| 20 |
|
return ( x >= 0 ) ? floor( x + 0.5 ) : ceil( x - 0.5 ); |
| 21 |
|
} |
| 22 |
|
|
| 23 |
+ |
inline double min( double a, double b ){ |
| 24 |
+ |
return (a < b ) ? a : b; |
| 25 |
+ |
} |
| 26 |
|
|
| 27 |
|
SimInfo* currentInfo; |
| 28 |
|
|
| 40 |
|
thermalTime = 0.0; |
| 41 |
|
currentTime = 0.0; |
| 42 |
|
rCut = 0.0; |
| 40 |
– |
origRcut = -1.0; |
| 43 |
|
ecr = 0.0; |
| 42 |
– |
origEcr = -1.0; |
| 44 |
|
est = 0.0; |
| 44 |
– |
oldEcr = 0.0; |
| 45 |
– |
oldRcut = 0.0; |
| 45 |
|
|
| 46 |
< |
haveOrigRcut = 0; |
| 47 |
< |
haveOrigEcr = 0; |
| 46 |
> |
haveRcut = 0; |
| 47 |
> |
haveEcr = 0; |
| 48 |
|
boxIsInit = 0; |
| 49 |
|
|
| 50 |
|
resetTime = 1e99; |
| 103 |
|
// [ 2 5 8 ] |
| 104 |
|
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
| 105 |
|
|
| 107 |
– |
|
| 106 |
|
if( !boxIsInit ) boxIsInit = 1; |
| 107 |
|
|
| 108 |
|
for(i=0; i < 3; i++) |
| 527 |
|
this->ndf = this->getNDF(); |
| 528 |
|
this->ndfRaw = this->getNDFraw(); |
| 529 |
|
this->ndfTrans = this->getNDFtranslational(); |
| 532 |
– |
} |
| 533 |
– |
|
| 534 |
– |
|
| 535 |
– |
void SimInfo::setRcut( double theRcut ){ |
| 536 |
– |
|
| 537 |
– |
rCut = theRcut; |
| 538 |
– |
checkCutOffs(); |
| 530 |
|
} |
| 531 |
|
|
| 532 |
|
void SimInfo::setDefaultRcut( double theRcut ){ |
| 533 |
|
|
| 534 |
< |
haveOrigRcut = 1; |
| 544 |
< |
origRcut = theRcut; |
| 534 |
> |
haveRcut = 1; |
| 535 |
|
rCut = theRcut; |
| 536 |
|
|
| 537 |
|
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 539 |
|
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 540 |
|
} |
| 541 |
|
|
| 552 |
– |
void SimInfo::setEcr( double theEcr ){ |
| 553 |
– |
|
| 554 |
– |
ecr = theEcr; |
| 555 |
– |
checkCutOffs(); |
| 556 |
– |
} |
| 557 |
– |
|
| 542 |
|
void SimInfo::setDefaultEcr( double theEcr ){ |
| 543 |
|
|
| 544 |
< |
haveOrigEcr = 1; |
| 545 |
< |
origEcr = theEcr; |
| 544 |
> |
haveEcr = 1; |
| 545 |
> |
ecr = theEcr; |
| 546 |
|
|
| 547 |
|
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 548 |
|
|
| 565 |
– |
ecr = theEcr; |
| 566 |
– |
|
| 549 |
|
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 550 |
|
} |
| 551 |
|
|
| 570 |
– |
void SimInfo::setEcr( double theEcr, double theEst ){ |
| 571 |
– |
|
| 572 |
– |
est = theEst; |
| 573 |
– |
setEcr( theEcr ); |
| 574 |
– |
} |
| 575 |
– |
|
| 552 |
|
void SimInfo::setDefaultEcr( double theEcr, double theEst ){ |
| 553 |
|
|
| 554 |
|
est = theEst; |
| 557 |
|
|
| 558 |
|
|
| 559 |
|
void SimInfo::checkCutOffs( void ){ |
| 584 |
– |
|
| 585 |
– |
int cutChanged = 0; |
| 560 |
|
|
| 561 |
|
if( boxIsInit ){ |
| 562 |
|
|
| 563 |
|
//we need to check cutOffs against the box |
| 564 |
< |
|
| 565 |
< |
//detect the change of rCut |
| 592 |
< |
if(( maxCutoff > rCut )&&(usePBC)){ |
| 593 |
< |
if( rCut < origRcut ){ |
| 594 |
< |
rCut = origRcut; |
| 595 |
< |
|
| 596 |
< |
if (rCut > maxCutoff) |
| 597 |
< |
rCut = maxCutoff; |
| 598 |
< |
|
| 599 |
< |
sprintf( painCave.errMsg, |
| 600 |
< |
"New Box size is setting the long range cutoff radius " |
| 601 |
< |
"to %lf at time %lf\n", |
| 602 |
< |
rCut, currentTime ); |
| 603 |
< |
painCave.isFatal = 0; |
| 604 |
< |
simError(); |
| 605 |
< |
} |
| 606 |
< |
} |
| 607 |
< |
else if ((rCut > maxCutoff)&&(usePBC)) { |
| 564 |
> |
|
| 565 |
> |
if( rCut > maxCutoff ){ |
| 566 |
|
sprintf( painCave.errMsg, |
| 567 |
< |
"New Box size is setting the long range cutoff radius " |
| 568 |
< |
"to %lf at time %lf\n", |
| 569 |
< |
maxCutoff, currentTime ); |
| 570 |
< |
painCave.isFatal = 0; |
| 567 |
> |
"Box size is too small for the long range cutoff radius, " |
| 568 |
> |
"%G, at time %G\n" |
| 569 |
> |
" [ %G %G %G ]\n" |
| 570 |
> |
" [ %G %G %G ]\n" |
| 571 |
> |
" [ %G %G %G ]\n", |
| 572 |
> |
rCut, currentTime, |
| 573 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 574 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 575 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 576 |
> |
painCave.isFatal = 1; |
| 577 |
|
simError(); |
| 614 |
– |
rCut = maxCutoff; |
| 578 |
|
} |
| 579 |
< |
|
| 580 |
< |
|
| 581 |
< |
//detect the change of ecr |
| 582 |
< |
if( maxCutoff > ecr ){ |
| 583 |
< |
if( ecr < origEcr ){ |
| 584 |
< |
ecr = origEcr; |
| 585 |
< |
if (ecr > maxCutoff) ecr = maxCutoff; |
| 586 |
< |
|
| 587 |
< |
sprintf( painCave.errMsg, |
| 588 |
< |
"New Box size is setting the electrostaticCutoffRadius " |
| 589 |
< |
"to %lf at time %lf\n", |
| 590 |
< |
ecr, currentTime ); |
| 591 |
< |
painCave.isFatal = 0; |
| 592 |
< |
simError(); |
| 579 |
> |
|
| 580 |
> |
if( haveEcr ){ |
| 581 |
> |
if( ecr > maxCutoff ){ |
| 582 |
> |
sprintf( painCave.errMsg, |
| 583 |
> |
"Box size is too small for the electrostatic cutoff radius, " |
| 584 |
> |
"%G, at time %G\n" |
| 585 |
> |
" [ %G %G %G ]\n" |
| 586 |
> |
" [ %G %G %G ]\n" |
| 587 |
> |
" [ %G %G %G ]\n", |
| 588 |
> |
ecr, currentTime, |
| 589 |
> |
Hmat[0][0], Hmat[0][1], Hmat[0][2], |
| 590 |
> |
Hmat[1][0], Hmat[1][1], Hmat[1][2], |
| 591 |
> |
Hmat[2][0], Hmat[2][1], Hmat[2][2]); |
| 592 |
> |
painCave.isFatal = 1; |
| 593 |
> |
simError(); |
| 594 |
|
} |
| 595 |
|
} |
| 632 |
– |
else if( ecr > maxCutoff){ |
| 633 |
– |
sprintf( painCave.errMsg, |
| 634 |
– |
"New Box size is setting the electrostaticCutoffRadius " |
| 635 |
– |
"to %lf at time %lf\n", |
| 636 |
– |
maxCutoff, currentTime ); |
| 637 |
– |
painCave.isFatal = 0; |
| 638 |
– |
simError(); |
| 639 |
– |
ecr = maxCutoff; |
| 640 |
– |
} |
| 641 |
– |
|
| 642 |
– |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
| 643 |
– |
|
| 644 |
– |
// rlist is the 1.0 plus max( rcut, ecr ) |
| 645 |
– |
|
| 646 |
– |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
| 647 |
– |
|
| 648 |
– |
if( cutChanged ){ |
| 649 |
– |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
| 650 |
– |
} |
| 651 |
– |
|
| 652 |
– |
oldEcr = ecr; |
| 653 |
– |
oldRcut = rCut; |
| 654 |
– |
|
| 596 |
|
} else { |
| 597 |
|
// initialize this stuff before using it, OK? |
| 598 |
|
sprintf( painCave.errMsg, |
