コード例 #1
0
// -----------------------------------------------------------------------------
//                     COPY STATE BACK TO CPU FROM OPENMM
// -----------------------------------------------------------------------------
static void
myGetOpenMMState(MyOpenMMData* omm, bool wantEnergy, 
                 double& timeInPs, double& energyInKcal,
                 MyAtomInfo atoms[])
{
    int infoMask = 0;
    infoMask = OpenMM::State::Positions;
    if (wantEnergy) {
        infoMask += OpenMM::State::Velocities; // for kinetic energy (cheap)
        infoMask += OpenMM::State::Energy;     // for pot. energy (expensive)
    }
    // Forces are also available (and cheap).

    const OpenMM::State state = omm->context->getState(infoMask);
    timeInPs = state.getTime(); // OpenMM time is in ps already

    // Copy OpenMM positions into atoms array and change units from nm to Angstroms.
    const std::vector<Vec3>& positionsInNm = state.getPositions();
    for (int i=0; i < (int)positionsInNm.size(); ++i)
        for (int j=0; j < 3; ++j)
            atoms[i].posInAng[j] = positionsInNm[i][j] * OpenMM::AngstromsPerNm;

    // If energy has been requested, obtain it and convert from kJ to kcal.
    energyInKcal = 0;
    if (wantEnergy) 
        energyInKcal = (state.getPotentialEnergy() + state.getKineticEnergy())
                        * OpenMM::KcalPerKJ;
}
コード例 #2
0
ファイル: HelloWaterBox.cpp プロジェクト: frobnitzem/openmm
// -----------------------------------------------------------------------------
//                     COPY STATE BACK TO CPU FROM OPENMM
// -----------------------------------------------------------------------------
static void
myGetOpenMMState(MyOpenMMData* omm, double& timeInPs,
                 std::vector<double>& atomPositionsInAng)
{
    const OpenMM::State state = omm->context->getState(OpenMM::State::Positions, true);
    timeInPs = state.getTime(); // OpenMM time is in ps already

    // Copy OpenMM positions into output array and change units from nm to Angstroms.
    const std::vector<Vec3>& positionsInNm = state.getPositions();
    atomPositionsInAng.resize(3*positionsInNm.size());
    for (int i=0; i < (int)positionsInNm.size(); ++i)
        for (int j=0; j < 3; ++j)
            atomPositionsInAng[3*i+j] = positionsInNm[i][j] * OpenMM::AngstromsPerNm;
}