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

Example 31 with Atom

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

the class ForceFieldEnergyOpenMM method updateAmoebaMultipoleForce.

/**
 * Updates the Amoeba electrostatic multipolar force for change in Use
 * flags.
 *
 * @param atoms Array of all Atoms in the system
 */
private void updateAmoebaMultipoleForce(Atom[] atoms) {
    ParticleMeshEwald pme = super.getPmeNode();
    int[][] axisAtom = pme.getAxisAtoms();
    double dipoleConversion = OpenMM_NmPerAngstrom;
    double quadrupoleConversion = OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom;
    double polarityConversion = OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom * OpenMM_NmPerAngstrom;
    double dampingFactorConversion = sqrt(OpenMM_NmPerAngstrom);
    double polarScale = 1.0;
    if (pme.getPolarizationType() == Polarization.NONE) {
        polarScale = 0.0;
    }
    PointerByReference dipoles = OpenMM_DoubleArray_create(3);
    PointerByReference quadrupoles = OpenMM_DoubleArray_create(9);
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        MultipoleType multipoleType = atom.getMultipoleType();
        PolarizeType polarType = atom.getPolarizeType();
        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;
        /**
         * Define the frame definition.
         */
        int axisType = OpenMM_AmoebaMultipoleForce_NoAxisType;
        switch(multipoleType.frameDefinition) {
            case ZONLY:
                axisType = OpenMM_AmoebaMultipoleForce_ZOnly;
                break;
            case ZTHENX:
                axisType = OpenMM_AmoebaMultipoleForce_ZThenX;
                break;
            case BISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_Bisector;
                break;
            case ZTHENBISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_ZBisect;
                break;
            case TRISECTOR:
                axisType = OpenMM_AmoebaMultipoleForce_ThreeFold;
                break;
            default:
                break;
        }
        /**
         * Load local multipole coefficients.
         */
        for (int j = 0; j < 3; j++) {
            OpenMM_DoubleArray_set(dipoles, j, multipoleType.dipole[j] * dipoleConversion * useFactor);
        }
        int l = 0;
        for (int j = 0; j < 3; j++) {
            for (int k = 0; k < 3; k++) {
                OpenMM_DoubleArray_set(quadrupoles, l++, multipoleType.quadrupole[j][k] * quadrupoleConversion / 3.0 * useFactor);
            }
        }
        // int zaxis = 0;
        int zaxis = 1;
        // int xaxis = 0;
        int xaxis = 1;
        // int yaxis = 0;
        int yaxis = 1;
        int[] refAtoms = axisAtom[i];
        if (refAtoms != null) {
            zaxis = refAtoms[0];
            if (refAtoms.length > 1) {
                xaxis = refAtoms[1];
                if (refAtoms.length > 2) {
                    yaxis = refAtoms[2];
                }
            }
        } else {
            axisType = OpenMM_AmoebaMultipoleForce_NoAxisType;
        }
        /**
         * Add the multipole.
         */
        OpenMM_AmoebaMultipoleForce_setMultipoleParameters(amoebaMultipoleForce, i, multipoleType.charge * useFactor, dipoles, quadrupoles, axisType, zaxis, xaxis, yaxis, polarType.thole, polarType.pdamp * dampingFactorConversion, polarType.polarizability * polarityConversion * polarScale * useFactor);
    }
    OpenMM_DoubleArray_destroy(dipoles);
    OpenMM_DoubleArray_destroy(quadrupoles);
    OpenMM_AmoebaMultipoleForce_updateParametersInContext(amoebaMultipoleForce, context);
}

Example 32 with Atom

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

the class ForceFieldEnergyOpenMM method fillGradients.

/**
 * Private method for internal use, so we don't have subclasses calling
 * super.energy, and this class delegating to the subclass's getGradients
 * method.
 *
 * @param g Gradient array to fill.
 * @return Gradient array.
 */
public double[] fillGradients(double[] g) {
    assert (g != null);
    int n = getNumberOfVariables();
    if (g.length < n) {
        g = new double[n];
    }
    int index = 0;
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom a = atoms[i];
        if (a.isActive()) {
            OpenMM_Vec3 posInNm = OpenMM_Vec3Array_get(forces, i);
            /**
             * Convert OpenMM Forces in KJ/Nm into an FFX gradient in
             * Kcal/A.
             */
            double gx = -posInNm.x * OpenMM_NmPerAngstrom * OpenMM_KcalPerKJ;
            double gy = -posInNm.y * OpenMM_NmPerAngstrom * OpenMM_KcalPerKJ;
            double gz = -posInNm.z * OpenMM_NmPerAngstrom * OpenMM_KcalPerKJ;
            if (Double.isNaN(gx) || Double.isInfinite(gx) || Double.isNaN(gy) || Double.isInfinite(gy) || Double.isNaN(gz) || Double.isInfinite(gz)) {
                /*String message = format("The gradient of atom %s is (%8.3f,%8.3f,%8.3f).",
                            a.toString(), gx, gy, gz);*/
                StringBuilder sb = new StringBuilder(format("The gradient of atom %s is (%8.3f,%8.3f,%8.3f).", a.toString(), gx, gy, gz));
                double[] vals = new double[3];
                a.getVelocity(vals);
                sb.append(format("\n Velocities: %8.3g %8.3g %8.3g", vals[0], vals[1], vals[2]));
                a.getAcceleration(vals);
                sb.append(format("\n Accelerations: %8.3g %8.3g %8.3g", vals[0], vals[1], vals[2]));
                a.getPreviousAcceleration(vals);
                sb.append(format("\n Previous accelerations: %8.3g %8.3g %8.3g", vals[0], vals[1], vals[2]));
                // logger.severe(message);
                throw new EnergyException(sb.toString());
            }
            a.setXYZGradient(gx, gy, gz);
            g[index++] = gx;
            g[index++] = gy;
            g[index++] = gz;
        }
    }
    return g;
}

Example 33 with Atom

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

the class ForceFieldEnergyOpenMM method getOpenMMAccelerations.

/**
 * getOpenMMAccelerations takes in a PointerByReference containing the force
 * information of the context. This method creates a Vec3Array that contains
 * the three dimensional information of the forces on the atoms. This method
 * then adds these values (divided by mass, effectively turning them into
 * accelerations) to a new double array a and returns it to the method call
 *
 * @param forces
 * @param numberOfVariables
 * @param mass
 * @return
 */
public double[] getOpenMMAccelerations(PointerByReference forces, int numberOfVariables, double[] mass, double[] a) {
    assert numberOfVariables == getNumberOfVariables();
    if (a == null || a.length < numberOfVariables) {
        a = new double[numberOfVariables];
    }
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        int offset = i * 3;
        OpenMM_Vec3 acc = OpenMM_Vec3Array_get(forces, i);
        a[offset] = (acc.x * 10.0) / mass[i];
        a[offset + 1] = (acc.y * 10.0) / mass[i + 1];
        a[offset + 2] = (acc.z * 10.0) / mass[i + 2];
        Atom atom = atoms[i];
        double[] acceleration = { a[offset], a[offset + 1], a[offset + 2] };
        atom.setAcceleration(acceleration);
    }
    return a;
}

Example 34 with Atom

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

the class ForceFieldEnergyOpenMM method addAmoebaVDWForce.

private void addAmoebaVDWForce() {
    VanDerWaals vdW = super.getVdwNode();
    if (vdW == null) {
        return;
    }
    amoebaVDWForce = OpenMM_AmoebaVdwForce_create();
    OpenMM_System_addForce(system, amoebaVDWForce);
    OpenMM_Force_setForceGroup(amoebaVDWForce, 1);
    VanDerWaalsForm vdwForm = vdW.getVDWForm();
    NonbondedCutoff nonbondedCutoff = vdW.getNonbondedCutoff();
    Crystal crystal = super.getCrystal();
    double radScale = 1.0;
    if (vdwForm.radiusSize == VanDerWaalsForm.RADIUS_SIZE.DIAMETER) {
        radScale = 0.5;
    }
    /**
     * Note that the API says it wants a SIGMA value.
     */
    if (vdwForm.radiusType == VanDerWaalsForm.RADIUS_TYPE.R_MIN) {
    // radScale *= 1.122462048309372981;
    }
    int[] ired = vdW.getReductionIndex();
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        VDWType vdwType = atom.getVDWType();
        OpenMM_AmoebaVdwForce_addParticle(amoebaVDWForce, ired[i], OpenMM_NmPerAngstrom * vdwType.radius * radScale, OpenMM_KJPerKcal * vdwType.wellDepth, vdwType.reductionFactor);
    }
    // OpenMM_AmoebaVdwForce_setSigmaCombiningRule(amoebaVdwForce, toPropertyForm(vdwForm.radiusRule.name()));
    // OpenMM_AmoebaVdwForce_setEpsilonCombiningRule(amoebaVdwForce, toPropertyForm(vdwForm.epsilonRule.name()));
    OpenMM_AmoebaVdwForce_setCutoffDistance(amoebaVDWForce, nonbondedCutoff.off * OpenMM_NmPerAngstrom);
    OpenMM_AmoebaVdwForce_setUseDispersionCorrection(amoebaVDWForce, OpenMM_Boolean.OpenMM_False);
    if (crystal.aperiodic()) {
        OpenMM_AmoebaVdwForce_setNonbondedMethod(amoebaVDWForce, OpenMM_AmoebaVdwForce_NonbondedMethod.OpenMM_AmoebaVdwForce_NoCutoff);
    } else {
        OpenMM_AmoebaVdwForce_setNonbondedMethod(amoebaVDWForce, OpenMM_AmoebaVdwForce_NonbondedMethod.OpenMM_AmoebaVdwForce_CutoffPeriodic);
    }
    /**
     * Create exclusion lists.
     */
    PointerByReference exclusions = OpenMM_IntArray_create(0);
    double[] mask = new double[nAtoms];
    Arrays.fill(mask, 1.0);
    for (int i = 0; i < nAtoms; i++) {
        OpenMM_IntArray_append(exclusions, i);
        vdW.applyMask(mask, i);
        for (int j = 0; j < nAtoms; j++) {
            if (mask[j] == 0.0) {
                OpenMM_IntArray_append(exclusions, j);
            }
        }
        vdW.removeMask(mask, i);
        OpenMM_AmoebaVdwForce_setParticleExclusions(amoebaVDWForce, i, exclusions);
        OpenMM_IntArray_resize(exclusions, 0);
    }
    OpenMM_IntArray_destroy(exclusions);
    logger.log(Level.INFO, " Added van der Waals force.");
}

Example 35 with Atom

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

the class ForceFieldEnergyOpenMM method addCustomNonbondedSoftcoreForce.

/**
 * 1.) Handle interactions between non-alchemical atoms with our default
 * OpenMM NonBondedForce. Note that alchemical atoms must have eps=0 to turn
 * them off in this force.
 * <p>
 * 2.) Handle interactions between alchemical atoms and mixed non-alchemical
 * <-> alchemical interactions with an OpenMM CustomNonBondedForce.
 */
private void addCustomNonbondedSoftcoreForce() {
    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;
    }
    // Sterics mixing rules.
    String stericsMixingRules = " epsilon = sqrt(epsilon1*epsilon2);";
    stericsMixingRules += " rmin = 0.5 * (sigma1 + sigma2) * 1.122462048309372981;";
    // Softcore Lennard-Jones, with a form equivalent to that used in FFX VanDerWaals class.
    String stericsEnergyExpression = "(vdw_lambda^beta)*epsilon*x*(x-2.0);";
    // Effective softcore distance for sterics.
    stericsEnergyExpression += " x = 1.0 / (alpha*(1.0-vdw_lambda)^2.0 + (r/rmin)^6.0);";
    // Define energy expression for sterics.
    String energyExpression = stericsEnergyExpression + stericsMixingRules;
    fixedChargeSoftcore = OpenMM_CustomNonbondedForce_create(energyExpression);
    // Get the Alpha and Beta constants from the VanDerWaals instance.
    double alpha = vdW.getAlpha();
    double beta = vdW.getBeta();
    logger.info(format(" Custom non-bonded force with alpha = %8.6f and beta = %8.6f", alpha, beta));
    OpenMM_CustomNonbondedForce_addGlobalParameter(fixedChargeSoftcore, "vdw_lambda", 1.0);
    OpenMM_CustomNonbondedForce_addGlobalParameter(fixedChargeSoftcore, "alpha", alpha);
    OpenMM_CustomNonbondedForce_addGlobalParameter(fixedChargeSoftcore, "beta", beta);
    OpenMM_CustomNonbondedForce_addPerParticleParameter(fixedChargeSoftcore, "sigma");
    OpenMM_CustomNonbondedForce_addPerParticleParameter(fixedChargeSoftcore, "epsilon");
    /**
     * Add particles.
     */
    PointerByReference alchemicalGroup = OpenMM_IntSet_create();
    PointerByReference nonAlchemicalGroup = OpenMM_IntSet_create();
    DoubleByReference charge = new DoubleByReference();
    DoubleByReference sigma = new DoubleByReference();
    DoubleByReference eps = new DoubleByReference();
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        OpenMM_NonbondedForce_getParticleParameters(fixedChargeNonBondedForce, i, charge, sigma, eps);
        if (atom.applyLambda()) {
            OpenMM_IntSet_insert(alchemicalGroup, i);
            logger.info(format(" Adding alchemical atom %s.", atom));
        } else {
            OpenMM_IntSet_insert(nonAlchemicalGroup, i);
        }
        PointerByReference particleParameters = OpenMM_DoubleArray_create(0);
        OpenMM_DoubleArray_append(particleParameters, sigma.getValue());
        OpenMM_DoubleArray_append(particleParameters, eps.getValue());
        OpenMM_CustomNonbondedForce_addParticle(fixedChargeSoftcore, particleParameters);
        OpenMM_DoubleArray_destroy(particleParameters);
    }
    OpenMM_CustomNonbondedForce_addInteractionGroup(fixedChargeSoftcore, alchemicalGroup, alchemicalGroup);
    OpenMM_CustomNonbondedForce_addInteractionGroup(fixedChargeSoftcore, alchemicalGroup, nonAlchemicalGroup);
    OpenMM_IntSet_destroy(alchemicalGroup);
    OpenMM_IntSet_destroy(nonAlchemicalGroup);
    Crystal crystal = super.getCrystal();
    if (crystal.aperiodic()) {
        OpenMM_CustomNonbondedForce_setNonbondedMethod(fixedChargeSoftcore, OpenMM_CustomNonbondedForce_NonbondedMethod.OpenMM_CustomNonbondedForce_NoCutoff);
    } else {
        OpenMM_CustomNonbondedForce_setNonbondedMethod(fixedChargeSoftcore, OpenMM_CustomNonbondedForce_NonbondedMethod.OpenMM_CustomNonbondedForce_CutoffPeriodic);
    }
    NonbondedCutoff nonbondedCutoff = vdW.getNonbondedCutoff();
    double off = nonbondedCutoff.off;
    double cut = nonbondedCutoff.cut;
    OpenMM_CustomNonbondedForce_setCutoffDistance(fixedChargeSoftcore, OpenMM_NmPerAngstrom * off);
    OpenMM_CustomNonbondedForce_setUseSwitchingFunction(fixedChargeSoftcore, OpenMM_True);
    OpenMM_CustomNonbondedForce_setSwitchingDistance(fixedChargeSoftcore, OpenMM_NmPerAngstrom * cut);
    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;
        }
    }
    // Add energy parameter derivative
    OpenMM_CustomNonbondedForce_addEnergyParameterDerivative(fixedChargeSoftcore, "vdw_lambda");
    OpenMM_System_addForce(system, fixedChargeSoftcore);
    logger.log(Level.INFO, String.format(" Added fixed charge softcore sterics force."));
    GeneralizedKirkwood gk = super.getGK();
    if (gk != null) {
        logger.severe(" OpenMM alchemical methods are not supported for GB.");
        addCustomGBForce();
    }
    // Not entirely sure how to initialize this portion
    alchemicalAlchemicalStericsForce = OpenMM_CustomBondForce_create(stericsEnergyExpression);
    nonAlchemicalAlchemicalStericsForce = OpenMM_CustomBondForce_create(stericsEnergyExpression);
    // allStericsForce = (alchemicalAlchemicalStericsForce + nonAlchemicalAlchemicalStericsForce);
    // Can be reduced to two lines if I can figure out how to combine the two custom bonded sterics forces
    OpenMM_CustomBondForce_addPerBondParameter(alchemicalAlchemicalStericsForce, "rmin");
    OpenMM_CustomBondForce_addPerBondParameter(alchemicalAlchemicalStericsForce, "epsilon");
    OpenMM_CustomBondForce_addGlobalParameter(alchemicalAlchemicalStericsForce, "vdw_lambda", 1.0);
    OpenMM_CustomBondForce_addGlobalParameter(alchemicalAlchemicalStericsForce, "alpha", alpha);
    OpenMM_CustomBondForce_addGlobalParameter(alchemicalAlchemicalStericsForce, "beta", beta);
    OpenMM_CustomBondForce_addPerBondParameter(nonAlchemicalAlchemicalStericsForce, "rmin");
    OpenMM_CustomBondForce_addPerBondParameter(nonAlchemicalAlchemicalStericsForce, "epsilon");
    OpenMM_CustomBondForce_addGlobalParameter(nonAlchemicalAlchemicalStericsForce, "vdw_lambda", 1.0);
    OpenMM_CustomBondForce_addGlobalParameter(nonAlchemicalAlchemicalStericsForce, "alpha", alpha);
    OpenMM_CustomBondForce_addGlobalParameter(nonAlchemicalAlchemicalStericsForce, "beta", beta);
    int range = OpenMM_NonbondedForce_getNumExceptions(fixedChargeNonBondedForce);
    IntByReference atomi = new IntByReference();
    IntByReference atomj = new IntByReference();
    int[][] torsionMask = vdW.getTorsionMask();
    for (int i = 0; i < range; i++) {
        OpenMM_NonbondedForce_getExceptionParameters(fixedChargeNonBondedForce, i, atomi, atomj, charge, sigma, eps);
        OpenMM_CustomNonbondedForce_addExclusion(fixedChargeSoftcore, atomi.getValue(), atomj.getValue());
        int[] maskI = torsionMask[atomi.getValue()];
        int jID = atomj.getValue();
        boolean epsException = false;
        for (int j = 0; j < maskI.length; j++) {
            if (maskI[j] == jID) {
                epsException = true;
                break;
            }
        }
        Atom atom1 = atoms[atomi.getValue()];
        Atom atom2 = atoms[atomj.getValue()];
        boolean bothAlchemical = false;
        boolean oneAlchemical = false;
        if (atom1.applyLambda() && atom2.applyLambda()) {
            bothAlchemical = true;
        } else if ((atom1.applyLambda() && !atom2.applyLambda()) || (!atom1.applyLambda() && atom2.applyLambda())) {
            oneAlchemical = true;
        }
        if (bothAlchemical) {
            if (epsException) {
                PointerByReference bondParameters = OpenMM_DoubleArray_create(0);
                OpenMM_DoubleArray_append(bondParameters, sigma.getValue() * 1.122462048309372981);
                OpenMM_DoubleArray_append(bondParameters, eps.getValue());
                OpenMM_CustomBondForce_addBond(alchemicalAlchemicalStericsForce, atomi.getValue(), atomj.getValue(), bondParameters);
                OpenMM_DoubleArray_destroy(bondParameters);
            }
        } else if (oneAlchemical) {
            if (epsException) {
                PointerByReference bondParameters = OpenMM_DoubleArray_create(0);
                OpenMM_DoubleArray_append(bondParameters, sigma.getValue() * 1.122462048309372981);
                OpenMM_DoubleArray_append(bondParameters, eps.getValue());
                OpenMM_CustomBondForce_addBond(nonAlchemicalAlchemicalStericsForce, atomi.getValue(), atomj.getValue(), bondParameters);
                OpenMM_DoubleArray_destroy(bondParameters);
            }
        }
    }
    /**
     *        for (int i = 0; i < range; i++){
     *            OpenMM_NonbondedForce_getExceptionParameters(fixedChargeNonBondedForce, i, atomi, atomj, charge, sigma, eps);
     *
     *            Atom atom1 = atoms[atomi.getValue()];
     *            Atom atom2 = atoms[atomj.getValue()];
     *
     *            if (atom1.applyLambda() || atom2.applyLambda()){
     *                OpenMM_NonbondedForce_setExceptionParameters(fixedChargeNonBondedForce, i, atomi.getValue(), atomj.getValue(), abs(0.0*charge.getValue()), sigma.getValue(), abs(0.0*eps.getValue()));
     *            }
     *        }
     */
    OpenMM_CustomBondForce_addEnergyParameterDerivative(alchemicalAlchemicalStericsForce, "vdw_lambda");
    OpenMM_CustomBondForce_addEnergyParameterDerivative(nonAlchemicalAlchemicalStericsForce, "vdw_lambda");
    OpenMM_System_addForce(system, alchemicalAlchemicalStericsForce);
    OpenMM_System_addForce(system, nonAlchemicalAlchemicalStericsForce);
}