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

Example 1 with ReciprocalSpace

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

the class ForceFieldEnergyOpenMM method addAmoebaMultipoleForce.

private void addAmoebaMultipoleForce() {
    ParticleMeshEwald pme = super.getPmeNode();
    if (pme == null) {
        return;
    }
    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);
    amoebaMultipoleForce = OpenMM_AmoebaMultipoleForce_create();
    double polarScale = 1.0;
    if (pme.getPolarizationType() != Polarization.MUTUAL) {
        OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Direct);
        if (pme.getPolarizationType() == Polarization.NONE) {
            polarScale = 0.0;
        }
    } else {
        ForceField forceField = molecularAssembly.getForceField();
        String algorithm = forceField.getString(ForceField.ForceFieldString.SCF_ALGORITHM, "CG");
        ParticleMeshEwald.SCFAlgorithm scfAlgorithm;
        try {
            algorithm = algorithm.replaceAll("-", "_").toUpperCase();
            scfAlgorithm = ParticleMeshEwald.SCFAlgorithm.valueOf(algorithm);
        } catch (Exception e) {
            scfAlgorithm = ParticleMeshEwald.SCFAlgorithm.CG;
        }
        switch(scfAlgorithm) {
            case EPT:
                logger.info(" Using extrapolated perturbation theory approximation instead of full SCF calculations. Not supported in FFX reference implementation.");
                OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Extrapolated);
                PointerByReference exptCoefficients = OpenMM_DoubleArray_create(4);
                OpenMM_DoubleArray_set(exptCoefficients, 0, -0.154);
                OpenMM_DoubleArray_set(exptCoefficients, 1, 0.017);
                OpenMM_DoubleArray_set(exptCoefficients, 2, 0.657);
                OpenMM_DoubleArray_set(exptCoefficients, 3, 0.475);
                OpenMM_AmoebaMultipoleForce_setExtrapolationCoefficients(amoebaMultipoleForce, exptCoefficients);
                OpenMM_DoubleArray_destroy(exptCoefficients);
                break;
            case CG:
            case SOR:
            default:
                OpenMM_AmoebaMultipoleForce_setPolarizationType(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_Mutual);
                break;
        }
    }
    PointerByReference dipoles = OpenMM_DoubleArray_create(3);
    PointerByReference quadrupoles = OpenMM_DoubleArray_create(9);
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        MultipoleType multipoleType = atom.getMultipoleType();
        PolarizeType polarType = atom.getPolarizeType();
        /**
         * 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;
        }
        double useFactor = 1.0;
        if (!atoms[i].getUse() || !atoms[i].getElectrostatics()) {
            // if (!atoms[i].getUse()) {
            useFactor = 0.0;
        }
        // Should be 1.0 at this point.
        double lambdaScale = lambda;
        if (!atom.applyLambda()) {
            lambdaScale = 1.0;
        }
        useFactor *= lambdaScale;
        /**
         * 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 * useFactor / 3.0);
            }
        }
        // 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;
            logger.info(String.format(" Atom type %s", atom.getAtomType().toString()));
        }
        double charge = multipoleType.charge * useFactor;
        /**
         * Add the multipole.
         */
        OpenMM_AmoebaMultipoleForce_addMultipole(amoebaMultipoleForce, charge, dipoles, quadrupoles, axisType, zaxis, xaxis, yaxis, polarType.thole, polarType.pdamp * dampingFactorConversion, polarType.polarizability * polarityConversion * polarScale);
    }
    OpenMM_DoubleArray_destroy(dipoles);
    OpenMM_DoubleArray_destroy(quadrupoles);
    Crystal crystal = super.getCrystal();
    if (!crystal.aperiodic()) {
        OpenMM_AmoebaMultipoleForce_setNonbondedMethod(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_PME);
        OpenMM_AmoebaMultipoleForce_setCutoffDistance(amoebaMultipoleForce, pme.getEwaldCutoff() * OpenMM_NmPerAngstrom);
        OpenMM_AmoebaMultipoleForce_setAEwald(amoebaMultipoleForce, pme.getEwaldCoefficient() / OpenMM_NmPerAngstrom);
        double ewaldTolerance = 1.0e-04;
        OpenMM_AmoebaMultipoleForce_setEwaldErrorTolerance(amoebaMultipoleForce, ewaldTolerance);
        PointerByReference gridDimensions = OpenMM_IntArray_create(3);
        ReciprocalSpace recip = pme.getReciprocalSpace();
        OpenMM_IntArray_set(gridDimensions, 0, recip.getXDim());
        OpenMM_IntArray_set(gridDimensions, 1, recip.getYDim());
        OpenMM_IntArray_set(gridDimensions, 2, recip.getZDim());
        OpenMM_AmoebaMultipoleForce_setPmeGridDimensions(amoebaMultipoleForce, gridDimensions);
        OpenMM_IntArray_destroy(gridDimensions);
    } else {
        OpenMM_AmoebaMultipoleForce_setNonbondedMethod(amoebaMultipoleForce, OpenMM_AmoebaMultipoleForce_NoCutoff);
    }
    OpenMM_AmoebaMultipoleForce_setMutualInducedMaxIterations(amoebaMultipoleForce, 500);
    OpenMM_AmoebaMultipoleForce_setMutualInducedTargetEpsilon(amoebaMultipoleForce, pme.getPolarEps());
    int[][] ip11 = pme.getPolarization11();
    int[][] ip12 = pme.getPolarization12();
    int[][] ip13 = pme.getPolarization13();
    ArrayList<Integer> list12 = new ArrayList<>();
    ArrayList<Integer> list13 = new ArrayList<>();
    ArrayList<Integer> list14 = new ArrayList<>();
    PointerByReference covalentMap = OpenMM_IntArray_create(0);
    for (int i = 0; i < nAtoms; i++) {
        Atom ai = atoms[i];
        list12.clear();
        list13.clear();
        list14.clear();
        for (Bond bond : ai.getBonds()) {
            int index = bond.get1_2(ai).getIndex() - 1;
            OpenMM_IntArray_append(covalentMap, index);
            list12.add(index);
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent12, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Angle angle : ai.getAngles()) {
            Atom ak = angle.get1_3(ai);
            if (ak != null) {
                int index = ak.getIndex() - 1;
                if (!list12.contains(index)) {
                    list13.add(index);
                    OpenMM_IntArray_append(covalentMap, index);
                }
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent13, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Torsion torsion : ai.getTorsions()) {
            Atom ak = torsion.get1_4(ai);
            if (ak != null) {
                int index = ak.getIndex() - 1;
                if (!list12.contains(index) && !list13.contains(index)) {
                    list14.add(index);
                    OpenMM_IntArray_append(covalentMap, index);
                }
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent14, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (Atom ak : ai.get1_5s()) {
            int index = ak.getIndex() - 1;
            if (!list12.contains(index) && !list13.contains(index) && !list14.contains(index)) {
                OpenMM_IntArray_append(covalentMap, index);
            }
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_Covalent15, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
        for (int j = 0; j < ip11[i].length; j++) {
            OpenMM_IntArray_append(covalentMap, ip11[i][j]);
        }
        OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i, OpenMM_AmoebaMultipoleForce_PolarizationCovalent11, covalentMap);
        OpenMM_IntArray_resize(covalentMap, 0);
    // for (int j = 0; j < ip12[i].length; j++) {
    // OpenMM_IntArray_append(covalentMap, ip12[i][j]);
    // }
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent12, covalentMap);
    // OpenMM_IntArray_resize(covalentMap, 0);
    // 
    // for (int j = 0; j < ip13[i].length; j++) {
    // OpenMM_IntArray_append(covalentMap, ip13[i][j]);
    // }
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent13, covalentMap);
    // OpenMM_IntArray_resize(covalentMap, 0);
    // 
    // OpenMM_AmoebaMultipoleForce_setCovalentMap(amoebaMultipoleForce, i,
    // OpenMM_AmoebaMultipoleForce_PolarizationCovalent14, covalentMap);
    }
    OpenMM_IntArray_destroy(covalentMap);
    OpenMM_System_addForce(system, amoebaMultipoleForce);
    OpenMM_Force_setForceGroup(amoebaMultipoleForce, 1);
    logger.log(Level.INFO, " Added polarizable multipole force.");
    GeneralizedKirkwood gk = super.getGK();
    if (gk != null) {
        addGKForce();
    }
}