Package gov.nih.mipav.model.structures.jama

Class SparseEigenvalue

java.lang.Object
gov.nih.mipav.model.structures.jama.SparseEigenvalue
All Implemented Interfaces:
Serializable
public class SparseEigenvalue extends Object implements Serializable
These sparse symmetric eigenvalue and eigenvector routines are ported from the FORTRAN ARPACK package. The license with the orginal ARPACK package is: BSD Software License Pertains to ARPACK and P_ARPACK Copyright (c) 1996-2008 Rice University. Developed by D.C. Sorensen, R.B. Lehoucq, C. Yang, and K. Maschhoff. All rights reserved. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: - Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. - Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer listed in this license in the documentation and/or other materials provided with the distribution. - Neither the name of the copyright holders nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
Author:
ilb
See Also:

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    private boolean
    dgetv0_first
     
    private boolean
    dgetv0_inits
     
    private int[]
    dgetv0_iseed
     
    private int
    dgetv0_iter
     
    private int
    dgetv0_msglvl
     
    private boolean
    dgetv0_orth
     
    private double
    dgetv0_rnorm0
     
    private boolean
    dsaitr_first
     
    private int[]
    dsaitr_ierr
     
    private int
    dsaitr_ipj
     
    private int
    dsaitr_irj
     
    private int
    dsaitr_iter
     
    private int
    dsaitr_itry
     
    private int
    dsaitr_ivj
     
    private int
    dsaitr_j
     
    private int
    dsaitr_msglvl
     
    private boolean
    dsaitr_orth1
     
    private boolean
    dsaitr_orth2
     
    private double
    dsaitr_rnorm1
     
    private boolean
    dsaitr_rstart
     
    private double
    dsaitr_safmin
     
    private boolean
    dsaitr_step3
     
    private boolean
    dsaitr_step4
     
    private double
    dsaitr_wnorm
     
    private double
    dsapps_epsmch
     
    private boolean
    dsapps_first
     
    private boolean
    dsaup2_cnorm
     
    private double
    dsaup2_eps23
     
    private boolean
    dsaup2_getv0
     
    private boolean
    dsaup2_initv
     
    private int
    dsaup2_iter
     
    private int
    dsaup2_kplusp
     
    private int
    dsaup2_msglvl
     
    private int[]
    dsaup2_nconv
     
    private int
    dsaup2_nev0
     
    private int
    dsaup2_np0
     
    private double[]
    dsaup2_rnorm
     
    private boolean
    dsaup2_update
     
    private boolean
    dsaup2_ushift
     
    private int
    dsaupd_bounds
     
    private int
    dsaupd_ierr
     
    private int
    dsaupd_ih
     
    private int
    dsaupd_iq
     
    private int
    dsaupd_ishift
     
    private int
    dsaupd_iupd
     
    private int
    dsaupd_iw
     
    private int
    dsaupd_ldh
     
    private int
    dsaupd_ldq
     
    private int
    dsaupd_mode
     
    private int
    dsaupd_msglvl
     
    private int[]
    dsaupd_mxiter
     
    private int
    dsaupd_nb
     
    private int[]
    dsaupd_nev0
     
    private int
    dsaupd_next
     
    private int[]
    dsaupd_np
     
    private int
    dsaupd_ritz
     
    (package private) GeneralizedEigenvalue
    ge
     
    (package private) LinearEquations
    le
     
    private int
    mgetv0
     
    private int
    msaitr
     
    private int
    msapps
     
    private int
    msaup2
     
    private int
    msaupd
     
    private int
    mseigt
     
    private int
    mseupd
     
    private int
    msgets
     
    private int
    nbx
     
    (package private) DecimalFormat
    nf
     
    private int
    nitref
     
    private int
    nopx
     
    private int
    nrorth
     
    private int
    nrstrt
     
    private long
    t0
     
    private long
    t1
     
    private long
    t2
     
    private long
    t3
     
    private long
    t4
     
    private long
    t5
     
    private double
    tgetv0
     
    private double
    titref
     
    private double
    tmvbx
     
    private double
    tmvopx
     
    private double
    tsaitr
     
    private double
    tsapps
     
    private double
    tsaup2
     
    private double
    tsaupd
     
    private double
    tsconv
     
    private double
    tseigt
     
    private double
    tsgets
     
    private ViewUserInterface
    UI
     

  • Constructor Summary

    Constructors
    Constructor
    Description
    SparseEigenvalue()
    Creates a new SparseEigenvalue object.

  • Method Summary

    Modifier and Type
    Method
    Description
    private void
    atv(int m, int n, double[] w, double[] y)
     
    private void
    av(int nx, double[] v, double[] w)
     
    private void
    av2(int n, double[] v, double[] w)
     
    private void
    av3(int n, double[] v, double[] w)
     
    private void
    av4(int n, double[] v, double[] w)
     
    private void
    av5(int n, double[] v, double[] w)
     
    private void
    av6(int n, double[] v, double[] w)
     
    private void
    avsimp(int nx, double[] v, double[] w)
     
    private void
    avsvd(int m, int n, double[] x, double[] w)
     
    private void
    dchkgt(boolean[] dotype, int nn, int[] nval, int nns, int[] nsval, double thresh, double[] a, double[] af, double[] b, double[] x, double[] xact, double[] work, double[] rwork, int[] iwork)
     
    void
    dchkgt_test()
    This dchkgt_test routine is a port of a portion of the version 3.4.1 LAPACK test routine DCHKAA by Univ. of Tennessee, Univ.
    private void
    dgetv0(int[] ido, String bmat, int itry, boolean initv, int n, int j, double[][] v, int ldv, double[] resid, double[] rnorm, int[] ipntr, double[] workd, int[] ierr)
     
    private void
    dgtcon(char NORM, int N, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, double ANORM, double[] RCOND, double[] WORK, int[] IWORK, int[] INFO)
     
    private void
    dgtrfs(char trans, int n, int nrhs, double[] dl, double[] d, double[] du, double[] dlf, double[] df, double[] duf, double[] du2, int[] ipiv, double[][] b, int ldb, double[][] x, int ldx, double[] ferr, double[] berr, double[] work, int[] iwork, int[] info)
     
    private void
    dgtt01(int n, double[] dl, double[] d, double[] du, double[] dlf, double[] df, double[] duf, double[] du2, int[] ipiv, double[][] work, int ldwork, double[] rwork, double[] resid)
     
    private void
    dgtt02(char TRANS, int N, int NRHS, double[] DL, double[] D, double[] DU, double[][] X, int LDX, double[][] B, int LDB, double[] RWORK, double[] RESID)
     
    private void
    dgtt05(char trans, int n, int nrhs, double[] dl, double[] d, double[] du, double[][] b, int ldb, double[][] x, int ldx, double[][] xact, int ldxact, double[] ferr, double[] berr, double[] reslts)
     
    private void
    dgttrf(int N, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, int[] INFO)
     
    private void
    dgttrs(char TRANS, int N, int NRHS, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, double[][] B, int LDB, int[] INFO)
     
    private void
    DGTTS2(int ITRANS, int N, int NRHS, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, double[][] B, int LDB)
     
    private void
    dlagtm(char trans, int n, int nrhs, double alpha, double[] dl, double[] d, double[] du, double[][] x, int ldx, double beta, double[][] b, int ldb)
     
    private double
    dlangt(char norm, int n, double[] dl, double[] d, double[] du)
     
    private void
    dsaitr(int[] ido, String bmat, int n, int k, int np, int mode, double[] resid, double[] rnorm, double[][] v, int ldv, double[][] h, int ldh, int[] ipntr, double[] workd, int[] info)
     
    private void
    dsapps(int n, int kev, int np, double[] shift, double[][] v, int ldv, double[][] h, int ldh, double[] resid, double[][] q, int ldq, double[] workd)
     
    private void
    dsaup2(int[] ido, String bmat, int n, String which, int[] nev, int[] np, double[] tol, double[] resid, int mode, int iupd, int ishift, int[] mxiter, double[][] v, int ldv, double[][] h, int ldh, double[] ritz, double[] bounds, double[][] q, int ldq, double[] workl, int[] ipntr, double[] workd, int[] info)
     
    void
    dsaupd(int[] ido, String bmat, int n, String which, int nev, double[] tol, double[] resid, int ncv, double[][] v, int ldv, int[] iparam, int[] ipntr, double[] workd, double[] workl, int lworkl, int[] info)
     
    private void
    dsconv(int n, double[] ritz, double[] bounds, double tol, int[] nconv)
     
    void
    dsdrv1()
     
    void
    dsdrv2()
     
    void
    dsdrv3()
     
    void
    dsdrv4()
     
    void
    dsdrv5()
     
    void
    dsdrv6()
     
    private void
    dseigt(double rnorm, int n, double[][] h, int ldh, double[] eig, double[] bounds, double[] workl, int[] ierr)
     
    private void
    dsesrt(String which, boolean apply, int n, double[] x, int na, double[][] a, int lda)
     
    void
    dseupd(boolean rvec, String howmny, boolean[] select, double[] d, double[][] z, int ldz, double sigma, String bmat, int n, String which, int nev, double tol, double[] resid, int ncv, double[][] v, int ldv, int[] iparam, int[] ipntr, double[] workd, double[] workl, int lworkl, int[] info)
     
    private void
    dsgets(int ishift, String which, int kev, int np, double[] ritz, double[] bounds, double[] shifts)
     
    private void
    dsortr(String which, boolean apply, int n, double[] x1, double[] x2)
     
    void
    dssimp()
     
    private void
    dstats()
     
    private void
    dstqrb(int n, double[] d, double[] e, double[] z, double[] work, int[] info)
     
    void
    dsvd()
     
    private void
    matMult(int n, double[][] A, double[] x, double[] y)
     
    private void
    mv3(int n, double[] v, double[] w)
     
    private void
    mv4(int n, double[] v, double[] w)
     
    private void
    mv5(int n, double[] v, double[] w)
     
    private void
    mv6(int n, double[] v, double[] w)
     
    private void
    printHeader()
     
    void
    simpleEigenvalue(double[][] A, int nev, String which, double[] tol, int ncv, double[] d, double[][] Z)
    Calculate requested eigenvalues and eigenvectors of a matrix
    void
    simpleEigenvalueTest1()
     
    private void
    tv(int nx, double[] x, double[] y)
     
    private void
    tvsimp(int nx, double[] x, double[] y)
     

    Methods inherited from class java.lang.Object

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

  • Field Details

    • ge

      GeneralizedEigenvalue ge

    • le

      LinearEquations le

    • UI

      private ViewUserInterface UI

    • nf

      DecimalFormat nf

    • dsaupd_bounds

      private int dsaupd_bounds

    • dsaupd_ierr

      private int dsaupd_ierr

    • dsaupd_ih

      private int dsaupd_ih

    • dsaupd_iq

      private int dsaupd_iq

    • dsaupd_ishift

      private int dsaupd_ishift

    • dsaupd_iupd

      private int dsaupd_iupd

    • dsaupd_iw

      private int dsaupd_iw

    • dsaupd_ldh

      private int dsaupd_ldh

    • dsaupd_ldq

      private int dsaupd_ldq

    • dsaupd_msglvl

      private int dsaupd_msglvl

    • dsaupd_mxiter

      private int[] dsaupd_mxiter

    • dsaupd_mode

      private int dsaupd_mode

    • dsaupd_nb

      private int dsaupd_nb

    • dsaupd_nev0

      private int[] dsaupd_nev0

    • dsaupd_next

      private int dsaupd_next

    • dsaupd_np

      private int[] dsaupd_np

    • dsaupd_ritz

      private int dsaupd_ritz

    • t0

      private long t0

    • t1

      private long t1

    • t2

      private long t2

    • t3

      private long t3

    • t4

      private long t4

    • t5

      private long t5

    • nopx

      private int nopx

    • nbx

      private int nbx

    • nrorth

      private int nrorth

    • nitref

      private int nitref

    • nrstrt

      private int nrstrt

    • tsaupd

      private double tsaupd

    • tsaup2

      private double tsaup2

    • tsaitr

      private double tsaitr

    • tseigt

      private double tseigt

    • tsgets

      private double tsgets

    • tsapps

      private double tsapps

    • tsconv

      private double tsconv

    • titref

      private double titref

    • tgetv0

      private double tgetv0

    • tmvopx

      private double tmvopx

    • tmvbx

      private double tmvbx

    • mgetv0

      private int mgetv0

    • msaupd

      private int msaupd

    • msaup2

      private int msaup2

    • msaitr

      private int msaitr

    • mseigt

      private int mseigt

    • msapps

      private int msapps

    • msgets

      private int msgets

    • mseupd

      private int mseupd

    • dsaup2_cnorm

      private boolean dsaup2_cnorm

    • dsaup2_getv0

      private boolean dsaup2_getv0

    • dsaup2_initv

      private boolean dsaup2_initv

    • dsaup2_update

      private boolean dsaup2_update

    • dsaup2_ushift

      private boolean dsaup2_ushift

    • dsaup2_iter

      private int dsaup2_iter

    • dsaup2_kplusp

      private int dsaup2_kplusp

    • dsaup2_msglvl

      private int dsaup2_msglvl

    • dsaup2_nconv

      private int[] dsaup2_nconv

    • dsaup2_nev0

      private int dsaup2_nev0

    • dsaup2_np0

      private int dsaup2_np0

    • dsaup2_rnorm

      private double[] dsaup2_rnorm

    • dsaup2_eps23

      private double dsaup2_eps23

    • dgetv0_first

      private boolean dgetv0_first

    • dgetv0_inits

      private boolean dgetv0_inits

    • dgetv0_orth

      private boolean dgetv0_orth

    • dgetv0_iseed

      private int[] dgetv0_iseed

    • dgetv0_iter

      private int dgetv0_iter

    • dgetv0_msglvl

      private int dgetv0_msglvl

    • dgetv0_rnorm0

      private double dgetv0_rnorm0

    • dsaitr_orth1

      private boolean dsaitr_orth1

    • dsaitr_orth2

      private boolean dsaitr_orth2

    • dsaitr_rstart

      private boolean dsaitr_rstart

    • dsaitr_step3

      private boolean dsaitr_step3

    • dsaitr_step4

      private boolean dsaitr_step4

    • dsaitr_first

      private boolean dsaitr_first

    • dsaitr_ierr

      private int[] dsaitr_ierr

    • dsaitr_ipj

      private int dsaitr_ipj

    • dsaitr_irj

      private int dsaitr_irj

    • dsaitr_ivj

      private int dsaitr_ivj

    • dsaitr_iter

      private int dsaitr_iter

    • dsaitr_itry

      private int dsaitr_itry

    • dsaitr_j

      private int dsaitr_j

    • dsaitr_msglvl

      private int dsaitr_msglvl

    • dsaitr_rnorm1

      private double dsaitr_rnorm1

    • dsaitr_safmin

      private double dsaitr_safmin

    • dsaitr_wnorm

      private double dsaitr_wnorm

    • dsapps_epsmch

      private double dsapps_epsmch

    • dsapps_first

      private boolean dsapps_first

  • Constructor Details

    • SparseEigenvalue

      public SparseEigenvalue()
      Creates a new SparseEigenvalue object.

  • Method Details

    • simpleEigenvalueTest1

      public void simpleEigenvalueTest1()

    • simpleEigenvalue

      public void simpleEigenvalue(double[][] A, int nev, String which, double[] tol, int ncv, double[] d, double[][] Z)
      Calculate requested eigenvalues and eigenvectors of a matrix
      Parameters:
      A - Symmetric real matrix for which eigenvalues and eigenvectors will be calculated n = A.length = A[0].length
      nev - Number of eigenvalues and accompanying eigenvectors to be calculated
      which - WHICH must be one of "LM", "SM", "LA", "SA" or "BE" largest and smallest magnitudes, largest and smallest amplitudes, both ends of the spectrum
      tol - determines the stopping criterion. Expect | abs(lambdaC - lambdaT) invalid input: '<' tol*abs(lambdaC) computed true If tol .le. 0, then tol invalid input: '<'- macheps (machine precision) is used.
      ncv - The largest number of basis vectors that will be used in the Implicitly Restarted Arnoldi Process. Work per major iteration is proportional to n*ncv*ncv. As a rule of thumb, ncv >= 2 * nev is reasonable. ncv must be >= nev+1 and ncv must be invalid input: '<'= n.
      d - User supplied array of size nev will hold the calculated eigenvalues
      Z - User supplied array of size [A.length][nev] to hold the calculated eigenvalues

    • matMult

      private void matMult(int n, double[][] A, double[] x, double[] y)

    • dssimp

      public void dssimp()

    • avsimp

      private void avsimp(int nx, double[] v, double[] w)

    • tvsimp

      private void tvsimp(int nx, double[] x, double[] y)

    • dsvd

      public void dsvd()

    • avsvd

      private void avsvd(int m, int n, double[] x, double[] w)

    • atv

      private void atv(int m, int n, double[] w, double[] y)

    • dsdrv1

      public void dsdrv1()

    • av

      private void av(int nx, double[] v, double[] w)

    • tv

      private void tv(int nx, double[] x, double[] y)

    • dsdrv2

      public void dsdrv2()

    • av2

      private void av2(int n, double[] v, double[] w)

    • dsdrv3

      public void dsdrv3()

    • mv3

      private void mv3(int n, double[] v, double[] w)

    • av3

      private void av3(int n, double[] v, double[] w)

    • dsdrv4

      public void dsdrv4()

    • mv4

      private void mv4(int n, double[] v, double[] w)

    • av4

      private void av4(int n, double[] v, double[] w)

    • dsdrv5

      public void dsdrv5()

    • mv5

      private void mv5(int n, double[] v, double[] w)

    • av5

      private void av5(int n, double[] v, double[] w)

    • dsdrv6

      public void dsdrv6()

    • mv6

      private void mv6(int n, double[] v, double[] w)

    • av6

      private void av6(int n, double[] v, double[] w)

    • dchkgt_test

      public void dchkgt_test()
      This dchkgt_test routine is a port of a portion of the version 3.4.1 LAPACK test routine DCHKAA by Univ. of Tennessee, Univ. Of California Berkeley and NAG Ltd., April, 2012. and some values from the test data file dtest.in. Received message In dchkgt all 2694 tests run passed the threshold.

    • dchkgt

      private void dchkgt(boolean[] dotype, int nn, int[] nval, int nns, int[] nsval, double thresh, double[] a, double[] af, double[] b, double[] x, double[] xact, double[] work, double[] rwork, int[] iwork)

    • dgtt05

      private void dgtt05(char trans, int n, int nrhs, double[] dl, double[] d, double[] du, double[][] b, int ldb, double[][] x, int ldx, double[][] xact, int ldxact, double[] ferr, double[] berr, double[] reslts)

    • dgtrfs

      private void dgtrfs(char trans, int n, int nrhs, double[] dl, double[] d, double[] du, double[] dlf, double[] df, double[] duf, double[] du2, int[] ipiv, double[][] b, int ldb, double[][] x, int ldx, double[] ferr, double[] berr, double[] work, int[] iwork, int[] info)

    • dgtt02

      private void dgtt02(char TRANS, int N, int NRHS, double[] DL, double[] D, double[] DU, double[][] X, int LDX, double[][] B, int LDB, double[] RWORK, double[] RESID)

    • printHeader

      private void printHeader()

    • dlagtm

      private void dlagtm(char trans, int n, int nrhs, double alpha, double[] dl, double[] d, double[] du, double[][] x, int ldx, double beta, double[][] b, int ldb)

    • dgtcon

      private void dgtcon(char NORM, int N, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, double ANORM, double[] RCOND, double[] WORK, int[] IWORK, int[] INFO)

    • dgtt01

      private void dgtt01(int n, double[] dl, double[] d, double[] du, double[] dlf, double[] df, double[] duf, double[] du2, int[] ipiv, double[][] work, int ldwork, double[] rwork, double[] resid)

    • dlangt

      private double dlangt(char norm, int n, double[] dl, double[] d, double[] du)

    • dgttrf

      private void dgttrf(int N, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, int[] INFO)

    • dgttrs

      private void dgttrs(char TRANS, int N, int NRHS, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, double[][] B, int LDB, int[] INFO)

    • DGTTS2

      private void DGTTS2(int ITRANS, int N, int NRHS, double[] DL, double[] D, double[] DU, double[] DU2, int[] IPIV, double[][] B, int LDB)

    • dseupd

      public void dseupd(boolean rvec, String howmny, boolean[] select, double[] d, double[][] z, int ldz, double sigma, String bmat, int n, String which, int nev, double tol, double[] resid, int ncv, double[][] v, int ldv, int[] iparam, int[] ipntr, double[] workd, double[] workl, int lworkl, int[] info)

    • dsesrt

      private void dsesrt(String which, boolean apply, int n, double[] x, int na, double[][] a, int lda)

    • dsaupd

      public void dsaupd(int[] ido, String bmat, int n, String which, int nev, double[] tol, double[] resid, int ncv, double[][] v, int ldv, int[] iparam, int[] ipntr, double[] workd, double[] workl, int lworkl, int[] info)

    • dsaup2

      private void dsaup2(int[] ido, String bmat, int n, String which, int[] nev, int[] np, double[] tol, double[] resid, int mode, int iupd, int ishift, int[] mxiter, double[][] v, int ldv, double[][] h, int ldh, double[] ritz, double[] bounds, double[][] q, int ldq, double[] workl, int[] ipntr, double[] workd, int[] info)

    • dsapps

      private void dsapps(int n, int kev, int np, double[] shift, double[][] v, int ldv, double[][] h, int ldh, double[] resid, double[][] q, int ldq, double[] workd)

    • dsconv

      private void dsconv(int n, double[] ritz, double[] bounds, double tol, int[] nconv)

    • dsgets

      private void dsgets(int ishift, String which, int kev, int np, double[] ritz, double[] bounds, double[] shifts)

    • dsortr

      private void dsortr(String which, boolean apply, int n, double[] x1, double[] x2)

    • dseigt

      private void dseigt(double rnorm, int n, double[][] h, int ldh, double[] eig, double[] bounds, double[] workl, int[] ierr)

    • dstqrb

      private void dstqrb(int n, double[] d, double[] e, double[] z, double[] work, int[] info)

    • dsaitr

      private void dsaitr(int[] ido, String bmat, int n, int k, int np, int mode, double[] resid, double[] rnorm, double[][] v, int ldv, double[][] h, int ldh, int[] ipntr, double[] workd, int[] info)

    • dgetv0

      private void dgetv0(int[] ido, String bmat, int itry, boolean initv, int n, int j, double[][] v, int ldv, double[] resid, double[] rnorm, int[] ipntr, double[] workd, int[] ierr)

    • dstats

      private void dstats()