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SpatialSearch.h File Reference

#include "ResizeArray.h"

Go to the source code of this file.

Compounds

struct  GridSearchPair
 linked list of atom index pairs generated by the vmd_gridsearch1 and vmd_gridsearch2 XXX on 64-bit machines the next pointers are as large as the atom index data in each node, so half of the memory is wasted in pointer chasing. Calling malloc/free once per pair when building the linked list is a severe multithreading scalability bottleneck due to OS-level mutex locks in malloc/free and/or the kernel VM. On Linux, it is also problematic due to the threaded version of malloc allocating huge blocks and fragmenting memory tremendously. This implementation should not be used for any threaded code. More...

struct  GridSearchPairlist
 Linked list of ResizeArrays containing pairlists, optimized for multithreading. Compared with the GridSearchPair linked list, The list of ResizeArrays uses half as much memory per pair, reduces the malloc calls so they are logarithmic rather than linear with the number of bonds, and reduces free call count to one per-thread down from one per-bond. Since the ResizeArray results in a contiguous block of memory, the traversal coherency is also significantly improved. Ultimately we should convert all of the grid search routines to use this type of data structure, or one like it. More...


Functions

int make_neighborlist (int **nbrlist, int xb, int yb, int zb)
 Build neighborlist. More...

GridSearchPairvmd_gridsearch1 (const float *pos, int n, const int *on, float dist, int allow_double_counting, 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. More...

GridSearchPairvmd_gridsearch2 (const float *pos, int natoms, const int *A, const int *B, float pairdist, int maxpairs)
 Grid search for two different sets of atoms in same molecule. (will eventually be obsoleted by the faster and more useful vmd_gridsearch3). right now, is still needed by measure hbonds (until problems resolved) The maxpairs parameter is set to -1 for no-limit pairlist calculation, or a maximum value otherwise. More...

GridSearchPairvmd_gridsearch3 (const float *posA, int natomsA, const int *A, const float *posB, int natomsB, const int *B, float pairdist, int allow_double_counting, int maxpairs)
 Grid search for two different sets of atoms and/or molecules. By default, if (posA == posB), all bonds are unique. Otherwise, double-counting is allowed. This can be overridden by setting the allow_double_counting param (true=1, false=0, or default=-1). The maxpairs parameter is set to -1 for no-limit pairlist calculation, or a maximum value otherwise. More...

void find_minmax_all (const float *pos, int n, float *min, float *max)
 Find axis-aligned bounding box for all atoms in the list. More...

int find_minmax_selected (int n, const int *flgs, const float *pos, float &_xmin, float &_ymin, float &_zmin, float &_xmax, float &_ymax, float &_zmax)
 Find axis-aligned bounding box for selected atoms in the list Return true if minmax was found, false if all flags are zero. More...

void find_minmax (const float *pos, int n, const int *on, float *min, float *max, int *oncount)
 Find axis-aligned bounding box for selected atoms in the list. More...

void find_within (const float *xyz, int *flgs, const int *others, int num, float r)
 Find selected atoms within a specified distance of a second set of points. More...


Function Documentation

void find_minmax const float *    pos,
int    n,
const int *    on,
float *    min,
float *    max,
int *    oncount
 

Find axis-aligned bounding box for selected atoms in the list.

Definition at line 117 of file SpatialSearch.C.

Referenced by vmd_gridsearch1, vmd_gridsearch2, and vmd_gridsearch3.

void find_minmax_all const float *    pos,
int    n,
float *    min,
float *    max
 

Find axis-aligned bounding box for all atoms in the list.

Definition at line 43 of file SpatialSearch.C.

Referenced by vmd_gridsearch_bonds.

int find_minmax_selected int    n,
const int *    flgs,
const float *    pos,
float &    _xmin,
float &    _ymin,
float &    _zmin,
float &    _xmax,
float &    _ymax,
float &    _zmax
 

Find axis-aligned bounding box for selected atoms in the list Return true if minmax was found, false if all flags are zero.

Definition at line 74 of file SpatialSearch.C.

References n, and num.

Referenced by find_within.

void find_within const float *    xyz,
int *    flgs,
const int *    others,
int    num,
float    r
 

Find selected atoms within a specified distance of a second set of points.

Definition at line 984 of file SpatialSearch.C.

Referenced by measure_pbc_neighbors.

int make_neighborlist int **    nbrlist,
int    xb,
int    yb,
int    zb
 

Build neighborlist.

Definition at line 168 of file SpatialSearch.C.

Referenced by vmd_gridsearch1, vmd_gridsearch2, and vmd_gridsearch_bonds.

GridSearchPair* vmd_gridsearch1 const float *    pos,
int    n,
const int *    on,
float    dist,
int    allow_double_counting,
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.

Definition at line 273 of file SpatialSearch.C.

Referenced by measure_clustsize, measure_sasa, measure_sasa_perresidue, measure_sasa_thread, and vmd_gridsearch3.

GridSearchPair* vmd_gridsearch2 const float *    pos,
int    natoms,
const int *    A,
const int *    B,
float    pairdist,
int    maxpairs
 

Grid search for two different sets of atoms in same molecule. (will eventually be obsoleted by the faster and more useful vmd_gridsearch3). right now, is still needed by measure hbonds (until problems resolved) The maxpairs parameter is set to -1 for no-limit pairlist calculation, or a maximum value otherwise.

Definition at line 476 of file SpatialSearch.C.

Referenced by measure_hbonds.

GridSearchPair* vmd_gridsearch3 const float *    posA,
int    natomsA,
const int *    A,
const float *    posB,
int    natomsB,
const int *    B,
float    pairdist,
int    allow_double_counting,
int    maxpairs
 

Grid search for two different sets of atoms and/or molecules. By default, if (posA == posB), all bonds are unique. Otherwise, double-counting is allowed. This can be overridden by setting the allow_double_counting param (true=1, false=0, or default=-1). The maxpairs parameter is set to -1 for no-limit pairlist calculation, or a maximum value otherwise.

Definition at line 684 of file SpatialSearch.C.

Referenced by VolMapCreateDistance::compute_frame, contacts, measure_pointset_overlap, and vmd_measure_contacts.


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