Gromacs
2020.4
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This file declares functions for domdec to use while managing communication of atoms required for special purposes.
Classes | |
class | gmx::HashedMap< T > |
Unordered key to value mapping. More... | |
struct | gmx_specatsend_t |
The communication setup along a single dimension. More... | |
struct | gmx_domdec_specat_comm_t |
Struct with setup and buffers for special atom communication. More... | |
Functions | |
void | dd_move_f_specat (gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac, rvec *f, rvec *fshift) |
Communicates the force for special atoms, the shift forces are reduced with fshift != NULL. | |
void | dd_move_x_specat (gmx_domdec_t *dd, gmx_domdec_specat_comm_t *spac, const matrix box, rvec *x0, rvec *x1, gmx_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 | ( | gmx_domdec_t * | dd, |
gmx_domdec_specat_comm_t * | spac, | ||
const matrix | box, | ||
rvec * | x0, | ||
rvec * | x1, | ||
gmx_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 |