struct SettleParameters
{
//! Mass of oxygen atom
- float mO;
+ float mO;
//! Mass of hydrogen atom
- float mH;
+ float mH;
//! Relative hydrogen mass (i.e. mH/(mO+2*mH))
- float wh;
+ float wh;
//! Target distance between oxygen and hydrogen
- float dOH;
+ float dOH;
//! Target distance between hydrogen atoms
- float dHH;
+ float dHH;
//! Double relative H mass times height of the H-O-H triangle.
- float ra;
+ float ra;
//! Height of the H-O-H triangle minus ra.
- float rb;
+ float rb;
//! Half the H-H distance.
- float rc;
+ float rc;
//! Reciprocal H-H distance
- float irc2;
+ float irc2;
/* Parameters below are used for projection */
//! Reciprocal oxygen mass
- float imO;
+ float imO;
//! Reciprocal hydrogen mass
- float imH;
+ float imH;
//! Reciprocal O-H distance
- float invdOH;
+ float invdOH;
//! Reciprocal H-H distance (again)
- float invdHH;
+ float invdHH;
//! Reciprocal projection matrix
- matrix invmat;
+ matrix invmat;
};
/*! \brief Initializes a projection matrix.
* \param[in] dHH Target H-H bond length
* \param[out] inverseCouplingMatrix Inverse bond coupling matrix for the projection version of SETTLE
*/
-static void initializeProjectionMatrix(const real invmO, const real invmH,
- const real dOH, const real dHH,
- matrix inverseCouplingMatrix)
+static void initializeProjectionMatrix(const real invmO,
+ const real invmH,
+ const real dOH,
+ const real dHH,
+ matrix inverseCouplingMatrix)
{
// We normalize the inverse masses with invmO for the matrix inversion.
// so we can keep using masses of almost zero for frozen particles,
// without running out of the float range in invertMatrix.
double invmORelative = 1.0;
- double invmHRelative = invmH/static_cast<double>(invmO);
- double distanceRatio = dHH/static_cast<double>(dOH);
+ double invmHRelative = invmH / static_cast<double>(invmO);
+ double distanceRatio = dHH / static_cast<double>(dOH);
/* Construct the constraint coupling matrix */
matrix mat;
mat[0][0] = invmORelative + invmHRelative;
- mat[0][1] = invmORelative*(1.0 - 0.5*gmx::square(distanceRatio));
- mat[0][2] = invmHRelative*0.5*distanceRatio;
+ mat[0][1] = invmORelative * (1.0 - 0.5 * gmx::square(distanceRatio));
+ mat[0][2] = invmHRelative * 0.5 * distanceRatio;
mat[1][1] = mat[0][0];
mat[1][2] = mat[0][2];
mat[2][2] = invmHRelative + invmHRelative;
gmx::invertMatrix(mat, inverseCouplingMatrix);
- msmul(inverseCouplingMatrix, 1/invmO, inverseCouplingMatrix);
+ msmul(inverseCouplingMatrix, 1 / invmO, inverseCouplingMatrix);
}
/*! \brief Initializes settle parameters.
* \param[in] dHH Target H-H bond length
*/
gmx_unused // Temporary solution to keep clang happy
-static void initSettleParameters(SettleParameters *p,
- const real mO, const real mH,
- const real dOH, const real dHH)
+ static void
+ initSettleParameters(SettleParameters* p, const real mO, const real mH, const real dOH, const real dHH)
{
// We calculate parameters in double precision to minimize errors.
// The velocity correction applied during SETTLE coordinate constraining
// depending on what the compiler does with the code.
double wohh;
- real invmO = 1.0/mO;
- real invmH = 1.0/mH;
+ real invmO = 1.0 / mO;
+ real invmH = 1.0 / mH;
p->mO = mO;
p->mH = mH;
- wohh = mO + 2.0*mH;
- p->wh = mH/wohh;
+ wohh = mO + 2.0 * mH;
+ p->wh = mH / wohh;
p->dOH = dOH;
p->dHH = dHH;
- double rc = dHH/2.0;
- double ra = 2.0*mH*std::sqrt(dOH*dOH - rc*rc)/wohh;
- p->rb = std::sqrt(dOH*dOH - rc*rc) - ra;
+ double rc = dHH / 2.0;
+ double ra = 2.0 * mH * std::sqrt(dOH * dOH - rc * rc) / wohh;
+ p->rb = std::sqrt(dOH * dOH - rc * rc) - ra;
p->rc = rc;
p->ra = ra;
- p->irc2 = 1.0/dHH;
+ p->irc2 = 1.0 / dHH;
// For projection: inverse masses and coupling matrix inversion
- p->imO = invmO;
- p->imH = invmH;
+ p->imO = invmO;
+ p->imH = invmH;
- p->invdOH = 1.0/dOH;
- p->invdHH = 1.0/dHH;
+ p->invdOH = 1.0 / dOH;
+ p->invdHH = 1.0 / dHH;
initializeProjectionMatrix(invmO, invmH, dOH, dHH, p->invmat);
}
class SettleCuda
{
- public:
- /*! \brief Create SETTLE object
- *
- * Extracts masses for oxygen and hydrogen as well as the O-H and H-H target distances
- * from the topology data (mtop), check their values for consistency and calls the
- * following constructor.
- *
- * \param[in] mtop Topology of the system to gen the masses for O and H atoms and
- * target O-H and H-H distances. These values are also checked for
- * consistency.
- * \param[in] commandStream Device stream to use.
- */
- SettleCuda(const gmx_mtop_t &mtop,
- CommandStream commandStream);
+public:
+ /*! \brief Create SETTLE object
+ *
+ * Extracts masses for oxygen and hydrogen as well as the O-H and H-H target distances
+ * from the topology data (mtop), check their values for consistency and calls the
+ * following constructor.
+ *
+ * \param[in] mtop Topology of the system to gen the masses for O and H atoms and
+ * target O-H and H-H distances. These values are also checked for
+ * consistency.
+ * \param[in] commandStream Device stream to use.
+ */
+ SettleCuda(const gmx_mtop_t& mtop, CommandStream commandStream);
- ~SettleCuda();
+ ~SettleCuda();
- /*! \brief Apply SETTLE.
- *
- * Applies SETTLE to coordinates and velocities, stored on GPU. Data at pointers d_xp and
- * d_v change in the GPU memory. The results are not automatically copied back to the CPU
- * memory. Method uses this class data structures which should be updated when needed using
- * update method.
- *
- * \param[in] d_x Coordinates before timestep (in GPU memory)
- * \param[in,out] d_xp Coordinates after timestep (in GPU memory). The
- * resulting constrained coordinates will be saved here.
- * \param[in] updateVelocities If the velocities should be updated.
- * \param[in,out] d_v Velocities to update (in GPU 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 apply(const float3 *d_x,
- float3 *d_xp,
- const bool updateVelocities,
- float3 *d_v,
- const real invdt,
- const bool computeVirial,
- tensor virialScaled);
+ /*! \brief Apply SETTLE.
+ *
+ * Applies SETTLE to coordinates and velocities, stored on GPU. Data at pointers d_xp and
+ * d_v change in the GPU memory. The results are not automatically copied back to the CPU
+ * memory. Method uses this class data structures which should be updated when needed using
+ * update method.
+ *
+ * \param[in] d_x Coordinates before timestep (in GPU memory)
+ * \param[in,out] d_xp Coordinates after timestep (in GPU memory). The
+ * resulting constrained coordinates will be saved here.
+ * \param[in] updateVelocities If the velocities should be updated.
+ * \param[in,out] d_v Velocities to update (in GPU 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 apply(const float3* d_x,
+ float3* d_xp,
+ const bool updateVelocities,
+ float3* d_v,
+ const real invdt,
+ const bool computeVirial,
+ tensor virialScaled);
- /*! \brief
- * Update data-structures (e.g. after NB search step).
- *
- * Updates the constraints data and copies it to the GPU. Should be
- * called if the particles were sorted, redistributed between domains, etc.
- * Does not recycle the data preparation routines from the CPU version.
- * All three atoms from single water molecule should be handled by the same GPU.
- *
- * SETTLEs atom ID's is taken from idef.il[F_SETTLE].iatoms.
- *
- * \param[in] idef System topology
- * \param[in] md Atoms data. Can be used to update masses if needed (not used now).
- */
- void set(const t_idef &idef,
- const t_mdatoms &md);
+ /*! \brief
+ * Update data-structures (e.g. after NB search step).
+ *
+ * Updates the constraints data and copies it to the GPU. Should be
+ * called if the particles were sorted, redistributed between domains, etc.
+ * Does not recycle the data preparation routines from the CPU version.
+ * All three atoms from single water molecule should be handled by the same GPU.
+ *
+ * SETTLEs atom ID's is taken from idef.il[F_SETTLE].iatoms.
+ *
+ * \param[in] idef System topology
+ * \param[in] md Atoms data. Can be used to update masses if needed (not used now).
+ */
+ void set(const t_idef& idef, const t_mdatoms& md);
- /*! \brief
- * Update PBC data.
- *
- * Converts pbc data from t_pbc into the PbcAiuc format and stores the latter.
- *
- * \todo PBC should not be handled by constraints.
- *
- * \param[in] pbc The PBC data in t_pbc format.
- */
- void setPbc(const t_pbc *pbc);
+ /*! \brief
+ * Update PBC data.
+ *
+ * Converts pbc data from t_pbc into the PbcAiuc format and stores the latter.
+ *
+ * \todo PBC should not be handled by constraints.
+ *
+ * \param[in] pbc The PBC data in t_pbc format.
+ */
+ void setPbc(const t_pbc* pbc);
- private:
+private:
+ //! CUDA stream
+ CommandStream commandStream_;
+ //! Periodic boundary data
+ PbcAiuc pbcAiuc_;
- //! CUDA stream
- CommandStream commandStream_;
- //! Periodic boundary data
- PbcAiuc pbcAiuc_;
+ //! Scaled virial tensor (9 reals, GPU)
+ std::vector<float> h_virialScaled_;
+ //! Scaled virial tensor (9 reals, GPU)
+ float* d_virialScaled_;
- //! Scaled virial tensor (9 reals, GPU)
- std::vector<float> h_virialScaled_;
- //! Scaled virial tensor (9 reals, GPU)
- float *d_virialScaled_;
+ //! Number of settles
+ int numSettles_ = 0;
- //! Number of settles
- int numSettles_ = 0;
+ //! Indexes of atoms (.x for oxygen, .y and.z for hydrogens, CPU)
+ std::vector<int3> h_atomIds_;
+ //! Indexes of atoms (.x for oxygen, .y and.z for hydrogens, GPU)
+ int3* d_atomIds_;
+ //! Current size of the array of atom IDs
+ int numAtomIds_ = -1;
+ //! Allocated size for the array of atom IDs
+ int numAtomIdsAlloc_ = -1;
- //! Indexes of atoms (.x for oxygen, .y and.z for hydrogens, CPU)
- std::vector<int3> h_atomIds_;
- //! Indexes of atoms (.x for oxygen, .y and.z for hydrogens, GPU)
- int3 *d_atomIds_;
- //! Current size of the array of atom IDs
- int numAtomIds_ = -1;
- //! Allocated size for the array of atom IDs
- int numAtomIdsAlloc_ = -1;
-
- //! Settle parameters
- SettleParameters settleParameters_;
+ //! Settle parameters
+ SettleParameters settleParameters_;
};
} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff