1 |
mmeineke |
558 |
#include <iostream> |
2 |
gezelter |
829 |
#include <stdlib.h> |
3 |
|
|
#include <math.h> |
4 |
mmeineke |
558 |
|
5 |
|
|
#ifdef IS_MPI |
6 |
|
|
#include "mpiSimulation.hpp" |
7 |
|
|
#include <unistd.h> |
8 |
|
|
#endif //is_mpi |
9 |
|
|
|
10 |
chuckv |
892 |
#ifdef PROFILE |
11 |
|
|
#include "mdProfile.hpp" |
12 |
|
|
#endif // profile |
13 |
|
|
|
14 |
mmeineke |
558 |
#include "Integrator.hpp" |
15 |
|
|
#include "simError.h" |
16 |
|
|
|
17 |
|
|
|
18 |
tim |
725 |
template<typename T> Integrator<T>::Integrator(SimInfo* theInfo, |
19 |
|
|
ForceFields* the_ff){ |
20 |
mmeineke |
558 |
info = theInfo; |
21 |
|
|
myFF = the_ff; |
22 |
|
|
isFirst = 1; |
23 |
|
|
|
24 |
|
|
molecules = info->molecules; |
25 |
|
|
nMols = info->n_mol; |
26 |
|
|
|
27 |
|
|
// give a little love back to the SimInfo object |
28 |
tim |
725 |
|
29 |
|
|
if (info->the_integrator != NULL){ |
30 |
|
|
delete info->the_integrator; |
31 |
|
|
} |
32 |
tim |
837 |
|
33 |
mmeineke |
558 |
nAtoms = info->n_atoms; |
34 |
|
|
|
35 |
|
|
// check for constraints |
36 |
tim |
725 |
|
37 |
|
|
constrainedA = NULL; |
38 |
|
|
constrainedB = NULL; |
39 |
mmeineke |
558 |
constrainedDsqr = NULL; |
40 |
tim |
725 |
moving = NULL; |
41 |
|
|
moved = NULL; |
42 |
|
|
oldPos = NULL; |
43 |
|
|
|
44 |
mmeineke |
558 |
nConstrained = 0; |
45 |
|
|
|
46 |
|
|
checkConstraints(); |
47 |
|
|
} |
48 |
|
|
|
49 |
tim |
725 |
template<typename T> Integrator<T>::~Integrator(){ |
50 |
|
|
if (nConstrained){ |
51 |
mmeineke |
558 |
delete[] constrainedA; |
52 |
|
|
delete[] constrainedB; |
53 |
|
|
delete[] constrainedDsqr; |
54 |
|
|
delete[] moving; |
55 |
|
|
delete[] moved; |
56 |
mmeineke |
561 |
delete[] oldPos; |
57 |
mmeineke |
558 |
} |
58 |
|
|
} |
59 |
|
|
|
60 |
tim |
725 |
template<typename T> void Integrator<T>::checkConstraints(void){ |
61 |
mmeineke |
558 |
isConstrained = 0; |
62 |
|
|
|
63 |
tim |
725 |
Constraint* temp_con; |
64 |
|
|
Constraint* dummy_plug; |
65 |
mmeineke |
558 |
temp_con = new Constraint[info->n_SRI]; |
66 |
|
|
nConstrained = 0; |
67 |
|
|
int constrained = 0; |
68 |
tim |
725 |
|
69 |
mmeineke |
558 |
SRI** theArray; |
70 |
tim |
725 |
for (int i = 0; i < nMols; i++){ |
71 |
|
|
theArray = (SRI * *) molecules[i].getMyBonds(); |
72 |
|
|
for (int j = 0; j < molecules[i].getNBonds(); j++){ |
73 |
mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
74 |
mmeineke |
594 |
|
75 |
tim |
725 |
if (constrained){ |
76 |
|
|
dummy_plug = theArray[j]->get_constraint(); |
77 |
|
|
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
78 |
|
|
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
79 |
|
|
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
80 |
mmeineke |
594 |
|
81 |
tim |
725 |
nConstrained++; |
82 |
|
|
constrained = 0; |
83 |
|
|
} |
84 |
mmeineke |
558 |
} |
85 |
|
|
|
86 |
tim |
725 |
theArray = (SRI * *) molecules[i].getMyBends(); |
87 |
|
|
for (int j = 0; j < molecules[i].getNBends(); j++){ |
88 |
mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
89 |
tim |
725 |
|
90 |
|
|
if (constrained){ |
91 |
|
|
dummy_plug = theArray[j]->get_constraint(); |
92 |
|
|
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
93 |
|
|
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
94 |
|
|
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
95 |
|
|
|
96 |
|
|
nConstrained++; |
97 |
|
|
constrained = 0; |
98 |
mmeineke |
558 |
} |
99 |
|
|
} |
100 |
|
|
|
101 |
tim |
725 |
theArray = (SRI * *) molecules[i].getMyTorsions(); |
102 |
|
|
for (int j = 0; j < molecules[i].getNTorsions(); j++){ |
103 |
mmeineke |
558 |
constrained = theArray[j]->is_constrained(); |
104 |
tim |
725 |
|
105 |
|
|
if (constrained){ |
106 |
|
|
dummy_plug = theArray[j]->get_constraint(); |
107 |
|
|
temp_con[nConstrained].set_a(dummy_plug->get_a()); |
108 |
|
|
temp_con[nConstrained].set_b(dummy_plug->get_b()); |
109 |
|
|
temp_con[nConstrained].set_dsqr(dummy_plug->get_dsqr()); |
110 |
|
|
|
111 |
|
|
nConstrained++; |
112 |
|
|
constrained = 0; |
113 |
mmeineke |
558 |
} |
114 |
|
|
} |
115 |
|
|
} |
116 |
|
|
|
117 |
tim |
725 |
if (nConstrained > 0){ |
118 |
mmeineke |
558 |
isConstrained = 1; |
119 |
|
|
|
120 |
tim |
725 |
if (constrainedA != NULL) |
121 |
|
|
delete[] constrainedA; |
122 |
|
|
if (constrainedB != NULL) |
123 |
|
|
delete[] constrainedB; |
124 |
|
|
if (constrainedDsqr != NULL) |
125 |
|
|
delete[] constrainedDsqr; |
126 |
mmeineke |
558 |
|
127 |
tim |
725 |
constrainedA = new int[nConstrained]; |
128 |
|
|
constrainedB = new int[nConstrained]; |
129 |
mmeineke |
558 |
constrainedDsqr = new double[nConstrained]; |
130 |
tim |
725 |
|
131 |
|
|
for (int i = 0; i < nConstrained; i++){ |
132 |
mmeineke |
558 |
constrainedA[i] = temp_con[i].get_a(); |
133 |
|
|
constrainedB[i] = temp_con[i].get_b(); |
134 |
|
|
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
135 |
|
|
} |
136 |
|
|
|
137 |
tim |
725 |
|
138 |
mmeineke |
558 |
// save oldAtoms to check for lode balanceing later on. |
139 |
tim |
725 |
|
140 |
mmeineke |
558 |
oldAtoms = nAtoms; |
141 |
tim |
725 |
|
142 |
mmeineke |
558 |
moving = new int[nAtoms]; |
143 |
tim |
725 |
moved = new int[nAtoms]; |
144 |
mmeineke |
558 |
|
145 |
tim |
725 |
oldPos = new double[nAtoms * 3]; |
146 |
mmeineke |
558 |
} |
147 |
tim |
725 |
|
148 |
mmeineke |
558 |
delete[] temp_con; |
149 |
|
|
} |
150 |
|
|
|
151 |
|
|
|
152 |
tim |
725 |
template<typename T> void Integrator<T>::integrate(void){ |
153 |
mmeineke |
558 |
|
154 |
tim |
725 |
double runTime = info->run_time; |
155 |
|
|
double sampleTime = info->sampleTime; |
156 |
|
|
double statusTime = info->statusTime; |
157 |
mmeineke |
558 |
double thermalTime = info->thermalTime; |
158 |
mmeineke |
746 |
double resetTime = info->resetTime; |
159 |
mmeineke |
558 |
|
160 |
mmeineke |
746 |
|
161 |
mmeineke |
558 |
double currSample; |
162 |
|
|
double currThermal; |
163 |
|
|
double currStatus; |
164 |
mmeineke |
746 |
double currReset; |
165 |
tim |
837 |
|
166 |
mmeineke |
558 |
int calcPot, calcStress; |
167 |
|
|
|
168 |
tim |
725 |
tStats = new Thermo(info); |
169 |
|
|
statOut = new StatWriter(info); |
170 |
|
|
dumpOut = new DumpWriter(info); |
171 |
mmeineke |
558 |
|
172 |
mmeineke |
561 |
atoms = info->atoms; |
173 |
|
|
|
174 |
|
|
dt = info->dt; |
175 |
mmeineke |
558 |
dt2 = 0.5 * dt; |
176 |
|
|
|
177 |
mmeineke |
784 |
readyCheck(); |
178 |
|
|
|
179 |
mmeineke |
558 |
// initialize the forces before the first step |
180 |
|
|
|
181 |
tim |
677 |
calcForce(1, 1); |
182 |
tim |
781 |
|
183 |
|
|
if (nConstrained){ |
184 |
|
|
preMove(); |
185 |
|
|
constrainA(); |
186 |
tim |
837 |
calcForce(1, 1); |
187 |
tim |
781 |
constrainB(); |
188 |
|
|
} |
189 |
mmeineke |
843 |
|
190 |
tim |
725 |
if (info->setTemp){ |
191 |
tim |
677 |
thermalize(); |
192 |
mmeineke |
558 |
} |
193 |
tim |
725 |
|
194 |
mmeineke |
558 |
calcPot = 0; |
195 |
|
|
calcStress = 0; |
196 |
mmeineke |
711 |
currSample = sampleTime + info->getTime(); |
197 |
|
|
currThermal = thermalTime+ info->getTime(); |
198 |
|
|
currStatus = statusTime + info->getTime(); |
199 |
mmeineke |
746 |
currReset = resetTime + info->getTime(); |
200 |
mmeineke |
558 |
|
201 |
tim |
725 |
dumpOut->writeDump(info->getTime()); |
202 |
|
|
statOut->writeStat(info->getTime()); |
203 |
mmeineke |
559 |
|
204 |
|
|
|
205 |
|
|
#ifdef IS_MPI |
206 |
tim |
725 |
strcpy(checkPointMsg, "The integrator is ready to go."); |
207 |
mmeineke |
559 |
MPIcheckPoint(); |
208 |
|
|
#endif // is_mpi |
209 |
|
|
|
210 |
tim |
725 |
while (info->getTime() < runTime){ |
211 |
|
|
if ((info->getTime() + dt) >= currStatus){ |
212 |
mmeineke |
558 |
calcPot = 1; |
213 |
|
|
calcStress = 1; |
214 |
|
|
} |
215 |
mmeineke |
561 |
|
216 |
chuckv |
892 |
#ifdef PROFILE |
217 |
|
|
startProfile( pro1 ); |
218 |
|
|
#endif |
219 |
|
|
|
220 |
tim |
725 |
integrateStep(calcPot, calcStress); |
221 |
|
|
|
222 |
chuckv |
892 |
#ifdef PROFILE |
223 |
|
|
endProfile( pro1 ); |
224 |
|
|
|
225 |
|
|
startProfile( pro2 ); |
226 |
|
|
#endif // profile |
227 |
|
|
|
228 |
mmeineke |
643 |
info->incrTime(dt); |
229 |
mmeineke |
558 |
|
230 |
tim |
725 |
if (info->setTemp){ |
231 |
|
|
if (info->getTime() >= currThermal){ |
232 |
|
|
thermalize(); |
233 |
|
|
currThermal += thermalTime; |
234 |
mmeineke |
558 |
} |
235 |
|
|
} |
236 |
|
|
|
237 |
tim |
725 |
if (info->getTime() >= currSample){ |
238 |
|
|
dumpOut->writeDump(info->getTime()); |
239 |
mmeineke |
558 |
currSample += sampleTime; |
240 |
|
|
} |
241 |
|
|
|
242 |
tim |
725 |
if (info->getTime() >= currStatus){ |
243 |
tim |
837 |
statOut->writeStat(info->getTime()); |
244 |
|
|
calcPot = 0; |
245 |
mmeineke |
558 |
calcStress = 0; |
246 |
|
|
currStatus += statusTime; |
247 |
tim |
837 |
} |
248 |
mmeineke |
559 |
|
249 |
mmeineke |
746 |
if (info->resetIntegrator){ |
250 |
|
|
if (info->getTime() >= currReset){ |
251 |
|
|
this->resetIntegrator(); |
252 |
|
|
currReset += resetTime; |
253 |
|
|
} |
254 |
|
|
} |
255 |
chuckv |
892 |
|
256 |
|
|
#ifdef PROFILE |
257 |
|
|
endProfile( pro2 ); |
258 |
|
|
#endif //profile |
259 |
mmeineke |
746 |
|
260 |
mmeineke |
559 |
#ifdef IS_MPI |
261 |
tim |
725 |
strcpy(checkPointMsg, "successfully took a time step."); |
262 |
mmeineke |
559 |
MPIcheckPoint(); |
263 |
|
|
#endif // is_mpi |
264 |
mmeineke |
558 |
} |
265 |
|
|
|
266 |
|
|
|
267 |
mmeineke |
804 |
// write the last frame |
268 |
|
|
dumpOut->writeDump(info->getTime()); |
269 |
|
|
|
270 |
mmeineke |
561 |
delete dumpOut; |
271 |
|
|
delete statOut; |
272 |
mmeineke |
558 |
} |
273 |
|
|
|
274 |
tim |
725 |
template<typename T> void Integrator<T>::integrateStep(int calcPot, |
275 |
|
|
int calcStress){ |
276 |
mmeineke |
558 |
// Position full step, and velocity half step |
277 |
chuckv |
892 |
|
278 |
|
|
#ifdef PROFILE |
279 |
|
|
startProfile(pro3); |
280 |
|
|
#endif //profile |
281 |
|
|
|
282 |
tim |
725 |
preMove(); |
283 |
mmeineke |
558 |
|
284 |
chuckv |
892 |
#ifdef PROFILE |
285 |
|
|
endProfile(pro3); |
286 |
|
|
|
287 |
|
|
startProfile(pro4); |
288 |
|
|
#endif // profile |
289 |
|
|
|
290 |
mmeineke |
558 |
moveA(); |
291 |
|
|
|
292 |
chuckv |
892 |
#ifdef PROFILE |
293 |
|
|
endProfile(pro4); |
294 |
|
|
|
295 |
|
|
startProfile(pro5); |
296 |
|
|
#endif//profile |
297 |
tim |
725 |
|
298 |
|
|
|
299 |
mmeineke |
614 |
#ifdef IS_MPI |
300 |
tim |
725 |
strcpy(checkPointMsg, "Succesful moveA\n"); |
301 |
mmeineke |
614 |
MPIcheckPoint(); |
302 |
|
|
#endif // is_mpi |
303 |
|
|
|
304 |
tim |
725 |
|
305 |
mmeineke |
558 |
// calc forces |
306 |
|
|
|
307 |
tim |
725 |
calcForce(calcPot, calcStress); |
308 |
mmeineke |
558 |
|
309 |
mmeineke |
614 |
#ifdef IS_MPI |
310 |
tim |
725 |
strcpy(checkPointMsg, "Succesful doForces\n"); |
311 |
mmeineke |
614 |
MPIcheckPoint(); |
312 |
|
|
#endif // is_mpi |
313 |
|
|
|
314 |
chuckv |
892 |
#ifdef PROFILE |
315 |
|
|
endProfile( pro5 ); |
316 |
tim |
725 |
|
317 |
chuckv |
892 |
startProfile( pro6 ); |
318 |
|
|
#endif //profile |
319 |
|
|
|
320 |
mmeineke |
558 |
// finish the velocity half step |
321 |
tim |
725 |
|
322 |
mmeineke |
558 |
moveB(); |
323 |
tim |
725 |
|
324 |
chuckv |
892 |
#ifdef PROFILE |
325 |
|
|
endProfile(pro6); |
326 |
|
|
#endif // profile |
327 |
tim |
725 |
|
328 |
mmeineke |
614 |
#ifdef IS_MPI |
329 |
tim |
725 |
strcpy(checkPointMsg, "Succesful moveB\n"); |
330 |
mmeineke |
614 |
MPIcheckPoint(); |
331 |
|
|
#endif // is_mpi |
332 |
mmeineke |
558 |
} |
333 |
|
|
|
334 |
|
|
|
335 |
tim |
725 |
template<typename T> void Integrator<T>::moveA(void){ |
336 |
gezelter |
600 |
int i, j; |
337 |
mmeineke |
558 |
DirectionalAtom* dAtom; |
338 |
gezelter |
600 |
double Tb[3], ji[3]; |
339 |
|
|
double vel[3], pos[3], frc[3]; |
340 |
|
|
double mass; |
341 |
mmeineke |
558 |
|
342 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
343 |
|
|
atoms[i]->getVel(vel); |
344 |
|
|
atoms[i]->getPos(pos); |
345 |
|
|
atoms[i]->getFrc(frc); |
346 |
mmeineke |
567 |
|
347 |
gezelter |
600 |
mass = atoms[i]->getMass(); |
348 |
mmeineke |
594 |
|
349 |
tim |
725 |
for (j = 0; j < 3; j++){ |
350 |
gezelter |
600 |
// velocity half step |
351 |
tim |
725 |
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
352 |
gezelter |
600 |
// position whole step |
353 |
|
|
pos[j] += dt * vel[j]; |
354 |
|
|
} |
355 |
mmeineke |
594 |
|
356 |
tim |
725 |
atoms[i]->setVel(vel); |
357 |
|
|
atoms[i]->setPos(pos); |
358 |
gezelter |
600 |
|
359 |
tim |
725 |
if (atoms[i]->isDirectional()){ |
360 |
|
|
dAtom = (DirectionalAtom *) atoms[i]; |
361 |
mmeineke |
558 |
|
362 |
|
|
// get and convert the torque to body frame |
363 |
mmeineke |
597 |
|
364 |
tim |
725 |
dAtom->getTrq(Tb); |
365 |
|
|
dAtom->lab2Body(Tb); |
366 |
|
|
|
367 |
mmeineke |
558 |
// get the angular momentum, and propagate a half step |
368 |
gezelter |
600 |
|
369 |
tim |
725 |
dAtom->getJ(ji); |
370 |
gezelter |
600 |
|
371 |
tim |
725 |
for (j = 0; j < 3; j++) |
372 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
373 |
tim |
725 |
|
374 |
mmeineke |
778 |
this->rotationPropagation( dAtom, ji ); |
375 |
gezelter |
600 |
|
376 |
tim |
725 |
dAtom->setJ(ji); |
377 |
|
|
} |
378 |
mmeineke |
558 |
} |
379 |
mmeineke |
768 |
|
380 |
|
|
if (nConstrained){ |
381 |
|
|
constrainA(); |
382 |
|
|
} |
383 |
mmeineke |
558 |
} |
384 |
|
|
|
385 |
|
|
|
386 |
tim |
725 |
template<typename T> void Integrator<T>::moveB(void){ |
387 |
gezelter |
600 |
int i, j; |
388 |
mmeineke |
558 |
DirectionalAtom* dAtom; |
389 |
gezelter |
600 |
double Tb[3], ji[3]; |
390 |
|
|
double vel[3], frc[3]; |
391 |
|
|
double mass; |
392 |
mmeineke |
558 |
|
393 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
394 |
|
|
atoms[i]->getVel(vel); |
395 |
|
|
atoms[i]->getFrc(frc); |
396 |
mmeineke |
558 |
|
397 |
gezelter |
600 |
mass = atoms[i]->getMass(); |
398 |
|
|
|
399 |
mmeineke |
558 |
// velocity half step |
400 |
tim |
725 |
for (j = 0; j < 3; j++) |
401 |
|
|
vel[j] += (dt2 * frc[j] / mass) * eConvert; |
402 |
gezelter |
600 |
|
403 |
tim |
725 |
atoms[i]->setVel(vel); |
404 |
mmeineke |
597 |
|
405 |
tim |
725 |
if (atoms[i]->isDirectional()){ |
406 |
|
|
dAtom = (DirectionalAtom *) atoms[i]; |
407 |
|
|
|
408 |
tim |
837 |
// get and convert the torque to body frame |
409 |
gezelter |
600 |
|
410 |
tim |
725 |
dAtom->getTrq(Tb); |
411 |
|
|
dAtom->lab2Body(Tb); |
412 |
gezelter |
600 |
|
413 |
|
|
// get the angular momentum, and propagate a half step |
414 |
|
|
|
415 |
tim |
725 |
dAtom->getJ(ji); |
416 |
gezelter |
600 |
|
417 |
tim |
725 |
for (j = 0; j < 3; j++) |
418 |
gezelter |
600 |
ji[j] += (dt2 * Tb[j]) * eConvert; |
419 |
mmeineke |
597 |
|
420 |
tim |
725 |
|
421 |
|
|
dAtom->setJ(ji); |
422 |
mmeineke |
558 |
} |
423 |
|
|
} |
424 |
mmeineke |
768 |
|
425 |
|
|
if (nConstrained){ |
426 |
|
|
constrainB(); |
427 |
|
|
} |
428 |
mmeineke |
558 |
} |
429 |
|
|
|
430 |
tim |
725 |
template<typename T> void Integrator<T>::preMove(void){ |
431 |
gezelter |
600 |
int i, j; |
432 |
|
|
double pos[3]; |
433 |
mmeineke |
558 |
|
434 |
tim |
725 |
if (nConstrained){ |
435 |
|
|
for (i = 0; i < nAtoms; i++){ |
436 |
|
|
atoms[i]->getPos(pos); |
437 |
mmeineke |
561 |
|
438 |
tim |
725 |
for (j = 0; j < 3; j++){ |
439 |
|
|
oldPos[3 * i + j] = pos[j]; |
440 |
gezelter |
600 |
} |
441 |
|
|
} |
442 |
tim |
725 |
} |
443 |
gezelter |
600 |
} |
444 |
|
|
|
445 |
tim |
645 |
template<typename T> void Integrator<T>::constrainA(){ |
446 |
mmeineke |
787 |
int i, j; |
447 |
mmeineke |
558 |
int done; |
448 |
gezelter |
600 |
double posA[3], posB[3]; |
449 |
|
|
double velA[3], velB[3]; |
450 |
mmeineke |
572 |
double pab[3]; |
451 |
|
|
double rab[3]; |
452 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
453 |
mmeineke |
558 |
double rma, rmb; |
454 |
|
|
double dx, dy, dz; |
455 |
mmeineke |
561 |
double rpab; |
456 |
mmeineke |
558 |
double rabsq, pabsq, rpabsq; |
457 |
|
|
double diffsq; |
458 |
|
|
double gab; |
459 |
|
|
int iteration; |
460 |
|
|
|
461 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
462 |
mmeineke |
558 |
moving[i] = 0; |
463 |
tim |
725 |
moved[i] = 1; |
464 |
mmeineke |
558 |
} |
465 |
mmeineke |
567 |
|
466 |
mmeineke |
558 |
iteration = 0; |
467 |
|
|
done = 0; |
468 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
469 |
mmeineke |
558 |
done = 1; |
470 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
471 |
mmeineke |
558 |
a = constrainedA[i]; |
472 |
|
|
b = constrainedB[i]; |
473 |
mmeineke |
563 |
|
474 |
tim |
725 |
ax = (a * 3) + 0; |
475 |
|
|
ay = (a * 3) + 1; |
476 |
|
|
az = (a * 3) + 2; |
477 |
mmeineke |
563 |
|
478 |
tim |
725 |
bx = (b * 3) + 0; |
479 |
|
|
by = (b * 3) + 1; |
480 |
|
|
bz = (b * 3) + 2; |
481 |
|
|
|
482 |
|
|
if (moved[a] || moved[b]){ |
483 |
|
|
atoms[a]->getPos(posA); |
484 |
|
|
atoms[b]->getPos(posB); |
485 |
|
|
|
486 |
|
|
for (j = 0; j < 3; j++) |
487 |
gezelter |
600 |
pab[j] = posA[j] - posB[j]; |
488 |
mmeineke |
567 |
|
489 |
tim |
725 |
//periodic boundary condition |
490 |
mmeineke |
567 |
|
491 |
tim |
725 |
info->wrapVector(pab); |
492 |
mmeineke |
572 |
|
493 |
tim |
725 |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
494 |
mmeineke |
558 |
|
495 |
tim |
725 |
rabsq = constrainedDsqr[i]; |
496 |
|
|
diffsq = rabsq - pabsq; |
497 |
mmeineke |
567 |
|
498 |
tim |
725 |
// the original rattle code from alan tidesley |
499 |
|
|
if (fabs(diffsq) > (tol * rabsq * 2)){ |
500 |
|
|
rab[0] = oldPos[ax] - oldPos[bx]; |
501 |
|
|
rab[1] = oldPos[ay] - oldPos[by]; |
502 |
|
|
rab[2] = oldPos[az] - oldPos[bz]; |
503 |
mmeineke |
558 |
|
504 |
tim |
725 |
info->wrapVector(rab); |
505 |
mmeineke |
567 |
|
506 |
tim |
725 |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
507 |
mmeineke |
558 |
|
508 |
tim |
725 |
rpabsq = rpab * rpab; |
509 |
mmeineke |
558 |
|
510 |
mmeineke |
563 |
|
511 |
tim |
725 |
if (rpabsq < (rabsq * -diffsq)){ |
512 |
mmeineke |
558 |
#ifdef IS_MPI |
513 |
tim |
725 |
a = atoms[a]->getGlobalIndex(); |
514 |
|
|
b = atoms[b]->getGlobalIndex(); |
515 |
mmeineke |
558 |
#endif //is_mpi |
516 |
tim |
725 |
sprintf(painCave.errMsg, |
517 |
|
|
"Constraint failure in constrainA at atom %d and %d.\n", a, |
518 |
|
|
b); |
519 |
|
|
painCave.isFatal = 1; |
520 |
|
|
simError(); |
521 |
|
|
} |
522 |
mmeineke |
558 |
|
523 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
524 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
525 |
mmeineke |
567 |
|
526 |
tim |
725 |
gab = diffsq / (2.0 * (rma + rmb) * rpab); |
527 |
mmeineke |
567 |
|
528 |
mmeineke |
572 |
dx = rab[0] * gab; |
529 |
|
|
dy = rab[1] * gab; |
530 |
|
|
dz = rab[2] * gab; |
531 |
mmeineke |
558 |
|
532 |
tim |
725 |
posA[0] += rma * dx; |
533 |
|
|
posA[1] += rma * dy; |
534 |
|
|
posA[2] += rma * dz; |
535 |
mmeineke |
558 |
|
536 |
tim |
725 |
atoms[a]->setPos(posA); |
537 |
mmeineke |
558 |
|
538 |
tim |
725 |
posB[0] -= rmb * dx; |
539 |
|
|
posB[1] -= rmb * dy; |
540 |
|
|
posB[2] -= rmb * dz; |
541 |
gezelter |
600 |
|
542 |
tim |
725 |
atoms[b]->setPos(posB); |
543 |
gezelter |
600 |
|
544 |
mmeineke |
558 |
dx = dx / dt; |
545 |
|
|
dy = dy / dt; |
546 |
|
|
dz = dz / dt; |
547 |
|
|
|
548 |
tim |
725 |
atoms[a]->getVel(velA); |
549 |
mmeineke |
558 |
|
550 |
tim |
725 |
velA[0] += rma * dx; |
551 |
|
|
velA[1] += rma * dy; |
552 |
|
|
velA[2] += rma * dz; |
553 |
mmeineke |
558 |
|
554 |
tim |
725 |
atoms[a]->setVel(velA); |
555 |
gezelter |
600 |
|
556 |
tim |
725 |
atoms[b]->getVel(velB); |
557 |
gezelter |
600 |
|
558 |
tim |
725 |
velB[0] -= rmb * dx; |
559 |
|
|
velB[1] -= rmb * dy; |
560 |
|
|
velB[2] -= rmb * dz; |
561 |
gezelter |
600 |
|
562 |
tim |
725 |
atoms[b]->setVel(velB); |
563 |
gezelter |
600 |
|
564 |
tim |
725 |
moving[a] = 1; |
565 |
|
|
moving[b] = 1; |
566 |
|
|
done = 0; |
567 |
|
|
} |
568 |
mmeineke |
558 |
} |
569 |
|
|
} |
570 |
tim |
725 |
|
571 |
|
|
for (i = 0; i < nAtoms; i++){ |
572 |
mmeineke |
558 |
moved[i] = moving[i]; |
573 |
|
|
moving[i] = 0; |
574 |
|
|
} |
575 |
|
|
|
576 |
|
|
iteration++; |
577 |
|
|
} |
578 |
|
|
|
579 |
tim |
725 |
if (!done){ |
580 |
|
|
sprintf(painCave.errMsg, |
581 |
|
|
"Constraint failure in constrainA, too many iterations: %d\n", |
582 |
|
|
iteration); |
583 |
mmeineke |
558 |
painCave.isFatal = 1; |
584 |
|
|
simError(); |
585 |
|
|
} |
586 |
mmeineke |
768 |
|
587 |
mmeineke |
558 |
} |
588 |
|
|
|
589 |
tim |
725 |
template<typename T> void Integrator<T>::constrainB(void){ |
590 |
mmeineke |
787 |
int i, j; |
591 |
mmeineke |
558 |
int done; |
592 |
gezelter |
600 |
double posA[3], posB[3]; |
593 |
|
|
double velA[3], velB[3]; |
594 |
mmeineke |
558 |
double vxab, vyab, vzab; |
595 |
mmeineke |
572 |
double rab[3]; |
596 |
mmeineke |
563 |
int a, b, ax, ay, az, bx, by, bz; |
597 |
mmeineke |
558 |
double rma, rmb; |
598 |
|
|
double dx, dy, dz; |
599 |
mmeineke |
787 |
double rvab; |
600 |
mmeineke |
558 |
double gab; |
601 |
|
|
int iteration; |
602 |
|
|
|
603 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
604 |
mmeineke |
558 |
moving[i] = 0; |
605 |
|
|
moved[i] = 1; |
606 |
|
|
} |
607 |
|
|
|
608 |
|
|
done = 0; |
609 |
mmeineke |
561 |
iteration = 0; |
610 |
tim |
725 |
while (!done && (iteration < maxIteration)){ |
611 |
mmeineke |
567 |
done = 1; |
612 |
|
|
|
613 |
tim |
725 |
for (i = 0; i < nConstrained; i++){ |
614 |
mmeineke |
558 |
a = constrainedA[i]; |
615 |
|
|
b = constrainedB[i]; |
616 |
|
|
|
617 |
tim |
725 |
ax = (a * 3) + 0; |
618 |
|
|
ay = (a * 3) + 1; |
619 |
|
|
az = (a * 3) + 2; |
620 |
mmeineke |
563 |
|
621 |
tim |
725 |
bx = (b * 3) + 0; |
622 |
|
|
by = (b * 3) + 1; |
623 |
|
|
bz = (b * 3) + 2; |
624 |
mmeineke |
563 |
|
625 |
tim |
725 |
if (moved[a] || moved[b]){ |
626 |
|
|
atoms[a]->getVel(velA); |
627 |
|
|
atoms[b]->getVel(velB); |
628 |
mmeineke |
558 |
|
629 |
tim |
725 |
vxab = velA[0] - velB[0]; |
630 |
|
|
vyab = velA[1] - velB[1]; |
631 |
|
|
vzab = velA[2] - velB[2]; |
632 |
gezelter |
600 |
|
633 |
tim |
725 |
atoms[a]->getPos(posA); |
634 |
|
|
atoms[b]->getPos(posB); |
635 |
gezelter |
600 |
|
636 |
tim |
725 |
for (j = 0; j < 3; j++) |
637 |
gezelter |
600 |
rab[j] = posA[j] - posB[j]; |
638 |
mmeineke |
558 |
|
639 |
tim |
725 |
info->wrapVector(rab); |
640 |
mmeineke |
558 |
|
641 |
tim |
725 |
rma = 1.0 / atoms[a]->getMass(); |
642 |
|
|
rmb = 1.0 / atoms[b]->getMass(); |
643 |
mmeineke |
558 |
|
644 |
tim |
725 |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
645 |
gezelter |
600 |
|
646 |
tim |
725 |
gab = -rvab / ((rma + rmb) * constrainedDsqr[i]); |
647 |
gezelter |
600 |
|
648 |
tim |
725 |
if (fabs(gab) > tol){ |
649 |
|
|
dx = rab[0] * gab; |
650 |
|
|
dy = rab[1] * gab; |
651 |
|
|
dz = rab[2] * gab; |
652 |
|
|
|
653 |
|
|
velA[0] += rma * dx; |
654 |
|
|
velA[1] += rma * dy; |
655 |
|
|
velA[2] += rma * dz; |
656 |
|
|
|
657 |
|
|
atoms[a]->setVel(velA); |
658 |
|
|
|
659 |
|
|
velB[0] -= rmb * dx; |
660 |
|
|
velB[1] -= rmb * dy; |
661 |
|
|
velB[2] -= rmb * dz; |
662 |
|
|
|
663 |
|
|
atoms[b]->setVel(velB); |
664 |
|
|
|
665 |
|
|
moving[a] = 1; |
666 |
|
|
moving[b] = 1; |
667 |
|
|
done = 0; |
668 |
|
|
} |
669 |
mmeineke |
558 |
} |
670 |
|
|
} |
671 |
|
|
|
672 |
tim |
725 |
for (i = 0; i < nAtoms; i++){ |
673 |
mmeineke |
558 |
moved[i] = moving[i]; |
674 |
|
|
moving[i] = 0; |
675 |
|
|
} |
676 |
tim |
725 |
|
677 |
mmeineke |
558 |
iteration++; |
678 |
|
|
} |
679 |
|
|
|
680 |
tim |
725 |
if (!done){ |
681 |
|
|
sprintf(painCave.errMsg, |
682 |
|
|
"Constraint failure in constrainB, too many iterations: %d\n", |
683 |
|
|
iteration); |
684 |
mmeineke |
558 |
painCave.isFatal = 1; |
685 |
|
|
simError(); |
686 |
tim |
725 |
} |
687 |
mmeineke |
558 |
} |
688 |
|
|
|
689 |
mmeineke |
778 |
template<typename T> void Integrator<T>::rotationPropagation |
690 |
|
|
( DirectionalAtom* dAtom, double ji[3] ){ |
691 |
|
|
|
692 |
|
|
double angle; |
693 |
|
|
double A[3][3], I[3][3]; |
694 |
|
|
|
695 |
|
|
// use the angular velocities to propagate the rotation matrix a |
696 |
|
|
// full time step |
697 |
|
|
|
698 |
|
|
dAtom->getA(A); |
699 |
|
|
dAtom->getI(I); |
700 |
tim |
837 |
|
701 |
|
|
// rotate about the x-axis |
702 |
mmeineke |
778 |
angle = dt2 * ji[0] / I[0][0]; |
703 |
tim |
837 |
this->rotate( 1, 2, angle, ji, A ); |
704 |
|
|
|
705 |
mmeineke |
778 |
// rotate about the y-axis |
706 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
707 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
708 |
tim |
837 |
|
709 |
mmeineke |
778 |
// rotate about the z-axis |
710 |
|
|
angle = dt * ji[2] / I[2][2]; |
711 |
|
|
this->rotate( 0, 1, angle, ji, A); |
712 |
tim |
837 |
|
713 |
mmeineke |
778 |
// rotate about the y-axis |
714 |
|
|
angle = dt2 * ji[1] / I[1][1]; |
715 |
|
|
this->rotate( 2, 0, angle, ji, A ); |
716 |
tim |
837 |
|
717 |
mmeineke |
778 |
// rotate about the x-axis |
718 |
|
|
angle = dt2 * ji[0] / I[0][0]; |
719 |
|
|
this->rotate( 1, 2, angle, ji, A ); |
720 |
tim |
837 |
|
721 |
|
|
dAtom->setA( A ); |
722 |
mmeineke |
778 |
} |
723 |
|
|
|
724 |
tim |
725 |
template<typename T> void Integrator<T>::rotate(int axes1, int axes2, |
725 |
|
|
double angle, double ji[3], |
726 |
|
|
double A[3][3]){ |
727 |
|
|
int i, j, k; |
728 |
mmeineke |
558 |
double sinAngle; |
729 |
|
|
double cosAngle; |
730 |
|
|
double angleSqr; |
731 |
|
|
double angleSqrOver4; |
732 |
|
|
double top, bottom; |
733 |
|
|
double rot[3][3]; |
734 |
|
|
double tempA[3][3]; |
735 |
|
|
double tempJ[3]; |
736 |
|
|
|
737 |
|
|
// initialize the tempA |
738 |
|
|
|
739 |
tim |
725 |
for (i = 0; i < 3; i++){ |
740 |
|
|
for (j = 0; j < 3; j++){ |
741 |
gezelter |
600 |
tempA[j][i] = A[i][j]; |
742 |
mmeineke |
558 |
} |
743 |
|
|
} |
744 |
|
|
|
745 |
|
|
// initialize the tempJ |
746 |
|
|
|
747 |
tim |
725 |
for (i = 0; i < 3; i++) |
748 |
|
|
tempJ[i] = ji[i]; |
749 |
|
|
|
750 |
mmeineke |
558 |
// initalize rot as a unit matrix |
751 |
|
|
|
752 |
|
|
rot[0][0] = 1.0; |
753 |
|
|
rot[0][1] = 0.0; |
754 |
|
|
rot[0][2] = 0.0; |
755 |
|
|
|
756 |
|
|
rot[1][0] = 0.0; |
757 |
|
|
rot[1][1] = 1.0; |
758 |
|
|
rot[1][2] = 0.0; |
759 |
tim |
725 |
|
760 |
mmeineke |
558 |
rot[2][0] = 0.0; |
761 |
|
|
rot[2][1] = 0.0; |
762 |
|
|
rot[2][2] = 1.0; |
763 |
tim |
725 |
|
764 |
mmeineke |
558 |
// use a small angle aproximation for sin and cosine |
765 |
|
|
|
766 |
tim |
725 |
angleSqr = angle * angle; |
767 |
mmeineke |
558 |
angleSqrOver4 = angleSqr / 4.0; |
768 |
|
|
top = 1.0 - angleSqrOver4; |
769 |
|
|
bottom = 1.0 + angleSqrOver4; |
770 |
|
|
|
771 |
|
|
cosAngle = top / bottom; |
772 |
|
|
sinAngle = angle / bottom; |
773 |
|
|
|
774 |
|
|
rot[axes1][axes1] = cosAngle; |
775 |
|
|
rot[axes2][axes2] = cosAngle; |
776 |
|
|
|
777 |
|
|
rot[axes1][axes2] = sinAngle; |
778 |
|
|
rot[axes2][axes1] = -sinAngle; |
779 |
tim |
725 |
|
780 |
mmeineke |
558 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
781 |
tim |
725 |
|
782 |
|
|
for (i = 0; i < 3; i++){ |
783 |
mmeineke |
558 |
ji[i] = 0.0; |
784 |
tim |
725 |
for (k = 0; k < 3; k++){ |
785 |
mmeineke |
558 |
ji[i] += rot[i][k] * tempJ[k]; |
786 |
|
|
} |
787 |
|
|
} |
788 |
|
|
|
789 |
tim |
837 |
// rotate the Rotation matrix acording to: |
790 |
mmeineke |
558 |
// A[][] = A[][] * transpose(rot[][]) |
791 |
|
|
|
792 |
|
|
|
793 |
mmeineke |
561 |
// NOte for as yet unknown reason, we are performing the |
794 |
mmeineke |
558 |
// calculation as: |
795 |
|
|
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
796 |
|
|
|
797 |
tim |
725 |
for (i = 0; i < 3; i++){ |
798 |
|
|
for (j = 0; j < 3; j++){ |
799 |
gezelter |
600 |
A[j][i] = 0.0; |
800 |
tim |
725 |
for (k = 0; k < 3; k++){ |
801 |
|
|
A[j][i] += tempA[i][k] * rot[j][k]; |
802 |
mmeineke |
558 |
} |
803 |
|
|
} |
804 |
|
|
} |
805 |
|
|
} |
806 |
tim |
677 |
|
807 |
tim |
725 |
template<typename T> void Integrator<T>::calcForce(int calcPot, int calcStress){ |
808 |
|
|
myFF->doForces(calcPot, calcStress); |
809 |
tim |
677 |
} |
810 |
|
|
|
811 |
|
|
template<typename T> void Integrator<T>::thermalize(){ |
812 |
tim |
725 |
tStats->velocitize(); |
813 |
tim |
677 |
} |
814 |
tim |
763 |
|
815 |
|
|
template<typename T> double Integrator<T>::getConservedQuantity(void){ |
816 |
|
|
return tStats->getTotalE(); |
817 |
mmeineke |
768 |
} |
818 |
tim |
837 |
template<typename T> string Integrator<T>::getAdditionalParameters(void){ |
819 |
|
|
//By default, return a null string |
820 |
|
|
//The reason we use string instead of char* is that if we use char*, we will |
821 |
|
|
//return a pointer point to local variable which might cause problem |
822 |
|
|
return string(); |
823 |
|
|
} |