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v_base.cc
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1 // Voro++, a 3D cell-based Voronoi library
2 //
3 // Author : Chris H. Rycroft (LBL / UC Berkeley)
4 // Email : chr@alum.mit.edu
5 // Date : August 30th 2011
6
7 /** \file v_base.cc
8 * \brief Function implementations for the base Voronoi container class. */
9
10 #include "v_base.hh"
11 #include "config.hh"
12
13 namespace voro {
14
15 /** This function is called during container construction. The routine scans
16 * all of the worklists in the wl[] array. For a given worklist of blocks
17 * labeled \f$w_1\f$ to \f$w_n\f$, it computes a sequence \f$r_0\f$ to
18 * \f$r_n\f$ so that $r_i$ is the minimum distance to all the blocks
19 * \f$w_{j}\f$ where \f$j>i\f$ and all blocks outside the worklist. The values
20 * of \f$r_n\f$ is calculated first, as the minimum distance to any block in
21 * the shell surrounding the worklist. The \f$r_i\f$ are then computed in
22 * reverse order by considering the distance to \f$w_{i+1}\f$. */
23 voro_base::voro_base(int nx_,int ny_,int nz_,double boxx_,double boxy_,double boxz_) :
24 nx(nx_), ny(ny_), nz(nz_), nxy(nx_*ny_), nxyz(nxy*nz_), boxx(boxx_), boxy(boxy_), boxz(boxz_),
25 xsp(1/boxx_), ysp(1/boxy_), zsp(1/boxz_), mrad(new double[wl_hgridcu*wl_seq_length]) {
26 const unsigned int b1=1<<21,b2=1<<22,b3=1<<24,b4=1<<25,b5=1<<27,b6=1<<28;
27 const double xstep=boxx/wl_fgrid,ystep=boxy/wl_fgrid,zstep=boxz/wl_fgrid;
28 int i,j,k,lx,ly,lz,q;
29 unsigned int f,*e=const_cast<unsigned int*> (wl);
30 double xlo,ylo,zlo,xhi,yhi,zhi,minr,*radp=mrad;
31 for(zlo=0,zhi=zstep,lz=0;lz<wl_hgrid;zlo=zhi,zhi+=zstep,lz++) {
32 for(ylo=0,yhi=ystep,ly=0;ly<wl_hgrid;ylo=yhi,yhi+=ystep,ly++) {
33 for(xlo=0,xhi=xstep,lx=0;lx<wl_hgrid;xlo=xhi,xhi+=xstep,lx++) {
34 minr=large_number;
35 for(q=e[0]+1;q<wl_seq_length;q++) {
36 f=e[q];
37 i=(f&127)-64;
38 j=(f>>7&127)-64;
39 k=(f>>14&127)-64;
40 if((f&b2)==b2) {
41 compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i-1,j,k);
42 if((f&b1)==0) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i+1,j,k);
43 } else if((f&b1)==b1) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i+1,j,k);
44 if((f&b4)==b4) {
45 compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j-1,k);
46 if((f&b3)==0) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j+1,k);
47 } else if((f&b3)==b3) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j+1,k);
48 if((f&b6)==b6) {
49 compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k-1);
50 if((f&b5)==0) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k+1);
51 } else if((f&b5)==b5) compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k+1);
52 }
53 q--;
54 while(q>0) {
55 radp[q]=minr;
56 f=e[q];
57 i=(f&127)-64;
58 j=(f>>7&127)-64;
59 k=(f>>14&127)-64;
60 compute_minimum(minr,xlo,xhi,ylo,yhi,zlo,zhi,i,j,k);
61 q--;
62 }
63 *radp=minr;
64 e+=wl_seq_length;
65 radp+=wl_seq_length;
66 }
67 }
68 }
69 }
70
71 /** Computes the minimum distance from a subregion to a given block. If this distance
72 * is smaller than the value of minr, then it passes
73 * \param[in,out] minr a pointer to the current minimum distance. If the distance
74 * computed in this function is smaller, then this distance is
75 * set to the new one.
76 * \param[out] (xlo,ylo,zlo) the lower coordinates of the subregion being
77 * considered.
78 * \param[out] (xhi,yhi,zhi) the upper coordinates of the subregion being
79 * considered.
80 * \param[in] (ti,tj,tk) the coordinates of the block. */
81 void voro_base::compute_minimum(double &minr,double &xlo,double &xhi,double &ylo,double &yhi,double &zlo,double &zhi,int ti,int tj,int tk) {
82 double radsq,temp;
83 if(ti>0) {temp=boxx*ti-xhi;radsq=temp*temp;}
84 else if(ti<0) {temp=xlo-boxx*(1+ti);radsq=temp*temp;}
85 else radsq=0;
86
87 if(tj>0) {temp=boxy*tj-yhi;radsq+=temp*temp;}
88 else if(tj<0) {temp=ylo-boxy*(1+tj);radsq+=temp*temp;}
89
90 if(tk>0) {temp=boxz*tk-zhi;radsq+=temp*temp;}
91 else if(tk<0) {temp=zlo-boxz*(1+tk);radsq+=temp*temp;}
92
93 if(radsq<minr) minr=radsq;
94 }
95
96 /** Checks to see whether "%n" appears in a format sequence to determine
97 * whether neighbor information is required or not.
98 * \param[in] format the format string to check.
99 * \return True if a "%n" is found, false otherwise. */
100 bool voro_base::contains_neighbor(const char *format) {
101 char *fmp=(const_cast<char*>(format));
102
103 // Check to see if "%n" appears in the format sequence
104 while(*fmp!=0) {
105 if(*fmp=='%') {
106 fmp++;
107 if(*fmp=='n') return true;
108 else if(*fmp==0) return false;
109 }
110 fmp++;
111 }
112
113 return false;
114 }
115
116 #include "v_base_wl.cc"
117
118 }
voro::voro_base::boxy
const double boxy
Definition: v_base.hh:43
config.hh
Master configuration file for setting various compile-time options.
v_base_wl.cc
The table of block worklists that are used during the cell computation, which is part of the voro_bas...
voro::voro_base::mrad
double * mrad
Definition: v_base.hh:55
voro::voro_base::voro_base
voro_base(int nx_, int ny_, int nz_, double boxx_, double boxy_, double boxz_)
Definition: v_base.cc:23
voro::voro_base::contains_neighbor
bool contains_neighbor(const char *format)
Definition: v_base.cc:100
voro::voro_base::boxx
const double boxx
Definition: v_base.hh:41
voro::voro_base::wl
static const unsigned int wl[wl_seq_length *wl_hgridcu]
Definition: v_base.hh:57
voro::voro_base::boxz
const double boxz
Definition: v_base.hh:45
v_base.hh
Header file for the base Voronoi container class.