Gromacs
2026.0-dev-20241204-d69d709
|
#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/math/vec.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 "domdec_internal.h"
This file definees functions for DD to write PDB files e.g. when reporting problems.
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 t_commrec *cr, int natoms, const rvec x[], const matrix box) |
Dump a pdb file with the current DD home + communicated atoms. More... | |
void write_dd_pdb | ( | const char * | fn, |
int64_t | step, | ||
const char * | title, | ||
const gmx_mtop_t & | mtop, | ||
const t_commrec * | cr, | ||
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.