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

Example 1 with NonPolar

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

the class ForceFieldEnergyOpenMM method addGKForce.

private void addGKForce() {
    GeneralizedKirkwood gk = super.getGK();
    amoebaGeneralizedKirkwoodForce = OpenMM_AmoebaGeneralizedKirkwoodForce_create();
    OpenMM_AmoebaGeneralizedKirkwoodForce_setSolventDielectric(amoebaGeneralizedKirkwoodForce, 78.3);
    OpenMM_AmoebaGeneralizedKirkwoodForce_setSoluteDielectric(amoebaGeneralizedKirkwoodForce, 1.0);
    double[] overlapScale = gk.getOverlapScale();
    double[] baseRadii = gk.getBaseRadii();
    Atom[] atoms = molecularAssembly.getAtomArray();
    int nAtoms = atoms.length;
    for (int i = 0; i < nAtoms; i++) {
        MultipoleType multipoleType = atoms[i].getMultipoleType();
        OpenMM_AmoebaGeneralizedKirkwoodForce_addParticle(amoebaGeneralizedKirkwoodForce, multipoleType.charge, OpenMM_NmPerAngstrom * baseRadii[i], overlapScale[i]);
    }
    OpenMM_AmoebaGeneralizedKirkwoodForce_setProbeRadius(amoebaGeneralizedKirkwoodForce, 1.4 * OpenMM_NmPerAngstrom);
    NonPolar nonpolar = gk.getNonPolarModel();
    switch(nonpolar) {
        case BORN_SOLV:
        case BORN_CAV_DISP:
        default:
            // Configure a Born Radii based surface area term.
            double surfaceTension = gk.getSurfaceTension() * OpenMM_KJPerKcal * OpenMM_AngstromsPerNm * OpenMM_AngstromsPerNm;
            OpenMM_AmoebaGeneralizedKirkwoodForce_setIncludeCavityTerm(amoebaGeneralizedKirkwoodForce, OpenMM_True);
            OpenMM_AmoebaGeneralizedKirkwoodForce_setSurfaceAreaFactor(amoebaGeneralizedKirkwoodForce, -surfaceTension);
            break;
        case CAV:
        case CAV_DISP:
        case HYDROPHOBIC_PMF:
        case NONE:
            // This NonPolar model does not use a Born Radii based surface area term.
            OpenMM_AmoebaGeneralizedKirkwoodForce_setIncludeCavityTerm(amoebaGeneralizedKirkwoodForce, OpenMM_False);
            break;
    }
    OpenMM_System_addForce(system, amoebaGeneralizedKirkwoodForce);
    switch(nonpolar) {
        case CAV_DISP:
        case BORN_CAV_DISP:
            addWCAForce();
            break;
        case CAV:
        case HYDROPHOBIC_PMF:
        case BORN_SOLV:
        case NONE:
        default:
    }
    logger.log(Level.INFO, " Added generalized Kirkwood force.");
}