#include "gromacs/math/vectypes.h"
#include "gromacs/utility/basedefinitions.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, gmx_int64_t step, t_commrec *cr, rvec xs[], rvec v[], matrix box, gmx_edsam_t ed) |
| Applies essential dynamics constrains as defined in the .edi input file. More...
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gmx_edsam_t | ed_open (int natoms, edsamstate_t *EDstate, int nfile, const t_filenm fnm[], unsigned long Flags, const gmx_output_env_t *oenv, t_commrec *cr) |
| Reads in the .edi file containing the essential dynamics and flooding data. More...
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void | init_edsam (const gmx_mtop_t *mtop, const t_inputrec *ir, t_commrec *cr, gmx_edsam_t ed, rvec x[], matrix box, edsamstate_t *EDstate) |
| Initializes the essential dynamics and flooding module. More...
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void | dd_make_local_ed_indices (gmx_domdec_t *dd, gmx_edsam_t ed) |
| Make a selection of the home atoms for the ED groups. More...
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void | do_flood (t_commrec *cr, const t_inputrec *ir, rvec x[], rvec force[], gmx_edsam_t ed, matrix box, gmx_int64_t step, gmx_bool bNS) |
| Evaluate the flooding potential(s) and forces as requested in the .edi input file. More...
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void | done_ed (gmx_edsam_t *ed) |
| Clean up. More...
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Abstract type for essential dynamics.
The main type is defined only in edsam.c
void dd_make_local_ed_indices |
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gmx_domdec_t * |
dd, |
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gmx_edsam_t |
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. |
void do_edsam |
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const t_inputrec * |
ir, |
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gmx_int64_t |
step, |
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t_commrec * |
cr, |
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rvec |
xs[], |
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rvec |
v[], |
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matrix |
box, |
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gmx_edsam_t |
ed |
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) |
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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. |
xs | The local positions on this processor. |
v | The local velocities. |
box | The simulation box. |
ed | The essential dynamics data. |
void do_flood |
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t_commrec * |
cr, |
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const t_inputrec * |
ir, |
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rvec |
x[], |
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rvec |
force[], |
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gmx_edsam_t |
ed, |
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matrix |
box, |
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gmx_int64_t |
step, |
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gmx_bool |
bNS |
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) |
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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. |
x | 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? |
Clean up.
- Parameters
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ed | The essential dynamics data |
gmx_edsam_t ed_open |
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int |
natoms, |
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edsamstate_t * |
EDstate, |
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int |
nfile, |
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const t_filenm |
fnm[], |
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unsigned long |
Flags, |
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const gmx_output_env_t * |
oenv, |
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t_commrec * |
cr |
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) |
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Reads in the .edi file containing the essential dynamics and flooding data.
This function opens the ED input and output files, reads in all datasets it finds in the input file, and cross-checks whether the .edi file information is consistent with the essential dynamics data found in the checkpoint file (if present). gmx make_edi can be used to create an .edi input file.
- Parameters
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natoms | Number of atoms of the whole MD system. |
EDstate | Essential dynamics and flooding data stored in the checkpoint file. |
nfile | Number of entries (files) in the fnm structure. |
fnm | The filenames struct; it contains also the names of the essential dynamics and flooding in + output files. |
Flags | Flags passed over from main, used to determine whether we are appending. |
oenv | Needed to open the output xvgr file. |
cr | Data needed for MPI communication. |
- Returns
- Pointer to the initialized essential dynamics / flooding data.
void init_edsam |
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const gmx_mtop_t * |
mtop, |
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const t_inputrec * |
ir, |
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t_commrec * |
cr, |
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gmx_edsam_t |
ed, |
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rvec |
x[], |
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matrix |
box, |
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edsamstate_t * |
EDstate |
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) |
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Initializes the essential dynamics and flooding module.
- Parameters
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mtop | Molecular topology. |
ir | MD input parameter record. |
cr | Data needed for MPI communication. |
ed | The essential dynamics data. |
x | Positions of the whole MD system. |
box | The simulation box. |
EDstate | ED data stored in the checkpoint file. |