コード例 #1
0
ファイル: mlinpckd.c プロジェクト: Chauamtran/apbs-pdb2pqr
VPUBLIC void Vdpbsl(double *abd, int *lda, int *n, int *m, double *b) {

    double t;
    int k, kb, la, lb, lm;

    MAT2(abd, *lda, 1);

    for (k=1; k<=*n; k++) {
        lm = VMIN2(k-1, *m);
        la = *m + 1 - lm;
        lb = k - lm;
        t = Vddot(lm, RAT2(abd, la, k ), 1, RAT(b, lb), 1 );
        VAT(b, k) = (VAT(b, k) - t) / VAT2(abd, *m+1, k);
    }

    // Solve R*X = Y
    for (kb=1; kb<=*n; kb++) {

        k = *n + 1 - kb;
        lm = VMIN2(k-1, *m);
        la = *m + 1 - lm;
        lb = k - lm;
        VAT(b, k) /= VAT2(abd, *m+1, k);
        t = -VAT(b, k);
        Vdaxpy(lm, t, RAT2(abd, la, k), 1, RAT(b, lb), 1);
    }
}
コード例 #2
0
ファイル: mikpckd.c プロジェクト: bottlecherry/apbs-pdb2pqr
VPUBLIC void Vprtmatd(int *nx, int *ny, int *nz,
                      int *ipc, double *rpc, double *ac) {

    int numdia;

    MAT2(ac, *nx * *ny * *nz, 1);

    WARN_UNTESTED;

    // Do the printing
    numdia = VAT(ipc, 11);
    if (numdia == 7) {
        Vprtmatd7(nx, ny, nz,
                  ipc, rpc,
                  RAT2(ac, 1, 1), RAT2(ac, 1, 2), RAT2(ac, 1, 3), RAT2(ac, 1, 4));
    } else if (numdia == 27) {
        Vprtmatd27(nx, ny, nz,
                   ipc, rpc,
                   RAT2(ac, 1,  1), RAT2(ac, 1,  2), RAT2(ac, 1,  3), RAT2(ac, 1,  4),
                   RAT2(ac, 1,  5), RAT2(ac, 1,  6),
                   RAT2(ac, 1,  7), RAT2(ac, 1,  8), RAT2(ac, 1,  9), RAT2(ac, 1, 10),
                   RAT2(ac, 1, 11), RAT2(ac, 1, 12), RAT2(ac, 1, 13), RAT2(ac, 1, 14));
    } else {
        Vnm_print(2, "Vprtmatd: invalid stencil type given: %d\n", numdia);
    }
}
コード例 #3
0
ファイル: mikpckd.c プロジェクト: bottlecherry/apbs-pdb2pqr
VPUBLIC void Vazeros(int *nx, int *ny, int *nz, double *x) {

    int i, n;
    int nproc = 1;

    n = *nx * *ny * *nz;

    #pragma omp parallel for private(i)
    for (i=1; i<=n; i++)
        VAT(x, i) = 0.0;
}
コード例 #4
0
ファイル: mikpckd.c プロジェクト: bottlecherry/apbs-pdb2pqr
VPUBLIC void Vaxrand(int *nx, int *ny, int *nz, double *x) {

    int n, i, ii, ipara, ivect, iflag;
    int nproc = 1;
    double xdum;

    WARN_UNTESTED;

    // Find parallel loops (ipara), remainder (ivect)
    n = *nx * *ny * *nz;
    ipara = n / nproc;
    ivect = n % nproc;
    iflag = 1;
    xdum  = (double)(VRAND);

    // Do parallel loops
    for (ii=1; ii<=nproc; ii++)
        for (i=1+(ipara*(ii-1)); i<=ipara*ii; i++)
            VAT(x, i) = (double)(VRAND);

    // Do vector loops
    for (i=ipara*nproc+1; i<=n; i++)
        VAT(x, i) = (double)(VRAND);
}
コード例 #5
0
ファイル: newtond.c プロジェクト: ASCM/apbs-pdb2pqr
VPUBLIC void Vnewton(int *nx, int *ny, int *nz,
        double *x, int *iz,
        double *w0, double *w1, double *w2, double *w3,
        int *istop, int *itmax, int *iters, int *ierror,
        int *nlev, int *ilev, int *nlev_real,
        int *mgsolv, int *iok, int *iinfo,
        double *epsiln, double *errtol, double *omega,
        int *nu1, int *nu2, int *mgsmoo,
        double *cprime,  double *rhs, double *xtmp,
        int *ipc, double *rpc,
        double *pc, double *ac, double *cc, double *fc, double *tru) {

    int level, lev;
    int itmax_s, iters_s, ierror_s, iok_s, iinfo_s, istop_s;
    double errtol_s, ord, bigc;
    double rsden, rsnrm, orsnrm;

    double xnorm_old, xnorm_new, damp, xnorm_med, xnorm_den;
    double rho_max, rho_min, rho_max_mod, rho_min_mod, errtol_p;
    int iter_d, itmax_d, mode, idamp, ipkey;
    int itmax_p, iters_p, iok_p, iinfo_p;

    // Utility and temproary parameters
    double alpha;

    MAT2(iz, 50, 1);

    // Recover level information
    level = 1;
    lev   = (*ilev - 1) + level;

    // Do some i/o if requested
    if (*iinfo > 1) {
        VMESSAGE3("Starting: (%d, %d, %d)", *nx, *ny, *nz);
    }

    if (*iok != 0) {
        Vprtstp(*iok, -1, 0.0, 0.0, 0.0);
    }

    /**************************************************************
     *** note: if (iok!=0) then:  use a stopping test.          ***
     ***       else:  use just the itmax to stop iteration.     ***
     **************************************************************
     *** istop=0 most efficient (whatever it is)                ***
     *** istop=1 relative residual                              ***
     *** istop=2 rms difference of successive iterates          ***
     *** istop=3 relative true error (provided for testing)     ***
     **************************************************************/

    // Compute denominator for stopping criterion
    if (*istop == 0) {
         rsden = 1.0;
    } else if (*istop == 1) {

        // Compute initial residual with zero initial guess
        // this is analogous to the linear case where one can
        // simply take norm of rhs for a zero initial guess

        Vazeros(nx, ny, nz, w1);

        Vnmresid(nx, ny, nz,
                RAT(ipc, VAT2(iz, 5, lev)), RAT(rpc, VAT2(iz, 6, lev)),
                RAT( ac, VAT2(iz, 7, lev)), RAT( cc, VAT2(iz, 1, lev)),
                RAT( fc, VAT2(iz, 1, lev)),
                w1, w2, w3);
        rsden = Vxnrm1(nx, ny, nz, w2);
    } else if (*istop == 2) {
        rsden = VSQRT( *nx * *ny * *nz);
    } else if (*istop == 3) {
        rsden = Vxnrm2(nx, ny, nz, RAT(tru, VAT2(iz, 1, lev)));
    } else if (*istop == 4) {
        rsden = Vxnrm2(nx, ny, nz, RAT(tru, VAT2(iz, 1, lev)));
    } else if (*istop == 5) {
        Vnmatvec(nx, ny, nz,
                RAT(ipc, VAT2(iz, 5, lev)), RAT(rpc, VAT2(iz, 6, lev)),
                RAT( ac, VAT2(iz, 7, lev)), RAT( cc, VAT2(iz, 1, lev)),
                RAT(tru, VAT2(iz, 1, lev)),
                w1, w2);
        rsden = VSQRT(Vxdot(nx, ny, nz, RAT(tru, VAT2(iz, 1, lev)), w1));
    } else {
        VABORT_MSG1("Bad istop value: %d\n", *istop);
    }

    if (rsden == 0.0) {
        rsden = 1.0;
        VWARN_MSG0(rsden != 0, "rhs is zero");
    }
    rsnrm = rsden;
    orsnrm = rsnrm;

    if (*iok != 0) {
        Vprtstp(*iok, 0, rsnrm, rsden, orsnrm);
    }

    /*********************************************************************
     *** begin newton iteration
     *********************************************************************/

    // Now compute residual with the initial guess

    Vnmresid(nx, ny, nz,
            RAT(ipc, VAT2(iz, 5, lev)), RAT(rpc, VAT2(iz, 6, lev)),
            RAT( ac, VAT2(iz, 7, lev)), RAT( cc, VAT2(iz, 1, lev)),
            RAT( fc, VAT2(iz, 1, lev)), RAT(  x, VAT2(iz, 1, lev)),
            w0, w2);
    xnorm_old = Vxnrm1(nx, ny, nz, w0);
    if (*iok != 0) {
        xnorm_den = rsden;
    } else {
        xnorm_den = xnorm_old;
    }



    /*********************************************************************
     *** begin the loop
     *********************************************************************/

    // Setup for the looping
    VMESSAGE0("Damping enabled");
    idamp  = 1;
    *iters  = 0;

    //30
    while(1) {

        (*iters)++;

        // Save iterate if stop test will use it on next iter
        if (*istop == 2) {
            Vxcopy(nx, ny, nz,
                    RAT(x, VAT2(iz, 1, lev)), RAT(tru, VAT2(iz, 1, lev)));
        }

        // Compute the current jacobian system and rhs
        ipkey = VAT(ipc, 10);
        Vgetjac(nx, ny, nz, nlev_real, iz, ilev, &ipkey,
                x, w0, cprime, rhs, cc, pc);

        // Determine number of correct digits in current residual
        // Algorithm 5.3 in the thesis, test version (1')
        // Global-superlinear convergence
        bigc = 1.0;
        ord  = 2.0;

        /* NAB 06-18-01:  If complex problems are not converging, set this to
         * machine epsilon.  This makes it use the exact jacobian rather than
         * the appropriate form (as here)
         */
         errtol_s  = VMIN2((0.9 * xnorm_old), (bigc * VPOW(xnorm_old, ord)));
         VMESSAGE1("Using errtol_s: %f", errtol_s);

        // Do a linear multigrid solve of the newton equations
        Vazeros(nx, ny, nz, RAT(xtmp, VAT2(iz, 1, lev)));

        itmax_s   = 1000;
        istop_s   = 0;
        iters_s   = 0;
        ierror_s  = 0;

        // NAB 06-18-01 -- What this used to be:
        iok_s     = 0;
        iinfo_s   = 0;
        if ((*iinfo >= 2) && (*ilev == 1))
            iok_s = 2;

        // What it's changed to:
        if (*iinfo >= 2)
            iinfo_s = *iinfo;
        iok_s = 2;

        // End of NAB hack.

        Vmvcs(nx, ny, nz,
                xtmp, iz,
                w0, w1, w2, w3,
                &istop_s, &itmax_s, &iters_s, &ierror_s,
                nlev, ilev, nlev_real, mgsolv,
                &iok_s, &iinfo_s,
                epsiln, &errtol_s, omega,
                nu1, nu2, mgsmoo,
                ipc, rpc, pc, ac, cprime, rhs, tru);

        /**************************************************************
         *** note: rhs and cprime are now available as temp vectors ***
         **************************************************************/

        // If damping is still enabled -- doit
        if (idamp == 1) {

            // Try the correction
            Vxcopy(nx, ny, nz,
                    RAT(x, VAT2(iz, 1, lev)), w1);
            damp = 1.0;
            Vxaxpy(nx, ny, nz, &damp, RAT(xtmp, VAT2(iz, 1, lev)), w1);

            Vnmresid(nx, ny, nz,
                    RAT(ipc, VAT2(iz, 5, lev)), RAT(rpc, VAT2(iz, 6, lev)),
                    RAT( ac, VAT2(iz, 7, lev)), RAT( cc, VAT2(iz, 1, lev)),
                    RAT( fc, VAT2(iz, 1, lev)),
                    w1, w0,
                    RAT(rhs, VAT2(iz, 1, lev)));
            xnorm_new = Vxnrm1(nx, ny, nz, w0);

            // Damping is still enabled -- doit
            damp    = 1.0;
            iter_d  = 0;
            itmax_d = 10;
            mode    = 0;

            VMESSAGE1("Attempting damping, relres = %f", xnorm_new / xnorm_den);

            while(iter_d < itmax_d) {
                if (mode == 0) {
                    if (xnorm_new < xnorm_old) {
                        mode = 1;
                    }
                } else if (xnorm_new > xnorm_med) {
                        break;
                }

                // Keep old soln and residual around, and its norm
                Vxcopy(nx, ny, nz, w1, w2);
                Vxcopy(nx, ny, nz, w0, w3);
                xnorm_med = xnorm_new;

                // New damped correction, residual, and its norm
                Vxcopy(nx, ny, nz,
                        RAT(x, VAT2(iz, 1, lev)), w1);
                damp = damp / 2.0;
                Vxaxpy(nx, ny, nz, &damp, RAT(xtmp, VAT2(iz, 1, lev)), w1);

                Vnmresid(nx, ny, nz,
                        RAT(ipc, VAT2(iz, 5, lev)), RAT(rpc, VAT2(iz, 6, lev)),
                        RAT( ac, VAT2(iz, 7, lev)), RAT( cc, VAT2(iz, 1, lev)),
                        RAT( fc, VAT2(iz, 1, lev)),
                        w1, w0,
                        RAT(rhs, VAT2(iz, 1, lev)));
                xnorm_new = Vxnrm1(nx, ny, nz, w0);

               // Next iter...
               iter_d = iter_d + 1;
               VMESSAGE1("Attempting damping, relres = %f",
                   xnorm_new / xnorm_den);

            }

            Vxcopy(nx, ny, nz, w2, RAT(x, VAT2(iz, 1, lev)));
            Vxcopy(nx, ny, nz, w3, w0);
            xnorm_new = xnorm_med;
            xnorm_old = xnorm_new;

            VMESSAGE1("Damping accepted, relres = %f", xnorm_new / xnorm_den);

            // Determine whether or not to disable damping
            if ((iter_d - 1) == 0) {
                VMESSAGE0("Damping disabled");
               idamp = 0;
            }
         } else {

            // Damping is disabled -- accept the newton step
            damp = 1.0;

            Vxaxpy(nx, ny, nz, &damp,
                    RAT(xtmp, VAT2(iz, 1, lev)), RAT(x, VAT2(iz, 1, lev)));

            Vnmresid(nx, ny, nz,
                    RAT(ipc, VAT2(iz, 5, lev)), RAT(rpc, VAT2(iz, 6, lev)),
                    RAT( ac, VAT2(iz, 7, lev)), RAT( cc, VAT2(iz, 1, lev)),
                    RAT( fc, VAT2(iz, 1, lev)), RAT(  x, VAT2(iz, 1, lev)),
                    w0,
                    RAT(rhs, VAT2(iz, 1, lev)));

            xnorm_new = Vxnrm1(nx, ny, nz, w0);
            xnorm_old = xnorm_new;
         }

         // Compute/check the current stopping test ***
         if (iok != 0) {

             orsnrm = rsnrm;

             if (*istop == 0) {
                rsnrm = xnorm_new;
             } else if (*istop == 1) {
                rsnrm = xnorm_new;
            } else if (*istop == 2) {
               Vxcopy(nx, ny, nz, RAT(tru, VAT2(iz, 1, lev)), w1);
               alpha = -1.0;
               Vxaxpy(nx, ny, nz, &alpha, RAT(x, VAT2(iz, 1, lev)), w1);
               rsnrm = Vxnrm1(nx, ny, nz, w1);
            } else if (*istop == 3) {
               Vxcopy(nx, ny, nz, RAT(tru, VAT2(iz, 1, lev)), w1);
               alpha = -1.0;
               Vxaxpy(nx, ny, nz, &alpha, RAT(x, VAT2(iz, 1, lev)), w1);
               rsnrm = Vxnrm2(nx, ny, nz, w1);
            } else if (*istop == 4) {
               Vxcopy(nx, ny, nz, RAT(tru, VAT2(iz, 1, lev)), w1);
               alpha = -1.0;
               Vxaxpy(nx, ny, nz, &alpha, RAT(x, VAT2(iz, 1, lev)), w1);
               rsnrm = Vxnrm2(nx, ny, nz, w1);
            } else if (*istop == 5) {
               Vxcopy(nx, ny, nz, RAT(tru, VAT2(iz, 1, lev)), w1);
               alpha = -1.0;
               Vxaxpy(nx, ny, nz, &alpha, RAT(x, VAT2(iz, 1, lev)), w1);
               Vnmatvec(nx, ny, nz,
                       RAT(ipc, VAT2(iz, 5, lev)), RAT(rpc, VAT2(iz, 6, lev)),
                       RAT( ac, VAT2(iz, 7, lev)), RAT( cc, VAT2(iz, 1, lev)),
                       w1, w2, w3);
               rsnrm = VSQRT(Vxdot(nx, ny, nz, w1, w2));
            } else {
                VABORT_MSG1("Bad istop value: %d", *istop);
            }

             Vprtstp(*iok, *iters, rsnrm, rsden, orsnrm);

            if ((rsnrm/rsden) <= *errtol)
                break;
        }

        // Check iteration count ***
        if (*iters >= *itmax)
            break;
    }

    // Condition estimate of final jacobian
    if (*iinfo > 2) {

        Vnm_print(2, "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n");
        Vnm_print(2, "% Vnewton: JACOBIAN ANALYSIS ==> (%d, %d, %d)\n",
                *nx, *ny, *nz );

        // Largest eigenvalue of the jacobian matrix
        Vnm_print(2, "% Vnewton: Power calculating rho(JAC)\n");
        itmax_p   = 1000;
        errtol_p  = 1.0e-4;
        iters_p   = 0;
        iinfo_p   = *iinfo;

        Vpower(nx, ny, nz,
                iz, ilev,
                ipc, rpc, ac, cprime,
                w0, w1, w2, w3,
                &rho_max, &rho_max_mod,
                &errtol_p, &itmax_p, &iters_p, &iinfo_p);

        Vnm_print(2, "% Vnewton: power iters   = %d\n", iters_p);
        Vnm_print(2, "% Vnewton: power eigmax  = %d\n", rho_max);
        Vnm_print(2, "% Vnewton: power (MODEL) = %d\n", rho_max_mod);

        // Smallest eigenvalue of the system matrix A ***
        Vnm_print(2, "% Vnewton: ipower calculating lambda_min(JAC)...\n");
        itmax_p   = 1000;
        errtol_p  = 1.0e-4;
        iters_p   = 0;
        iinfo_p   = *iinfo;

        Vazeros(nx, ny, nz, xtmp);

        Vipower(nx, ny, nz,
                xtmp, iz,
                w0, w1, w2, w3,
                rhs, &rho_min, &rho_min_mod,
                &errtol_p, &itmax_p, &iters_p,
                nlev, ilev, nlev_real, mgsolv,
                &iok_p, &iinfo_p,
                epsiln, errtol, omega,
                nu1, nu2, mgsmoo,
                ipc, rpc,
                pc, ac, cprime, tru);

        Vnm_print(2, "% Vnewton: ipower iters   = %d\n", iters_p);
        Vnm_print(2, "% Vnewton: ipower eigmin  = %d\n", rho_min);
        Vnm_print(2, "% Vnewton: ipower (MODEL) = %d\n", rho_min_mod);

        // Condition number estimate
        Vnm_print(2, "% Vnewton: condition number  = %f\n",
                (double)rho_max / rho_min);
        Vnm_print(2, "% Vnewton: condition (MODEL) = %f\n",
                (double)rho_max_mod / rho_min_mod);
        Vnm_print(2, "%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%\n");
    }
}
コード例 #6
0
ファイル: mlinpckd.c プロジェクト: Chauamtran/apbs-pdb2pqr
VPUBLIC void Vdaxpy(int n, double da,
        double *dx, int incx,
        double *dy, int incy) {

    int i, ix, iy, m, mp1;

    if (n <= 0)
        return;

    if (da == 0)
        return;

    if (incx == 1 && incy == 1) {

        m = n % 4;
        if (m != 0) {

            for (i=1; i<=m; i++)
                VAT(dy, i) += da * VAT(dx, i);
        }

        if (n < 4)
            return;

        mp1 = m + 1;

        for (i=mp1; i<=n; i+=4) {

            VAT(dy, i  ) += da * VAT(dx, i  );
            VAT(dy, i+1) += da * VAT(dx, i+1);
            VAT(dy, i+2) += da * VAT(dx, i+2);
            VAT(dy, i+3) += da * VAT(dx, i+3);
        }
    } else {

        ix = 1;
        if (incx < 0 )
            ix = (-n + 1) * incx + 1;

        iy = 1;
        if (incy < 0 )
            iy = (-n + 1) * incy + 1;

        for (i=1; i<=n; i++) {

            VAT(dy, iy) += da * VAT(dx, ix);
            ix += incx;
            iy += incy;
        }
    }
}
コード例 #7
0
ファイル: mlinpckd.c プロジェクト: Chauamtran/apbs-pdb2pqr
VPUBLIC double Vddot(int n, double *dx, int incx, double *dy, int incy) {

    double dtemp;
    int i, ix, iy, m, mp1;

    double ddot = 0.0;
    dtemp = 0.0;

    if (n <= 0)
        return ddot;

    if (incx == 1 && incy == 1) {

        m = n % 5;

        if (m != 0) {

            for (i=1; i<=m; i++)
                dtemp += VAT(dx, i) * VAT(dy, i);

            if (n < 5) {
                ddot = dtemp;
                return ddot;
            }
        }

        mp1 = m + 1;

        for (i=mp1; i<=n; i+=5)
            dtemp += VAT(dx,   i) * VAT(dy,   i)
                  +  VAT(dx, i+1) * VAT(dy, i+1)
                  +  VAT(dx, i+2) * VAT(dy, i+2)
                  +  VAT(dx, i+3) * VAT(dy, i+3)
                  +  VAT(dx, i+4) * VAT(dy, i+4);
    } else {

        ix = 1;
        if (incx < 0)
            ix = (-n + 1) * incx + 1;

        iy = 1;
        if (incy < 0)
            iy = (-n + 1) * incy + 1;

        for (i=1; i<=n; i++) {
            ix += incx;
            iy += incy;
        }
    }

    ddot = dtemp;
    return ddot;
}