if(GMX_USE_CUDA)
gmx_add_libgromacs_sources(
leapfrog_cuda_impl.cu
- lincs_cuda_impl.cu
+ lincs_cuda.cu
settle_cuda_impl.cu
update_constrain_cuda_impl.cu
)
*/
#include "gmxpre.h"
-#include "lincs_cuda_impl.h"
+#include "lincs_cuda.cuh"
#include <assert.h>
#include <stdio.h>
#include "gromacs/gpu_utils/vectype_ops.cuh"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/constr.h"
-#include "gromacs/mdlib/lincs_cuda.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_aiuc_cuda.cuh"
#include "gromacs/topology/ifunc.h"
return kernelPtr;
}
-void LincsCuda::Impl::apply(const float3 *d_x,
- float3 *d_xp,
- const bool updateVelocities,
- float3 *d_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled)
+void LincsCuda::apply(const float3 *d_x,
+ float3 *d_xp,
+ const bool updateVelocities,
+ float3 *d_v,
+ const real invdt,
+ const bool computeVirial,
+ tensor virialScaled)
{
ensureNoPendingCudaError("In CUDA version of LINCS");
return;
}
-void LincsCuda::Impl::copyApplyCopy(const int numAtoms,
- const rvec *h_x,
- rvec *h_xp,
- bool updateVelocities,
- rvec *h_v,
- real invdt,
- bool computeVirial,
- tensor virialScaled)
-{
-
- float3 *d_x, *d_xp, *d_v;
-
- allocateDeviceBuffer(&d_x, numAtoms, nullptr);
- allocateDeviceBuffer(&d_xp, numAtoms, nullptr);
- allocateDeviceBuffer(&d_v, numAtoms, nullptr);
-
- copyToDeviceBuffer(&d_x, (float3*)h_x, 0, numAtoms, stream_, GpuApiCallBehavior::Sync, nullptr);
- copyToDeviceBuffer(&d_xp, (float3*)h_xp, 0, numAtoms, stream_, GpuApiCallBehavior::Sync, nullptr);
- if (updateVelocities)
- {
- copyToDeviceBuffer(&d_v, (float3*)h_v, 0, numAtoms, stream_, GpuApiCallBehavior::Sync, nullptr);
- }
- apply(d_x, d_xp,
- updateVelocities, d_v, invdt,
- computeVirial, virialScaled);
-
- copyFromDeviceBuffer((float3*)h_xp, &d_xp, 0, numAtoms, stream_, GpuApiCallBehavior::Sync, nullptr);
- if (updateVelocities)
- {
- copyFromDeviceBuffer((float3*)h_v, &d_v, 0, numAtoms, stream_, GpuApiCallBehavior::Sync, nullptr);
- }
-
- freeDeviceBuffer(&d_x);
- freeDeviceBuffer(&d_xp);
- freeDeviceBuffer(&d_v);
-}
-
-LincsCuda::Impl::Impl(int numIterations,
- int expansionOrder)
+LincsCuda::LincsCuda(int numIterations,
+ int expansionOrder)
{
kernelParams_.numIterations = numIterations;
kernelParams_.expansionOrder = expansionOrder;
}
-LincsCuda::Impl::~Impl()
+LincsCuda::~LincsCuda()
{
freeDeviceBuffer(&kernelParams_.d_virialScaled);
return counted;
}
-void LincsCuda::Impl::set(const t_idef &idef,
- const t_mdatoms &md)
+void LincsCuda::set(const t_idef &idef,
+ const t_mdatoms &md)
{
int numAtoms = md.nr;
// List of constrained atoms (CPU memory)
}
-void LincsCuda::Impl::setPbc(const t_pbc *pbc)
-{
- setPbcAiuc(pbc->ndim_ePBC, pbc->box, &kernelParams_.pbcAiuc);
-}
-
-LincsCuda::LincsCuda(const int numIterations,
- const int expansionOrder)
- : impl_(new Impl(numIterations, expansionOrder))
-{
-}
-
-LincsCuda::~LincsCuda() = default;
-
-void LincsCuda::copyApplyCopy(const int numAtoms,
- const rvec *h_x,
- rvec *h_xp,
- const bool updateVelocities,
- rvec *h_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled)
-{
- impl_->copyApplyCopy(numAtoms, h_x, h_xp,
- updateVelocities, h_v, invdt,
- computeVirial, virialScaled);
-}
-
void LincsCuda::setPbc(const t_pbc *pbc)
{
- impl_->setPbc(pbc);
-}
-
-void LincsCuda::set(const t_idef &idef,
- const t_mdatoms &md)
-{
- impl_->set(idef, md);
+ setPbcAiuc(pbc->ndim_ePBC, pbc->box, &kernelParams_.pbcAiuc);
}
} // namespace gmx
* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
-/*! \internal \file
+/*! \libinternal \file
*
- * \brief Declares CUDA implementation class for LINCS
- *
- * This header file is needed to include from both the device-side
- * kernels file, and the host-side management code.
+ * \brief Declaration of high-level functions of CUDA implementation of LINCS.
*
* \author Artem Zhmurov <zhmurov@gmail.com>
*
* \ingroup module_mdlib
+ * \inlibraryapi
*/
-#ifndef GMX_MDLIB_LINCS_CUDA_IMPL_H
-#define GMX_MDLIB_LINCS_CUDA_IMPL_H
-
+#ifndef GMX_MDLIB_LINCS_CUDA_CUH
+#define GMX_MDLIB_LINCS_CUDA_CUH
#include "gromacs/mdlib/constr.h"
-#include "gromacs/mdlib/lincs_cuda.h"
#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/pbcutil/pbc_aiuc_cuda.cuh"
+#include "gromacs/pbcutil/pbc_aiuc.h"
#include "gromacs/topology/idef.h"
+#include "gromacs/utility/classhelpers.h"
namespace gmx
{
};
/*! \internal \brief Class with interfaces and data for CUDA version of LINCS. */
-class LincsCuda::Impl
+class LincsCuda
{
public:
* \param[in] numIterations Number of iteration for the correction of the projection.
* \param[in] expansionOrder Order of the matrix inversion algorithm.
*/
- Impl(int numIterations,
- int expansionOrder);
+ LincsCuda(int numIterations,
+ int expansionOrder);
/*! \brief Destructor.*/
- ~Impl();
+ ~LincsCuda();
/*! \brief Apply LINCS.
*
const bool computeVirial,
tensor virialScaled);
- /*! \brief Apply LINCS to the coordinates/velocities stored in CPU memory.
- *
- * This method should not be used in any code-path, where performance is of any value.
- * Only suitable for test and will be removed in future patch sets.
- * Allocates GPU memory, copies data from CPU, applies LINCS to coordinates and,
- * if requested, to velocities, copies the results back, frees GPU memory.
- * Method uses this class data structures which should be filled with set() and setPbc()
- * methods.
- *
- * \todo Remove this method
- *
- * \param[in] numAtoms Number of atoms
- * \param[in] h_x Coordinates before timestep (in CPU memory)
- * \param[in,out] h_xp Coordinates after timestep (in CPU memory). The
- * resulting constrained coordinates will be saved here.
- * \param[in] updateVelocities If the velocities should be updated.
- * \param[in,out] h_v Velocities to update (in CPU memory, can be nullptr
- * if not updated)
- * \param[in] invdt Reciprocal timestep (to scale Lagrange
- * multipliers when velocities are updated)
- * \param[in] computeVirial If virial should be updated.
- * \param[in,out] virialScaled Scaled virial tensor to be updated.
- */
- void copyApplyCopy(const int numAtoms,
- const rvec *h_x,
- rvec *h_xp,
- const bool updateVelocities,
- rvec *h_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled);
-
/*! \brief
* Update data-structures (e.g. after NB search step).
*
};
-} // namespace gmx
+} // namespace gmx
-#endif
+#endif // GMX_MDLIB_LINCS_CUDA_CUH
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \libinternal \file
- *
- * \brief Declaration of high-level functions of CUDA implementation of LINCS.
- *
- * \todo This should only list interfaces needed for libgromacs clients.
- *
- * \author Artem Zhmurov <zhmurov@gmail.com>
- *
- * \ingroup module_mdlib
- * \inlibraryapi
- */
-#ifndef GMX_MDLIB_LINCS_CUDA_H
-#define GMX_MDLIB_LINCS_CUDA_H
-
-
-#include "gromacs/mdlib/constr.h"
-#include "gromacs/mdtypes/mdatom.h"
-#include "gromacs/topology/idef.h"
-#include "gromacs/utility/classhelpers.h"
-
-namespace gmx
-{
-
-class LincsCuda
-{
-
- public:
- /*! \brief Constructor.
- *
- * \param[in] numIterations Number of iteration for the correction of the projection.
- * \param[in] expansionOrder Order of the matrix inversion algorithm.
- */
- LincsCuda(int numIterations,
- int expansionOrder);
- ~LincsCuda();
-
- /*! \brief Apply LINCS to the coordinates/velocities stored in CPU memory.
- *
- * This method should not be used in any code-path, where performance is of any value.
- * Only suitable for test and will be removed in future patch sets.
- * Allocates GPU memory, copies data from CPU, applies LINCS to coordinates and,
- * if requested, to velocities, copies the results back, frees GPU memory.
- * Method uses this class data structures which should be filled with set() and setPbc()
- * methods.
- *
- * \todo Remove this method
- *
- * \param[in] numAtoms Number of atoms
- * \param[in] h_x Coordinates before timestep (in CPU memory)
- * \param[in,out] h_xp Coordinates after timestep (in CPU memory). The
- * resulting constrained coordinates will be saved here.
- * \param[in] updateVelocities If the velocities should be updated.
- * \param[in,out] h_v Velocities to update (in CPU memory, can be nullptr
- * if not updated)
- * \param[in] invdt Reciprocal timestep (to scale Lagrange
- * multipliers when velocities are updated)
- * \param[in] computeVirial If virial should be updated.
- * \param[in,out] virialScaled Scaled virial tensor to be updated.
- */
- void copyApplyCopy(int numAtoms,
- const rvec *h_x,
- rvec *h_xp,
- bool updateVelocities,
- rvec *h_v,
- real invdt,
- bool computeVirial,
- tensor virialScaled);
-
- /*! \brief
- * Update data-structures (e.g. after NB search step).
- *
- * Updates the constraints data. Should be called if the particles were sorted,
- * redistributed between domains, etc.
- *
- * Information about constraints should be taken from:
- * idef.il[F_CONSTR].iatoms --- type (T) of constraint and two atom indexes (i1, i2)
- * idef.iparams[T].constr.dA --- target length for constraint of type T
- * From t_mdatom, the code should take:
- * md.invmass --- array of inverse square root of masses for each atom in the system.
- *
- * \param[in] idef Local topology data to get information on constraints from.
- * \param[in] md Atoms data to get atom masses from.
- */
- void set(const t_idef &idef,
- const t_mdatoms &md);
-
- /*! \brief
- * Update PBC data.
- *
- * \param[in] pbc The PBC data in t_pbc format.
- */
- void setPbc(const t_pbc *pbc);
-
- /*! \brief Class with hardware-specific interfaces and implementations.*/
- class Impl;
-
- private:
- gmx::PrivateImplPointer<Impl> impl_;
-
-};
-
-} // namespace gmx
-
-#endif
+++ /dev/null
-/*
- * This file is part of the GROMACS molecular simulation package.
- *
- * Copyright (c) 2019, by the GROMACS development team, led by
- * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
- * and including many others, as listed in the AUTHORS file in the
- * top-level source directory and at http://www.gromacs.org.
- *
- * GROMACS is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1
- * of the License, or (at your option) any later version.
- *
- * GROMACS is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with GROMACS; if not, see
- * http://www.gnu.org/licenses, or write to the Free Software Foundation,
- * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
- *
- * If you want to redistribute modifications to GROMACS, please
- * consider that scientific software is very special. Version
- * control is crucial - bugs must be traceable. We will be happy to
- * consider code for inclusion in the official distribution, but
- * derived work must not be called official GROMACS. Details are found
- * in the README & COPYING files - if they are missing, get the
- * official version at http://www.gromacs.org.
- *
- * To help us fund GROMACS development, we humbly ask that you cite
- * the research papers on the package. Check out http://www.gromacs.org.
- */
-/*! \internal \file
- *
- * \brief May be used to implement LINCS CUDA interfaces for non-GPU builds.
- *
- * Currently, reports and exits if any of the interfaces are called.
- * May replace CPU LINCS module in future. Currently used to satisfy
- * compiler on systems, where CUDA is not available.
- *
- * \author Artem Zhmurov <zhmurov@gmail.com>
- *
- * \ingroup module_mdlib
- */
-#include "gmxpre.h"
-
-#include "config.h"
-
-#include "gromacs/mdlib/lincs_cuda.h"
-
-#if GMX_GPU != GMX_GPU_CUDA
-
-namespace gmx
-{
-
-class LincsCuda::Impl
-{
-};
-
-LincsCuda::LincsCuda(gmx_unused int numIterations,
- gmx_unused int expansionOrder)
- : impl_(nullptr)
-{
- GMX_ASSERT(false, "A CPU stub for LINCS was called insted of the correct implementation.");
-}
-
-LincsCuda::~LincsCuda() = default;
-
-void LincsCuda::copyApplyCopy(gmx_unused int numAtoms,
- gmx_unused const rvec *h_x,
- gmx_unused rvec *h_xp,
- gmx_unused bool updateVelocities,
- gmx_unused rvec *h_v,
- gmx_unused real invdt,
- gmx_unused bool computeVirial,
- gmx_unused tensor virialScaled)
-{
- GMX_ASSERT(false, "A CPU stub for LINCS was called insted of the correct implementation.");
-}
-
-void LincsCuda::set(gmx_unused const t_idef &idef,
- gmx_unused const t_mdatoms &md)
-{
- GMX_ASSERT(false, "A CPU stub for LINCS was called insted of the correct implementation.");
-}
-
-void LincsCuda::setPbc(gmx_unused const t_pbc *pbc)
-{
- GMX_ASSERT(false, "A CPU stub for LINCS was called insted of the correct implementation.");
-}
-
-} // namespace gmx
-
-#endif /* GMX_GPU != GMX_GPU_CUDA */
# To help us fund GROMACS development, we humbly ask that you cite
# the research papers on the package. Check out http://www.gromacs.org.
+file(GLOB MDLIB_TEST_SOURCES
+ constr_impl.cpp
+ )
+
+if (GMX_USE_CUDA)
+ file(GLOB MDLIB_TEST_CUDA_SOURCES
+ constr_impl.cu
+ )
+endif()
+
gmx_add_unit_test(MdlibUnitTest mdlib-test
calc_verletbuf.cpp
constr.cpp
shake.cpp
simulationsignal.cpp
updategroups.cpp
- updategroupscog.cpp)
+ updategroupscog.cpp
+ ${MDLIB_TEST_SOURCES})
+
+# TODO: Make CUDA source to compile inside the testing framework
+gmx_add_libgromacs_sources(${MDLIB_TEST_CUDA_SOURCES})
\ No newline at end of file
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/gmxlib/nrnb.h"
-#include "gromacs/gmxlib/nonbonded/nonbonded.h"
-#include "gromacs/gpu_utils/gpu_utils.h"
#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vec.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdlib/lincs.h"
-#include "gromacs/mdlib/lincs_cuda.h"
#include "gromacs/mdlib/shake.h"
#include "gromacs/mdrunutility/multisim.h"
#include "gromacs/mdtypes/commrec.h"
#include "testutils/refdata.h"
#include "testutils/testasserts.h"
+#include "constr_impl.h"
+
namespace gmx
{
namespace test
{
-/*! \brief
- * Constraints test data structure.
- *
- * Structure to collect all the necessary data, including system coordinates and topology,
- * constraints information, etc. The structure can be reset and reused.
- */
-struct ConstraintsTestData
+ConstraintsTestData::ConstraintsTestData(const std::string &title,
+ int numAtoms, std::vector<real> masses,
+ std::vector<int> constraints, std::vector<real> constraintsR0,
+ bool computeVirial, tensor virialScaledRef,
+ bool compute_dHdLambda, float dHdLambdaRef,
+ real initialTime, real timestep,
+ const std::vector<RVec> &x, const std::vector<RVec> &xPrime, const std::vector<RVec> &v,
+ real shakeTolerance, gmx_bool shakeUseSOR,
+ int lincsNumIterations, int lincsExpansionOrder, real lincsWarnAngle)
{
- public:
- //! Human-friendly name for a system
- std::string title_;
- //! Number of atoms
- int numAtoms_;
- //! Topology
- gmx_mtop_t mtop_;
- //! Masses
- std::vector<real> masses_;
- //! Inverse masses
- std::vector<real> invmass_;
- //! Communication record
- t_commrec cr_;
- //! Input record (info that usually in .mdp file)
- t_inputrec ir_;
- //! Local topology
- t_idef idef_;
- //! MD atoms
- t_mdatoms md_;
- //! Multisim data
- gmx_multisim_t ms_;
- //! Computational time array (normally used to benchmark performance)
- t_nrnb nrnb_;
-
- //! Inverse timestep
- real invdt_;
- //! Number of flexible constraints
- int nflexcon_ = 0;
- //! Whether the virial should be computed
- bool computeVirial_;
- //! Scaled virial
- tensor virialScaled_;
- //! Scaled virial (reference values)
- tensor virialScaledRef_;
- //! If the free energy is computed
- bool compute_dHdLambda_;
- //! For free energy computation
- real dHdLambda_;
- //! For free energy computation (reference value)
- real dHdLambdaRef_;
-
- //! Coordinates before the timestep
- PaddedVector<RVec> x_;
- //! Coordinates after timestep, output for the constraints
- PaddedVector<RVec> xPrime_;
- //! Backup for coordinates (for reset)
- PaddedVector<RVec> xPrime0_;
- //! Intermediate set of coordinates (normally used for projection correction)
- PaddedVector<RVec> xPrime2_;
- //! Velocities
- PaddedVector<RVec> v_;
- //! Backup for velocities (for reset)
- PaddedVector<RVec> v0_;
-
- //! Constraints data (type1-i1-j1-type2-i2-j2-...)
- std::vector<int> constraints_;
- //! Target lengths for all constraint types
- std::vector<real> constraintsR0_;
-
- /*! \brief
- * Constructor for the object with all parameters and variables needed by constraints algorithms.
- *
- * This constructor assembles stubs for all the data structures, required to initialize
- * and apply LINCS and SHAKE constraints. The coordinates and velocities before constraining
- * are saved to allow for reset. The constraints data are stored for testing after constraints
- * were applied.
- *
- * \param[in] title Human-friendly name of the system.
- * \param[in] numAtoms Number of atoms in the system.
- * \param[in] masses Atom masses. Size of this vector should be equal to numAtoms.
- * \param[in] constraints List of constraints, organized in triples of integers.
- * First integer is the index of type for a constraint, second
- * and third are the indices of constrained atoms. The types
- * of constraints should be sequential but not necessarily
- * start from zero (which is the way they normally are in
- * GROMACS).
- * \param[in] constraintsR0 Target values for bond lengths for bonds of each type. The
- * size of this vector should be equal to the total number of
- * unique types in constraints vector.
- * \param[in] computeVirial Whether the virial should be computed.
- * \param[in] virialScaledRef Reference values for scaled virial tensor.
- * \param[in] compute_dHdLambda Whether free energy should be computed.
- * \param[in] dHdLambdaRef Reference value for dHdLambda.
- * \param[in] initialTime Initial time.
- * \param[in] timestep Timestep.
- * \param[in] x Coordinates before integration step.
- * \param[in] xPrime Coordinates after integration step, but before constraining.
- * \param[in] v Velocities before constraining.
- * \param[in] shakeTolerance Target tolerance for SHAKE.
- * \param[in] shakeUseSOR Use successive over-relaxation method for SHAKE iterations.
- * The general formula is:
- * x_n+1 = (1-omega)*x_n + omega*f(x_n),
- * where omega = 1 if SOR is off and may be < 1 if SOR is on.
- * \param[in] lincsNumIterations Number of iterations used to compute the inverse matrix.
- * \param[in] lincsExpansionOrder The order for algorithm that adjusts the direction of the
- * bond after constraints are applied.
- * \param[in] lincsWarnAngle The threshold value for the change in bond angle. When
- * exceeded the program will issue a warning.
- *
- */
- ConstraintsTestData(const std::string &title,
- int numAtoms, std::vector<real> masses,
- std::vector<int> constraints, std::vector<real> constraintsR0,
- bool computeVirial, tensor virialScaledRef,
- bool compute_dHdLambda, float dHdLambdaRef,
- real initialTime, real timestep,
- const std::vector<RVec> &x, const std::vector<RVec> &xPrime, const std::vector<RVec> &v,
- real shakeTolerance, gmx_bool shakeUseSOR,
- int lincsNumIterations, int lincsExpansionOrder, real lincsWarnAngle)
+ // This is to trick Gerrit
+ {
{
title_ = title; // Human-friendly name of the system
numAtoms_ = numAtoms; // Number of atoms
ir_.nProjOrder = lincsExpansionOrder;
ir_.LincsWarnAngle = lincsWarnAngle;
}
+ }
+}
- /*! \brief
- * Reset the data structure so it can be reused.
- *
- * Set the coordinates and velocities back to their values before
- * constraining. The scaled virial tensor and dHdLambda are zeroed.
- *
- */
- void reset()
- {
- xPrime_ = xPrime0_;
- xPrime2_ = xPrime0_;
- v_ = v0_;
+/*! \brief
+ * Reset the data structure so it can be reused.
+ *
+ * Set the coordinates and velocities back to their values before
+ * constraining. The scaled virial tensor and dHdLambda are zeroed.
+ *
+ */
+void ConstraintsTestData::reset()
+{
+ xPrime_ = xPrime0_;
+ xPrime2_ = xPrime0_;
+ v_ = v0_;
- if (computeVirial_)
+ if (computeVirial_)
+ {
+ for (int i = 0; i < DIM; i++)
+ {
+ for (int j = 0; j < DIM; j++)
{
- for (int i = 0; i < DIM; i++)
- {
- for (int j = 0; j < DIM; j++)
- {
- virialScaled_[i][j] = 0;
- }
- }
+ virialScaled_[i][j] = 0;
}
- dHdLambda_ = 0;
}
+ }
+ dHdLambda_ = 0;
+}
- /*! \brief
- * Cleaning up the memory.
- */
- ~ConstraintsTestData()
- {
- sfree(idef_.il[F_CONSTR].iatoms);
- sfree(idef_.iparams);
- }
+/*! \brief
+ * Cleaning up the memory.
+ */
+ConstraintsTestData::~ConstraintsTestData()
+{
+ sfree(idef_.il[F_CONSTR].iatoms);
+ sfree(idef_.iparams);
+}
-};
+namespace
+{
/*! \brief The two-dimensional parameter space for test.
*
*/
typedef std::tuple<std::string, std::string> ConstraintsTestParameters;
-/*! \brief Names of all availible algorithms
- */
-static std::vector<std::string> algorithmsNames;
+//! Names of all availible algorithms
+std::vector<std::string> algorithmsNames;
-/*! \brief Method that fills and returns algorithmNames to the test macros.
- *
- */
-static std::vector<std::string> getAlgorithmsNames()
+//! Method that fills and returns algorithmNames to the test macros.
+std::vector<std::string> getAlgorithmsNames()
{
algorithmsNames.emplace_back("SHAKE");
algorithmsNames.emplace_back("LINCS");
algorithms_["SHAKE"] = applyShake;
// LINCS
algorithms_["LINCS"] = applyLincs;
- // LINCS using CUDA (will be called only if CUDA is available)
+ // LINCS using CUDA (will only be called if CUDA is available)
algorithms_["LINCS_CUDA"] = applyLincsCuda;
}
- /*! \brief
- * Initialize and apply SHAKE constraints.
- *
- * \param[in] testData Test data structure.
- * \param[in] pbc Periodic boundary data (not used in SHAKE).
- */
- static void applyShake(ConstraintsTestData *testData, t_pbc gmx_unused pbc)
- {
- shakedata* shaked = shake_init();
- make_shake_sblock_serial(shaked, &testData->idef_, testData->md_);
- bool success = constrain_shake(
- nullptr,
- shaked,
- testData->invmass_.data(),
- testData->idef_,
- testData->ir_,
- as_rvec_array(testData->x_.data()),
- as_rvec_array(testData->xPrime_.data()),
- as_rvec_array(testData->xPrime2_.data()),
- &testData->nrnb_,
- testData->md_.lambda,
- &testData->dHdLambda_,
- testData->invdt_,
- as_rvec_array(testData->v_.data()),
- testData->computeVirial_,
- testData->virialScaled_,
- false,
- gmx::ConstraintVariable::Positions);
- EXPECT_TRUE(success) << "Test failed with a false return value in SHAKE.";
- done_shake(shaked);
- }
-
- /*! \brief
- * Initialize and apply LINCS constraints.
- *
- * \param[in] testData Test data structure.
- * \param[in] pbc Periodic boundary data.
- */
- static void applyLincs(ConstraintsTestData *testData, t_pbc pbc)
- {
-
- Lincs *lincsd;
- int maxwarn = 100;
- int warncount_lincs = 0;
- gmx_omp_nthreads_set(emntLINCS, 1);
-
- // Make blocka structure for faster LINCS setup
- std::vector<t_blocka> at2con_mt;
- at2con_mt.reserve(testData->mtop_.moltype.size());
- for (const gmx_moltype_t &moltype : testData->mtop_.moltype)
- {
- // This function is in constr.cpp
- at2con_mt.push_back(make_at2con(moltype,
- testData->mtop_.ffparams.iparams,
- flexibleConstraintTreatment(EI_DYNAMICS(testData->ir_.eI))));
- }
- // Initialize LINCS
- lincsd = init_lincs(nullptr, testData->mtop_,
- testData->nflexcon_, at2con_mt,
- false,
- testData->ir_.nLincsIter, testData->ir_.nProjOrder);
- set_lincs(testData->idef_, testData->md_, EI_DYNAMICS(testData->ir_.eI), &testData->cr_, lincsd);
-
- // Evaluate constraints
- bool sucess = constrain_lincs(false, testData->ir_, 0, lincsd, testData->md_,
- &testData->cr_,
- &testData->ms_,
- as_rvec_array(testData->x_.data()),
- as_rvec_array(testData->xPrime_.data()),
- as_rvec_array(testData->xPrime2_.data()),
- pbc.box, &pbc,
- testData->md_.lambda, &testData->dHdLambda_,
- testData->invdt_,
- as_rvec_array(testData->v_.data()),
- testData->computeVirial_, testData->virialScaled_,
- gmx::ConstraintVariable::Positions,
- &testData->nrnb_,
- maxwarn, &warncount_lincs);
- EXPECT_TRUE(sucess) << "Test failed with a false return value in LINCS.";
- EXPECT_EQ(warncount_lincs, 0) << "There were warnings in LINCS.";
- for (unsigned int i = 0; i < testData->mtop_.moltype.size(); i++)
- {
- sfree(at2con_mt.at(i).index);
- sfree(at2con_mt.at(i).a);
- }
- done_lincs(lincsd);
- }
-
- /*! \brief
- * Initialize and apply LINCS constraints on CUDA-enabled GPU.
- *
- * \param[in] testData Test data structure.
- * \param[in] pbc Periodic boundary data.
- */
- static void applyLincsCuda(ConstraintsTestData *testData, t_pbc pbc)
- {
- std::string errorMessage;
- GMX_RELEASE_ASSERT(GMX_GPU == GMX_GPU_CUDA,
- "The test for CUDA version of LINCS was called non-CUDA build.");
- GMX_RELEASE_ASSERT(canDetectGpus(&errorMessage),
- "The test for CUDA version of LINCS was called on host that is not CUDA capable.");
-
- auto lincsCuda = std::make_unique<LincsCuda>(testData->ir_.nLincsIter,
- testData->ir_.nProjOrder);
- lincsCuda->set(testData->idef_, testData->md_);
- lincsCuda->setPbc(&pbc);
- lincsCuda->copyApplyCopy(testData->numAtoms_,
- as_rvec_array(testData->x_.data()),
- as_rvec_array(testData->xPrime_.data()),
- true,
- as_rvec_array(testData->v_.data()),
- testData->invdt_,
- testData->computeVirial_,
- testData->virialScaled_);
- }
-
/*! \brief
* The test on the final length of constrained bonds.
*
::testing::Combine(::testing::Values("PBCNone", "PBCXYZ"),
::testing::ValuesIn(getAlgorithmsNames())));
+} // namespace
} // namespace test
} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Function to run SHAKE and LINCS on CPU.
+ *
+ * Functions used in the test to apply constraints on the test data:
+ * CPU-based implementation and a stub for GPU-based implementation.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ * \ingroup module_mdlib
+ */
+
+#include "gmxpre.h"
+
+#include "constr_impl.h"
+
+#include "config.h"
+
+#include <assert.h>
+
+#include <cmath>
+
+#include <algorithm>
+#include <unordered_map>
+#include <vector>
+
+#include <gtest/gtest.h>
+
+#include "gromacs/math/paddedvector.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/lincs.h"
+#include "gromacs/mdlib/shake.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/unique_cptr.h"
+
+#include "testutils/testasserts.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/*! \brief
+ * Initialize and apply SHAKE constraints.
+ *
+ * \param[in] testData Test data structure.
+ * \param[in] pbc Periodic boundary data.
+ */
+void applyShake(ConstraintsTestData *testData, t_pbc gmx_unused pbc)
+{
+ shakedata* shaked = shake_init();
+ make_shake_sblock_serial(shaked, &testData->idef_, testData->md_);
+ bool success = constrain_shake(
+ nullptr,
+ shaked,
+ testData->invmass_.data(),
+ testData->idef_,
+ testData->ir_,
+ as_rvec_array(testData->x_.data()),
+ as_rvec_array(testData->xPrime_.data()),
+ as_rvec_array(testData->xPrime2_.data()),
+ &testData->nrnb_,
+ testData->md_.lambda,
+ &testData->dHdLambda_,
+ testData->invdt_,
+ as_rvec_array(testData->v_.data()),
+ testData->computeVirial_,
+ testData->virialScaled_,
+ false,
+ gmx::ConstraintVariable::Positions);
+ EXPECT_TRUE(success) << "Test failed with a false return value in SHAKE.";
+ done_shake(shaked);
+}
+
+/*! \brief
+ * Initialize and apply LINCS constraints.
+ *
+ * \param[in] testData Test data structure.
+ * \param[in] pbc Periodic boundary data.
+ */
+void applyLincs(ConstraintsTestData *testData, t_pbc pbc)
+{
+
+ Lincs *lincsd;
+ int maxwarn = 100;
+ int warncount_lincs = 0;
+ gmx_omp_nthreads_set(emntLINCS, 1);
+
+ // Make blocka structure for faster LINCS setup
+ std::vector<t_blocka> at2con_mt;
+ at2con_mt.reserve(testData->mtop_.moltype.size());
+ for (const gmx_moltype_t &moltype : testData->mtop_.moltype)
+ {
+ // This function is in constr.cpp
+ at2con_mt.push_back(make_at2con(moltype,
+ testData->mtop_.ffparams.iparams,
+ flexibleConstraintTreatment(EI_DYNAMICS(testData->ir_.eI))));
+ }
+ // Initialize LINCS
+ lincsd = init_lincs(nullptr, testData->mtop_,
+ testData->nflexcon_, at2con_mt,
+ false,
+ testData->ir_.nLincsIter, testData->ir_.nProjOrder);
+ set_lincs(testData->idef_, testData->md_, EI_DYNAMICS(testData->ir_.eI), &testData->cr_, lincsd);
+
+ // Evaluate constraints
+ bool success = constrain_lincs(false, testData->ir_, 0, lincsd, testData->md_,
+ &testData->cr_,
+ &testData->ms_,
+ as_rvec_array(testData->x_.data()),
+ as_rvec_array(testData->xPrime_.data()),
+ as_rvec_array(testData->xPrime2_.data()),
+ pbc.box, &pbc,
+ testData->md_.lambda, &testData->dHdLambda_,
+ testData->invdt_,
+ as_rvec_array(testData->v_.data()),
+ testData->computeVirial_, testData->virialScaled_,
+ gmx::ConstraintVariable::Positions,
+ &testData->nrnb_,
+ maxwarn, &warncount_lincs);
+ EXPECT_TRUE(success) << "Test failed with a false return value in LINCS.";
+ EXPECT_EQ(warncount_lincs, 0) << "There were warnings in LINCS.";
+ for (unsigned int i = 0; i < testData->mtop_.moltype.size(); i++)
+ {
+ sfree(at2con_mt.at(i).index);
+ sfree(at2con_mt.at(i).a);
+ }
+ done_lincs(lincsd);
+}
+
+#if GMX_GPU != GMX_GPU_CUDA
+/*! \brief
+ * Stub for LINCS constraints on CUDA-enabled GPU to satisfy compiler.
+ *
+ * \param[in] testData Test data structure.
+ * \param[in] pbc Periodic boundary data.
+ */
+void applyLincsCuda(ConstraintsTestData gmx_unused *testData, t_pbc gmx_unused pbc)
+{
+ FAIL() << "Dummy LINCS CUDA function was called instead of the real one.";
+}
+#endif
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief Subroutines to run LINCS on GPU
+ *
+ * Copies data to GPU, runs LINCS and copies the results back.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ * \ingroup module_mdlib
+ */
+#include "gmxpre.h"
+
+#include "constr_impl.h"
+
+#include <assert.h>
+
+#include <cmath>
+
+#include <algorithm>
+#include <unordered_map>
+#include <vector>
+
+#include "gromacs/gpu_utils/devicebuffer.cuh"
+#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/lincs_cuda.cuh"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/utility/unique_cptr.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/*! \brief
+ * Initialize and apply LINCS constraints on CUDA-enabled GPU.
+ *
+ * \param[in] testData Test data structure.
+ * \param[in] pbc Periodic boundary data.
+ */
+void applyLincsCuda(ConstraintsTestData *testData, t_pbc pbc)
+{
+ auto lincsCuda = std::make_unique<LincsCuda>(testData->ir_.nLincsIter,
+ testData->ir_.nProjOrder);
+
+ bool updateVelocities = true;
+ int numAtoms = testData->numAtoms_;
+ float3 *d_x, *d_xp, *d_v;
+
+ lincsCuda->set(testData->idef_, testData->md_);
+ lincsCuda->setPbc(&pbc);
+
+ allocateDeviceBuffer(&d_x, numAtoms, nullptr);
+ allocateDeviceBuffer(&d_xp, numAtoms, nullptr);
+ allocateDeviceBuffer(&d_v, numAtoms, nullptr);
+
+ copyToDeviceBuffer(&d_x, (float3*)(testData->x_.data()), 0, numAtoms, nullptr, GpuApiCallBehavior::Sync, nullptr);
+ copyToDeviceBuffer(&d_xp, (float3*)(testData->xPrime_.data()), 0, numAtoms, nullptr, GpuApiCallBehavior::Sync, nullptr);
+ if (updateVelocities)
+ {
+ copyToDeviceBuffer(&d_v, (float3*)(testData->v_.data()), 0, numAtoms, nullptr, GpuApiCallBehavior::Sync, nullptr);
+ }
+ lincsCuda->apply(d_x, d_xp,
+ updateVelocities, d_v, testData->invdt_,
+ testData->computeVirial_, testData->virialScaled_);
+
+ copyFromDeviceBuffer((float3*)(testData->xPrime_.data()), &d_xp, 0, numAtoms, nullptr, GpuApiCallBehavior::Sync, nullptr);
+ if (updateVelocities)
+ {
+ copyFromDeviceBuffer((float3*)(testData->v_.data()), &d_v, 0, numAtoms, nullptr, GpuApiCallBehavior::Sync, nullptr);
+ }
+
+ freeDeviceBuffer(&d_x);
+ freeDeviceBuffer(&d_xp);
+ freeDeviceBuffer(&d_v);
+}
+
+} // namespace test
+} // namespace gmx
--- /dev/null
+/*
+ * This file is part of the GROMACS molecular simulation package.
+ *
+ * Copyright (c) 2018,2019, by the GROMACS development team, led by
+ * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
+ * and including many others, as listed in the AUTHORS file in the
+ * top-level source directory and at http://www.gromacs.org.
+ *
+ * GROMACS is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ *
+ * GROMACS is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public
+ * License along with GROMACS; if not, see
+ * http://www.gnu.org/licenses, or write to the Free Software Foundation,
+ * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+ *
+ * If you want to redistribute modifications to GROMACS, please
+ * consider that scientific software is very special. Version
+ * control is crucial - bugs must be traceable. We will be happy to
+ * consider code for inclusion in the official distribution, but
+ * derived work must not be called official GROMACS. Details are found
+ * in the README & COPYING files - if they are missing, get the
+ * official version at http://www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the research papers on the package. Check out http://www.gromacs.org.
+ */
+/*! \internal \file
+ * \brief SHAKE and LINCS tests header.
+ *
+ * Contains description and constructor for the test data accumulating object,
+ * declares CPU- and GPU-based functions used to apply SHAKE or LINCS on the
+ * test data.
+ *
+ * \author Artem Zhmurov <zhmurov@gmail.com>
+ * \ingroup module_mdlib
+ */
+
+#ifndef GMX_MDLIB_TESTS_CONSTR_IMPL_H
+#define GMX_MDLIB_TESTS_CONSTR_IMPL_H
+
+#include "gmxpre.h"
+
+#include <assert.h>
+
+#include <cmath>
+
+#include <algorithm>
+#include <unordered_map>
+#include <vector>
+
+#include "gromacs/fileio/gmxfio.h"
+#include "gromacs/gmxlib/nrnb.h"
+#include "gromacs/gmxlib/nonbonded/nonbonded.h"
+#include "gromacs/gpu_utils/gpu_utils.h"
+#include "gromacs/math/paddedvector.h"
+#include "gromacs/math/vec.h"
+#include "gromacs/math/vectypes.h"
+#include "gromacs/mdlib/constr.h"
+#include "gromacs/mdlib/gmx_omp_nthreads.h"
+#include "gromacs/mdlib/lincs.h"
+#include "gromacs/mdlib/shake.h"
+#include "gromacs/mdrunutility/multisim.h"
+#include "gromacs/mdtypes/commrec.h"
+#include "gromacs/mdtypes/inputrec.h"
+#include "gromacs/mdtypes/mdatom.h"
+#include "gromacs/pbcutil/pbc.h"
+#include "gromacs/topology/block.h"
+#include "gromacs/topology/idef.h"
+#include "gromacs/topology/ifunc.h"
+#include "gromacs/topology/topology.h"
+#include "gromacs/utility/smalloc.h"
+#include "gromacs/utility/stringutil.h"
+#include "gromacs/utility/unique_cptr.h"
+
+namespace gmx
+{
+namespace test
+{
+
+/* \brief
+ * Constraints test data structure.
+ *
+ * Structure to collect all the necessary data, including system coordinates and topology,
+ * constraints information, etc. The structure can be reset and reused.
+ */
+class ConstraintsTestData
+{
+ public:
+ //! Human-friendly name for a system
+ std::string title_;
+ //! Number of atoms
+ int numAtoms_;
+ //! Topology
+ gmx_mtop_t mtop_;
+ //! Masses
+ std::vector<real> masses_;
+ //! Inverse masses
+ std::vector<real> invmass_;
+ //! Communication record
+ t_commrec cr_;
+ //! Input record (info that usually in .mdp file)
+ t_inputrec ir_;
+ //! Local topology
+ t_idef idef_;
+ //! MD atoms
+ t_mdatoms md_;
+ //! Multisim data
+ gmx_multisim_t ms_;
+ //! Computational time array (normally used to benchmark performance)
+ t_nrnb nrnb_;
+
+ //! Inverse timestep
+ real invdt_;
+ //! Number of flexible constraints
+ int nflexcon_ = 0;
+ //! Whether the virial should be computed
+ bool computeVirial_;
+ //! Scaled virial
+ tensor virialScaled_;
+ //! Scaled virial (reference values)
+ tensor virialScaledRef_;
+ //! If the free energy is computed
+ bool compute_dHdLambda_;
+ //! For free energy computation
+ real dHdLambda_;
+ //! For free energy computation (reference value)
+ real dHdLambdaRef_;
+
+ //! Coordinates before the timestep
+ PaddedVector<RVec> x_;
+ //! Coordinates after timestep, output for the constraints
+ PaddedVector<RVec> xPrime_;
+ //! Backup for coordinates (for reset)
+ PaddedVector<RVec> xPrime0_;
+ //! Intermediate set of coordinates (normally used for projection correction)
+ PaddedVector<RVec> xPrime2_;
+ //! Velocities
+ PaddedVector<RVec> v_;
+ //! Backup for velocities (for reset)
+ PaddedVector<RVec> v0_;
+
+ //! Constraints data (type1-i1-j1-type2-i2-j2-...)
+ std::vector<int> constraints_;
+ //! Target lengths for all constraint types
+ std::vector<real> constraintsR0_;
+
+ /*! \brief
+ * Constructor for the object with all parameters and variables needed by constraints algorithms.
+ *
+ * This constructor assembles stubs for all the data structures, required to initialize
+ * and apply LINCS and SHAKE constraints. The coordinates and velocities before constraining
+ * are saved to allow for reset. The constraints data are stored for testing after constraints
+ * were applied.
+ *
+ * \param[in] title Human-friendly name of the system.
+ * \param[in] numAtoms Number of atoms in the system.
+ * \param[in] masses Atom masses. Size of this vector should be equal to numAtoms.
+ * \param[in] constraints List of constraints, organized in triples of integers.
+ * First integer is the index of type for a constraint, second
+ * and third are the indices of constrained atoms. The types
+ * of constraints should be sequential but not necessarily
+ * start from zero (which is the way they normally are in
+ * GROMACS).
+ * \param[in] constraintsR0 Target values for bond lengths for bonds of each type. The
+ * size of this vector should be equal to the total number of
+ * unique types in constraints vector.
+ * \param[in] computeVirial Whether the virial should be computed.
+ * \param[in] virialScaledRef Reference values for scaled virial tensor.
+ * \param[in] compute_dHdLambda Whether free energy should be computed.
+ * \param[in] dHdLambdaRef Reference value for dHdLambda.
+ * \param[in] initialTime Initial time.
+ * \param[in] timestep Timestep.
+ * \param[in] x Coordinates before integration step.
+ * \param[in] xPrime Coordinates after integration step, but before constraining.
+ * \param[in] v Velocities before constraining.
+ * \param[in] shakeTolerance Target tolerance for SHAKE.
+ * \param[in] shakeUseSOR Use successive over-relaxation method for SHAKE iterations.
+ * The general formula is:
+ * x_n+1 = (1-omega)*x_n + omega*f(x_n),
+ * where omega = 1 if SOR is off and may be < 1 if SOR is on.
+ * \param[in] lincsNumIterations Number of iterations used to compute the inverse matrix.
+ * \param[in] lincsExpansionOrder The order for algorithm that adjusts the direction of the
+ * bond after constraints are applied.
+ * \param[in] lincsWarnAngle The threshold value for the change in bond angle. When
+ * exceeded the program will issue a warning.
+ *
+ */
+ ConstraintsTestData(const std::string &title,
+ int numAtoms, std::vector<real> masses,
+ std::vector<int> constraints, std::vector<real> constraintsR0,
+ bool computeVirial, tensor virialScaledRef,
+ bool compute_dHdLambda, float dHdLambdaRef,
+ real initialTime, real timestep,
+ const std::vector<RVec> &x, const std::vector<RVec> &xPrime, const std::vector<RVec> &v,
+ real shakeTolerance, gmx_bool shakeUseSOR,
+ int lincsNumIterations, int lincsExpansionOrder, real lincsWarnAngle);
+
+ /*! \brief
+ * Reset the data structure so it can be reused.
+ *
+ * Set the coordinates and velocities back to their values before
+ * constraining. The scaled virial tensor and dHdLambda are zeroed.
+ *
+ */
+ void reset();
+
+ /*! \brief
+ * Cleaning up the memory.
+ */
+ ~ConstraintsTestData();
+};
+
+/*! \brief Apply SHAKE constraints to the test data.
+ */
+void applyShake(ConstraintsTestData *testData, t_pbc pbc);
+/*! \brief Apply LINCS constraints to the test data.
+ */
+void applyLincs(ConstraintsTestData *testData, t_pbc pbc);
+/*! \brief Apply CUDA version of LINCS constraints to the test data.
+ *
+ * All the data is copied to the GPU device, then LINCS is applied and
+ * the resulting coordinates are copied back.
+ */
+void applyLincsCuda(ConstraintsTestData *testData, t_pbc pbc);
+
+} // namespace test
+} // namespace gmx
+
+#endif // GMX_MDLIB_TESTS_CONSTR_IMPL_H
#include "gromacs/gpu_utils/gputraits.cuh"
#include "gromacs/gpu_utils/vectype_ops.cuh"
#include "gromacs/math/vec.h"
+#include "gromacs/mdlib/lincs_cuda.cuh"
#include "gromacs/mdlib/update_constrain_cuda.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/pbcutil/pbc_aiuc_cuda.cuh"
#include "leapfrog_cuda_impl.h"
-#include "lincs_cuda_impl.h"
#include "settle_cuda_impl.h"
namespace gmx
GMX_RELEASE_ASSERT(numAtoms == mtop.natoms, "State and topology number of atoms should be the same.");
integrator_ = std::make_unique<LeapFrogCuda::Impl>();
- lincsCuda_ = std::make_unique<LincsCuda::Impl>(ir.nLincsIter, ir.nProjOrder);
+ lincsCuda_ = std::make_unique<LincsCuda>(ir.nLincsIter, ir.nProjOrder);
settleCuda_ = std::make_unique<SettleCuda::Impl>(mtop);
}
#ifndef GMX_MDLIB_UPDATE_CONSTRAIN_CUDA_IMPL_H
#define GMX_MDLIB_UPDATE_CONSTRAIN_CUDA_IMPL_H
+#include "gromacs/mdlib/lincs_cuda.cuh"
#include "gromacs/mdlib/update_constrain_cuda.h"
#include "gromacs/mdtypes/inputrec.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/idef.h"
#include "leapfrog_cuda_impl.h"
-#include "lincs_cuda_impl.h"
#include "settle_cuda_impl.h"
namespace gmx
//! Leap-Frog integrator
std::unique_ptr<LeapFrogCuda::Impl> integrator_;
//! LINCS CUDA object to use for non-water constraints
- std::unique_ptr<LincsCuda::Impl> lincsCuda_;
+ std::unique_ptr<LincsCuda> lincsCuda_;
//! SETTLE CUDA object for water constrains
std::unique_ptr<SettleCuda::Impl> settleCuda_;
* \param[out] pbcAiuc Pointer to PbcAiuc structure to be initialized.
*
*/
-static void setPbcAiuc(int numPbcDim,
- const matrix box,
- PbcAiuc *pbcAiuc)
+static inline
+void setPbcAiuc(int numPbcDim,
+ const matrix box,
+ PbcAiuc *pbcAiuc)
{
pbcAiuc->invBoxDiagZ = 0.0f;
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