Examples with EnergyException ffx.potential.utils.EnergyException used on opensource projects

Example 16 with EnergyException

use of ffx.potential.utils.EnergyException in project ffx by mjschnie.

the class ParticleMeshEwaldCart method scfByPCG.

private int scfByPCG(boolean print, long startTime) {
    long directTime = System.nanoTime() - startTime;
    /**
     * A request of 0 SCF cycles simplifies mutual polarization to direct
     * polarization.
     */
    StringBuilder sb = null;
    if (print) {
        sb = new StringBuilder("\n Self-Consistent Field\n" + " Iter  RMS Change (Debye)  Time\n");
    }
    /**
     * Find the induced dipole field due to direct dipoles (or predicted
     * induced dipoles from previous steps).
     */
    computeInduceDipoleField();
    try {
        /**
         * Set initial conjugate gradient residual (a field).
         *
         * Store the current induced dipoles and load the residual induced
         * dipole
         */
        parallelTeam.execute(pcgInitRegion1);
        /**
         * Compute preconditioner.
         */
        if (nSymm > 1) {
            parallelTeam.execute(expandInducedDipolesRegion);
        }
        parallelTeam.execute(inducedDipolePreconditionerRegion);
        /**
         * Revert to the stored induce dipoles.
         *
         * Set initial conjugate vector (induced dipoles).
         */
        parallelTeam.execute(pcgInitRegion2);
    } catch (Exception e) {
        String message = "Exception initializing preconditioned CG.";
        logger.log(Level.SEVERE, message, e);
    }
    /**
     * Conjugate gradient iteration of the mutual induced dipoles.
     */
    int completedSCFCycles = 0;
    int maxSCFCycles = 1000;
    double eps = 100.0;
    double previousEps;
    boolean done = false;
    while (!done) {
        long cycleTime = -System.nanoTime();
        /**
         * Store a copy of the current induced dipoles, then set the induced
         * dipoles to the conjugate vector.
         */
        for (int i = 0; i < nAtoms; i++) {
            vec[0][i] = inducedDipole[0][i][0];
            vec[1][i] = inducedDipole[0][i][1];
            vec[2][i] = inducedDipole[0][i][2];
            inducedDipole[0][i][0] = conj[0][i];
            inducedDipole[0][i][1] = conj[1][i];
            inducedDipole[0][i][2] = conj[2][i];
            vecCR[0][i] = inducedDipoleCR[0][i][0];
            vecCR[1][i] = inducedDipoleCR[0][i][1];
            vecCR[2][i] = inducedDipoleCR[0][i][2];
            inducedDipoleCR[0][i][0] = conjCR[0][i];
            inducedDipoleCR[0][i][1] = conjCR[1][i];
            inducedDipoleCR[0][i][2] = conjCR[2][i];
        }
        /**
         * Find the induced dipole field.
         */
        computeInduceDipoleField();
        try {
            /**
             * Revert the induced dipoles to the saved values, then save the
             * new residual field.
             *
             * Compute dot product of the conjugate vector and new residual.
             *
             * Reduce the residual field, add to the induced dipoles based
             * on the scaled conjugate vector and finally set the induced
             * dipoles to the polarizability times the residual field.
             */
            parallelTeam.execute(pcgIterRegion1);
            /**
             * Compute preconditioner.
             */
            if (nSymm > 1) {
                parallelTeam.execute(expandInducedDipolesRegion);
            }
            parallelTeam.execute(inducedDipolePreconditionerRegion);
            /**
             * Revert the induced dipoles to the saved values.
             *
             * Compute the dot product of the residual and preconditioner.
             *
             * Update the conjugate vector and sum the square of the
             * residual field.
             */
            pcgIterRegion2.sum = pcgIterRegion1.sumShared.get();
            pcgIterRegion2.sumCR = pcgIterRegion1.sumCRShared.get();
            parallelTeam.execute(pcgIterRegion2);
        } catch (Exception e) {
            String message = "Exception in first CG iteration region.";
            logger.log(Level.SEVERE, message, e);
        }
        previousEps = eps;
        // eps = max(eps, epsCR);
        eps = max(pcgIterRegion2.epsShared.get(), pcgIterRegion2.epsCRShared.get());
        completedSCFCycles++;
        eps = MultipoleType.DEBYE * sqrt(eps / (double) nAtoms);
        cycleTime += System.nanoTime();
        if (print) {
            sb.append(format(" %4d     %15.10f %7.4f\n", completedSCFCycles, eps, cycleTime * TO_SECONDS));
        }
        /**
         * If the RMS Debye change increases, fail the SCF process.
         */
        if (eps > previousEps) {
            if (sb != null) {
                logger.warning(sb.toString());
            }
            String message = format("Fatal SCF convergence failure: (%10.5f > %10.5f)\n", eps, previousEps);
            throw new EnergyException(message, false);
        }
        /**
         * The SCF should converge well before the max iteration check.
         * Otherwise, fail the SCF process.
         */
        if (completedSCFCycles >= maxSCFCycles) {
            if (sb != null) {
                logger.warning(sb.toString());
            }
            String message = format("Maximum SCF iterations reached: (%d)\n", completedSCFCycles);
            throw new EnergyException(message, false);
        }
        /**
         * Check if the convergence criteria has been achieved.
         */
        if (eps < poleps) {
            done = true;
        }
    }
    if (print) {
        sb.append(format(" Direct:                  %7.4f\n", TO_SECONDS * directTime));
        startTime = System.nanoTime() - startTime;
        sb.append(format(" Total:                   %7.4f", startTime * TO_SECONDS));
        logger.info(sb.toString());
    /**
     * for (int i = 0; i < nAtoms; i++) { double dx =
     * MultipoleType.DEBYE * inducedDipole[0][i][0]; double dy =
     * MultipoleType.DEBYE * inducedDipole[0][i][1]; double dz =
     * MultipoleType.DEBYE * inducedDipole[0][i][2]; double norm =
     * sqrt(dx * dx + dy * dy + dz * dz); logger.info(format("ind %d
     * %16.6f %16.6f %16.6f %16.6f", i + 1, dx, dy, dz, norm)); dx =
     * MultipoleType.DEBYE * inducedDipoleCR[0][i][0]; dy =
     * MultipoleType.DEBYE * inducedDipoleCR[0][i][1]; dz =
     * MultipoleType.DEBYE * inducedDipoleCR[0][i][2]; norm = sqrt(dx *
     * dx + dy * dy + dz * dz); logger.info(format("inp %d %16.6f %16.6f
     * %16.6f %16.6f", i + 1, dx, dy, dz, norm)); }
     */
    }
    /**
     * Find the final induced dipole field.
     */
    computeInduceDipoleField();
    return completedSCFCycles;
}

Example 17 with EnergyException

use of ffx.potential.utils.EnergyException in project ffx by mjschnie.

the class ParticleMeshEwaldQI method scfBySOR.

/**
 * Converge the SCF using Successive Over-Relaxation (SOR).
 */
private int scfBySOR(boolean print, long startTime) {
    long directTime = System.nanoTime() - startTime;
    /**
     * A request of 0 SCF cycles simplifies mutual polarization to direct
     * polarization.
     */
    StringBuilder sb = null;
    if (print) {
        sb = new StringBuilder("\n Self-Consistent Field\n" + " Iter  RMS Change (Debye)  Time\n");
    }
    int completedSCFCycles = 0;
    int maxSCFCycles = 1000;
    double eps = 100.0;
    double previousEps;
    boolean done = false;
    while (!done) {
        long cycleTime = -System.nanoTime();
        try {
            if (reciprocalSpaceTerm && aewald > 0.0) {
                reciprocalSpace.splineInducedDipoles(inducedDipole, inducedDipoleCR, use);
            }
            sectionTeam.execute(inducedDipoleFieldRegion);
            if (reciprocalSpaceTerm && aewald > 0.0) {
                reciprocalSpace.computeInducedPhi(cartesianDipolePhi, cartesianDipolePhiCR);
            }
            if (generalizedKirkwoodTerm) {
                /**
                 * GK field.
                 */
                gkEnergyTotal = -System.nanoTime();
                generalizedKirkwood.computeInducedGKField();
                gkEnergyTotal += System.nanoTime();
                logger.fine(format(" Computed GK induced field %8.3f (sec)", gkEnergyTotal * 1.0e-9));
            }
            parallelTeam.execute(sorRegion);
            if (nSymm > 1) {
                parallelTeam.execute(expandInducedDipolesRegion);
            }
        } catch (RuntimeException ex) {
            logger.warning("Exception computing mutual induced dipoles.");
            throw ex;
        } catch (Exception ex) {
            logger.log(Level.SEVERE, "Exception computing mutual induced dipoles.", ex);
        }
        completedSCFCycles++;
        previousEps = eps;
        eps = sorRegion.getEps();
        eps = MultipoleType.DEBYE * sqrt(eps / (double) nAtoms);
        cycleTime += System.nanoTime();
        if (print) {
            sb.append(format(" %4d     %15.10f %7.4f\n", completedSCFCycles, eps, cycleTime * TO_SECONDS));
        }
        /**
         * If the RMS Debye change increases, fail the SCF process.
         */
        if (eps > previousEps) {
            if (sb != null) {
                logger.warning(sb.toString());
            }
            String message = format("Fatal SCF convergence failure: (%10.5f > %10.5f)\n", eps, previousEps);
            throw new EnergyException(message, false);
        }
        /**
         * The SCF should converge well before the max iteration check.
         * Otherwise, fail the SCF process.
         */
        if (completedSCFCycles >= maxSCFCycles) {
            if (sb != null) {
                logger.warning(sb.toString());
            }
            String message = format("Maximum SCF iterations reached: (%d)\n", completedSCFCycles);
            throw new EnergyException(message, false);
        }
        /**
         * Check if the convergence criteria has been achieved.
         */
        if (eps < poleps) {
            done = true;
        }
    }
    if (print) {
        sb.append(format(" Direct:                  %7.4f\n", TO_SECONDS * directTime));
        startTime = System.nanoTime() - startTime;
        sb.append(format(" Total:                   %7.4f", startTime * TO_SECONDS));
        logger.info(sb.toString());
    }
    return completedSCFCycles;
}

Example 18 with EnergyException

use of ffx.potential.utils.EnergyException in project ffx by mjschnie.

the class ParticleMeshEwaldQI method scfByPCG.

private int scfByPCG(boolean print, long startTime) {
    long directTime = System.nanoTime() - startTime;
    /**
     * A request of 0 SCF cycles simplifies mutual polarization to direct
     * polarization.
     */
    StringBuilder sb = null;
    if (print) {
        sb = new StringBuilder("\n Self-Consistent Field\n" + " Iter  RMS Change (Debye)  Time\n");
    }
    /**
     * Find the induced dipole field due to direct dipoles (or predicted
     * induced dipoles from previous steps).
     */
    computeInduceDipoleField();
    try {
        /**
         * Set initial conjugate gradient residual (a field).
         *
         * Store the current induced dipoles and load the residual induced
         * dipole
         */
        parallelTeam.execute(pcgInitRegion1);
        /**
         * Compute preconditioner.
         */
        if (nSymm > 1) {
            parallelTeam.execute(expandInducedDipolesRegion);
        }
        parallelTeam.execute(inducedDipolePreconditionerRegion);
        /**
         * Revert to the stored induce dipoles.
         *
         * Set initial conjugate vector (induced dipoles).
         */
        parallelTeam.execute(pcgInitRegion2);
    } catch (Exception e) {
        String message = "Exception initializing preconditioned CG.";
        logger.log(Level.SEVERE, message, e);
    }
    /**
     * Conjugate gradient iteration of the mutual induced dipoles.
     */
    int completedSCFCycles = 0;
    int maxSCFCycles = 1000;
    double eps = 100.0;
    double previousEps;
    boolean done = false;
    while (!done) {
        long cycleTime = -System.nanoTime();
        /**
         * Store a copy of the current induced dipoles, then set the induced
         * dipoles to the conjugate vector.
         */
        for (int i = 0; i < nAtoms; i++) {
            vec[0][i] = inducedDipole[0][i][0];
            vec[1][i] = inducedDipole[0][i][1];
            vec[2][i] = inducedDipole[0][i][2];
            inducedDipole[0][i][0] = conj[0][i];
            inducedDipole[0][i][1] = conj[1][i];
            inducedDipole[0][i][2] = conj[2][i];
            vecCR[0][i] = inducedDipoleCR[0][i][0];
            vecCR[1][i] = inducedDipoleCR[0][i][1];
            vecCR[2][i] = inducedDipoleCR[0][i][2];
            inducedDipoleCR[0][i][0] = conjCR[0][i];
            inducedDipoleCR[0][i][1] = conjCR[1][i];
            inducedDipoleCR[0][i][2] = conjCR[2][i];
        }
        /**
         * Find the induced dipole field.
         */
        computeInduceDipoleField();
        try {
            /**
             * Revert the induced dipoles to the saved values, then save the
             * new residual field.
             *
             * Compute dot product of the conjugate vector and new residual.
             *
             * Reduce the residual field, add to the induced dipoles based
             * on the scaled conjugate vector and finally set the induced
             * dipoles to the polarizability times the residual field.
             */
            parallelTeam.execute(pcgIterRegion1);
            /**
             * Compute preconditioner.
             */
            if (nSymm > 1) {
                parallelTeam.execute(expandInducedDipolesRegion);
            }
            parallelTeam.execute(inducedDipolePreconditionerRegion);
            /**
             * Revert the induced dipoles to the saved values.
             *
             * Compute the dot product of the residual and preconditioner.
             *
             * Update the conjugate vector and sum the square of the
             * residual field.
             */
            pcgIterRegion2.sum = pcgIterRegion1.sumShared.get();
            pcgIterRegion2.sumCR = pcgIterRegion1.sumCRShared.get();
            parallelTeam.execute(pcgIterRegion2);
        } catch (Exception e) {
            String message = "Exception in first CG iteration region.";
            logger.log(Level.SEVERE, message, e);
        }
        previousEps = eps;
        // eps = max(eps, epsCR);
        eps = max(pcgIterRegion2.epsShared.get(), pcgIterRegion2.epsCRShared.get());
        completedSCFCycles++;
        eps = MultipoleType.DEBYE * sqrt(eps / (double) nAtoms);
        cycleTime += System.nanoTime();
        if (print) {
            sb.append(format(" %4d     %15.10f %7.4f\n", completedSCFCycles, eps, cycleTime * TO_SECONDS));
        }
        /**
         * If the RMS Debye change increases, fail the SCF process.
         */
        if (eps > previousEps) {
            if (sb != null) {
                logger.warning(sb.toString());
            }
            String message = format("Fatal SCF convergence failure: (%10.5f > %10.5f)\n", eps, previousEps);
            throw new EnergyException(message, false);
        }
        /**
         * The SCF should converge well before the max iteration check.
         * Otherwise, fail the SCF process.
         */
        if (completedSCFCycles >= maxSCFCycles) {
            if (sb != null) {
                logger.warning(sb.toString());
            }
            String message = format("Maximum SCF iterations reached: (%d)\n", completedSCFCycles);
            throw new EnergyException(message, false);
        }
        /**
         * Check if the convergence criteria has been achieved.
         */
        if (eps < poleps) {
            done = true;
        }
    }
    if (print) {
        sb.append(format(" Direct:                  %7.4f\n", TO_SECONDS * directTime));
        startTime = System.nanoTime() - startTime;
        sb.append(format(" Total:                   %7.4f", startTime * TO_SECONDS));
        logger.info(sb.toString());
    }
    /**
     * Find the final induced dipole field.
     */
    computeInduceDipoleField();
    return completedSCFCycles;
}