dump.cpp File Reference

#include "gmxpre.h"
#include "dump.h"
#include <cstdio>
#include <array>
#include <filesystem>
#include <memory>
#include <vector>
#include "gromacs/domdec/domdec_network.h"
#include "gromacs/domdec/domdec_struct.h"
#include "gromacs/fileio/gmxfio.h"
#include "gromacs/fileio/pdbio.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/mdtypes/md_enums.h"
#include "gromacs/pbcutil/pbc.h"
#include "gromacs/topology/mtop_lookup.h"
#include "gromacs/topology/topology_enums.h"
#include "gromacs/utility/cstringutil.h"
#include "gromacs/utility/real.h"
#include "gromacs/utility/vec.h"
#include "domdec_internal.h"

Include dependency graph for dump.cpp:

Description

This file definees functions for DD to write PDB files e.g. when reporting problems.

Author

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

Functions
void	write_dd_grid_pdb (const char *fn, int64_t step, gmx_domdec_t *dd, matrix box, gmx_ddbox_t *ddbox)
	Write the DD grid to a PDB file.
void	write_dd_pdb (const char *fn, int64_t step, const char *title, const gmx_mtop_t &mtop, const gmx_domdec_t &dd, int natoms, const rvec x[], const matrix box)
	Dump a pdb file with the current DD home + communicated atoms. More...

Function Documentation

void write_dd_pdb	(	const char *	fn,
		int64_t	step,
		const char *	title,
		const gmx_mtop_t &	mtop,
		const gmx_domdec_t &	dd,
		int	natoms,
		const rvec	x[],
		const matrix	box
	)

Dump a pdb file with the current DD home + communicated atoms.

When natoms=-1, dump all known atoms.