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

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