java.lang.Object
- org.openscience.cdk.math.qm.GaussiansBasis

All Implemented Interfaces:

IBasis

Direct Known Subclasses:

SimpleBasisSet
```
public class GaussiansBasis
extends Object
implements IBasis
```
This class contains the information to use gauss function as a base for calculation of quantum mechanics. The function is defined as:
```
 f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2)
 
```
S = <phi_i|phi_j>
J = <d/dr phi_i | d/dr phi_j>
V = <phi_i | 1/r | phi_j>
Author:

Stephan Michels <stephan@vern.chem.tu-berlin.de>

Source code:
main

Belongs to CDK module:
qm

Keywords:

Gaussian basis set

Created on:

2001-06-14

Constructor Summary

Constructors
Constructor	Description
`GaussiansBasis()`
`GaussiansBasis(int[] nx, int[] ny, int[] nz, double[] alpha, Vector[] r, IAtom[] atoms)`	Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`double`	`calcD(double normi, double normj, double alphai, double alphaj, Vector ri, Vector rj)`
`double`	`calcG(int n, double t, double alphai, double alphaj, double xi, double xj, double xN)`	Transfer equation for the calculation of core potentials
`double`	`calcG(int n, int m, double u, double alphai, double alphaj, double alphak, double alphal, double xi, double xj, double xk, double xl)`	Transfer equation for a four center integral.
`double`	`calcI(int i, int j, int k, int l)`	Calculates a two eletron fout center integral I = <chi_i chi_j \| 1/r12 \| chi_k chi_l >.
`double`	`calcI(int ni, int nj, int nk, int nl, double u, double alphai, double alphaj, double alphak, double alphal, double xi, double xj, double xk, double xl)`	Transfer equation for a four center integral.
`double`	`calcJ(int i, int j)`	Calculates the impulse J = -<d/dr chi_i \| d/dr chi_j>.
`double`	`calcJ(int ni, int nj, double alphai, double alphaj, double xi, double xj)`	Transfer equation the the calculation of the impulse
`double`	`calcS(int i, int j)`	Calculate the overlap integral S = <phi_i\|phi_j>.
`double`	`calcV(int i, int j)`	Calculates the core potential.
`double`	`calcV(int i, int j, Vector rN, double Z)`	Calculates the core potential.
`double`	`getMaxX()`	Gets the dimension of the volume, which describes the base.
`double`	`getMaxY()`	Gets the dimension of the volume, which describes the base.
`double`	`getMaxZ()`	Gets the dimension of the volume, which describes the base.
`double`	`getMinX()`	Gets the dimension of the volume, which describes the base.
`double`	`getMinY()`	Gets the dimension of the volume, which describes the base.
`double`	`getMinZ()`	Gets the dimension of the volume, which describes the base.
`Vector`	`getPosition(int index)`	Gets the position of a base.
`int`	`getSize()`	Gets the number of base vectors.
`double`	`getValue(int index, double x, double y, double z)`	Calculates the function value an (x,y,z).
`Vector`	`getValues(int index, Matrix m)`	Calculates the function values.
`protected void`	`setBasis(int[] nx, int[] ny, int[] nz, double[] alpha, Vector[] r, IAtom[] atoms)`	Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).

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

Constructor Detail

GaussiansBasis
```
public GaussiansBasis()
```

GaussiansBasis

public GaussiansBasis(int[] nx,
                      int[] ny,
                      int[] nz,
                      double[] alpha,
                      Vector[] r,
                      IAtom[] atoms)

Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).

Parameters:: atoms - The atom will need to calculate the core potential

Method Detail

setBasis

protected void setBasis(int[] nx,
                        int[] ny,
                        int[] nz,
                        double[] alpha,
                        Vector[] r,
                        IAtom[] atoms)

Set up basis with gauss funktions f(x,y,z) = (x-rx)^nx * (y-ry)^ny * (z-rz)^nz * exp(-alpha*(r-ri)^2).

Parameters:: atoms - The atom will need to calculate the core potential

getSize
```
public int getSize()
```
Gets the number of base vectors.

Specified by:

getSize in interface IBasis

getMinX
```
public double getMinX()
```
Gets the dimension of the volume, which describes the base.

Specified by:

getMinX in interface IBasis

getMaxX
```
public double getMaxX()
```
Gets the dimension of the volume, which describes the base.

Specified by:

getMaxX in interface IBasis

getMinY
```
public double getMinY()
```
Gets the dimension of the volume, which describes the base.

Specified by:

getMinY in interface IBasis

getMaxY
```
public double getMaxY()
```
Gets the dimension of the volume, which describes the base.

Specified by:

getMaxY in interface IBasis

getMinZ
```
public double getMinZ()
```
Gets the dimension of the volume, which describes the base.

Specified by:

getMinZ in interface IBasis

getMaxZ
```
public double getMaxZ()
```
Gets the dimension of the volume, which describes the base.

Specified by:

getMaxZ in interface IBasis

getValue

public double getValue(int index,
                       double x,
                       double y,
                       double z)

Calculates the function value an (x,y,z).

Specified by:: getValue in interface IBasis
Parameters:: index - The number of the base

getValues
```
public Vector getValues(int index,
                        Matrix m)
```
Calculates the function values.

Specified by:

getValues in interface IBasis

Parameters:

index - The number of the base

getPosition

public Vector getPosition(int index)

Gets the position of a base.

calcD

public double calcD(double normi,
                    double normj,
                    double alphai,
                    double alphaj,
                    Vector ri,
                    Vector rj)

calcS
```
public double calcS(int i,
                    int j)
```
Description copied from interface: IBasis

Calculate the overlap integral S = <phi_i|phi_j>.

Specified by:

calcS in interface IBasis

Parameters:

i - Index of the first base

j - Index of the second base

calcJ

public double calcJ(int ni,
                    int nj,
                    double alphai,
                    double alphaj,
                    double xi,
                    double xj)

Transfer equation the the calculation of the impulse

calcJ
```
public double calcJ(int i,
                    int j)
```
Description copied from interface: IBasis

Calculates the impulse J = -<d/dr chi_i | d/dr chi_j>.

Specified by:

calcJ in interface IBasis

Parameters:

i - Index of the first base

j - Index of the second base

calcG

public double calcG(int n,
                    double t,
                    double alphai,
                    double alphaj,
                    double xi,
                    double xj,
                    double xN)

Transfer equation for the calculation of core potentials

calcV
```
public double calcV(int i,
                    int j,
                    Vector rN,
                    double Z)
```
Calculates the core potential. It use a 10 point Simpson formula.

Parameters:

i - Index of the first base

j - Index of the second base

rN - Position the core potential

Z - Atomic number of the nucleous

calcV
```
public double calcV(int i,
                    int j)
```
Calculates the core potential. It use a 10 point Simpson formula.

Specified by:

calcV in interface IBasis

Parameters:

i - Index of the first base

j - Index of the second base

calcG

public double calcG(int n,
                    int m,
                    double u,
                    double alphai,
                    double alphaj,
                    double alphak,
                    double alphal,
                    double xi,
                    double xj,
                    double xk,
                    double xl)

Transfer equation for a four center integral.

calcI

public double calcI(int ni,
                    int nj,
                    int nk,
                    int nl,
                    double u,
                    double alphai,
                    double alphaj,
                    double alphak,
                    double alphal,
                    double xi,
                    double xj,
                    double xk,
                    double xl)

Transfer equation for a four center integral.

calcI
```
public double calcI(int i,
                    int j,
                    int k,
                    int l)
```
Description copied from interface: IBasis

Calculates a two eletron fout center integral I = <chi_i chi_j | 1/r12 | chi_k chi_l >.

Specified by:

calcI in interface IBasis

Parameters:

i - Index of the first base

j - Index of the second base

k - Index of the third base

l - Index of the fourth base

Class GaussiansBasis

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

GaussiansBasis

GaussiansBasis

Method Detail

setBasis

getSize

getMinX

getMaxX

getMinY

getMaxY

getMinZ

getMaxZ

getValue

getValues

getPosition

calcD

calcS

calcJ

calcJ

calcG

calcV

calcV

calcG

calcI

calcI