1 |
mmeineke |
561 |
#include <iostream> |
2 |
|
|
|
3 |
|
|
using namespace std; |
4 |
|
|
|
5 |
mmeineke |
670 |
#include "simError.h" |
6 |
gezelter |
409 |
#include "Atom.hpp" |
7 |
|
|
|
8 |
mmeineke |
670 |
Atom::Atom(int theIndex, SimState* theConfig) { |
9 |
|
|
|
10 |
|
|
myConfig = theConfig; |
11 |
|
|
hasCoords = false; |
12 |
mmeineke |
707 |
|
13 |
gezelter |
409 |
c_n_hyd = 0; |
14 |
|
|
has_dipole = 0; |
15 |
|
|
is_VDW = 0; |
16 |
|
|
is_LJ = 0; |
17 |
chrisfen |
999 |
is_charged = 0; |
18 |
gezelter |
409 |
|
19 |
|
|
index = theIndex; |
20 |
mmeineke |
670 |
offset = 0; |
21 |
gezelter |
409 |
offsetX = offset; |
22 |
|
|
offsetY = offset+1; |
23 |
|
|
offsetZ = offset+2; |
24 |
|
|
|
25 |
mmeineke |
670 |
Axx = 0; |
26 |
gezelter |
409 |
Axy = Axx+1; |
27 |
|
|
Axz = Axx+2; |
28 |
|
|
|
29 |
|
|
Ayx = Axx+3; |
30 |
|
|
Ayy = Axx+4; |
31 |
|
|
Ayz = Axx+5; |
32 |
|
|
|
33 |
|
|
Azx = Axx+6; |
34 |
|
|
Azy = Axx+7; |
35 |
|
|
Azz = Axx+8; |
36 |
|
|
} |
37 |
|
|
|
38 |
mmeineke |
670 |
void Atom::setIndex(int theIndex) { |
39 |
|
|
index = theIndex; |
40 |
|
|
} |
41 |
mmeineke |
413 |
|
42 |
mmeineke |
670 |
void Atom::setCoords(void){ |
43 |
|
|
|
44 |
|
|
if( myConfig->isAllocated() ){ |
45 |
|
|
|
46 |
mmeineke |
690 |
|
47 |
mmeineke |
670 |
myConfig->getAtomPointers( index, |
48 |
|
|
&pos, |
49 |
|
|
&vel, |
50 |
|
|
&frc, |
51 |
|
|
&trq, |
52 |
|
|
&Amat, |
53 |
|
|
&mu, |
54 |
|
|
&ul ); |
55 |
gezelter |
409 |
} |
56 |
mmeineke |
670 |
else{ |
57 |
|
|
sprintf( painCave.errMsg, |
58 |
|
|
"Attempted to set Atom %d coordinates with an unallocated " |
59 |
mmeineke |
787 |
"SimState object.\n", index ); |
60 |
mmeineke |
670 |
painCave.isFatal = 1; |
61 |
|
|
simError(); |
62 |
|
|
} |
63 |
gezelter |
409 |
|
64 |
mmeineke |
670 |
hasCoords = true; |
65 |
gezelter |
409 |
|
66 |
|
|
} |
67 |
|
|
|
68 |
mmeineke |
670 |
// void Atom::addAtoms(int nAdded, double* Apos, double* Avel, double* Afrc, |
69 |
|
|
// double* Atrq, double* AAmat, double* Amu, |
70 |
|
|
// double* Aul) { |
71 |
gezelter |
409 |
|
72 |
mmeineke |
670 |
// int nNew = nElements+nAdded; |
73 |
gezelter |
409 |
|
74 |
mmeineke |
670 |
// double* new_pos = new double[nNew*3]; |
75 |
|
|
// double* new_vel = new double[nNew*3]; |
76 |
|
|
// double* new_frc = new double[nNew*3]; |
77 |
|
|
// double* new_trq = new double[nNew*3]; |
78 |
|
|
// double* new_Amat = new double[nNew*9]; |
79 |
|
|
// double* new_mu = new double[nNew]; |
80 |
|
|
// double* new_ul = new double[nNew*3]; |
81 |
|
|
// int i, j; |
82 |
gezelter |
409 |
|
83 |
mmeineke |
670 |
// for (i = 0; i < 3*nElements; i++) { |
84 |
|
|
// new_pos[i] = pos[i]; |
85 |
|
|
// new_vel[i] = vel[i]; |
86 |
|
|
// new_frc[i] = frc[i]; |
87 |
|
|
// new_trq[i] = trq[i]; |
88 |
|
|
// new_ul[i] = ul[i]; |
89 |
|
|
// } |
90 |
gezelter |
409 |
|
91 |
mmeineke |
670 |
// for(i = 0; i < 3*nAdded; i++) { |
92 |
|
|
// j = i + 3*nElements; |
93 |
|
|
// new_pos[j] = Apos[i]; |
94 |
|
|
// new_vel[j] = Avel[i]; |
95 |
|
|
// new_frc[j] = Afrc[i]; |
96 |
|
|
// new_trq[j] = Atrq[i]; |
97 |
|
|
// new_ul[j] = Aul[i]; |
98 |
|
|
// } |
99 |
gezelter |
409 |
|
100 |
mmeineke |
670 |
// for (i = 0; i < 9*nElements; i++) { |
101 |
|
|
// new_Amat[i] = Amat[i]; |
102 |
|
|
// } |
103 |
gezelter |
409 |
|
104 |
mmeineke |
670 |
// for(i = 0; i < 9*nAdded; i++) { |
105 |
|
|
// j = i + 9*nElements; |
106 |
|
|
// new_Amat[j] = AAmat[i]; |
107 |
|
|
// } |
108 |
gezelter |
409 |
|
109 |
mmeineke |
670 |
// for (i = 0; i < nElements; i++) { |
110 |
|
|
// new_mu[i] = mu[i]; |
111 |
|
|
// } |
112 |
gezelter |
409 |
|
113 |
mmeineke |
670 |
// for(i = 0; i < nAdded; i++) { |
114 |
|
|
// j = i + nElements; |
115 |
|
|
// new_mu[j] = Amu[i]; |
116 |
|
|
// } |
117 |
gezelter |
409 |
|
118 |
mmeineke |
670 |
// delete[] pos; |
119 |
|
|
// delete[] vel; |
120 |
|
|
// delete[] frc; |
121 |
|
|
// delete[] trq; |
122 |
|
|
// delete[] Amat; |
123 |
|
|
// delete[] mu; |
124 |
gezelter |
409 |
|
125 |
mmeineke |
670 |
// pos = new_pos; |
126 |
|
|
// vel = new_vel; |
127 |
|
|
// frc = new_frc; |
128 |
|
|
// trq = new_trq; |
129 |
|
|
// ul = new_ul; |
130 |
|
|
// Amat = new_Amat; |
131 |
|
|
// mu = new_mu; |
132 |
gezelter |
409 |
|
133 |
mmeineke |
670 |
// nElements = nNew; |
134 |
|
|
// } |
135 |
gezelter |
409 |
|
136 |
mmeineke |
670 |
// void Atom::deleteAtom(int theIndex) { |
137 |
|
|
// deleteRange(theIndex, theIndex); |
138 |
|
|
// } |
139 |
gezelter |
409 |
|
140 |
mmeineke |
670 |
// void Atom::deleteRange(int startIndex, int stopIndex) { |
141 |
gezelter |
409 |
|
142 |
mmeineke |
670 |
// int nNew = nElements-(stopIndex-startIndex+1); |
143 |
gezelter |
409 |
|
144 |
mmeineke |
670 |
// double* new_pos = new double[nNew*3]; |
145 |
|
|
// double* new_vel = new double[nNew*3]; |
146 |
|
|
// double* new_frc = new double[nNew*3]; |
147 |
|
|
// double* new_trq = new double[nNew*3]; |
148 |
|
|
// double* new_Amat = new double[nNew*9]; |
149 |
|
|
// double* new_mu = new double[nNew]; |
150 |
|
|
// double* new_ul = new double[nNew*3]; |
151 |
|
|
// int i, j; |
152 |
gezelter |
409 |
|
153 |
mmeineke |
670 |
// for (i = 0; i < 3*startIndex; i++) { |
154 |
|
|
// new_pos[i] = pos[i]; |
155 |
|
|
// new_vel[i] = vel[i]; |
156 |
|
|
// new_frc[i] = frc[i]; |
157 |
|
|
// new_trq[i] = trq[i]; |
158 |
|
|
// new_ul[i] = ul[i]; |
159 |
|
|
// } |
160 |
gezelter |
409 |
|
161 |
mmeineke |
670 |
// for(i = 3*(stopIndex + 1); i < 3*nElements; i++) { |
162 |
|
|
// j = i - 3*startIndex + 1; |
163 |
|
|
// new_pos[j] = pos[i]; |
164 |
|
|
// new_vel[j] = vel[i]; |
165 |
|
|
// new_frc[j] = frc[i]; |
166 |
|
|
// new_trq[j] = trq[i]; |
167 |
|
|
// new_ul[j] = ul[i]; |
168 |
|
|
// } |
169 |
gezelter |
409 |
|
170 |
mmeineke |
670 |
// for (i = 0; i < 9*startIndex; i++) { |
171 |
|
|
// new_Amat[i] = Amat[i]; |
172 |
|
|
// } |
173 |
gezelter |
409 |
|
174 |
mmeineke |
670 |
// for(i = 9*(stopIndex + 1); i < 9*nElements; i++) { |
175 |
|
|
// j = i - 9*startIndex + 1; |
176 |
|
|
// new_Amat[j] = Amat[i]; |
177 |
|
|
// } |
178 |
gezelter |
409 |
|
179 |
mmeineke |
670 |
// for (i = 0; i < startIndex; i++) { |
180 |
|
|
// new_mu[i] = mu[i]; |
181 |
|
|
// } |
182 |
gezelter |
409 |
|
183 |
mmeineke |
670 |
// for(i = (stopIndex+1); i < nElements; i++) { |
184 |
|
|
// j = i - startIndex + 1; |
185 |
|
|
// new_mu[j] = mu[i]; |
186 |
|
|
// } |
187 |
gezelter |
409 |
|
188 |
mmeineke |
670 |
// delete[] pos; |
189 |
|
|
// delete[] vel; |
190 |
|
|
// delete[] frc; |
191 |
|
|
// delete[] trq; |
192 |
|
|
// delete[] Amat; |
193 |
|
|
// delete[] mu; |
194 |
gezelter |
409 |
|
195 |
mmeineke |
670 |
// pos = new_pos; |
196 |
|
|
// vel = new_vel; |
197 |
|
|
// frc = new_frc; |
198 |
|
|
// trq = new_trq; |
199 |
|
|
// ul = new_ul; |
200 |
|
|
// Amat = new_Amat; |
201 |
|
|
// mu = new_mu; |
202 |
gezelter |
409 |
|
203 |
mmeineke |
670 |
// nElements = nNew; |
204 |
|
|
// } |
205 |
mmeineke |
599 |
|
206 |
|
|
|
207 |
|
|
void Atom::getPos( double theP[3] ){ |
208 |
|
|
|
209 |
mmeineke |
670 |
if( hasCoords ){ |
210 |
|
|
theP[0] = pos[offsetX]; |
211 |
|
|
theP[1] = pos[offsetY]; |
212 |
|
|
theP[2] = pos[offsetZ]; |
213 |
|
|
} |
214 |
|
|
else{ |
215 |
|
|
|
216 |
|
|
sprintf( painCave.errMsg, |
217 |
|
|
"Attempt to get Pos for atom %d before coords set.\n", |
218 |
|
|
index ); |
219 |
|
|
painCave.isFatal = 1; |
220 |
|
|
simError(); |
221 |
|
|
} |
222 |
mmeineke |
599 |
} |
223 |
|
|
|
224 |
|
|
void Atom::setPos( double theP[3] ){ |
225 |
|
|
|
226 |
mmeineke |
670 |
if( hasCoords ){ |
227 |
|
|
pos[offsetX] = theP[0]; |
228 |
|
|
pos[offsetY] = theP[1]; |
229 |
|
|
pos[offsetZ] = theP[2]; |
230 |
|
|
} |
231 |
|
|
else{ |
232 |
|
|
|
233 |
|
|
sprintf( painCave.errMsg, |
234 |
|
|
"Attempt to set Pos for atom %d before coords set.\n", |
235 |
|
|
index ); |
236 |
|
|
painCave.isFatal = 1; |
237 |
|
|
simError(); |
238 |
|
|
} |
239 |
mmeineke |
599 |
} |
240 |
|
|
|
241 |
|
|
void Atom::getVel( double theV[3] ){ |
242 |
|
|
|
243 |
mmeineke |
670 |
if( hasCoords ){ |
244 |
|
|
theV[0] = vel[offsetX]; |
245 |
|
|
theV[1] = vel[offsetY]; |
246 |
|
|
theV[2] = vel[offsetZ]; |
247 |
|
|
} |
248 |
|
|
else{ |
249 |
|
|
|
250 |
|
|
sprintf( painCave.errMsg, |
251 |
|
|
"Attempt to get vel for atom %d before coords set.\n", |
252 |
|
|
index ); |
253 |
|
|
painCave.isFatal = 1; |
254 |
|
|
simError(); |
255 |
|
|
} |
256 |
|
|
|
257 |
mmeineke |
599 |
} |
258 |
|
|
|
259 |
|
|
void Atom::setVel( double theV[3] ){ |
260 |
|
|
|
261 |
mmeineke |
670 |
if( hasCoords ){ |
262 |
|
|
vel[offsetX] = theV[0]; |
263 |
|
|
vel[offsetY] = theV[1]; |
264 |
|
|
vel[offsetZ] = theV[2]; |
265 |
|
|
} |
266 |
|
|
else{ |
267 |
|
|
|
268 |
|
|
sprintf( painCave.errMsg, |
269 |
|
|
"Attempt to set vel for atom %d before coords set.\n", |
270 |
|
|
index ); |
271 |
|
|
painCave.isFatal = 1; |
272 |
|
|
simError(); |
273 |
|
|
} |
274 |
mmeineke |
599 |
} |
275 |
|
|
|
276 |
|
|
void Atom::getFrc( double theF[3] ){ |
277 |
|
|
|
278 |
mmeineke |
670 |
if( hasCoords ){ |
279 |
|
|
theF[0] = frc[offsetX]; |
280 |
|
|
theF[1] = frc[offsetY]; |
281 |
|
|
theF[2] = frc[offsetZ]; |
282 |
|
|
} |
283 |
|
|
else{ |
284 |
|
|
|
285 |
|
|
sprintf( painCave.errMsg, |
286 |
|
|
"Attempt to get frc for atom %d before coords set.\n", |
287 |
|
|
index ); |
288 |
|
|
painCave.isFatal = 1; |
289 |
|
|
simError(); |
290 |
|
|
} |
291 |
mmeineke |
599 |
} |
292 |
|
|
|
293 |
|
|
void Atom::addFrc( double theF[3] ){ |
294 |
|
|
|
295 |
mmeineke |
670 |
if( hasCoords ){ |
296 |
|
|
frc[offsetX] += theF[0]; |
297 |
|
|
frc[offsetY] += theF[1]; |
298 |
|
|
frc[offsetZ] += theF[2]; |
299 |
|
|
} |
300 |
|
|
else{ |
301 |
|
|
|
302 |
|
|
sprintf( painCave.errMsg, |
303 |
|
|
"Attempt to add frc for atom %d before coords set.\n", |
304 |
|
|
index ); |
305 |
|
|
painCave.isFatal = 1; |
306 |
|
|
simError(); |
307 |
|
|
} |
308 |
mmeineke |
599 |
} |
309 |
mmeineke |
670 |
|
310 |
|
|
|
311 |
|
|
void GeneralAtom::zeroForces( void ){ |
312 |
|
|
|
313 |
|
|
|
314 |
|
|
if( hasCoords ){ |
315 |
|
|
frc[offsetX] = 0.0; |
316 |
|
|
frc[offsetY] = 0.0; |
317 |
|
|
frc[offsetZ] = 0.0; |
318 |
|
|
} |
319 |
|
|
else{ |
320 |
|
|
|
321 |
|
|
sprintf( painCave.errMsg, |
322 |
|
|
"Attempt to zero frc for atom %d before coords set.\n", |
323 |
|
|
index ); |
324 |
|
|
painCave.isFatal = 1; |
325 |
|
|
simError(); |
326 |
|
|
} |
327 |
|
|
} |