1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
|
/////////////////////////////////////////////////////////////
// //
// Copyright (c) 2003-2011 by The University of Queensland //
// Earth Systems Science Computational Centre (ESSCC) //
// http://www.uq.edu.au/esscc //
// //
// Primary Business: Brisbane, Queensland, Australia //
// Licensed under the Open Software License version 3.0 //
// http://www.opensource.org/licenses/osl-3.0.php //
// //
/////////////////////////////////////////////////////////////
#include "Geometry/SimpleNTable3D.h"
/*!
Return the grid index of a position.
\param pos the position
\warning does not check if pos is within space
*/
int CSimple3DNTable::index(const Vec3& pos) const
{
int ix=int((pos.X()-m_p0.X())/m_dim);
int iy=int((pos.Y()-m_p0.Y())/m_dim);
int iz=int((pos.Z()-m_p0.Z())/m_dim);
int idx=ix+m_xsize*iy+iz*m_xsize*m_ysize;
return idx;
}
/*!
Get all indices to which a particle at a given position will be added.
\param pos the position
\warning does not check if pos is within space
*/
vector<int> CSimple3DNTable::allidx(const Vec3& pos) const
{
vector<int> res;
int ix=int((pos.X()-m_p0.X())/m_dim);
int iy=int((pos.Y()-m_p0.Y())/m_dim);
int iz=int((pos.Z()-m_p0.Z())/m_dim);
int idx=ix+m_xsize*iy+iz*m_xsize*m_ysize;
res.push_back(idx);
// iz-layer
if(ix>0){
res.push_back(idx-1);
if(iy>0){
res.push_back(idx-m_xsize-1);
}
if(iy<m_ysize-1){
res.push_back(idx+m_xsize-1);
}
}
if(ix<m_xsize-1){
res.push_back(idx+1);
if(iy>0){
res.push_back(idx-m_xsize+1);
}
if(iy<m_ysize-1){
res.push_back(idx+m_xsize+1);
}
}
if(iy>0){
res.push_back(idx-m_xsize);
}
if(iy<m_ysize-1){
res.push_back(idx+m_xsize);
}
// iz-1 layer
if(iz>0){
int idb=idx-m_xsize*m_ysize;
res.push_back(idb);
if(ix>0){
res.push_back(idb-1);
if(iy>0){
res.push_back(idb-m_xsize-1);
}
if(iy<m_ysize-1){
res.push_back(idb+m_xsize-1);
}
}
if(ix<m_xsize-1){
res.push_back(idb+1);
if(iy>0){
res.push_back(idb-m_xsize+1);
}
if(iy<m_ysize-1){
res.push_back(idb+m_xsize+1);
}
}
if(iy>0){
res.push_back(idb-m_xsize);
}
if(iy<m_ysize-1){
res.push_back(idb+m_xsize);
}
}
// iz+1 layer
if(iz<m_zsize-1){
int idb=idx+m_xsize*m_ysize;
res.push_back(idb);
if(ix>0){
res.push_back(idb-1);
if(iy>0){
res.push_back(idb-m_xsize-1);
}
if(iy<m_ysize-1){
res.push_back(idb+m_xsize-1);
}
}
if(ix<m_xsize-1){
res.push_back(idb+1);
if(iy>0){
res.push_back(idb-m_xsize+1);
}
if(iy<m_ysize-1){
res.push_back(idb+m_xsize+1);
}
}
if(iy>0){
res.push_back(idb-m_xsize);
}
if(iy<m_ysize-1){
res.push_back(idb+m_xsize);
}
}
return res;
}
/*!
insert circular images of the particle
\param cbp the particle
*/
void CSimple3DNTable::insertParticleCircular(SimpleParticle cbp)
{
if(m_xcirc){
if (int((cbp.getPos().X()-m_p0.X())/m_dim)==1) {
cbp.moveTo(cbp.getPos()+m_xshift);
const vector<int> idx=allidx(cbp.getPos());
for(vector<int>::const_iterator citer=idx.begin();citer!=idx.end();citer++){
m_data[*citer].push_back(cbp);
}
} else if (int((cbp.getPos().X()-m_p0.X())/m_dim)==m_xsize-2) {
cbp.moveTo(cbp.getPos()-m_xshift);
const vector<int> idx=allidx(cbp.getPos());
for(vector<int>::const_iterator citer=idx.begin();citer!=idx.end();citer++){
m_data[*citer].push_back(cbp);
}
}
}
}
/*!
Constructor
\param pos position of the (xmin,ymin,zmin) point
\param dim size of the space
\param r grid spacing
*/
CSimple3DNTable::CSimple3DNTable(const Vec3& pos,const Vec3& dim ,double r ,bool xcirc,bool ycirc,bool zcirc)
{
//cout << "CSimple3DNTable(" << pos << " , " << dim << " , " << r << ")" << endl;
m_xsize=int(ceil(dim.X()/r));
m_ysize=int(ceil(dim.Y()/r));
m_zsize=int(ceil(dim.Z()/r));
m_xcirc=xcirc;
m_ycirc=ycirc;
m_zcirc=zcirc;
m_p0=pos;
m_dim=r;
// pad in circular directions
if (m_xcirc) {
m_xsize+=2;
m_p0-=Vec3(r,0.0,0.0);
m_xshift=Vec3(dim.X(),0.0,0.0);
}
if (m_ycirc) {
m_ysize+=2;
m_p0-=Vec3(0.0,r,0.0);
m_yshift=Vec3(0.0,dim.Y(),0.0);
}
if (m_zcirc) {
m_zsize+=2;
m_p0-=Vec3(0.0,0.0,r);
m_yshift=Vec3(0.0,0.0,dim.Z());
}
//cout << "NT size : " << m_xsize << " , " << m_ysize << " , " << m_zsize << endl;
m_data=new vector<SimpleParticle>[m_xsize*m_ysize*m_zsize];
}
/*!
Put all interactions into a set
\param iset the set into which to put them
\param dmax max distance for the creation of an interaction
*/
void CSimple3DNTable::getInteractions(set<BasicInteraction,BILess>& iset, double dmax)
{
for(int i=0;i<m_xsize;i++){
for(int j=0;j<m_ysize;j++){
for(int k=0;k<m_zsize;k++){
int idx=i+m_xsize*j+k*m_xsize*m_ysize;
//cout << "-- " << i << " , " << j << " , " << idx << endl;
if(m_data[idx].size()>=2){
for(vector<SimpleParticle>::iterator iter=m_data[idx].begin();
iter!=m_data[idx].end()-1;
iter++)
{
for (
vector<SimpleParticle>::iterator iter2=iter+1;
iter2!=m_data[idx].end();
iter2++)
{
// cout << "Pair: " << iter->getID() << " - " << iter2 ->getID() << endl;
if((iter->getPos()-iter2->getPos()).norm() < dmax*(iter->getRad()+iter2->getRad()))
{
iset.insert(BasicInteraction(iter->getID(),iter2->getID()));
}
}
}
}
}
}
}
}
// debugging only
void CSimple3DNTable::print()
{
for(int i=0;i<m_xsize;i++){
for(int j=0;j<m_ysize;j++){
for(int k=0;k<m_zsize;k++){
int idx=i+m_xsize*j+k*m_xsize*m_ysize;
//cout << "-- " << i << " , " << j << " , " << " , " << j << " , " << idx << endl;
for(vector<SimpleParticle>::iterator iter=m_data[idx].begin();
iter!=m_data[idx].end();
iter++){
cout << iter->getPos() << " , " << iter->getRad() << endl;
}
}
}
}
}
|
