11 |
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#include "simError.h" |
12 |
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13 |
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14 |
< |
Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ |
14 |
> |
template<typename T> Integrator<T>::Integrator( SimInfo *theInfo, ForceFields* the_ff ) { |
15 |
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|
16 |
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info = theInfo; |
17 |
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myFF = the_ff; |
41 |
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checkConstraints(); |
42 |
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} |
43 |
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|
44 |
< |
Integrator::~Integrator() { |
44 |
> |
template<typename T> Integrator<T>::~Integrator() { |
45 |
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46 |
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if( nConstrained ){ |
47 |
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delete[] constrainedA; |
54 |
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55 |
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} |
56 |
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57 |
< |
void Integrator::checkConstraints( void ){ |
57 |
> |
template<typename T> void Integrator<T>::checkConstraints( void ){ |
58 |
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59 |
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60 |
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isConstrained = 0; |
72 |
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for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 |
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74 |
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constrained = theArray[j]->is_constrained(); |
75 |
< |
|
75 |
> |
|
76 |
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if(constrained){ |
77 |
< |
|
77 |
> |
|
78 |
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dummy_plug = theArray[j]->get_constraint(); |
79 |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
80 |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
82 |
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|
83 |
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nConstrained++; |
84 |
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constrained = 0; |
85 |
< |
} |
85 |
> |
} |
86 |
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} |
87 |
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88 |
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theArray = (SRI**) molecules[i].getMyBends(); |
155 |
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} |
156 |
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157 |
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158 |
< |
void Integrator::integrate( void ){ |
158 |
> |
template<typename T> void Integrator<T>::integrate( void ){ |
159 |
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160 |
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int i, j; // loop counters |
161 |
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|
167 |
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double currSample; |
168 |
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double currThermal; |
169 |
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double currStatus; |
170 |
– |
double currTime; |
170 |
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171 |
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int calcPot, calcStress; |
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int isError; |
173 |
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175 |
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176 |
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174 |
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tStats = new Thermo( info ); |
175 |
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statOut = new StatWriter( info ); |
176 |
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dumpOut = new DumpWriter( info ); |
183 |
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184 |
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// initialize the forces before the first step |
185 |
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186 |
< |
myFF->doForces(1,1); |
186 |
> |
calcForce(1, 1); |
187 |
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|
188 |
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if( info->setTemp ){ |
189 |
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|
190 |
< |
tStats->velocitize(); |
190 |
> |
thermalize(); |
191 |
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} |
192 |
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196 |
– |
dumpOut->writeDump( 0.0 ); |
197 |
– |
statOut->writeStat( 0.0 ); |
198 |
– |
|
193 |
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calcPot = 0; |
194 |
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calcStress = 0; |
195 |
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currSample = sampleTime; |
196 |
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currThermal = thermalTime; |
197 |
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currStatus = statusTime; |
204 |
– |
currTime = 0.0;; |
198 |
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|
199 |
+ |
dumpOut->writeDump( info->getTime() ); |
200 |
+ |
statOut->writeStat( info->getTime() ); |
201 |
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202 |
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readyCheck(); |
203 |
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207 |
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MPIcheckPoint(); |
208 |
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#endif // is_mpi |
209 |
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210 |
< |
|
216 |
< |
pos = Atom::getPosArray(); |
217 |
< |
vel = Atom::getVelArray(); |
218 |
< |
frc = Atom::getFrcArray(); |
219 |
< |
trq = Atom::getTrqArray(); |
220 |
< |
Amat = Atom::getAmatArray(); |
210 |
> |
while( info->getTime() < runTime ){ |
211 |
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212 |
< |
while( currTime < runTime ){ |
223 |
< |
|
224 |
< |
if( (currTime+dt) >= currStatus ){ |
212 |
> |
if( (info->getTime()+dt) >= currStatus ){ |
213 |
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calcPot = 1; |
214 |
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calcStress = 1; |
215 |
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} |
216 |
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|
217 |
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integrateStep( calcPot, calcStress ); |
218 |
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|
219 |
< |
currTime += dt; |
219 |
> |
info->incrTime(dt); |
220 |
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|
221 |
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if( info->setTemp ){ |
222 |
< |
if( currTime >= currThermal ){ |
223 |
< |
tStats->velocitize(); |
222 |
> |
if( info->getTime() >= currThermal ){ |
223 |
> |
thermalize(); |
224 |
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currThermal += thermalTime; |
225 |
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} |
226 |
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} |
227 |
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|
228 |
< |
if( currTime >= currSample ){ |
229 |
< |
dumpOut->writeDump( currTime ); |
228 |
> |
if( info->getTime() >= currSample ){ |
229 |
> |
dumpOut->writeDump( info->getTime() ); |
230 |
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currSample += sampleTime; |
231 |
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} |
232 |
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|
233 |
< |
if( currTime >= currStatus ){ |
234 |
< |
statOut->writeStat( currTime ); |
233 |
> |
if( info->getTime() >= currStatus ){ |
234 |
> |
statOut->writeStat( info->getTime() ); |
235 |
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calcPot = 0; |
236 |
|
calcStress = 0; |
237 |
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currStatus += statusTime; |
245 |
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|
246 |
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} |
247 |
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|
248 |
< |
dumpOut->writeFinal(); |
248 |
> |
dumpOut->writeFinal(info->getTime()); |
249 |
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|
250 |
|
delete dumpOut; |
251 |
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delete statOut; |
252 |
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} |
253 |
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|
254 |
< |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
254 |
> |
template<typename T> void Integrator<T>::integrateStep( int calcPot, int calcStress ){ |
255 |
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256 |
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257 |
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|
261 |
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moveA(); |
262 |
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if( nConstrained ) constrainA(); |
263 |
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|
264 |
+ |
|
265 |
+ |
#ifdef IS_MPI |
266 |
+ |
strcpy( checkPointMsg, "Succesful moveA\n" ); |
267 |
+ |
MPIcheckPoint(); |
268 |
+ |
#endif // is_mpi |
269 |
+ |
|
270 |
+ |
|
271 |
|
// calc forces |
272 |
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|
273 |
< |
myFF->doForces(calcPot,calcStress); |
273 |
> |
calcForce(calcPot,calcStress); |
274 |
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|
275 |
+ |
#ifdef IS_MPI |
276 |
+ |
strcpy( checkPointMsg, "Succesful doForces\n" ); |
277 |
+ |
MPIcheckPoint(); |
278 |
+ |
#endif // is_mpi |
279 |
+ |
|
280 |
+ |
|
281 |
|
// finish the velocity half step |
282 |
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|
283 |
|
moveB(); |
284 |
|
if( nConstrained ) constrainB(); |
285 |
< |
|
285 |
> |
|
286 |
> |
#ifdef IS_MPI |
287 |
> |
strcpy( checkPointMsg, "Succesful moveB\n" ); |
288 |
> |
MPIcheckPoint(); |
289 |
> |
#endif // is_mpi |
290 |
> |
|
291 |
> |
|
292 |
|
} |
293 |
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|
294 |
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|
295 |
< |
void Integrator::moveA( void ){ |
295 |
> |
template<typename T> void Integrator<T>::moveA( void ){ |
296 |
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|
297 |
< |
int i,j,k; |
291 |
< |
int atomIndex, aMatIndex; |
297 |
> |
int i, j; |
298 |
|
DirectionalAtom* dAtom; |
299 |
< |
double Tb[3]; |
300 |
< |
double ji[3]; |
299 |
> |
double Tb[3], ji[3]; |
300 |
> |
double A[3][3], I[3][3]; |
301 |
|
double angle; |
302 |
+ |
double vel[3], pos[3], frc[3]; |
303 |
+ |
double mass; |
304 |
|
|
305 |
+ |
for( i=0; i<nAtoms; i++ ){ |
306 |
|
|
307 |
+ |
atoms[i]->getVel( vel ); |
308 |
+ |
atoms[i]->getPos( pos ); |
309 |
+ |
atoms[i]->getFrc( frc ); |
310 |
|
|
311 |
< |
for( i=0; i<nAtoms; i++ ){ |
300 |
< |
atomIndex = i * 3; |
301 |
< |
aMatIndex = i * 9; |
311 |
> |
mass = atoms[i]->getMass(); |
312 |
|
|
313 |
< |
// velocity half step |
314 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
315 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
313 |
> |
for (j=0; j < 3; j++) { |
314 |
> |
// velocity half step |
315 |
> |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
316 |
> |
// position whole step |
317 |
> |
pos[j] += dt * vel[j]; |
318 |
> |
} |
319 |
|
|
320 |
< |
// position whole step |
321 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) pos[j] += dt * vel[j]; |
322 |
< |
|
320 |
> |
atoms[i]->setVel( vel ); |
321 |
> |
atoms[i]->setPos( pos ); |
322 |
> |
|
323 |
|
if( atoms[i]->isDirectional() ){ |
324 |
|
|
325 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
326 |
|
|
327 |
|
// get and convert the torque to body frame |
328 |
|
|
329 |
< |
Tb[0] = dAtom->getTx(); |
317 |
< |
Tb[1] = dAtom->getTy(); |
318 |
< |
Tb[2] = dAtom->getTz(); |
319 |
< |
|
329 |
> |
dAtom->getTrq( Tb ); |
330 |
|
dAtom->lab2Body( Tb ); |
331 |
< |
|
331 |
> |
|
332 |
|
// get the angular momentum, and propagate a half step |
333 |
< |
|
334 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
335 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
336 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
333 |
> |
|
334 |
> |
dAtom->getJ( ji ); |
335 |
> |
|
336 |
> |
for (j=0; j < 3; j++) |
337 |
> |
ji[j] += (dt2 * Tb[j]) * eConvert; |
338 |
|
|
339 |
|
// use the angular velocities to propagate the rotation matrix a |
340 |
|
// full time step |
341 |
< |
|
341 |
> |
|
342 |
> |
dAtom->getA(A); |
343 |
> |
dAtom->getI(I); |
344 |
> |
|
345 |
|
// rotate about the x-axis |
346 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
347 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
348 |
< |
|
346 |
> |
angle = dt2 * ji[0] / I[0][0]; |
347 |
> |
this->rotate( 1, 2, angle, ji, A ); |
348 |
> |
|
349 |
|
// rotate about the y-axis |
350 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
351 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
350 |
> |
angle = dt2 * ji[1] / I[1][1]; |
351 |
> |
this->rotate( 2, 0, angle, ji, A ); |
352 |
|
|
353 |
|
// rotate about the z-axis |
354 |
< |
angle = dt * ji[2] / dAtom->getIzz(); |
355 |
< |
this->rotate( 0, 1, angle, ji, &Amat[aMatIndex] ); |
354 |
> |
angle = dt * ji[2] / I[2][2]; |
355 |
> |
this->rotate( 0, 1, angle, ji, A); |
356 |
|
|
357 |
|
// rotate about the y-axis |
358 |
< |
angle = dt2 * ji[1] / dAtom->getIyy(); |
359 |
< |
this->rotate( 2, 0, angle, ji, &Amat[aMatIndex] ); |
358 |
> |
angle = dt2 * ji[1] / I[1][1]; |
359 |
> |
this->rotate( 2, 0, angle, ji, A ); |
360 |
|
|
361 |
|
// rotate about the x-axis |
362 |
< |
angle = dt2 * ji[0] / dAtom->getIxx(); |
363 |
< |
this->rotate( 1, 2, angle, ji, &Amat[aMatIndex] ); |
362 |
> |
angle = dt2 * ji[0] / I[0][0]; |
363 |
> |
this->rotate( 1, 2, angle, ji, A ); |
364 |
|
|
365 |
< |
dAtom->setJx( ji[0] ); |
366 |
< |
dAtom->setJy( ji[1] ); |
367 |
< |
dAtom->setJz( ji[2] ); |
368 |
< |
} |
369 |
< |
|
365 |
> |
|
366 |
> |
dAtom->setJ( ji ); |
367 |
> |
dAtom->setA( A ); |
368 |
> |
|
369 |
> |
} |
370 |
|
} |
371 |
|
} |
372 |
|
|
373 |
|
|
374 |
< |
void Integrator::moveB( void ){ |
375 |
< |
int i,j,k; |
362 |
< |
int atomIndex; |
374 |
> |
template<typename T> void Integrator<T>::moveB( void ){ |
375 |
> |
int i, j; |
376 |
|
DirectionalAtom* dAtom; |
377 |
< |
double Tb[3]; |
378 |
< |
double ji[3]; |
377 |
> |
double Tb[3], ji[3]; |
378 |
> |
double vel[3], frc[3]; |
379 |
> |
double mass; |
380 |
|
|
381 |
|
for( i=0; i<nAtoms; i++ ){ |
382 |
< |
atomIndex = i * 3; |
382 |
> |
|
383 |
> |
atoms[i]->getVel( vel ); |
384 |
> |
atoms[i]->getFrc( frc ); |
385 |
|
|
386 |
< |
// velocity half step |
371 |
< |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
372 |
< |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
386 |
> |
mass = atoms[i]->getMass(); |
387 |
|
|
388 |
+ |
// velocity half step |
389 |
+ |
for (j=0; j < 3; j++) |
390 |
+ |
vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
391 |
+ |
|
392 |
+ |
atoms[i]->setVel( vel ); |
393 |
+ |
|
394 |
|
if( atoms[i]->isDirectional() ){ |
395 |
< |
|
395 |
> |
|
396 |
|
dAtom = (DirectionalAtom *)atoms[i]; |
397 |
< |
|
398 |
< |
// get and convert the torque to body frame |
399 |
< |
|
400 |
< |
Tb[0] = dAtom->getTx(); |
381 |
< |
Tb[1] = dAtom->getTy(); |
382 |
< |
Tb[2] = dAtom->getTz(); |
383 |
< |
|
397 |
> |
|
398 |
> |
// get and convert the torque to body frame |
399 |
> |
|
400 |
> |
dAtom->getTrq( Tb ); |
401 |
|
dAtom->lab2Body( Tb ); |
402 |
+ |
|
403 |
+ |
// get the angular momentum, and propagate a half step |
404 |
+ |
|
405 |
+ |
dAtom->getJ( ji ); |
406 |
+ |
|
407 |
+ |
for (j=0; j < 3; j++) |
408 |
+ |
ji[j] += (dt2 * Tb[j]) * eConvert; |
409 |
|
|
410 |
< |
// get the angular momentum, and complete the angular momentum |
411 |
< |
// half step |
388 |
< |
|
389 |
< |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
390 |
< |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
391 |
< |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
392 |
< |
|
393 |
< |
dAtom->setJx( ji[0] ); |
394 |
< |
dAtom->setJy( ji[1] ); |
395 |
< |
dAtom->setJz( ji[2] ); |
410 |
> |
|
411 |
> |
dAtom->setJ( ji ); |
412 |
|
} |
413 |
|
} |
398 |
– |
|
414 |
|
} |
415 |
|
|
416 |
< |
void Integrator::preMove( void ){ |
417 |
< |
int i; |
416 |
> |
template<typename T> void Integrator<T>::preMove( void ){ |
417 |
> |
int i, j; |
418 |
> |
double pos[3]; |
419 |
|
|
420 |
|
if( nConstrained ){ |
421 |
|
|
422 |
< |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
423 |
< |
} |
424 |
< |
} |
422 |
> |
for(i=0; i < nAtoms; i++) { |
423 |
> |
|
424 |
> |
atoms[i]->getPos( pos ); |
425 |
|
|
426 |
< |
void Integrator::constrainA(){ |
426 |
> |
for (j = 0; j < 3; j++) { |
427 |
> |
oldPos[3*i + j] = pos[j]; |
428 |
> |
} |
429 |
|
|
430 |
+ |
} |
431 |
+ |
} |
432 |
+ |
} |
433 |
+ |
|
434 |
+ |
template<typename T> void Integrator<T>::constrainA(){ |
435 |
+ |
|
436 |
|
int i,j,k; |
437 |
|
int done; |
438 |
< |
double pxab, pyab, pzab; |
439 |
< |
double rxab, ryab, rzab; |
438 |
> |
double posA[3], posB[3]; |
439 |
> |
double velA[3], velB[3]; |
440 |
> |
double pab[3]; |
441 |
> |
double rab[3]; |
442 |
|
int a, b, ax, ay, az, bx, by, bz; |
443 |
|
double rma, rmb; |
444 |
|
double dx, dy, dz; |
448 |
|
double gab; |
449 |
|
int iteration; |
450 |
|
|
451 |
< |
|
426 |
< |
|
427 |
< |
for( i=0; i<nAtoms; i++){ |
428 |
< |
|
451 |
> |
for( i=0; i<nAtoms; i++){ |
452 |
|
moving[i] = 0; |
453 |
|
moved[i] = 1; |
454 |
|
} |
472 |
|
bz = (b*3) + 2; |
473 |
|
|
474 |
|
if( moved[a] || moved[b] ){ |
475 |
< |
|
476 |
< |
pxab = pos[ax] - pos[bx]; |
477 |
< |
pyab = pos[ay] - pos[by]; |
478 |
< |
pzab = pos[az] - pos[bz]; |
479 |
< |
|
475 |
> |
|
476 |
> |
atoms[a]->getPos( posA ); |
477 |
> |
atoms[b]->getPos( posB ); |
478 |
> |
|
479 |
> |
for (j = 0; j < 3; j++ ) |
480 |
> |
pab[j] = posA[j] - posB[j]; |
481 |
> |
|
482 |
|
//periodic boundary condition |
458 |
– |
pxab = pxab - info->box_x * copysign(1, pxab) |
459 |
– |
* (int)( fabs(pxab / info->box_x) + 0.5); |
460 |
– |
pyab = pyab - info->box_y * copysign(1, pyab) |
461 |
– |
* (int)( fabs(pyab / info->box_y) + 0.5); |
462 |
– |
pzab = pzab - info->box_z * copysign(1, pzab) |
463 |
– |
* (int)( fabs(pzab / info->box_z) + 0.5); |
483 |
|
|
484 |
< |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
484 |
> |
info->wrapVector( pab ); |
485 |
|
|
486 |
+ |
pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
487 |
+ |
|
488 |
|
rabsq = constrainedDsqr[i]; |
489 |
|
diffsq = rabsq - pabsq; |
490 |
|
|
491 |
|
// the original rattle code from alan tidesley |
492 |
|
if (fabs(diffsq) > (tol*rabsq*2)) { |
493 |
< |
rxab = oldPos[ax] - oldPos[bx]; |
494 |
< |
ryab = oldPos[ay] - oldPos[by]; |
495 |
< |
rzab = oldPos[az] - oldPos[bz]; |
493 |
> |
rab[0] = oldPos[ax] - oldPos[bx]; |
494 |
> |
rab[1] = oldPos[ay] - oldPos[by]; |
495 |
> |
rab[2] = oldPos[az] - oldPos[bz]; |
496 |
|
|
497 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
477 |
< |
* (int)( fabs(rxab / info->box_x) + 0.5); |
478 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
479 |
< |
* (int)( fabs(ryab / info->box_y) + 0.5); |
480 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
481 |
< |
* (int)( fabs(rzab / info->box_z) + 0.5); |
497 |
> |
info->wrapVector( rab ); |
498 |
|
|
499 |
< |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
499 |
> |
rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
500 |
|
|
501 |
|
rpabsq = rpab * rpab; |
502 |
|
|
519 |
|
|
520 |
|
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
521 |
|
|
522 |
< |
dx = rxab * gab; |
523 |
< |
dy = ryab * gab; |
524 |
< |
dz = rzab * gab; |
522 |
> |
dx = rab[0] * gab; |
523 |
> |
dy = rab[1] * gab; |
524 |
> |
dz = rab[2] * gab; |
525 |
|
|
526 |
< |
pos[ax] += rma * dx; |
527 |
< |
pos[ay] += rma * dy; |
528 |
< |
pos[az] += rma * dz; |
526 |
> |
posA[0] += rma * dx; |
527 |
> |
posA[1] += rma * dy; |
528 |
> |
posA[2] += rma * dz; |
529 |
|
|
530 |
< |
pos[bx] -= rmb * dx; |
515 |
< |
pos[by] -= rmb * dy; |
516 |
< |
pos[bz] -= rmb * dz; |
530 |
> |
atoms[a]->setPos( posA ); |
531 |
|
|
532 |
+ |
posB[0] -= rmb * dx; |
533 |
+ |
posB[1] -= rmb * dy; |
534 |
+ |
posB[2] -= rmb * dz; |
535 |
+ |
|
536 |
+ |
atoms[b]->setPos( posB ); |
537 |
+ |
|
538 |
|
dx = dx / dt; |
539 |
|
dy = dy / dt; |
540 |
|
dz = dz / dt; |
541 |
|
|
542 |
< |
vel[ax] += rma * dx; |
523 |
< |
vel[ay] += rma * dy; |
524 |
< |
vel[az] += rma * dz; |
542 |
> |
atoms[a]->getVel( velA ); |
543 |
|
|
544 |
< |
vel[bx] -= rmb * dx; |
545 |
< |
vel[by] -= rmb * dy; |
546 |
< |
vel[bz] -= rmb * dz; |
544 |
> |
velA[0] += rma * dx; |
545 |
> |
velA[1] += rma * dy; |
546 |
> |
velA[2] += rma * dz; |
547 |
> |
|
548 |
> |
atoms[a]->setVel( velA ); |
549 |
|
|
550 |
+ |
atoms[b]->getVel( velB ); |
551 |
+ |
|
552 |
+ |
velB[0] -= rmb * dx; |
553 |
+ |
velB[1] -= rmb * dy; |
554 |
+ |
velB[2] -= rmb * dz; |
555 |
+ |
|
556 |
+ |
atoms[b]->setVel( velB ); |
557 |
+ |
|
558 |
|
moving[a] = 1; |
559 |
|
moving[b] = 1; |
560 |
|
done = 0; |
582 |
|
|
583 |
|
} |
584 |
|
|
585 |
< |
void Integrator::constrainB( void ){ |
585 |
> |
template<typename T> void Integrator<T>::constrainB( void ){ |
586 |
|
|
587 |
|
int i,j,k; |
588 |
|
int done; |
589 |
+ |
double posA[3], posB[3]; |
590 |
+ |
double velA[3], velB[3]; |
591 |
|
double vxab, vyab, vzab; |
592 |
< |
double rxab, ryab, rzab; |
592 |
> |
double rab[3]; |
593 |
|
int a, b, ax, ay, az, bx, by, bz; |
594 |
|
double rma, rmb; |
595 |
|
double dx, dy, dz; |
623 |
|
bz = (b*3) + 2; |
624 |
|
|
625 |
|
if( moved[a] || moved[b] ){ |
596 |
– |
|
597 |
– |
vxab = vel[ax] - vel[bx]; |
598 |
– |
vyab = vel[ay] - vel[by]; |
599 |
– |
vzab = vel[az] - vel[bz]; |
626 |
|
|
627 |
< |
rxab = pos[ax] - pos[bx]; |
628 |
< |
ryab = pos[ay] - pos[by]; |
629 |
< |
rzab = pos[az] - pos[bz]; |
630 |
< |
|
627 |
> |
atoms[a]->getVel( velA ); |
628 |
> |
atoms[b]->getVel( velB ); |
629 |
> |
|
630 |
> |
vxab = velA[0] - velB[0]; |
631 |
> |
vyab = velA[1] - velB[1]; |
632 |
> |
vzab = velA[2] - velB[2]; |
633 |
|
|
634 |
< |
rxab = rxab - info->box_x * copysign(1, rxab) |
635 |
< |
* (int)( fabs(rxab / info->box_x) + 0.5); |
636 |
< |
ryab = ryab - info->box_y * copysign(1, ryab) |
637 |
< |
* (int)( fabs(ryab / info->box_y) + 0.5); |
638 |
< |
rzab = rzab - info->box_z * copysign(1, rzab) |
639 |
< |
* (int)( fabs(rzab / info->box_z) + 0.5); |
634 |
> |
atoms[a]->getPos( posA ); |
635 |
> |
atoms[b]->getPos( posB ); |
636 |
> |
|
637 |
> |
for (j = 0; j < 3; j++) |
638 |
> |
rab[j] = posA[j] - posB[j]; |
639 |
> |
|
640 |
> |
info->wrapVector( rab ); |
641 |
|
|
642 |
|
rma = 1.0 / atoms[a]->getMass(); |
643 |
|
rmb = 1.0 / atoms[b]->getMass(); |
644 |
|
|
645 |
< |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
645 |
> |
rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
646 |
|
|
647 |
|
gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
648 |
|
|
649 |
|
if (fabs(gab) > tol) { |
650 |
|
|
651 |
< |
dx = rxab * gab; |
652 |
< |
dy = ryab * gab; |
653 |
< |
dz = rzab * gab; |
654 |
< |
|
655 |
< |
vel[ax] += rma * dx; |
656 |
< |
vel[ay] += rma * dy; |
657 |
< |
vel[az] += rma * dz; |
651 |
> |
dx = rab[0] * gab; |
652 |
> |
dy = rab[1] * gab; |
653 |
> |
dz = rab[2] * gab; |
654 |
> |
|
655 |
> |
velA[0] += rma * dx; |
656 |
> |
velA[1] += rma * dy; |
657 |
> |
velA[2] += rma * dz; |
658 |
|
|
659 |
< |
vel[bx] -= rmb * dx; |
660 |
< |
vel[by] -= rmb * dy; |
661 |
< |
vel[bz] -= rmb * dz; |
659 |
> |
atoms[a]->setVel( velA ); |
660 |
> |
|
661 |
> |
velB[0] -= rmb * dx; |
662 |
> |
velB[1] -= rmb * dy; |
663 |
> |
velB[2] -= rmb * dz; |
664 |
> |
|
665 |
> |
atoms[b]->setVel( velB ); |
666 |
|
|
667 |
|
moving[a] = 1; |
668 |
|
moving[b] = 1; |
678 |
|
|
679 |
|
iteration++; |
680 |
|
} |
681 |
< |
|
681 |
> |
|
682 |
|
if( !done ){ |
683 |
|
|
684 |
|
|
691 |
|
|
692 |
|
} |
693 |
|
|
694 |
+ |
template<typename T> void Integrator<T>::rotate( int axes1, int axes2, double angle, double ji[3], |
695 |
+ |
double A[3][3] ){ |
696 |
|
|
662 |
– |
|
663 |
– |
|
664 |
– |
|
665 |
– |
|
666 |
– |
|
667 |
– |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
668 |
– |
double A[9] ){ |
669 |
– |
|
697 |
|
int i,j,k; |
698 |
|
double sinAngle; |
699 |
|
double cosAngle; |
708 |
|
|
709 |
|
for(i=0; i<3; i++){ |
710 |
|
for(j=0; j<3; j++){ |
711 |
< |
tempA[j][i] = A[3*i + j]; |
711 |
> |
tempA[j][i] = A[i][j]; |
712 |
|
} |
713 |
|
} |
714 |
|
|
765 |
|
|
766 |
|
for(i=0; i<3; i++){ |
767 |
|
for(j=0; j<3; j++){ |
768 |
< |
A[3*j + i] = 0.0; |
768 |
> |
A[j][i] = 0.0; |
769 |
|
for(k=0; k<3; k++){ |
770 |
< |
A[3*j + i] += tempA[i][k] * rot[j][k]; |
770 |
> |
A[j][i] += tempA[i][k] * rot[j][k]; |
771 |
|
} |
772 |
|
} |
773 |
|
} |
774 |
|
} |
775 |
+ |
|
776 |
+ |
template<typename T> void Integrator<T>::calcForce( int calcPot, int calcStress ){ |
777 |
+ |
myFF->doForces(calcPot,calcStress); |
778 |
+ |
|
779 |
+ |
} |
780 |
+ |
|
781 |
+ |
template<typename T> void Integrator<T>::thermalize(){ |
782 |
+ |
tStats->velocitize(); |
783 |
+ |
} |