Gromacs
2020.4
|
Contains functions relevant to simulation setup in MD drivers.
Functions | |
void | make_local_shells (const t_commrec *cr, const t_mdatoms *md, gmx_shellfc_t *shfc) |
Gets the local shell with domain decomposition. More... | |
void | mdAlgorithmsSetupAtomData (const t_commrec *cr, const t_inputrec *ir, const gmx_mtop_t &top_global, gmx_localtop_t *top, t_forcerec *fr, t_graph **graph, gmx::MDAtoms *mdAtoms, gmx::Constraints *constr, gmx_vsite_t *vsite, gmx_shellfc_t *shellfc) |
Sets atom data for several MD algorithms. More... | |
void make_local_shells | ( | const t_commrec * | cr, |
const t_mdatoms * | md, | ||
gmx_shellfc_t * | shfc | ||
) |
Gets the local shell with domain decomposition.
[in] | cr | Communication record |
[in] | md | The MD atom data |
[in,out] | shfc | The shell/flexible-constraint data |
void mdAlgorithmsSetupAtomData | ( | const t_commrec * | cr, |
const t_inputrec * | ir, | ||
const gmx_mtop_t & | top_global, | ||
gmx_localtop_t * | top, | ||
t_forcerec * | fr, | ||
t_graph ** | graph, | ||
gmx::MDAtoms * | mdAtoms, | ||
gmx::Constraints * | constr, | ||
gmx_vsite_t * | vsite, | ||
gmx_shellfc_t * | shellfc | ||
) |
Sets atom data for several MD algorithms.
Most MD algorithms require two different setup calls: one for initialization and parameter setting and one for atom data setup. This routine sets the atom data for the (locally available) atoms. This is called at the start of serial runs and during domain decomposition.
[in] | cr | Communication record |
[in] | ir | Input parameter record |
[in] | top_global | The global topology |
[in,out] | top | The local topology |
[in,out] | fr | The force calculation parameter/data record |
[out] | graph | The molecular graph, can be NULL |
[out] | mdAtoms | The MD atom data |
[in,out] | constr | The constraints handler, can be NULL |
[in,out] | vsite | The virtual site data, can be NULL |
[in,out] | shellfc | The shell/flexible-constraint data, can be NULL |