#include <memory>
#include "gromacs/math/vectypes.h"
Declares functions to calculate both essential dynamics constraints as well as flooding potentials and forces.
- Authors
- Bert de Groot bgroo.nosp@m.t@gw.nosp@m.dg.de, Oliver Lange olive.nosp@m.r.la.nosp@m.nge@t.nosp@m.um.d.nosp@m.e, Carsten Kutzner ckutz.nosp@m.ne@g.nosp@m.wdg.d.nosp@m.e
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void | do_edsam (const t_inputrec *ir, int64_t step, const t_commrec *cr, gmx::ArrayRef< gmx::RVec > coords, gmx::ArrayRef< gmx::RVec > velocities, const matrix box, gmx_edsam *ed) |
| Applies essential dynamics constrains as defined in the .edi input file. More...
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std::unique_ptr
< gmx::EssentialDynamics > | init_edsam (const gmx::MDLogger &mdlog, const char *ediFileName, const char *edoFileName, const gmx_mtop_t &mtop, const t_inputrec &ir, const t_commrec *cr, gmx::Constraints *constr, const t_state *globalState, ObservablesHistory *oh, const gmx_output_env_t *oenv, gmx::StartingBehavior startingBehavior) |
| Initializes the essential dynamics and flooding module. More...
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void | dd_make_local_ed_indices (gmx_domdec_t *dd, gmx_edsam *ed) |
| Make a selection of the home atoms for the ED groups. More...
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void | do_flood (const t_commrec *cr, const t_inputrec &ir, gmx::ArrayRef< const gmx::RVec > coords, gmx::ArrayRef< gmx::RVec > force, gmx_edsam *ed, const matrix box, int64_t step, bool bNS) |
| Evaluate the flooding potential(s) and forces as requested in the .edi input file. More...
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void dd_make_local_ed_indices |
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gmx_domdec_t * |
dd, |
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gmx_edsam * |
ed |
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Make a selection of the home atoms for the ED groups.
Should be called at every domain decomposition.
- Parameters
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dd | Domain decomposition data. |
ed | Essential dynamics and flooding data. |
Applies essential dynamics constrains as defined in the .edi input file.
- Parameters
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ir | MD input parameter record. |
step | Number of the time step. |
cr | Data needed for MPI communication. |
coords | The local positions on this processor. |
velocities | The local velocities. |
box | The simulation box. |
ed | The essential dynamics data. |
Evaluate the flooding potential(s) and forces as requested in the .edi input file.
- Parameters
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cr | Data needed for MPI communication. |
ir | MD input parameter record. |
coords | Positions on the local processor. |
force | Forcefield forces to which the flooding forces are added. |
ed | The essential dynamics data. |
box | The simulation box. |
step | Number of the time step. |
bNS | Are we in a neighbor searching step? |
std::unique_ptr<gmx::EssentialDynamics> init_edsam |
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const gmx::MDLogger & |
mdlog, |
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const char * |
ediFileName, |
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const char * |
edoFileName, |
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const gmx_mtop_t & |
mtop, |
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const t_inputrec & |
ir, |
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const t_commrec * |
cr, |
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gmx::Constraints * |
constr, |
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const t_state * |
globalState, |
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ObservablesHistory * |
oh, |
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const gmx_output_env_t * |
oenv, |
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gmx::StartingBehavior |
startingBehavior |
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Initializes the essential dynamics and flooding module.
- Parameters
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mdlog | Logger. |
ediFileName | Essential dynamics input file. |
edoFileName | Output file for essential dynamics data. |
mtop | Molecular topology. |
ir | MD input parameter record. |
cr | Data needed for MPI communication. |
constr | Data structure keeping the constraint information. |
globalState | The global state, only used on the main rank. |
oh | The observables history container. |
oenv | The output environment information. |
startingBehavior | Describes whether this is a restart appending to output files |
- Returns
- A pointer to the ED data structure.