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root/group/trunk/OOPSE/libmdtools/Atom.cpp
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Comparing trunk/OOPSE/libmdtools/Atom.cpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

# Line 2 | Line 2 | using namespace std;
2  
3   using namespace std;
4  
5 + #include "simError.h"
6   #include "Atom.hpp"
7  
8 < double* Atom::pos; // the position array
9 < double* Atom::vel; // the velocity array
10 < double* Atom::frc; // the forc array
11 < double* Atom::trq; // the torque vector  ( space fixed )
11 < double* Atom::Amat; // the rotation matrix
12 < double* Atom::mu;   // the array of dipole moments
13 < double* Atom::ul;   // the lab frame unit directional vector
14 < int Atom::nElements;
8 > Atom::Atom(int theIndex, SimState* theConfig) {
9 >  
10 >  myConfig = theConfig;
11 >  hasCoords = false;
12  
16 – Atom::Atom(int theIndex) {
13    c_n_hyd = 0;
14    has_dipole = 0;
15    is_VDW = 0;
16    is_LJ = 0;
17    
18    index = theIndex;
19 <  offset = 3 * index;
19 >  offset = 0;
20    offsetX = offset;
21    offsetY = offset+1;
22    offsetZ = offset+2;
23    
24 <  Axx = index*9;
24 >  Axx = 0;
25    Axy = Axx+1;
26    Axz = Axx+2;
27    
# Line 38 | Line 34 | void Atom::createArrays (int the_nElements) {
34    Azz = Axx+8;
35   }
36  
41 – void Atom::createArrays (int the_nElements) {
42 –  int i;
43 –  
44 –  nElements = the_nElements;
45 –
46 –  pos = new double[nElements*3];
47 –  vel = new double[nElements*3];
48 –  frc = new double[nElements*3];
49 –  trq = new double[nElements*3];
50 –  Amat = new double[nElements*9];
51 –  mu = new double[nElements];
52 –  ul = new double[nElements*3];
53 –  
54 –  // init directional values to zero
55 –  
56 –  for( i=0; i<nElements; i++){
57 –    trq[i] = 0.0;
58 –    trq[i+1] = 0.0;
59 –    trq[i+2] = 0.0;
60 –    
61 –    Amat[i] = 1.0;
62 –    Amat[i+1] = 0.0;
63 –    Amat[i+2] = 0.0;
64 –    
65 –    Amat[i+3] = 0.0;
66 –    Amat[i+4] = 1.0;
67 –    Amat[i+5] = 0.0;
68 –    
69 –    Amat[i+6] = 0.0;
70 –    Amat[i+7] = 0.0;
71 –    Amat[i+8] = 1.0;
72 –    
73 –    mu[i] = 0.0;    
74 –    
75 –    ul[i] = 1.0;
76 –    ul[i+1] = 0.0;
77 –    ul[i+2] = 0.0;
78 –  }
79 – }
80 –
81 – void Atom::destroyArrays(void) {
82 –  delete[] pos;
83 –  delete[] vel;
84 –  delete[] frc;
85 –  delete[] trq;
86 –  delete[] Amat;
87 –  delete[] mu;
88 – }
89 –
37   void Atom::setIndex(int theIndex) {
38    index = theIndex;
92 –  offset = index*3;
93 –  offsetX = offset;
94 –  offsetY = offset+1;
95 –  offsetZ = offset+2;
96 –  
97 –  Axx = index*9;
98 –  Axy = Axx+1;
99 –  Axz = Axx+2;
100 –  
101 –  Ayx = Axx+3;
102 –  Ayy = Axx+4;
103 –  Ayz = Axx+5;
104 –  
105 –  Azx = Axx+6;
106 –  Azy = Axx+7;
107 –  Azz = Axx+8;
39   }
40  
41 < void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
111 <                   double* Atrq, double* AAmat, double* Amu,
112 <                   double* Aul) {
41 > void Atom::setCoords(void){
42  
43 <  int nNew = nElements+nAdded;
43 >  if( myConfig->isAllocated() ){
44  
116 –  double* new_pos = new double[nNew*3];
117 –  double* new_vel = new double[nNew*3];
118 –  double* new_frc = new double[nNew*3];
119 –  double* new_trq = new double[nNew*3];
120 –  double* new_Amat = new double[nNew*9];
121 –  double* new_mu = new double[nNew];
122 –  double* new_ul = new double[nNew*3];
123 –  int i, j;
124 –  
125 –  for (i = 0; i < 3*nElements; i++) {
126 –    new_pos[i] = pos[i];
127 –    new_vel[i] = vel[i];
128 –    new_frc[i] = frc[i];
129 –    new_trq[i] = trq[i];
130 –    new_ul[i] = ul[i];
131 –  }
45  
46 <  for(i = 0; i < 3*nAdded; i++) {
47 <    j = i + 3*nElements;
48 <    new_pos[j] = Apos[i];
49 <    new_vel[j] = Avel[i];
50 <    new_frc[j] = Afrc[i];
51 <    new_trq[j] = Atrq[i];
52 <    new_ul[j] = Aul[i];
46 >    myConfig->getAtomPointers( index,
47 >                     &pos,
48 >                     &vel,
49 >                     &frc,
50 >                     &trq,
51 >                     &Amat,
52 >                     &mu,  
53 >                     &ul );
54    }
55 <
56 <  for (i = 0; i < 9*nElements; i++) {
57 <    new_Amat[i] = Amat[i];
55 >  else{
56 >    sprintf( painCave.errMsg,
57 >             "Attempted to set Atom %d  coordinates with an unallocated "
58 >             "SimState object.\n", index );
59 >    painCave.isFatal = 1;
60 >    simError();
61    }
62  
63 <  for(i = 0; i < 9*nAdded; i++) {
147 <    j = i + 9*nElements;
148 <    new_Amat[j] = AAmat[i];
149 <  }
63 >  hasCoords = true;
64  
151 –  for (i = 0; i < nElements; i++) {
152 –    new_mu[i] = mu[i];
153 –  }
154 –
155 –  for(i = 0; i < nAdded; i++) {
156 –    j = i + nElements;
157 –    new_mu[j] = Amu[i];
158 –  }
159 –
160 –  delete[] pos;
161 –  delete[] vel;
162 –  delete[] frc;
163 –  delete[] trq;
164 –  delete[] Amat;
165 –  delete[] mu;
166 –
167 –  pos = new_pos;
168 –  vel = new_vel;
169 –  frc = new_frc;
170 –  trq = new_trq;
171 –  ul = new_ul;
172 –  Amat = new_Amat;
173 –  mu = new_mu;
174 –
175 –  nElements = nNew;
65   }
66  
67 < void Atom::deleteAtom(int theIndex) {
68 <  deleteRange(theIndex, theIndex);
69 < }
67 > // void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc,
68 > //                    double* Atrq, double* AAmat, double* Amu,
69 > //                    double* Aul) {
70  
71 < void Atom::deleteRange(int startIndex, int stopIndex) {
183 <
184 <  int nNew = nElements-(stopIndex-startIndex+1);
71 > //   int nNew = nElements+nAdded;
72  
73 <  double* new_pos = new double[nNew*3];
74 <  double* new_vel = new double[nNew*3];
75 <  double* new_frc = new double[nNew*3];
76 <  double* new_trq = new double[nNew*3];
77 <  double* new_Amat = new double[nNew*9];
78 <  double* new_mu = new double[nNew];
79 <  double* new_ul = new double[nNew*3];
80 <  int i, j;
73 > //   double* new_pos = new double[nNew*3];
74 > //   double* new_vel = new double[nNew*3];
75 > //   double* new_frc = new double[nNew*3];
76 > //   double* new_trq = new double[nNew*3];
77 > //   double* new_Amat = new double[nNew*9];
78 > //   double* new_mu = new double[nNew];
79 > //   double* new_ul = new double[nNew*3];
80 > //   int i, j;
81    
82 <  for (i = 0; i < 3*startIndex; i++) {
83 <    new_pos[i] = pos[i];
84 <    new_vel[i] = vel[i];
85 <    new_frc[i] = frc[i];
86 <    new_trq[i] = trq[i];
87 <    new_ul[i] = ul[i];
88 <  }
82 > //   for (i = 0; i < 3*nElements; i++) {
83 > //     new_pos[i] = pos[i];
84 > //     new_vel[i] = vel[i];
85 > //     new_frc[i] = frc[i];
86 > //     new_trq[i] = trq[i];
87 > //     new_ul[i] = ul[i];
88 > //   }
89  
90 <  for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
91 <    j = i - 3*startIndex + 1;
92 <    new_pos[j] = pos[i];
93 <    new_vel[j] = vel[i];
94 <    new_frc[j] = frc[i];
95 <    new_trq[j] = trq[i];
96 <    new_ul[j] = ul[i];
97 <  }
90 > //   for(i = 0; i < 3*nAdded; i++) {
91 > //     j = i + 3*nElements;
92 > //     new_pos[j] = Apos[i];
93 > //     new_vel[j] = Avel[i];
94 > //     new_frc[j] = Afrc[i];
95 > //     new_trq[j] = Atrq[i];
96 > //     new_ul[j] = Aul[i];
97 > //   }
98  
99 <  for (i = 0; i < 9*startIndex; i++) {
100 <    new_Amat[i] = Amat[i];
101 <  }
99 > //   for (i = 0; i < 9*nElements; i++) {
100 > //     new_Amat[i] = Amat[i];
101 > //   }
102  
103 <  for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
104 <    j = i - 9*startIndex + 1;
105 <    new_Amat[j] = Amat[i];
106 <  }
103 > //   for(i = 0; i < 9*nAdded; i++) {
104 > //     j = i + 9*nElements;
105 > //     new_Amat[j] = AAmat[i];
106 > //   }
107  
108 <  for (i = 0; i < startIndex; i++) {
109 <    new_mu[i] = mu[i];
108 > //   for (i = 0; i < nElements; i++) {
109 > //     new_mu[i] = mu[i];
110 > //   }
111 >
112 > //   for(i = 0; i < nAdded; i++) {
113 > //     j = i + nElements;
114 > //     new_mu[j] = Amu[i];
115 > //   }
116 >
117 > //   delete[] pos;
118 > //   delete[] vel;
119 > //   delete[] frc;
120 > //   delete[] trq;
121 > //   delete[] Amat;
122 > //   delete[] mu;
123 >
124 > //   pos = new_pos;
125 > //   vel = new_vel;
126 > //   frc = new_frc;
127 > //   trq = new_trq;
128 > //   ul = new_ul;
129 > //   Amat = new_Amat;
130 > //   mu = new_mu;
131 >
132 > //   nElements = nNew;
133 > // }
134 >
135 > // void Atom::deleteAtom(int theIndex) {
136 > //   deleteRange(theIndex, theIndex);
137 > // }
138 >
139 > // void Atom::deleteRange(int startIndex, int stopIndex) {
140 >
141 > //   int nNew = nElements-(stopIndex-startIndex+1);
142 >
143 > //   double* new_pos = new double[nNew*3];
144 > //   double* new_vel = new double[nNew*3];
145 > //   double* new_frc = new double[nNew*3];
146 > //   double* new_trq = new double[nNew*3];
147 > //   double* new_Amat = new double[nNew*9];
148 > //   double* new_mu = new double[nNew];
149 > //   double* new_ul = new double[nNew*3];
150 > //   int i, j;
151 >  
152 > //   for (i = 0; i < 3*startIndex; i++) {
153 > //     new_pos[i] = pos[i];
154 > //     new_vel[i] = vel[i];
155 > //     new_frc[i] = frc[i];
156 > //     new_trq[i] = trq[i];
157 > //     new_ul[i] = ul[i];
158 > //   }
159 >
160 > //   for(i = 3*(stopIndex + 1); i < 3*nElements; i++) {
161 > //     j = i - 3*startIndex + 1;
162 > //     new_pos[j] = pos[i];
163 > //     new_vel[j] = vel[i];
164 > //     new_frc[j] = frc[i];
165 > //     new_trq[j] = trq[i];
166 > //     new_ul[j] = ul[i];
167 > //   }
168 >
169 > //   for (i = 0; i < 9*startIndex; i++) {
170 > //     new_Amat[i] = Amat[i];
171 > //   }
172 >
173 > //   for(i = 9*(stopIndex + 1); i < 9*nElements; i++) {
174 > //     j = i - 9*startIndex + 1;
175 > //     new_Amat[j] = Amat[i];
176 > //   }
177 >
178 > //   for (i = 0; i < startIndex; i++) {
179 > //     new_mu[i] = mu[i];
180 > //   }
181 >
182 > //   for(i = (stopIndex+1); i < nElements; i++) {
183 > //     j = i - startIndex + 1;
184 > //     new_mu[j] = mu[i];
185 > //   }
186 >
187 > //   delete[] pos;
188 > //   delete[] vel;
189 > //   delete[] frc;
190 > //   delete[] trq;
191 > //   delete[] Amat;
192 > //   delete[] mu;
193 >
194 > //   pos = new_pos;
195 > //   vel = new_vel;
196 > //   frc = new_frc;
197 > //   trq = new_trq;
198 > //   ul = new_ul;
199 > //   Amat = new_Amat;
200 > //   mu = new_mu;
201 >
202 > //   nElements = nNew;
203 > // }
204 >
205 >
206 > void Atom::getPos( double theP[3] ){
207 >  
208 >  if( hasCoords ){
209 >    theP[0] = pos[offsetX];
210 >    theP[1] = pos[offsetY];
211 >    theP[2] = pos[offsetZ];
212    }
213 +  else{
214  
215 <  for(i = (stopIndex+1); i < nElements; i++) {
216 <    j = i - startIndex + 1;
217 <    new_mu[j] = mu[i];
215 >    sprintf( painCave.errMsg,
216 >             "Attempt to get Pos for atom %d before coords set.\n",
217 >             index );
218 >    painCave.isFatal = 1;
219 >    simError();
220    }
221 + }
222  
223 <  delete[] pos;
224 <  delete[] vel;
225 <  delete[] frc;
226 <  delete[] trq;
227 <  delete[] Amat;
228 <  delete[] mu;
223 > void Atom::setPos( double theP[3] ){
224 >  
225 >  if( hasCoords ){
226 >    pos[offsetX] = theP[0];
227 >    pos[offsetY] = theP[1];
228 >    pos[offsetZ] = theP[2];
229 >  }
230 >  else{
231  
232 <  pos = new_pos;
233 <  vel = new_vel;
234 <  frc = new_frc;
235 <  trq = new_trq;
236 <  ul = new_ul;
237 <  Amat = new_Amat;
238 <  mu = new_mu;
232 >    sprintf( painCave.errMsg,
233 >             "Attempt to set Pos for atom %d before coords set.\n",
234 >             index );
235 >    painCave.isFatal = 1;
236 >    simError();
237 >  }
238 > }
239  
240 <  nElements = nNew;
240 > void Atom::getVel( double theV[3] ){
241 >  
242 >  if( hasCoords ){
243 >    theV[0] = vel[offsetX];
244 >    theV[1] = vel[offsetY];
245 >    theV[2] = vel[offsetZ];
246 >  }
247 >  else{
248 >    
249 >    sprintf( painCave.errMsg,
250 >             "Attempt to get vel for atom %d before coords set.\n",
251 >             index );
252 >    painCave.isFatal = 1;
253 >    simError();
254 >  }
255 >
256   }
257 +
258 + void Atom::setVel( double theV[3] ){
259 +  
260 +  if( hasCoords ){
261 +    vel[offsetX] = theV[0];
262 +    vel[offsetY] = theV[1];
263 +    vel[offsetZ] = theV[2];
264 +  }
265 +  else{
266 +    
267 +    sprintf( painCave.errMsg,
268 +             "Attempt to set vel for atom %d before coords set.\n",
269 +             index );
270 +    painCave.isFatal = 1;
271 +    simError();
272 +  }
273 + }
274 +
275 + void Atom::getFrc( double theF[3] ){
276 +  
277 +  if( hasCoords ){
278 +    theF[0] = frc[offsetX];
279 +    theF[1] = frc[offsetY];
280 +    theF[2] = frc[offsetZ];
281 +  }
282 +  else{
283 +    
284 +    sprintf( painCave.errMsg,
285 +             "Attempt to get frc for atom %d before coords set.\n",
286 +             index );
287 +    painCave.isFatal = 1;
288 +    simError();
289 +  }
290 + }
291 +
292 + void Atom::addFrc( double theF[3] ){
293 +  
294 +  if( hasCoords ){
295 +    frc[offsetX] += theF[0];
296 +    frc[offsetY] += theF[1];
297 +    frc[offsetZ] += theF[2];
298 +  }
299 +  else{
300 +    
301 +    sprintf( painCave.errMsg,
302 +             "Attempt to add frc for atom %d before coords set.\n",
303 +             index );
304 +    painCave.isFatal = 1;
305 +    simError();
306 +  }
307 + }
308 +
309 +
310 + void GeneralAtom::zeroForces( void ){
311 +  
312 +  
313 +  if( hasCoords ){
314 +    frc[offsetX] = 0.0;
315 +    frc[offsetY] = 0.0;
316 +    frc[offsetZ] = 0.0;
317 +  }
318 +  else{
319 +    
320 +    sprintf( painCave.errMsg,
321 +             "Attempt to zero frc for atom %d before coords set.\n",
322 +             index );
323 +    painCave.isFatal = 1;
324 +    simError();
325 +  }
326 + }

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