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SpatialSearch.C File Reference

#include <stdio.h>
#include <math.h>
#include <stdlib.h>
#include "BondSearch.h"
#include "Timestep.h"
#include "BaseMolecule.h"
#include "Molecule.h"
#include "Inform.h"
#include "VMDThreads.h"
#include <ctype.h>
#include <string.h>

Go to the source code of this file.

Compounds

struct  AtomEntry
struct  FindWithinData

Defines

#define MAXGRIDDIM   31

Typedefs

typedef ResizeArray< AtomEntry > atomlist

Functions

void add_link (GridSearchPair *link, int i, int j)
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...

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

int make_neighborlist_sym (int **nbrlist, int xb, int yb, int zb)
GridSearchPair * vmd_gridsearch1 (const float *pos, int natoms, const int *on, float pairdist, 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...

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. More...

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. More...

void * find_within_routine (void *v)
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...

Define Documentation

#define MAXGRIDDIM   31
 

Definition at line 914 of file SpatialSearch.C.

Referenced by find_within.

Typedef Documentation

typedef ResizeArray<AtomEntry> atomlist
 

Definition at line 896 of file SpatialSearch.C.

Function Documentation

void add_link (  GridSearchPair *    link,
int    i,
int    j
)  [static]
 

Definition at line 39 of file SpatialSearch.C.

References GridSearchPair::ind1, GridSearchPair::ind2, GridSearchPair::next, and NULL.

Referenced by vmd_gridsearch1, vmd_gridsearch2, and vmd_gridsearch3.

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 113 of file SpatialSearch.C.

References NULL.

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 46 of file SpatialSearch.C.

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 77 of file SpatialSearch.C.

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 915 of file SpatialSearch.C.

References ResizeArray< AtomEntry >::append, data, find_minmax_selected, find_within_routine, FindWithinData::flgatoms, FindWithinData::flgs, MAXGRIDDIM, FindWithinData::nthreads, NULL, num, FindWithinData::otheratoms, FindWithinData::r2, FindWithinData::tid, FindWithinData::totb, vmd_thread_create, vmd_thread_join, vmd_thread_numprocessors, vmd_thread_t, FindWithinData::xb, FindWithinData::xytotb, FindWithinData::xyz, FindWithinData::yb, and FindWithinData::zb.

void * find_within_routine (  void *    v )  [static]
 

Definition at line 1045 of file SpatialSearch.C.

References data, FindWithinData::flgatoms, FindWithinData::flgs, AtomEntry::index, FindWithinData::nthreads, NULL, ResizeArray< AtomEntry >::num, FindWithinData::otheratoms, FindWithinData::r2, FindWithinData::tid, FindWithinData::totb, AtomEntry::x, FindWithinData::xb, FindWithinData::xytotb, AtomEntry::y, FindWithinData::yb, AtomEntry::z, and FindWithinData::zb.

Referenced by find_within.

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

Build neighborlist.

Definition at line 164 of file SpatialSearch.C.

References NULL.

int make_neighborlist_sym (  int **    nbrlist,
int    xb,
int    yb,
int    zb
)  [static]
 

Definition at line 212 of file SpatialSearch.C.

References NULL.

Referenced by vmd_gridsearch3.

GridSearchPair* vmd_gridsearch1 (  const float *    pos,
int    natoms,
const int *    on,
float    pairdist,
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 269 of file SpatialSearch.C.

References add_link, distance2, find_minmax, make_neighborlist, msg_timer_create, msg_timer_destroy, msg_timer_timeout, GridSearchPair::next, NULL, num, and vec_sub.

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 453 of file SpatialSearch.C.

References add_link, distance2, find_minmax, make_neighborlist, GridSearchPair::next, NULL, num, and vec_sub.

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 642 of file SpatialSearch.C.

References add_link, distance2, find_minmax, make_neighborlist_sym, GridSearchPair::next, NULL, num, vec_sub, and vmd_gridsearch1.

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