#include "gromacs/utility/real.h"
//! Max number of zones in domain decomposition
-#define DD_MAXZONE 8
+#define DD_MAXZONE 8
//! Max number of izones in domain decomposition
#define DD_MAXIZONE 4
namespace gmx
{
-template <typename T> class HashedMap;
+template<typename T>
+class HashedMap;
class LocalAtomSetManager;
class GpuHaloExchange;
-}
+} // namespace gmx
/*! \internal
* \brief Pair interaction zone and atom range for an i-zone
struct DDPairInteractionRanges
{
//! The index of this i-zone in the i-zone list
- int iZoneIndex = -1;
+ int iZoneIndex = -1;
//! The range of j-zones
gmx::Range<int> jZoneRange;
//! The i-atom range
//! The j-atom range
gmx::Range<int> jAtomRange;
//! Minimum shifts to consider
- ivec shift0 = { };
+ ivec shift0 = {};
//! Maximum shifts to consider
- ivec shift1 = { };
+ ivec shift1 = {};
};
-typedef struct {
+typedef struct
+{
/* Zone lower corner in triclinic coordinates */
- rvec x0 = { };
+ rvec x0 = {};
/* Zone upper corner in triclinic coordinates */
- rvec x1 = { };
+ rvec x1 = {};
/* Zone bounding box lower corner in Cartesian coords */
- rvec bb_x0 = { };
+ rvec bb_x0 = {};
/* Zone bounding box upper corner in Cartesian coords */
- rvec bb_x1 = { };
+ rvec bb_x1 = {};
} gmx_domdec_zone_size_t;
-struct gmx_domdec_zones_t {
+struct gmx_domdec_zones_t
+{
/* The number of zones including the home zone */
- int n = 0;
+ int n = 0;
/* The shift of the zones with respect to the home zone */
- ivec shift[DD_MAXZONE] = { };
+ ivec shift[DD_MAXZONE] = {};
/* The charge group boundaries for the zones */
- int cg_range[DD_MAXZONE+1] = { };
+ int cg_range[DD_MAXZONE + 1] = {};
/* The pair interaction zone and atom ranges per each i-zone */
std::vector<DDPairInteractionRanges> iZones;
/* Boundaries of the zones */
- gmx_domdec_zone_size_t size[DD_MAXZONE];
+ gmx_domdec_zone_size_t size[DD_MAXZONE];
/* The cg density of the home zone */
- real dens_zone0 = 0;
+ real dens_zone0 = 0;
};
-struct gmx_ddbox_t {
+struct gmx_ddbox_t
+{
int npbcdim;
int nboundeddim;
rvec box0;
struct UnitCellInfo
{
//! Constructor
- UnitCellInfo(const t_inputrec &ir);
+ UnitCellInfo(const t_inputrec& ir);
//! We have PBC from dim 0 (X) up to npbcdim
- int npbcdim;
+ int npbcdim;
//! The system is bounded from 0 (X) to numBoundedDimensions
- int numBoundedDimensions;
+ int numBoundedDimensions;
//! Tells whether the box bounding the atoms is dynamic
bool ddBoxIsDynamic;
//! Screw PBC?
bool haveScrewPBC;
};
-struct gmx_domdec_t { //NOLINT(clang-analyzer-optin.performance.Padding)
+struct gmx_domdec_t
+{ //NOLINT(clang-analyzer-optin.performance.Padding)
//! Constructor, only partial for now
- gmx_domdec_t(const t_inputrec &ir);
+ gmx_domdec_t(const t_inputrec& ir);
/* The DD particle-particle nodes only */
/* The communication setup within the communicator all
* defined in dd->comm in domdec.c
*/
- int nnodes = 0;
- MPI_Comm mpi_comm_all = MPI_COMM_NULL;
+ int nnodes = 0;
+ MPI_Comm mpi_comm_all = MPI_COMM_NULL;
/* The local DD cell index and rank */
- ivec ci = { 0, 0, 0 };
- int rank = 0;
- ivec master_ci = { 0, 0, 0 };
- int masterrank = 0;
+ ivec ci = { 0, 0, 0 };
+ int rank = 0;
+ ivec master_ci = { 0, 0, 0 };
+ int masterrank = 0;
/* Communication with the PME only nodes */
- int pme_nodeid = 0;
- gmx_bool pme_receive_vir_ener = false;
- gmx_pme_comm_n_box_t *cnb = nullptr;
- int nreq_pme = 0;
- MPI_Request req_pme[8];
+ int pme_nodeid = 0;
+ gmx_bool pme_receive_vir_ener = false;
+ gmx_pme_comm_n_box_t* cnb = nullptr;
+ int nreq_pme = 0;
+ MPI_Request req_pme[8];
/* Properties of the unit cell */
UnitCellInfo unitCellInfo;
/* The communication setup, identical for each cell, cartesian index */
- ivec nc = { 0, 0, 0 };
- int ndim = 0;
- ivec dim = { 0, 0, 0 }; /* indexed by 0 to ndim */
+ ivec nc = { 0, 0, 0 };
+ int ndim = 0;
+ ivec dim = { 0, 0, 0 }; /* indexed by 0 to ndim */
/* Forward and backward neighboring cells, indexed by 0 to ndim */
- int neighbor[DIM][2] = { { 0, 0 }, { 0, 0 }, { 0, 0 } };
+ int neighbor[DIM][2] = { { 0, 0 }, { 0, 0 }, { 0, 0 } };
/* Only available on the master node */
std::unique_ptr<AtomDistribution> ma;
/* Global atom number to interaction list */
- gmx_reverse_top_t *reverse_top = nullptr;
- int nbonded_global = 0;
- int nbonded_local = 0;
+ gmx_reverse_top_t* reverse_top = nullptr;
+ int nbonded_global = 0;
+ int nbonded_local = 0;
/* Whether we have non-self exclusion */
bool haveExclusions = false;
/* Vsite stuff */
- gmx::HashedMap<int> *ga2la_vsite = nullptr;
- gmx_domdec_specat_comm_t *vsite_comm = nullptr;
- std::vector<int> vsite_requestedGlobalAtomIndices;
+ gmx::HashedMap<int>* ga2la_vsite = nullptr;
+ gmx_domdec_specat_comm_t* vsite_comm = nullptr;
+ std::vector<int> vsite_requestedGlobalAtomIndices;
/* Constraint stuff */
- gmx_domdec_constraints_t *constraints = nullptr;
- gmx_domdec_specat_comm_t *constraint_comm = nullptr;
+ gmx_domdec_constraints_t* constraints = nullptr;
+ gmx_domdec_specat_comm_t* constraint_comm = nullptr;
/* The number of home atom groups */
- int ncg_home = 0;
+ int ncg_home = 0;
/* Global atom group indices for the home and all non-home groups */
- std::vector<int> globalAtomGroupIndices;
+ std::vector<int> globalAtomGroupIndices;
/* Index from the local atoms to the global atoms, covers home and received zones */
std::vector<int> globalAtomIndices;
/* Global atom number to local atom number list */
- gmx_ga2la_t *ga2la = nullptr;
+ gmx_ga2la_t* ga2la = nullptr;
/* Communication stuff */
- gmx_domdec_comm_t *comm = nullptr;
+ gmx_domdec_comm_t* comm = nullptr;
/* The partioning count, to keep track of the state */
int64_t ddp_count = 0;
/* The managed atom sets that are updated in domain decomposition */
- gmx::LocalAtomSetManager * atomSets = nullptr;
+ gmx::LocalAtomSetManager* atomSets = nullptr;
/* gmx_pme_recv_f buffer */
std::vector<gmx::RVec> pmeForceReceiveBuffer;
};
//! Are we the master node for domain decomposition
-static inline bool DDMASTER(const gmx_domdec_t &dd)
+static inline bool DDMASTER(const gmx_domdec_t& dd)
{
return dd.rank == dd.masterrank;
};
//! Are we the master node for domain decomposition, deprecated
-static inline bool DDMASTER(const gmx_domdec_t *dd)
+static inline bool DDMASTER(const gmx_domdec_t* dd)
{
return dd->rank == dd->masterrank;
};
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