*
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* Copyright (c) 2001-2004, The GROMACS development team.
- * Copyright (c) 2013,2014,2015,2016,2017,2018,2019, by the GROMACS development team, led by
+ * Copyright (c) 2013,2014,2015,2016,2017 The GROMACS development team.
+ * Copyright (c) 2018,2019,2020,2021, 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.
* 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 Implements the VirtualSitesHandler class and vsite standalone functions
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_mdlib
+ */
+
#include "gmxpre.h"
#include "vsite.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/gmx_omp_nthreads.h"
#include "gromacs/mdtypes/commrec.h"
-#include "gromacs/mdtypes/mdatom.h"
#include "gromacs/pbcutil/ishift.h"
-#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/timing/wallcycle.h"
#include "gromacs/topology/ifunc.h"
*
* Any remaining vsites are assigned to a separate master thread task.
*/
+namespace gmx
+{
-using gmx::RVec;
+//! VirialHandling is often used outside VirtualSitesHandler class members
+using VirialHandling = VirtualSitesHandler::VirialHandling;
-static void init_ilist(t_ilist *ilist)
+/*! \brief Information on PBC and domain decomposition for virtual sites
+ */
+struct DomainInfo
{
- for (int i = 0; i < F_NRE; i++)
+public:
+ //! Constructs without PBC and DD
+ DomainInfo() = default;
+
+ //! Constructs with PBC and DD, if !=nullptr
+ DomainInfo(PbcType pbcType, bool haveInterUpdateGroupVirtualSites, gmx_domdec_t* domdec) :
+ pbcType_(pbcType),
+ useMolPbc_(pbcType != PbcType::No && haveInterUpdateGroupVirtualSites),
+ domdec_(domdec)
{
- ilist[i].nr = 0;
- ilist[i].nalloc = 0;
- ilist[i].iatoms = nullptr;
}
-}
-/*! \brief List of atom indices belonging to a task */
-struct AtomIndex {
+ //! Returns whether we are using domain decomposition with more than 1 DD rank
+ bool useDomdec() const { return (domdec_ != nullptr); }
+
+ //! The pbc type
+ const PbcType pbcType_ = PbcType::No;
+ //! Whether molecules are broken over PBC
+ const bool useMolPbc_ = false;
+ //! Pointer to the domain decomposition struct, nullptr without PP DD
+ const gmx_domdec_t* domdec_ = nullptr;
+};
+
+/*! \brief List of atom indices belonging to a task
+ */
+struct AtomIndex
+{
//! List of atom indices
std::vector<int> atom;
};
-/*! \brief Data structure for thread tasks that use constructing atoms outside their own atom range */
+/*! \brief Data structure for thread tasks that use constructing atoms outside their own atom range
+ */
struct InterdependentTask
{
//! The interaction lists, only vsite entries are used
- t_ilist ilist[F_NRE];
+ InteractionLists ilist;
//! Thread/task-local force buffer
- std::vector<RVec> force;
+ std::vector<RVec> force;
//! The atom indices of the vsites of our task
- std::vector<int> vsite;
+ std::vector<int> vsite;
//! Flags if elements in force are spread to or not
- std::vector<bool> use;
+ std::vector<bool> use;
//! The number of entries set to true in use
- int nuse;
+ int nuse = 0;
//! Array of atoms indices, size nthreads, covering all nuse set elements in use
std::vector<AtomIndex> atomIndex;
//! List of tasks (force blocks) this task spread forces to
- std::vector<int> spreadTask;
+ std::vector<int> spreadTask;
//! List of tasks that write to this tasks force block range
- std::vector<int> reduceTask;
-
- InterdependentTask()
- {
- init_ilist(ilist);
- nuse = 0;
- }
+ std::vector<int> reduceTask;
};
-/*! \brief Vsite thread task data structure */
+/*! \brief Vsite thread task data structure
+ */
struct VsiteThread
{
//! Start of atom range of this task
- int rangeStart;
+ int rangeStart;
//! End of atom range of this task
- int rangeEnd;
+ int rangeEnd;
//! The interaction lists, only vsite entries are used
- t_ilist ilist[F_NRE];
+ std::array<InteractionList, F_NRE> ilist;
//! Local fshift accumulation buffer
- rvec fshift[SHIFTS];
+ std::array<RVec, c_numShiftVectors> fshift;
//! Local virial dx*df accumulation buffer
- matrix dxdf;
+ matrix dxdf;
//! Tells if interdependent task idTask should be used (in addition to the rest of this task), this bool has the same value on all threads
- bool useInterdependentTask;
+ bool useInterdependentTask;
//! Data for vsites that involve constructing atoms in the atom range of other threads/tasks
InterdependentTask idTask;
/*! \brief Constructor */
VsiteThread()
{
- rangeStart = -1;
- rangeEnd = -1;
- init_ilist(ilist);
- clear_rvecs(SHIFTS, fshift);
+ rangeStart = -1;
+ rangeEnd = -1;
+ for (auto& elem : fshift)
+ {
+ elem = { 0.0_real, 0.0_real, 0.0_real };
+ }
clear_mat(dxdf);
useInterdependentTask = false;
}
};
+
+/*! \brief Information on how the virtual site work is divided over thread tasks
+ */
+class ThreadingInfo
+{
+public:
+ //! Constructor, retrieves the number of threads to use from gmx_omp_nthreads.h
+ ThreadingInfo();
+
+ //! Returns the number of threads to use for vsite operations
+ int numThreads() const { return numThreads_; }
+
+ //! Returns the thread data for the given thread
+ const VsiteThread& threadData(int threadIndex) const { return *tData_[threadIndex]; }
+
+ //! Returns the thread data for the given thread
+ VsiteThread& threadData(int threadIndex) { return *tData_[threadIndex]; }
+
+ //! Returns the thread data for vsites that depend on non-local vsites
+ const VsiteThread& threadDataNonLocalDependent() const { return *tData_[numThreads_]; }
+
+ //! Returns the thread data for vsites that depend on non-local vsites
+ VsiteThread& threadDataNonLocalDependent() { return *tData_[numThreads_]; }
+
+ //! Set VSites and distribute VSite work over threads, should be called after DD partitioning
+ void setVirtualSites(ArrayRef<const InteractionList> ilist,
+ ArrayRef<const t_iparams> iparams,
+ int numAtoms,
+ int homenr,
+ ArrayRef<const ParticleType> ptype,
+ bool useDomdec);
+
+private:
+ //! Number of threads used for vsite operations
+ const int numThreads_;
+ //! Thread local vsites and work structs
+ std::vector<std::unique_ptr<VsiteThread>> tData_;
+ //! Work array for dividing vsites over threads
+ std::vector<int> taskIndex_;
+};
+
+/*! \brief Impl class for VirtualSitesHandler
+ */
+class VirtualSitesHandler::Impl
+{
+public:
+ //! Constructor, domdec should be nullptr without DD
+ Impl(const gmx_mtop_t& mtop,
+ gmx_domdec_t* domdec,
+ PbcType pbcType,
+ ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType);
+
+ //! Returns the number of virtual sites acting over multiple update groups
+ int numInterUpdategroupVirtualSites() const { return numInterUpdategroupVirtualSites_; }
+
+ //! Set VSites and distribute VSite work over threads, should be called after DD partitioning
+ void setVirtualSites(ArrayRef<const InteractionList> ilist,
+ int numAtoms,
+ int homenr,
+ ArrayRef<const ParticleType> ptype);
+
+ /*! \brief Create positions of vsite atoms based for the local system
+ *
+ * \param[in,out] x The coordinates
+ * \param[in,out] v The velocities, needed if operation requires it
+ * \param[in] box The box
+ * \param[in] operation Whether we calculate positions, velocities, or both
+ */
+ void construct(ArrayRef<RVec> x, ArrayRef<RVec> v, const matrix box, VSiteOperation operation) const;
+
+ /*! \brief Spread the force operating on the vsite atoms on the surrounding atoms.
+ *
+ * vsite should point to a valid object.
+ * The virialHandling parameter determines how virial contributions are handled.
+ * If this is set to Linear, shift forces are accumulated into fshift.
+ * If this is set to NonLinear, non-linear contributions are added to virial.
+ * This non-linear correction is required when the virial is not calculated
+ * afterwards from the particle position and forces, but in a different way,
+ * as for instance for the PME mesh contribution.
+ */
+ void spreadForces(ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ VirialHandling virialHandling,
+ ArrayRef<RVec> fshift,
+ matrix virial,
+ t_nrnb* nrnb,
+ const matrix box,
+ gmx_wallcycle* wcycle);
+
+private:
+ //! The number of vsites that cross update groups, when =0 no PBC treatment is needed
+ const int numInterUpdategroupVirtualSites_;
+ //! PBC and DD information
+ const DomainInfo domainInfo_;
+ //! The interaction parameters
+ const ArrayRef<const t_iparams> iparams_;
+ //! The interaction lists
+ ArrayRef<const InteractionList> ilists_;
+ //! Information for handling vsite threading
+ ThreadingInfo threadingInfo_;
+};
+
+VirtualSitesHandler::~VirtualSitesHandler() = default;
+
+int VirtualSitesHandler::numInterUpdategroupVirtualSites() const
+{
+ return impl_->numInterUpdategroupVirtualSites();
+}
+
/*! \brief Returns the sum of the vsite ilist sizes over all vsite types
*
* \param[in] ilist The interaction list
*/
-template <typename T>
-static int vsiteIlistNrCount(const T *ilist)
+static int vsiteIlistNrCount(ArrayRef<const InteractionList> ilist)
{
int nr = 0;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
return nr;
}
-static int pbc_rvec_sub(const t_pbc *pbc, const rvec xi, const rvec xj, rvec dx)
+//! Computes the distance between xi and xj, pbc is used when pbc!=nullptr
+static int pbc_rvec_sub(const t_pbc* pbc, const rvec xi, const rvec xj, rvec dx)
{
if (pbc)
{
else
{
rvec_sub(xi, xj, dx);
- return CENTRAL;
+ return c_centralShiftIndex;
}
}
+//! Returns the 1/norm(x)
+static inline real inverseNorm(const rvec x)
+{
+ return gmx::invsqrt(iprod(x, x));
+}
+
+//! Whether we're calculating the virtual site position
+enum class VSiteCalculatePosition
+{
+ Yes,
+ No
+};
+//! Whether we're calculating the virtual site velocity
+enum class VSiteCalculateVelocity
+{
+ Yes,
+ No
+};
+
+#ifndef DOXYGEN
/* Vsite construction routines */
-static void constr_vsite2(const rvec xi, const rvec xj, rvec x, real a, const t_pbc *pbc)
+// GCC 8 falsely flags unused variables if constexpr prunes a code path, fixed in GCC 9
+// https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85827
+// clang-format off
+GCC_DIAGNOSTIC_IGNORE(-Wunused-but-set-parameter)
+// clang-format on
+
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite1(const rvec xi, rvec x, const rvec vi, rvec v)
+{
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ copy_rvec(xi, x);
+ /* TOTAL: 0 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ copy_rvec(vi, v);
+ }
+}
+
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void
+constr_vsite2(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc, const rvec vi, const rvec vj, rvec v)
{
- real b = 1 - a;
+ const real b = 1 - a;
/* 1 flop */
- if (pbc)
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ if (pbc)
+ {
+ rvec dx;
+ pbc_dx_aiuc(pbc, xj, xi, dx);
+ x[XX] = xi[XX] + a * dx[XX];
+ x[YY] = xi[YY] + a * dx[YY];
+ x[ZZ] = xi[ZZ] + a * dx[ZZ];
+ }
+ else
+ {
+ x[XX] = b * xi[XX] + a * xj[XX];
+ x[YY] = b * xi[YY] + a * xj[YY];
+ x[ZZ] = b * xi[ZZ] + a * xj[ZZ];
+ /* 9 Flops */
+ }
+ /* TOTAL: 10 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
{
- rvec dx;
- pbc_dx_aiuc(pbc, xj, xi, dx);
- x[XX] = xi[XX] + a*dx[XX];
- x[YY] = xi[YY] + a*dx[YY];
- x[ZZ] = xi[ZZ] + a*dx[ZZ];
+ v[XX] = b * vi[XX] + a * vj[XX];
+ v[YY] = b * vi[YY] + a * vj[YY];
+ v[ZZ] = b * vi[ZZ] + a * vj[ZZ];
}
- else
+}
+
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void
+constr_vsite2FD(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc, const rvec vi, const rvec vj, rvec v)
+{
+ rvec xij = { 0 };
+ pbc_rvec_sub(pbc, xj, xi, xij);
+ /* 3 flops */
+
+ const real invNormXij = inverseNorm(xij);
+ const real b = a * invNormXij;
+ /* 6 + 10 flops */
+
+ if (calculatePosition == VSiteCalculatePosition::Yes)
{
- x[XX] = b*xi[XX] + a*xj[XX];
- x[YY] = b*xi[YY] + a*xj[YY];
- x[ZZ] = b*xi[ZZ] + a*xj[ZZ];
- /* 9 Flops */
+ x[XX] = xi[XX] + b * xij[XX];
+ x[YY] = xi[YY] + b * xij[YY];
+ x[ZZ] = xi[ZZ] + b * xij[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 25 flops */
}
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec_sub(vj, vi, vij);
+ const real vijDotXij = iprod(vij, xij);
- /* TOTAL: 10 flops */
+ v[XX] = vi[XX] + b * (vij[XX] - xij[XX] * vijDotXij * invNormXij * invNormXij);
+ v[YY] = vi[YY] + b * (vij[YY] - xij[YY] * vijDotXij * invNormXij * invNormXij);
+ v[ZZ] = vi[ZZ] + b * (vij[ZZ] - xij[ZZ] * vijDotXij * invNormXij * invNormXij);
+ }
}
-static void constr_vsite3(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b,
- const t_pbc *pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
{
- real c = 1 - a - b;
+ const real c = 1 - a - b;
/* 2 flops */
- if (pbc)
+ if (calculatePosition == VSiteCalculatePosition::Yes)
{
- rvec dxj, dxk;
+ if (pbc)
+ {
+ rvec dxj, dxk;
- pbc_dx_aiuc(pbc, xj, xi, dxj);
- pbc_dx_aiuc(pbc, xk, xi, dxk);
- x[XX] = xi[XX] + a*dxj[XX] + b*dxk[XX];
- x[YY] = xi[YY] + a*dxj[YY] + b*dxk[YY];
- x[ZZ] = xi[ZZ] + a*dxj[ZZ] + b*dxk[ZZ];
+ pbc_dx_aiuc(pbc, xj, xi, dxj);
+ pbc_dx_aiuc(pbc, xk, xi, dxk);
+ x[XX] = xi[XX] + a * dxj[XX] + b * dxk[XX];
+ x[YY] = xi[YY] + a * dxj[YY] + b * dxk[YY];
+ x[ZZ] = xi[ZZ] + a * dxj[ZZ] + b * dxk[ZZ];
+ }
+ else
+ {
+ x[XX] = c * xi[XX] + a * xj[XX] + b * xk[XX];
+ x[YY] = c * xi[YY] + a * xj[YY] + b * xk[YY];
+ x[ZZ] = c * xi[ZZ] + a * xj[ZZ] + b * xk[ZZ];
+ /* 15 Flops */
+ }
+ /* TOTAL: 17 flops */
}
- else
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
{
- x[XX] = c*xi[XX] + a*xj[XX] + b*xk[XX];
- x[YY] = c*xi[YY] + a*xj[YY] + b*xk[YY];
- x[ZZ] = c*xi[ZZ] + a*xj[ZZ] + b*xk[ZZ];
- /* 15 Flops */
+ v[XX] = c * vi[XX] + a * vj[XX] + b * vk[XX];
+ v[YY] = c * vi[YY] + a * vj[YY] + b * vk[YY];
+ v[ZZ] = c * vi[ZZ] + a * vj[ZZ] + b * vk[ZZ];
}
-
- /* TOTAL: 17 flops */
}
-static void constr_vsite3FD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b,
- const t_pbc *pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3FD(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
{
rvec xij, xjk, temp;
- real c;
pbc_rvec_sub(pbc, xj, xi, xij);
pbc_rvec_sub(pbc, xk, xj, xjk);
/* 6 flops */
/* temp goes from i to a point on the line jk */
- temp[XX] = xij[XX] + a*xjk[XX];
- temp[YY] = xij[YY] + a*xjk[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ];
+ temp[XX] = xij[XX] + a * xjk[XX];
+ temp[YY] = xij[YY] + a * xjk[YY];
+ temp[ZZ] = xij[ZZ] + a * xjk[ZZ];
/* 6 flops */
- c = b*gmx::invsqrt(iprod(temp, temp));
+ const real invNormTemp = inverseNorm(temp);
+ const real c = b * invNormTemp;
/* 6 + 10 flops */
- x[XX] = xi[XX] + c*temp[XX];
- x[YY] = xi[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + c*temp[ZZ];
- /* 6 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + c * temp[XX];
+ x[YY] = xi[YY] + c * temp[YY];
+ x[ZZ] = xi[ZZ] + c * temp[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 34 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vjk = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vj, vjk);
+ const rvec tempV = { vij[XX] + a * vjk[XX], vij[YY] + a * vjk[YY], vij[ZZ] + a * vjk[ZZ] };
+ const real tempDotTempV = iprod(temp, tempV);
- /* TOTAL: 34 flops */
+ v[XX] = vi[XX] + c * (tempV[XX] - temp[XX] * tempDotTempV * invNormTemp * invNormTemp);
+ v[YY] = vi[YY] + c * (tempV[YY] - temp[YY] * tempDotTempV * invNormTemp * invNormTemp);
+ v[ZZ] = vi[ZZ] + c * (tempV[ZZ] - temp[ZZ] * tempDotTempV * invNormTemp * invNormTemp);
+ }
}
-static void constr_vsite3FAD(const rvec xi, const rvec xj, const rvec xk, rvec x, real a, real b, const t_pbc *pbc)
-{
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3FAD(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
+{ // Note: a = d * cos(theta)
+ // b = d * sin(theta)
rvec xij, xjk, xp;
- real a1, b1, c1, invdij;
pbc_rvec_sub(pbc, xj, xi, xij);
pbc_rvec_sub(pbc, xk, xj, xjk);
/* 6 flops */
- invdij = gmx::invsqrt(iprod(xij, xij));
- c1 = invdij * invdij * iprod(xij, xjk);
- xp[XX] = xjk[XX] - c1*xij[XX];
- xp[YY] = xjk[YY] - c1*xij[YY];
- xp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
- a1 = a*invdij;
- b1 = b*gmx::invsqrt(iprod(xp, xp));
+ const real invdij = inverseNorm(xij);
+ const real xijDotXjk = iprod(xij, xjk);
+ const real c1 = invdij * invdij * xijDotXjk;
+ xp[XX] = xjk[XX] - c1 * xij[XX];
+ xp[YY] = xjk[YY] - c1 * xij[YY];
+ xp[ZZ] = xjk[ZZ] - c1 * xij[ZZ];
+ const real a1 = a * invdij;
+ const real invNormXp = inverseNorm(xp);
+ const real b1 = b * invNormXp;
/* 45 */
- x[XX] = xi[XX] + a1*xij[XX] + b1*xp[XX];
- x[YY] = xi[YY] + a1*xij[YY] + b1*xp[YY];
- x[ZZ] = xi[ZZ] + a1*xij[ZZ] + b1*xp[ZZ];
- /* 12 Flops */
-
- /* TOTAL: 63 flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + a1 * xij[XX] + b1 * xp[XX];
+ x[YY] = xi[YY] + a1 * xij[YY] + b1 * xp[YY];
+ x[ZZ] = xi[ZZ] + a1 * xij[ZZ] + b1 * xp[ZZ];
+ /* 12 Flops */
+ /* TOTAL: 63 flops */
+ }
+
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vjk = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vj, vjk);
+
+ const real vijDotXjkPlusXijDotVjk = iprod(vij, xjk) + iprod(xij, vjk);
+ const real xijDotVij = iprod(xij, vij);
+ const real invNormXij2 = invdij * invdij;
+
+ rvec vp = { 0 };
+ vp[XX] = vjk[XX]
+ - xij[XX] * invNormXij2
+ * (vijDotXjkPlusXijDotVjk - invNormXij2 * xijDotXjk * xijDotVij * 2)
+ - vij[XX] * xijDotXjk * invNormXij2;
+ vp[YY] = vjk[YY]
+ - xij[YY] * invNormXij2
+ * (vijDotXjkPlusXijDotVjk - invNormXij2 * xijDotXjk * xijDotVij * 2)
+ - vij[YY] * xijDotXjk * invNormXij2;
+ vp[ZZ] = vjk[ZZ]
+ - xij[ZZ] * invNormXij2
+ * (vijDotXjkPlusXijDotVjk - invNormXij2 * xijDotXjk * xijDotVij * 2)
+ - vij[ZZ] * xijDotXjk * invNormXij2;
+
+ const real xpDotVp = iprod(xp, vp);
+
+ v[XX] = vi[XX] + a1 * (vij[XX] - xij[XX] * xijDotVij * invdij * invdij)
+ + b1 * (vp[XX] - xp[XX] * xpDotVp * invNormXp * invNormXp);
+ v[YY] = vi[YY] + a1 * (vij[YY] - xij[YY] * xijDotVij * invdij * invdij)
+ + b1 * (vp[YY] - xp[YY] * xpDotVp * invNormXp * invNormXp);
+ v[ZZ] = vi[ZZ] + a1 * (vij[ZZ] - xij[ZZ] * xijDotVij * invdij * invdij)
+ + b1 * (vp[ZZ] - xp[ZZ] * xpDotVp * invNormXp * invNormXp);
+ }
}
-static void constr_vsite3OUT(const rvec xi, const rvec xj, const rvec xk, rvec x,
- real a, real b, real c, const t_pbc *pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite3OUT(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ rvec x,
+ real a,
+ real b,
+ real c,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ rvec v)
{
rvec xij, xik, temp;
cprod(xij, xik, temp);
/* 15 Flops */
- x[XX] = xi[XX] + a*xij[XX] + b*xik[XX] + c*temp[XX];
- x[YY] = xi[YY] + a*xij[YY] + b*xik[YY] + c*temp[YY];
- x[ZZ] = xi[ZZ] + a*xij[ZZ] + b*xik[ZZ] + c*temp[ZZ];
- /* 18 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + a * xij[XX] + b * xik[XX] + c * temp[XX];
+ x[YY] = xi[YY] + a * xij[YY] + b * xik[YY] + c * temp[YY];
+ x[ZZ] = xi[ZZ] + a * xij[ZZ] + b * xik[ZZ] + c * temp[ZZ];
+ /* 18 Flops */
+ /* TOTAL: 33 flops */
+ }
+
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vik = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vi, vik);
+
+ rvec temp1 = { 0 };
+ rvec temp2 = { 0 };
+ cprod(vij, xik, temp1);
+ cprod(xij, vik, temp2);
- /* TOTAL: 33 flops */
+ v[XX] = vi[XX] + a * vij[XX] + b * vik[XX] + c * (temp1[XX] + temp2[XX]);
+ v[YY] = vi[YY] + a * vij[YY] + b * vik[YY] + c * (temp1[YY] + temp2[YY]);
+ v[ZZ] = vi[ZZ] + a * vij[ZZ] + b * vik[ZZ] + c * (temp1[ZZ] + temp2[ZZ]);
+ }
}
-static void constr_vsite4FD(const rvec xi, const rvec xj, const rvec xk, const rvec xl, rvec x,
- real a, real b, real c, const t_pbc *pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite4FD(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ const rvec xl,
+ rvec x,
+ real a,
+ real b,
+ real c,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ const rvec vl,
+ rvec v)
{
rvec xij, xjk, xjl, temp;
real d;
/* 9 flops */
/* temp goes from i to a point on the plane jkl */
- temp[XX] = xij[XX] + a*xjk[XX] + b*xjl[XX];
- temp[YY] = xij[YY] + a*xjk[YY] + b*xjl[YY];
- temp[ZZ] = xij[ZZ] + a*xjk[ZZ] + b*xjl[ZZ];
+ temp[XX] = xij[XX] + a * xjk[XX] + b * xjl[XX];
+ temp[YY] = xij[YY] + a * xjk[YY] + b * xjl[YY];
+ temp[ZZ] = xij[ZZ] + a * xjk[ZZ] + b * xjl[ZZ];
/* 12 flops */
- d = c*gmx::invsqrt(iprod(temp, temp));
+ const real invRm = inverseNorm(temp);
+ d = c * invRm;
/* 6 + 10 flops */
- x[XX] = xi[XX] + d*temp[XX];
- x[YY] = xi[YY] + d*temp[YY];
- x[ZZ] = xi[ZZ] + d*temp[ZZ];
- /* 6 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + d * temp[XX];
+ x[YY] = xi[YY] + d * temp[YY];
+ x[ZZ] = xi[ZZ] + d * temp[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 43 flops */
+ }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vjk = { 0 };
+ rvec vjl = { 0 };
+
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vj, vjk);
+ rvec_sub(vl, vj, vjl);
+
+ rvec vm = { 0 };
+ vm[XX] = vij[XX] + a * vjk[XX] + b * vjl[XX];
+ vm[YY] = vij[YY] + a * vjk[YY] + b * vjl[YY];
+ vm[ZZ] = vij[ZZ] + a * vjk[ZZ] + b * vjl[ZZ];
- /* TOTAL: 43 flops */
+ const real vmDotRm = iprod(vm, temp);
+ v[XX] = vi[XX] + d * (vm[XX] - temp[XX] * vmDotRm * invRm * invRm);
+ v[YY] = vi[YY] + d * (vm[YY] - temp[YY] * vmDotRm * invRm * invRm);
+ v[ZZ] = vi[ZZ] + d * (vm[ZZ] - temp[ZZ] * vmDotRm * invRm * invRm);
+ }
}
-static void constr_vsite4FDN(const rvec xi, const rvec xj, const rvec xk, const rvec xl, rvec x,
- real a, real b, real c, const t_pbc *pbc)
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void constr_vsite4FDN(const rvec xi,
+ const rvec xj,
+ const rvec xk,
+ const rvec xl,
+ rvec x,
+ real a,
+ real b,
+ real c,
+ const t_pbc* pbc,
+ const rvec vi,
+ const rvec vj,
+ const rvec vk,
+ const rvec vl,
+ rvec v)
{
rvec xij, xik, xil, ra, rb, rja, rjb, rm;
real d;
pbc_rvec_sub(pbc, xl, xi, xil);
/* 9 flops */
- ra[XX] = a*xik[XX];
- ra[YY] = a*xik[YY];
- ra[ZZ] = a*xik[ZZ];
+ ra[XX] = a * xik[XX];
+ ra[YY] = a * xik[YY];
+ ra[ZZ] = a * xik[ZZ];
- rb[XX] = b*xil[XX];
- rb[YY] = b*xil[YY];
- rb[ZZ] = b*xil[ZZ];
+ rb[XX] = b * xil[XX];
+ rb[YY] = b * xil[YY];
+ rb[ZZ] = b * xil[ZZ];
/* 6 flops */
cprod(rja, rjb, rm);
/* 9 flops */
- d = c*gmx::invsqrt(norm2(rm));
+ const real invNormRm = inverseNorm(rm);
+ d = c * invNormRm;
/* 5+5+1 flops */
- x[XX] = xi[XX] + d*rm[XX];
- x[YY] = xi[YY] + d*rm[YY];
- x[ZZ] = xi[ZZ] + d*rm[ZZ];
- /* 6 Flops */
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[XX] = xi[XX] + d * rm[XX];
+ x[YY] = xi[YY] + d * rm[YY];
+ x[ZZ] = xi[ZZ] + d * rm[ZZ];
+ /* 6 Flops */
+ /* TOTAL: 47 flops */
+ }
- /* TOTAL: 47 flops */
-}
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ rvec vij = { 0 };
+ rvec vik = { 0 };
+ rvec vil = { 0 };
+ rvec_sub(vj, vi, vij);
+ rvec_sub(vk, vi, vik);
+ rvec_sub(vl, vi, vil);
+
+ rvec vja = { 0 };
+ rvec vjb = { 0 };
+ vja[XX] = a * vik[XX] - vij[XX];
+ vja[YY] = a * vik[YY] - vij[YY];
+ vja[ZZ] = a * vik[ZZ] - vij[ZZ];
+ vjb[XX] = b * vil[XX] - vij[XX];
+ vjb[YY] = b * vil[YY] - vij[YY];
+ vjb[ZZ] = b * vil[ZZ] - vij[ZZ];
-static int constr_vsiten(const t_iatom *ia, const t_iparams ip[],
- rvec *x, const t_pbc *pbc)
+ rvec temp1 = { 0 };
+ rvec temp2 = { 0 };
+ cprod(vja, rjb, temp1);
+ cprod(rja, vjb, temp2);
+
+ rvec vm = { 0 };
+ vm[XX] = temp1[XX] + temp2[XX];
+ vm[YY] = temp1[YY] + temp2[YY];
+ vm[ZZ] = temp1[ZZ] + temp2[ZZ];
+
+ const real rmDotVm = iprod(rm, vm);
+ v[XX] = vi[XX] + d * (vm[XX] - rm[XX] * rmDotVm * invNormRm * invNormRm);
+ v[YY] = vi[YY] + d * (vm[YY] - rm[YY] * rmDotVm * invNormRm * invNormRm);
+ v[ZZ] = vi[ZZ] + d * (vm[ZZ] - rm[ZZ] * rmDotVm * invNormRm * invNormRm);
+ }
+}
+
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static int constr_vsiten(const t_iatom* ia,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<RVec> x,
+ const t_pbc* pbc,
+ ArrayRef<RVec> v)
{
rvec x1, dx;
dvec dsum;
- int n3, av, ai;
real a;
+ dvec dvsum = { 0 };
+ rvec v1 = { 0 };
- n3 = 3*ip[ia[0]].vsiten.n;
- av = ia[1];
- ai = ia[2];
+ const int n3 = 3 * ip[ia[0]].vsiten.n;
+ const int av = ia[1];
+ int ai = ia[2];
copy_rvec(x[ai], x1);
+ copy_rvec(v[ai], v1);
clear_dvec(dsum);
for (int i = 3; i < n3; i += 3)
{
- ai = ia[i+2];
+ ai = ia[i + 2];
a = ip[ia[i]].vsiten.a;
- if (pbc)
+ if (calculatePosition == VSiteCalculatePosition::Yes)
{
- pbc_dx_aiuc(pbc, x[ai], x1, dx);
+ if (pbc)
+ {
+ pbc_dx_aiuc(pbc, x[ai], x1, dx);
+ }
+ else
+ {
+ rvec_sub(x[ai], x1, dx);
+ }
+ dsum[XX] += a * dx[XX];
+ dsum[YY] += a * dx[YY];
+ dsum[ZZ] += a * dx[ZZ];
+ /* 9 Flops */
}
- else
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
{
- rvec_sub(x[ai], x1, dx);
+ rvec_sub(v[ai], v1, dx);
+ dvsum[XX] += a * dx[XX];
+ dvsum[YY] += a * dx[YY];
+ dvsum[ZZ] += a * dx[ZZ];
+ /* 9 Flops */
}
- dsum[XX] += a*dx[XX];
- dsum[YY] += a*dx[YY];
- dsum[ZZ] += a*dx[ZZ];
- /* 9 Flops */
}
- x[av][XX] = x1[XX] + dsum[XX];
- x[av][YY] = x1[YY] + dsum[YY];
- x[av][ZZ] = x1[ZZ] + dsum[ZZ];
+ if (calculatePosition == VSiteCalculatePosition::Yes)
+ {
+ x[av][XX] = x1[XX] + dsum[XX];
+ x[av][YY] = x1[YY] + dsum[YY];
+ x[av][ZZ] = x1[ZZ] + dsum[ZZ];
+ }
+
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ v[av][XX] = v1[XX] + dvsum[XX];
+ v[av][YY] = v1[YY] + dvsum[YY];
+ v[av][ZZ] = v1[ZZ] + dvsum[ZZ];
+ }
return n3;
}
+// End GCC 8 bug
+GCC_DIAGNOSTIC_RESET
+
+#endif // DOXYGEN
-/*! \brief PBC modes for vsite construction and spreading */
+//! PBC modes for vsite construction and spreading
enum class PbcMode
{
- all, // Apply normal, simple PBC for all vsites
- chargeGroup, // Keep vsite in the same periodic image as the rest of it's charge group
- none // No PBC treatment needed
+ all, //!< Apply normal, simple PBC for all vsites
+ none //!< No PBC treatment needed
};
/*! \brief Returns the PBC mode based on the system PBC and vsite properties
*
* \param[in] pbcPtr A pointer to a PBC struct or nullptr when no PBC treatment is required
- * \param[in] vsite A pointer to the vsite struct, can be nullptr
*/
-static PbcMode getPbcMode(const t_pbc *pbcPtr,
- const gmx_vsite_t *vsite)
+static PbcMode getPbcMode(const t_pbc* pbcPtr)
{
if (pbcPtr == nullptr)
{
return PbcMode::none;
}
- else if (vsite != nullptr && vsite->bHaveChargeGroups)
- {
- return PbcMode::chargeGroup;
- }
else
{
return PbcMode::all;
}
}
-static void construct_vsites_thread(const gmx_vsite_t *vsite,
- rvec x[],
- real dt, rvec *v,
- const t_iparams ip[], const t_ilist ilist[],
- const t_pbc *pbc_null)
+/*! \brief Executes the vsite construction task for a single thread
+ *
+ * \tparam operation Whether we are calculating positions, velocities, or both
+ * \param[in,out] x Coordinates to construct vsites for
+ * \param[in,out] v Velocities are generated for virtual sites if `operation` requires it
+ * \param[in] ip Interaction parameters for all interaction, only vsite parameters are used
+ * \param[in] ilist The interaction lists, only vsites are usesd
+ * \param[in] pbc_null PBC struct, used for PBC distance calculations when !=nullptr
+ */
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void construct_vsites_thread(ArrayRef<RVec> x,
+ ArrayRef<RVec> v,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const InteractionList> ilist,
+ const t_pbc* pbc_null)
{
- real inv_dt;
- if (v != nullptr)
- {
- inv_dt = 1.0/dt;
- }
- else
- {
- inv_dt = 1.0;
- }
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ GMX_RELEASE_ASSERT(!v.empty(),
+ "Can't calculate velocities without access to velocity vector.");
+ }
+
+ // Work around clang bug (unfixed as of Feb 2021)
+ // https://bugs.llvm.org/show_bug.cgi?id=35450
+ // clang-format off
+ CLANG_DIAGNOSTIC_IGNORE(-Wunused-lambda-capture)
+ // clang-format on
+ // GCC 8 falsely flags unused variables if constexpr prunes a code path, fixed in GCC 9
+ // https://gcc.gnu.org/bugzilla/show_bug.cgi?id=85827
+ // clang-format off
+ GCC_DIAGNOSTIC_IGNORE(-Wunused-but-set-parameter)
+ // clang-format on
+ // getVOrNull returns a velocity rvec if we need it, nullptr otherwise.
+ auto getVOrNull = [v](int idx) -> real* {
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ return v[idx].as_vec();
+ }
+ else
+ {
+ return nullptr;
+ }
+ };
+ GCC_DIAGNOSTIC_RESET
+ CLANG_DIAGNOSTIC_RESET
- const PbcMode pbcMode = getPbcMode(pbc_null, vsite);
+ const PbcMode pbcMode = getPbcMode(pbc_null);
/* We need another pbc pointer, as with charge groups we switch per vsite */
- const t_pbc *pbc_null2 = pbc_null;
- gmx::ArrayRef<const int> vsite_pbc;
+ const t_pbc* pbc_null2 = pbc_null;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- if (ilist[ftype].nr == 0)
+ if (ilist[ftype].empty())
{
continue;
}
- { // TODO remove me
- int nra = interaction_function[ftype].nratoms;
- int inc = 1 + nra;
- int nr = ilist[ftype].nr;
-
- const t_iatom *ia = ilist[ftype].iatoms;
+ { // TODO remove me
+ int nra = interaction_function[ftype].nratoms;
+ int inc = 1 + nra;
+ int nr = ilist[ftype].size();
- if (pbcMode == PbcMode::chargeGroup)
- {
- vsite_pbc = (*vsite->vsite_pbc_loc)[ftype - c_ftypeVsiteStart];
- }
+ const t_iatom* ia = ilist[ftype].iatoms.data();
- for (int i = 0; i < nr; )
+ for (int i = 0; i < nr;)
{
- int tp = ia[0];
+ int tp = ia[0];
/* The vsite and constructing atoms */
- int avsite = ia[1];
- int ai = ia[2];
+ int avsite = ia[1];
+ int ai = ia[2];
/* Constants for constructing vsites */
- real a1 = ip[tp].vsite.a;
- /* Check what kind of pbc we need to use */
- int pbc_atom;
- rvec xpbc;
- if (pbcMode == PbcMode::all)
- {
- /* No charge groups, vsite follows its own pbc */
- pbc_atom = avsite;
- copy_rvec(x[avsite], xpbc);
- }
- else if (pbcMode == PbcMode::chargeGroup)
- {
- pbc_atom = vsite_pbc[i/(1 + nra)];
- if (pbc_atom > -2)
- {
- if (pbc_atom >= 0)
- {
- /* We need to copy the coordinates here,
- * single for single atom cg's pbc_atom
- * is the vsite itself.
- */
- copy_rvec(x[pbc_atom], xpbc);
- }
- pbc_null2 = pbc_null;
- }
- else
- {
- pbc_null2 = nullptr;
- }
- }
- else
- {
- pbc_atom = -2;
- }
+ real a1 = ip[tp].vsite.a;
/* Copy the old position */
rvec xv;
copy_rvec(x[avsite], xv);
real b1, c1;
switch (ftype)
{
+ case F_VSITE1:
+ constr_vsite1<calculatePosition, calculateVelocity>(
+ x[ai], x[avsite], getVOrNull(ai), getVOrNull(avsite));
+ break;
case F_VSITE2:
aj = ia[3];
- constr_vsite2(x[ai], x[aj], x[avsite], a1, pbc_null2);
+ constr_vsite2<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[avsite],
+ a1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(avsite));
+ break;
+ case F_VSITE2FD:
+ aj = ia[3];
+ constr_vsite2FD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[avsite],
+ a1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(avsite));
break;
case F_VSITE3:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
- constr_vsite3(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ constr_vsite3<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE3FD:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
- constr_vsite3FD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ constr_vsite3FD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE3FAD:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
- constr_vsite3FAD(x[ai], x[aj], x[ak], x[avsite], a1, b1, pbc_null2);
+ constr_vsite3FAD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE3OUT:
aj = ia[3];
ak = ia[4];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite3OUT(x[ai], x[aj], x[ak], x[avsite], a1, b1, c1, pbc_null2);
+ constr_vsite3OUT<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[avsite],
+ a1,
+ b1,
+ c1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(avsite));
break;
case F_VSITE4FD:
aj = ia[3];
al = ia[5];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite4FD(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
- pbc_null2);
+ constr_vsite4FD<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[al],
+ x[avsite],
+ a1,
+ b1,
+ c1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(al),
+ getVOrNull(avsite));
break;
case F_VSITE4FDN:
aj = ia[3];
al = ia[5];
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- constr_vsite4FDN(x[ai], x[aj], x[ak], x[al], x[avsite], a1, b1, c1,
- pbc_null2);
+ constr_vsite4FDN<calculatePosition, calculateVelocity>(x[ai],
+ x[aj],
+ x[ak],
+ x[al],
+ x[avsite],
+ a1,
+ b1,
+ c1,
+ pbc_null2,
+ getVOrNull(ai),
+ getVOrNull(aj),
+ getVOrNull(ak),
+ getVOrNull(al),
+ getVOrNull(avsite));
break;
case F_VSITEN:
- inc = constr_vsiten(ia, ip, x, pbc_null2);
+ inc = constr_vsiten<calculatePosition, calculateVelocity>(ia, ip, x, pbc_null2, v);
break;
default:
- gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
- ftype, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d", ftype, __FILE__, __LINE__);
}
- if (pbc_atom >= 0)
+ if (pbcMode == PbcMode::all)
{
- /* Match the pbc of this vsite to the rest of its charge group */
+ /* Keep the vsite in the same periodic image as before */
rvec dx;
- int ishift = pbc_dx_aiuc(pbc_null, x[avsite], xpbc, dx);
- if (ishift != CENTRAL)
+ int ishift = pbc_dx_aiuc(pbc_null, x[avsite], xv, dx);
+ if (ishift != c_centralShiftIndex)
{
- rvec_add(xpbc, dx, x[avsite]);
+ rvec_add(xv, dx, x[avsite]);
}
}
- if (v != nullptr)
- {
- /* Calculate velocity of vsite... */
- rvec vv;
- rvec_sub(x[avsite], xv, vv);
- svmul(inv_dt, vv, v[avsite]);
- }
/* Increment loop variables */
- i += inc;
+ i += inc;
ia += inc;
}
}
}
}
-void construct_vsites(const gmx_vsite_t *vsite,
- rvec x[],
- real dt, rvec *v,
- const t_iparams ip[], const t_ilist ilist[],
- int ePBC, gmx_bool bMolPBC,
- const t_commrec *cr,
- const matrix box)
+/*! \brief Dispatch the vsite construction tasks for all threads
+ *
+ * \param[in] threadingInfo Used to divide work over threads when != nullptr
+ * \param[in,out] x Coordinates to construct vsites for
+ * \param[in,out] v When not empty, velocities are generated for virtual sites
+ * \param[in] ip Interaction parameters for all interaction, only vsite parameters are used
+ * \param[in] ilist The interaction lists, only vsites are usesd
+ * \param[in] domainInfo Information about PBC and DD
+ * \param[in] box Used for PBC when PBC is set in domainInfo
+ */
+template<VSiteCalculatePosition calculatePosition, VSiteCalculateVelocity calculateVelocity>
+static void construct_vsites(const ThreadingInfo* threadingInfo,
+ ArrayRef<RVec> x,
+ ArrayRef<RVec> v,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const InteractionList> ilist,
+ const DomainInfo& domainInfo,
+ const matrix box)
{
- const bool useDomdec = (vsite != nullptr && vsite->useDomdec);
- GMX_ASSERT(!useDomdec || (cr != nullptr && DOMAINDECOMP(cr)), "When vsites are set up with domain decomposition, we need a valid commrec");
- // TODO: Remove this assertion when we remove charge groups
- GMX_ASSERT(vsite != nullptr || ePBC == epbcNONE, "Without a vsite struct we can not do PBC (in case we have charge groups)");
+ const bool useDomdec = domainInfo.useDomdec();
- t_pbc pbc, *pbc_null;
+ t_pbc pbc, *pbc_null;
- /* We only need to do pbc when we have inter-cg vsites.
+ /* We only need to do pbc when we have inter update-group vsites.
* Note that with domain decomposition we do not need to apply PBC here
* when we have at least 3 domains along each dimension. Currently we
* do not optimize this case.
*/
- if (ePBC != epbcNONE && (useDomdec || bMolPBC) &&
- !(vsite != nullptr && vsite->n_intercg_vsite == 0))
+ if (domainInfo.pbcType_ != PbcType::No && domainInfo.useMolPbc_)
{
/* This is wasting some CPU time as we now do this multiple times
* per MD step.
*/
ivec null_ivec;
clear_ivec(null_ivec);
- pbc_null = set_pbc_dd(&pbc, ePBC,
- useDomdec ? cr->dd->nc : null_ivec,
- FALSE, box);
+ pbc_null = set_pbc_dd(
+ &pbc, domainInfo.pbcType_, useDomdec ? domainInfo.domdec_->numCells : null_ivec, FALSE, box);
}
else
{
if (useDomdec)
{
- dd_move_x_vsites(cr->dd, box, x);
+ if (calculateVelocity == VSiteCalculateVelocity::Yes)
+ {
+ dd_move_x_and_v_vsites(
+ *domainInfo.domdec_, box, as_rvec_array(x.data()), as_rvec_array(v.data()));
+ }
+ else
+ {
+ dd_move_x_vsites(*domainInfo.domdec_, box, as_rvec_array(x.data()));
+ }
}
- if (vsite == nullptr || vsite->nthreads == 1)
+ if (threadingInfo == nullptr || threadingInfo->numThreads() == 1)
{
- construct_vsites_thread(vsite,
- x, dt, v,
- ip, ilist,
- pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(x, v, ip, ilist, pbc_null);
}
else
{
-#pragma omp parallel num_threads(vsite->nthreads)
+#pragma omp parallel num_threads(threadingInfo->numThreads())
{
try
{
const int th = gmx_omp_get_thread_num();
- const VsiteThread &tData = *vsite->tData[th];
- GMX_ASSERT(tData.rangeStart >= 0, "The thread data should be initialized before calling construct_vsites");
+ const VsiteThread& tData = threadingInfo->threadData(th);
+ GMX_ASSERT(tData.rangeStart >= 0,
+ "The thread data should be initialized before calling construct_vsites");
- construct_vsites_thread(vsite,
- x, dt, v,
- ip, tData.ilist,
- pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(
+ x, v, ip, tData.ilist, pbc_null);
if (tData.useInterdependentTask)
{
/* Here we don't need a barrier (unlike the spreading),
* since both tasks only construct vsites from particles,
* or local vsites, not from non-local vsites.
*/
- construct_vsites_thread(vsite,
- x, dt, v,
- ip, tData.idTask.ilist,
- pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(
+ x, v, ip, tData.idTask.ilist, pbc_null);
}
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Now we can construct the vsites that might depend on other vsites */
- construct_vsites_thread(vsite,
- x, dt, v,
- ip, vsite->tData[vsite->nthreads]->ilist,
- pbc_null);
+ construct_vsites_thread<calculatePosition, calculateVelocity>(
+ x, v, ip, threadingInfo->threadDataNonLocalDependent().ilist, pbc_null);
+ }
+}
+
+void VirtualSitesHandler::Impl::construct(ArrayRef<RVec> x,
+ ArrayRef<RVec> v,
+ const matrix box,
+ VSiteOperation operation) const
+{
+ switch (operation)
+ {
+ case VSiteOperation::Positions:
+ construct_vsites<VSiteCalculatePosition::Yes, VSiteCalculateVelocity::No>(
+ &threadingInfo_, x, v, iparams_, ilists_, domainInfo_, box);
+ break;
+ case VSiteOperation::Velocities:
+ construct_vsites<VSiteCalculatePosition::No, VSiteCalculateVelocity::Yes>(
+ &threadingInfo_, x, v, iparams_, ilists_, domainInfo_, box);
+ break;
+ case VSiteOperation::PositionsAndVelocities:
+ construct_vsites<VSiteCalculatePosition::Yes, VSiteCalculateVelocity::Yes>(
+ &threadingInfo_, x, v, iparams_, ilists_, domainInfo_, box);
+ break;
+ default: gmx_fatal(FARGS, "Unknown virtual site operation");
}
}
-static void spread_vsite2(const t_iatom ia[], real a,
- const rvec x[],
- rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g)
+void VirtualSitesHandler::construct(ArrayRef<RVec> x, ArrayRef<RVec> v, const matrix box, VSiteOperation operation) const
+{
+ impl_->construct(x, v, box, operation);
+}
+
+void constructVirtualSites(ArrayRef<RVec> x, ArrayRef<const t_iparams> ip, ArrayRef<const InteractionList> ilist)
+
+{
+ // No PBC, no DD
+ const DomainInfo domainInfo;
+ construct_vsites<VSiteCalculatePosition::Yes, VSiteCalculateVelocity::No>(
+ nullptr, x, {}, ip, ilist, domainInfo, nullptr);
+}
+
+#ifndef DOXYGEN
+/* Force spreading routines */
+
+static void spread_vsite1(const t_iatom ia[], ArrayRef<RVec> f)
+{
+ const int av = ia[1];
+ const int ai = ia[2];
+
+ f[av] += f[ai];
+}
+
+template<VirialHandling virialHandling>
+static void spread_vsite2(const t_iatom ia[],
+ real a,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ const t_pbc* pbc)
{
rvec fi, fj, dx;
t_iatom av, ai, aj;
- ivec di;
- int siv, sij;
av = ia[1];
ai = ia[2];
aj = ia[3];
svmul(1 - a, f[av], fi);
- svmul( a, f[av], fj);
+ svmul(a, f[av], fj);
/* 7 flop */
rvec_inc(f[ai], fi);
rvec_inc(f[aj], fj);
/* 6 Flops */
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, av), di);
- siv = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), di);
- sij = IVEC2IS(di);
- }
- else if (pbc)
+ if (virialHandling == VirialHandling::Pbc)
{
- siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
- sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
- }
- else
- {
- siv = CENTRAL;
- sij = CENTRAL;
- }
+ int siv;
+ int sij;
+ if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
+ sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
+ }
+ else
+ {
+ siv = c_centralShiftIndex;
+ sij = c_centralShiftIndex;
+ }
- if (fshift && (siv != CENTRAL || sij != CENTRAL))
- {
- rvec_inc(fshift[siv], f[av]);
- rvec_dec(fshift[CENTRAL], fi);
- rvec_dec(fshift[sij], fj);
+ if (siv != c_centralShiftIndex || sij != c_centralShiftIndex)
+ {
+ rvec_inc(fshift[siv], f[av]);
+ rvec_dec(fshift[c_centralShiftIndex], fi);
+ rvec_dec(fshift[sij], fj);
+ }
}
/* TOTAL: 13 flops */
}
-void constructVsitesGlobal(const gmx_mtop_t &mtop,
- gmx::ArrayRef<gmx::RVec> x)
+void constructVirtualSitesGlobal(const gmx_mtop_t& mtop, gmx::ArrayRef<gmx::RVec> x)
{
GMX_ASSERT(x.ssize() >= mtop.natoms, "x should contain the whole system");
- GMX_ASSERT(!mtop.moleculeBlockIndices.empty(), "molblock indices are needed in constructVsitesGlobal");
+ GMX_ASSERT(!mtop.moleculeBlockIndices.empty(),
+ "molblock indices are needed in constructVsitesGlobal");
for (size_t mb = 0; mb < mtop.molblock.size(); mb++)
{
- const gmx_molblock_t &molb = mtop.molblock[mb];
- const gmx_moltype_t &molt = mtop.moltype[molb.type];
- if (vsiteIlistNrCount(molt.ilist.data()) > 0)
+ const gmx_molblock_t& molb = mtop.molblock[mb];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
+ if (vsiteIlistNrCount(molt.ilist) > 0)
{
int atomOffset = mtop.moleculeBlockIndices[mb].globalAtomStart;
for (int mol = 0; mol < molb.nmol; mol++)
{
- t_ilist ilist[F_NRE];
- for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
- {
- ilist[ftype].nr = molt.ilist[ftype].size();
- ilist[ftype].iatoms = const_cast<t_iatom *>(molt.ilist[ftype].iatoms.data());
- }
-
- construct_vsites(nullptr, as_rvec_array(x.data()) + atomOffset,
- 0.0, nullptr,
- mtop.ffparams.iparams.data(), ilist,
- epbcNONE, TRUE, nullptr, nullptr);
+ constructVirtualSites(
+ x.subArray(atomOffset, molt.atoms.nr), mtop.ffparams.iparams, molt.ilist);
atomOffset += molt.atoms.nr;
}
}
}
}
-static void spread_vsite3(const t_iatom ia[], real a, real b,
- const rvec x[],
- rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g)
+template<VirialHandling virialHandling>
+static void spread_vsite2FD(const t_iatom ia[],
+ real a,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ const t_pbc* pbc)
{
- rvec fi, fj, fk, dx;
- int av, ai, aj, ak;
- ivec di;
- int siv, sij, sik;
+ const int av = ia[1];
+ const int ai = ia[2];
+ const int aj = ia[3];
+ rvec fv;
+ copy_rvec(f[av], fv);
+
+ rvec xij;
+ int sji = pbc_rvec_sub(pbc, x[aj], x[ai], xij);
+ /* 6 flops */
+
+ const real invDistance = inverseNorm(xij);
+ const real b = a * invDistance;
+ /* 4 + ?10? flops */
+
+ const real fproj = iprod(xij, fv) * invDistance * invDistance;
+
+ rvec fj;
+ fj[XX] = b * (fv[XX] - fproj * xij[XX]);
+ fj[YY] = b * (fv[YY] - fproj * xij[YY]);
+ fj[ZZ] = b * (fv[ZZ] - fproj * xij[ZZ]);
+ /* 9 */
+
+ /* b is already calculated in constr_vsite2FD
+ storing b somewhere will save flops. */
+
+ f[ai][XX] += fv[XX] - fj[XX];
+ f[ai][YY] += fv[YY] - fj[YY];
+ f[ai][ZZ] += fv[ZZ] - fj[ZZ];
+ f[aj][XX] += fj[XX];
+ f[aj][YY] += fj[YY];
+ f[aj][ZZ] += fj[ZZ];
+ /* 9 Flops */
+
+ if (virialHandling == VirialHandling::Pbc)
+ {
+ int svi;
+ if (pbc)
+ {
+ rvec xvi;
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = c_centralShiftIndex;
+ }
+
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex)
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[c_centralShiftIndex][XX] += fv[XX] - fj[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - fj[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - fj[ZZ];
+ fshift[sji][XX] += fj[XX];
+ fshift[sji][YY] += fj[YY];
+ fshift[sji][ZZ] += fj[ZZ];
+ }
+ }
+
+ if (virialHandling == VirialHandling::NonLinear)
+ {
+ /* Under this condition, the virial for the current forces is not
+ * calculated from the redistributed forces. This means that
+ * the effect of non-linear virtual site constructions on the virial
+ * needs to be added separately. This contribution can be calculated
+ * in many ways, but the simplest and cheapest way is to use
+ * the first constructing atom ai as a reference position in space:
+ * subtract (xv-xi)*fv and add (xj-xi)*fj.
+ */
+ rvec xiv;
+
+ pbc_rvec_sub(pbc, x[av], x[ai], xiv);
+
+ for (int i = 0; i < DIM; i++)
+ {
+ for (int j = 0; j < DIM; j++)
+ {
+ /* As xix is a linear combination of j and k, use that here */
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * fj[j];
+ }
+ }
+ }
+
+ /* TOTAL: 38 flops */
+}
+
+template<VirialHandling virialHandling>
+static void spread_vsite3(const t_iatom ia[],
+ real a,
+ real b,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ const t_pbc* pbc)
+{
+ rvec fi, fj, fk, dx;
+ int av, ai, aj, ak;
av = ia[1];
ai = ia[2];
ak = ia[4];
svmul(1 - a - b, f[av], fi);
- svmul( a, f[av], fj);
- svmul( b, f[av], fk);
+ svmul(a, f[av], fj);
+ svmul(b, f[av], fk);
/* 11 flops */
rvec_inc(f[ai], fi);
rvec_inc(f[ak], fk);
/* 9 Flops */
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, ia[1]), di);
- siv = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, aj), di);
- sij = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, ak), di);
- sik = IVEC2IS(di);
- }
- else if (pbc)
- {
- siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
- sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
- sik = pbc_dx_aiuc(pbc, x[ai], x[ak], dx);
- }
- else
+ if (virialHandling == VirialHandling::Pbc)
{
- siv = CENTRAL;
- sij = CENTRAL;
- sik = CENTRAL;
- }
+ int siv;
+ int sij;
+ int sik;
+ if (pbc)
+ {
+ siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
+ sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
+ sik = pbc_dx_aiuc(pbc, x[ai], x[ak], dx);
+ }
+ else
+ {
+ siv = c_centralShiftIndex;
+ sij = c_centralShiftIndex;
+ sik = c_centralShiftIndex;
+ }
- if (fshift && (siv != CENTRAL || sij != CENTRAL || sik != CENTRAL))
- {
- rvec_inc(fshift[siv], f[av]);
- rvec_dec(fshift[CENTRAL], fi);
- rvec_dec(fshift[sij], fj);
- rvec_dec(fshift[sik], fk);
+ if (siv != c_centralShiftIndex || sij != c_centralShiftIndex || sik != c_centralShiftIndex)
+ {
+ rvec_inc(fshift[siv], f[av]);
+ rvec_dec(fshift[c_centralShiftIndex], fi);
+ rvec_dec(fshift[sij], fj);
+ rvec_dec(fshift[sik], fk);
+ }
}
/* TOTAL: 20 flops */
}
-static void spread_vsite3FD(const t_iatom ia[], real a, real b,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+template<VirialHandling virialHandling>
+static void spread_vsite3FD(const t_iatom ia[],
+ real a,
+ real b,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ const t_pbc* pbc)
{
- real c, invl, fproj, a1;
+ real fproj, a1;
rvec xvi, xij, xjk, xix, fv, temp;
t_iatom av, ai, aj, ak;
- int svi, sji, skj;
- ivec di;
+ int sji, skj;
av = ia[1];
ai = ia[2];
/* 6 flops */
/* xix goes from i to point x on the line jk */
- xix[XX] = xij[XX]+a*xjk[XX];
- xix[YY] = xij[YY]+a*xjk[YY];
- xix[ZZ] = xij[ZZ]+a*xjk[ZZ];
+ xix[XX] = xij[XX] + a * xjk[XX];
+ xix[YY] = xij[YY] + a * xjk[YY];
+ xix[ZZ] = xij[ZZ] + a * xjk[ZZ];
/* 6 flops */
- invl = gmx::invsqrt(iprod(xix, xix));
- c = b*invl;
+ const real invDistance = inverseNorm(xix);
+ const real c = b * invDistance;
/* 4 + ?10? flops */
- fproj = iprod(xix, fv)*invl*invl; /* = (xix . f)/(xix . xix) */
+ fproj = iprod(xix, fv) * invDistance * invDistance; /* = (xix . f)/(xix . xix) */
- temp[XX] = c*(fv[XX]-fproj*xix[XX]);
- temp[YY] = c*(fv[YY]-fproj*xix[YY]);
- temp[ZZ] = c*(fv[ZZ]-fproj*xix[ZZ]);
+ temp[XX] = c * (fv[XX] - fproj * xix[XX]);
+ temp[YY] = c * (fv[YY] - fproj * xix[YY]);
+ temp[ZZ] = c * (fv[ZZ] - fproj * xix[ZZ]);
/* 16 */
/* c is already calculated in constr_vsite3FD
storing c somewhere will save 26 flops! */
- a1 = 1 - a;
+ a1 = 1 - a;
f[ai][XX] += fv[XX] - temp[XX];
f[ai][YY] += fv[YY] - temp[YY];
f[ai][ZZ] += fv[ZZ] - temp[ZZ];
- f[aj][XX] += a1*temp[XX];
- f[aj][YY] += a1*temp[YY];
- f[aj][ZZ] += a1*temp[ZZ];
- f[ak][XX] += a*temp[XX];
- f[ak][YY] += a*temp[YY];
- f[ak][ZZ] += a*temp[ZZ];
+ f[aj][XX] += a1 * temp[XX];
+ f[aj][YY] += a1 * temp[YY];
+ f[aj][ZZ] += a1 * temp[ZZ];
+ f[ak][XX] += a * temp[XX];
+ f[ak][YY] += a * temp[YY];
+ f[ak][ZZ] += a * temp[ZZ];
/* 19 Flops */
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
- skj = IVEC2IS(di);
- }
- else if (pbc)
+ if (virialHandling == VirialHandling::Pbc)
{
- svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
- }
- else
- {
- svi = CENTRAL;
- }
+ int svi;
+ if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = c_centralShiftIndex;
+ }
- if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
- {
- rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - (1 + a)*temp[XX];
- fshift[CENTRAL][YY] += fv[YY] - (1 + a)*temp[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - (1 + a)*temp[ZZ];
- fshift[ sji][XX] += temp[XX];
- fshift[ sji][YY] += temp[YY];
- fshift[ sji][ZZ] += temp[ZZ];
- fshift[ skj][XX] += a*temp[XX];
- fshift[ skj][YY] += a*temp[YY];
- fshift[ skj][ZZ] += a*temp[ZZ];
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || skj != c_centralShiftIndex)
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[c_centralShiftIndex][XX] += fv[XX] - (1 + a) * temp[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - (1 + a) * temp[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - (1 + a) * temp[ZZ];
+ fshift[sji][XX] += temp[XX];
+ fshift[sji][YY] += temp[YY];
+ fshift[sji][ZZ] += temp[ZZ];
+ fshift[skj][XX] += a * temp[XX];
+ fshift[skj][YY] += a * temp[YY];
+ fshift[skj][ZZ] += a * temp[ZZ];
+ }
}
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
- /* When VirCorr=TRUE, the virial for the current forces is not
+ /* Under this condition, the virial for the current forces is not
* calculated from the redistributed forces. This means that
* the effect of non-linear virtual site constructions on the virial
* needs to be added separately. This contribution can be calculated
for (int j = 0; j < DIM; j++)
{
/* As xix is a linear combination of j and k, use that here */
- dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xix[i] * temp[j];
}
}
}
/* TOTAL: 61 flops */
}
-static void spread_vsite3FAD(const t_iatom ia[], real a, real b,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+template<VirialHandling virialHandling>
+static void spread_vsite3FAD(const t_iatom ia[],
+ real a,
+ real b,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ const t_pbc* pbc)
{
rvec xvi, xij, xjk, xperp, Fpij, Fppp, fv, f1, f2, f3;
real a1, b1, c1, c2, invdij, invdij2, invdp, fproj;
t_iatom av, ai, aj, ak;
- int svi, sji, skj, d;
- ivec di;
+ int sji, skj;
av = ia[1];
ai = ia[2];
skj = pbc_rvec_sub(pbc, x[ak], x[aj], xjk);
/* 6 flops */
- invdij = gmx::invsqrt(iprod(xij, xij));
+ invdij = inverseNorm(xij);
invdij2 = invdij * invdij;
c1 = iprod(xij, xjk) * invdij2;
- xperp[XX] = xjk[XX] - c1*xij[XX];
- xperp[YY] = xjk[YY] - c1*xij[YY];
- xperp[ZZ] = xjk[ZZ] - c1*xij[ZZ];
+ xperp[XX] = xjk[XX] - c1 * xij[XX];
+ xperp[YY] = xjk[YY] - c1 * xij[YY];
+ xperp[ZZ] = xjk[ZZ] - c1 * xij[ZZ];
/* xperp in plane ijk, perp. to ij */
- invdp = gmx::invsqrt(iprod(xperp, xperp));
- a1 = a*invdij;
- b1 = b*invdp;
+ invdp = inverseNorm(xperp);
+ a1 = a * invdij;
+ b1 = b * invdp;
/* 45 flops */
/* a1, b1 and c1 are already calculated in constr_vsite3FAD
storing them somewhere will save 45 flops! */
- fproj = iprod(xij, fv)*invdij2;
- svmul(fproj, xij, Fpij); /* proj. f on xij */
- svmul(iprod(xperp, fv)*invdp*invdp, xperp, Fppp); /* proj. f on xperp */
- svmul(b1*fproj, xperp, f3);
+ fproj = iprod(xij, fv) * invdij2;
+ svmul(fproj, xij, Fpij); /* proj. f on xij */
+ svmul(iprod(xperp, fv) * invdp * invdp, xperp, Fppp); /* proj. f on xperp */
+ svmul(b1 * fproj, xperp, f3);
/* 23 flops */
rvec_sub(fv, Fpij, f1); /* f1 = f - Fpij */
rvec_sub(f1, Fppp, f2); /* f2 = f - Fpij - Fppp */
- for (d = 0; (d < DIM); d++)
+ for (int d = 0; d < DIM; d++)
{
f1[d] *= a1;
f2[d] *= b1;
}
/* 12 flops */
- c2 = 1 + c1;
- f[ai][XX] += fv[XX] - f1[XX] + c1*f2[XX] + f3[XX];
- f[ai][YY] += fv[YY] - f1[YY] + c1*f2[YY] + f3[YY];
- f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1*f2[ZZ] + f3[ZZ];
- f[aj][XX] += f1[XX] - c2*f2[XX] - f3[XX];
- f[aj][YY] += f1[YY] - c2*f2[YY] - f3[YY];
- f[aj][ZZ] += f1[ZZ] - c2*f2[ZZ] - f3[ZZ];
- f[ak][XX] += f2[XX];
- f[ak][YY] += f2[YY];
- f[ak][ZZ] += f2[ZZ];
+ c2 = 1 + c1;
+ f[ai][XX] += fv[XX] - f1[XX] + c1 * f2[XX] + f3[XX];
+ f[ai][YY] += fv[YY] - f1[YY] + c1 * f2[YY] + f3[YY];
+ f[ai][ZZ] += fv[ZZ] - f1[ZZ] + c1 * f2[ZZ] + f3[ZZ];
+ f[aj][XX] += f1[XX] - c2 * f2[XX] - f3[XX];
+ f[aj][YY] += f1[YY] - c2 * f2[YY] - f3[YY];
+ f[aj][ZZ] += f1[ZZ] - c2 * f2[ZZ] - f3[ZZ];
+ f[ak][XX] += f2[XX];
+ f[ak][YY] += f2[YY];
+ f[ak][ZZ] += f2[ZZ];
/* 30 Flops */
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
- skj = IVEC2IS(di);
- }
- else if (pbc)
- {
- svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
- }
- else
+ if (virialHandling == VirialHandling::Pbc)
{
- svi = CENTRAL;
- }
+ int svi;
- if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL))
- {
- rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - f1[XX] - (1-c1)*f2[XX] + f3[XX];
- fshift[CENTRAL][YY] += fv[YY] - f1[YY] - (1-c1)*f2[YY] + f3[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - f1[ZZ] - (1-c1)*f2[ZZ] + f3[ZZ];
- fshift[ sji][XX] += f1[XX] - c1 *f2[XX] - f3[XX];
- fshift[ sji][YY] += f1[YY] - c1 *f2[YY] - f3[YY];
- fshift[ sji][ZZ] += f1[ZZ] - c1 *f2[ZZ] - f3[ZZ];
- fshift[ skj][XX] += f2[XX];
- fshift[ skj][YY] += f2[YY];
- fshift[ skj][ZZ] += f2[ZZ];
+ if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = c_centralShiftIndex;
+ }
+
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || skj != c_centralShiftIndex)
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[c_centralShiftIndex][XX] += fv[XX] - f1[XX] - (1 - c1) * f2[XX] + f3[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - f1[YY] - (1 - c1) * f2[YY] + f3[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - f1[ZZ] - (1 - c1) * f2[ZZ] + f3[ZZ];
+ fshift[sji][XX] += f1[XX] - c1 * f2[XX] - f3[XX];
+ fshift[sji][YY] += f1[YY] - c1 * f2[YY] - f3[YY];
+ fshift[sji][ZZ] += f1[ZZ] - c1 * f2[ZZ] - f3[ZZ];
+ fshift[skj][XX] += f2[XX];
+ fshift[skj][YY] += f2[YY];
+ fshift[skj][ZZ] += f2[ZZ];
+ }
}
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
rvec xiv;
- int i, j;
-
pbc_rvec_sub(pbc, x[av], x[ai], xiv);
- for (i = 0; i < DIM; i++)
+ for (int i = 0; i < DIM; i++)
{
- for (j = 0; j < DIM; j++)
+ for (int j = 0; j < DIM; j++)
{
/* Note that xik=xij+xjk, so we have to add xij*f2 */
- dxdf[i][j] +=
- -xiv[i]*fv[j]
- + xij[i]*(f1[j] + (1 - c2)*f2[j] - f3[j])
- + xjk[i]*f2[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * (f1[j] + (1 - c2) * f2[j] - f3[j])
+ + xjk[i] * f2[j];
}
}
}
/* TOTAL: 113 flops */
}
-static void spread_vsite3OUT(const t_iatom ia[], real a, real b, real c,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+template<VirialHandling virialHandling>
+static void spread_vsite3OUT(const t_iatom ia[],
+ real a,
+ real b,
+ real c,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ const t_pbc* pbc)
{
- rvec xvi, xij, xik, fv, fj, fk;
- real cfx, cfy, cfz;
- int av, ai, aj, ak;
- ivec di;
- int svi, sji, ski;
+ rvec xvi, xij, xik, fv, fj, fk;
+ real cfx, cfy, cfz;
+ int av, ai, aj, ak;
+ int sji, ski;
av = ia[1];
ai = ia[2];
copy_rvec(f[av], fv);
- cfx = c*fv[XX];
- cfy = c*fv[YY];
- cfz = c*fv[ZZ];
+ cfx = c * fv[XX];
+ cfy = c * fv[YY];
+ cfz = c * fv[ZZ];
/* 3 Flops */
- fj[XX] = a*fv[XX] - xik[ZZ]*cfy + xik[YY]*cfz;
- fj[YY] = xik[ZZ]*cfx + a*fv[YY] - xik[XX]*cfz;
- fj[ZZ] = -xik[YY]*cfx + xik[XX]*cfy + a*fv[ZZ];
+ fj[XX] = a * fv[XX] - xik[ZZ] * cfy + xik[YY] * cfz;
+ fj[YY] = xik[ZZ] * cfx + a * fv[YY] - xik[XX] * cfz;
+ fj[ZZ] = -xik[YY] * cfx + xik[XX] * cfy + a * fv[ZZ];
- fk[XX] = b*fv[XX] + xij[ZZ]*cfy - xij[YY]*cfz;
- fk[YY] = -xij[ZZ]*cfx + b*fv[YY] + xij[XX]*cfz;
- fk[ZZ] = xij[YY]*cfx - xij[XX]*cfy + b*fv[ZZ];
+ fk[XX] = b * fv[XX] + xij[ZZ] * cfy - xij[YY] * cfz;
+ fk[YY] = -xij[ZZ] * cfx + b * fv[YY] + xij[XX] * cfz;
+ fk[ZZ] = xij[YY] * cfx - xij[XX] * cfy + b * fv[ZZ];
/* 30 Flops */
f[ai][XX] += fv[XX] - fj[XX] - fk[XX];
rvec_inc(f[ak], fk);
/* 15 Flops */
- if (g)
+ if (virialHandling == VirialHandling::Pbc)
{
- ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, ai), di);
- ski = IVEC2IS(di);
- }
- else if (pbc)
- {
- svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
- }
- else
- {
- svi = CENTRAL;
- }
+ int svi;
+ if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = c_centralShiftIndex;
+ }
- if (fshift && (svi != CENTRAL || sji != CENTRAL || ski != CENTRAL))
- {
- rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX];
- fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
- rvec_inc(fshift[sji], fj);
- rvec_inc(fshift[ski], fk);
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || ski != c_centralShiftIndex)
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[c_centralShiftIndex][XX] += fv[XX] - fj[XX] - fk[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - fj[YY] - fk[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ];
+ rvec_inc(fshift[sji], fj);
+ rvec_inc(fshift[ski], fk);
+ }
}
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
rvec xiv;
{
for (int j = 0; j < DIM; j++)
{
- dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * fj[j] + xik[i] * fk[j];
}
}
}
/* TOTAL: 54 flops */
}
-static void spread_vsite4FD(const t_iatom ia[], real a, real b, real c,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+template<VirialHandling virialHandling>
+static void spread_vsite4FD(const t_iatom ia[],
+ real a,
+ real b,
+ real c,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ const t_pbc* pbc)
{
- real d, invl, fproj, a1;
- rvec xvi, xij, xjk, xjl, xix, fv, temp;
- int av, ai, aj, ak, al;
- ivec di;
- int svi, sji, skj, slj, m;
+ real fproj, a1;
+ rvec xvi, xij, xjk, xjl, xix, fv, temp;
+ int av, ai, aj, ak, al;
+ int sji, skj, slj, m;
av = ia[1];
ai = ia[2];
/* xix goes from i to point x on the plane jkl */
for (m = 0; m < DIM; m++)
{
- xix[m] = xij[m] + a*xjk[m] + b*xjl[m];
+ xix[m] = xij[m] + a * xjk[m] + b * xjl[m];
}
/* 12 flops */
- invl = gmx::invsqrt(iprod(xix, xix));
- d = c*invl;
+ const real invDistance = inverseNorm(xix);
+ const real d = c * invDistance;
/* 4 + ?10? flops */
copy_rvec(f[av], fv);
- fproj = iprod(xix, fv)*invl*invl; /* = (xix . f)/(xix . xix) */
+ fproj = iprod(xix, fv) * invDistance * invDistance; /* = (xix . f)/(xix . xix) */
for (m = 0; m < DIM; m++)
{
- temp[m] = d*(fv[m] - fproj*xix[m]);
+ temp[m] = d * (fv[m] - fproj * xix[m]);
}
/* 16 */
for (m = 0; m < DIM; m++)
{
f[ai][m] += fv[m] - temp[m];
- f[aj][m] += a1*temp[m];
- f[ak][m] += a*temp[m];
- f[al][m] += b*temp[m];
+ f[aj][m] += a1 * temp[m];
+ f[ak][m] += a * temp[m];
+ f[al][m] += b * temp[m];
}
/* 26 Flops */
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ia[1]), SHIFT_IVEC(g, ai), di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
- sji = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, aj), di);
- skj = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, al), SHIFT_IVEC(g, aj), di);
- slj = IVEC2IS(di);
- }
- else if (pbc)
- {
- svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
- }
- else
+ if (virialHandling == VirialHandling::Pbc)
{
- svi = CENTRAL;
- }
+ int svi;
+ if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = c_centralShiftIndex;
+ }
- if (fshift &&
- (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL))
- {
- rvec_dec(fshift[svi], fv);
- for (m = 0; m < DIM; m++)
+ if (svi != c_centralShiftIndex || sji != c_centralShiftIndex || skj != c_centralShiftIndex
+ || slj != c_centralShiftIndex)
{
- fshift[CENTRAL][m] += fv[m] - (1 + a + b)*temp[m];
- fshift[ sji][m] += temp[m];
- fshift[ skj][m] += a*temp[m];
- fshift[ slj][m] += b*temp[m];
+ rvec_dec(fshift[svi], fv);
+ for (m = 0; m < DIM; m++)
+ {
+ fshift[c_centralShiftIndex][m] += fv[m] - (1 + a + b) * temp[m];
+ fshift[sji][m] += temp[m];
+ fshift[skj][m] += a * temp[m];
+ fshift[slj][m] += b * temp[m];
+ }
}
}
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
rvec xiv;
int i, j;
{
for (j = 0; j < DIM; j++)
{
- dxdf[i][j] += -xiv[i]*fv[j] + xix[i]*temp[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xix[i] * temp[j];
}
}
}
/* TOTAL: 77 flops */
}
-
-static void spread_vsite4FDN(const t_iatom ia[], real a, real b, real c,
- const rvec x[],
- rvec f[], rvec fshift[],
- gmx_bool VirCorr, matrix dxdf,
- const t_pbc *pbc, const t_graph *g)
+template<VirialHandling virialHandling>
+static void spread_vsite4FDN(const t_iatom ia[],
+ real a,
+ real b,
+ real c,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ const t_pbc* pbc)
{
rvec xvi, xij, xik, xil, ra, rb, rja, rjb, rab, rm, rt;
rvec fv, fj, fk, fl;
real invrm, denom;
real cfx, cfy, cfz;
- ivec di;
int av, ai, aj, ak, al;
- int svi, sij, sik, sil;
+ int sij, sik, sil;
/* DEBUG: check atom indices */
av = ia[1];
sil = pbc_rvec_sub(pbc, x[al], x[ai], xil);
/* 9 flops */
- ra[XX] = a*xik[XX];
- ra[YY] = a*xik[YY];
- ra[ZZ] = a*xik[ZZ];
+ ra[XX] = a * xik[XX];
+ ra[YY] = a * xik[YY];
+ ra[ZZ] = a * xik[ZZ];
- rb[XX] = b*xil[XX];
- rb[YY] = b*xil[YY];
- rb[ZZ] = b*xil[ZZ];
+ rb[XX] = b * xil[XX];
+ rb[YY] = b * xil[YY];
+ rb[ZZ] = b * xil[ZZ];
/* 6 flops */
cprod(rja, rjb, rm);
/* 9 flops */
- invrm = gmx::invsqrt(norm2(rm));
- denom = invrm*invrm;
+ invrm = inverseNorm(rm);
+ denom = invrm * invrm;
/* 5+5+2 flops */
- cfx = c*invrm*fv[XX];
- cfy = c*invrm*fv[YY];
- cfz = c*invrm*fv[ZZ];
+ cfx = c * invrm * fv[XX];
+ cfy = c * invrm * fv[YY];
+ cfz = c * invrm * fv[ZZ];
/* 6 Flops */
cprod(rm, rab, rt);
rt[ZZ] *= denom;
/* 3flops */
- fj[XX] = ( -rm[XX]*rt[XX]) * cfx + ( rab[ZZ]-rm[YY]*rt[XX]) * cfy + (-rab[YY]-rm[ZZ]*rt[XX]) * cfz;
- fj[YY] = (-rab[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( rab[XX]-rm[ZZ]*rt[YY]) * cfz;
- fj[ZZ] = ( rab[YY]-rm[XX]*rt[ZZ]) * cfx + (-rab[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
+ fj[XX] = (-rm[XX] * rt[XX]) * cfx + (rab[ZZ] - rm[YY] * rt[XX]) * cfy
+ + (-rab[YY] - rm[ZZ] * rt[XX]) * cfz;
+ fj[YY] = (-rab[ZZ] - rm[XX] * rt[YY]) * cfx + (-rm[YY] * rt[YY]) * cfy
+ + (rab[XX] - rm[ZZ] * rt[YY]) * cfz;
+ fj[ZZ] = (rab[YY] - rm[XX] * rt[ZZ]) * cfx + (-rab[XX] - rm[YY] * rt[ZZ]) * cfy
+ + (-rm[ZZ] * rt[ZZ]) * cfz;
/* 30 flops */
cprod(rjb, rm, rt);
/* 9 flops */
- rt[XX] *= denom*a;
- rt[YY] *= denom*a;
- rt[ZZ] *= denom*a;
+ rt[XX] *= denom * a;
+ rt[YY] *= denom * a;
+ rt[ZZ] *= denom * a;
/* 3flops */
- fk[XX] = ( -rm[XX]*rt[XX]) * cfx + (-a*rjb[ZZ]-rm[YY]*rt[XX]) * cfy + ( a*rjb[YY]-rm[ZZ]*rt[XX]) * cfz;
- fk[YY] = ( a*rjb[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + (-a*rjb[XX]-rm[ZZ]*rt[YY]) * cfz;
- fk[ZZ] = (-a*rjb[YY]-rm[XX]*rt[ZZ]) * cfx + ( a*rjb[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
+ fk[XX] = (-rm[XX] * rt[XX]) * cfx + (-a * rjb[ZZ] - rm[YY] * rt[XX]) * cfy
+ + (a * rjb[YY] - rm[ZZ] * rt[XX]) * cfz;
+ fk[YY] = (a * rjb[ZZ] - rm[XX] * rt[YY]) * cfx + (-rm[YY] * rt[YY]) * cfy
+ + (-a * rjb[XX] - rm[ZZ] * rt[YY]) * cfz;
+ fk[ZZ] = (-a * rjb[YY] - rm[XX] * rt[ZZ]) * cfx + (a * rjb[XX] - rm[YY] * rt[ZZ]) * cfy
+ + (-rm[ZZ] * rt[ZZ]) * cfz;
/* 36 flops */
cprod(rm, rja, rt);
/* 9 flops */
- rt[XX] *= denom*b;
- rt[YY] *= denom*b;
- rt[ZZ] *= denom*b;
+ rt[XX] *= denom * b;
+ rt[YY] *= denom * b;
+ rt[ZZ] *= denom * b;
/* 3flops */
- fl[XX] = ( -rm[XX]*rt[XX]) * cfx + ( b*rja[ZZ]-rm[YY]*rt[XX]) * cfy + (-b*rja[YY]-rm[ZZ]*rt[XX]) * cfz;
- fl[YY] = (-b*rja[ZZ]-rm[XX]*rt[YY]) * cfx + ( -rm[YY]*rt[YY]) * cfy + ( b*rja[XX]-rm[ZZ]*rt[YY]) * cfz;
- fl[ZZ] = ( b*rja[YY]-rm[XX]*rt[ZZ]) * cfx + (-b*rja[XX]-rm[YY]*rt[ZZ]) * cfy + ( -rm[ZZ]*rt[ZZ]) * cfz;
+ fl[XX] = (-rm[XX] * rt[XX]) * cfx + (b * rja[ZZ] - rm[YY] * rt[XX]) * cfy
+ + (-b * rja[YY] - rm[ZZ] * rt[XX]) * cfz;
+ fl[YY] = (-b * rja[ZZ] - rm[XX] * rt[YY]) * cfx + (-rm[YY] * rt[YY]) * cfy
+ + (b * rja[XX] - rm[ZZ] * rt[YY]) * cfz;
+ fl[ZZ] = (b * rja[YY] - rm[XX] * rt[ZZ]) * cfx + (-b * rja[XX] - rm[YY] * rt[ZZ]) * cfy
+ + (-rm[ZZ] * rt[ZZ]) * cfz;
/* 36 flops */
f[ai][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
rvec_inc(f[al], fl);
/* 21 flops */
- if (g)
+ if (virialHandling == VirialHandling::Pbc)
{
- ivec_sub(SHIFT_IVEC(g, av), SHIFT_IVEC(g, ai), di);
- svi = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, aj), SHIFT_IVEC(g, ai), di);
- sij = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, ak), SHIFT_IVEC(g, ai), di);
- sik = IVEC2IS(di);
- ivec_sub(SHIFT_IVEC(g, al), SHIFT_IVEC(g, ai), di);
- sil = IVEC2IS(di);
- }
- else if (pbc)
- {
- svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
- }
- else
- {
- svi = CENTRAL;
- }
+ int svi;
+ if (pbc)
+ {
+ svi = pbc_rvec_sub(pbc, x[av], x[ai], xvi);
+ }
+ else
+ {
+ svi = c_centralShiftIndex;
+ }
- if (fshift && (svi != CENTRAL || sij != CENTRAL || sik != CENTRAL || sil != CENTRAL))
- {
- rvec_dec(fshift[svi], fv);
- fshift[CENTRAL][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
- fshift[CENTRAL][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
- fshift[CENTRAL][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
- rvec_inc(fshift[sij], fj);
- rvec_inc(fshift[sik], fk);
- rvec_inc(fshift[sil], fl);
+ if (svi != c_centralShiftIndex || sij != c_centralShiftIndex || sik != c_centralShiftIndex
+ || sil != c_centralShiftIndex)
+ {
+ rvec_dec(fshift[svi], fv);
+ fshift[c_centralShiftIndex][XX] += fv[XX] - fj[XX] - fk[XX] - fl[XX];
+ fshift[c_centralShiftIndex][YY] += fv[YY] - fj[YY] - fk[YY] - fl[YY];
+ fshift[c_centralShiftIndex][ZZ] += fv[ZZ] - fj[ZZ] - fk[ZZ] - fl[ZZ];
+ rvec_inc(fshift[sij], fj);
+ rvec_inc(fshift[sik], fk);
+ rvec_inc(fshift[sil], fl);
+ }
}
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
rvec xiv;
int i, j;
{
for (j = 0; j < DIM; j++)
{
- dxdf[i][j] += -xiv[i]*fv[j] + xij[i]*fj[j] + xik[i]*fk[j] + xil[i]*fl[j];
+ dxdf[i][j] += -xiv[i] * fv[j] + xij[i] * fj[j] + xik[i] * fk[j] + xil[i] * fl[j];
}
}
}
/* Total: 207 flops (Yuck!) */
}
-
-static int spread_vsiten(const t_iatom ia[], const t_iparams ip[],
- const rvec x[],
- rvec f[], rvec fshift[],
- const t_pbc *pbc, const t_graph *g)
+template<VirialHandling virialHandling>
+static int spread_vsiten(const t_iatom ia[],
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ const t_pbc* pbc)
{
rvec xv, dx, fi;
int n3, av, i, ai;
real a;
- ivec di;
int siv;
- n3 = 3*ip[ia[0]].vsiten.n;
+ n3 = 3 * ip[ia[0]].vsiten.n;
av = ia[1];
copy_rvec(x[av], xv);
for (i = 0; i < n3; i += 3)
{
- ai = ia[i+2];
- if (g)
- {
- ivec_sub(SHIFT_IVEC(g, ai), SHIFT_IVEC(g, av), di);
- siv = IVEC2IS(di);
- }
- else if (pbc)
+ ai = ia[i + 2];
+ if (pbc)
{
siv = pbc_dx_aiuc(pbc, x[ai], xv, dx);
}
else
{
- siv = CENTRAL;
+ siv = c_centralShiftIndex;
}
a = ip[ia[i]].vsiten.a;
svmul(a, f[av], fi);
rvec_inc(f[ai], fi);
- if (fshift && siv != CENTRAL)
+
+ if (virialHandling == VirialHandling::Pbc && siv != c_centralShiftIndex)
{
rvec_inc(fshift[siv], fi);
- rvec_dec(fshift[CENTRAL], fi);
+ rvec_dec(fshift[c_centralShiftIndex], fi);
}
/* 6 Flops */
}
return n3;
}
+#endif // DOXYGEN
-static int vsite_count(const t_ilist *ilist, int ftype)
+//! Returns the number of virtual sites in the interaction list, for VSITEN the number of atoms
+static int vsite_count(ArrayRef<const InteractionList> ilist, int ftype)
{
if (ftype == F_VSITEN)
{
- return ilist[ftype].nr/3;
+ return ilist[ftype].size() / 3;
}
else
{
- return ilist[ftype].nr/(1 + interaction_function[ftype].nratoms);
+ return ilist[ftype].size() / (1 + interaction_function[ftype].nratoms);
}
}
-static void spread_vsite_f_thread(const gmx_vsite_t *vsite,
- const rvec x[],
- rvec f[], rvec *fshift,
- gmx_bool VirCorr, matrix dxdf,
- t_iparams ip[], const t_ilist ilist[],
- const t_graph *g, const t_pbc *pbc_null)
+//! Executes the force spreading task for a single thread
+template<VirialHandling virialHandling>
+static void spreadForceForThread(ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const InteractionList> ilist,
+ const t_pbc* pbc_null)
{
- const PbcMode pbcMode = getPbcMode(pbc_null, vsite);
+ const PbcMode pbcMode = getPbcMode(pbc_null);
/* We need another pbc pointer, as with charge groups we switch per vsite */
- const t_pbc *pbc_null2 = pbc_null;
+ const t_pbc* pbc_null2 = pbc_null;
gmx::ArrayRef<const int> vsite_pbc;
/* this loop goes backwards to be able to build *
* higher type vsites from lower types */
for (int ftype = c_ftypeVsiteEnd - 1; ftype >= c_ftypeVsiteStart; ftype--)
{
- if (ilist[ftype].nr == 0)
+ if (ilist[ftype].empty())
{
continue;
}
- { // TODO remove me
- int nra = interaction_function[ftype].nratoms;
- int inc = 1 + nra;
- int nr = ilist[ftype].nr;
+ { // TODO remove me
+ int nra = interaction_function[ftype].nratoms;
+ int inc = 1 + nra;
+ int nr = ilist[ftype].size();
- const t_iatom *ia = ilist[ftype].iatoms;
+ const t_iatom* ia = ilist[ftype].iatoms.data();
if (pbcMode == PbcMode::all)
{
pbc_null2 = pbc_null;
}
- else if (pbcMode == PbcMode::chargeGroup)
- {
- if (vsite->vsite_pbc_loc)
- {
- vsite_pbc = (*vsite->vsite_pbc_loc)[ftype - c_ftypeVsiteStart];
- }
- }
- for (int i = 0; i < nr; )
+ for (int i = 0; i < nr;)
{
- if (!vsite_pbc.empty())
- {
- if (vsite_pbc[i/(1 + nra)] > -2)
- {
- pbc_null2 = pbc_null;
- }
- else
- {
- pbc_null2 = nullptr;
- }
- }
-
int tp = ia[0];
/* Constants for constructing */
/* Construct the vsite depending on type */
switch (ftype)
{
+ case F_VSITE1: spread_vsite1(ia, f); break;
case F_VSITE2:
- spread_vsite2(ia, a1, x, f, fshift, pbc_null2, g);
+ spread_vsite2<virialHandling>(ia, a1, x, f, fshift, pbc_null2);
+ break;
+ case F_VSITE2FD:
+ spread_vsite2FD<virialHandling>(ia, a1, x, f, fshift, dxdf, pbc_null2);
break;
case F_VSITE3:
b1 = ip[tp].vsite.b;
- spread_vsite3(ia, a1, b1, x, f, fshift, pbc_null2, g);
+ spread_vsite3<virialHandling>(ia, a1, b1, x, f, fshift, pbc_null2);
break;
case F_VSITE3FD:
b1 = ip[tp].vsite.b;
- spread_vsite3FD(ia, a1, b1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ spread_vsite3FD<virialHandling>(ia, a1, b1, x, f, fshift, dxdf, pbc_null2);
break;
case F_VSITE3FAD:
b1 = ip[tp].vsite.b;
- spread_vsite3FAD(ia, a1, b1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ spread_vsite3FAD<virialHandling>(ia, a1, b1, x, f, fshift, dxdf, pbc_null2);
break;
case F_VSITE3OUT:
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- spread_vsite3OUT(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ spread_vsite3OUT<virialHandling>(ia, a1, b1, c1, x, f, fshift, dxdf, pbc_null2);
break;
case F_VSITE4FD:
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- spread_vsite4FD(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ spread_vsite4FD<virialHandling>(ia, a1, b1, c1, x, f, fshift, dxdf, pbc_null2);
break;
case F_VSITE4FDN:
b1 = ip[tp].vsite.b;
c1 = ip[tp].vsite.c;
- spread_vsite4FDN(ia, a1, b1, c1, x, f, fshift, VirCorr, dxdf, pbc_null2, g);
+ spread_vsite4FDN<virialHandling>(ia, a1, b1, c1, x, f, fshift, dxdf, pbc_null2);
break;
case F_VSITEN:
- inc = spread_vsiten(ia, ip, x, f, fshift, pbc_null2, g);
+ inc = spread_vsiten<virialHandling>(ia, ip, x, f, fshift, pbc_null2);
break;
default:
- gmx_fatal(FARGS, "No such vsite type %d in %s, line %d",
- ftype, __FILE__, __LINE__);
+ gmx_fatal(FARGS, "No such vsite type %d in %s, line %d", ftype, __FILE__, __LINE__);
}
clear_rvec(f[ia[1]]);
/* Increment loop variables */
- i += inc;
+ i += inc;
ia += inc;
}
}
}
}
-/*! \brief Clears the task force buffer elements that are written by task idTask */
-static void clearTaskForceBufferUsedElements(InterdependentTask *idTask)
+//! Wrapper function for calling the templated thread-local spread function
+static void spreadForceWrapper(ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ const VirialHandling virialHandling,
+ ArrayRef<RVec> fshift,
+ matrix dxdf,
+ const bool clearDxdf,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const InteractionList> ilist,
+ const t_pbc* pbc_null)
+{
+ if (virialHandling == VirialHandling::NonLinear && clearDxdf)
+ {
+ clear_mat(dxdf);
+ }
+
+ switch (virialHandling)
+ {
+ case VirialHandling::None:
+ spreadForceForThread<VirialHandling::None>(x, f, fshift, dxdf, ip, ilist, pbc_null);
+ break;
+ case VirialHandling::Pbc:
+ spreadForceForThread<VirialHandling::Pbc>(x, f, fshift, dxdf, ip, ilist, pbc_null);
+ break;
+ case VirialHandling::NonLinear:
+ spreadForceForThread<VirialHandling::NonLinear>(x, f, fshift, dxdf, ip, ilist, pbc_null);
+ break;
+ }
+}
+
+//! Clears the task force buffer elements that are written by task idTask
+static void clearTaskForceBufferUsedElements(InterdependentTask* idTask)
{
int ntask = idTask->spreadTask.size();
for (int ti = 0; ti < ntask; ti++)
{
- const AtomIndex *atomList = &idTask->atomIndex[idTask->spreadTask[ti]];
+ const AtomIndex* atomList = &idTask->atomIndex[idTask->spreadTask[ti]];
int natom = atomList->atom.size();
- RVec *force = idTask->force.data();
+ RVec* force = idTask->force.data();
for (int i = 0; i < natom; i++)
{
clear_rvec(force[atomList->atom[i]]);
}
}
-void spread_vsite_f(const gmx_vsite_t *vsite,
- const rvec * gmx_restrict x,
- rvec * gmx_restrict f, rvec * gmx_restrict fshift,
- gmx_bool VirCorr, matrix vir,
- t_nrnb *nrnb, const t_idef *idef,
- int ePBC, gmx_bool bMolPBC, const t_graph *g, const matrix box,
- const t_commrec *cr, gmx_wallcycle *wcycle)
+void VirtualSitesHandler::Impl::spreadForces(ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ const VirialHandling virialHandling,
+ ArrayRef<RVec> fshift,
+ matrix virial,
+ t_nrnb* nrnb,
+ const matrix box,
+ gmx_wallcycle* wcycle)
{
- wallcycle_start(wcycle, ewcVSITESPREAD);
- const bool useDomdec = vsite->useDomdec;
- GMX_ASSERT(!useDomdec || (cr != nullptr && DOMAINDECOMP(cr)), "When vsites are set up with domain decomposition, we need a valid commrec");
+ wallcycle_start(wcycle, WallCycleCounter::VsiteSpread);
+
+ const bool useDomdec = domainInfo_.useDomdec();
t_pbc pbc, *pbc_null;
- /* We only need to do pbc when we have inter-cg vsites */
- if ((useDomdec || bMolPBC) && vsite->n_intercg_vsite)
+ if (domainInfo_.useMolPbc_)
{
/* This is wasting some CPU time as we now do this multiple times
* per MD step.
*/
- pbc_null = set_pbc_dd(&pbc, ePBC, useDomdec ? cr->dd->nc : nullptr, FALSE, box);
+ pbc_null = set_pbc_dd(
+ &pbc, domainInfo_.pbcType_, useDomdec ? domainInfo_.domdec_->numCells : nullptr, FALSE, box);
}
else
{
if (useDomdec)
{
- dd_clear_f_vsites(cr->dd, f);
+ dd_clear_f_vsites(*domainInfo_.domdec_, f);
}
- if (vsite->nthreads == 1)
+ const int numThreads = threadingInfo_.numThreads();
+
+ if (numThreads == 1)
{
matrix dxdf;
- if (VirCorr)
- {
- clear_mat(dxdf);
- }
- spread_vsite_f_thread(vsite,
- x, f, fshift,
- VirCorr, dxdf,
- idef->iparams, idef->il,
- g, pbc_null);
+ spreadForceWrapper(x, f, virialHandling, fshift, dxdf, true, iparams_, ilists_, pbc_null);
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
for (int i = 0; i < DIM; i++)
{
for (int j = 0; j < DIM; j++)
{
- vir[i][j] += -0.5*dxdf[i][j];
+ virial[i][j] += -0.5 * dxdf[i][j];
}
}
}
else
{
/* First spread the vsites that might depend on non-local vsites */
- if (VirCorr)
- {
- clear_mat(vsite->tData[vsite->nthreads]->dxdf);
- }
- spread_vsite_f_thread(vsite,
- x, f, fshift,
- VirCorr, vsite->tData[vsite->nthreads]->dxdf,
- idef->iparams,
- vsite->tData[vsite->nthreads]->ilist,
- g, pbc_null);
-
-#pragma omp parallel num_threads(vsite->nthreads)
+ auto& nlDependentVSites = threadingInfo_.threadDataNonLocalDependent();
+ spreadForceWrapper(x,
+ f,
+ virialHandling,
+ fshift,
+ nlDependentVSites.dxdf,
+ true,
+ iparams_,
+ nlDependentVSites.ilist,
+ pbc_null);
+
+#pragma omp parallel num_threads(numThreads)
{
try
{
int thread = gmx_omp_get_thread_num();
- VsiteThread &tData = *vsite->tData[thread];
+ VsiteThread& tData = threadingInfo_.threadData(thread);
- rvec *fshift_t;
- if (thread == 0 || fshift == nullptr)
- {
- fshift_t = fshift;
- }
- else
+ ArrayRef<RVec> fshift_t;
+ if (virialHandling == VirialHandling::Pbc)
{
- fshift_t = tData.fshift;
-
- for (int i = 0; i < SHIFTS; i++)
+ if (thread == 0)
{
- clear_rvec(fshift_t[i]);
+ fshift_t = fshift;
+ }
+ else
+ {
+ fshift_t = tData.fshift;
+
+ for (int i = 0; i < c_numShiftVectors; i++)
+ {
+ clear_rvec(fshift_t[i]);
+ }
}
- }
- if (VirCorr)
- {
- clear_mat(tData.dxdf);
}
if (tData.useInterdependentTask)
* This is done using a thread-local force buffer force.
* First we need to copy the input vsite forces to force.
*/
- InterdependentTask *idTask = &tData.idTask;
+ InterdependentTask* idTask = &tData.idTask;
/* Clear the buffer elements set by our task during
* the last call to spread_vsite_f.
int nvsite = idTask->vsite.size();
for (int i = 0; i < nvsite; i++)
{
- copy_rvec(f[idTask->vsite[i]],
- idTask->force[idTask->vsite[i]]);
+ copy_rvec(f[idTask->vsite[i]], idTask->force[idTask->vsite[i]]);
}
- spread_vsite_f_thread(vsite,
- x, as_rvec_array(idTask->force.data()), fshift_t,
- VirCorr, tData.dxdf,
- idef->iparams,
- tData.idTask.ilist,
- g, pbc_null);
+ spreadForceWrapper(x,
+ idTask->force,
+ virialHandling,
+ fshift_t,
+ tData.dxdf,
+ true,
+ iparams_,
+ tData.idTask.ilist,
+ pbc_null);
/* We need a barrier before reducing forces below
* that have been produced by a different thread above.
int ntask = idTask->reduceTask.size();
for (int ti = 0; ti < ntask; ti++)
{
- const InterdependentTask *idt_foreign = &vsite->tData[idTask->reduceTask[ti]]->idTask;
- const AtomIndex *atomList = &idt_foreign->atomIndex[thread];
- const RVec *f_foreign = idt_foreign->force.data();
+ const InterdependentTask& idt_foreign =
+ threadingInfo_.threadData(idTask->reduceTask[ti]).idTask;
+ const AtomIndex& atomList = idt_foreign.atomIndex[thread];
+ const RVec* f_foreign = idt_foreign.force.data();
- int natom = atomList->atom.size();
- for (int i = 0; i < natom; i++)
+ for (int ind : atomList.atom)
{
- int ind = atomList->atom[i];
rvec_inc(f[ind], f_foreign[ind]);
/* Clearing of f_foreign is done at the next step */
}
}
/* Spread the vsites that spread locally only */
- spread_vsite_f_thread(vsite,
- x, f, fshift_t,
- VirCorr, tData.dxdf,
- idef->iparams,
- tData.ilist,
- g, pbc_null);
+ spreadForceWrapper(
+ x, f, virialHandling, fshift_t, tData.dxdf, false, iparams_, tData.ilist, pbc_null);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- if (fshift != nullptr)
+ if (virialHandling == VirialHandling::Pbc)
{
- for (int th = 1; th < vsite->nthreads; th++)
+ for (int th = 1; th < numThreads; th++)
{
- for (int i = 0; i < SHIFTS; i++)
+ for (int i = 0; i < c_numShiftVectors; i++)
{
- rvec_inc(fshift[i], vsite->tData[th]->fshift[i]);
+ rvec_inc(fshift[i], threadingInfo_.threadData(th).fshift[i]);
}
}
}
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
- for (int th = 0; th < vsite->nthreads + 1; th++)
+ for (int th = 0; th < numThreads + 1; th++)
{
/* MSVC doesn't like matrix references, so we use a pointer */
- const matrix *dxdf = &vsite->tData[th]->dxdf;
+ const matrix& dxdf = threadingInfo_.threadData(th).dxdf;
for (int i = 0; i < DIM; i++)
{
for (int j = 0; j < DIM; j++)
{
- vir[i][j] += -0.5*(*dxdf)[i][j];
+ virial[i][j] += -0.5 * dxdf[i][j];
}
}
}
if (useDomdec)
{
- dd_move_f_vsites(cr->dd, f, fshift);
+ dd_move_f_vsites(*domainInfo_.domdec_, f, fshift);
}
- inc_nrnb(nrnb, eNR_VSITE2, vsite_count(idef->il, F_VSITE2));
- inc_nrnb(nrnb, eNR_VSITE3, vsite_count(idef->il, F_VSITE3));
- inc_nrnb(nrnb, eNR_VSITE3FD, vsite_count(idef->il, F_VSITE3FD));
- inc_nrnb(nrnb, eNR_VSITE3FAD, vsite_count(idef->il, F_VSITE3FAD));
- inc_nrnb(nrnb, eNR_VSITE3OUT, vsite_count(idef->il, F_VSITE3OUT));
- inc_nrnb(nrnb, eNR_VSITE4FD, vsite_count(idef->il, F_VSITE4FD));
- inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(idef->il, F_VSITE4FDN));
- inc_nrnb(nrnb, eNR_VSITEN, vsite_count(idef->il, F_VSITEN));
+ inc_nrnb(nrnb, eNR_VSITE1, vsite_count(ilists_, F_VSITE1));
+ inc_nrnb(nrnb, eNR_VSITE2, vsite_count(ilists_, F_VSITE2));
+ inc_nrnb(nrnb, eNR_VSITE2FD, vsite_count(ilists_, F_VSITE2FD));
+ inc_nrnb(nrnb, eNR_VSITE3, vsite_count(ilists_, F_VSITE3));
+ inc_nrnb(nrnb, eNR_VSITE3FD, vsite_count(ilists_, F_VSITE3FD));
+ inc_nrnb(nrnb, eNR_VSITE3FAD, vsite_count(ilists_, F_VSITE3FAD));
+ inc_nrnb(nrnb, eNR_VSITE3OUT, vsite_count(ilists_, F_VSITE3OUT));
+ inc_nrnb(nrnb, eNR_VSITE4FD, vsite_count(ilists_, F_VSITE4FD));
+ inc_nrnb(nrnb, eNR_VSITE4FDN, vsite_count(ilists_, F_VSITE4FDN));
+ inc_nrnb(nrnb, eNR_VSITEN, vsite_count(ilists_, F_VSITEN));
- wallcycle_stop(wcycle, ewcVSITESPREAD);
+ wallcycle_stop(wcycle, WallCycleCounter::VsiteSpread);
}
-/*! \brief Returns the an array with charge-group indices for each atom
+/*! \brief Returns the an array with group indices for each atom
*
- * \param[in] chargeGroups The charge group block struct
+ * \param[in] grouping The paritioning of the atom range into atom groups
*/
-static std::vector<int> atom2cg(const t_block &chargeGroups)
+static std::vector<int> makeAtomToGroupMapping(const gmx::RangePartitioning& grouping)
{
- std::vector<int> a2cg(chargeGroups.index[chargeGroups.nr], 0);
+ std::vector<int> atomToGroup(grouping.fullRange().end(), 0);
- for (int chargeGroup = 0; chargeGroup < chargeGroups.nr; chargeGroup++)
+ for (int group = 0; group < grouping.numBlocks(); group++)
{
- std::fill(a2cg.begin() + chargeGroups.index[chargeGroup],
- a2cg.begin() + chargeGroups.index[chargeGroup + 1],
- chargeGroup);
+ auto block = grouping.block(group);
+ std::fill(atomToGroup.begin() + block.begin(), atomToGroup.begin() + block.end(), group);
}
- return a2cg;
+ return atomToGroup;
}
-int count_intercg_vsites(const gmx_mtop_t *mtop)
+int countNonlinearVsites(const gmx_mtop_t& mtop)
{
- int n_intercg_vsite = 0;
- for (const gmx_molblock_t &molb : mtop->molblock)
+ int numNonlinearVsites = 0;
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- const gmx_moltype_t &molt = mtop->moltype[molb.type];
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
- std::vector<int> a2cg = atom2cg(molt.cgs);
- for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
+ for (const auto& ilist : extractILists(molt.ilist, IF_VSITE))
{
- const int nral = NRAL(ftype);
- const InteractionList &il = molt.ilist[ftype];
- for (int i = 0; i < il.size(); i += 1 + nral)
+ if (ilist.functionType != F_VSITE2 && ilist.functionType != F_VSITE3
+ && ilist.functionType != F_VSITEN)
{
- int cg = a2cg[il.iatoms[1 + i]];
- for (int a = 1; a < nral; a++)
- {
- if (a2cg[il.iatoms[1 + a]] != cg)
- {
- n_intercg_vsite += molb.nmol;
- break;
- }
- }
+ numNonlinearVsites += molb.nmol * ilist.iatoms.size() / (1 + NRAL(ilist.functionType));
}
}
}
- return n_intercg_vsite;
+ return numNonlinearVsites;
}
-template <typename T>
-static VsitePbc
-get_vsite_pbc(const t_iparams *iparams, const T *ilist,
- const t_atom *atom, const t_mdatoms *md,
- const t_block &cgs)
+void VirtualSitesHandler::spreadForces(ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ const VirialHandling virialHandling,
+ ArrayRef<RVec> fshift,
+ matrix virial,
+ t_nrnb* nrnb,
+ const matrix box,
+ gmx_wallcycle* wcycle)
{
- /* Make an atom to charge group index */
- std::vector<int> a2cg = atom2cg(cgs);
+ impl_->spreadForces(x, f, virialHandling, fshift, virial, nrnb, box, wcycle);
+}
- /* Make an array that tells if the pbc of an atom is set */
- std::vector<bool> pbc_set(cgs.index[cgs.nr], false);
- /* PBC is set for all non vsites */
- for (int a = 0; a < cgs.index[cgs.nr]; a++)
+int countInterUpdategroupVsites(const gmx_mtop_t& mtop,
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingsPerMoleculeType)
+{
+ int n_intercg_vsite = 0;
+ for (const gmx_molblock_t& molb : mtop.molblock)
{
- if ((atom && atom[a].ptype != eptVSite) ||
- (md && md->ptype[a] != eptVSite))
+ const gmx_moltype_t& molt = mtop.moltype[molb.type];
+
+ std::vector<int> atomToGroup;
+ if (!updateGroupingsPerMoleculeType.empty())
{
- pbc_set[a] = true;
+ atomToGroup = makeAtomToGroupMapping(updateGroupingsPerMoleculeType[molb.type]);
}
- }
-
- VsitePbc vsite_pbc;
-
- for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
- {
- { // TODO remove me
- int nral = NRAL(ftype);
- const T &il = ilist[ftype];
-
- std::vector<int> &vsite_pbc_f = vsite_pbc[ftype - F_VSITE2];
- vsite_pbc_f.resize(il.size()/(1 + nral));
-
- int i = 0;
- while (i < il.size())
+ for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
+ {
+ const int nral = NRAL(ftype);
+ const InteractionList& il = molt.ilist[ftype];
+ for (int i = 0; i < il.size(); i += 1 + nral)
{
- int vsi = i/(1 + nral);
- t_iatom vsite = il.iatoms[i + 1];
- int cg_v = a2cg[vsite];
- /* A value of -2 signals that this vsite and its contructing
- * atoms are all within the same cg, so no pbc is required.
- */
- vsite_pbc_f[vsi] = -2;
- /* Check if constructing atoms are outside the vsite's cg */
- int nc3 = 0;
- if (ftype == F_VSITEN)
- {
- nc3 = 3*iparams[il.iatoms[i]].vsiten.n;
- for (int j = 0; j < nc3; j += 3)
- {
- if (a2cg[il.iatoms[i + j + 2]] != cg_v)
- {
- vsite_pbc_f[vsi] = -1;
- }
- }
- }
- else
+ bool isInterGroup = atomToGroup.empty();
+ if (!isInterGroup)
{
+ const int group = atomToGroup[il.iatoms[1 + i]];
for (int a = 1; a < nral; a++)
{
- if (a2cg[il.iatoms[i + 1 + a]] != cg_v)
+ if (atomToGroup[il.iatoms[1 + a]] != group)
{
- vsite_pbc_f[vsi] = -1;
- }
- }
- }
- if (vsite_pbc_f[vsi] == -1)
- {
- /* Check if this is the first processed atom of a vsite only cg */
- gmx_bool bViteOnlyCG_and_FirstAtom = TRUE;
- for (int a = cgs.index[cg_v]; a < cgs.index[cg_v + 1]; a++)
- {
- /* Non-vsites already have pbc set, so simply check for pbc_set */
- if (pbc_set[a])
- {
- bViteOnlyCG_and_FirstAtom = FALSE;
+ isInterGroup = true;
break;
}
}
- if (bViteOnlyCG_and_FirstAtom)
- {
- /* First processed atom of a vsite only charge group.
- * The pbc of the input coordinates to construct_vsites
- * should be preserved.
- */
- vsite_pbc_f[vsi] = vsite;
- }
- else if (cg_v != a2cg[il.iatoms[1 + i + 1]])
- {
- /* This vsite has a different charge group index
- * than it's first constructing atom
- * and the charge group has more than one atom,
- * search for the first normal particle
- * or vsite that already had its pbc defined.
- * If nothing is found, use full pbc for this vsite.
- */
- for (int a = cgs.index[cg_v]; a < cgs.index[cg_v + 1]; a++)
- {
- if (a != vsite && pbc_set[a])
- {
- vsite_pbc_f[vsi] = a;
- if (gmx_debug_at)
- {
- fprintf(debug, "vsite %d match pbc with atom %d\n",
- vsite+1, a+1);
- }
- break;
- }
- }
- if (gmx_debug_at)
- {
- fprintf(debug, "vsite atom %d cg %d - %d pbc atom %d\n",
- vsite+1, cgs.index[cg_v] + 1, cgs.index[cg_v + 1],
- vsite_pbc_f[vsi] + 1);
- }
- }
}
- if (ftype == F_VSITEN)
+ if (isInterGroup)
{
- /* The other entries in vsite_pbc_f are not used for center vsites */
- i += nc3;
+ n_intercg_vsite += molb.nmol;
}
- else
- {
- i += 1 + nral;
- }
-
- /* This vsite now has its pbc defined */
- pbc_set[vsite] = true;
}
}
}
- return vsite_pbc;
+ return n_intercg_vsite;
}
-
-std::unique_ptr<gmx_vsite_t>
-initVsite(const gmx_mtop_t &mtop,
- const t_commrec *cr)
+std::unique_ptr<VirtualSitesHandler> makeVirtualSitesHandler(const gmx_mtop_t& mtop,
+ const t_commrec* cr,
+ PbcType pbcType,
+ ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType)
{
GMX_RELEASE_ASSERT(cr != nullptr, "We need a valid commrec");
- std::unique_ptr<gmx_vsite_t> vsite;
+ std::unique_ptr<VirtualSitesHandler> vsite;
/* check if there are vsites */
int nvsite = 0;
{
if (interaction_function[ftype].flags & IF_VSITE)
{
- GMX_ASSERT(ftype >= c_ftypeVsiteStart && ftype < c_ftypeVsiteEnd, "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
+ GMX_ASSERT(ftype >= c_ftypeVsiteStart && ftype < c_ftypeVsiteEnd,
+ "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
- nvsite += gmx_mtop_ftype_count(&mtop, ftype);
+ nvsite += gmx_mtop_ftype_count(mtop, ftype);
}
else
{
- GMX_ASSERT(ftype < c_ftypeVsiteStart || ftype >= c_ftypeVsiteEnd, "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
+ GMX_ASSERT(ftype < c_ftypeVsiteStart || ftype >= c_ftypeVsiteEnd,
+ "c_ftypeVsiteStart and/or c_ftypeVsiteEnd do not have correct values");
}
}
return vsite;
}
- vsite = std::make_unique<gmx_vsite_t>();
-
- vsite->n_intercg_vsite = count_intercg_vsites(&mtop);
-
- vsite->bHaveChargeGroups = (ncg_mtop(&mtop) < mtop.natoms);
-
- vsite->useDomdec = (DOMAINDECOMP(cr) && cr->dd->nnodes > 1);
-
- /* If we don't have charge groups, the vsite follows its own pbc.
- *
- * With charge groups, each vsite needs to follow the pbc of the charge
- * group. Thus we need to keep track of PBC. Here we assume that without
- * domain decomposition all molecules are whole (which will not be
- * the case with periodic molecules).
- */
- if (vsite->bHaveChargeGroups &&
- vsite->n_intercg_vsite > 0 &&
- DOMAINDECOMP(cr))
- {
- vsite->vsite_pbc_molt.resize(mtop.moltype.size());
- for (size_t mt = 0; mt < mtop.moltype.size(); mt++)
- {
- const gmx_moltype_t &molt = mtop.moltype[mt];
- vsite->vsite_pbc_molt[mt] = get_vsite_pbc(mtop.ffparams.iparams.data(),
- molt.ilist.data(),
- molt.atoms.atom, nullptr,
- molt.cgs);
- }
-
- vsite->vsite_pbc_loc = std::make_unique<VsitePbc>();
- }
-
- vsite->nthreads = gmx_omp_nthreads_get(emntVSITE);
+ return std::make_unique<VirtualSitesHandler>(mtop, cr->dd, pbcType, updateGroupingPerMoleculeType);
+}
- if (vsite->nthreads > 1)
+ThreadingInfo::ThreadingInfo() : numThreads_(gmx_omp_nthreads_get(ModuleMultiThread::VirtualSite))
+{
+ if (numThreads_ > 1)
{
/* We need one extra thread data structure for the overlap vsites */
- vsite->tData.resize(vsite->nthreads + 1);
-#pragma omp parallel for num_threads(vsite->nthreads) schedule(static)
- for (int thread = 0; thread < vsite->nthreads; thread++)
+ tData_.resize(numThreads_ + 1);
+#pragma omp parallel for num_threads(numThreads_) schedule(static)
+ for (int thread = 0; thread < numThreads_; thread++)
{
try
{
- vsite->tData[thread] = std::make_unique<VsiteThread>();
+ tData_[thread] = std::make_unique<VsiteThread>();
- InterdependentTask &idTask = vsite->tData[thread]->idTask;
+ InterdependentTask& idTask = tData_[thread]->idTask;
idTask.nuse = 0;
- idTask.atomIndex.resize(vsite->nthreads);
+ idTask.atomIndex.resize(numThreads_);
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- if (vsite->nthreads > 1)
+ if (numThreads_ > 1)
{
- vsite->tData[vsite->nthreads] = std::make_unique<VsiteThread>();
+ tData_[numThreads_] = std::make_unique<VsiteThread>();
}
}
-
- return vsite;
}
-gmx_vsite_t::gmx_vsite_t()
+VirtualSitesHandler::Impl::Impl(const gmx_mtop_t& mtop,
+ gmx_domdec_t* domdec,
+ const PbcType pbcType,
+ const ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType) :
+ numInterUpdategroupVirtualSites_(countInterUpdategroupVsites(mtop, updateGroupingPerMoleculeType)),
+ domainInfo_({ pbcType, pbcType != PbcType::No && numInterUpdategroupVirtualSites_ > 0, domdec }),
+ iparams_(mtop.ffparams.iparams)
{
}
-gmx_vsite_t::~gmx_vsite_t()
+VirtualSitesHandler::VirtualSitesHandler(const gmx_mtop_t& mtop,
+ gmx_domdec_t* domdec,
+ const PbcType pbcType,
+ const ArrayRef<const RangePartitioning> updateGroupingPerMoleculeType) :
+ impl_(new Impl(mtop, domdec, pbcType, updateGroupingPerMoleculeType))
{
}
-static inline void flagAtom(InterdependentTask *idTask, int atom,
- int thread, int nthread, int natperthread)
+//! Flag that atom \p atom which is home in another task, if it has not already been added before
+static inline void flagAtom(InterdependentTask* idTask, const int atom, const int numThreads, const int numAtomsPerThread)
{
if (!idTask->use[atom])
{
idTask->use[atom] = true;
- thread = atom/natperthread;
+ int thread = atom / numAtomsPerThread;
/* Assign all non-local atom force writes to thread 0 */
- if (thread >= nthread)
+ if (thread >= numThreads)
{
- thread = 0;
+ thread = 0;
}
idTask->atomIndex[thread].atom.push_back(atom);
}
}
-/*\brief Here we try to assign all vsites that are in our local range.
+/*! \brief Here we try to assign all vsites that are in our local range.
*
* Our task local atom range is tData->rangeStart - tData->rangeEnd.
* Vsites that depend only on local atoms, as indicated by taskIndex[]==thread,
* taskIndex[] is set for all vsites in our range, either to our local tasks
* or to the single last task as taskIndex[]=2*nthreads.
*/
-static void assignVsitesToThread(VsiteThread *tData,
- int thread,
- int nthread,
- int natperthread,
- gmx::ArrayRef<int> taskIndex,
- const t_ilist *ilist,
- const t_iparams *ip,
- const unsigned short *ptype)
+static void assignVsitesToThread(VsiteThread* tData,
+ int thread,
+ int nthread,
+ int natperthread,
+ gmx::ArrayRef<int> taskIndex,
+ ArrayRef<const InteractionList> ilist,
+ ArrayRef<const t_iparams> ip,
+ ArrayRef<const ParticleType> ptype)
{
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- tData->ilist[ftype].nr = 0;
- tData->idTask.ilist[ftype].nr = 0;
+ tData->ilist[ftype].clear();
+ tData->idTask.ilist[ftype].clear();
- int nral1 = 1 + NRAL(ftype);
- int inc = nral1;
- t_iatom *iat = ilist[ftype].iatoms;
- for (int i = 0; i < ilist[ftype].nr; )
+ const int nral1 = 1 + NRAL(ftype);
+ const int* iat = ilist[ftype].iatoms.data();
+ for (int i = 0; i < ilist[ftype].size();)
{
- if (ftype == F_VSITEN)
- {
- /* The 3 below is from 1+NRAL(ftype)=3 */
- inc = ip[iat[i]].vsiten.n*3;
- }
+ /* Get the number of iatom entries in this virtual site.
+ * The 3 below for F_VSITEN is from 1+NRAL(ftype)=3
+ */
+ const int numIAtoms = (ftype == F_VSITEN ? ip[iat[i]].vsiten.n * 3 : nral1);
- if (iat[1 + i] < tData->rangeStart ||
- iat[1 + i] >= tData->rangeEnd)
+ if (iat[1 + i] < tData->rangeStart || iat[1 + i] >= tData->rangeEnd)
{
/* This vsite belongs to a different thread */
- i += inc;
+ i += numIAtoms;
continue;
}
for (int j = i + 2; j < i + nral1; j++)
{
/* Do a range check to avoid a harmless race on taskIndex */
- if (iat[j] < tData->rangeStart ||
- iat[j] >= tData->rangeEnd ||
- taskIndex[iat[j]] != thread)
+ if (iat[j] < tData->rangeStart || iat[j] >= tData->rangeEnd || taskIndex[iat[j]] != thread)
{
- if (!tData->useInterdependentTask ||
- ptype[iat[j]] == eptVSite)
+ if (!tData->useInterdependentTask || ptype[iat[j]] == ParticleType::VSite)
{
/* At least one constructing atom is a vsite
* that is not assigned to the same thread.
* Put this vsite into a separate task.
*/
- task = 2*nthread;
+ task = 2 * nthread;
break;
}
}
else
{
- for (int j = i + 2; j < i + inc; j += 3)
+ for (int j = i + 2; j < i + numIAtoms; j += 3)
{
/* Do a range check to avoid a harmless race on taskIndex */
- if (iat[j] < tData->rangeStart ||
- iat[j] >= tData->rangeEnd ||
- taskIndex[iat[j]] != thread)
+ if (iat[j] < tData->rangeStart || iat[j] >= tData->rangeEnd || taskIndex[iat[j]] != thread)
{
- GMX_ASSERT(ptype[iat[j]] != eptVSite, "A vsite to be assigned in assignVsitesToThread has a vsite as a constructing atom that does not belong to our task, such vsites should be assigned to the single 'master' task");
+ GMX_ASSERT(ptype[iat[j]] != ParticleType::VSite,
+ "A vsite to be assigned in assignVsitesToThread has a vsite as "
+ "a constructing atom that does not belong to our task, such "
+ "vsites should be assigned to the single 'master' task");
- task = nthread + thread;
+ if (tData->useInterdependentTask)
+ {
+ // Assign to the interdependent task
+ task = nthread + thread;
+ }
+ else
+ {
+ // Assign to the separate, non-parallel task
+ task = 2 * nthread;
+ }
}
}
}
/* Update this vsite's thread index entry */
- taskIndex[iat[1+i]] = task;
+ taskIndex[iat[1 + i]] = task;
if (task == thread || task == nthread + thread)
{
/* Copy this vsite to the thread data struct of thread */
- t_ilist *il_task;
+ InteractionList* il_task;
if (task == thread)
{
il_task = &tData->ilist[ftype];
{
il_task = &tData->idTask.ilist[ftype];
}
- /* Ensure we have sufficient memory allocated */
- if (il_task->nr + inc > il_task->nalloc)
- {
- il_task->nalloc = over_alloc_large(il_task->nr + inc);
- srenew(il_task->iatoms, il_task->nalloc);
- }
/* Copy the vsite data to the thread-task local array */
- for (int j = i; j < i + inc; j++)
- {
- il_task->iatoms[il_task->nr++] = iat[j];
- }
+ il_task->push_back(iat[i], numIAtoms - 1, iat + i + 1);
if (task == nthread + thread)
{
- /* This vsite write outside our own task force block.
+ /* This vsite writes outside our own task force block.
* Put it into the interdependent task list and flag
* the atoms involved for reduction.
*/
{
for (int j = i + 2; j < i + nral1; j++)
{
- flagAtom(&tData->idTask, iat[j],
- thread, nthread, natperthread);
+ flagAtom(&tData->idTask, iat[j], nthread, natperthread);
}
}
else
{
- for (int j = i + 2; j < i + inc; j += 3)
+ for (int j = i + 2; j < i + numIAtoms; j += 3)
{
- flagAtom(&tData->idTask, iat[j],
- thread, nthread, natperthread);
+ flagAtom(&tData->idTask, iat[j], nthread, natperthread);
}
}
}
}
- i += inc;
+ i += numIAtoms;
}
}
}
/*! \brief Assign all vsites with taskIndex[]==task to task tData */
-static void assignVsitesToSingleTask(VsiteThread *tData,
- int task,
- gmx::ArrayRef<const int> taskIndex,
- const t_ilist *ilist,
- const t_iparams *ip)
+static void assignVsitesToSingleTask(VsiteThread* tData,
+ int task,
+ gmx::ArrayRef<const int> taskIndex,
+ ArrayRef<const InteractionList> ilist,
+ ArrayRef<const t_iparams> ip)
{
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- tData->ilist[ftype].nr = 0;
- tData->idTask.ilist[ftype].nr = 0;
+ tData->ilist[ftype].clear();
+ tData->idTask.ilist[ftype].clear();
- int nral1 = 1 + NRAL(ftype);
- int inc = nral1;
- t_iatom *iat = ilist[ftype].iatoms;
- t_ilist *il_task = &tData->ilist[ftype];
+ int nral1 = 1 + NRAL(ftype);
+ int inc = nral1;
+ const int* iat = ilist[ftype].iatoms.data();
+ InteractionList* il_task = &tData->ilist[ftype];
- for (int i = 0; i < ilist[ftype].nr; )
+ for (int i = 0; i < ilist[ftype].size();)
{
if (ftype == F_VSITEN)
{
/* The 3 below is from 1+NRAL(ftype)=3 */
- inc = ip[iat[i]].vsiten.n*3;
+ inc = ip[iat[i]].vsiten.n * 3;
}
/* Check if the vsite is assigned to our task */
if (taskIndex[iat[1 + i]] == task)
{
- /* Ensure we have sufficient memory allocated */
- if (il_task->nr + inc > il_task->nalloc)
- {
- il_task->nalloc = over_alloc_large(il_task->nr + inc);
- srenew(il_task->iatoms, il_task->nalloc);
- }
/* Copy the vsite data to the thread-task local array */
- for (int j = i; j < i + inc; j++)
- {
- il_task->iatoms[il_task->nr++] = iat[j];
- }
+ il_task->push_back(iat[i], inc - 1, iat + i + 1);
}
i += inc;
}
}
-void split_vsites_over_threads(const t_ilist *ilist,
- const t_iparams *ip,
- const t_mdatoms *mdatoms,
- gmx_vsite_t *vsite)
+void ThreadingInfo::setVirtualSites(ArrayRef<const InteractionList> ilists,
+ ArrayRef<const t_iparams> iparams,
+ const int numAtoms,
+ const int homenr,
+ ArrayRef<const ParticleType> ptype,
+ const bool useDomdec)
{
- int vsite_atom_range, natperthread;
-
- if (vsite->nthreads == 1)
+ if (numThreads_ <= 1)
{
/* Nothing to do */
return;
* uniformly in each domain along the major dimension, usually x,
* it will also perform well.
*/
- if (!vsite->useDomdec)
+ int vsite_atom_range;
+ int natperthread;
+ if (!useDomdec)
{
vsite_atom_range = -1;
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- { // TODO remove me
+ { // TODO remove me
if (ftype != F_VSITEN)
{
- int nral1 = 1 + NRAL(ftype);
- const t_iatom *iat = ilist[ftype].iatoms;
- for (int i = 0; i < ilist[ftype].nr; i += nral1)
+ int nral1 = 1 + NRAL(ftype);
+ ArrayRef<const int> iat = ilists[ftype].iatoms;
+ for (int i = 0; i < ilists[ftype].size(); i += nral1)
{
for (int j = i + 1; j < i + nral1; j++)
{
}
else
{
- int vs_ind_end;
+ int vs_ind_end;
- const t_iatom *iat = ilist[ftype].iatoms;
+ ArrayRef<const int> iat = ilists[ftype].iatoms;
- int i = 0;
- while (i < ilist[ftype].nr)
+ int i = 0;
+ while (i < ilists[ftype].size())
{
/* The 3 below is from 1+NRAL(ftype)=3 */
- vs_ind_end = i + ip[iat[i]].vsiten.n*3;
+ vs_ind_end = i + iparams[iat[i]].vsiten.n * 3;
- vsite_atom_range = std::max(vsite_atom_range, iat[i+1]);
+ vsite_atom_range = std::max(vsite_atom_range, iat[i + 1]);
while (i < vs_ind_end)
{
- vsite_atom_range = std::max(vsite_atom_range, iat[i+2]);
- i += 3;
+ vsite_atom_range = std::max(vsite_atom_range, iat[i + 2]);
+ i += 3;
}
}
}
}
}
vsite_atom_range++;
- natperthread = (vsite_atom_range + vsite->nthreads - 1)/vsite->nthreads;
+ natperthread = (vsite_atom_range + numThreads_ - 1) / numThreads_;
}
else
{
* When assigning vsites to threads, we should take care that the last
* threads also covers the non-local range.
*/
- vsite_atom_range = mdatoms->nr;
- natperthread = (mdatoms->homenr + vsite->nthreads - 1)/vsite->nthreads;
+ vsite_atom_range = numAtoms;
+ natperthread = (homenr + numThreads_ - 1) / numThreads_;
}
if (debug)
{
- fprintf(debug, "virtual site thread dist: natoms %d, range %d, natperthread %d\n", mdatoms->nr, vsite_atom_range, natperthread);
+ fprintf(debug,
+ "virtual site thread dist: natoms %d, range %d, natperthread %d\n",
+ numAtoms,
+ vsite_atom_range,
+ natperthread);
}
/* To simplify the vsite assignment, we make an index which tells us
* to which task particles, both non-vsites and vsites, are assigned.
*/
- vsite->taskIndex.resize(mdatoms->nr);
+ taskIndex_.resize(numAtoms);
/* Initialize the task index array. Here we assign the non-vsite
* particles to task=thread, so we easily figure out if vsites
* depend on local and/or non-local particles in assignVsitesToThread.
*/
- gmx::ArrayRef<int> taskIndex = vsite->taskIndex;
{
- int thread = 0;
- for (int i = 0; i < mdatoms->nr; i++)
+ int thread = 0;
+ for (int i = 0; i < numAtoms; i++)
{
- if (mdatoms->ptype[i] == eptVSite)
+ if (ptype[i] == ParticleType::VSite)
{
/* vsites are not assigned to a task yet */
- taskIndex[i] = -1;
+ taskIndex_[i] = -1;
}
else
{
/* assign non-vsite particles to task thread */
- taskIndex[i] = thread;
+ taskIndex_[i] = thread;
}
- if (i == (thread + 1)*natperthread && thread < vsite->nthreads)
+ if (i == (thread + 1) * natperthread && thread < numThreads_)
{
thread++;
}
}
}
-#pragma omp parallel num_threads(vsite->nthreads)
+#pragma omp parallel num_threads(numThreads_)
{
try
{
int thread = gmx_omp_get_thread_num();
- VsiteThread &tData = *vsite->tData[thread];
+ VsiteThread& tData = *tData_[thread];
/* Clear the buffer use flags that were set before */
if (tData.useInterdependentTask)
{
- InterdependentTask &idTask = tData.idTask;
+ InterdependentTask& idTask = tData.idTask;
/* To avoid an extra OpenMP barrier in spread_vsite_f,
* we clear the force buffer at the next step,
clearTaskForceBufferUsedElements(&idTask);
idTask.vsite.resize(0);
- for (int t = 0; t < vsite->nthreads; t++)
+ for (int t = 0; t < numThreads_; t++)
{
- AtomIndex &atomIndex = idTask.atomIndex[t];
+ AtomIndex& atomIndex = idTask.atomIndex[t];
int natom = atomIndex.atom.size();
for (int i = 0; i < natom; i++)
{
}
/* To avoid large f_buf allocations of #threads*vsite_atom_range
- * we don't use task2 with more than 200000 atoms. This doesn't
- * affect performance, since with such a large range relatively few
- * vsites will end up in the separate task.
- * Note that useTask2 should be the same for all threads.
+ * we don't use the interdependent tasks with more than 200000 atoms.
+ * This doesn't affect performance, since with such a large range
+ * relatively few vsites will end up in the separate task.
+ * Note that useInterdependentTask should be the same for all threads.
*/
- tData.useInterdependentTask = (vsite_atom_range <= 200000);
+ const int c_maxNumLocalAtomsForInterdependentTask = 200000;
+ tData.useInterdependentTask = (vsite_atom_range <= c_maxNumLocalAtomsForInterdependentTask);
if (tData.useInterdependentTask)
{
size_t natoms_use_in_vsites = vsite_atom_range;
- InterdependentTask &idTask = tData.idTask;
+ InterdependentTask& idTask = tData.idTask;
/* To avoid resizing and re-clearing every nstlist steps,
* we never down size the force buffer.
*/
- if (natoms_use_in_vsites > idTask.force.size() ||
- natoms_use_in_vsites > idTask.use.size())
+ if (natoms_use_in_vsites > idTask.force.size() || natoms_use_in_vsites > idTask.use.size())
{
idTask.force.resize(natoms_use_in_vsites, { 0, 0, 0 });
idTask.use.resize(natoms_use_in_vsites, false);
}
/* Assign all vsites that can execute independently on threads */
- tData.rangeStart = thread *natperthread;
- if (thread < vsite->nthreads - 1)
+ tData.rangeStart = thread * natperthread;
+ if (thread < numThreads_ - 1)
{
- tData.rangeEnd = (thread + 1)*natperthread;
+ tData.rangeEnd = (thread + 1) * natperthread;
}
else
{
/* The last thread should cover up to the end of the range */
- tData.rangeEnd = mdatoms->nr;
+ tData.rangeEnd = numAtoms;
}
- assignVsitesToThread(&tData,
- thread, vsite->nthreads,
- natperthread,
- taskIndex,
- ilist, ip, mdatoms->ptype);
+ assignVsitesToThread(
+ &tData, thread, numThreads_, natperthread, taskIndex_, ilists, iparams, ptype);
if (tData.useInterdependentTask)
{
* scaling at high thread counts we therefore construct
* an index to only loop over the actually affected tasks.
*/
- InterdependentTask &idTask = tData.idTask;
+ InterdependentTask& idTask = tData.idTask;
/* Ensure assignVsitesToThread finished on other threads */
#pragma omp barrier
idTask.spreadTask.resize(0);
idTask.reduceTask.resize(0);
- for (int t = 0; t < vsite->nthreads; t++)
+ for (int t = 0; t < numThreads_; t++)
{
/* Do we write to the force buffer of task t? */
if (!idTask.atomIndex[t].atom.empty())
idTask.spreadTask.push_back(t);
}
/* Does task t write to our force buffer? */
- if (!vsite->tData[t]->idTask.atomIndex[thread].atom.empty())
+ if (!tData_[t]->idTask.atomIndex[thread].atom.empty())
{
idTask.reduceTask.push_back(t);
}
}
}
}
- GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR;
+ GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Assign all remaining vsites, that will have taskIndex[]=2*vsite->nthreads,
* to a single task that will not run in parallel with other tasks.
*/
- assignVsitesToSingleTask(vsite->tData[vsite->nthreads].get(),
- 2*vsite->nthreads,
- taskIndex,
- ilist, ip);
+ assignVsitesToSingleTask(tData_[numThreads_].get(), 2 * numThreads_, taskIndex_, ilists, iparams);
- if (debug && vsite->nthreads > 1)
+ if (debug && numThreads_ > 1)
{
- fprintf(debug, "virtual site useInterdependentTask %d, nuse:\n",
- static_cast<int>(vsite->tData[0]->useInterdependentTask));
- for (int th = 0; th < vsite->nthreads + 1; th++)
+ fprintf(debug,
+ "virtual site useInterdependentTask %d, nuse:\n",
+ static_cast<int>(tData_[0]->useInterdependentTask));
+ for (int th = 0; th < numThreads_ + 1; th++)
{
- fprintf(debug, " %4d", vsite->tData[th]->idTask.nuse);
+ fprintf(debug, " %4d", tData_[th]->idTask.nuse);
}
fprintf(debug, "\n");
for (int ftype = c_ftypeVsiteStart; ftype < c_ftypeVsiteEnd; ftype++)
{
- if (ilist[ftype].nr > 0)
+ if (!ilists[ftype].empty())
{
- fprintf(debug, "%-20s thread dist:",
- interaction_function[ftype].longname);
- for (int th = 0; th < vsite->nthreads + 1; th++)
+ fprintf(debug, "%-20s thread dist:", interaction_function[ftype].longname);
+ for (int th = 0; th < numThreads_ + 1; th++)
{
- fprintf(debug, " %4d %4d ",
- vsite->tData[th]->ilist[ftype].nr,
- vsite->tData[th]->idTask.ilist[ftype].nr);
+ fprintf(debug,
+ " %4d %4d ",
+ tData_[th]->ilist[ftype].size(),
+ tData_[th]->idTask.ilist[ftype].size());
}
fprintf(debug, "\n");
}
}
#ifndef NDEBUG
- int nrOrig = vsiteIlistNrCount(ilist);
+ int nrOrig = vsiteIlistNrCount(ilists);
int nrThreaded = 0;
- for (int th = 0; th < vsite->nthreads + 1; th++)
+ for (int th = 0; th < numThreads_ + 1; th++)
{
- nrThreaded +=
- vsiteIlistNrCount(vsite->tData[th]->ilist) +
- vsiteIlistNrCount(vsite->tData[th]->idTask.ilist);
+ nrThreaded += vsiteIlistNrCount(tData_[th]->ilist) + vsiteIlistNrCount(tData_[th]->idTask.ilist);
}
- GMX_ASSERT(nrThreaded == nrOrig, "The number of virtual sites assigned to all thread task has to match the total number of virtual sites");
+ GMX_ASSERT(nrThreaded == nrOrig,
+ "The number of virtual sites assigned to all thread task has to match the total "
+ "number of virtual sites");
#endif
}
-void set_vsite_top(gmx_vsite_t *vsite,
- const gmx_localtop_t *top,
- const t_mdatoms *md)
+void VirtualSitesHandler::Impl::setVirtualSites(ArrayRef<const InteractionList> ilists,
+ const int numAtoms,
+ const int homenr,
+ ArrayRef<const ParticleType> ptype)
{
- if (vsite->n_intercg_vsite > 0 && vsite->bHaveChargeGroups)
- {
- vsite->vsite_pbc_loc = std::make_unique<VsitePbc>();
- *vsite->vsite_pbc_loc = get_vsite_pbc(top->idef.iparams,
- top->idef.il, nullptr, md,
- top->cgs);
- }
+ ilists_ = ilists;
- if (vsite->nthreads > 1)
- {
- if (vsite->bHaveChargeGroups)
- {
- gmx_fatal(FARGS, "The combination of threading, virtual sites and charge groups is not implemented");
- }
+ threadingInfo_.setVirtualSites(ilists, iparams_, numAtoms, homenr, ptype, domainInfo_.useDomdec());
+}
- split_vsites_over_threads(top->idef.il, top->idef.iparams,
- md, vsite);
- }
+void VirtualSitesHandler::setVirtualSites(ArrayRef<const InteractionList> ilists,
+ const int numAtoms,
+ const int homenr,
+ ArrayRef<const ParticleType> ptype)
+{
+ impl_->setVirtualSites(ilists, numAtoms, homenr, ptype);
}
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff