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BondSearch.h File Reference

#include "ResizeArray.h"
#include "SpatialSearch.h"

Go to the source code of this file.

Functions

GridSearchPairlist * vmd_gridsearch_bonds (const float *pos, const float *radii, int n, float dist, int maxpairs)

Grid search for the case of a single set of atoms. It ignore pairs between atoms with identical coords. The maxpairs parameter is set to -1 for no-limit pairlist calculation, or a maximum value otherwise. This is the same code as gridsearch1(), but simplified and hopefully a bit faster. More...

int vmd_bond_search (BaseMolecule *mol, const Timestep *ts, float cutoff, int dupcheck)

Compute bonds for the molecule using the given timestep (which must not be NULL) and adds them to the given molecule. Return success. The code currently calls gridsearch1 with a pairlist limit of 27 * natoms, which should easily be sufficient for any real structure. More...

int vmd_bondsearch_thr (const float *pos, const float *radii, GridSearchPairlist *cur, int totb, int **boxatom, int *numinbox, int **nbrlist, int maxpairs, float pairdist)

Multithreaded bond search worker routine handles spawning and joining all of the worker threads, and merging their results into a single list. More...

Function Documentation

int vmd_bond_search ( BaseMolecule * mol,

const Timestep * ts,

float cutoff,

int dupcheck

)

Compute bonds for the molecule using the given timestep (which must not be NULL) and adds them to the given molecule. Return success. The code currently calls gridsearch1 with a pairlist limit of 27 * natoms, which should easily be sufficient for any real structure.

Definition at line 373 of file BondSearch.C.
Referenced by DrawMolecule::append_frame, and DrawMolecule::recalc_bonds.

int vmd_bondsearch_thr ( const float * pos,

const float * radii,

GridSearchPairlist * cur,

int totb,

int ** boxatom,

int * numinbox,

int ** nbrlist,

int maxpairs,

float pairdist

)

Multithreaded bond search worker routine handles spawning and joining all of the worker threads, and merging their results into a single list.

Definition at line 210 of file BondSearch.C.
Referenced by vmd_gridsearch_bonds.

GridSearchPairlist* vmd_gridsearch_bonds ( const float * pos,

const float * radii,

int n,

float dist,

int maxpairs

)

Grid search for the case of a single set of atoms. It ignore pairs between atoms with identical coords. The maxpairs parameter is set to -1 for no-limit pairlist calculation, or a maximum value otherwise. This is the same code as gridsearch1(), but simplified and hopefully a bit faster.

Definition at line 37 of file BondSearch.C.
References n.
Referenced by vmd_bond_search.

Generated on Thu Oct 30 02:45:54 2025 for VMD (current) by

Functions
GridSearchPairlist *	vmd_gridsearch_bonds (const float pos, const float radii, int n, float dist, int maxpairs)
	Grid search for the case of a single set of atoms. It ignore pairs between atoms with identical coords. The maxpairs parameter is set to -1 for no-limit pairlist calculation, or a maximum value otherwise. This is the same code as gridsearch1(), but simplified and hopefully a bit faster. More...
int	vmd_bond_search (BaseMolecule mol, const Timestep ts, float cutoff, int dupcheck)
	Compute bonds for the molecule using the given timestep (which must not be NULL) and adds them to the given molecule. Return success. The code currently calls gridsearch1 with a pairlist limit of 27 * natoms, which should easily be sufficient for any real structure. More...
int	vmd_bondsearch_thr (const float pos, const float radii, GridSearchPairlist cur, int totb, int boxatom, int numinbox, int **nbrlist, int maxpairs, float pairdist)
	Multithreaded bond search worker routine handles spawning and joining all of the worker threads, and merging their results into a single list. More...