1 |
#include <iostream> |
2 |
#include <cstdlib> |
3 |
|
4 |
#ifdef IS_MPI |
5 |
#include "mpiSimulation.hpp" |
6 |
#include <unistd.h> |
7 |
#endif //is_mpi |
8 |
|
9 |
#include "Integrator.hpp" |
10 |
#include "simError.h" |
11 |
|
12 |
|
13 |
Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ |
14 |
|
15 |
info = theInfo; |
16 |
myFF = the_ff; |
17 |
isFirst = 1; |
18 |
|
19 |
molecules = info->molecules; |
20 |
nMols = info->n_mol; |
21 |
|
22 |
// give a little love back to the SimInfo object |
23 |
|
24 |
if( info->the_integrator != NULL ) delete info->the_integrator; |
25 |
info->the_integrator = this; |
26 |
|
27 |
nAtoms = info->n_atoms; |
28 |
|
29 |
// check for constraints |
30 |
|
31 |
constrainedA = NULL; |
32 |
constrainedB = NULL; |
33 |
constrainedDsqr = NULL; |
34 |
moving = NULL; |
35 |
moved = NULL; |
36 |
prePos = NULL; |
37 |
|
38 |
nConstrained = 0; |
39 |
|
40 |
checkConstraints(); |
41 |
} |
42 |
|
43 |
Integrator::~Integrator() { |
44 |
|
45 |
if( nConstrained ){ |
46 |
delete[] constrainedA; |
47 |
delete[] constrainedB; |
48 |
delete[] constrainedDsqr; |
49 |
delete[] moving; |
50 |
delete[] moved; |
51 |
delete[] prePos; |
52 |
k |
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} |
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|
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} |
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|
57 |
void Integrator::checkConstraints( void ){ |
58 |
|
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|
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isConstrained = 0; |
61 |
|
62 |
Constraint *temp_con; |
63 |
Constraint *dummy_plug; |
64 |
temp_con = new Constraint[info->n_SRI]; |
65 |
nConstrained = 0; |
66 |
int constrained = 0; |
67 |
|
68 |
SRI** theArray; |
69 |
for(int i = 0; i < nMols; i++){ |
70 |
|
71 |
theArray = (SRI**) molecules[i].getMyBonds(); |
72 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
73 |
|
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constrained = theArray[j]->is_constrained(); |
75 |
|
76 |
if(constrained){ |
77 |
|
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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() ); |
81 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
82 |
|
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyBends(); |
89 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
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|
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constrained = theArray[j]->is_constrained(); |
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|
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if(constrained){ |
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|
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dummy_plug = theArray[j]->get_constraint(); |
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temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
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temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
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temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
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|
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nConstrained++; |
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constrained = 0; |
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} |
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} |
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|
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theArray = (SRI**) molecules[i].getMyTorsions(); |
106 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
107 |
|
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constrained = theArray[j]->is_constrained(); |
109 |
|
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if(constrained){ |
111 |
|
112 |
dummy_plug = theArray[j]->get_constraint(); |
113 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
114 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
115 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
116 |
|
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nConstrained++; |
118 |
constrained = 0; |
119 |
} |
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} |
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} |
122 |
|
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if(nConstrained > 0){ |
124 |
|
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isConstrained = 1; |
126 |
|
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if(constrainedA != NULL ) delete[] constrainedA; |
128 |
if(constrainedB != NULL ) delete[] constrainedB; |
129 |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
130 |
|
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constrainedA = new int[nConstrained]; |
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constrainedB = new int[nConstrained]; |
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constrainedDsqr = new double[nConstrained]; |
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|
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for( int i = 0; i < nConstrained; i++){ |
136 |
|
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constrainedA[i] = temp_con[i].get_a(); |
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constrainedB[i] = temp_con[i].get_b(); |
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constrainedDsqr[i] = temp_con[i].get_dsqr(); |
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} |
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|
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|
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// save oldAtoms to check for lode balanceing later on. |
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|
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oldAtoms = nAtoms; |
146 |
|
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moving = new int[nAtoms]; |
148 |
moved = new int[nAtoms]; |
149 |
|
150 |
prePos = new double[nAtoms*3]; |
151 |
} |
152 |
|
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delete[] temp_con; |
154 |
} |
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|
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|
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void Integrator::integrate( void ){ |
158 |
|
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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 |
165 |
|
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double vx, vy, vz; // the velocities |
167 |
double vx2, vy2, vz2; // the square of the velocities |
168 |
double rx, ry, rz; // the postitions |
169 |
|
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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; |
178 |
double runTime = info->run_time; |
179 |
double sampleTime = info->sampleTime; |
180 |
double statusTime = info->statusTime; |
181 |
double thermalTime = info->thermalTime; |
182 |
|
183 |
double currSample; |
184 |
double currThermal; |
185 |
double currStatus; |
186 |
double currTime; |
187 |
|
188 |
int calcPot, calcStress; |
189 |
int isError; |
190 |
|
191 |
tStats = new Thermo( info ); |
192 |
e_out = new StatWriter( info ); |
193 |
dump_out = new DumpWriter( info ); |
194 |
|
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Atom** atoms = info->atoms; |
196 |
DirectionalAtom* dAtom; |
197 |
dt2 = 0.5 * dt; |
198 |
|
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// initialize the forces before the first step |
200 |
|
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myFF->doForces(1,1); |
202 |
|
203 |
if( info->setTemp ){ |
204 |
|
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tStats->velocitize(); |
206 |
} |
207 |
|
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dump_out->writeDump( 0.0 ); |
209 |
e_out->writeStat( 0.0 ); |
210 |
|
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calcPot = 0; |
212 |
calcStress = 0; |
213 |
currSample = sampleTime; |
214 |
currThermal = thermalTime; |
215 |
currStatus = statusTime; |
216 |
currTime = 0.0;; |
217 |
|
218 |
while( currTime < runTime ){ |
219 |
|
220 |
if( (currTime+dt) >= currStatus ){ |
221 |
calcPot = 1; |
222 |
calcStress = 1; |
223 |
} |
224 |
|
225 |
integrateStep( calcPot, calcStress ); |
226 |
|
227 |
currTime += dt; |
228 |
|
229 |
if( info->setTemp ){ |
230 |
if( currTime >= currThermal ){ |
231 |
tStats->velocitize(); |
232 |
currThermal += thermalTime; |
233 |
} |
234 |
} |
235 |
|
236 |
if( currTime >= currSample ){ |
237 |
dump_out->writeDump( currTime ); |
238 |
currSample += sampleTime; |
239 |
} |
240 |
|
241 |
if( currTime >= currStatus ){ |
242 |
e_out->writeStat( time * dt ); |
243 |
calcPot = 0; |
244 |
calcStress = 0; |
245 |
currStatus += statusTime; |
246 |
} |
247 |
} |
248 |
|
249 |
dump_out->writeFinal(); |
250 |
|
251 |
delete dump_out; |
252 |
delete e_out; |
253 |
} |
254 |
|
255 |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
256 |
|
257 |
// Position full step, and velocity half step |
258 |
|
259 |
preMove(); |
260 |
moveA(); |
261 |
if( nConstrained ) constrainA(); |
262 |
|
263 |
// calc forces |
264 |
|
265 |
myFF->doForces(calcPot,calcStress); |
266 |
|
267 |
// finish the velocity half step |
268 |
|
269 |
moveB(); |
270 |
if( nConstrained ) constrainB(); |
271 |
|
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} |
273 |
|
274 |
|
275 |
void Integrator::moveA( void ){ |
276 |
|
277 |
int i,j,k; |
278 |
int atomIndex, aMatIndex; |
279 |
DirectionalAtom* dAtom; |
280 |
double Tb[3]; |
281 |
double ji[3]; |
282 |
|
283 |
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; |
290 |
|
291 |
// position whole step |
292 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
293 |
pos[j] += dt * vel[j]; |
294 |
|
295 |
|
296 |
if( atoms[i]->isDirectional() ){ |
297 |
|
298 |
dAtom = (DirectionalAtom *)atoms[i]; |
299 |
|
300 |
// get and convert the torque to body frame |
301 |
|
302 |
Tb[0] = dAtom->getTx(); |
303 |
Tb[1] = dAtom->getTy(); |
304 |
Tb[2] = dAtom->getTz(); |
305 |
|
306 |
dAtom->lab2Body( Tb ); |
307 |
|
308 |
// get the angular momentum, and propagate a half step |
309 |
|
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 |
|
314 |
// use the angular velocities to propagate the rotation matrix a |
315 |
// full time step |
316 |
|
317 |
// rotate about the x-axis |
318 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
319 |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
320 |
|
321 |
// rotate about the y-axis |
322 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
323 |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
324 |
|
325 |
// rotate about the z-axis |
326 |
angle = dt * ji[2] / dAtom->getIzz(); |
327 |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
328 |
|
329 |
// rotate about the y-axis |
330 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
331 |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
332 |
|
333 |
// rotate about the x-axis |
334 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
335 |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
336 |
|
337 |
dAtom->setJx( ji[0] ); |
338 |
dAtom->setJy( ji[1] ); |
339 |
dAtom->setJz( ji[2] ); |
340 |
} |
341 |
|
342 |
} |
343 |
} |
344 |
|
345 |
|
346 |
void Integrator::moveB( void ){ |
347 |
int i,j,k; |
348 |
int atomIndex; |
349 |
DirectionalAtom* dAtom; |
350 |
double Tb[3]; |
351 |
double ji[3]; |
352 |
|
353 |
for( i=0; i<nAtoms; i++ ){ |
354 |
atomIndex = i * 3; |
355 |
|
356 |
// velocity half step |
357 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
358 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
359 |
|
360 |
if( atoms[i]->isDirectional() ){ |
361 |
|
362 |
dAtom = (DirectionalAtom *)atoms[i]; |
363 |
|
364 |
// get and convert the torque to body frame |
365 |
|
366 |
Tb[0] = dAtom->getTx(); |
367 |
Tb[1] = dAtom->getTy(); |
368 |
Tb[2] = dAtom->getTz(); |
369 |
|
370 |
dAtom->lab2Body( Tb ); |
371 |
|
372 |
// get the angular momentum, and complete the angular momentum |
373 |
// 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] ); |
386 |
} |
387 |
} |
388 |
|
389 |
} |
390 |
|
391 |
void Integrator::preMove( void ){ |
392 |
int i; |
393 |
|
394 |
if( nConstrained ){ |
395 |
if( oldAtoms != nAtoms ){ |
396 |
|
397 |
// save oldAtoms to check for lode balanceing later on. |
398 |
|
399 |
oldAtoms = nAtoms; |
400 |
|
401 |
delete[] moving; |
402 |
delete[] moved; |
403 |
delete[] oldPos; |
404 |
|
405 |
moving = new int[nAtoms]; |
406 |
moved = new int[nAtoms]; |
407 |
|
408 |
oldPos = new double[nAtoms*3]; |
409 |
} |
410 |
|
411 |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
412 |
} |
413 |
} |
414 |
|
415 |
void Integrator::constrainA(){ |
416 |
|
417 |
int i,j,k; |
418 |
int done; |
419 |
double pxab, pyab, pzab; |
420 |
double rxab, ryab, rzab; |
421 |
int a, b; |
422 |
double rma, rmb; |
423 |
double dx, dy, dz; |
424 |
double rabsq, pabsq, rpabsq; |
425 |
double diffsq; |
426 |
double gab; |
427 |
int iteration; |
428 |
|
429 |
|
430 |
|
431 |
for( i=0; i<nAtoms; i++){ |
432 |
|
433 |
moving[i] = 0; |
434 |
moved[i] = 1; |
435 |
} |
436 |
|
437 |
|
438 |
iteration = 0; |
439 |
done = 0; |
440 |
while( !done && (iteration < maxIteration )){ |
441 |
|
442 |
done = 1; |
443 |
for(i=0; i<nConstrained; i++){ |
444 |
|
445 |
a = constrainedA[i]; |
446 |
b = constrainedB[i]; |
447 |
|
448 |
if( moved[a] || moved[b] ){ |
449 |
|
450 |
pxab = pos[3*a+0] - pos[3*b+0]; |
451 |
pyab = pos[3*a+1] - pos[3*b+1]; |
452 |
pzab = pos[3*a+2] - pos[3*b+2]; |
453 |
|
454 |
//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; |
465 |
|
466 |
// the original rattle code from alan tidesley |
467 |
if (fabs(diffsq) > tol*rabsq*2) { |
468 |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
469 |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
470 |
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); |
478 |
|
479 |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
480 |
rpabsq = rpab * rpab; |
481 |
|
482 |
|
483 |
if (rpabsq < (rabsq * -diffsq)){ |
484 |
#ifdef IS_MPI |
485 |
a = atoms[a]->getGlobalIndex(); |
486 |
b = atoms[b]->getGlobalIndex(); |
487 |
#endif //is_mpi |
488 |
sprintf( painCave.errMsg, |
489 |
"Constraint failure in constrainA at atom %d and %d\n.", |
490 |
a, b ); |
491 |
painCave.isFatal = 1; |
492 |
simError(); |
493 |
} |
494 |
|
495 |
rma = 1.0 / atoms[a]->getMass(); |
496 |
rmb = 1.0 / atoms[b]->getMass(); |
497 |
|
498 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
499 |
dx = rxab * gab; |
500 |
dy = ryab * gab; |
501 |
dz = rzab * gab; |
502 |
|
503 |
pos[3*a+0] += rma * dx; |
504 |
pos[3*a+1] += rma * dy; |
505 |
pos[3*a+2] += rma * dz; |
506 |
|
507 |
pos[3*b+0] -= rmb * dx; |
508 |
pos[3*b+1] -= rmb * dy; |
509 |
pos[3*b+2] -= rmb * dz; |
510 |
|
511 |
dx = dx / dt; |
512 |
dy = dy / dt; |
513 |
dz = dz / dt; |
514 |
|
515 |
vel[3*a+0] += rma * dx; |
516 |
vel[3*a+1] += rma * dy; |
517 |
vel[3*a+2] += rma * dz; |
518 |
|
519 |
vel[3*b+0] -= rmb * dx; |
520 |
vel[3*b+1] -= rmb * dy; |
521 |
vel[3*b+2] -= rmb * dz; |
522 |
|
523 |
moving[a] = 1; |
524 |
moving[b] = 1; |
525 |
done = 0; |
526 |
} |
527 |
} |
528 |
} |
529 |
|
530 |
for(i=0; i<nAtoms; i++){ |
531 |
|
532 |
moved[i] = moving[i]; |
533 |
moving[i] = 0; |
534 |
} |
535 |
|
536 |
iteration++; |
537 |
} |
538 |
|
539 |
if( !done ){ |
540 |
|
541 |
sprintf( painCae.errMsg, |
542 |
"Constraint failure in constrainA, too many iterations: %d\n", |
543 |
iterations ); |
544 |
painCave.isFatal = 1; |
545 |
simError(); |
546 |
} |
547 |
|
548 |
} |
549 |
|
550 |
void Integrator::constrainB( void ){ |
551 |
|
552 |
int i,j,k; |
553 |
int done; |
554 |
double vxab, vyab, vzab; |
555 |
double rxab, ryab, rzab; |
556 |
int a, b; |
557 |
double rma, rmb; |
558 |
double dx, dy, dz; |
559 |
double rabsq, pabsq, rvab; |
560 |
double diffsq; |
561 |
double gab; |
562 |
int iteration; |
563 |
|
564 |
for(i=0; i<nAtom; i++){ |
565 |
moving[i] = 0; |
566 |
moved[i] = 1; |
567 |
} |
568 |
|
569 |
done = 0; |
570 |
while( !done && (iteration < maxIteration ) ){ |
571 |
|
572 |
for(i=0; i<nConstrained; i++){ |
573 |
|
574 |
a = constrainedA[i]; |
575 |
b = constrainedB[i]; |
576 |
|
577 |
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]; |
582 |
|
583 |
rxab = pos[3*a+0] - pos[3*b+0];q |
584 |
ryab = pos[3*a+1] - pos[3*b+1]; |
585 |
rzab = pos[3*a+2] - pos[3*b+2]; |
586 |
|
587 |
rxab = rxab - info->box_x * copysign(1, rxab) |
588 |
* 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); |
593 |
|
594 |
rma = 1.0 / atoms[a]->getMass(); |
595 |
rmb = 1.0 / atoms[b]->getMass(); |
596 |
|
597 |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
598 |
|
599 |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
600 |
|
601 |
if (fabs(gab) > tol) { |
602 |
|
603 |
dx = rxab * gab; |
604 |
dy = ryab * gab; |
605 |
dz = rzab * gab; |
606 |
|
607 |
vel[3*a+0] += rma * dx; |
608 |
vel[3*a+1] += rma * dy; |
609 |
vel[3*a+2] += rma * dz; |
610 |
|
611 |
vel[3*b+0] -= rmb * dx; |
612 |
vel[3*b+1] -= rmb * dy; |
613 |
vel[3*b+2] -= rmb * dz; |
614 |
|
615 |
moving[a] = 1; |
616 |
moving[b] = 1; |
617 |
done = 0; |
618 |
} |
619 |
} |
620 |
} |
621 |
|
622 |
for(i=0; i<nAtoms; i++){ |
623 |
moved[i] = moving[i]; |
624 |
moving[i] = 0; |
625 |
} |
626 |
|
627 |
iteration++; |
628 |
} |
629 |
|
630 |
if( !done ){ |
631 |
|
632 |
|
633 |
sprintf( painCae.errMsg, |
634 |
"Constraint failure in constrainB, too many iterations: %d\n", |
635 |
iterations ); |
636 |
painCave.isFatal = 1; |
637 |
simError(); |
638 |
} |
639 |
|
640 |
} |
641 |
|
642 |
|
643 |
|
644 |
|
645 |
|
646 |
|
647 |
|
648 |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
649 |
double A[3][3] ){ |
650 |
|
651 |
int i,j,k; |
652 |
double sinAngle; |
653 |
double cosAngle; |
654 |
double angleSqr; |
655 |
double angleSqrOver4; |
656 |
double top, bottom; |
657 |
double rot[3][3]; |
658 |
double tempA[3][3]; |
659 |
double tempJ[3]; |
660 |
|
661 |
// initialize the tempA |
662 |
|
663 |
for(i=0; i<3; i++){ |
664 |
for(j=0; j<3; j++){ |
665 |
tempA[j][i] = A[i][j]; |
666 |
} |
667 |
} |
668 |
|
669 |
// initialize the tempJ |
670 |
|
671 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
672 |
|
673 |
// initalize rot as a unit matrix |
674 |
|
675 |
rot[0][0] = 1.0; |
676 |
rot[0][1] = 0.0; |
677 |
rot[0][2] = 0.0; |
678 |
|
679 |
rot[1][0] = 0.0; |
680 |
rot[1][1] = 1.0; |
681 |
rot[1][2] = 0.0; |
682 |
|
683 |
rot[2][0] = 0.0; |
684 |
rot[2][1] = 0.0; |
685 |
rot[2][2] = 1.0; |
686 |
|
687 |
// use a small angle aproximation for sin and cosine |
688 |
|
689 |
angleSqr = angle * angle; |
690 |
angleSqrOver4 = angleSqr / 4.0; |
691 |
top = 1.0 - angleSqrOver4; |
692 |
bottom = 1.0 + angleSqrOver4; |
693 |
|
694 |
cosAngle = top / bottom; |
695 |
sinAngle = angle / bottom; |
696 |
|
697 |
rot[axes1][axes1] = cosAngle; |
698 |
rot[axes2][axes2] = cosAngle; |
699 |
|
700 |
rot[axes1][axes2] = sinAngle; |
701 |
rot[axes2][axes1] = -sinAngle; |
702 |
|
703 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
704 |
|
705 |
for(i=0; i<3; i++){ |
706 |
ji[i] = 0.0; |
707 |
for(k=0; k<3; k++){ |
708 |
ji[i] += rot[i][k] * tempJ[k]; |
709 |
} |
710 |
} |
711 |
|
712 |
// rotate the Rotation matrix acording to: |
713 |
// A[][] = A[][] * transpose(rot[][]) |
714 |
|
715 |
|
716 |
// NOte for as yet unknown reason, we are setting the performing the |
717 |
// calculation as: |
718 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
719 |
|
720 |
for(i=0; i<3; i++){ |
721 |
for(j=0; j<3; j++){ |
722 |
A[j][i] = 0.0; |
723 |
for(k=0; k<3; k++){ |
724 |
A[j][i] += tempA[i][k] * rot[j][k]; |
725 |
} |
726 |
} |
727 |
} |
728 |
} |