Gromacs
2018.8
|
Declares functions to enforce rotational motion upon a group of particles.
Functions | |
void | init_rot (FILE *fplog, t_inputrec *ir, int nfile, const t_filenm fnm[], struct t_commrec *cr, const t_state *globalState, gmx_mtop_t *mtop, const gmx_output_env_t *oenv, const MdrunOptions &mdrunOptions) |
Initializes the enforced rotation groups. More... | |
void | dd_make_local_rotation_groups (struct gmx_domdec_t *dd, t_rot *rot) |
Make a selection of the home atoms for all enforced rotation groups. More... | |
void | do_rotation (struct t_commrec *cr, t_inputrec *ir, matrix box, rvec x[], real t, gmx_int64_t step, gmx_bool bNS) |
Calculates the enforced rotation potential(s). More... | |
real | add_rot_forces (t_rot *rot, rvec f[], struct t_commrec *cr, gmx_int64_t step, real t) |
Add the enforced rotation forces to the official force array. More... | |
void | finish_rot (t_rot *rot) |
Close the enforced rotation output files. More... | |
Add the enforced rotation forces to the official force array.
Adds the forces from enforced rotation potential to the local forces and sums up the contributions to the rotation potential from all the nodes. Since this needs communication, this routine should be called after the short range forces have been evaluated (in order not to spoil cycle counts). This routine also outputs data to the rotation output files (e.g. the potential, the angle of the group(s), and torques).
rot | Pointer to all the enforced rotation data. |
f | The local forces to which the rotational forces have to be added. |
cr | Pointer to MPI communication data. |
step | The time step, used for output. |
t | Time, used for output. |
void dd_make_local_rotation_groups | ( | struct gmx_domdec_t * | dd, |
t_rot * | rot | ||
) |
Make a selection of the home atoms for all enforced rotation groups.
This routine is similar to dd_make_local_pull_groups, but works only with domain decomposition. It should be called at every domain decomposition.
dd | Structure containing domain decomposition data. |
rot | Pointer to all the enforced rotation data. |
void do_rotation | ( | struct t_commrec * | cr, |
t_inputrec * | ir, | ||
matrix | box, | ||
rvec | x[], | ||
real | t, | ||
gmx_int64_t | step, | ||
gmx_bool | bNS | ||
) |
Calculates the enforced rotation potential(s).
This is the main enforced rotation module which is called during every time step. Here the rotation potential as well as the resulting forces are calculated.
cr | Pointer to MPI communication data. |
ir | Struct containing MD input parameters, among those |
box | Simulation box, needed to make group whole. |
x | The positions of all the local particles. |
t | Time. |
step | The time step. |
bNS | After domain decomposition / neighbor searching several local arrays have to be updated (masses, shifts) |
void finish_rot | ( | t_rot * | rot | ) |
Close the enforced rotation output files.
rot | Pointer to all the enforced rotation data. |
void init_rot | ( | FILE * | fplog, |
t_inputrec * | ir, | ||
int | nfile, | ||
const t_filenm | fnm[], | ||
struct t_commrec * | cr, | ||
const t_state * | globalState, | ||
gmx_mtop_t * | mtop, | ||
const gmx_output_env_t * | oenv, | ||
const MdrunOptions & | mdrunOptions | ||
) |
Initializes the enforced rotation groups.
This routine does the memory allocation for various helper arrays, opens the output files etc.
fplog | General output file, normally md.log. |
ir | Struct containing MD input parameters, among those also the enforced rotation parameters. |
nfile | Number of entries in the fnm structure. |
fnm | The filenames struct containing also the names of the rotation output files. |
cr | Pointer to MPI communication data. |
globalState | The global state, only used on the master rank. |
mtop | Molecular topology. |
oenv | Needed to open the rotation output xvgr file. |
mdrunOptions | Options for mdrun. |