#include "gromacs/gpu_utils/devicebuffer_datatype.h"
#include "gromacs/math/vectypes.h"
-#include "gromacs/utility/arrayref.h"
-#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"
-struct cginfo_mb_t;
struct gmx_domdec_t;
struct gmx_ddbox_t;
struct gmx_domdec_zones_t;
struct gmx_localtop_t;
struct gmx_mtop_t;
-struct t_block;
-struct t_blocka;
struct t_commrec;
struct t_forcerec;
struct t_inputrec;
namespace gmx
{
+struct AtomInfoWithinMoleculeBlock;
class DeviceStreamManager;
class ForceWithShiftForces;
+class LocalTopologyChecker;
class MDLogger;
class RangePartitioning;
class VirtualSitesHandler;
+template<typename>
+class ArrayRef;
} // namespace gmx
/*! \brief Returns the global topology atom number belonging to local atom index i.
*/
int ddglatnr(const gmx_domdec_t* dd, int i);
-/*! \brief Returns a list of update group partitioning for each molecule type or empty when update groups are not used */
-gmx::ArrayRef<const gmx::RangePartitioning> getUpdateGroupingPerMoleculetype(const gmx_domdec_t& dd);
-
/*! \brief Store the global cg indices of the home cgs in state,
*
* This means it can be reset, even after a new DD partitioning.
*/
-void dd_store_state(struct gmx_domdec_t* dd, t_state* state);
+void dd_store_state(const gmx_domdec_t& dd, t_state* state);
/*! \brief Returns a pointer to the gmx_domdec_zones_t struct */
struct gmx_domdec_zones_t* domdec_zones(struct gmx_domdec_t* dd);
int dd_numHomeAtoms(const gmx_domdec_t& dd);
/*! \brief Returns the atom range in the local state for atoms that need to be present in mdatoms */
-int dd_natoms_mdatoms(const gmx_domdec_t* dd);
+int dd_natoms_mdatoms(const gmx_domdec_t& dd);
/*! \brief Returns the atom range in the local state for atoms involved in virtual sites */
-int dd_natoms_vsite(const gmx_domdec_t* dd);
+int dd_natoms_vsite(const gmx_domdec_t& dd);
/*! \brief Sets the atom range for atom in the local state for atoms received in constraints communication */
-void dd_get_constraint_range(const gmx_domdec_t* dd, int* at_start, int* at_end);
+void dd_get_constraint_range(const gmx_domdec_t& dd, int* at_start, int* at_end);
/*! \libinternal \brief Struct for passing around the number of PME domains */
struct NumPmeDomains
std::vector<int> get_pme_ddranks(const t_commrec* cr, int pmenodeid);
/*! \brief Returns the maximum shift for coordinate communication in PME, dim x */
-int dd_pme_maxshift_x(const gmx_domdec_t* dd);
+int dd_pme_maxshift_x(const gmx_domdec_t& dd);
/*! \brief Returns the maximum shift for coordinate communication in PME, dim y */
-int dd_pme_maxshift_y(const gmx_domdec_t* dd);
-
-/*! \brief Return whether constraints, not including settles, cross domain boundaries */
-bool ddHaveSplitConstraints(const gmx_domdec_t& dd);
+int dd_pme_maxshift_y(const gmx_domdec_t& dd);
/*! \brief Return whether update groups are used */
bool ddUsesUpdateGroups(const gmx_domdec_t& dd);
-/*! \brief Initialize data structures for bonded interactions */
-void dd_init_bondeds(FILE* fplog,
- gmx_domdec_t* dd,
- const gmx_mtop_t& mtop,
- const gmx::VirtualSitesHandler* vsite,
- const t_inputrec* ir,
- gmx_bool bBCheck,
- gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
-
/*! \brief Returns whether molecules are always whole, i.e. not broken by PBC */
bool dd_moleculesAreAlwaysWhole(const gmx_domdec_t& dd);
/*! \brief Returns if we need to do pbc for calculating bonded interactions */
-gmx_bool dd_bonded_molpbc(const gmx_domdec_t* dd, PbcType pbcType);
+bool dd_bonded_molpbc(const gmx_domdec_t& dd, PbcType pbcType);
/*! \brief Change the DD non-bonded communication cut-off.
*
* \param[in] x Position vector, used for computing the dimensions of the system
* \param[in] cutoffRequested The requested atom to atom cut-off distance, usually the pair-list cutoff distance
*/
-gmx_bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
+bool change_dd_cutoff(t_commrec* cr, const matrix box, gmx::ArrayRef<const gmx::RVec> x, real cutoffRequested);
/*! \brief Set up communication for averaging GPU wait times over domains
*
const matrix box,
gmx::ArrayRef<gmx::RVec> x0,
gmx::ArrayRef<gmx::RVec> x1,
- gmx_bool bX1IsCoord);
+ bool bX1IsCoord);
/*! \brief Communicates the coordinates involved in virtual sites */
void dd_move_x_vsites(const gmx_domdec_t& dd, const matrix box, rvec* x);
+/*! \brief Communicates the positions and velocities involved in virtual sites */
+void dd_move_x_and_v_vsites(const gmx_domdec_t& dd, const matrix box, rvec* x, rvec* v);
/*! \brief Returns the local atom count array for all constraints
*
*/
gmx::ArrayRef<const int> dd_constraints_nlocalatoms(const gmx_domdec_t* dd);
-/* In domdec_top.c */
-
-/*! \brief Print error output when interactions are missing */
-[[noreturn]] void dd_print_missing_interactions(const gmx::MDLogger& mdlog,
- t_commrec* cr,
- int local_count,
- const gmx_mtop_t* top_global,
- const gmx_localtop_t* top_local,
- gmx::ArrayRef<const gmx::RVec> x,
- const matrix box);
-
-/*! \brief Generate and store the reverse topology */
-void dd_make_reverse_top(FILE* fplog,
- gmx_domdec_t* dd,
- const gmx_mtop_t* mtop,
- const gmx::VirtualSitesHandler* vsite,
- const t_inputrec* ir,
- gmx_bool bBCheck);
-
-/*! \brief Generate the local topology and virtual site data */
-void dd_make_local_top(struct gmx_domdec_t* dd,
- struct gmx_domdec_zones_t* zones,
- int npbcdim,
- matrix box,
- rvec cellsize_min,
- const ivec npulse,
- t_forcerec* fr,
- rvec* cgcm_or_x,
- const gmx_mtop_t& top,
- gmx_localtop_t* ltop);
-
-/*! \brief Sort ltop->ilist when we are doing free energy. */
-void dd_sort_local_top(gmx_domdec_t* dd, const t_mdatoms* mdatoms, gmx_localtop_t* ltop);
-
-/*! \brief Construct local state */
-void dd_init_local_state(struct gmx_domdec_t* dd, const t_state* state_global, t_state* local_state);
+/*! Const getter for the local topology checker
+ *
+ * \returns Const handle to local topology checker */
+const gmx::LocalTopologyChecker& dd_localTopologyChecker(const gmx_domdec_t& dd);
-/*! \brief Generate a list of links between atoms that are linked by bonded interactions
+/*! Getter for the local topology checker
*
- * Also stores whether atoms are linked in \p cginfo_mb.
- */
-t_blocka* makeBondedLinks(const gmx_mtop_t& mtop, gmx::ArrayRef<cginfo_mb_t> cginfo_mb);
-
-/*! \brief Calculate the maximum distance involved in 2-body and multi-body bonded interactions */
-void dd_bonded_cg_distance(const gmx::MDLogger& mdlog,
- const gmx_mtop_t* mtop,
- const t_inputrec* ir,
- gmx::ArrayRef<const gmx::RVec> x,
- const matrix box,
- gmx_bool bBCheck,
- real* r_2b,
- real* r_mb);
+ * \returns Handle to local topology checker */
+gmx::LocalTopologyChecker* dd_localTopologyChecker(gmx_domdec_t* dd);
+
+/*! \brief Construct local state */
+void dd_init_local_state(const gmx_domdec_t& dd, const t_state* state_global, t_state* local_state);
/*! \brief Construct the GPU halo exchange object(s).
*
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