# | Line 1 | Line 1 | |
---|---|---|
1 | #include <iostream> | |
2 | #include <cstdlib> | |
3 | + | #include <cmath> |
4 | ||
5 | #ifdef IS_MPI | |
6 | #include "mpiSimulation.hpp" | |
# | Line 10 | Line 11 | |
11 | #include "simError.h" | |
12 | ||
13 | ||
14 | < | Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ |
14 | > | Integrator::Integrator( SimInfo *theInfo, ForceFields* the_ff ){ |
15 | ||
16 | info = theInfo; | |
17 | myFF = the_ff; | |
# | Line 33 | Line 34 | Integrator::Integrator( SimInfo* theInfo, ForceFields* | |
34 | constrainedDsqr = NULL; | |
35 | moving = NULL; | |
36 | moved = NULL; | |
37 | < | prePos = NULL; |
37 | > | oldPos = NULL; |
38 | ||
39 | nConstrained = 0; | |
40 | ||
# | Line 48 | Line 49 | Integrator::~Integrator() { | |
49 | delete[] constrainedDsqr; | |
50 | delete[] moving; | |
51 | delete[] moved; | |
52 | < | delete[] prePos; |
52 | < | k |
52 | > | delete[] oldPos; |
53 | } | |
54 | ||
55 | } | |
# | Line 72 | Line 72 | void Integrator::checkConstraints( void ){ | |
72 | for(int j=0; j<molecules[i].getNBonds(); j++){ | |
73 | ||
74 | constrained = theArray[j]->is_constrained(); | |
75 | < | |
75 | > | |
76 | if(constrained){ | |
77 | < | |
77 | > | |
78 | dummy_plug = theArray[j]->get_constraint(); | |
79 | temp_con[nConstrained].set_a( dummy_plug->get_a() ); | |
80 | temp_con[nConstrained].set_b( dummy_plug->get_b() ); | |
# | Line 82 | Line 82 | void Integrator::checkConstraints( void ){ | |
82 | ||
83 | nConstrained++; | |
84 | constrained = 0; | |
85 | < | } |
85 | > | } |
86 | } | |
87 | ||
88 | theArray = (SRI**) molecules[i].getMyBends(); | |
# | Line 137 | Line 137 | void Integrator::checkConstraints( void ){ | |
137 | constrainedA[i] = temp_con[i].get_a(); | |
138 | constrainedB[i] = temp_con[i].get_b(); | |
139 | constrainedDsqr[i] = temp_con[i].get_dsqr(); | |
140 | + | |
141 | } | |
142 | ||
143 | ||
# | Line 147 | Line 148 | void Integrator::checkConstraints( void ){ | |
148 | moving = new int[nAtoms]; | |
149 | moved = new int[nAtoms]; | |
150 | ||
151 | < | prePos = new double[nAtoms*3]; |
151 | > | oldPos = new double[nAtoms*3]; |
152 | } | |
153 | ||
154 | delete[] temp_con; | |
# | Line 157 | Line 158 | void Integrator::integrate( void ){ | |
158 | void Integrator::integrate( void ){ | |
159 | ||
160 | int i, j; // loop counters | |
160 | – | double kE = 0.0; // the kinetic energy |
161 | – | double rot_kE; |
162 | – | double trans_kE; |
163 | – | int tl; // the time loop conter |
164 | – | double dt2; // half the dt |
161 | ||
166 | – | double vx, vy, vz; // the velocities |
167 | – | double vx2, vy2, vz2; // the square of the velocities |
168 | – | double rx, ry, rz; // the postitions |
169 | – | |
170 | – | double ji[3]; // the body frame angular momentum |
171 | – | double jx2, jy2, jz2; // the square of the angular momentums |
172 | – | double Tb[3]; // torque in the body frame |
173 | – | double angle; // the angle through which to rotate the rotation matrix |
174 | – | double A[3][3]; // the rotation matrix |
175 | – | double press[9]; |
176 | – | |
177 | – | double dt = info->dt; |
162 | double runTime = info->run_time; | |
163 | double sampleTime = info->sampleTime; | |
164 | double statusTime = info->statusTime; | |
# | Line 183 | Line 167 | void Integrator::integrate( void ){ | |
167 | double currSample; | |
168 | double currThermal; | |
169 | double currStatus; | |
186 | – | double currTime; |
170 | ||
171 | int calcPot, calcStress; | |
172 | int isError; | |
173 | ||
174 | tStats = new Thermo( info ); | |
175 | < | e_out = new StatWriter( info ); |
176 | < | dump_out = new DumpWriter( info ); |
175 | > | statOut = new StatWriter( info ); |
176 | > | dumpOut = new DumpWriter( info ); |
177 | ||
178 | < | Atom** atoms = info->atoms; |
178 | > | atoms = info->atoms; |
179 | DirectionalAtom* dAtom; | |
180 | + | |
181 | + | dt = info->dt; |
182 | dt2 = 0.5 * dt; | |
183 | ||
184 | // initialize the forces before the first step | |
# | Line 205 | Line 190 | void Integrator::integrate( void ){ | |
190 | tStats->velocitize(); | |
191 | } | |
192 | ||
208 | – | dump_out->writeDump( 0.0 ); |
209 | – | e_out->writeStat( 0.0 ); |
210 | – | |
193 | calcPot = 0; | |
194 | calcStress = 0; | |
195 | currSample = sampleTime; | |
196 | currThermal = thermalTime; | |
197 | currStatus = statusTime; | |
216 | – | currTime = 0.0;; |
198 | ||
199 | < | while( currTime < runTime ){ |
199 | > | dumpOut->writeDump( info->currTime ); |
200 | > | statOut->writeStat( info->currTime ); |
201 | ||
202 | < | if( (currTime+dt) >= currStatus ){ |
202 | > | readyCheck(); |
203 | > | |
204 | > | #ifdef IS_MPI |
205 | > | strcpy( checkPointMsg, |
206 | > | "The integrator is ready to go." ); |
207 | > | MPIcheckPoint(); |
208 | > | #endif // is_mpi |
209 | > | |
210 | > | while( info->currTime < runTime ){ |
211 | > | |
212 | > | if( (info->currTime+dt) >= currStatus ){ |
213 | calcPot = 1; | |
214 | calcStress = 1; | |
215 | } | |
216 | < | |
216 | > | |
217 | integrateStep( calcPot, calcStress ); | |
218 | ||
219 | < | currTime += dt; |
219 | > | info->currTime += dt; |
220 | > | info->setTime(info->currTime); |
221 | ||
222 | if( info->setTemp ){ | |
223 | < | if( currTime >= currThermal ){ |
223 | > | if( info->currTime >= currThermal ){ |
224 | tStats->velocitize(); | |
225 | currThermal += thermalTime; | |
226 | } | |
227 | } | |
228 | ||
229 | < | if( currTime >= currSample ){ |
230 | < | dump_out->writeDump( currTime ); |
229 | > | if( info->currTime >= currSample ){ |
230 | > | dumpOut->writeDump( info->currTime ); |
231 | currSample += sampleTime; | |
232 | } | |
233 | ||
234 | < | if( currTime >= currStatus ){ |
235 | < | e_out->writeStat( time * dt ); |
234 | > | if( info->currTime >= currStatus ){ |
235 | > | statOut->writeStat( info->currTime ); |
236 | calcPot = 0; | |
237 | calcStress = 0; | |
238 | currStatus += statusTime; | |
239 | } | |
247 | – | } |
240 | ||
241 | < | dump_out->writeFinal(); |
241 | > | #ifdef IS_MPI |
242 | > | strcpy( checkPointMsg, |
243 | > | "successfully took a time step." ); |
244 | > | MPIcheckPoint(); |
245 | > | #endif // is_mpi |
246 | ||
247 | < | delete dump_out; |
248 | < | delete e_out; |
247 | > | } |
248 | > | |
249 | > | dumpOut->writeFinal(info->currTime); |
250 | > | |
251 | > | delete dumpOut; |
252 | > | delete statOut; |
253 | } | |
254 | ||
255 | void Integrator::integrateStep( int calcPot, int calcStress ){ | |
256 | ||
257 | + | |
258 | + | |
259 | // Position full step, and velocity half step | |
260 | ||
261 | < | //preMove(); |
261 | > | preMove(); |
262 | moveA(); | |
263 | if( nConstrained ) constrainA(); | |
264 | ||
265 | + | |
266 | + | #ifdef IS_MPI |
267 | + | strcpy( checkPointMsg, "Succesful moveA\n" ); |
268 | + | MPIcheckPoint(); |
269 | + | #endif // is_mpi |
270 | + | |
271 | + | |
272 | // calc forces | |
273 | ||
274 | myFF->doForces(calcPot,calcStress); | |
275 | ||
276 | + | #ifdef IS_MPI |
277 | + | strcpy( checkPointMsg, "Succesful doForces\n" ); |
278 | + | MPIcheckPoint(); |
279 | + | #endif // is_mpi |
280 | + | |
281 | + | |
282 | // finish the velocity half step | |
283 | ||
284 | moveB(); | |
285 | if( nConstrained ) constrainB(); | |
286 | < | |
286 | > | |
287 | > | #ifdef IS_MPI |
288 | > | strcpy( checkPointMsg, "Succesful moveB\n" ); |
289 | > | MPIcheckPoint(); |
290 | > | #endif // is_mpi |
291 | > | |
292 | > | |
293 | } | |
294 | ||
295 | ||
296 | void Integrator::moveA( void ){ | |
297 | ||
298 | < | int i,j,k; |
278 | < | int atomIndex, aMatIndex; |
298 | > | int i, j; |
299 | DirectionalAtom* dAtom; | |
300 | < | double Tb[3]; |
301 | < | double ji[3]; |
300 | > | double Tb[3], ji[3]; |
301 | > | double A[3][3], I[3][3]; |
302 | > | double angle; |
303 | > | double vel[3], pos[3], frc[3]; |
304 | > | double mass; |
305 | ||
306 | for( i=0; i<nAtoms; i++ ){ | |
284 | – | atomIndex = i * 3; |
285 | – | aMatIndex = i * 9; |
286 | – | |
287 | – | // velocity half step |
288 | – | for( j=atomIndex; j<(atomIndex+3); j++ ) |
289 | – | vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
307 | ||
308 | < | // position whole step |
309 | < | for( j=atomIndex; j<(atomIndex+3); j++ ) |
308 | > | atoms[i]->getVel( vel ); |
309 | > | atoms[i]->getPos( pos ); |
310 | > | atoms[i]->getFrc( frc ); |
311 | > | |
312 | > | mass = atoms[i]->getMass(); |
313 | > | |
314 | > | for (j=0; j < 3; j++) { |
315 | > | // velocity half step |
316 | > | vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
317 | > | // position whole step |
318 | pos[j] += dt * vel[j]; | |
319 | + | } |
320 | ||
321 | < | |
321 | > | atoms[i]->setVel( vel ); |
322 | > | atoms[i]->setPos( pos ); |
323 | > | |
324 | if( atoms[i]->isDirectional() ){ | |
325 | ||
326 | dAtom = (DirectionalAtom *)atoms[i]; | |
327 | ||
328 | // get and convert the torque to body frame | |
329 | ||
330 | < | Tb[0] = dAtom->getTx(); |
303 | < | Tb[1] = dAtom->getTy(); |
304 | < | Tb[2] = dAtom->getTz(); |
305 | < | |
330 | > | dAtom->getTrq( Tb ); |
331 | dAtom->lab2Body( Tb ); | |
332 | < | |
332 | > | |
333 | // get the angular momentum, and propagate a half step | |
334 | + | |
335 | + | dAtom->getJ( ji ); |
336 | + | |
337 | + | for (j=0; j < 3; j++) |
338 | + | ji[j] += (dt2 * Tb[j]) * eConvert; |
339 | ||
310 | – | ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
311 | – | ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
312 | – | ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
313 | – | |
340 | // use the angular velocities to propagate the rotation matrix a | |
341 | // full time step | |
342 | < | |
342 | > | |
343 | > | dAtom->getA(A); |
344 | > | dAtom->getI(I); |
345 | > | |
346 | // rotate about the x-axis | |
347 | < | angle = dt2 * ji[0] / dAtom->getIxx(); |
348 | < | this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
349 | < | |
347 | > | angle = dt2 * ji[0] / I[0][0]; |
348 | > | this->rotate( 1, 2, angle, ji, A ); |
349 | > | |
350 | // rotate about the y-axis | |
351 | < | angle = dt2 * ji[1] / dAtom->getIyy(); |
352 | < | this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
351 | > | angle = dt2 * ji[1] / I[1][1]; |
352 | > | this->rotate( 2, 0, angle, ji, A ); |
353 | ||
354 | // rotate about the z-axis | |
355 | < | angle = dt * ji[2] / dAtom->getIzz(); |
356 | < | this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
355 | > | angle = dt * ji[2] / I[2][2]; |
356 | > | this->rotate( 0, 1, angle, ji, A); |
357 | ||
358 | // rotate about the y-axis | |
359 | < | angle = dt2 * ji[1] / dAtom->getIyy(); |
360 | < | this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
359 | > | angle = dt2 * ji[1] / I[1][1]; |
360 | > | this->rotate( 2, 0, angle, ji, A ); |
361 | ||
362 | // rotate about the x-axis | |
363 | < | angle = dt2 * ji[0] / dAtom->getIxx(); |
364 | < | this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
363 | > | angle = dt2 * ji[0] / I[0][0]; |
364 | > | this->rotate( 1, 2, angle, ji, A ); |
365 | ||
366 | < | dAtom->setJx( ji[0] ); |
367 | < | dAtom->setJy( ji[1] ); |
368 | < | dAtom->setJz( ji[2] ); |
369 | < | } |
370 | < | |
366 | > | |
367 | > | dAtom->setJ( ji ); |
368 | > | dAtom->setA( A ); |
369 | > | |
370 | > | } |
371 | } | |
372 | } | |
373 | ||
374 | ||
375 | void Integrator::moveB( void ){ | |
376 | < | int i,j,k; |
348 | < | int atomIndex; |
376 | > | int i, j; |
377 | DirectionalAtom* dAtom; | |
378 | < | double Tb[3]; |
379 | < | double ji[3]; |
378 | > | double Tb[3], ji[3]; |
379 | > | double vel[3], frc[3]; |
380 | > | double mass; |
381 | ||
382 | for( i=0; i<nAtoms; i++ ){ | |
383 | < | atomIndex = i * 3; |
383 | > | |
384 | > | atoms[i]->getVel( vel ); |
385 | > | atoms[i]->getFrc( frc ); |
386 | ||
387 | < | // velocity half step |
357 | < | for( j=atomIndex; j<(atomIndex+3); j++ ) |
358 | < | vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
387 | > | mass = atoms[i]->getMass(); |
388 | ||
389 | + | // velocity half step |
390 | + | for (j=0; j < 3; j++) |
391 | + | vel[j] += ( dt2 * frc[j] / mass ) * eConvert; |
392 | + | |
393 | + | atoms[i]->setVel( vel ); |
394 | + | |
395 | if( atoms[i]->isDirectional() ){ | |
396 | < | |
396 | > | |
397 | dAtom = (DirectionalAtom *)atoms[i]; | |
398 | < | |
399 | < | // get and convert the torque to body frame |
400 | < | |
401 | < | Tb[0] = dAtom->getTx(); |
367 | < | Tb[1] = dAtom->getTy(); |
368 | < | Tb[2] = dAtom->getTz(); |
369 | < | |
398 | > | |
399 | > | // get and convert the torque to body frame |
400 | > | |
401 | > | dAtom->getTrq( Tb ); |
402 | dAtom->lab2Body( Tb ); | |
403 | + | |
404 | + | // get the angular momentum, and propagate a half step |
405 | + | |
406 | + | dAtom->getJ( ji ); |
407 | + | |
408 | + | for (j=0; j < 3; j++) |
409 | + | ji[j] += (dt2 * Tb[j]) * eConvert; |
410 | ||
411 | < | // get the angular momentum, and complete the angular momentum |
412 | < | // half step |
374 | < | |
375 | < | ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
376 | < | ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
377 | < | ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
378 | < | |
379 | < | jx2 = ji[0] * ji[0]; |
380 | < | jy2 = ji[1] * ji[1]; |
381 | < | jz2 = ji[2] * ji[2]; |
382 | < | |
383 | < | dAtom->setJx( ji[0] ); |
384 | < | dAtom->setJy( ji[1] ); |
385 | < | dAtom->setJz( ji[2] ); |
411 | > | |
412 | > | dAtom->setJ( ji ); |
413 | } | |
414 | } | |
388 | – | |
415 | } | |
416 | ||
417 | void Integrator::preMove( void ){ | |
418 | < | int i; |
418 | > | int i, j; |
419 | > | double pos[3]; |
420 | ||
421 | if( nConstrained ){ | |
422 | < | if( oldAtoms != nAtoms ){ |
423 | < | |
424 | < | // save oldAtoms to check for lode balanceing later on. |
425 | < | |
426 | < | oldAtoms = nAtoms; |
427 | < | |
428 | < | delete[] moving; |
429 | < | delete[] moved; |
430 | < | delete[] oldPos; |
404 | < | |
405 | < | moving = new int[nAtoms]; |
406 | < | moved = new int[nAtoms]; |
407 | < | |
408 | < | oldPos = new double[nAtoms*3]; |
422 | > | |
423 | > | for(i=0; i < nAtoms; i++) { |
424 | > | |
425 | > | atoms[i]->getPos( pos ); |
426 | > | |
427 | > | for (j = 0; j < 3; j++) { |
428 | > | oldPos[3*i + j] = pos[j]; |
429 | > | } |
430 | > | |
431 | } | |
432 | < | |
433 | < | for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
412 | < | } |
413 | < | } |
432 | > | } |
433 | > | } |
434 | ||
435 | void Integrator::constrainA(){ | |
436 | ||
437 | int i,j,k; | |
438 | int done; | |
439 | < | double pxab, pyab, pzab; |
440 | < | double rxab, ryab, rzab; |
441 | < | int a, b; |
439 | > | double posA[3], posB[3]; |
440 | > | double velA[3], velB[3]; |
441 | > | double pab[3]; |
442 | > | double rab[3]; |
443 | > | int a, b, ax, ay, az, bx, by, bz; |
444 | double rma, rmb; | |
445 | double dx, dy, dz; | |
446 | + | double rpab; |
447 | double rabsq, pabsq, rpabsq; | |
448 | double diffsq; | |
449 | double gab; | |
450 | int iteration; | |
451 | ||
452 | < | |
430 | < | |
431 | < | for( i=0; i<nAtoms; i++){ |
432 | < | |
452 | > | for( i=0; i<nAtoms; i++){ |
453 | moving[i] = 0; | |
454 | moved[i] = 1; | |
455 | } | |
456 | < | |
437 | < | |
456 | > | |
457 | iteration = 0; | |
458 | done = 0; | |
459 | while( !done && (iteration < maxIteration )){ | |
# | Line 444 | Line 463 | void Integrator::constrainA(){ | |
463 | ||
464 | a = constrainedA[i]; | |
465 | b = constrainedB[i]; | |
466 | < | |
466 | > | |
467 | > | ax = (a*3) + 0; |
468 | > | ay = (a*3) + 1; |
469 | > | az = (a*3) + 2; |
470 | > | |
471 | > | bx = (b*3) + 0; |
472 | > | by = (b*3) + 1; |
473 | > | bz = (b*3) + 2; |
474 | > | |
475 | if( moved[a] || moved[b] ){ | |
476 | < | |
477 | < | pxab = pos[3*a+0] - pos[3*b+0]; |
478 | < | pyab = pos[3*a+1] - pos[3*b+1]; |
479 | < | pzab = pos[3*a+2] - pos[3*b+2]; |
476 | > | |
477 | > | atoms[a]->getPos( posA ); |
478 | > | atoms[b]->getPos( posB ); |
479 | > | |
480 | > | for (j = 0; j < 3; j++ ) |
481 | > | pab[j] = posA[j] - posB[j]; |
482 | > | |
483 | > | //periodic boundary condition |
484 | ||
485 | < | //periodic boundary condition |
455 | < | pxab = pxab - info->box_x * copysign(1, pxab) |
456 | < | * int(pxab / info->box_x + 0.5); |
457 | < | pyab = pyab - info->box_y * copysign(1, pyab) |
458 | < | * int(pyab / info->box_y + 0.5); |
459 | < | pzab = pzab - info->box_z * copysign(1, pzab) |
460 | < | * int(pzab / info->box_z + 0.5); |
461 | < | |
462 | < | pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
463 | < | rabsq = constraintedDsqr[i]; |
464 | < | diffsq = pabsq - rabsq; |
485 | > | info->wrapVector( pab ); |
486 | ||
487 | + | pabsq = pab[0] * pab[0] + pab[1] * pab[1] + pab[2] * pab[2]; |
488 | + | |
489 | + | rabsq = constrainedDsqr[i]; |
490 | + | diffsq = rabsq - pabsq; |
491 | + | |
492 | // the original rattle code from alan tidesley | |
493 | < | if (fabs(diffsq) > tol*rabsq*2) { |
494 | < | rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
495 | < | ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
496 | < | rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
471 | < | |
472 | < | rxab = rxab - info->box_x * copysign(1, rxab) |
473 | < | * int(rxab / info->box_x + 0.5); |
474 | < | ryab = ryab - info->box_y * copysign(1, ryab) |
475 | < | * int(ryab / info->box_y + 0.5); |
476 | < | rzab = rzab - info->box_z * copysign(1, rzab) |
477 | < | * int(rzab / info->box_z + 0.5); |
493 | > | if (fabs(diffsq) > (tol*rabsq*2)) { |
494 | > | rab[0] = oldPos[ax] - oldPos[bx]; |
495 | > | rab[1] = oldPos[ay] - oldPos[by]; |
496 | > | rab[2] = oldPos[az] - oldPos[bz]; |
497 | ||
498 | < | rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
498 | > | info->wrapVector( rab ); |
499 | > | |
500 | > | rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
501 | > | |
502 | rpabsq = rpab * rpab; | |
503 | ||
504 | ||
505 | if (rpabsq < (rabsq * -diffsq)){ | |
506 | + | |
507 | #ifdef IS_MPI | |
508 | a = atoms[a]->getGlobalIndex(); | |
509 | b = atoms[b]->getGlobalIndex(); | |
510 | #endif //is_mpi | |
511 | sprintf( painCave.errMsg, | |
512 | < | "Constraint failure in constrainA at atom %d and %d\n.", |
512 | > | "Constraint failure in constrainA at atom %d and %d.\n", |
513 | a, b ); | |
514 | painCave.isFatal = 1; | |
515 | simError(); | |
# | Line 494 | Line 517 | void Integrator::constrainA(){ | |
517 | ||
518 | rma = 1.0 / atoms[a]->getMass(); | |
519 | rmb = 1.0 / atoms[b]->getMass(); | |
520 | < | |
520 | > | |
521 | gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); | |
499 | – | dx = rxab * gab; |
500 | – | dy = ryab * gab; |
501 | – | dz = rzab * gab; |
522 | ||
523 | < | pos[3*a+0] += rma * dx; |
524 | < | pos[3*a+1] += rma * dy; |
525 | < | pos[3*a+2] += rma * dz; |
523 | > | dx = rab[0] * gab; |
524 | > | dy = rab[1] * gab; |
525 | > | dz = rab[2] * gab; |
526 | ||
527 | < | pos[3*b+0] -= rmb * dx; |
528 | < | pos[3*b+1] -= rmb * dy; |
529 | < | pos[3*b+2] -= rmb * dz; |
527 | > | posA[0] += rma * dx; |
528 | > | posA[1] += rma * dy; |
529 | > | posA[2] += rma * dz; |
530 | > | |
531 | > | atoms[a]->setPos( posA ); |
532 | > | |
533 | > | posB[0] -= rmb * dx; |
534 | > | posB[1] -= rmb * dy; |
535 | > | posB[2] -= rmb * dz; |
536 | > | |
537 | > | atoms[b]->setPos( posB ); |
538 | ||
539 | dx = dx / dt; | |
540 | dy = dy / dt; | |
541 | dz = dz / dt; | |
542 | ||
543 | < | vel[3*a+0] += rma * dx; |
516 | < | vel[3*a+1] += rma * dy; |
517 | < | vel[3*a+2] += rma * dz; |
543 | > | atoms[a]->getVel( velA ); |
544 | ||
545 | < | vel[3*b+0] -= rmb * dx; |
546 | < | vel[3*b+1] -= rmb * dy; |
547 | < | vel[3*b+2] -= rmb * dz; |
545 | > | velA[0] += rma * dx; |
546 | > | velA[1] += rma * dy; |
547 | > | velA[2] += rma * dz; |
548 | ||
549 | + | atoms[a]->setVel( velA ); |
550 | + | |
551 | + | atoms[b]->getVel( velB ); |
552 | + | |
553 | + | velB[0] -= rmb * dx; |
554 | + | velB[1] -= rmb * dy; |
555 | + | velB[2] -= rmb * dz; |
556 | + | |
557 | + | atoms[b]->setVel( velB ); |
558 | + | |
559 | moving[a] = 1; | |
560 | moving[b] = 1; | |
561 | done = 0; | |
# | Line 538 | Line 574 | void Integrator::constrainA(){ | |
574 | ||
575 | if( !done ){ | |
576 | ||
577 | < | sprintf( painCae.errMsg, |
577 | > | sprintf( painCave.errMsg, |
578 | "Constraint failure in constrainA, too many iterations: %d\n", | |
579 | < | iterations ); |
579 | > | iteration ); |
580 | painCave.isFatal = 1; | |
581 | simError(); | |
582 | } | |
# | Line 551 | Line 587 | void Integrator::constrainB( void ){ | |
587 | ||
588 | int i,j,k; | |
589 | int done; | |
590 | + | double posA[3], posB[3]; |
591 | + | double velA[3], velB[3]; |
592 | double vxab, vyab, vzab; | |
593 | < | double rxab, ryab, rzab; |
594 | < | int a, b; |
593 | > | double rab[3]; |
594 | > | int a, b, ax, ay, az, bx, by, bz; |
595 | double rma, rmb; | |
596 | double dx, dy, dz; | |
597 | double rabsq, pabsq, rvab; | |
# | Line 561 | Line 599 | void Integrator::constrainB( void ){ | |
599 | double gab; | |
600 | int iteration; | |
601 | ||
602 | < | for(i=0; i<nAtom; i++){ |
602 | > | for(i=0; i<nAtoms; i++){ |
603 | moving[i] = 0; | |
604 | moved[i] = 1; | |
605 | } | |
606 | ||
607 | done = 0; | |
608 | + | iteration = 0; |
609 | while( !done && (iteration < maxIteration ) ){ | |
610 | ||
611 | + | done = 1; |
612 | + | |
613 | for(i=0; i<nConstrained; i++){ | |
614 | ||
615 | a = constrainedA[i]; | |
616 | b = constrainedB[i]; | |
617 | ||
618 | + | ax = (a*3) + 0; |
619 | + | ay = (a*3) + 1; |
620 | + | az = (a*3) + 2; |
621 | + | |
622 | + | bx = (b*3) + 0; |
623 | + | by = (b*3) + 1; |
624 | + | bz = (b*3) + 2; |
625 | + | |
626 | if( moved[a] || moved[b] ){ | |
578 | – | |
579 | – | vxab = vel[3*a+0] - vel[3*b+0]; |
580 | – | vyab = vel[3*a+1] - vel[3*b+1]; |
581 | – | vzab = vel[3*a+2] - vel[3*b+2]; |
627 | ||
628 | < | rxab = pos[3*a+0] - pos[3*b+0];q |
629 | < | ryab = pos[3*a+1] - pos[3*b+1]; |
630 | < | rzab = pos[3*a+2] - pos[3*b+2]; |
631 | < | |
632 | < | rxab = rxab - info->box_x * copysign(1, rxab) |
633 | < | * int(rxab / info->box_x + 0.5); |
589 | < | ryab = ryab - info->box_y * copysign(1, ryab) |
590 | < | * int(ryab / info->box_y + 0.5); |
591 | < | rzab = rzab - info->box_z * copysign(1, rzab) |
592 | < | * int(rzab / info->box_z + 0.5); |
628 | > | atoms[a]->getVel( velA ); |
629 | > | atoms[b]->getVel( velB ); |
630 | > | |
631 | > | vxab = velA[0] - velB[0]; |
632 | > | vyab = velA[1] - velB[1]; |
633 | > | vzab = velA[2] - velB[2]; |
634 | ||
635 | + | atoms[a]->getPos( posA ); |
636 | + | atoms[b]->getPos( posB ); |
637 | + | |
638 | + | for (j = 0; j < 3; j++) |
639 | + | rab[j] = posA[j] - posB[j]; |
640 | + | |
641 | + | info->wrapVector( rab ); |
642 | + | |
643 | rma = 1.0 / atoms[a]->getMass(); | |
644 | rmb = 1.0 / atoms[b]->getMass(); | |
645 | ||
646 | < | rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
646 | > | rvab = rab[0] * vxab + rab[1] * vyab + rab[2] * vzab; |
647 | ||
648 | < | gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
648 | > | gab = -rvab / ( ( rma + rmb ) * constrainedDsqr[i] ); |
649 | ||
650 | if (fabs(gab) > tol) { | |
651 | ||
652 | < | dx = rxab * gab; |
653 | < | dy = ryab * gab; |
654 | < | dz = rzab * gab; |
655 | < | |
656 | < | vel[3*a+0] += rma * dx; |
657 | < | vel[3*a+1] += rma * dy; |
658 | < | vel[3*a+2] += rma * dz; |
652 | > | dx = rab[0] * gab; |
653 | > | dy = rab[1] * gab; |
654 | > | dz = rab[2] * gab; |
655 | > | |
656 | > | velA[0] += rma * dx; |
657 | > | velA[1] += rma * dy; |
658 | > | velA[2] += rma * dz; |
659 | ||
660 | < | vel[3*b+0] -= rmb * dx; |
661 | < | vel[3*b+1] -= rmb * dy; |
662 | < | vel[3*b+2] -= rmb * dz; |
660 | > | atoms[a]->setVel( velA ); |
661 | > | |
662 | > | velB[0] -= rmb * dx; |
663 | > | velB[1] -= rmb * dy; |
664 | > | velB[2] -= rmb * dz; |
665 | > | |
666 | > | atoms[b]->setVel( velB ); |
667 | ||
668 | moving[a] = 1; | |
669 | moving[b] = 1; | |
# | Line 626 | Line 679 | void Integrator::constrainB( void ){ | |
679 | ||
680 | iteration++; | |
681 | } | |
682 | < | |
682 | > | |
683 | if( !done ){ | |
684 | ||
685 | ||
686 | < | sprintf( painCae.errMsg, |
686 | > | sprintf( painCave.errMsg, |
687 | "Constraint failure in constrainB, too many iterations: %d\n", | |
688 | < | iterations ); |
688 | > | iteration ); |
689 | painCave.isFatal = 1; | |
690 | simError(); | |
691 | } | |
692 | ||
693 | } | |
694 | ||
642 | – | |
643 | – | |
644 | – | |
645 | – | |
646 | – | |
647 | – | |
695 | void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], | |
696 | double A[3][3] ){ | |
697 | ||
# | Line 713 | Line 760 | void Integrator::rotate( int axes1, int axes2, double | |
760 | // A[][] = A[][] * transpose(rot[][]) | |
761 | ||
762 | ||
763 | < | // NOte for as yet unknown reason, we are setting the performing the |
763 | > | // NOte for as yet unknown reason, we are performing the |
764 | // calculation as: | |
765 | // transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) | |
766 |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |