# | 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 | > | delete[] oldPos; |
53 | } | |
54 | ||
55 | } | |
# | Line 71 | 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 81 | Line 82 | void Integrator::checkConstraints( void ){ | |
82 | ||
83 | nConstrained++; | |
84 | constrained = 0; | |
85 | < | } |
85 | > | } |
86 | } | |
87 | ||
88 | theArray = (SRI**) molecules[i].getMyBends(); | |
# | Line 136 | 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 146 | 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 156 | Line 158 | void Integrator::integrate( void ){ | |
158 | void Integrator::integrate( void ){ | |
159 | ||
160 | int i, j; // loop counters | |
159 | – | double kE = 0.0; // the kinetic energy |
160 | – | double rot_kE; |
161 | – | double trans_kE; |
162 | – | int tl; // the time loop conter |
163 | – | double dt2; // half the dt |
161 | ||
165 | – | double vx, vy, vz; // the velocities |
166 | – | double vx2, vy2, vz2; // the square of the velocities |
167 | – | double rx, ry, rz; // the postitions |
168 | – | |
169 | – | double ji[3]; // the body frame angular momentum |
170 | – | double jx2, jy2, jz2; // the square of the angular momentums |
171 | – | double Tb[3]; // torque in the body frame |
172 | – | double angle; // the angle through which to rotate the rotation matrix |
173 | – | double A[3][3]; // the rotation matrix |
174 | – | double press[9]; |
175 | – | |
176 | – | double dt = info->dt; |
162 | double runTime = info->run_time; | |
163 | double sampleTime = info->sampleTime; | |
164 | double statusTime = info->statusTime; | |
# | Line 182 | Line 167 | void Integrator::integrate( void ){ | |
167 | double currSample; | |
168 | double currThermal; | |
169 | double currStatus; | |
185 | – | 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 204 | Line 190 | void Integrator::integrate( void ){ | |
190 | tStats->velocitize(); | |
191 | } | |
192 | ||
207 | – | dump_out->writeDump( 0.0 ); |
208 | – | e_out->writeStat( 0.0 ); |
209 | – | |
193 | calcPot = 0; | |
194 | calcStress = 0; | |
195 | currSample = sampleTime; | |
196 | currThermal = thermalTime; | |
197 | currStatus = statusTime; | |
215 | – | currTime = 0.0;; |
198 | ||
199 | + | dumpOut->writeDump( info->getTime() ); |
200 | + | statOut->writeStat( info->getTime() ); |
201 | ||
202 | readyCheck(); | |
203 | ||
# | Line 223 | Line 207 | void Integrator::integrate( void ){ | |
207 | MPIcheckPoint(); | |
208 | #endif // is_mpi | |
209 | ||
210 | < | while( currTime < runTime ){ |
210 | > | while( info->getTime() < runTime ){ |
211 | ||
212 | < | if( (currTime+dt) >= currStatus ){ |
212 | > | if( (info->getTime()+dt) >= currStatus ){ |
213 | calcPot = 1; | |
214 | calcStress = 1; | |
215 | } | |
216 | < | |
216 | > | |
217 | integrateStep( calcPot, calcStress ); | |
218 | ||
219 | < | currTime += dt; |
219 | > | info->incrTime(dt); |
220 | ||
221 | if( info->setTemp ){ | |
222 | < | if( currTime >= currThermal ){ |
222 | > | if( info->getTime() >= currThermal ){ |
223 | tStats->velocitize(); | |
224 | currThermal += thermalTime; | |
225 | } | |
226 | } | |
227 | ||
228 | < | if( currTime >= currSample ){ |
229 | < | dump_out->writeDump( currTime ); |
228 | > | if( info->getTime() >= currSample ){ |
229 | > | dumpOut->writeDump( info->getTime() ); |
230 | currSample += sampleTime; | |
231 | } | |
232 | ||
233 | < | if( currTime >= currStatus ){ |
234 | < | e_out->writeStat( time * dt ); |
233 | > | if( info->getTime() >= currStatus ){ |
234 | > | statOut->writeStat( info->getTime() ); |
235 | calcPot = 0; | |
236 | calcStress = 0; | |
237 | currStatus += statusTime; | |
# | Line 261 | Line 245 | void Integrator::integrate( void ){ | |
245 | ||
246 | } | |
247 | ||
248 | < | dump_out->writeFinal(); |
248 | > | dumpOut->writeFinal(info->getTime()); |
249 | ||
250 | < | delete dump_out; |
251 | < | delete e_out; |
250 | > | delete dumpOut; |
251 | > | delete statOut; |
252 | } | |
253 | ||
254 | void Integrator::integrateStep( int calcPot, int calcStress ){ | |
255 | ||
256 | + | |
257 | + | |
258 | // Position full step, and velocity half step | |
259 | ||
260 | < | //preMove(); |
260 | > | preMove(); |
261 | moveA(); | |
262 | if( nConstrained ) constrainA(); | |
263 | ||
264 | + | |
265 | + | #ifdef IS_MPI |
266 | + | strcpy( checkPointMsg, "Succesful moveA\n" ); |
267 | + | MPIcheckPoint(); |
268 | + | #endif // is_mpi |
269 | + | |
270 | + | |
271 | // calc forces | |
272 | ||
273 | myFF->doForces(calcPot,calcStress); | |
274 | ||
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 | ||
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 | ||
294 | ||
295 | void Integrator::moveA( void ){ | |
296 | ||
297 | < | int i,j,k; |
293 | < | 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++ ){ | |
299 | – | atomIndex = i * 3; |
300 | – | aMatIndex = i * 9; |
301 | – | |
302 | – | // velocity half step |
303 | – | for( j=atomIndex; j<(atomIndex+3); j++ ) |
304 | – | vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
306 | ||
307 | < | // position whole step |
308 | < | for( j=atomIndex; j<(atomIndex+3); j++ ) |
307 | > | atoms[i]->getVel( vel ); |
308 | > | atoms[i]->getPos( pos ); |
309 | > | atoms[i]->getFrc( frc ); |
310 | > | |
311 | > | mass = atoms[i]->getMass(); |
312 | > | |
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 | < | |
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(); |
318 | < | Tb[1] = dAtom->getTy(); |
319 | < | Tb[2] = dAtom->getTz(); |
320 | < | |
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; |
363 | < | int atomIndex; |
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 |
372 | < | for( j=atomIndex; j<(atomIndex+3); j++ ) |
373 | < | 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(); |
382 | < | Tb[1] = dAtom->getTy(); |
383 | < | Tb[2] = dAtom->getTz(); |
384 | < | |
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 |
389 | < | |
390 | < | ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
391 | < | ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
392 | < | ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
393 | < | |
394 | < | jx2 = ji[0] * ji[0]; |
395 | < | jy2 = ji[1] * ji[1]; |
396 | < | jz2 = ji[2] * ji[2]; |
397 | < | |
398 | < | dAtom->setJx( ji[0] ); |
399 | < | dAtom->setJy( ji[1] ); |
400 | < | dAtom->setJz( ji[2] ); |
410 | > | |
411 | > | dAtom->setJ( ji ); |
412 | } | |
413 | } | |
403 | – | |
414 | } | |
415 | ||
416 | void Integrator::preMove( void ){ | |
417 | < | int i; |
417 | > | int i, j; |
418 | > | double pos[3]; |
419 | ||
420 | if( nConstrained ){ | |
421 | < | if( oldAtoms != nAtoms ){ |
422 | < | |
423 | < | // save oldAtoms to check for lode balanceing later on. |
424 | < | |
425 | < | oldAtoms = nAtoms; |
426 | < | |
427 | < | delete[] moving; |
428 | < | delete[] moved; |
429 | < | delete[] oldPos; |
419 | < | |
420 | < | moving = new int[nAtoms]; |
421 | < | moved = new int[nAtoms]; |
422 | < | |
423 | < | oldPos = new double[nAtoms*3]; |
421 | > | |
422 | > | for(i=0; i < nAtoms; i++) { |
423 | > | |
424 | > | atoms[i]->getPos( pos ); |
425 | > | |
426 | > | for (j = 0; j < 3; j++) { |
427 | > | oldPos[3*i + j] = pos[j]; |
428 | > | } |
429 | > | |
430 | } | |
431 | < | |
432 | < | for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
427 | < | } |
428 | < | } |
431 | > | } |
432 | > | } |
433 | ||
434 | void Integrator::constrainA(){ | |
435 | ||
436 | int i,j,k; | |
437 | int done; | |
438 | < | double pxab, pyab, pzab; |
439 | < | double rxab, ryab, rzab; |
440 | < | int a, b; |
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; | |
445 | + | double rpab; |
446 | double rabsq, pabsq, rpabsq; | |
447 | double diffsq; | |
448 | double gab; | |
449 | int iteration; | |
450 | ||
451 | < | |
445 | < | |
446 | < | for( i=0; i<nAtoms; i++){ |
447 | < | |
451 | > | for( i=0; i<nAtoms; i++){ |
452 | moving[i] = 0; | |
453 | moved[i] = 1; | |
454 | } | |
455 | < | |
452 | < | |
455 | > | |
456 | iteration = 0; | |
457 | done = 0; | |
458 | while( !done && (iteration < maxIteration )){ | |
# | Line 459 | Line 462 | void Integrator::constrainA(){ | |
462 | ||
463 | a = constrainedA[i]; | |
464 | b = constrainedB[i]; | |
465 | < | |
465 | > | |
466 | > | ax = (a*3) + 0; |
467 | > | ay = (a*3) + 1; |
468 | > | az = (a*3) + 2; |
469 | > | |
470 | > | bx = (b*3) + 0; |
471 | > | by = (b*3) + 1; |
472 | > | bz = (b*3) + 2; |
473 | > | |
474 | if( moved[a] || moved[b] ){ | |
475 | < | |
476 | < | pxab = pos[3*a+0] - pos[3*b+0]; |
477 | < | pyab = pos[3*a+1] - pos[3*b+1]; |
478 | < | pzab = pos[3*a+2] - pos[3*b+2]; |
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 |
483 | ||
484 | < | //periodic boundary condition |
470 | < | pxab = pxab - info->box_x * copysign(1, pxab) |
471 | < | * int(pxab / info->box_x + 0.5); |
472 | < | pyab = pyab - info->box_y * copysign(1, pyab) |
473 | < | * int(pyab / info->box_y + 0.5); |
474 | < | pzab = pzab - info->box_z * copysign(1, pzab) |
475 | < | * int(pzab / info->box_z + 0.5); |
476 | < | |
477 | < | pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
478 | < | rabsq = constraintedDsqr[i]; |
479 | < | diffsq = pabsq - rabsq; |
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[3*a+0] - oldPos[3*b+0]; |
494 | < | ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
495 | < | rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
486 | < | |
487 | < | rxab = rxab - info->box_x * copysign(1, rxab) |
488 | < | * int(rxab / info->box_x + 0.5); |
489 | < | ryab = ryab - info->box_y * copysign(1, ryab) |
490 | < | * int(ryab / info->box_y + 0.5); |
491 | < | rzab = rzab - info->box_z * copysign(1, rzab) |
492 | < | * int(rzab / info->box_z + 0.5); |
492 | > | if (fabs(diffsq) > (tol*rabsq*2)) { |
493 | > | rab[0] = oldPos[ax] - oldPos[bx]; |
494 | > | rab[1] = oldPos[ay] - oldPos[by]; |
495 | > | rab[2] = oldPos[az] - oldPos[bz]; |
496 | ||
497 | < | rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
497 | > | info->wrapVector( rab ); |
498 | > | |
499 | > | rpab = rab[0] * pab[0] + rab[1] * pab[1] + rab[2] * pab[2]; |
500 | > | |
501 | rpabsq = rpab * rpab; | |
502 | ||
503 | ||
504 | if (rpabsq < (rabsq * -diffsq)){ | |
505 | + | |
506 | #ifdef IS_MPI | |
507 | a = atoms[a]->getGlobalIndex(); | |
508 | b = atoms[b]->getGlobalIndex(); | |
509 | #endif //is_mpi | |
510 | sprintf( painCave.errMsg, | |
511 | < | "Constraint failure in constrainA at atom %d and %d\n.", |
511 | > | "Constraint failure in constrainA at atom %d and %d.\n", |
512 | a, b ); | |
513 | painCave.isFatal = 1; | |
514 | simError(); | |
# | Line 509 | Line 516 | void Integrator::constrainA(){ | |
516 | ||
517 | rma = 1.0 / atoms[a]->getMass(); | |
518 | rmb = 1.0 / atoms[b]->getMass(); | |
519 | < | |
519 | > | |
520 | gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); | |
514 | – | dx = rxab * gab; |
515 | – | dy = ryab * gab; |
516 | – | dz = rzab * gab; |
521 | ||
522 | < | pos[3*a+0] += rma * dx; |
523 | < | pos[3*a+1] += rma * dy; |
524 | < | pos[3*a+2] += rma * dz; |
522 | > | dx = rab[0] * gab; |
523 | > | dy = rab[1] * gab; |
524 | > | dz = rab[2] * gab; |
525 | ||
526 | < | pos[3*b+0] -= rmb * dx; |
527 | < | pos[3*b+1] -= rmb * dy; |
528 | < | pos[3*b+2] -= rmb * dz; |
526 | > | posA[0] += rma * dx; |
527 | > | posA[1] += rma * dy; |
528 | > | posA[2] += rma * dz; |
529 | ||
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[3*a+0] += rma * dx; |
531 | < | vel[3*a+1] += rma * dy; |
532 | < | vel[3*a+2] += rma * dz; |
542 | > | atoms[a]->getVel( velA ); |
543 | ||
544 | < | vel[3*b+0] -= rmb * dx; |
545 | < | vel[3*b+1] -= rmb * dy; |
546 | < | vel[3*b+2] -= 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; | |
# | Line 553 | Line 573 | void Integrator::constrainA(){ | |
573 | ||
574 | if( !done ){ | |
575 | ||
576 | < | sprintf( painCae.errMsg, |
576 | > | sprintf( painCave.errMsg, |
577 | "Constraint failure in constrainA, too many iterations: %d\n", | |
578 | < | iterations ); |
578 | > | iteration ); |
579 | painCave.isFatal = 1; | |
580 | simError(); | |
581 | } | |
# | Line 566 | Line 586 | void Integrator::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; |
593 | < | int a, b; |
592 | > | double rab[3]; |
593 | > | int a, b, ax, ay, az, bx, by, bz; |
594 | double rma, rmb; | |
595 | double dx, dy, dz; | |
596 | double rabsq, pabsq, rvab; | |
# | Line 576 | Line 598 | void Integrator::constrainB( void ){ | |
598 | double gab; | |
599 | int iteration; | |
600 | ||
601 | < | for(i=0; i<nAtom; i++){ |
601 | > | for(i=0; i<nAtoms; i++){ |
602 | moving[i] = 0; | |
603 | moved[i] = 1; | |
604 | } | |
605 | ||
606 | done = 0; | |
607 | + | iteration = 0; |
608 | while( !done && (iteration < maxIteration ) ){ | |
609 | ||
610 | + | done = 1; |
611 | + | |
612 | for(i=0; i<nConstrained; i++){ | |
613 | ||
614 | a = constrainedA[i]; | |
615 | b = constrainedB[i]; | |
616 | ||
617 | + | ax = (a*3) + 0; |
618 | + | ay = (a*3) + 1; |
619 | + | az = (a*3) + 2; |
620 | + | |
621 | + | bx = (b*3) + 0; |
622 | + | by = (b*3) + 1; |
623 | + | bz = (b*3) + 2; |
624 | + | |
625 | if( moved[a] || moved[b] ){ | |
593 | – | |
594 | – | vxab = vel[3*a+0] - vel[3*b+0]; |
595 | – | vyab = vel[3*a+1] - vel[3*b+1]; |
596 | – | vzab = vel[3*a+2] - vel[3*b+2]; |
626 | ||
627 | < | rxab = pos[3*a+0] - pos[3*b+0];q |
628 | < | ryab = pos[3*a+1] - pos[3*b+1]; |
629 | < | rzab = pos[3*a+2] - pos[3*b+2]; |
630 | < | |
631 | < | rxab = rxab - info->box_x * copysign(1, rxab) |
632 | < | * int(rxab / info->box_x + 0.5); |
604 | < | ryab = ryab - info->box_y * copysign(1, ryab) |
605 | < | * int(ryab / info->box_y + 0.5); |
606 | < | rzab = rzab - info->box_z * copysign(1, rzab) |
607 | < | * int(rzab / info->box_z + 0.5); |
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 | + | 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 ) * constraintsDsqr[i] ); |
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[3*a+0] += rma * dx; |
656 | < | vel[3*a+1] += rma * dy; |
657 | < | vel[3*a+2] += 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[3*b+0] -= rmb * dx; |
660 | < | vel[3*b+1] -= rmb * dy; |
661 | < | vel[3*b+2] -= 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; | |
# | Line 641 | Line 678 | void Integrator::constrainB( void ){ | |
678 | ||
679 | iteration++; | |
680 | } | |
681 | < | |
681 | > | |
682 | if( !done ){ | |
683 | ||
684 | ||
685 | < | sprintf( painCae.errMsg, |
685 | > | sprintf( painCave.errMsg, |
686 | "Constraint failure in constrainB, too many iterations: %d\n", | |
687 | < | iterations ); |
687 | > | iteration ); |
688 | painCave.isFatal = 1; | |
689 | simError(); | |
690 | } | |
691 | ||
692 | } | |
693 | ||
657 | – | |
658 | – | |
659 | – | |
660 | – | |
661 | – | |
662 | – | |
694 | void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], | |
695 | double A[3][3] ){ | |
696 | ||
# | Line 728 | Line 759 | void Integrator::rotate( int axes1, int axes2, double | |
759 | // A[][] = A[][] * transpose(rot[][]) | |
760 | ||
761 | ||
762 | < | // NOte for as yet unknown reason, we are setting the performing the |
762 | > | // NOte for as yet unknown reason, we are performing the |
763 | // calculation as: | |
764 | // transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) | |
765 |
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