* To help us fund GROMACS development, we humbly ask that you cite
* the research papers on the package. Check out http://www.gromacs.org.
*/
+/*! \libinternal \file
+ * \brief Implements the VirtualSitesHandler class and vsite standalone functions
+ *
+ * \author Berk Hess <hess@kth.se>
+ * \ingroup module_mdlib
+ * \inlibraryapi
+ */
+
#include "gmxpre.h"
#include "vsite.h"
* Any remaining vsites are assigned to a separate master thread task.
*/
-using gmx::ArrayRef;
-using gmx::RVec;
+namespace gmx
+{
+
+//! VirialHandling is often used outside VirtualSitesHandler class members
+using VirialHandling = VirtualSitesHandler::VirialHandling;
+
+/*! \libinternal
+ * \brief Information on PBC and domain decomposition for virtual sites
+ */
+struct DomainInfo
+{
+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)
+ {
+ }
+
+ //! Returns whether we are using domain decomposition with more than 1 DD rank
+ bool useDomdec() const { return (domdec_ != nullptr); }
-/*! \brief List of atom indices belonging to a task */
+ //! 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;
+};
+
+/*! \libinternal
+ * \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 */
+/*! \libinternal
+ * \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
std::vector<int> reduceTask;
};
-/*! \brief Vsite thread task data structure */
+/*! \libinternal
+ * \brief Vsite thread task data structure
+ */
struct VsiteThread
{
//! Start of atom range of this task
//! The interaction lists, only vsite entries are used
std::array<InteractionList, F_NRE> ilist;
//! Local fshift accumulation buffer
- rvec fshift[SHIFTS];
+ std::array<RVec, SHIFTS> fshift;
//! Local virial dx*df accumulation buffer
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
{
rangeStart = -1;
rangeEnd = -1;
- clear_rvecs(SHIFTS, fshift);
+ for (auto& elem : fshift)
+ {
+ elem = { 0.0_real, 0.0_real, 0.0_real };
+ }
clear_mat(dxdf);
useInterdependentTask = false;
}
};
+
+/*! \libinternal
+ * \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,
+ const t_mdatoms& mdatoms,
+ 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_;
+};
+
+/*! \libinternal
+ * \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);
+
+ //! 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, const t_mdatoms& mdatoms);
+
+ /*! \brief Create positions of vsite atoms based for the local system
+ *
+ * \param[in,out] x The coordinates
+ * \param[in] dt The time step
+ * \param[in,out] v When != nullptr, velocities for vsites are set as displacement/dt
+ * \param[in] box The box
+ */
+ void construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) 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
return nr;
}
+//! 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)
}
}
+//! Returns the 1/norm(x)
static inline real inverseNorm(const rvec x)
{
return gmx::invsqrt(iprod(x, x));
}
+#ifndef DOXYGEN
/* Vsite construction routines */
static void constr_vsite2(const rvec xi, const rvec xj, rvec x, real a, const t_pbc* pbc)
/* TOTAL: 47 flops */
}
-
-static int constr_vsiten(const t_iatom* ia, ArrayRef<const t_iparams> ip, rvec* x, const t_pbc* pbc)
+static int constr_vsiten(const t_iatom* ia, ArrayRef<const t_iparams> ip, ArrayRef<RVec> x, const t_pbc* pbc)
{
rvec x1, dx;
dvec dsum;
return n3;
}
-/*! \brief PBC modes for vsite construction and spreading */
+#endif // DOXYGEN
+
+//! PBC modes for vsite construction and spreading
enum class PbcMode
{
- all, // Apply normal, simple PBC for all vsites
- 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
}
}
-static void construct_vsites_thread(rvec x[],
- real dt,
- rvec* v,
+/*! \brief Executes the vsite construction task for a single thread
+ *
+ * \param[in,out] x Coordinates to construct vsites for
+ * \param[in] dt Time step, needed when v is not empty
+ * \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] pbc_null PBC struct, used for PBC distance calculations when !=nullptr
+ */
+static void construct_vsites_thread(ArrayRef<RVec> x,
+ const real dt,
+ ArrayRef<RVec> v,
ArrayRef<const t_iparams> ip,
ArrayRef<const InteractionList> ilist,
const t_pbc* pbc_null)
{
real inv_dt;
- if (v != nullptr)
+ if (!v.empty())
{
inv_dt = 1.0 / dt;
}
rvec_add(xv, dx, x[avsite]);
}
}
- if (v != nullptr)
+ if (!v.empty())
{
/* Calculate velocity of vsite... */
rvec vv;
}
}
-void construct_vsites(const gmx_vsite_t* vsite,
- rvec x[],
- real dt,
- rvec* v,
- ArrayRef<const t_iparams> ip,
- ArrayRef<const InteractionList> ilist,
- PbcType pbcType,
- 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] dt Time step, needed when v is not empty
+ * \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
+ */
+static void construct_vsites(const ThreadingInfo* threadingInfo,
+ ArrayRef<RVec> x,
+ real dt,
+ 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 || pbcType == PbcType::No,
- "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;
- /* 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 (pbcType != PbcType::No && (useDomdec || bMolPBC)
- && !(vsite != nullptr && vsite->numInterUpdategroupVsites == 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, pbcType, useDomdec ? cr->dd->numCells : 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);
+ 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(x, dt, 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];
+ const VsiteThread& tData = threadingInfo->threadData(th);
GMX_ASSERT(tData.rangeStart >= 0,
"The thread data should be initialized before calling construct_vsites");
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
/* Now we can construct the vsites that might depend on other vsites */
- construct_vsites_thread(x, dt, v, ip, vsite->tData[vsite->nthreads]->ilist, pbc_null);
+ construct_vsites_thread(x, dt, v, ip, threadingInfo->threadDataNonLocalDependent().ilist, pbc_null);
}
}
-static void spread_vsite2(const t_iatom ia[], real a, const rvec x[], rvec f[], rvec fshift[], const t_pbc* pbc)
+void VirtualSitesHandler::Impl::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
+{
+ construct_vsites(&threadingInfo_, x, dt, v, iparams_, ilists_, domainInfo_, box);
+}
+
+void VirtualSitesHandler::construct(ArrayRef<RVec> x, real dt, ArrayRef<RVec> v, const matrix box) const
+{
+ impl_->construct(x, dt, v, box);
+}
+
+void constructVirtualSites(ArrayRef<RVec> x, ArrayRef<const t_iparams> ip, ArrayRef<const InteractionList> ilist)
+
+{
+ // No PBC, no DD
+ const DomainInfo domainInfo;
+ construct_vsites(nullptr, x, 0, {}, ip, ilist, domainInfo, nullptr);
+}
+
+#ifndef DOXYGEN
+/* Force spreading routines */
+
+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;
- int siv, sij;
av = ia[1];
ai = ia[2];
rvec_inc(f[aj], fj);
/* 6 Flops */
- if (pbc)
- {
- siv = pbc_dx_aiuc(pbc, x[ai], x[av], dx);
- sij = pbc_dx_aiuc(pbc, x[ai], x[aj], dx);
- }
- else
+ if (virialHandling == VirialHandling::Pbc)
{
- 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 = CENTRAL;
+ sij = CENTRAL;
+ }
- if (fshift && (siv != CENTRAL || sij != CENTRAL))
- {
- rvec_inc(fshift[siv], f[av]);
- rvec_dec(fshift[CENTRAL], fi);
- rvec_dec(fshift[sij], fj);
+ if (siv != CENTRAL || sij != CENTRAL)
+ {
+ rvec_inc(fshift[siv], f[av]);
+ rvec_dec(fshift[CENTRAL], 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(),
int atomOffset = mtop.moleculeBlockIndices[mb].globalAtomStart;
for (int mol = 0; mol < molb.nmol; mol++)
{
- construct_vsites(nullptr, as_rvec_array(x.data()) + atomOffset, 0.0, nullptr,
- mtop.ffparams.iparams, molt.ilist, PbcType::No, TRUE, nullptr, nullptr);
+ constructVirtualSites(x.subArray(atomOffset, molt.atoms.nr), mtop.ffparams.iparams,
+ molt.ilist);
atomOffset += molt.atoms.nr;
}
}
}
}
-static void spread_vsite2FD(const t_iatom ia[],
- real a,
- const rvec x[],
- rvec f[],
- rvec fshift[],
- gmx_bool VirCorr,
- matrix dxdf,
- const t_pbc* pbc)
+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)
{
const int av = ia[1];
const int ai = ia[2];
f[aj][ZZ] += fj[ZZ];
/* 9 Flops */
- if (fshift)
+ if (virialHandling == VirialHandling::Pbc)
{
int svi;
if (pbc)
}
}
- 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
/* TOTAL: 38 flops */
}
-static void spread_vsite3(const t_iatom ia[], real a, real b, const rvec x[], rvec f[], rvec fshift[], const t_pbc* pbc)
+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;
- int siv, sij, sik;
av = ia[1];
ai = ia[2];
rvec_inc(f[ak], fk);
/* 9 Flops */
- 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 = CENTRAL;
+ sij = CENTRAL;
+ sik = CENTRAL;
+ }
- 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 != 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);
+ }
}
/* 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)
+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 fproj, a1;
rvec xvi, xij, xjk, xix, fv, temp;
t_iatom av, ai, aj, ak;
- int svi, sji, skj;
+ int sji, skj;
av = ia[1];
ai = ia[2];
f[ak][ZZ] += a * temp[ZZ];
/* 19 Flops */
- 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 = CENTRAL;
+ }
- 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 != 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 (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
/* 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)
+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;
+ int sji, skj;
av = ia[1];
ai = ia[2];
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;
f[ak][ZZ] += f2[ZZ];
/* 30 Flops */
- 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 = CENTRAL;
+ }
+
+ if (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 (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])
/* 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)
+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;
- int svi, sji, ski;
+ int sji, ski;
av = ia[1];
ai = ia[2];
rvec_inc(f[ak], fk);
/* 15 Flops */
- 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 = CENTRAL;
+ }
- 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 != 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 (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
rvec xiv;
/* 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)
+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 fproj, a1;
rvec xvi, xij, xjk, xjl, xix, fv, temp;
int av, ai, aj, ak, al;
- int svi, sji, skj, slj, m;
+ int sji, skj, slj, m;
av = ia[1];
ai = ia[2];
}
/* 26 Flops */
- 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 = CENTRAL;
+ }
- if (fshift && (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL))
- {
- rvec_dec(fshift[svi], fv);
- for (m = 0; m < DIM; m++)
+ if (svi != CENTRAL || sji != CENTRAL || skj != CENTRAL || slj != CENTRAL)
{
- 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[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];
+ }
}
}
- if (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
rvec xiv;
int i, 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)
+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;
int av, ai, aj, ak, al;
- int svi, sij, sik, sil;
+ int sij, sik, sil;
/* DEBUG: check atom indices */
av = ia[1];
rvec_inc(f[al], fl);
/* 21 flops */
- 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 = CENTRAL;
+ }
- 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 != 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 (VirCorr)
+ if (virialHandling == VirialHandling::NonLinear)
{
rvec xiv;
int i, j;
/* Total: 207 flops (Yuck!) */
}
-
+template<VirialHandling virialHandling>
static int spread_vsiten(const t_iatom ia[],
ArrayRef<const t_iparams> ip,
- const rvec x[],
- rvec f[],
- rvec fshift[],
+ ArrayRef<const RVec> x,
+ ArrayRef<RVec> f,
+ ArrayRef<RVec> fshift,
const t_pbc* pbc)
{
rvec xv, dx, fi;
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 != CENTRAL)
{
rvec_inc(fshift[siv], fi);
rvec_dec(fshift[CENTRAL], fi);
return n3;
}
+#endif // DOXYGEN
+//! 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)
}
}
-static void spread_vsite_f_thread(const rvec x[],
- rvec f[],
- rvec* fshift,
- gmx_bool VirCorr,
- matrix dxdf,
- ArrayRef<const t_iparams> ip,
- ArrayRef<const InteractionList> ilist,
- 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);
/* We need another pbc pointer, as with charge groups we switch per vsite */
/* Construct the vsite depending on type */
switch (ftype)
{
- case F_VSITE2: spread_vsite2(ia, a1, x, f, fshift, pbc_null2); break;
+ case F_VSITE2:
+ spread_vsite2<virialHandling>(ia, a1, x, f, fshift, pbc_null2);
+ break;
case F_VSITE2FD:
- spread_vsite2FD(ia, a1, x, f, fshift, VirCorr, dxdf, pbc_null2);
+ 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);
+ 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);
+ 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);
+ 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);
+ 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);
+ 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);
+ spread_vsite4FDN<virialHandling>(ia, a1, b1, c1, x, f, fshift, dxdf, pbc_null2);
+ break;
+ case F_VSITEN:
+ inc = spread_vsiten<virialHandling>(ia, ip, x, f, fshift, pbc_null2);
break;
- case F_VSITEN: inc = spread_vsiten(ia, ip, x, f, fshift, pbc_null2); break;
default:
gmx_fatal(FARGS, "No such vsite type %d in %s, line %d", ftype, __FILE__, __LINE__);
}
}
}
-/*! \brief Clears the task force buffer elements that are written by task 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();
}
}
-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 InteractionDefinitions& idef,
- PbcType pbcType,
- gmx_bool bMolPBC,
- 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");
+
+ 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->numInterUpdategroupVsites)
+ 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, pbcType, useDomdec ? cr->dd->numCells : 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(x, f, fshift, VirCorr, dxdf, idef.iparams, idef.il, 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(x, f, fshift, VirCorr, vsite->tData[vsite->nthreads]->dxdf,
- idef.iparams, vsite->tData[vsite->nthreads]->ilist, pbc_null);
+ auto& nlDependentVSites = threadingInfo_.threadDataNonLocalDependent();
+ spreadForceWrapper(x, f, virialHandling, fshift, nlDependentVSites.dxdf, true, iparams_,
+ nlDependentVSites.ilist, pbc_null);
-#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 = 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 < SHIFTS; i++)
+ {
+ clear_rvec(fshift_t[i]);
+ }
}
- }
- if (VirCorr)
- {
- clear_mat(tData.dxdf);
}
if (tData.useInterdependentTask)
{
copy_rvec(f[idTask->vsite[i]], idTask->force[idTask->vsite[i]]);
}
- spread_vsite_f_thread(x, as_rvec_array(idTask->force.data()), fshift_t, VirCorr,
- tData.dxdf, idef.iparams, tData.idTask.ilist, 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(x, f, fshift_t, VirCorr, tData.dxdf, idef.iparams,
- tData.ilist, pbc_null);
+ spreadForceWrapper(x, f, virialHandling, fshift_t, tData.dxdf, false, iparams_,
+ tData.ilist, pbc_null);
}
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++)
{
- 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_VSITE2FD, vsite_count(idef.il, F_VSITE2FD));
- 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_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);
}
return numNonlinearVsites;
}
+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)
+{
+ impl_->spreadForces(x, f, virialHandling, fshift, virial, nrnb, box, wcycle);
+}
+
int countInterUpdategroupVsites(const gmx_mtop_t& mtop,
gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype)
{
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)
{
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;
return vsite;
}
- vsite = std::make_unique<gmx_vsite_t>();
-
- gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype;
- if (DOMAINDECOMP(cr))
- {
- updateGroupingPerMoleculetype = getUpdateGroupingPerMoleculetype(*cr->dd);
- }
- vsite->numInterUpdategroupVsites = countInterUpdategroupVsites(mtop, updateGroupingPerMoleculetype);
-
- vsite->useDomdec = (DOMAINDECOMP(cr) && cr->dd->nnodes > 1);
-
- vsite->nthreads = gmx_omp_nthreads_get(emntVSITE);
+ return std::make_unique<VirtualSitesHandler>(mtop, cr->dd, pbcType);
+}
- if (vsite->nthreads > 1)
+ThreadingInfo::ThreadingInfo() : numThreads_(gmx_omp_nthreads_get(emntVSITE))
+{
+ 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
}
- if (vsite->nthreads > 1)
+ if (numThreads_ > 1)
{
- vsite->tData[vsite->nthreads] = std::make_unique<VsiteThread>();
+ tData_[numThreads_] = std::make_unique<VsiteThread>();
}
}
+}
+
+//! Returns the number of inter update-group vsites
+static int getNumInterUpdategroupVsites(const gmx_mtop_t& mtop, const gmx_domdec_t* domdec)
+{
+ gmx::ArrayRef<const gmx::RangePartitioning> updateGroupingPerMoleculetype;
+ if (domdec)
+ {
+ updateGroupingPerMoleculetype = getUpdateGroupingPerMoleculetype(*domdec);
+ }
- return vsite;
+ return countInterUpdategroupVsites(mtop, updateGroupingPerMoleculetype);
}
-gmx_vsite_t::gmx_vsite_t() {}
+VirtualSitesHandler::Impl::Impl(const gmx_mtop_t& mtop, gmx_domdec_t* domdec, const PbcType pbcType) :
+ numInterUpdategroupVirtualSites_(getNumInterUpdategroupVsites(mtop, domdec)),
+ 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) :
+ impl_(new Impl(mtop, domdec, pbcType))
+{
+}
-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;
}
}
}
-/*\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,
{
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)
{
- flagAtom(&tData->idTask, iat[j], thread, nthread, natperthread);
+ flagAtom(&tData->idTask, iat[j], nthread, natperthread);
}
}
}
}
}
-void split_vsites_over_threads(ArrayRef<const InteractionList> ilist,
- ArrayRef<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 t_mdatoms& mdatoms,
+ 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++)
if (ftype != F_VSITEN)
{
int nral1 = 1 + NRAL(ftype);
- ArrayRef<const int> iat = ilist[ftype].iatoms;
- for (int i = 0; i < ilist[ftype].size(); i += nral1)
+ 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++)
{
{
int vs_ind_end;
- ArrayRef<const int> iat = ilist[ftype].iatoms;
+ ArrayRef<const int> iat = ilists[ftype].iatoms;
int i = 0;
- while (i < ilist[ftype].size())
+ 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]);
while (i < vs_ind_end)
}
}
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 = mdatoms.nr;
+ natperthread = (mdatoms.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);
+ mdatoms.nr, 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(mdatoms.nr);
/* 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++)
+ for (int i = 0; i < mdatoms.nr; i++)
{
- if (mdatoms->ptype[i] == eptVSite)
+ if (mdatoms.ptype[i] == eptVSite)
{
/* 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)
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];
int natom = atomIndex.atom.size();
/* Assign all vsites that can execute independently on threads */
tData.rangeStart = thread * natperthread;
- if (thread < vsite->nthreads - 1)
+ if (thread < numThreads_ - 1)
{
tData.rangeEnd = (thread + 1) * natperthread;
}
else
{
/* The last thread should cover up to the end of the range */
- tData.rangeEnd = mdatoms->nr;
+ tData.rangeEnd = mdatoms.nr;
}
- assignVsitesToThread(&tData, thread, vsite->nthreads, natperthread, taskIndex, ilist,
- ip, mdatoms->ptype);
+ assignVsitesToThread(&tData, thread, numThreads_, natperthread, taskIndex_, ilists,
+ iparams, mdatoms.ptype);
if (tData.useInterdependentTask)
{
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);
}
/* 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++)
+ 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].empty())
+ if (!ilists[ftype].empty())
{
fprintf(debug, "%-20s thread dist:", interaction_function[ftype].longname);
- for (int th = 0; th < vsite->nthreads + 1; th++)
+ for (int th = 0; th < numThreads_ + 1; th++)
{
- fprintf(debug, " %4d %4d ", vsite->tData[th]->ilist[ftype].size(),
- vsite->tData[th]->idTask.ilist[ftype].size());
+ 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 "
#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 t_mdatoms& mdatoms)
{
- if (vsite->nthreads > 1)
- {
- split_vsites_over_threads(top->idef.il, top->idef.iparams, md, vsite);
- }
+ ilists_ = ilists;
+
+ threadingInfo_.setVirtualSites(ilists, iparams_, mdatoms, domainInfo_.useDomdec());
}
+
+void VirtualSitesHandler::setVirtualSites(ArrayRef<const InteractionList> ilists, const t_mdatoms& mdatoms)
+{
+ impl_->setVirtualSites(ilists, mdatoms);
+}
+
+} // namespace gmx
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff