Multiple //!< Multiple T-scaling values, need to use T-group indices
};
+/*! \brief Different variants of the Parrinello-Rahman velocity scaling
+ *
+ * This is needed to template the kernel
+ * \todo Unify with similar enum in CPU update module
+ */
+enum class VelocityScalingType
+{
+ None, //!< Do not apply velocity scaling (not a PR-coupling run or step)
+ Diagonal, //!< Apply velocity scaling using a diagonal matrix
+ Full //!< Apply velocity scaling using a full matrix
+};
+
/*! \brief Main kernel for Leap-Frog integrator.
*
* Each GPU thread works with a single particle. Empty declaration is needed to
* \todo Check if the force should be set to zero here.
* \todo This kernel can also accumulate incidental temperatures for each atom.
*
- * \tparam numTempScaleValues The number of different T-couple values
- * \param[in] numAtoms Total number of atoms.
- * \param[in] gm_x Coordinates before the timestep
- * \param[out] gm_xp Coordinates after the timestep.
- * \param[in,out] gm_v Velocities to update.
- * \param[in] gm_f Atomic forces.
- * \param[in] gm_inverseMasses Reciprocal masses.
- * \param[in] dt Timestep.
- * \param[in] gm_lambdas Temperature scaling factors (one per group)
- * \param[in] gm_tempScaleGroups Mapping of atoms into groups.
+ * \tparam numTempScaleValues The number of different T-couple values.
+ * \tparam velocityScaling Type of the Parrinello-Rahman velocity rescaling.
+ * \param[in] numAtoms Total number of atoms.
+ * \param[in] gm_x Coordinates before the timestep
+ * \param[out] gm_xp Coordinates after the timestep.
+ * \param[in,out] gm_v Velocities to update.
+ * \param[in] gm_f Atomic forces.
+ * \param[in] gm_inverseMasses Reciprocal masses.
+ * \param[in] dt Timestep.
+ * \param[in] gm_lambdas Temperature scaling factors (one per group)
+ * \param[in] gm_tempScaleGroups Mapping of atoms into groups.
+ * \param[in] dtPressureCouple Time step for pressure coupling
+ * \param[in] velocityScalingMatrixDiagonal Diagonal elements of Parrinello-Rahman velocity scaling matrix
*/
-template<NumTempScaleValues numTempScaleValues>
+template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>
__launch_bounds__(c_maxThreadsPerBlock)
__global__ void leapfrog_kernel(const int numAtoms,
const float3* __restrict__ gm_x,
const float* __restrict__ gm_inverseMasses,
const float dt,
const float* __restrict__ gm_lambdas,
- const unsigned short* __restrict__ gm_tempScaleGroups);
+ const unsigned short* __restrict__ gm_tempScaleGroups,
+ const float3 velocityScalingMatrixDiagonal);
-template<NumTempScaleValues numTempScaleValues>
+template<NumTempScaleValues numTempScaleValues, VelocityScalingType velocityScaling>
__launch_bounds__(c_maxThreadsPerBlock)
__global__ void leapfrog_kernel(const int numAtoms,
const float3* __restrict__ gm_x,
const float* __restrict__ gm_inverseMasses,
const float dt,
const float* __restrict__ gm_lambdas,
- const unsigned short* __restrict__ gm_tempScaleGroups)
+ const unsigned short* __restrict__ gm_tempScaleGroups,
+ const float3 velocityScalingMatrixDiagonal)
{
int threadIndex = blockIdx.x*blockDim.x + threadIdx.x;
if (threadIndex < numAtoms)
{
- float3 xi = gm_x[threadIndex];
- float3 vi = gm_v[threadIndex];
- float3 fi = gm_f[threadIndex];
- float imi = gm_inverseMasses[threadIndex];
- float imidt = imi*dt;
+ float3 x = gm_x[threadIndex];
+ float3 v = gm_v[threadIndex];
+ float3 f = gm_f[threadIndex];
+ float im = gm_inverseMasses[threadIndex];
+ float imdt = im*dt;
- if (numTempScaleValues != NumTempScaleValues::None)
+ if (numTempScaleValues != NumTempScaleValues::None || velocityScaling != VelocityScalingType::None)
{
- float lambda = 1.0F;
- if (numTempScaleValues == NumTempScaleValues::Single)
+ float3 vp = v;
+
+ if (numTempScaleValues != NumTempScaleValues::None)
{
- lambda = gm_lambdas[0];
+ float lambda = 1.0F;
+ if (numTempScaleValues == NumTempScaleValues::Single)
+ {
+ lambda = gm_lambdas[0];
+ }
+ else if (numTempScaleValues == NumTempScaleValues::Multiple)
+ {
+ int tempScaleGroup = gm_tempScaleGroups[threadIndex];
+ lambda = gm_lambdas[tempScaleGroup];
+ }
+ vp *= lambda;
}
- if (numTempScaleValues == NumTempScaleValues::Multiple)
+
+ if (velocityScaling == VelocityScalingType::Diagonal)
{
- int tempScaleGroup = gm_tempScaleGroups[threadIndex];
- lambda = gm_lambdas[tempScaleGroup];
+ vp.x -= velocityScalingMatrixDiagonal.x*v.x;
+ vp.y -= velocityScalingMatrixDiagonal.y*v.y;
+ vp.z -= velocityScalingMatrixDiagonal.z*v.z;
}
- vi *= lambda;
+
+ v = vp;
}
- vi += fi*imidt;
- xi += vi*dt;
- gm_v[threadIndex] = vi;
- gm_xp[threadIndex] = xi;
+
+ v += f*imdt;
+
+ x += v*dt;
+ gm_v[threadIndex] = v;
+ gm_xp[threadIndex] = x;
}
return;
}
* If zero is passed as an argument, it is assumed that no temperature coupling groups are used.
*
* \param[in] numTempScaleValues Numer of temperature coupling groups in the system
+ * \param[in] velocityScaling Type of the Parrinello-Rahman velocity scaling
*
* \retrun Pointer to CUDA kernel
*/
-inline auto selectLeapFrogKernelPtr(int numTempScaleValues)
+inline auto selectLeapFrogKernelPtr(int numTempScaleValues, VelocityScalingType velocityScaling)
{
- auto kernelPtr = leapfrog_kernel<NumTempScaleValues::None>;
+ auto kernelPtr = leapfrog_kernel<NumTempScaleValues::None, VelocityScalingType::None>;
- if (numTempScaleValues == 0)
- {
- kernelPtr = leapfrog_kernel<NumTempScaleValues::None>;
- }
- else if (numTempScaleValues == 1)
+ if (velocityScaling == VelocityScalingType::None)
{
- kernelPtr = leapfrog_kernel<NumTempScaleValues::Single>;
+ if (numTempScaleValues == 0)
+ {
+ kernelPtr = leapfrog_kernel<NumTempScaleValues::None, VelocityScalingType::None>;
+ }
+ else if (numTempScaleValues == 1)
+ {
+ kernelPtr = leapfrog_kernel<NumTempScaleValues::Single, VelocityScalingType::None>;
+ }
+ else if (numTempScaleValues > 1)
+ {
+ kernelPtr = leapfrog_kernel<NumTempScaleValues::Multiple, VelocityScalingType::None>;
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(false, "Number of temperature coupling groups should be greater than zero (zero for no coupling).");
+ }
}
- else if (numTempScaleValues > 1)
+ else
+ if (velocityScaling == VelocityScalingType::Diagonal)
{
- kernelPtr = leapfrog_kernel<NumTempScaleValues::Multiple>;
+ if (numTempScaleValues == 0)
+ {
+ kernelPtr = leapfrog_kernel<NumTempScaleValues::None, VelocityScalingType::Diagonal>;
+ }
+ else if (numTempScaleValues == 1)
+ {
+ kernelPtr = leapfrog_kernel<NumTempScaleValues::Single, VelocityScalingType::Diagonal>;
+ }
+ else if (numTempScaleValues > 1)
+ {
+ kernelPtr = leapfrog_kernel<NumTempScaleValues::Multiple, VelocityScalingType::Diagonal>;
+ }
+ else
+ {
+ GMX_RELEASE_ASSERT(false, "Number of temperature coupling groups should be greater than zero (zero for no coupling).");
+ }
}
else
{
- GMX_RELEASE_ASSERT(false, "Number of temperature coupling groups should be greater than zero or zero for no coupling.");
+ GMX_RELEASE_ASSERT(false, "Only isotropic Parrinello-Rahman pressure coupling is supported.");
}
return kernelPtr;
}
const float3 *d_f,
const real dt,
const bool doTempCouple,
- gmx::ArrayRef<const t_grp_tcstat> tcstat)
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ const bool doPressureCouple,
+ const float dtPressureCouple,
+ const matrix velocityScalingMatrix)
{
ensureNoPendingCudaError("In CUDA version of Leap-Frog integrator");
- auto kernelPtr = leapfrog_kernel<NumTempScaleValues::None>;
-
- if (doTempCouple)
+ auto kernelPtr = leapfrog_kernel<NumTempScaleValues::None, VelocityScalingType::None>;
+ if (doTempCouple || doPressureCouple)
{
- GMX_ASSERT(numTempScaleValues_ == ssize(h_lambdas_), "Number of temperature scaling factors changed since it was set for the last time.");
- for (int i = 0; i < numTempScaleValues_; i++)
+ if (doTempCouple)
+ {
+ GMX_ASSERT(numTempScaleValues_ == ssize(h_lambdas_), "Number of temperature scaling factors changed since it was set for the last time.");
+ for (int i = 0; i < numTempScaleValues_; i++)
+ {
+ h_lambdas_[i] = tcstat[i].lambda;
+ }
+ copyToDeviceBuffer(&d_lambdas_, h_lambdas_.data(),
+ 0, numTempScaleValues_, stream_, GpuApiCallBehavior::Async, nullptr);
+ }
+ VelocityScalingType velocityScaling = VelocityScalingType::None;
+ if (doPressureCouple)
{
- h_lambdas_[i] = tcstat[i].lambda;
+ velocityScaling = VelocityScalingType::Diagonal;
+ GMX_ASSERT(velocityScalingMatrix[YY][XX] == 0 && velocityScalingMatrix[ZZ][XX] == 0 && velocityScalingMatrix[ZZ][YY] == 0 &&
+ velocityScalingMatrix[XX][YY] == 0 && velocityScalingMatrix[XX][ZZ] == 0 && velocityScalingMatrix[YY][ZZ] == 0,
+ "Fully anisotropic Parrinello-Rahman pressure coupling is not yet supported in GPU version of Leap-Frog integrator.");
+ velocityScalingMatrixDiagonal_ = make_float3(dtPressureCouple*velocityScalingMatrix[XX][XX],
+ dtPressureCouple*velocityScalingMatrix[YY][YY],
+ dtPressureCouple*velocityScalingMatrix[ZZ][ZZ]);
}
- copyToDeviceBuffer(&d_lambdas_, h_lambdas_.data(),
- 0, numTempScaleValues_, stream_, GpuApiCallBehavior::Async, nullptr);
- kernelPtr = selectLeapFrogKernelPtr(numTempScaleValues_);
+ kernelPtr = selectLeapFrogKernelPtr(numTempScaleValues_, velocityScaling);
}
const auto kernelArgs = prepareGpuKernelArguments(kernelPtr, kernelLaunchConfig_,
&d_v,
&d_f,
&d_inverseMasses_, &dt,
- &d_lambdas_, &d_tempScaleGroups_);
+ &d_lambdas_, &d_tempScaleGroups_,
+ &velocityScalingMatrixDiagonal_);
launchGpuKernel(kernelPtr, kernelLaunchConfig_, nullptr, "leapfrog_kernel", kernelArgs);
return;
* Integrates the equation of motion using Leap-Frog algorithm.
* Updates coordinates and velocities on the GPU.
*
- * \param[in] d_x Initial coordinates.
- * \param[out] d_xp Place to save the resulting coordinates to.
- * \param[in,out] d_v Velocities (will be updated).
- * \param[in] d_f Forces.
- * \param[in] dt Timestep.
- * \param[in] doTempCouple If the temperature coupling should be applied.
- * \param[in] tcstat Temperature coupling data.
+ * \param[in] d_x Initial coordinates.
+ * \param[out] d_xp Place to save the resulting coordinates to.
+ * \param[in,out] d_v Velocities (will be updated).
+ * \param[in] d_f Forces.
+ * \param[in] dt Timestep.
+ * \param[in] doTempCouple If the temperature coupling should be applied.
+ * \param[in] tcstat Temperature coupling data.
+ * \param[in] doPressureCouple If the temperature coupling should be applied.
+ * \param[in] dtPressureCouple Period between pressure coupling steps
+ * \param[in] velocityScalingMatrix Parrinello-Rahman velocity scaling matrix
*/
void integrate(const float3 *d_x,
float3 *d_xp,
const float3 *d_f,
const real dt,
const bool doTempCouple,
- gmx::ArrayRef<const t_grp_tcstat> tcstat);
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ const bool doPressureCouple,
+ const float dtPressureCouple,
+ const matrix velocityScalingMatrix);
/*! \brief Set the integrator
*
//! Maximum size of the temperature coupling groups array
int numTempScaleGroupsAlloc_ = -1;
+ //! Vector with diagonal elements of the pressure coupling velocity rescale factors
+ float3 velocityScalingMatrixDiagonal_;
+
};
} //namespace gmx
rvec f;
//! Number of temperature coupling group (zero for no temperature coupling)
int numTCoupleGroups;
+ //! Number of steps between pressure coupling steps (zero for no pressure coupling).
+ int nstpcouple;
};
//! The set of parameters combinations to run the test on
-const LeapFrogTestParameters parametersSets[] = {{ 1, 0.001, 1, {0.0, 0.0, 0.0}, {0.0, 0.0, 0.0}, 0}, // Zero velocity and force
- { 1, 0.001, 1, {0.0, 0.0, 0.0}, {-3.0, 2.0, -1.0}, 0}, // Zero velocity
- { 1, 0.001, 1, {1.0, -2.0, 3.0}, {0.0, 0.0, 0.0}, 0}, // Zero force
- { 1, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0}, // 1 particle
- { 10, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0}, // 10 particles
- {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0}, // 100 particles
- {300, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0}, // 300 particles
- { 1, 0.0005, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0}, // 0.0005 ps timestep
- { 1, 0.001, 10, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0}, // 10 step
- { 1, 0.001, 100, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0}, // 100 steps
- {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 1}, // 1 temperature couple group
- {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 2}, // 2 temperature couple groups
- {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 10}}; // 10 temperature couple groups
+const LeapFrogTestParameters parametersSets[] = {{ 1, 0.001, 1, {0.0, 0.0, 0.0}, { 0.0, 0.0, 0.0}, 0, 0}, // Zero velocity and force
+ { 1, 0.001, 1, {0.0, 0.0, 0.0}, {-3.0, 2.0, -1.0}, 0, 0}, // Zero velocity
+ { 1, 0.001, 1, {1.0, -2.0, 3.0}, { 0.0, 0.0, 0.0}, 0, 0}, // Zero force
+ { 1, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 0}, // 1 particle
+ { 10, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 0}, // 10 particles
+ {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 0}, // 100 particles
+ {300, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 0}, // 300 particles
+ { 1, 0.0005, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 0}, // 0.0005 ps timestep
+ { 1, 0.001, 10, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 0}, // 10 step
+ { 1, 0.001, 100, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 0}, // 100 steps
+ {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 1, 0}, // 1 temperature couple group
+ {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 2, 0}, // 2 temperature couple groups
+ {100, 0.001, 1, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 10, 0}, // 10 temperature couple groups
+ {100, 0.001, 10, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 1}, // With pressure coupling
+ {100, 0.001, 10, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 2, 1}, // With both temperature and pressure coupling
+ {100, 0.001, 10, {1.0, -2.0, 3.0}, {-3.0, 2.0, -1.0}, 0, 3}}; // Do pressure coupling not on every step
+
/*! \brief Test fixture for LeapFrog integrator.
LeapFrogTestParameters parameters = GetParam();
- std::string testDescription = formatString("Testing %s with %d atoms for %d timesteps with %d temperature coupling groups (dt = %f, v0=(%f, %f, %f), f0=(%f, %f, %f))",
+ std::string testDescription = formatString("Testing %s with %d atoms for %d timesteps with %d temperature coupling groups and %s pressure coupling (dt = %f, v0=(%f, %f, %f), f0=(%f, %f, %f), nstpcouple = %d)",
runnerName.c_str(),
- parameters.numAtoms, parameters.numSteps, parameters.numTCoupleGroups, parameters.timestep,
+ parameters.numAtoms, parameters.numSteps, parameters.numTCoupleGroups,
+ parameters.nstpcouple == 0 ? "without" : "with",
+ parameters.timestep,
parameters.v[XX], parameters.v[YY], parameters.v[ZZ],
- parameters.f[XX], parameters.f[YY], parameters.f[ZZ]);
+ parameters.f[XX], parameters.f[YY], parameters.f[ZZ],
+ parameters.nstpcouple);
SCOPED_TRACE(testDescription);
std::unique_ptr<LeapFrogTestData> testData =
- std::make_unique<LeapFrogTestData>(parameters.numAtoms, parameters.timestep, parameters.v, parameters.f, parameters.numTCoupleGroups);
+ std::make_unique<LeapFrogTestData>(parameters.numAtoms, parameters.timestep,
+ parameters.v, parameters.f,
+ parameters.numTCoupleGroups,
+ parameters.nstpcouple);
runner.second(testData.get(), parameters.numSteps);
FloatingPointTolerance tolerance = absoluteTolerance(parameters.numSteps*0.000005);
// Test against the analytical solution (without temperature coupling)
- if (parameters.numTCoupleGroups == 0)
+ if (parameters.numTCoupleGroups == 0 && parameters.nstpcouple == 0)
{
testAgainstAnalyticalSolution(tolerance, *testData, totalTime);
}
namespace test
{
-LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, const rvec f0, int numTCoupleGroups) :
+LeapFrogTestData::LeapFrogTestData(int numAtoms, real timestep, const rvec v0, const rvec f0, int numTCoupleGroups, int nstpcouple) :
numAtoms_(numAtoms),
timestep_(timestep),
x0_(numAtoms),
}
}
- // Data needed for current CPU-based implementation
inputRecord_.eI = eiMD;
inputRecord_.delta_t = timestep_;
- inputRecord_.epc = epcNO;
state_.flags = 0;
mdAtoms_.havePartiallyFrozenAtoms = false;
mdAtoms_.cFREEZE = nullptr;
- prVScalingMatrix_[XX][XX] = 1.0;
- prVScalingMatrix_[XX][YY] = 0.0;
- prVScalingMatrix_[XX][ZZ] = 0.0;
+ update_ = std::make_unique<Update>(&inputRecord_, nullptr);
+ update_->setNumAtoms(numAtoms);
+
+ doPressureCouple_ = (nstpcouple != 0);
- prVScalingMatrix_[YY][XX] = 0.0;
- prVScalingMatrix_[YY][YY] = 1.0;
- prVScalingMatrix_[YY][ZZ] = 0.0;
+ if (doPressureCouple_)
+ {
+ inputRecord_.epc = epcPARRINELLORAHMAN;
+ inputRecord_.nstpcouple = nstpcouple;
+ dtPressureCouple_ = inputRecord_.nstpcouple*inputRecord_.delta_t;
- prVScalingMatrix_[ZZ][XX] = 0.0;
- prVScalingMatrix_[ZZ][YY] = 0.0;
- prVScalingMatrix_[ZZ][ZZ] = 1.0;
+ velocityScalingMatrix_[XX][XX] = 1.2;
+ velocityScalingMatrix_[XX][YY] = 0.0;
+ velocityScalingMatrix_[XX][ZZ] = 0.0;
+
+ velocityScalingMatrix_[YY][XX] = 0.0;
+ velocityScalingMatrix_[YY][YY] = 0.8;
+ velocityScalingMatrix_[YY][ZZ] = 0.0;
+
+ velocityScalingMatrix_[ZZ][XX] = 0.0;
+ velocityScalingMatrix_[ZZ][YY] = 0.0;
+ velocityScalingMatrix_[ZZ][ZZ] = 0.9;
+ }
+ else
+ {
+ inputRecord_.epc = epcNO;
+ velocityScalingMatrix_[XX][XX] = 1.0;
+ velocityScalingMatrix_[XX][YY] = 0.0;
+ velocityScalingMatrix_[XX][ZZ] = 0.0;
+
+ velocityScalingMatrix_[YY][XX] = 0.0;
+ velocityScalingMatrix_[YY][YY] = 1.0;
+ velocityScalingMatrix_[YY][ZZ] = 0.0;
+
+ velocityScalingMatrix_[ZZ][XX] = 0.0;
+ velocityScalingMatrix_[ZZ][YY] = 0.0;
+ velocityScalingMatrix_[ZZ][ZZ] = 1.0;
+ }
- update_ = std::make_unique<Update>(&inputRecord_, nullptr);
- update_->setNumAtoms(numAtoms);
}
LeapFrogTestData::~LeapFrogTestData()
/*! \internal \file
* \brief Tests for the Leap-Frog integrator
*
- * \todo Prepare for temperature and pressure controlled integrators.
+ * \todo Add anisotropic Parrinello-Rahman and other pressure coupling schemes
* \todo Add PBC handling test.
* \todo Reference values tests.
*
t_fcdata forceCalculationData_;
//! Kinetic energy data (to disable non-equilibrium MD integration)
gmx_ekindata_t kineticEnergyData_;
- //! Parrinnello-Rahman velocity rescalling matrix
- matrix prVScalingMatrix_;
//! Update data
std::unique_ptr<Update> update_;
//! Number of temperature coupling groups
int numTCoupleGroups_;
+ //! If the pressure coupling is enabled
+ bool doPressureCouple_;
+ //! Period between pressure coupling steps
+ float dtPressureCouple_;
+ //! Matrix for Parrinello-Rahman velocity scaling
+ matrix velocityScalingMatrix_;
/*! \brief Constructor.
*
* \param[in] v0 Initial velocity (same for all particles)
* \param[in] f0 External constant force, acting on all particles
* \param[in] numTCoupleGroups Number of temperature coupling groups (zero for no temperature coupling)
+ * \param[in] nstpcouple Number of steps between pressure coupling steps (zero for no pressure coupling)
*/
- LeapFrogTestData(int numAtoms, real timestep, const rvec v0, const rvec f0, int numTCoupleGroups);
+ LeapFrogTestData(int numAtoms, real timestep, const rvec v0, const rvec f0,
+ int numTCoupleGroups, int nstpcouple);
~LeapFrogTestData();
};
testData->f_,
&testData->forceCalculationData_,
&testData->kineticEnergyData_,
- testData->prVScalingMatrix_,
+ testData->velocityScalingMatrix_,
testData->update_.get(),
etrtNONE,
nullptr,
#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/leapfrog_cuda.cuh"
+#include "gromacs/mdlib/stat.h"
#include "gromacs/mdtypes/group.h"
namespace gmx
bool doTempCouple = testData->numTCoupleGroups_ > 0;
for (int step = 0; step < numSteps; step++)
{
-
- integrator->integrate(d_x, d_xp, d_v, d_f, testData->timestep_, doTempCouple, testData->kineticEnergyData_.tcstat);
+ // This follows the logic of the CPU-based implementation
+ bool doPressureCouple = testData->doPressureCouple_ && do_per_step(step + testData->inputRecord_.nstpcouple - 1, testData->inputRecord_.nstpcouple);
+ integrator->integrate(d_x, d_xp, d_v, d_f, testData->timestep_,
+ doTempCouple, testData->kineticEnergyData_.tcstat,
+ doPressureCouple, testData->dtPressureCouple_, testData->velocityScalingMatrix_);
copyFromDeviceBuffer(h_xp, &d_xp, 0, numAtoms, nullptr, GpuApiCallBehavior::Sync, nullptr);
copyToDeviceBuffer(&d_x, h_xp, 0, numAtoms, nullptr, GpuApiCallBehavior::Sync, nullptr);
--- /dev/null
+<?xml version="1.0"?>
+<?xml-stylesheet type="text/xsl" href="referencedata.xsl"?>
+<ReferenceData>
+ <Sequence Name="FinalPositions">
+ <Int Name="Length">100</Int>
+ <Atom>
+ <Real Name="XX">0.0097698296075089917</Real>
+ <Real Name="YY">6.4801975255594693</Real>
+ <Real Name="ZZ">0.029797048462235041</Real>
+ </Atom>
+ <Atom>
+ <Real Name="XX">1.009852033319113</Real>
+ <Real Name="YY">5.480142657348507</Real>
+ <Real Name="ZZ">0.029824474345716775</Real>
+ </Atom>
+ <Atom>
+ <Real Name="XX">2.0098794345563151</Real>
+ <Real Name="YY">4.4801243679448515</Real>
+ <Real Name="ZZ">0.029833616306877371</Real>
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* This will extract temperature scaling factors from tcstat, transform them into the plain
* array and call the normal integrate method.
*
- * \param[in] dt Timestep
- * \param[in] updateVelocities If the velocities should be constrained.
- * \param[in] computeVirial If virial should be updated.
- * \param[out] virial Place to save virial tensor.
- * \param[in] doTempCouple If the temperature coupling should be performed.
- * \param[in] tcstat Temperature coupling data.
+ * \param[in] dt Timestep
+ * \param[in] updateVelocities If the velocities should be constrained.
+ * \param[in] computeVirial If virial should be updated.
+ * \param[out] virial Place to save virial tensor.
+ * \param[in] doTempCouple If the temperature coupling should be performed.
+ * \param[in] tcstat Temperature coupling data.
+ * \param[in] doPressureCouple If the temperature coupling should be applied.
+ * \param[in] dtPressureCouple Period between pressure coupling steps
+ * \param[in] velocityScalingMatrix Parrinello-Rahman velocity scaling matrix
*/
void integrate(real dt,
bool updateVelocities,
bool computeVirial,
tensor virial,
bool doTempCouple,
- gmx::ArrayRef<const t_grp_tcstat> tcstat);
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ bool doPressureCouple,
+ float dtPressureCouple,
+ const matrix velocityScalingMatrix);
/*! \brief
* Update data-structures (e.g. after NB search step).
gmx_unused const bool computeVirial,
gmx_unused tensor virialScaled,
gmx_unused const bool doTempCouple,
- gmx_unused gmx::ArrayRef<const t_grp_tcstat> tcstat)
+ gmx_unused gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ gmx_unused const bool doPressureCouple,
+ gmx_unused const float dtPressureCouple,
+ gmx_unused const matrix velocityScalingMatrix)
{
GMX_ASSERT(false, "A CPU stub for UpdateConstrain was called insted of the correct implementation.");
}
const bool computeVirial,
tensor virial,
const bool doTempCouple,
- gmx::ArrayRef<const t_grp_tcstat> tcstat)
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ const bool doPressureCouple,
+ const float dtPressureCouple,
+ const matrix velocityScalingMatrix)
{
// Clearing virial matrix
// TODO There is no point in having separate virial matrix for constraints
clear_mat(virial);
- integrator_->integrate(d_x_, d_xp_, d_v_, d_f_, dt, doTempCouple, tcstat);
+ integrator_->integrate(d_x_, d_xp_, d_v_, d_f_, dt,
+ doTempCouple, tcstat,
+ doPressureCouple, dtPressureCouple, velocityScalingMatrix);
lincsCuda_->apply(d_x_, d_xp_,
updateVelocities, d_v_, 1.0/dt,
computeVirial, virial);
const bool computeVirial,
tensor virialScaled,
const bool doTempCouple,
- gmx::ArrayRef<const t_grp_tcstat> tcstat)
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ const bool doPressureCouple,
+ const float dtPressureCouple,
+ const matrix pRVScalingMatrix)
{
- impl_->integrate(dt, updateVelocities, computeVirial, virialScaled, doTempCouple, tcstat);
+ impl_->integrate(dt, updateVelocities, computeVirial, virialScaled,
+ doTempCouple, tcstat,
+ doPressureCouple, dtPressureCouple, pRVScalingMatrix);
}
void UpdateConstrainCuda::set(const t_idef &idef,
* 2. This is the temperature coupling step.
* Parameters virial/lambdas can be nullptr if computeVirial/doTempCouple are false.
*
- * \param[in] dt Timestep
- * \param[in] updateVelocities If the velocities should be constrained.
- * \param[in] computeVirial If virial should be updated.
- * \param[out] virial Place to save virial tensor.
- * \param[in] doTempCouple If the temperature coupling should be performed.
- * \param[in] tcstat Temperature coupling data.
+ * \param[in] dt Timestep
+ * \param[in] updateVelocities If the velocities should be constrained.
+ * \param[in] computeVirial If virial should be updated.
+ * \param[out] virial Place to save virial tensor.
+ * \param[in] doTempCouple If the temperature coupling should be performed.
+ * \param[in] tcstat Temperature coupling data.
+ * \param[in] doPressureCouple If the temperature coupling should be applied.
+ * \param[in] dtPressureCouple Period between pressure coupling steps
+ * \param[in] velocityScalingMatrix Parrinello-Rahman velocity scaling matrix
*/
void integrate(const real dt,
const bool updateVelocities,
const bool computeVirial,
tensor virial,
const bool doTempCouple,
- gmx::ArrayRef<const t_grp_tcstat> tcstat);
+ gmx::ArrayRef<const t_grp_tcstat> tcstat,
+ const bool doPressureCouple,
+ const float dtPressureCouple,
+ const matrix velocityScalingMatrix);
/*! \brief
* Update data-structures (e.g. after NB search step).
{
GMX_RELEASE_ASSERT(ir->eI == eiMD, "Only md integrator is supported on the GPU.");
GMX_RELEASE_ASSERT(ir->etc != etcNOSEHOOVER, "Nose Hoover temperature coupling is not supported on the GPU.");
- GMX_RELEASE_ASSERT(ir->epc == epcNO, "Pressure coupling is not supported on the GPU.");
+ GMX_RELEASE_ASSERT(ir->epc == epcNO || ir->epc == epcPARRINELLORAHMAN, "Only Parrinello Rahman pressure control is supported on the GPU.");
GMX_RELEASE_ASSERT(!mdatoms->haveVsites, "Virtual sites are not supported on the GPU");
GMX_RELEASE_ASSERT(ed == nullptr, "Essential dynamics is not supported with GPU-based update constraints.");
GMX_LOG(mdlog.info).asParagraph().
integrator->copyVelocitiesToGpu(state->v.rvec_array());
integrator->copyForcesToGpu(as_rvec_array(f.data()));
- // This applies Leap-Frog, LINCS and SETTLE in a succession
- bool doTempCouple = (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
+ bool doTempCouple = (ir->etc != etcNO && do_per_step(step + ir->nsttcouple - 1, ir->nsttcouple));
+ bool doPressureCouple = (ir->epc == epcPARRINELLORAHMAN && do_per_step(step + ir->nstpcouple - 1, ir->nstpcouple));
- integrator->integrate(ir->delta_t, true, bCalcVir, shake_vir, doTempCouple, ekind->tcstat);
+ // This applies Leap-Frog, LINCS and SETTLE in succession
+ integrator->integrate(ir->delta_t, true, bCalcVir, shake_vir,
+ doTempCouple, ekind->tcstat,
+ doPressureCouple, ir->nstpcouple*ir->delta_t, M);
integrator->copyCoordinatesFromGpu(state->x.rvec_array());
integrator->copyVelocitiesFromGpu(state->v.rvec_array());
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff