#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/ga2la.h"
+#include "gromacs/domdec/localtopologychecker.h"
#include "gromacs/domdec/options.h"
+#include "gromacs/domdec/reversetopology.h"
#include "gromacs/gmxlib/network.h"
#include "gromacs/math/vec.h"
#include "gromacs/mdlib/forcerec.h"
#include "gromacs/mdtypes/state.h"
#include "gromacs/pbcutil/mshift.h"
#include "gromacs/pbcutil/pbc.h"
-#include "gromacs/topology/ifunc.h"
#include "gromacs/topology/mtop_util.h"
#include "gromacs/topology/topsort.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/exceptions.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
-#include "gromacs/utility/listoflists.h"
#include "gromacs/utility/logger.h"
#include "gromacs/utility/smalloc.h"
#include "gromacs/utility/strconvert.h"
/*! \brief The number of integer item in the local state, used for broadcasting of the state */
#define NITEM_DD_INIT_LOCAL_STATE 5
-struct reverse_ilist_t
-{
- std::vector<int> index; /* Index for each atom into il */
- std::vector<int> il; /* ftype|type|a0|...|an|ftype|... */
- int numAtomsInMolecule; /* The number of atoms in this molecule */
-};
-
-struct MolblockIndices
-{
- int a_start;
- int a_end;
- int natoms_mol;
- int type;
-};
-
-/*! \brief Struct for thread local work data for local topology generation */
-struct thread_work_t
-{
- /*! \brief Constructor
- *
- * \param[in] ffparams The interaction parameters, the lifetime of the created object should not exceed the lifetime of the passed parameters
- */
- thread_work_t(const gmx_ffparams_t& ffparams) : idef(ffparams) {}
-
- InteractionDefinitions idef; /**< Partial local topology */
- std::unique_ptr<gmx::VsitePbc> vsitePbc = nullptr; /**< vsite PBC structure */
- int numBondedInteractions = 0; /**< The number of bonded interactions observed */
- ListOfLists<int> excl; /**< List of exclusions */
-};
-
-/*! \brief Options for setting up gmx_reverse_top_t */
-struct ReverseTopOptions
-{
- //! Constructor, constraints and settles are not including with a single argument
- ReverseTopOptions(DDBondedChecking ddBondedChecking,
- bool includeConstraints = false,
- bool includeSettles = false) :
- ddBondedChecking(ddBondedChecking),
- includeConstraints(includeConstraints),
- includeSettles(includeSettles)
- {
- }
-
- //! \brief For which bonded interactions to check assignments
- const DDBondedChecking ddBondedChecking;
- //! \brief Whether constraints are stored in this reverse top
- const bool includeConstraints;
- //! \brief Whether settles are stored in this reverse top
- const bool includeSettles;
-};
-
/*! \brief Struct for the reverse topology: links bonded interactions to atoms */
struct gmx_reverse_top_t::Impl
{
//! Options for the setup of this reverse topology
const ReverseTopOptions options;
//! Are there interaction of type F_POSRES and/or F_FBPOSRES
- bool havePositionRestraints;
+ bool hasPositionRestraints;
//! \brief Are there bondeds/exclusions between atoms?
bool bInterAtomicInteractions = false;
//! \brief Reverse ilist for all moltypes
for (int ftype = 0; ftype < F_NRE; ftype++)
{
- if (dd_check_ftype(ftype, rt.impl_->options))
+ if (dd_check_ftype(ftype, rt.options()))
{
flagInteractionsForType(
ftype, idef.il[ftype], ril, atomRange, numAtomsPerMolecule, cr->dd->globalAtomIndices, isAssigned);
a_end = a_start + molb.nmol * moltype.atoms.nr;
const gmx::Range<int> atomRange(a_start, a_end);
- auto warning = printMissingInteractionsMolblock(
- cr, rt, *(moltype.name), rt.impl_->ril_mt[molb.type], atomRange, moltype.atoms.nr, molb.nmol, idef);
+ auto warning = printMissingInteractionsMolblock(cr,
+ rt,
+ *(moltype.name),
+ rt.interactionListForMoleculeType(molb.type),
+ atomRange,
+ moltype.atoms.nr,
+ molb.nmol,
+ idef);
GMX_LOG(mdlog.warning).appendText(warning);
}
"decomposition cells");
const int ndiff_tot = numBondedInteractionsOverAllDomains
- - dd->reverse_top->impl_->expectedNumGlobalBondedInteractions;
+ - dd->reverse_top->expectedNumGlobalBondedInteractions();
for (int ftype = 0; ftype < F_NRE; ftype++)
{
if (DDMASTER(dd))
{
GMX_LOG(mdlog.warning).appendText("A list of missing interactions:");
- int rest_global = dd->reverse_top->impl_->expectedNumGlobalBondedInteractions;
+ int rest_global = dd->reverse_top->expectedNumGlobalBondedInteractions();
int rest = numBondedInteractionsOverAllDomains;
for (int ftype = 0; ftype < F_NRE; ftype++)
{
* into F_CONSTR. So in the if statement we skip F_CONSTRNC
* and add these constraints when doing F_CONSTR.
*/
- if (dd_check_ftype(ftype, dd->reverse_top->impl_->options) && ftype != F_CONSTRNC)
+ if (dd_check_ftype(ftype, dd->reverse_top->options()) && ftype != F_CONSTRNC)
{
int n = gmx_mtop_ftype_count(top_global, ftype);
if (ftype == F_CONSTR)
"two-body cut-off distance (%g nm), see option -rdd, for pairs and tabulated bonds "
"also see option -ddcheck",
-ndiff_tot,
- dd->reverse_top->impl_->expectedNumGlobalBondedInteractions,
+ dd->reverse_top->expectedNumGlobalBondedInteractions(),
dd_cutoff_multibody(dd),
dd_cutoff_twobody(dd));
}
return maxNumExcls;
}
-//! Options for linking atoms in make_reverse_ilist
-enum class AtomLinkRule
-{
- FirstAtom, //!< Link all interactions to the first atom in the atom list
- AllAtomsInBondeds //!< Link bonded interactions to all atoms involved, don't link vsites
-};
-
/*! \brief Run the reverse ilist generation and store it in r_il when \p bAssign = TRUE */
static int low_make_reverse_ilist(const InteractionLists& il_mt,
const t_atom* atom,
gmx_reverse_top_t::~gmx_reverse_top_t() {}
+const ReverseTopOptions& gmx_reverse_top_t::options() const
+{
+ return impl_->options;
+}
+
+const reverse_ilist_t& gmx_reverse_top_t::interactionListForMoleculeType(int moleculeType) const
+{
+ return impl_->ril_mt[moleculeType];
+}
+
+int gmx_reverse_top_t::expectedNumGlobalBondedInteractions() const
+{
+ return impl_->expectedNumGlobalBondedInteractions;
+}
+
+ArrayRef<const MolblockIndices> gmx_reverse_top_t::molblockIndices() const
+{
+ return impl_->mbi;
+}
+
+bool gmx_reverse_top_t::hasIntermolecularInteractions() const
+{
+ return impl_->bIntermolecularInteractions;
+}
+
+const reverse_ilist_t& gmx_reverse_top_t::interactionListForIntermolecularInteractions() const
+{
+ return impl_->ril_intermol;
+}
+
+bool gmx_reverse_top_t::hasInterAtomicInteractions() const
+{
+ return impl_->bInterAtomicInteractions;
+}
+
+bool gmx_reverse_top_t::hasPositionRestraints() const
+{
+ return impl_->hasPositionRestraints;
+}
+
+ArrayRef<thread_work_t> gmx_reverse_top_t::threadWorkObjects() const
+{
+ return impl_->th_work;
+}
+
+bool gmx_reverse_top_t::doSorting() const
+{
+ return impl_->ilsort != ilsortNO_FE;
+}
+
/*! \brief Generate the reverse topology */
gmx_reverse_top_t::Impl::Impl(const gmx_mtop_t& mtop,
const bool useFreeEnergy,
const ReverseTopOptions& reverseTopOptions) :
options(reverseTopOptions),
- havePositionRestraints(
- gmx_mtop_ftype_count(mtop, F_POSRES) + gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0),
+ hasPositionRestraints(gmx_mtop_ftype_count(mtop, F_POSRES) + gmx_mtop_ftype_count(mtop, F_FBPOSRES) > 0),
bInterAtomicInteractions(mtop.bIntermolecularInteractions)
{
bInterAtomicInteractions = mtop.bIntermolecularInteractions;
int mol = 0;
int atomIndexInMolecule = 0;
- const auto ddBondedChecking = rt->impl_->options.ddBondedChecking;
+ const auto ddBondedChecking = rt->options().ddBondedChecking;
int numBondedInteractions = 0;
{
/* Get the global atom number */
const int globalAtomIndex = globalAtomIndices[i];
- global_atomnr_to_moltype_ind(rt->impl_->mbi, globalAtomIndex, &mb, &mt, &mol, &atomIndexInMolecule);
+ global_atomnr_to_moltype_ind(
+ rt->molblockIndices(), globalAtomIndex, &mb, &mt, &mol, &atomIndexInMolecule);
/* Check all intramolecular interactions assigned to this atom */
- gmx::ArrayRef<const int> index = rt->impl_->ril_mt[mt].index;
- gmx::ArrayRef<const t_iatom> rtil = rt->impl_->ril_mt[mt].il;
+ gmx::ArrayRef<const int> index = rt->interactionListForMoleculeType(mt).index;
+ gmx::ArrayRef<const t_iatom> rtil = rt->interactionListForMoleculeType(mt).il;
numBondedInteractions += assignInteractionsForAtom<InteractionConnectivity::Intramolecular>(
i,
ddBondedChecking);
// Assign position restraints, when present, for the home zone
- if (izone == 0 && rt->impl_->havePositionRestraints)
+ if (izone == 0 && rt->hasPositionRestraints())
{
- numBondedInteractions +=
- assignPositionRestraintsForAtom(i,
- mol,
- atomIndexInMolecule,
- rt->impl_->ril_mt[mt].numAtomsInMolecule,
- rtil,
- index[atomIndexInMolecule],
- index[atomIndexInMolecule + 1],
- molb[mb],
- ip_in,
- idef);
+ numBondedInteractions += assignPositionRestraintsForAtom(
+ i,
+ mol,
+ atomIndexInMolecule,
+ rt->interactionListForMoleculeType(mt).numAtomsInMolecule,
+ rtil,
+ index[atomIndexInMolecule],
+ index[atomIndexInMolecule + 1],
+ molb[mb],
+ ip_in,
+ idef);
}
- if (rt->impl_->bIntermolecularInteractions)
+ if (rt->hasIntermolecularInteractions())
{
/* Check all intermolecular interactions assigned to this atom */
- index = rt->impl_->ril_intermol.index;
- rtil = rt->impl_->ril_intermol.il;
+ index = rt->interactionListForIntermolecularInteractions().index;
+ rtil = rt->interactionListForIntermolecularInteractions().il;
numBondedInteractions += assignInteractionsForAtom<InteractionConnectivity::Intermolecular>(
i,
"The number of exclusion list should match the number of atoms in the range");
}
-/*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls */
-static void make_local_bondeds_excls(gmx_domdec_t* dd,
- gmx_domdec_zones_t* zones,
- const gmx_mtop_t& mtop,
- const int* cginfo,
- const bool checkDistanceMultiBody,
- const ivec rcheck,
- const gmx_bool checkDistanceTwoBody,
- const real cutoff,
- const t_pbc* pbc_null,
- ArrayRef<const RVec> coordinates,
- InteractionDefinitions* idef,
- ListOfLists<int>* lexcls)
+/*! \brief Generate and store all required local bonded interactions in \p idef and local exclusions in \p lexcls
+ *
+ * \returns Total count of bonded interactions in the local topology on this domain */
+static int make_local_bondeds_excls(gmx_domdec_t* dd,
+ gmx_domdec_zones_t* zones,
+ const gmx_mtop_t& mtop,
+ const int* cginfo,
+ const bool checkDistanceMultiBody,
+ const ivec rcheck,
+ const gmx_bool checkDistanceTwoBody,
+ const real cutoff,
+ const t_pbc* pbc_null,
+ ArrayRef<const RVec> coordinates,
+ InteractionDefinitions* idef,
+ ListOfLists<int>* lexcls)
{
int nzone_bondeds = 0;
- if (dd->reverse_top->impl_->bInterAtomicInteractions)
+ if (dd->reverse_top->hasInterAtomicInteractions())
{
nzone_bondeds = zones->n;
}
/* Clear the counts */
idef->clear();
- dd->reverse_top->impl_->numBondedInteractions = 0;
+ int numBondedInteractions = 0;
lexcls->clear();
const int cg0 = zones->cg_range[izone];
const int cg1 = zones->cg_range[izone + 1];
- const int numThreads = rt->impl_->th_work.size();
+ gmx::ArrayRef<thread_work_t> threadWorkObjects = rt->threadWorkObjects();
+ const int numThreads = threadWorkObjects.size();
#pragma omp parallel for num_threads(numThreads) schedule(static)
for (int thread = 0; thread < numThreads; thread++)
{
}
else
{
- idef_t = &rt->impl_->th_work[thread].idef;
+ idef_t = &threadWorkObjects[thread].idef;
idef_t->clear();
}
- rt->impl_->th_work[thread].numBondedInteractions =
+ threadWorkObjects[thread].numBondedInteractions =
make_bondeds_zone(rt,
dd->globalAtomIndices,
*dd->ga2la,
else
{
// Threads > 0 store in temporary storage, starting at list index 0
- excl_t = &rt->impl_->th_work[thread].excl;
+ excl_t = &threadWorkObjects[thread].excl;
excl_t->clear();
}
make_exclusions_zone(dd->globalAtomIndices,
*dd->ga2la,
zones,
- rt->impl_->mbi,
+ rt->molblockIndices(),
mtop.moltype,
cginfo,
excl_t,
GMX_CATCH_ALL_AND_EXIT_WITH_FATAL_ERROR
}
- if (rt->impl_->th_work.size() > 1)
+ if (threadWorkObjects.size() > 1)
{
- combine_idef(idef, rt->impl_->th_work);
+ combine_idef(idef, threadWorkObjects);
}
- for (const thread_work_t& th_work : rt->impl_->th_work)
+ for (const thread_work_t& th_work : threadWorkObjects)
{
- dd->reverse_top->impl_->numBondedInteractions += th_work.numBondedInteractions;
+ numBondedInteractions += th_work.numBondedInteractions;
}
if (izone < numIZonesForExclusions)
{
- for (std::size_t th = 1; th < rt->impl_->th_work.size(); th++)
+ for (std::size_t th = 1; th < threadWorkObjects.size(); th++)
{
- lexcls->appendListOfLists(rt->impl_->th_work[th].excl);
+ lexcls->appendListOfLists(threadWorkObjects[th].excl);
}
}
}
+ if (debug)
+ {
+ fprintf(debug, "We have %d exclusions\n", lexcls->numElements());
+ }
+
+ return numBondedInteractions;
+}
+
+void scheduleCheckOfLocalTopology(gmx_domdec_t* dd, const int numBondedInteractionsToReduce)
+{
+ dd->localTopologyChecker->numBondedInteractionsToReduce = numBondedInteractionsToReduce;
// Note that it's possible for this to still be true from the last
// time it was set, e.g. if repartitioning was triggered before
// global communication that would have acted on the true
// value. This could happen for example when replica exchange took
// place soon after a partition.
- dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions = true;
+ dd->localTopologyChecker->shouldCheckNumberOfBondedInteractions = true;
// Clear the old global value, which is now invalid
- dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.reset();
-
- if (debug)
- {
- fprintf(debug, "We have %d exclusions\n", lexcls->numElements());
- }
+ dd->localTopologyChecker->numBondedInteractionsOverAllDomains.reset();
}
bool shouldCheckNumberOfBondedInteractions(const gmx_domdec_t& dd)
{
- return dd.reverse_top->impl_->shouldCheckNumberOfBondedInteractions;
+ return dd.localTopologyChecker->shouldCheckNumberOfBondedInteractions;
}
int numBondedInteractions(const gmx_domdec_t& dd)
{
- return dd.reverse_top->impl_->numBondedInteractions;
+ return dd.localTopologyChecker->numBondedInteractionsToReduce;
}
void setNumberOfBondedInteractionsOverAllDomains(const gmx_domdec_t& dd, int newValue)
{
- GMX_RELEASE_ASSERT(!dd.reverse_top->impl_->numBondedInteractionsOverAllDomains.has_value(),
+ GMX_RELEASE_ASSERT(!dd.localTopologyChecker->numBondedInteractionsOverAllDomains.has_value(),
"Cannot set number of bonded interactions because it is already set");
- dd.reverse_top->impl_->numBondedInteractionsOverAllDomains.emplace(newValue);
+ dd.localTopologyChecker->numBondedInteractionsOverAllDomains.emplace(newValue);
}
void checkNumberOfBondedInteractions(const gmx::MDLogger& mdlog,
GMX_RELEASE_ASSERT(
DOMAINDECOMP(cr),
"No need to check number of bonded interactions when not using domain decomposition");
- if (cr->dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions)
+ if (cr->dd->localTopologyChecker->shouldCheckNumberOfBondedInteractions)
{
- GMX_RELEASE_ASSERT(cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.has_value(),
+ GMX_RELEASE_ASSERT(cr->dd->localTopologyChecker->numBondedInteractionsOverAllDomains.has_value(),
"The check for the total number of bonded interactions requires the "
"value to have been reduced across all domains");
- if (cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.value()
- != cr->dd->reverse_top->impl_->expectedNumGlobalBondedInteractions)
+ if (cr->dd->localTopologyChecker->numBondedInteractionsOverAllDomains.value()
+ != cr->dd->reverse_top->expectedNumGlobalBondedInteractions())
{
dd_print_missing_interactions(
mdlog,
cr,
- cr->dd->reverse_top->impl_->numBondedInteractionsOverAllDomains.value(),
+ cr->dd->localTopologyChecker->numBondedInteractionsOverAllDomains.value(),
top_global,
top_local,
x,
// Now that the value is set and the check complete, future
// global communication should not compute the value until
// after the next partitioning.
- cr->dd->reverse_top->impl_->shouldCheckNumberOfBondedInteractions = false;
+ cr->dd->localTopologyChecker->shouldCheckNumberOfBondedInteractions = false;
}
}
-void dd_make_local_top(gmx_domdec_t* dd,
- gmx_domdec_zones_t* zones,
- int npbcdim,
- matrix box,
- rvec cellsize_min,
- const ivec npulse,
- t_forcerec* fr,
- ArrayRef<const RVec> coordinates,
- const gmx_mtop_t& mtop,
- gmx_localtop_t* ltop)
+int dd_make_local_top(gmx_domdec_t* dd,
+ gmx_domdec_zones_t* zones,
+ int npbcdim,
+ matrix box,
+ rvec cellsize_min,
+ const ivec npulse,
+ t_forcerec* fr,
+ ArrayRef<const RVec> coordinates,
+ const gmx_mtop_t& mtop,
+ gmx_localtop_t* ltop)
{
real rc = -1;
ivec rcheck;
bool checkDistanceMultiBody = false;
bool checkDistanceTwoBody = false;
- if (dd->reverse_top->impl_->bInterAtomicInteractions)
+ if (dd->reverse_top->hasInterAtomicInteractions())
{
/* We need to check to which cell bondeds should be assigned */
rc = dd_cutoff_twobody(dd);
}
}
- make_local_bondeds_excls(dd,
- zones,
- mtop,
- fr->cginfo.data(),
- checkDistanceMultiBody,
- rcheck,
- checkDistanceTwoBody,
- rc,
- pbc_null,
- coordinates,
- <op->idef,
- <op->excls);
+ int numBondedInteractionsToReduce = make_local_bondeds_excls(dd,
+ zones,
+ mtop,
+ fr->cginfo.data(),
+ checkDistanceMultiBody,
+ rcheck,
+ checkDistanceTwoBody,
+ rc,
+ pbc_null,
+ coordinates,
+ <op->idef,
+ <op->excls);
/* The ilist is not sorted yet,
* we can only do this when we have the charge arrays.
*/
ltop->idef.ilsort = ilsortUNKNOWN;
+
+ return numBondedInteractionsToReduce;
}
void dd_sort_local_top(const gmx_domdec_t& dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop)
{
- if (dd.reverse_top->impl_->ilsort == ilsortNO_FE)
+ if (dd.reverse_top->doSorting())
{
- ltop->idef.ilsort = ilsortNO_FE;
+ gmx_sort_ilist_fe(<op->idef, mdatoms->chargeA, mdatoms->chargeB);
}
else
{
- gmx_sort_ilist_fe(<op->idef, mdatoms->chargeA, mdatoms->chargeB);
+ ltop->idef.ilsort = ilsortNO_FE;
}
}
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff