// -----------------------------------------------------------------------------
// 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;
}
void writeTimeSeries(int steps, const OpenMM::State& state, std::ofstream &ots, double qscore) {
ots << std::setw(8) << steps;
ots << ' ' << std::fixed << std::setw(8) << std::setprecision(3) << qscore;
ots << ' ' << std::fixed << std::setw(8) << state.getPotentialEnergy();
ots << ' ' << std::fixed << std::setw(8) << state.getKineticEnergy();
ots << '\n';
}