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