26 |
|
SimInfo::SimInfo(){ |
27 |
|
excludes = NULL; |
28 |
|
n_constraints = 0; |
29 |
+ |
nZconstraints = 0; |
30 |
|
n_oriented = 0; |
31 |
|
n_dipoles = 0; |
32 |
|
ndf = 0; |
48 |
|
haveOrigEcr = 0; |
49 |
|
boxIsInit = 0; |
50 |
|
|
51 |
+ |
resetTime = 1e99; |
52 |
|
|
53 |
|
|
54 |
|
usePBC = 0; |
280 |
|
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
281 |
|
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
282 |
|
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
283 |
+ |
} |
284 |
+ |
|
285 |
+ |
|
286 |
+ |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
287 |
+ |
|
288 |
+ |
out[0] = a[1] * b[2] - a[2] * b[1]; |
289 |
+ |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
290 |
+ |
out[2] = a[0] * b[1] - a[1] * b[0]; |
291 |
+ |
|
292 |
+ |
} |
293 |
+ |
|
294 |
+ |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
295 |
+ |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
296 |
|
} |
297 |
|
|
298 |
+ |
double SimInfo::length3(double a[3]){ |
299 |
+ |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
300 |
+ |
} |
301 |
+ |
|
302 |
|
void SimInfo::calcBoxL( void ){ |
303 |
|
|
304 |
|
double dx, dy, dz, dsq; |
313 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
314 |
|
dsq = dx*dx + dy*dy + dz*dz; |
315 |
|
boxL[0] = sqrt( dsq ); |
316 |
< |
maxCutoff = 0.5 * boxL[0]; |
316 |
> |
//maxCutoff = 0.5 * boxL[0]; |
317 |
|
|
318 |
|
// boxLy |
319 |
|
|
320 |
|
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
321 |
|
dsq = dx*dx + dy*dy + dz*dz; |
322 |
|
boxL[1] = sqrt( dsq ); |
323 |
< |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
323 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
324 |
|
|
325 |
+ |
|
326 |
|
// boxLz |
327 |
|
|
328 |
|
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
329 |
|
dsq = dx*dx + dy*dy + dz*dz; |
330 |
|
boxL[2] = sqrt( dsq ); |
331 |
< |
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
331 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
332 |
> |
|
333 |
> |
//calculate the max cutoff |
334 |
> |
maxCutoff = calcMaxCutOff(); |
335 |
|
|
336 |
|
checkCutOffs(); |
337 |
|
|
338 |
|
} |
339 |
+ |
|
340 |
+ |
|
341 |
+ |
double SimInfo::calcMaxCutOff(){ |
342 |
+ |
|
343 |
+ |
double ri[3], rj[3], rk[3]; |
344 |
+ |
double rij[3], rjk[3], rki[3]; |
345 |
+ |
double minDist; |
346 |
+ |
|
347 |
+ |
ri[0] = Hmat[0][0]; |
348 |
+ |
ri[1] = Hmat[1][0]; |
349 |
+ |
ri[2] = Hmat[2][0]; |
350 |
+ |
|
351 |
+ |
rj[0] = Hmat[0][1]; |
352 |
+ |
rj[1] = Hmat[1][1]; |
353 |
+ |
rj[2] = Hmat[2][1]; |
354 |
+ |
|
355 |
+ |
rk[0] = Hmat[0][2]; |
356 |
+ |
rk[1] = Hmat[1][2]; |
357 |
+ |
rk[2] = Hmat[2][2]; |
358 |
+ |
|
359 |
+ |
crossProduct3(ri,rj, rij); |
360 |
+ |
distXY = dotProduct3(rk,rij) / length3(rij); |
361 |
|
|
362 |
+ |
crossProduct3(rj,rk, rjk); |
363 |
+ |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
364 |
|
|
365 |
+ |
crossProduct3(rk,ri, rki); |
366 |
+ |
distZX = dotProduct3(rj,rki) / length3(rki); |
367 |
+ |
|
368 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
369 |
+ |
return minDist/2; |
370 |
+ |
|
371 |
+ |
} |
372 |
+ |
|
373 |
|
void SimInfo::wrapVector( double thePos[3] ){ |
374 |
|
|
375 |
|
int i, j, k; |
439 |
|
|
440 |
|
return ndfRaw; |
441 |
|
} |
442 |
< |
|
442 |
> |
|
443 |
> |
int SimInfo::getNDFtranslational() { |
444 |
> |
int ndfTrans_local, ndfTrans; |
445 |
> |
|
446 |
> |
ndfTrans_local = 3 * n_atoms - n_constraints; |
447 |
> |
|
448 |
> |
#ifdef IS_MPI |
449 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
450 |
> |
#else |
451 |
> |
ndfTrans = ndfTrans_local; |
452 |
> |
#endif |
453 |
> |
|
454 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
455 |
> |
|
456 |
> |
return ndfTrans; |
457 |
> |
} |
458 |
> |
|
459 |
|
void SimInfo::refreshSim(){ |
460 |
|
|
461 |
|
simtype fInfo; |
511 |
|
|
512 |
|
this->ndf = this->getNDF(); |
513 |
|
this->ndfRaw = this->getNDFraw(); |
514 |
< |
|
514 |
> |
this->ndfTrans = this->getNDFtranslational(); |
515 |
|
} |
516 |
|
|
517 |
|
|
547 |
|
void SimInfo::checkCutOffs( void ){ |
548 |
|
|
549 |
|
int cutChanged = 0; |
550 |
< |
|
480 |
< |
|
481 |
< |
|
550 |
> |
|
551 |
|
if( boxIsInit ){ |
552 |
|
|
553 |
|
//we need to check cutOffs against the box |
554 |
< |
|
554 |
> |
|
555 |
> |
//detect the change of rCut |
556 |
|
if(( maxCutoff > rCut )&&(usePBC)){ |
557 |
|
if( rCut < origRcut ){ |
558 |
< |
rCut = origRcut; |
559 |
< |
if (rCut > maxCutoff) rCut = maxCutoff; |
560 |
< |
|
561 |
< |
sprintf( painCave.errMsg, |
562 |
< |
"New Box size is setting the long range cutoff radius " |
563 |
< |
"to %lf\n", |
564 |
< |
rCut ); |
565 |
< |
painCave.isFatal = 0; |
566 |
< |
simError(); |
558 |
> |
rCut = origRcut; |
559 |
> |
|
560 |
> |
if (rCut > maxCutoff) |
561 |
> |
rCut = maxCutoff; |
562 |
> |
|
563 |
> |
sprintf( painCave.errMsg, |
564 |
> |
"New Box size is setting the long range cutoff radius " |
565 |
> |
"to %lf at time %lf\n", |
566 |
> |
rCut, currentTime ); |
567 |
> |
painCave.isFatal = 0; |
568 |
> |
simError(); |
569 |
|
} |
570 |
|
} |
571 |
< |
|
500 |
< |
if( maxCutoff > ecr ){ |
501 |
< |
if( ecr < origEcr ){ |
502 |
< |
rCut = origEcr; |
503 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
504 |
< |
|
505 |
< |
sprintf( painCave.errMsg, |
506 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
507 |
< |
"to %lf\n", |
508 |
< |
ecr ); |
509 |
< |
painCave.isFatal = 0; |
510 |
< |
simError(); |
511 |
< |
} |
512 |
< |
} |
513 |
< |
|
514 |
< |
|
515 |
< |
if ((rCut > maxCutoff)&&(usePBC)) { |
571 |
> |
else if ((rCut > maxCutoff)&&(usePBC)) { |
572 |
|
sprintf( painCave.errMsg, |
573 |
|
"New Box size is setting the long range cutoff radius " |
574 |
< |
"to %lf\n", |
575 |
< |
maxCutoff ); |
574 |
> |
"to %lf at time %lf\n", |
575 |
> |
maxCutoff, currentTime ); |
576 |
|
painCave.isFatal = 0; |
577 |
|
simError(); |
578 |
|
rCut = maxCutoff; |
579 |
|
} |
580 |
|
|
581 |
< |
if( ecr > maxCutoff){ |
581 |
> |
|
582 |
> |
//detect the change of ecr |
583 |
> |
if( maxCutoff > ecr ){ |
584 |
> |
if( ecr < origEcr ){ |
585 |
> |
ecr = origEcr; |
586 |
> |
if (ecr > maxCutoff) ecr = maxCutoff; |
587 |
> |
|
588 |
> |
sprintf( painCave.errMsg, |
589 |
> |
"New Box size is setting the electrostaticCutoffRadius " |
590 |
> |
"to %lf at time %lf\n", |
591 |
> |
ecr, currentTime ); |
592 |
> |
painCave.isFatal = 0; |
593 |
> |
simError(); |
594 |
> |
} |
595 |
> |
} |
596 |
> |
else if( ecr > maxCutoff){ |
597 |
|
sprintf( painCave.errMsg, |
598 |
|
"New Box size is setting the electrostaticCutoffRadius " |
599 |
< |
"to %lf\n", |
600 |
< |
maxCutoff ); |
599 |
> |
"to %lf at time %lf\n", |
600 |
> |
maxCutoff, currentTime ); |
601 |
|
painCave.isFatal = 0; |
602 |
|
simError(); |
603 |
|
ecr = maxCutoff; |
604 |
|
} |
605 |
|
|
606 |
+ |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
607 |
|
|
608 |
< |
} |
537 |
< |
|
538 |
< |
|
539 |
< |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
540 |
< |
|
541 |
< |
// rlist is the 1.0 plus max( rcut, ecr ) |
542 |
< |
|
543 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
544 |
< |
|
545 |
< |
if( cutChanged ){ |
608 |
> |
// rlist is the 1.0 plus max( rcut, ecr ) |
609 |
|
|
610 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
610 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
611 |
> |
|
612 |
> |
if( cutChanged ){ |
613 |
> |
|
614 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
615 |
> |
} |
616 |
> |
|
617 |
> |
oldEcr = ecr; |
618 |
> |
oldRcut = rCut; |
619 |
> |
|
620 |
> |
} else { |
621 |
> |
// initialize this stuff before using it, OK? |
622 |
> |
sprintf( painCave.errMsg, |
623 |
> |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
624 |
> |
painCave.isFatal = 1; |
625 |
> |
simError(); |
626 |
|
} |
627 |
< |
|
550 |
< |
oldEcr = ecr; |
551 |
< |
oldRcut = rCut; |
627 |
> |
|
628 |
|
} |
629 |
|
|
630 |
|
void SimInfo::addProperty(GenericData* prop){ |
674 |
|
return result; |
675 |
|
} |
676 |
|
|
677 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
678 |
+ |
double trace; |
679 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
680 |
|
|
681 |
+ |
return trace; |
682 |
+ |
} |