Examples with GeneralizedKirkwood ffx.potential.nonbonded.GeneralizedKirkwood used on opensource projects

Example 6 with GeneralizedKirkwood

use of ffx.potential.nonbonded.GeneralizedKirkwood in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method updateCustomGBForce.

/**
 * Updates the custom GB force for change in Use flags.
 *
 * @param atoms Array of all Atoms in the system
 */
private void updateCustomGBForce(Atom[] atoms) {
    GeneralizedKirkwood gk = super.getGK();
    double[] baseRadii = gk.getBaseRadii();
    double[] overlapScale = gk.getOverlapScale();
    PointerByReference doubleArray = OpenMM_DoubleArray_create(0);
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        double useFactor = 1.0;
        if (!atoms[i].getUse() || !atoms[i].getElectrostatics()) {
            // if (!atoms[i].getUse()) {
            useFactor = 0.0;
        }
        double lambdaScale = lambda;
        if (!atom.applyLambda()) {
            lambdaScale = 1.0;
        }
        useFactor *= lambdaScale;
        MultipoleType multipoleType = atom.getMultipoleType();
        double charge = multipoleType.charge * useFactor;
        double oScale = overlapScale[i] * useFactor;
        OpenMM_DoubleArray_append(doubleArray, charge);
        OpenMM_DoubleArray_append(doubleArray, OpenMM_NmPerAngstrom * baseRadii[i]);
        OpenMM_DoubleArray_append(doubleArray, oScale);
        OpenMM_CustomGBForce_setParticleParameters(customGBForce, i, doubleArray);
        OpenMM_DoubleArray_resize(doubleArray, 0);
    }
    OpenMM_DoubleArray_destroy(doubleArray);
    OpenMM_CustomGBForce_updateParametersInContext(customGBForce, context);
}

Example 7 with GeneralizedKirkwood

use of ffx.potential.nonbonded.GeneralizedKirkwood in project ffx by mjschnie.

the class ForceFieldEnergyOpenMM method addFixedChargeNonBondedForce.

/**
 * Uses arithmetic mean to define sigma and geometric mean for epsilon.
 */
private void addFixedChargeNonBondedForce() {
    VanDerWaals vdW = super.getVdwNode();
    if (vdW == null) {
        return;
    }
    /**
     * Only 6-12 LJ with arithmetic mean to define sigma and geometric mean
     * for epsilon is supported.
     */
    VanDerWaalsForm vdwForm = vdW.getVDWForm();
    if (vdwForm.vdwType != LENNARD_JONES || vdwForm.radiusRule != ARITHMETIC || vdwForm.epsilonRule != GEOMETRIC) {
        logger.info(format(" VDW Type:         %s", vdwForm.vdwType));
        logger.info(format(" VDW Radius Rule:  %s", vdwForm.radiusRule));
        logger.info(format(" VDW Epsilon Rule: %s", vdwForm.epsilonRule));
        logger.log(Level.SEVERE, String.format(" Unsuppporterd van der Waals functional form."));
        return;
    }
    fixedChargeNonBondedForce = OpenMM_NonbondedForce_create();
    /**
     * OpenMM vdW force requires a diameter (i.e. not radius).
     */
    double radScale = 1.0;
    if (vdwForm.radiusSize == RADIUS) {
        radScale = 2.0;
    }
    /**
     * OpenMM vdw force requires atomic sigma values (i.e. not r-min).
     */
    if (vdwForm.radiusType == R_MIN) {
        radScale /= 1.122462048309372981;
    }
    /**
     * Add particles.
     */
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        VDWType vdwType = atom.getVDWType();
        double sigma = OpenMM_NmPerAngstrom * vdwType.radius * radScale;
        double eps = OpenMM_KJPerKcal * vdwType.wellDepth;
        double charge = 0.0;
        MultipoleType multipoleType = atom.getMultipoleType();
        if (multipoleType != null && atoms[i].getElectrostatics()) {
            charge = multipoleType.charge;
        }
        OpenMM_NonbondedForce_addParticle(fixedChargeNonBondedForce, charge, sigma, eps);
    }
    /**
     * Define 1-4 scale factors.
     */
    double lj14Scale = vdwForm.getScale14();
    double coulomb14Scale = 1.0 / 1.2;
    ParticleMeshEwald pme = super.getPmeNode();
    Bond[] bonds = super.getBonds();
    if (bonds != null && bonds.length > 0) {
        int nBonds = bonds.length;
        PointerByReference bondArray;
        bondArray = OpenMM_BondArray_create(0);
        for (int i = 0; i < nBonds; i++) {
            Bond bond = bonds[i];
            int i1 = bond.getAtom(0).getXyzIndex() - 1;
            int i2 = bond.getAtom(1).getXyzIndex() - 1;
            OpenMM_BondArray_append(bondArray, i1, i2);
        }
        if (pme != null) {
            coulomb14Scale = pme.getScale14();
        }
        OpenMM_NonbondedForce_createExceptionsFromBonds(fixedChargeNonBondedForce, bondArray, coulomb14Scale, lj14Scale);
        OpenMM_BondArray_destroy(bondArray);
        int num = OpenMM_NonbondedForce_getNumExceptions(fixedChargeNonBondedForce);
        chargeExclusion = new boolean[num];
        vdWExclusion = new boolean[num];
        exceptionChargeProd = new double[num];
        exceptionEps = new double[num];
        IntByReference particle1 = new IntByReference();
        IntByReference particle2 = new IntByReference();
        DoubleByReference chargeProd = new DoubleByReference();
        DoubleByReference sigma = new DoubleByReference();
        DoubleByReference eps = new DoubleByReference();
        for (int i = 0; i < num; i++) {
            OpenMM_NonbondedForce_getExceptionParameters(fixedChargeNonBondedForce, i, particle1, particle2, chargeProd, sigma, eps);
            if (abs(chargeProd.getValue()) > 0.0) {
                chargeExclusion[i] = false;
                exceptionChargeProd[i] = chargeProd.getValue();
            } else {
                exceptionChargeProd[i] = 0.0;
                chargeExclusion[i] = true;
            }
            if (abs(eps.getValue()) > 0.0) {
                vdWExclusion[i] = false;
                exceptionEps[i] = eps.getValue();
            } else {
                vdWExclusion[i] = true;
                exceptionEps[i] = 0.0;
            }
        }
    }
    Crystal crystal = super.getCrystal();
    if (crystal.aperiodic()) {
        OpenMM_NonbondedForce_setNonbondedMethod(fixedChargeNonBondedForce, OpenMM_NonbondedForce_NonbondedMethod.OpenMM_NonbondedForce_NoCutoff);
    } else {
        OpenMM_NonbondedForce_setNonbondedMethod(fixedChargeNonBondedForce, OpenMM_NonbondedForce_NonbondedMethod.OpenMM_NonbondedForce_PME);
        if (pme != null) {
            // Units of the Ewald coefficient are A^-1; Multiply by AngstromsPerNM to convert to (Nm^-1).
            double aEwald = OpenMM_AngstromsPerNm * pme.getEwaldCoefficient();
            int nx = pme.getReciprocalSpace().getXDim();
            int ny = pme.getReciprocalSpace().getYDim();
            int nz = pme.getReciprocalSpace().getZDim();
            OpenMM_NonbondedForce_setPMEParameters(fixedChargeNonBondedForce, aEwald, nx, ny, nz);
        }
        NonbondedCutoff nonbondedCutoff = vdW.getNonbondedCutoff();
        double off = nonbondedCutoff.off;
        double cut = nonbondedCutoff.cut;
        OpenMM_NonbondedForce_setCutoffDistance(fixedChargeNonBondedForce, OpenMM_NmPerAngstrom * off);
        OpenMM_NonbondedForce_setUseSwitchingFunction(fixedChargeNonBondedForce, OpenMM_True);
        if (cut == off) {
            logger.warning(" OpenMM does not properly handle cutoffs where cut == off!");
            if (cut == Double.MAX_VALUE || cut == Double.POSITIVE_INFINITY) {
                logger.info(" Detected infinite or max-value cutoff; setting cut to 1E+40 for OpenMM.");
                cut = 1E40;
            } else {
                logger.info(String.format(" Detected cut %8.4g == off %8.4g; scaling cut to 0.99 of off for OpenMM.", cut, off));
                cut *= 0.99;
            }
        }
        OpenMM_NonbondedForce_setSwitchingDistance(fixedChargeNonBondedForce, OpenMM_NmPerAngstrom * cut);
    }
    OpenMM_NonbondedForce_setUseDispersionCorrection(fixedChargeNonBondedForce, OpenMM_False);
    // OpenMM_Force_setForceGroup(fixedChargeNonBondedForce, 1);
    OpenMM_System_addForce(system, fixedChargeNonBondedForce);
    logger.log(Level.INFO, String.format(" Added fixed charge non-bonded force."));
    GeneralizedKirkwood gk = super.getGK();
    if (gk != null) {
        addCustomGBForce();
    }
}