partition.h File Reference

#include "gromacs/math/paddedvector.h"
#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.h"
#include "gromacs/utility/real.h"

Include dependency graph for partition.h:

Description

This file declares functions for mdrun to call to make a new domain decomposition, and check it.

Author

Berk Hess hess@.nosp@m.kth..nosp@m.se

Functions
bool	check_grid_jump (int64_t step, const gmx_domdec_t *dd, real cutoff, const gmx_ddbox_t *ddbox, gmx_bool bFatal)
	Check whether the DD grid has moved too far for correctness.
void	print_dd_statistics (const t_commrec *cr, const t_inputrec *ir, FILE *fplog)
	Print statistics for domain decomposition communication.
void	dd_partition_system (FILE *fplog, const gmx::MDLogger &mdlog, int64_t step, const t_commrec *cr, gmx_bool bMasterState, int nstglobalcomm, t_state *state_global, const gmx_mtop_t *top_global, const t_inputrec *ir, t_state *state_local, PaddedVector< gmx::RVec > *f, gmx::MDAtoms *mdatoms, gmx_localtop_t *top_local, t_forcerec *fr, gmx_vsite_t *vsite, gmx::Constraints *constr, t_nrnb *nrnb, gmx_wallcycle *wcycle, gmx_bool bVerbose)
	Partition the system over the nodes. More...
void	checkNumberOfBondedInteractions (const gmx::MDLogger &mdlog, t_commrec *cr, int totalNumberOfBondedInteractions, const gmx_mtop_t *top_global, const gmx_localtop_t *top_local, const t_state *state, bool *shouldCheckNumberOfBondedInteractions)
	Check whether bonded interactions are missing, if appropriate. More...

Function Documentation

void checkNumberOfBondedInteractions	(	const gmx::MDLogger &	mdlog,
		t_commrec *	cr,
		int	totalNumberOfBondedInteractions,
		const gmx_mtop_t *	top_global,
		const gmx_localtop_t *	top_local,
		const t_state *	state,
		bool *	shouldCheckNumberOfBondedInteractions
	)

Check whether bonded interactions are missing, if appropriate.

Parameters

[in]	mdlog	Logger
[in]	cr	Communication object
[in]	totalNumberOfBondedInteractions	Result of the global reduction over the number of bonds treated in each domain
[in]	top_global	Global topology for the error message
[in]	top_local	Local topology for the error message
[in]	state	Global state for the error message
[in,out]	shouldCheckNumberOfBondedInteractions	Whether we should do the check. Always set to false.

void dd_partition_system	(	FILE *	fplog,
		const gmx::MDLogger &	mdlog,
		int64_t	step,
		const t_commrec *	cr,
		gmx_bool	bMasterState,
		int	nstglobalcomm,
		t_state *	state_global,
		const gmx_mtop_t *	top_global,
		const t_inputrec *	ir,
		t_state *	state_local,
		PaddedVector< gmx::RVec > *	f,
		gmx::MDAtoms *	mdatoms,
		gmx_localtop_t *	top_local,
		t_forcerec *	fr,
		gmx_vsite_t *	vsite,
		gmx::Constraints *	constr,
		t_nrnb *	nrnb,
		gmx_wallcycle *	wcycle,
		gmx_bool	bVerbose
	)

Partition the system over the nodes.

step is only used for printing error messages. If bMasterState==TRUE then state_global from the master node is used, else state_local is redistributed between the nodes. When f!=NULL, *f will be reallocated to the size of state_local.