry operators.

Since:

1.0

Author:

Michael J. Schnieders

See Also:

Field Summary

Fields

Modifier and Type

Field

Description

double

a

Length of the cell edge in the direction of the a basis vector.

double[][]

A

Matrix to convert from Cartesian to fractional coordinates.

double

A00

Entry in the A matrix.

double

A01

Entry in the A matrix.

double

A02

Entry in the A matrix.

double

A10

Entry in the A matrix.

double

A11

Entry in the A matrix.

double

A12

Entry in the A matrix.

double

A20

Entry in the A matrix.

double

A21

Entry in the A matrix.

double

A22

Entry in the A matrix.

final double[][]

Ai

Matrix to convert from fractional to Cartesian coordinates.

double

Ai00

Entry in the Ai matrix.

double

Ai01

Entry in the Ai matrix.

double

Ai02

Entry in the Ai matrix.

double

Ai10

Entry in the Ai matrix.

double

Ai11

Entry in the Ai matrix.

double

Ai12

Entry in the Ai matrix.

double

Ai20

Entry in the Ai matrix.

double

Ai21

Entry in the Ai matrix.

double

Ai22

Entry in the Ai matrix.

double

alpha

The interaxial lattice angle between b and c.

double

b

Length of the cell edge in the direction of the b basis vector.

double

beta

The interaxial lattice angle between a and c.

double

c

Length of the cell edge in the direction of the c basis vector.

double

dVdA

Change in the volume with respect to a.

double

dVdAlpha

Change in the volume with respect to alpha (in Radians).

double

dVdB

Change in the volume with respect to b.

double

dVdBeta

Change in the volume with respect to beta (in Radians).

double

dVdC

Change in the volume with respect to c.

double

dVdGamma

Change in the volume with respect to gamma (in Radians).

final double[][]

G

The direct space metric matrix.

double

gamma

The interaxial lattice angle between a and b.

double

interfacialRadiusA

Interfacial radius in the direction of the A-axis.

double

interfacialRadiusB

Interfacial radius in the direction of the B-axis.

double

interfacialRadiusC

Interfacial radius in the direction of the C-axis.

int[]

scaleB

Anisotropic bulk solvent B-factor scaling (0 or 1 for each component).

int

scaleN

Number of bulk solvent B-factor components.

final SpaceGroup

spaceGroup

The space group of the crystal.

double

volume

The crystal unit cell volume.
Constructor Summary

Constructors

Constructor

Description

Crystal(double a, double b, double c, double alpha, double beta, double gamma, int sgNumber)

The Crystal class encapsulates the lattice parameters and space group.

Crystal(double a, double b, double c, double alpha, double beta, double gamma, String sg)

The Crystal class encapsulates the lattice parameters and space group.
Method Summary

Modifier and Type

Method

Description

boolean

aperiodic()

aperiodic

void

applySymOp(double[] xyz, double[] mate, SymOp symOp)

Apply a fractional symmetry operator to one set of cartesian coordinates.

void

applySymOp(int n, double[] x, double[] y, double[] z, double[] mateX, double[] mateY, double[] mateZ, SymOp symOp)

Apply a fractional symmetry operator to an array of Cartesian coordinates.

void

applySymRot(double[] xyz, double[] mate, SymOp symOp)

Apply a fractional symmetry operator to one set of cartesian coordinates.

void

applyTransSymRot(int n, double[] x, double[] y, double[] z, double[] mateX, double[] mateY, double[] mateZ, SymOp symOp, double[][] rotmat)

Apply the transpose of a symmetry rotation to an array of Cartesian coordinates.

void

averageTensor(double[][] m, double[][] r)

averageTensor

void

averageTensor(double[] v, double[][] r)

averageTensor

boolean

changeUnitCellParameters(double a, double b, double c, double alpha, double beta, double gamma)

This method should be called to update the unit cell parameters of a crystal.

boolean

changeUnitCellParametersAndVolume(double a, double b, double c, double alpha, double beta, double gamma, double targetAUVolume)

This method should be called to update the unit cell parameters of a crystal.

static Crystal

checkProperties(org.apache.commons.configuration2.CompositeConfiguration properties)

checkProperties

boolean

equals(Object o)

Two crystals are equal only if all unit cell parameters are exactly the same.

double[]

getCellParametersFromVectors(double[][] cellVectors)

Set the unit cell parameters from unit cell vectors.

boolean

getCheckRestrictions()

Are space group restrictions being checked.

double

getDensity(double mass)

Compute the density of the system.

int

getNumSymOps()

Return the number of symmetry operators for this crystal.

double[]

getRandomCartTranslation()

Create a random Cartesian translation vector.

double

getSpecialPositionCutoff()

Getter for the field specialPositionCutoff.

double

getSpecialPositionCutoff2()

Getter for the field specialPositionCutoff2.

void

getTransformationOperator(SymOp symOp, double[][] rotmat)

Compute the total transformation operator R = ToCart * Rot * ToFrac.

Crystal

getUnitCell()

The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.

int

hashCode()

double

image(double[] xyz)

Apply the minimum image convention.

double

image(double[] xyz, double[] xyz2)

Apply the minimum image convention.

double

image(double dx, double dy, double dz)

Apply the minimum image convention.

double

invressq(HKL hkl)

invressq

double

minDistOverSymOps(double[] xyzA, double[] xyzB)

Minimum distance between two coordinates over all symmetry operators.

boolean

perturbCellVectors(double[][] dStrain)

Strain the unit cell vectors.

boolean

randomParameters(double density, double mass)

Randomly set the unit cell vectors respecting the specified density.

double

res(HKL hkl)

res

void

setAperiodic(boolean aperiodic)

Is this a finite system without periodic boundary conditions.

boolean

setCellVectors(double[][] cellVectors)

Set the unit cell vectors.

boolean

setCellVectorsAndVolume(double[][] cellVectors, double targetAUVolume)

Set the unit cell vectors.

void

setCheckRestrictions(boolean checkRestrictions)

Set whether to check space group restrictions.

void

setDensity(double density, double mass)

Set the unit cell vectors.

void

setSpecialPositionCutoff(double cutoff)

Setter for the field specialPositionCutoff.

void

toCartesianCoordinates(double[] xf, double[] x)

toCartesianCoordinates

void

toCartesianCoordinates(int n, double[] frac, double[] cart)

toCartesianCoordinates

void

toCartesianCoordinates(int n, double[] xf, double[] yf, double[] zf, double[] x, double[] y, double[] z)

toCartesianCoordinates

String

toCRYST1()

Return a CRYST1 record useful for writing a PDB file.

void

toFractionalCoordinates(double[] x, double[] xf)

toFractionalCoordinates

void

toFractionalCoordinates(int n, double[] cart, double[] frac)

toFractionalCoordinates

void

toFractionalCoordinates(int n, double[] x, double[] y, double[] z, double[] xf, double[] yf, double[] zf)

toFractionalCoordinates

void

toPrimaryCell(double[] in, double[] out)

toPrimaryCell

String

toShortString()

A String containing the unit cell parameters.

String

toString()

final void

updateCrystal()

Update all Crystal variables that are a function of unit cell parameters.

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

Field Details
- spaceGroup
  
  @FFXProperty(name="SpaceGroup", propertyGroup=UnitCellAndSpaceGroup, clazz=SpaceGroup.class, defaultValue="P1", description="This property defines the crystal space group used during structural manipulations and force field calculations.\n") public final SpaceGroup spaceGroup
  
  The space group of the crystal.
- a
  
  @FFXProperty(name="a-axis", propertyGroup=UnitCellAndSpaceGroup, defaultValue="None", description="Sets the value of the a-axis length for a crystal unit cell, or, equivalently,\nthe X-axis length for a periodic box (Angstroms).\n") public double a
  
  Length of the cell edge in the direction of the a basis vector.
- b
  
  @FFXProperty(name="b-axis", propertyGroup=UnitCellAndSpaceGroup, defaultValue="A-Axis", description="Sets the value of the b-axis length for a crystal unit cell, or, equivalently,\nthe Y-axis length for a periodic box (Angstroms).\n") public double b
  
  Length of the cell edge in the direction of the b basis vector.
- c
  
  @FFXProperty(name="c-axis", propertyGroup=UnitCellAndSpaceGroup, defaultValue="A-Axis", description="Sets the value of the c-axis length for a crystal unit cell, or, equivalently,\nthe Z-axis length for a periodic box (Angstroms).\n") public double c
  
  Length of the cell edge in the direction of the c basis vector.
- alpha
  
  @FFXProperty(name="alpha", propertyGroup=UnitCellAndSpaceGroup, defaultValue="90.0", description="Sets the value of the \u03b1-angle of a crystal unit cell, i.e.,\nthe angle between the b-axis and c-axis of a unit cell, or, equivalently,\nthe angle between the Y-axis and Z-axis of a periodic box.\n") public double alpha
  
  The interaxial lattice angle between b and c.
- beta
  
  @FFXProperty(name="beta", propertyGroup=UnitCellAndSpaceGroup, defaultValue="Alpha", description="Sets the value of the \u03b2-angle of a crystal unit cell, i.e.,\nthe angle between the a-axis and c-axis of a unit cell, or, equivalently,\nthe angle between the X-axis and Z-axis of a periodic box.\n") public double beta
  
  The interaxial lattice angle between a and c.
- gamma
  
  @FFXProperty(name="gamma", propertyGroup=UnitCellAndSpaceGroup, defaultValue="Alpha", description="Sets the value of the \u03b3-angle of a crystal unit cell, i.e.,\nthe angle between the a-axis and b-axis of a unit cell, or, equivalently,\nthe angle between the X-axis and Y-axis of a periodic box.\n") public double gamma
  
  The interaxial lattice angle between a and b.
- Ai
  
  public final double[][] Ai
  
  Matrix to convert from fractional to Cartesian coordinates.
  a-axis vector is the first row of A^(-1).
  b-axis vector is the second row of A^(-1).
  c-axis vector is the third row of A^(-1).
- G
  
  public final double[][] G
  
  The direct space metric matrix.
- volume
  
  public double volume
  
  The crystal unit cell volume.
- A
  
  public double[][] A
  
  Matrix to convert from Cartesian to fractional coordinates.
- A00
  
  public double A00
  
  Entry in the A matrix.
- A01
  
  public double A01
  
  Entry in the A matrix.
- A02
  
  public double A02
  
  Entry in the A matrix.
- A10
  
  public double A10
  
  Entry in the A matrix.
- A11
  
  public double A11
  
  Entry in the A matrix.
- A12
  
  public double A12
  
  Entry in the A matrix.
- A20
  
  public double A20
  
  Entry in the A matrix.
- A21
  
  public double A21
  
  Entry in the A matrix.
- A22
  
  public double A22
  
  Entry in the A matrix.
- interfacialRadiusA
  
  public double interfacialRadiusA
  
  Interfacial radius in the direction of the A-axis.
- interfacialRadiusB
  
  public double interfacialRadiusB
  
  Interfacial radius in the direction of the B-axis.
- interfacialRadiusC
  
  public double interfacialRadiusC
  
  Interfacial radius in the direction of the C-axis.
- scaleB
  
  public int[] scaleB
  
  Anisotropic bulk solvent B-factor scaling (0 or 1 for each component).
- scaleN
  
  public int scaleN
  
  Number of bulk solvent B-factor components.
- Ai00
  
  public double Ai00
  
  Entry in the Ai matrix.
- Ai01
  
  public double Ai01
  
  Entry in the Ai matrix.
- Ai02
  
  public double Ai02
  
  Entry in the Ai matrix.
- Ai10
  
  public double Ai10
  
  Entry in the Ai matrix.
- Ai11
  
  public double Ai11
  
  Entry in the Ai matrix.
- Ai12
  
  public double Ai12
  
  Entry in the Ai matrix.
- Ai20
  
  public double Ai20
  
  Entry in the Ai matrix.
- Ai21
  
  public double Ai21
  
  Entry in the Ai matrix.
- Ai22
  
  public double Ai22
  
  Entry in the Ai matrix.
- dVdA
  
  public double dVdA
  
  Change in the volume with respect to a.
- dVdB
  
  public double dVdB
  
  Change in the volume with respect to b.
- dVdC
  
  public double dVdC
  
  Change in the volume with respect to c.
- dVdAlpha
  
  public double dVdAlpha
  
  Change in the volume with respect to alpha (in Radians). This is set to zero if alpha is fixed.
- dVdBeta
  
  public double dVdBeta
  
  Change in the volume with respect to beta (in Radians). This is set to zero if beta is fixed.
- dVdGamma
  
  public double dVdGamma
  
  Change in the volume with respect to gamma (in Radians). This is set to zero if gamma is fixed.
Constructor Details
- Crystal
  
  public Crystal(double a, double b, double c, double alpha, double beta, double gamma, int sgNumber)
  
  The Crystal class encapsulates the lattice parameters and space group. Methods are available to apply the minimum image convention and to apply space group operators.
  
  Parameters:
  
  a - The a-axis length.
  
  b - The b-axis length.
  
  c - The c-axis length.
  
  alpha - The alpha angle.
  
  beta - The beta angle.
  
  gamma - The gamma angle.
  
  sgNumber - The space group number.
- Crystal
  
  public Crystal(double a, double b, double c, double alpha, double beta, double gamma, String sg)
  
  The Crystal class encapsulates the lattice parameters and space group. Methods are available to apply the minimum image convention and to apply space group operators.
  
  Parameters:
  
  a - The a-axis length.
  
  b - The b-axis length.
  
  c - The c-axis length.
  
  alpha - The alpha angle.
  
  beta - The beta angle.
  
  gamma - The gamma angle.
  
  sg - The space group symbol.
Method Details
- checkProperties
  
  public static Crystal checkProperties(org.apache.commons.configuration2.CompositeConfiguration properties)
  
  checkProperties
  
  Parameters:
  
  properties - a CompositeConfiguration object.
  
  Returns:
  
  a Crystal object.
- invressq
  
  public double invressq(HKL hkl)
  
  invressq
  
  Parameters:
  
  hkl - a HKL object.
  
  Returns:
  
  a double.
- res
  
  public double res(HKL hkl)
  
  res
  
  Parameters:
  
  hkl - a HKL object.
  
  Returns:
  
  a double.
- aperiodic
  
  public boolean aperiodic()
  
  aperiodic
  
  Returns:
  
  a boolean.
- applySymOp
  
  public void applySymOp(int n, double[] x, double[] y, double[] z, double[] mateX, double[] mateY, double[] mateZ, SymOp symOp)
  
  Apply a fractional symmetry operator to an array of Cartesian coordinates.
  If the arrays x, y or z are null or not of length n, an exception is thrown.
  If mateX, mateY or mateZ are null or not of length n, an exception is thrown.
  
  Parameters:
  
  n - Number of atoms.
  
  x - Input fractional x-coordinates.
  
  y - Input fractional y-coordinates.
  
  z - Input fractional z-coordinates.
  
  mateX - Output fractional x-coordinates.
  
  mateY - Output fractional y-coordinates.
  
  mateZ - Output fractional z-coordinates.
  
  symOp - The fractional symmetry operator.
- applySymOp
  
  public void applySymOp(double[] xyz, double[] mate, SymOp symOp)
  
  Apply a fractional symmetry operator to one set of cartesian coordinates.
  
  Parameters:
  
  xyz - Input cartesian coordinates.
  
  mate - Symmetry mate cartesian coordinates.
  
  symOp - The fractional symmetry operator.
- applySymRot
  
  public void applySymRot(double[] xyz, double[] mate, SymOp symOp)
  
  Apply a fractional symmetry operator to one set of cartesian coordinates.
  
  Parameters:
  
  xyz - Input cartesian coordinates.
  
  mate - Symmetry mate cartesian coordinates.
  
  symOp - The fractional symmetry operator.
- applyTransSymRot
  
  public void applyTransSymRot(int n, double[] x, double[] y, double[] z, double[] mateX, double[] mateY, double[] mateZ, SymOp symOp, double[][] rotmat)
  
  Apply the transpose of a symmetry rotation to an array of Cartesian coordinates.
  If the arrays x, y or z are null or not of length n, an exception is thrown.
  If mateX, mateY or mateZ are null or not of length n, an exception is thrown.
  
  Parameters:
  
  n - Number of atoms.
  
  x - Input x-coordinates.
  
  y - Input y-coordinates.
  
  z - Input z-coordinates.
  
  mateX - Output x-coordinates.
  
  mateY - Output y-coordinates.
  
  mateZ - Output z-coordinates.
  
  symOp - The symmetry operator.
  
  rotmat - an array of double.
- averageTensor
  
  public void averageTensor(double[][] m, double[][] r)
  
  averageTensor
  
  Parameters:
  
  m - an array of double.
  
  r - an array of double.
- averageTensor
  
  public void averageTensor(double[] v, double[][] r)
  
  averageTensor
  
  Parameters:
  
  v - an array of double.
  
  r - an array of double.
- changeUnitCellParameters
  
  public boolean changeUnitCellParameters(double a, double b, double c, double alpha, double beta, double gamma)
  
  This method should be called to update the unit cell parameters of a crystal. The proposed parameters will only be accepted if symmetry restrictions are satisfied. If so, all Crystal variables that depend on the unit cell parameters will be updated.
  
  Parameters:
  
  a - length of the a-axis.
  
  b - length of the b-axis.
  
  c - length of the c-axis.
  
  alpha - Angle between b-axis and c-axis.
  
  beta - Angle between a-axis and c-axis.
  
  gamma - Angle between a-axis and b-axis.
  
  Returns:
  
  The method return true if the parameters are accepted, false otherwise.
- changeUnitCellParametersAndVolume
  
  public boolean changeUnitCellParametersAndVolume(double a, double b, double c, double alpha, double beta, double gamma, double targetAUVolume)
  
  This method should be called to update the unit cell parameters of a crystal. The proposed parameters will only be accepted if symmetry restrictions are satisfied. If so, all Crystal variables that depend on the unit cell parameters will be updated.
  If the new parameters are accepted, the target asymmetric unit volume is achieved by uniformly scaling all lattice lengths.
  
  Parameters:
  
  a - length of the a-axis.
  
  b - length of the b-axis.
  
  c - length of the c-axis.
  
  alpha - Angle between b-axis and c-axis.
  
  beta - Angle between a-axis and c-axis.
  
  gamma - Angle between a-axis and b-axis.
  
  targetAUVolume - Target asymmetric unit volume.
  
  Returns:
  
  The method return true if the parameters are accepted, false otherwise.
- equals
  
  public boolean equals(Object o)
  
  Two crystals are equal only if all unit cell parameters are exactly the same.
  
  Overrides:
  
  equals in class Object
  
  Parameters:
  
  o - the Crystal to compare to.
  
  Returns:
  
  true if all unit cell parameters are exactly the same.
- getCheckRestrictions
  
  public boolean getCheckRestrictions()
  
  Are space group restrictions being checked.
  
  Returns:
  
  true if the restrictions are being checked.
- setCheckRestrictions
  
  public void setCheckRestrictions(boolean checkRestrictions)
  
  Set whether to check space group restrictions.
  
  Parameters:
  
  checkRestrictions - true to check restrictions.
- getDensity
  
  public double getDensity(double mass)
  
  Compute the density of the system.
  
  Parameters:
  
  mass - The total mass of the asymmetric unit.
  
  Returns:
  
  The density (g/cc)
- getNumSymOps
  
  public int getNumSymOps()
  
  Return the number of symmetry operators for this crystal.
  
  Returns:
  
  The number of symmetry operators.
- getRandomCartTranslation
  
  public double[] getRandomCartTranslation()
  
  Create a random Cartesian translation vector.
  First, a random fractional translation is created. Second, the random fractional operator is converted to Cartesian coordinates.
  
  Returns:
  
  A random Cartesian translation vector.
- getSpecialPositionCutoff
  
  public double getSpecialPositionCutoff()
  
  Getter for the field specialPositionCutoff.
  
  Returns:
  
  a double.
- getSpecialPositionCutoff2
  
  public double getSpecialPositionCutoff2()
  
  Getter for the field specialPositionCutoff2.
  
  Returns:
  
  a double.
- setSpecialPositionCutoff
  
  public void setSpecialPositionCutoff(double cutoff)
  
  Setter for the field specialPositionCutoff.
  
  Parameters:
  
  cutoff - a double.
- getTransformationOperator
  
  public void getTransformationOperator(SymOp symOp, double[][] rotmat)
  
  Compute the total transformation operator R = ToCart * Rot * ToFrac.
  
  Parameters:
  
  symOp - Symmetry operator to apply.
  
  rotmat - Resulting transformation operator R.
- getUnitCell
  
  public Crystal getUnitCell()
  
  The ReplicatesCrystal over-rides this method to return the unit cell rather than the ReplicateCell.
  
  Returns:
  
  The unit cell Crystal instance.
- hashCode
  
  public int hashCode()
  
  Overrides:
  
  hashCode in class Object
- image
  
  public double image(double[] xyz, double[] xyz2)
  
  Apply the minimum image convention.
  
  Parameters:
  
  xyz - the coordinates of the first atom.
  
  xyz2 - the coordinates of the second atom.
  
  Returns:
  
  the output distance squared.
- image
  
  public double image(double[] xyz)
  
  Apply the minimum image convention.
  
  Parameters:
  
  xyz - input distances that are over-written.
  
  Returns:
  
  the output distance squared.
- image
  
  public double image(double dx, double dy, double dz)
  
  Apply the minimum image convention.
  
  Parameters:
  
  dx - x-distance
  
  dy - y-distance
  
  dz - z-distance
  
  Returns:
  
  the output distance squared.
- minDistOverSymOps
  
  public double minDistOverSymOps(double[] xyzA, double[] xyzB)
  
  Minimum distance between two coordinates over all symmetry operators.
  
  Parameters:
  
  xyzA - Coordinate A
  
  xyzB - Coordinate B
  
  Returns:
  
  Minimum distance in crystal
- perturbCellVectors
  
  public boolean perturbCellVectors(double[][] dStrain)
  
  Strain the unit cell vectors.
  
  Parameters:
  
  dStrain - a 3x3 matrix of unitless Strain percentages.
  
  Returns:
  
  True if the perturbation of cell vectors succeeds.
- randomParameters
  
  public boolean randomParameters(double density, double mass)
  
  Randomly set the unit cell vectors respecting the specified density.
  
  Parameters:
  
  density - The target density.
  
  mass - The total mass of the asymmetric unit.
  
  Returns:
  
  True if the perturbation of cell vectors succeeds.
- setAperiodic
  
  public void setAperiodic(boolean aperiodic)
  
  Is this a finite system without periodic boundary conditions.
  
  Parameters:
  
  aperiodic - a boolean.
- getCellParametersFromVectors
  
  public double[] getCellParametersFromVectors(double[][] cellVectors)
  
  Set the unit cell parameters from unit cell vectors.
  
  Parameters:
  
  cellVectors - 3x3 matrix of unit cell vectors.
  
  Returns:
  
  The six unit cell parameters (a, b, c, alpha, beta, gamma).
- setCellVectors
  
  public boolean setCellVectors(double[][] cellVectors)
  
  Set the unit cell vectors.
  
  Parameters:
  
  cellVectors - 3x3 matrix of cell vectors.
  
  Returns:
  
  True if the perturbation of cell vectors succeeds.
- setCellVectorsAndVolume
  
  public boolean setCellVectorsAndVolume(double[][] cellVectors, double targetAUVolume)
  
  Set the unit cell vectors. Scale lattice lengths if necessary to hit the target volume.
  
  Parameters:
  
  cellVectors - 3x3 matrix of cell vectors.
  
  targetAUVolume - the target volume for the new cell Vectors.
  
  Returns:
  
  True if the perturbation of cell vectors succeeds.
- setDensity
  
  public void setDensity(double density, double mass)
  
  Set the unit cell vectors. Scale lattice lengths if necessary to hit the target volume.
  
  Parameters:
  
  density - The target density.
  
  mass - The total mass of the asymmetric unit.
- toCRYST1
  
  public String toCRYST1()
  
  Return a CRYST1 record useful for writing a PDB file.
  
  Returns:
  
  The CRYST1 record.
- toCartesianCoordinates
  
  public void toCartesianCoordinates(int n, double[] xf, double[] yf, double[] zf, double[] x, double[] y, double[] z)
  
  toCartesianCoordinates
  
  Parameters:
  
  n - an int.
  
  xf - an array of double for fractional x-coordinates.
  
  yf - an array of double for fractional y-coordinates.
  
  zf - an array of double for fractional z-coordinates.
  
  x - an array of double for cartesian x-coordinates.
  
  y - an array of double for cartesian y-coordinates.
  
  z - an array of double for cartesian z-coordinates.
- toCartesianCoordinates
  
  public void toCartesianCoordinates(int n, double[] frac, double[] cart)
  
  toCartesianCoordinates
  
  Parameters:
  
  n - an int.
  
  frac - an array of double for fractional coordinates.
  
  cart - an array of double for cartesian coordinates.
- toCartesianCoordinates
  
  public void toCartesianCoordinates(double[] xf, double[] x)
  
  toCartesianCoordinates
  
  Parameters:
  
  xf - an array of double for fractional coordinate.
  
  x - an array of double for cartesian coordinate.
- toFractionalCoordinates
  
  public void toFractionalCoordinates(int n, double[] x, double[] y, double[] z, double[] xf, double[] yf, double[] zf)
  
  toFractionalCoordinates
  
  Parameters:
  
  n - an int.
  
  x - an array of double for cartesian x-coordinates.
  
  y - an array of double for cartesian y-coordinates.
  
  z - an array of double for cartesian z-coordinates.
  
  xf - an array of double for fractional x-coordinates.
  
  yf - an array of double for fractional y-coordinates.
  
  zf - an array of double for fractional z-coordinates.
- toFractionalCoordinates
  
  public void toFractionalCoordinates(int n, double[] cart, double[] frac)
  
  toFractionalCoordinates
  
  Parameters:
  
  n - an int.
  
  cart - an array of double for cartesian coordinates.
  
  frac - an array of double for fractional coordinates.
- toFractionalCoordinates
  
  public void toFractionalCoordinates(double[] x, double[] xf)
  
  toFractionalCoordinates
  
  Parameters:
  
  x - an array of double for cartesian coordinate.
  
  xf - an array of double for fractional coordinate.
- toPrimaryCell
  
  public void toPrimaryCell(double[] in, double[] out)
  
  toPrimaryCell
  
  Parameters:
  
  in - an array of double.
  
  out - an array of double.
- toShortString
  
  public String toShortString()
  
  A String containing the unit cell parameters.
  
  Returns:
  
  A string with the unit cell parameters.
- toString
  
  public String toString()
  
  Overrides:
  
  toString in class Object
- updateCrystal
  
  public final void updateCrystal()
  
  Update all Crystal variables that are a function of unit cell parameters.

Class Crystal

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Details

spaceGroup

a

b

c

alpha

beta

gamma

Ai

G

volume

A

A00

A01

A02

A10

A11

A12

A20

A21

A22

interfacialRadiusA

interfacialRadiusB

interfacialRadiusC

scaleB

scaleN

Ai00

Ai01

Ai02

Ai10

Ai11

Ai12

Ai20

Ai21

Ai22

dVdA

dVdB

dVdC

dVdAlpha

dVdBeta

dVdGamma

Constructor Details

Crystal

Crystal

Method Details

checkProperties

invressq

res

aperiodic

applySymOp

applySymOp

applySymRot

applyTransSymRot

averageTensor

averageTensor

changeUnitCellParameters

changeUnitCellParametersAndVolume

equals

getCheckRestrictions

setCheckRestrictions

getDensity

getNumSymOps

getRandomCartTranslation

getSpecialPositionCutoff

getSpecialPositionCutoff2

setSpecialPositionCutoff

getTransformationOperator

getUnitCell

hashCode

image

image

image

minDistOverSymOps

perturbCellVectors

randomParameters