Examples with BondedTerm ffx.potential.bonded.BondedTerm used on opensource projects

Example 1 with BondedTerm

use of ffx.potential.bonded.BondedTerm in project ffx by mjschnie.

the class PhDiscount method crashDump.

/**
 * Attempt to print sources of catastrophic system heating.
 */
private void crashDump(RuntimeException error) {
    writeSnapshot(".meltdown-");
    ffe.energy(false, true);
    mola.getDescendants(BondedTerm.class).stream().filter(BondedTerm::isExtendedSystemMember).forEach(term -> {
        try {
            ((Bond) term).log();
        } catch (Exception ex) {
        }
        try {
            ((Angle) term).log();
        } catch (Exception ex) {
        }
        try {
            ((Torsion) term).log();
        } catch (Exception ex) {
        }
    });
    if (ffe.getVanDerWaalsEnergy() > 1000) {
        extendedAtoms = esvSystem.getExtendedAtoms();
        nAtomsExt = esvSystem.getExtendedAtoms().length;
        for (int i = 0; i < nAtomsExt; i++) {
            Atom ai = extendedAtoms[i];
            for (int j = 0; j < nAtomsExt; j++) {
                Atom aj = extendedAtoms[j];
                if (!esvSystem.isExtended(i) && !esvSystem.isExtended(j)) {
                    continue;
                }
                if (ai == aj || ai.getBond(aj) != null) {
                    continue;
                }
                double dist = FastMath.sqrt(FastMath.pow((aj.getX() - ai.getX()), 2) + FastMath.pow((aj.getY() - ai.getY()), 2) + FastMath.pow((aj.getZ() - ai.getZ()), 2));
                if (dist < 0.8 * (aj.getVDWR() + ai.getVDWR())) {
                    logger.warning(String.format("Close vdW contact for atoms: \n   %s\n   %s", aj, ai));
                }
            }
        }
    }
    throw error;
}

Example 2 with BondedTerm

use of ffx.potential.bonded.BondedTerm in project ffx by mjschnie.

the class ExtendedSystem method getDerivative.

private double getDerivative(int esvID) {
    final double temperature = (config.forceRoomTemp) ? ExtConstants.roomTemperature : currentTemperature;
    final boolean p = config.decomposeDeriv;
    ExtendedVariable esv = esvList.get(esvID);
    double esvDeriv = 0.0;
    final String format = " %-20.20s %2.2s %9.4f";
    if (config.biasTerm) {
        final double dBias = esv.getTotalBiasDeriv(temperature, true);
        if (p) {
            sb.append(format("  Biases:", "", dBias));
        }
        final double dDiscr = esv.getDiscrBiasDeriv();
        if (p) {
            sb.append(format("    Discretizer:", ">", dDiscr));
        }
        if (esv instanceof TitrationESV) {
            final double dPh = ((TitrationESV) esv).getPhBiasDeriv(temperature);
            if (p) {
                sb.append(format("    Acidostat:", ">", dPh));
            }
        }
        esvDeriv += dBias;
    }
    if (config.vanDerWaals) {
        final double dVdw = vdw.getEsvDerivative(esvID);
        if (p) {
            sb.append(format("  VanDerWaals:", "", dVdw));
        }
        esvDeriv += dVdw;
    }
    if (config.electrostatics) {
        final double permanent = pme.getEsvDeriv_Permanent(esvID);
        esvDeriv += permanent;
        if (p) {
            sb.append(format("  PermanentElec:", "", permanent));
        }
        double permReal = pme.getEsvDeriv_PermReal(esvID);
        double permSelf = pme.getEsvDeriv_PermSelf(esvID);
        double permRecip = pme.getEsvDeriv_PermRecip(esvID);
        if (p) {
            sb.append(format("    PermReal:", ">", permReal));
        }
        if (p) {
            sb.append(format("    PermRcpSelf:", ">", permSelf));
        }
        if (p) {
            sb.append(format("    PermRecipMpole:", ">", permRecip));
        }
        if (config.polarization) {
            final double induced = pme.getEsvDeriv_Induced(esvID);
            esvDeriv += induced;
            if (p) {
                sb.append(format("  Polarization:", "", induced));
            }
            double indReal = pme.getEsvDeriv_IndReal(esvID);
            double indSelf = pme.getEsvDeriv_IndSelf(esvID);
            double indRecip = pme.getEsvDeriv_IndRecip(esvID);
            if (p) {
                sb.append(format("    IndReal:", ">", indReal));
            }
            if (p) {
                sb.append(format("    IndSelf:", ">", indSelf));
            }
            if (p) {
                sb.append(format("    IndRecip:", ">", indRecip));
            }
        }
    }
    if (config.bonded) {
        final double dBonded = esv.getBondedDeriv();
        if (p) {
            sb.append(format("  Bonded:", "", dBonded));
        }
        esvDeriv += dBonded;
        /* If desired, decompose bonded contribution into component types from foreground and background. */
        if (config.decomposeBonded) {
            // Foreground portion:
            double fgSum = 0.0;
            HashMap<Class<? extends BondedTerm>, SharedDouble> fgMap = esv.getBondedDerivDecomp();
            for (SharedDouble dub : fgMap.values()) {
                fgSum += dub.get();
            }
            if (p) {
                sb.append(format("    Foreground:", ">", fgSum));
            }
            for (Class<? extends BondedTerm> clas : fgMap.keySet()) {
                if (p) {
                    sb.append(format("      " + clas.getName().replaceAll("ffx.potential.bonded.", "") + ":", ">>", fgMap.get(clas).get()));
                }
            }
            // Background portion:
            double bgSum = 0.0;
            HashMap<Class<? extends BondedTerm>, SharedDouble> bgMap = esv.getBackgroundBondedDerivDecomp();
            for (SharedDouble dub : bgMap.values()) {
                bgSum += dub.get();
            }
            if (p) {
                sb.append(format("    Background:", ">", bgSum));
            }
            for (Class<? extends BondedTerm> clas : bgMap.keySet()) {
                if (p) {
                    sb.append(format("      " + clas.getName().replaceAll("ffx.potential.bonded.", "") + ":", ">>", bgMap.get(clas).get()));
                }
            }
        }
    }
    if (Double.isNaN(esvDeriv) || !Double.isFinite(esvDeriv)) {
        logger.warning(format("NaN/Inf lambda derivative: %s", this));
    }
    if (p) {
        sb.insert(0, format(" %-21.21s %-2.2s %9.4f", format("dUd%s:", esv.getName()), "", esvDeriv));
    }
    if (p) {
        logger.info(sb.toString());
    }
    return esvDeriv;
}

Example 3 with BondedTerm

use of ffx.potential.bonded.BondedTerm in project ffx by mjschnie.

the class ExtendedVariable method updateBondedLambdas.

private void updateBondedLambdas() {
    if (!config.bonded) {
        return;
    }
    bondedDeriv.set(0.0);
    double Sl = getLambdaSwitch();
    double dSldL = getSwitchDeriv();
    for (BondedTerm bt1 : bondedFg) {
        if (config.decomposeBonded) {
            bt1.attachExtendedVariable(Sl, dSldL, bondedDeriv, fgBondedDerivDecomp);
            fgBondedDerivDecomp.clear();
        } else {
            bt1.attachExtendedVariable(Sl, dSldL, bondedDeriv);
        }
    }
    for (BondedTerm bt0 : bondedBg) {
        if (config.decomposeBonded) {
            bt0.attachExtendedVariable(1.0 - Sl, -dSldL, bondedDeriv, bgBondedDerivDecomp);
            bgBondedDerivDecomp.clear();
        } else {
            bt0.attachExtendedVariable(1.0 - Sl, -dSldL, bondedDeriv);
        }
    }
}