namespace gmx
{
-void UpdateConstrainCuda::Impl::integrate(GpuEventSynchronizer *fReadyOnDevice,
+void UpdateConstrainCuda::Impl::integrate(GpuEventSynchronizer* fReadyOnDevice,
const real dt,
const bool updateVelocities,
const bool computeVirial,
// Make sure that the forces are ready on device before proceeding with the update.
fReadyOnDevice->enqueueWaitEvent(commandStream_);
- // The integrate should save a copy of the current coordinates in d_xp_ and write updated once into d_x_.
- // The d_xp_ is only needed by constraints.
- integrator_->integrate(d_x_, d_xp_, d_v_, d_f_, dt,
- doTempCouple, tcstat,
- doPressureCouple, dtPressureCouple, velocityScalingMatrix);
+ // The integrate should save a copy of the current coordinates in d_xp_ and write updated once
+ // into d_x_. The d_xp_ is only needed by constraints.
+ integrator_->integrate(d_x_, d_xp_, d_v_, d_f_, dt, doTempCouple, tcstat, doPressureCouple,
+ dtPressureCouple, velocityScalingMatrix);
// Constraints need both coordinates before (d_x_) and after (d_xp_) update. However, after constraints
// are applied, the d_x_ can be discarded. So we intentionally swap the d_x_ and d_xp_ here to avoid the
// d_xp_ -> d_x_ copy after constraints. Note that the integrate saves them in the wrong order as well.
- lincsCuda_->apply(d_xp_, d_x_,
- updateVelocities, d_v_, 1.0/dt,
- computeVirial, virial);
- settleCuda_->apply(d_xp_, d_x_,
- updateVelocities, d_v_, 1.0/dt,
- computeVirial, virial);
+ lincsCuda_->apply(d_xp_, d_x_, updateVelocities, d_v_, 1.0 / dt, computeVirial, virial);
+ settleCuda_->apply(d_xp_, d_x_, updateVelocities, d_v_, 1.0 / dt, computeVirial, virial);
// scaledVirial -> virial (methods above returns scaled values)
- float scaleFactor = 0.5f/(dt*dt);
+ float scaleFactor = 0.5f / (dt * dt);
for (int i = 0; i < DIM; i++)
{
for (int j = 0; j < DIM; j++)
{
- virial[i][j] = scaleFactor*virial[i][j];
+ virial[i][j] = scaleFactor * virial[i][j];
}
}
return;
}
-UpdateConstrainCuda::Impl::Impl(const t_inputrec &ir,
- const gmx_mtop_t &mtop,
- const void *commandStream,
- GpuEventSynchronizer *xUpdatedOnDevice) :
+UpdateConstrainCuda::Impl::Impl(const t_inputrec& ir,
+ const gmx_mtop_t& mtop,
+ const void* commandStream,
+ GpuEventSynchronizer* xUpdatedOnDevice) :
coordinatesReady_(xUpdatedOnDevice)
{
GMX_ASSERT(xUpdatedOnDevice != nullptr, "The event synchronizer can not be nullptr.");
- commandStream != nullptr ? commandStream_ = *static_cast<const CommandStream*>(commandStream) : commandStream_ = nullptr;
+ commandStream != nullptr ? commandStream_ = *static_cast<const CommandStream*>(commandStream)
+ : commandStream_ = nullptr;
integrator_ = std::make_unique<LeapFrogCuda>(commandStream_);
lincsCuda_ = std::make_unique<LincsCuda>(ir.nLincsIter, ir.nProjOrder, commandStream_);
settleCuda_ = std::make_unique<SettleCuda>(mtop, commandStream_);
-
}
-UpdateConstrainCuda::Impl::~Impl()
-{
-}
+UpdateConstrainCuda::Impl::~Impl() {}
-void UpdateConstrainCuda::Impl::set(DeviceBuffer<float> d_x,
- DeviceBuffer<float> d_v,
- const DeviceBuffer<float> d_f,
- const t_idef &idef,
- const t_mdatoms &md,
- const int numTempScaleValues)
+void UpdateConstrainCuda::Impl::set(DeviceBuffer<float> d_x,
+ DeviceBuffer<float> d_v,
+ const DeviceBuffer<float> d_f,
+ const t_idef& idef,
+ const t_mdatoms& md,
+ const int numTempScaleValues)
{
GMX_ASSERT(d_x != nullptr, "Coordinates device buffer should not be null.");
GMX_ASSERT(d_v != nullptr, "Velocities device buffer should not be null.");
reallocateDeviceBuffer(&d_xp_, numAtoms_, &numXp_, &numXpAlloc_, nullptr);
- reallocateDeviceBuffer(&d_inverseMasses_, numAtoms_,
- &numInverseMasses_, &numInverseMassesAlloc_, nullptr);
+ reallocateDeviceBuffer(&d_inverseMasses_, numAtoms_, &numInverseMasses_,
+ &numInverseMassesAlloc_, nullptr);
// Integrator should also update something, but it does not even have a method yet
integrator_->set(md, numTempScaleValues, md.cTC);
settleCuda_->set(idef, md);
}
-void UpdateConstrainCuda::Impl::setPbc(const t_pbc *pbc)
+void UpdateConstrainCuda::Impl::setPbc(const t_pbc* pbc)
{
setPbcAiuc(pbc->ndim_ePBC, pbc->box, &pbcAiuc_);
integrator_->setPbc(pbc);
return coordinatesReady_;
}
-UpdateConstrainCuda::UpdateConstrainCuda(const t_inputrec &ir,
- const gmx_mtop_t &mtop,
- const void *commandStream,
- GpuEventSynchronizer *xUpdatedOnDevice)
- : impl_(new Impl(ir, mtop, commandStream, xUpdatedOnDevice))
+UpdateConstrainCuda::UpdateConstrainCuda(const t_inputrec& ir,
+ const gmx_mtop_t& mtop,
+ const void* commandStream,
+ GpuEventSynchronizer* xUpdatedOnDevice) :
+ impl_(new Impl(ir, mtop, commandStream, xUpdatedOnDevice))
{
}
UpdateConstrainCuda::~UpdateConstrainCuda() = default;
-void UpdateConstrainCuda::integrate(GpuEventSynchronizer *fReadyOnDevice,
+void UpdateConstrainCuda::integrate(GpuEventSynchronizer* fReadyOnDevice,
const real dt,
const bool updateVelocities,
const bool computeVirial,
const float dtPressureCouple,
const matrix velocityScalingMatrix)
{
- impl_->integrate(fReadyOnDevice,
- dt, updateVelocities, computeVirial, virialScaled,
- doTempCouple, tcstat,
- doPressureCouple, dtPressureCouple, velocityScalingMatrix);
+ impl_->integrate(fReadyOnDevice, dt, updateVelocities, computeVirial, virialScaled, doTempCouple,
+ tcstat, doPressureCouple, dtPressureCouple, velocityScalingMatrix);
}
-void UpdateConstrainCuda::set(DeviceBuffer<float> d_x,
- DeviceBuffer<float> d_v,
- const DeviceBuffer<float> d_f,
- const t_idef &idef,
- const t_mdatoms &md,
- const int numTempScaleValues)
+void UpdateConstrainCuda::set(DeviceBuffer<float> d_x,
+ DeviceBuffer<float> d_v,
+ const DeviceBuffer<float> d_f,
+ const t_idef& idef,
+ const t_mdatoms& md,
+ const int numTempScaleValues)
{
impl_->set(d_x, d_v, d_f, idef, md, numTempScaleValues);
}
-void UpdateConstrainCuda::setPbc(const t_pbc *pbc)
+void UpdateConstrainCuda::setPbc(const t_pbc* pbc)
{
impl_->setPbc(pbc);
}
return impl_->getCoordinatesReadySync();
}
-} //namespace gmx
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff