| 48 |
|
haveOrigEcr = 0; |
| 49 |
|
boxIsInit = 0; |
| 50 |
|
|
| 51 |
+ |
resetTime = 1e99; |
| 52 |
|
|
| 53 |
|
|
| 54 |
|
usePBC = 0; |
| 94 |
|
|
| 95 |
|
void SimInfo::setBoxM( double theBox[3][3] ){ |
| 96 |
|
|
| 97 |
< |
int i, j, status; |
| 97 |
< |
double smallestBoxL, maxCutoff; |
| 97 |
> |
int i, j; |
| 98 |
|
double FortranHmat[9]; // to preserve compatibility with Fortran the |
| 99 |
|
// ordering in the array is as follows: |
| 100 |
|
// [ 0 3 6 ] |
| 279 |
|
<< "[ " << A[0] << ", " << A[1] << ", " << A[2] << " ]\n" |
| 280 |
|
<< "[ " << A[3] << ", " << A[4] << ", " << A[5] << " ]\n" |
| 281 |
|
<< "[ " << A[6] << ", " << A[7] << ", " << A[8] << " ]\n"; |
| 282 |
+ |
} |
| 283 |
+ |
|
| 284 |
+ |
|
| 285 |
+ |
void SimInfo::crossProduct3(double a[3],double b[3], double out[3]){ |
| 286 |
+ |
|
| 287 |
+ |
out[0] = a[1] * b[2] - a[2] * b[1]; |
| 288 |
+ |
out[1] = a[2] * b[0] - a[0] * b[2] ; |
| 289 |
+ |
out[2] = a[0] * b[1] - a[1] * b[0]; |
| 290 |
+ |
|
| 291 |
+ |
} |
| 292 |
+ |
|
| 293 |
+ |
double SimInfo::dotProduct3(double a[3], double b[3]){ |
| 294 |
+ |
return a[0]*b[0] + a[1]*b[1]+ a[2]*b[2]; |
| 295 |
+ |
} |
| 296 |
+ |
|
| 297 |
+ |
double SimInfo::length3(double a[3]){ |
| 298 |
+ |
return sqrt(a[0]*a[0] + a[1]*a[1] + a[2]*a[2]); |
| 299 |
|
} |
| 300 |
|
|
| 301 |
|
void SimInfo::calcBoxL( void ){ |
| 302 |
|
|
| 303 |
|
double dx, dy, dz, dsq; |
| 287 |
– |
int i; |
| 304 |
|
|
| 305 |
|
// boxVol = Determinant of Hmat |
| 306 |
|
|
| 311 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
| 312 |
|
dsq = dx*dx + dy*dy + dz*dz; |
| 313 |
|
boxL[0] = sqrt( dsq ); |
| 314 |
< |
maxCutoff = 0.5 * boxL[0]; |
| 314 |
> |
//maxCutoff = 0.5 * boxL[0]; |
| 315 |
|
|
| 316 |
|
// boxLy |
| 317 |
|
|
| 318 |
|
dx = Hmat[0][1]; dy = Hmat[1][1]; dz = Hmat[2][1]; |
| 319 |
|
dsq = dx*dx + dy*dy + dz*dz; |
| 320 |
|
boxL[1] = sqrt( dsq ); |
| 321 |
< |
if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
| 321 |
> |
//if( (0.5 * boxL[1]) < maxCutoff ) maxCutoff = 0.5 * boxL[1]; |
| 322 |
|
|
| 323 |
+ |
|
| 324 |
|
// boxLz |
| 325 |
|
|
| 326 |
|
dx = Hmat[0][2]; dy = Hmat[1][2]; dz = Hmat[2][2]; |
| 327 |
|
dsq = dx*dx + dy*dy + dz*dz; |
| 328 |
|
boxL[2] = sqrt( dsq ); |
| 329 |
< |
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
| 329 |
> |
//if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
| 330 |
> |
|
| 331 |
> |
//calculate the max cutoff |
| 332 |
> |
maxCutoff = calcMaxCutOff(); |
| 333 |
|
|
| 334 |
|
checkCutOffs(); |
| 335 |
|
|
| 336 |
|
} |
| 337 |
|
|
| 338 |
|
|
| 339 |
+ |
double SimInfo::calcMaxCutOff(){ |
| 340 |
+ |
|
| 341 |
+ |
double ri[3], rj[3], rk[3]; |
| 342 |
+ |
double rij[3], rjk[3], rki[3]; |
| 343 |
+ |
double minDist; |
| 344 |
+ |
|
| 345 |
+ |
ri[0] = Hmat[0][0]; |
| 346 |
+ |
ri[1] = Hmat[1][0]; |
| 347 |
+ |
ri[2] = Hmat[2][0]; |
| 348 |
+ |
|
| 349 |
+ |
rj[0] = Hmat[0][1]; |
| 350 |
+ |
rj[1] = Hmat[1][1]; |
| 351 |
+ |
rj[2] = Hmat[2][1]; |
| 352 |
+ |
|
| 353 |
+ |
rk[0] = Hmat[0][2]; |
| 354 |
+ |
rk[1] = Hmat[1][2]; |
| 355 |
+ |
rk[2] = Hmat[2][2]; |
| 356 |
+ |
|
| 357 |
+ |
crossProduct3(ri,rj, rij); |
| 358 |
+ |
distXY = dotProduct3(rk,rij) / length3(rij); |
| 359 |
+ |
|
| 360 |
+ |
crossProduct3(rj,rk, rjk); |
| 361 |
+ |
distYZ = dotProduct3(ri,rjk) / length3(rjk); |
| 362 |
+ |
|
| 363 |
+ |
crossProduct3(rk,ri, rki); |
| 364 |
+ |
distZX = dotProduct3(rj,rki) / length3(rki); |
| 365 |
+ |
|
| 366 |
+ |
minDist = min(min(distXY, distYZ), distZX); |
| 367 |
+ |
return minDist/2; |
| 368 |
+ |
|
| 369 |
+ |
} |
| 370 |
+ |
|
| 371 |
|
void SimInfo::wrapVector( double thePos[3] ){ |
| 372 |
|
|
| 373 |
< |
int i, j, k; |
| 373 |
> |
int i; |
| 374 |
|
double scaled[3]; |
| 375 |
|
|
| 376 |
|
if( !orthoRhombic ){ |
| 545 |
|
void SimInfo::checkCutOffs( void ){ |
| 546 |
|
|
| 547 |
|
int cutChanged = 0; |
| 548 |
< |
|
| 497 |
< |
|
| 498 |
< |
|
| 548 |
> |
|
| 549 |
|
if( boxIsInit ){ |
| 550 |
|
|
| 551 |
|
//we need to check cutOffs against the box |
| 552 |
< |
|
| 552 |
> |
|
| 553 |
> |
//detect the change of rCut |
| 554 |
|
if(( maxCutoff > rCut )&&(usePBC)){ |
| 555 |
|
if( rCut < origRcut ){ |
| 556 |
< |
rCut = origRcut; |
| 557 |
< |
if (rCut > maxCutoff) rCut = maxCutoff; |
| 558 |
< |
|
| 559 |
< |
sprintf( painCave.errMsg, |
| 560 |
< |
"New Box size is setting the long range cutoff radius " |
| 561 |
< |
"to %lf\n", |
| 562 |
< |
rCut ); |
| 563 |
< |
painCave.isFatal = 0; |
| 564 |
< |
simError(); |
| 556 |
> |
rCut = origRcut; |
| 557 |
> |
|
| 558 |
> |
if (rCut > maxCutoff) |
| 559 |
> |
rCut = maxCutoff; |
| 560 |
> |
|
| 561 |
> |
sprintf( painCave.errMsg, |
| 562 |
> |
"New Box size is setting the long range cutoff radius " |
| 563 |
> |
"to %lf at time %lf\n", |
| 564 |
> |
rCut, currentTime ); |
| 565 |
> |
painCave.isFatal = 0; |
| 566 |
> |
simError(); |
| 567 |
|
} |
| 568 |
|
} |
| 569 |
< |
|
| 517 |
< |
if( maxCutoff > ecr ){ |
| 518 |
< |
if( ecr < origEcr ){ |
| 519 |
< |
ecr = origEcr; |
| 520 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
| 521 |
< |
|
| 522 |
< |
sprintf( painCave.errMsg, |
| 523 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
| 524 |
< |
"to %lf\n", |
| 525 |
< |
ecr ); |
| 526 |
< |
painCave.isFatal = 0; |
| 527 |
< |
simError(); |
| 528 |
< |
} |
| 529 |
< |
} |
| 530 |
< |
|
| 531 |
< |
|
| 532 |
< |
if ((rCut > maxCutoff)&&(usePBC)) { |
| 569 |
> |
else if ((rCut > maxCutoff)&&(usePBC)) { |
| 570 |
|
sprintf( painCave.errMsg, |
| 571 |
|
"New Box size is setting the long range cutoff radius " |
| 572 |
< |
"to %lf\n", |
| 573 |
< |
maxCutoff ); |
| 572 |
> |
"to %lf at time %lf\n", |
| 573 |
> |
maxCutoff, currentTime ); |
| 574 |
|
painCave.isFatal = 0; |
| 575 |
|
simError(); |
| 576 |
|
rCut = maxCutoff; |
| 577 |
|
} |
| 578 |
|
|
| 579 |
< |
if( ecr > maxCutoff){ |
| 579 |
> |
|
| 580 |
> |
//detect the change of ecr |
| 581 |
> |
if( maxCutoff > ecr ){ |
| 582 |
> |
if( ecr < origEcr ){ |
| 583 |
> |
ecr = origEcr; |
| 584 |
> |
if (ecr > maxCutoff) ecr = maxCutoff; |
| 585 |
> |
|
| 586 |
> |
sprintf( painCave.errMsg, |
| 587 |
> |
"New Box size is setting the electrostaticCutoffRadius " |
| 588 |
> |
"to %lf at time %lf\n", |
| 589 |
> |
ecr, currentTime ); |
| 590 |
> |
painCave.isFatal = 0; |
| 591 |
> |
simError(); |
| 592 |
> |
} |
| 593 |
> |
} |
| 594 |
> |
else if( ecr > maxCutoff){ |
| 595 |
|
sprintf( painCave.errMsg, |
| 596 |
|
"New Box size is setting the electrostaticCutoffRadius " |
| 597 |
< |
"to %lf\n", |
| 598 |
< |
maxCutoff ); |
| 597 |
> |
"to %lf at time %lf\n", |
| 598 |
> |
maxCutoff, currentTime ); |
| 599 |
|
painCave.isFatal = 0; |
| 600 |
|
simError(); |
| 601 |
|
ecr = maxCutoff; |
| 602 |
|
} |
| 603 |
|
|
| 552 |
– |
|
| 604 |
|
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
| 605 |
< |
|
| 605 |
> |
|
| 606 |
|
// rlist is the 1.0 plus max( rcut, ecr ) |
| 607 |
|
|
| 608 |
|
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 614 |
|
|
| 615 |
|
oldEcr = ecr; |
| 616 |
|
oldRcut = rCut; |
| 617 |
< |
|
| 617 |
> |
|
| 618 |
|
} else { |
| 619 |
|
// initialize this stuff before using it, OK? |
| 620 |
< |
sprintf( painCave.errMsg, |
| 621 |
< |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
| 622 |
< |
painCave.isFatal = 1; |
| 623 |
< |
simError(); |
| 620 |
> |
sprintf( painCave.errMsg, |
| 621 |
> |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
| 622 |
> |
painCave.isFatal = 1; |
| 623 |
> |
simError(); |
| 624 |
|
} |
| 625 |
< |
|
| 625 |
> |
|
| 626 |
|
} |
| 627 |
|
|
| 628 |
|
void SimInfo::addProperty(GenericData* prop){ |
