domdec_specatomcomm.cpp File Reference

#include "gmxpre.h"
#include "domdec_specatomcomm.h"
#include <cassert>
#include <cstdio>
#include <algorithm>
#include <array>
#include <filesystem>
#include <memory>
#include "gromacs/domdec/dlb.h"
#include "gromacs/domdec/domdec.h"
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/domdec/ga2la.h"
#include "gromacs/domdec/hashedmap.h"
#include "gromacs/domdec/partition.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/arrayref.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
#include "gromacs/utility/vec.h"

Include dependency graph for domdec_specatomcomm.cpp:

Description

This file implements functions for domdec to use while managing inter-atomic constraints.

Author

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

Functions
void	dd_move_f_specat (const gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac, gmx::RVec *f, gmx::RVec *fshift)
	Communicates the force for special atoms, the shift forces are reduced with fshift != NULL.
void	dd_move_x_specat (const gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac, const matrix box, gmx::RVec *x0, gmx::RVec *x1, bool bX1IsCoord)
	Communicates the coordinates for special atoms. More...
int	setup_specat_communication (gmx_domdec_t *dd, std::vector< int > *ireq, gmx_domdec_specat_comm_t *spac, gmx::HashedMap< int > *ga2la_specat, int at_start, int vbuf_fac, const char *specat_type, const char *add_err)
	Sets up the communication for special atoms. More...

Function Documentation

void dd_move_x_specat	(	const gmx_domdec_t *	dd,
		gmx_domdec_specat_comm_t *	spac,
		const matrix	box,
		gmx::RVec *	x0,
		gmx::RVec *	x1,
		bool	bX1IsCoord
	)

Communicates the coordinates for special atoms.

Parameters

[in]	dd	Domain decomposition struct
[in]	spac	Special atom communication struct
[in]	box	Box, used for pbc
[in,out]	x0	Vector to communicate
[in,out]	x1	Vector to communicate, when != NULL
[in]	bX1IsCoord	Tells is x1 is a coordinate vector (needs pbc)

int setup_specat_communication	(	gmx_domdec_t *	dd,
		std::vector< int > *	ireq,
		gmx_domdec_specat_comm_t *	spac,
		gmx::HashedMap< int > *	ga2la_specat,
		int	at_start,
		int	vbuf_fac,
		const char *	specat_type,
		const char *	add_err
	)

Sets up the communication for special atoms.

Parameters

[in]	dd	Domain decomposition struct
[in,out]	ireq	List of requested atom indices, updated due to aggregation
[in,out]	spac	Special atom communication struct
[out]	ga2la_specat	Global to local special atom index
[in]	at_start	Index in local state where to start storing communicated atoms
[in]	vbuf_fac	Buffer factor, 1 or 2 for communicating 1 or 2 vectors
[in]	specat_type	Name of the special atom, used for error message
[in]	add_err	Text to add at the end of error message when atoms can't be found