Gromacs
2024.4
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#include "gmxpre.h"
#include "domdec_specatomcomm.h"
#include <cassert>
#include <algorithm>
#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/math/vec.h"
#include "gromacs/mdtypes/commrec.h"
#include "gromacs/pbcutil/ishift.h"
#include "gromacs/utility/fatalerror.h"
#include "gromacs/utility/gmxassert.h"
This file implements functions for domdec to use while managing inter-atomic constraints.
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... | |
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.
[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.
[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 |