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

Example 26 with Atom

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

the class ForceFieldEnergyOpenMM method getOpenMMPositions.

/**
 * getOpenMMPositions takes in a PointerByReference containing the position
 * information of the context. This method creates a Vec3Array that contains
 * the three dimensional information of the positions of the atoms. The
 * method then adds these values to a new double array x and returns it to
 * the method call
 *
 * @param positions
 * @param numberOfVariables
 * @param x
 * @return x
 */
public double[] getOpenMMPositions(PointerByReference positions, int numberOfVariables, double[] x) {
    assert numberOfVariables == getNumberOfVariables();
    if (x == null || x.length < numberOfVariables) {
        x = new double[numberOfVariables];
    }
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        int offset = i * 3;
        OpenMM_Vec3 pos = OpenMM_Vec3Array_get(positions, i);
        x[offset] = pos.x * OpenMM_AngstromsPerNm;
        x[offset + 1] = pos.y * OpenMM_AngstromsPerNm;
        x[offset + 2] = pos.z * OpenMM_AngstromsPerNm;
        Atom atom = atoms[i];
        atom.moveTo(x[offset], x[offset + 1], x[offset + 2]);
    }
    return x;
}

Example 27 with Atom

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

the class ForceFieldEnergyOpenMM method addAtoms.

/**
 * Adds atoms from the molecular assembly to the OpenMM System and reports
 * to the user the number of particles added.
 */
private void addAtoms() throws Exception {
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    numParticles = 0;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        OpenMM_System_addParticle(system, atom.getMass());
        if (atom.getMass() <= 0.0) {
            throw new Exception(" Atom without mass greater than 0.");
        }
        numParticles++;
    }
    logger.log(Level.INFO, " Added particles ({0})", nAtoms);
}

Example 28 with Atom

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

the class ForceFieldEnergyOpenMM method updateFixedChargeNonBondedForce.

/**
 * Updates the fixed-charge non-bonded force for change in Use flags.
 *
 * @param atoms Array of all Atoms in the system
 * @param vdwLambdaTerm If true, set charges and eps values to zero for
 * Lambda atoms
 */
private void updateFixedChargeNonBondedForce(Atom[] atoms, boolean vdwLambdaTerm) {
    VanDerWaals vdW = super.getVdwNode();
    /**
     * 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.log(Level.SEVERE, String.format(" Unsuppporterd van der Waals functional form."));
        return;
    }
    /**
     * 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;
    }
    /**
     * Update parameters.
     */
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        boolean applyLambda = atom.applyLambda();
        double charge = Double.MIN_VALUE;
        MultipoleType multipoleType = atom.getMultipoleType();
        if (multipoleType != null && atoms[i].getElectrostatics()) {
            charge = multipoleType.charge;
            if (lambdaTerm && applyLambda) {
                charge *= lambda;
            }
        }
        VDWType vdwType = atom.getVDWType();
        double sigma = OpenMM_NmPerAngstrom * vdwType.radius * radScale;
        double eps = OpenMM_KJPerKcal * vdwType.wellDepth;
        if ((vdwLambdaTerm && applyLambda) || !atoms[i].getUse()) {
            eps = 0.0;
            charge = 0.0;
        }
        OpenMM_NonbondedForce_setParticleParameters(fixedChargeNonBondedForce, i, charge, sigma, eps);
    }
    // OpenMM_NonbondedForce_updateParametersInContext(fixedChargeNonBondedForce, context);
    /**
     * Update Exceptions.
     */
    IntByReference particle1 = new IntByReference();
    IntByReference particle2 = new IntByReference();
    DoubleByReference chargeProd = new DoubleByReference();
    DoubleByReference sigma = new DoubleByReference();
    DoubleByReference eps = new DoubleByReference();
    int numExceptions = OpenMM_NonbondedForce_getNumExceptions(fixedChargeNonBondedForce);
    for (int i = 0; i < numExceptions; i++) {
        /**
         * Only update exceptions.
         */
        if (chargeExclusion[i] && vdWExclusion[i]) {
            continue;
        }
        OpenMM_NonbondedForce_getExceptionParameters(fixedChargeNonBondedForce, i, particle1, particle2, chargeProd, sigma, eps);
        int i1 = particle1.getValue();
        int i2 = particle2.getValue();
        double qq = exceptionChargeProd[i];
        double epsilon = exceptionEps[i];
        Atom atom1 = atoms[i1];
        Atom atom2 = atoms[i2];
        double lambdaValue = lambda;
        if (lambda == 0.0) {
            lambdaValue = 1.0e-6;
        }
        if (atom1.applyLambda()) {
            qq *= lambdaValue;
            if (vdwLambdaTerm) {
                epsilon = 1.0e-6;
                qq = 1.0e-6;
            }
        }
        if (atom2.applyLambda()) {
            qq *= lambdaValue;
            if (vdwLambdaTerm) {
                epsilon = 1.0e-6;
                qq = 1.0e-6;
            }
        }
        if (!atom1.getUse() || !atom2.getUse()) {
            qq = 1.0e-6;
            epsilon = 1.0e-6;
        }
        OpenMM_NonbondedForce_setExceptionParameters(fixedChargeNonBondedForce, i, i1, i2, qq, sigma.getValue(), epsilon);
    /**
     * logger.info(format(" B Exception %d %d %d q=%10.8f s=%10.8f
     * e=%10.8f.", i, i1, i2, chargeProd.getValue(), sigma.getValue(),
     * eps.getValue()));
     *
     * logger.info(format(" E Exception %d %d %d q=%10.8f s=%10.8f
     * e=%10.8f.", i, i1, i2, qq, sigma.getValue(), epsilon));
     */
    }
    OpenMM_NonbondedForce_updateParametersInContext(fixedChargeNonBondedForce, context);
}

Example 29 with Atom

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

the class ForceFieldEnergyOpenMM method updateAmoebaVDWForce.

/**
 * Updates the AMOEBA van der Waals force for change in Use flags.
 *
 * @param atoms Array of all Atoms in the system
 */
private void updateAmoebaVDWForce(Atom[] atoms) {
    VanDerWaals vdW = super.getVdwNode();
    VanDerWaalsForm vdwForm = vdW.getVDWForm();
    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();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        Atom atom = atoms[i];
        VDWType vdwType = atom.getVDWType();
        double useFactor = 1.0;
        if (!atoms[i].getUse()) {
            useFactor = 0.0;
        }
        double eps = OpenMM_KJPerKcal * vdwType.wellDepth * useFactor;
        OpenMM_AmoebaVdwForce_setParticleParameters(amoebaVDWForce, i, ired[i], OpenMM_NmPerAngstrom * vdwType.radius * radScale, eps, vdwType.reductionFactor);
    }
    OpenMM_AmoebaVdwForce_updateParametersInContext(amoebaVDWForce, context);
}

Example 30 with Atom

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

the class ForceFieldEnergyOpenMM method addHarmonicRestraintForce.

/**
 * Adds harmonic restraints (CoordRestraint objects) to OpenMM as a custom
 * external force.
 */
private void addHarmonicRestraintForce() {
    for (CoordRestraint restraint : super.getCoordRestraints()) {
        double forceConst = restraint.getForceConstant();
        forceConst *= OpenMM_KJPerKcal;
        forceConst *= (OpenMM_AngstromsPerNm * OpenMM_AngstromsPerNm);
        Atom[] restAtoms = restraint.getAtoms();
        int nRestAts = restraint.getNumAtoms();
        double[][] oCoords = restraint.getOriginalCoordinates();
        for (int i = 0; i < nRestAts; i++) {
            oCoords[i][0] *= OpenMM_NmPerAngstrom;
            oCoords[i][1] *= OpenMM_NmPerAngstrom;
            oCoords[i][2] *= OpenMM_NmPerAngstrom;
        }
        PointerByReference theRestraint = OpenMM_CustomExternalForce_create("k*periodicdistance(x,y,z,x0,y0,z0)^2");
        OpenMM_CustomExternalForce_addGlobalParameter(theRestraint, "k", forceConst);
        OpenMM_CustomExternalForce_addPerParticleParameter(theRestraint, "x0");
        OpenMM_CustomExternalForce_addPerParticleParameter(theRestraint, "y0");
        OpenMM_CustomExternalForce_addPerParticleParameter(theRestraint, "z0");
        PointerByReference xyzOrigArray = OpenMM_DoubleArray_create(3);
        for (int i = 0; i < nRestAts; i++) {
            int ommIndex = restAtoms[i].getXyzIndex() - 1;
            for (int j = 0; j < 3; j++) {
                OpenMM_DoubleArray_set(xyzOrigArray, j, oCoords[i][j]);
            }
            OpenMM_CustomExternalForce_addParticle(theRestraint, ommIndex, xyzOrigArray);
        }
        OpenMM_DoubleArray_destroy(xyzOrigArray);
        OpenMM_System_addForce(system, theRestraint);
    }
}