Gromacs  2020.4
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Functions

Description

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...
 

Function Documentation

void make_local_shells ( const t_commrec *  cr,
const t_mdatoms md,
gmx_shellfc_t *  shfc 
)

Gets the local shell with domain decomposition.

Parameters
[in]crCommunication record
[in]mdThe MD atom data
[in,out]shfcThe 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.

Parameters
[in]crCommunication record
[in]irInput parameter record
[in]top_globalThe global topology
[in,out]topThe local topology
[in,out]frThe force calculation parameter/data record
[out]graphThe molecular graph, can be NULL
[out]mdAtomsThe MD atom data
[in,out]constrThe constraints handler, can be NULL
[in,out]vsiteThe virtual site data, can be NULL
[in,out]shellfcThe shell/flexible-constraint data, can be NULL