| 26 |
|
SimInfo::SimInfo(){ |
| 27 |
|
excludes = NULL; |
| 28 |
|
n_constraints = 0; |
| 29 |
+ |
nZconstraints = 0; |
| 30 |
|
n_oriented = 0; |
| 31 |
|
n_dipoles = 0; |
| 32 |
|
ndf = 0; |
| 33 |
|
ndfRaw = 0; |
| 34 |
+ |
nZconstraints = 0; |
| 35 |
|
the_integrator = NULL; |
| 36 |
|
setTemp = 0; |
| 37 |
|
thermalTime = 0.0; |
| 38 |
|
currentTime = 0.0; |
| 39 |
|
rCut = 0.0; |
| 40 |
+ |
origRcut = -1.0; |
| 41 |
|
ecr = 0.0; |
| 42 |
+ |
origEcr = -1.0; |
| 43 |
|
est = 0.0; |
| 44 |
|
oldEcr = 0.0; |
| 45 |
|
oldRcut = 0.0; |
| 58 |
|
useGB = 0; |
| 59 |
|
useEAM = 0; |
| 60 |
|
|
| 61 |
+ |
myConfiguration = new SimState(); |
| 62 |
+ |
|
| 63 |
|
wrapMeSimInfo( this ); |
| 64 |
|
} |
| 65 |
|
|
| 66 |
+ |
|
| 67 |
|
SimInfo::~SimInfo(){ |
| 68 |
|
|
| 69 |
+ |
delete myConfiguration; |
| 70 |
+ |
|
| 71 |
|
map<string, GenericData*>::iterator i; |
| 72 |
|
|
| 73 |
|
for(i = properties.begin(); i != properties.end(); i++) |
| 74 |
|
delete (*i).second; |
| 75 |
< |
|
| 67 |
< |
|
| 75 |
> |
|
| 76 |
|
} |
| 77 |
|
|
| 78 |
|
void SimInfo::setBox(double newBox[3]) { |
| 310 |
|
dsq = dx*dx + dy*dy + dz*dz; |
| 311 |
|
boxL[2] = sqrt( dsq ); |
| 312 |
|
if( (0.5 * boxL[2]) < maxCutoff ) maxCutoff = 0.5 * boxL[2]; |
| 313 |
+ |
|
| 314 |
+ |
checkCutOffs(); |
| 315 |
|
|
| 316 |
|
} |
| 317 |
|
|
| 366 |
|
ndf = ndf_local; |
| 367 |
|
#endif |
| 368 |
|
|
| 369 |
< |
ndf = ndf - 3; |
| 369 |
> |
ndf = ndf - 3 - nZconstraints; |
| 370 |
|
|
| 371 |
|
return ndf; |
| 372 |
|
} |
| 385 |
|
|
| 386 |
|
return ndfRaw; |
| 387 |
|
} |
| 388 |
< |
|
| 388 |
> |
|
| 389 |
> |
int SimInfo::getNDFtranslational() { |
| 390 |
> |
int ndfTrans_local, ndfTrans; |
| 391 |
> |
|
| 392 |
> |
ndfTrans_local = 3 * n_atoms - n_constraints; |
| 393 |
> |
|
| 394 |
> |
#ifdef IS_MPI |
| 395 |
> |
MPI_Allreduce(&ndfTrans_local,&ndfTrans,1,MPI_INT,MPI_SUM, MPI_COMM_WORLD); |
| 396 |
> |
#else |
| 397 |
> |
ndfTrans = ndfTrans_local; |
| 398 |
> |
#endif |
| 399 |
> |
|
| 400 |
> |
ndfTrans = ndfTrans - 3 - nZconstraints; |
| 401 |
> |
|
| 402 |
> |
return ndfTrans; |
| 403 |
> |
} |
| 404 |
> |
|
| 405 |
|
void SimInfo::refreshSim(){ |
| 406 |
|
|
| 407 |
|
simtype fInfo; |
| 457 |
|
|
| 458 |
|
this->ndf = this->getNDF(); |
| 459 |
|
this->ndfRaw = this->getNDFraw(); |
| 460 |
< |
|
| 460 |
> |
this->ndfTrans = this->getNDFtranslational(); |
| 461 |
|
} |
| 462 |
|
|
| 463 |
|
|
| 493 |
|
void SimInfo::checkCutOffs( void ){ |
| 494 |
|
|
| 495 |
|
int cutChanged = 0; |
| 496 |
< |
|
| 496 |
> |
|
| 497 |
|
if( boxIsInit ){ |
| 498 |
|
|
| 499 |
|
//we need to check cutOffs against the box |
| 500 |
|
|
| 501 |
< |
if( maxCutoff > rCut ){ |
| 501 |
> |
if(( maxCutoff > rCut )&&(usePBC)){ |
| 502 |
|
if( rCut < origRcut ){ |
| 503 |
|
rCut = origRcut; |
| 504 |
|
if (rCut > maxCutoff) rCut = maxCutoff; |
| 505 |
|
|
| 506 |
|
sprintf( painCave.errMsg, |
| 507 |
|
"New Box size is setting the long range cutoff radius " |
| 508 |
< |
"to %lf\n", |
| 509 |
< |
rCut ); |
| 508 |
> |
"to %lf at time %lf\n", |
| 509 |
> |
rCut, currentTime ); |
| 510 |
|
painCave.isFatal = 0; |
| 511 |
|
simError(); |
| 512 |
|
} |
| 513 |
|
} |
| 514 |
< |
|
| 514 |
> |
|
| 515 |
|
if( maxCutoff > ecr ){ |
| 516 |
|
if( ecr < origEcr ){ |
| 517 |
< |
rCut = origEcr; |
| 517 |
> |
ecr = origEcr; |
| 518 |
|
if (ecr > maxCutoff) ecr = maxCutoff; |
| 519 |
|
|
| 520 |
|
sprintf( painCave.errMsg, |
| 521 |
|
"New Box size is setting the electrostaticCutoffRadius " |
| 522 |
< |
"to %lf\n", |
| 523 |
< |
ecr ); |
| 522 |
> |
"to %lf at time %lf\n", |
| 523 |
> |
ecr, currentTime ); |
| 524 |
|
painCave.isFatal = 0; |
| 525 |
|
simError(); |
| 526 |
|
} |
| 527 |
|
} |
| 528 |
< |
|
| 529 |
< |
|
| 530 |
< |
if (rCut > maxCutoff) { |
| 528 |
> |
|
| 529 |
> |
|
| 530 |
> |
if ((rCut > maxCutoff)&&(usePBC)) { |
| 531 |
|
sprintf( painCave.errMsg, |
| 532 |
|
"New Box size is setting the long range cutoff radius " |
| 533 |
< |
"to %lf\n", |
| 534 |
< |
maxCutoff ); |
| 533 |
> |
"to %lf at time %lf\n", |
| 534 |
> |
maxCutoff, currentTime ); |
| 535 |
|
painCave.isFatal = 0; |
| 536 |
|
simError(); |
| 537 |
|
rCut = maxCutoff; |
| 538 |
|
} |
| 539 |
< |
|
| 539 |
> |
|
| 540 |
|
if( ecr > maxCutoff){ |
| 541 |
|
sprintf( painCave.errMsg, |
| 542 |
|
"New Box size is setting the electrostaticCutoffRadius " |
| 543 |
< |
"to %lf\n", |
| 544 |
< |
maxCutoff ); |
| 543 |
> |
"to %lf at time %lf\n", |
| 544 |
> |
maxCutoff, currentTime ); |
| 545 |
|
painCave.isFatal = 0; |
| 546 |
|
simError(); |
| 547 |
|
ecr = maxCutoff; |
| 548 |
|
} |
| 549 |
|
|
| 550 |
+ |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
| 551 |
|
|
| 552 |
< |
} |
| 526 |
< |
|
| 527 |
< |
|
| 528 |
< |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
| 529 |
< |
|
| 530 |
< |
// rlist is the 1.0 plus max( rcut, ecr ) |
| 531 |
< |
|
| 532 |
< |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 533 |
< |
|
| 534 |
< |
if( cutChanged ){ |
| 552 |
> |
// rlist is the 1.0 plus max( rcut, ecr ) |
| 553 |
|
|
| 554 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 554 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 555 |
> |
|
| 556 |
> |
if( cutChanged ){ |
| 557 |
> |
|
| 558 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 559 |
> |
} |
| 560 |
> |
|
| 561 |
> |
oldEcr = ecr; |
| 562 |
> |
oldRcut = rCut; |
| 563 |
> |
|
| 564 |
> |
} else { |
| 565 |
> |
// initialize this stuff before using it, OK? |
| 566 |
> |
sprintf( painCave.errMsg, |
| 567 |
> |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
| 568 |
> |
painCave.isFatal = 1; |
| 569 |
> |
simError(); |
| 570 |
|
} |
| 571 |
< |
|
| 539 |
< |
oldEcr = ecr; |
| 540 |
< |
oldRcut = rCut; |
| 571 |
> |
|
| 572 |
|
} |
| 573 |
|
|
| 574 |
|
void SimInfo::addProperty(GenericData* prop){ |
| 618 |
|
return result; |
| 619 |
|
} |
| 620 |
|
|
| 621 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
| 622 |
+ |
double trace; |
| 623 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
| 624 |
|
|
| 625 |
+ |
return trace; |
| 626 |
+ |
} |
