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; |
46 |
|
|
47 |
+ |
haveOrigRcut = 0; |
48 |
+ |
haveOrigEcr = 0; |
49 |
+ |
boxIsInit = 0; |
50 |
+ |
|
51 |
+ |
resetTime = 1e99; |
52 |
+ |
|
53 |
+ |
|
54 |
|
usePBC = 0; |
55 |
|
useLJ = 0; |
56 |
|
useSticky = 0; |
59 |
|
useGB = 0; |
60 |
|
useEAM = 0; |
61 |
|
|
62 |
+ |
myConfiguration = new SimState(); |
63 |
+ |
|
64 |
|
wrapMeSimInfo( this ); |
65 |
|
} |
66 |
|
|
67 |
+ |
|
68 |
+ |
SimInfo::~SimInfo(){ |
69 |
+ |
|
70 |
+ |
delete myConfiguration; |
71 |
+ |
|
72 |
+ |
map<string, GenericData*>::iterator i; |
73 |
+ |
|
74 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
75 |
+ |
delete (*i).second; |
76 |
+ |
|
77 |
+ |
} |
78 |
+ |
|
79 |
|
void SimInfo::setBox(double newBox[3]) { |
80 |
|
|
81 |
|
int i, j; |
103 |
|
// [ 2 5 8 ] |
104 |
|
double FortranHmatInv[9]; // the inverted Hmat (for Fortran); |
105 |
|
|
106 |
+ |
|
107 |
+ |
if( !boxIsInit ) boxIsInit = 1; |
108 |
|
|
109 |
|
for(i=0; i < 3; i++) |
110 |
|
for (j=0; j < 3; j++) Hmat[i][j] = theBox[i][j]; |
111 |
|
|
82 |
– |
// cerr |
83 |
– |
// << "setting Hmat ->\n" |
84 |
– |
// << "[ " << Hmat[0][0] << ", " << Hmat[0][1] << ", " << Hmat[0][2] << " ]\n" |
85 |
– |
// << "[ " << Hmat[1][0] << ", " << Hmat[1][1] << ", " << Hmat[1][2] << " ]\n" |
86 |
– |
// << "[ " << Hmat[2][0] << ", " << Hmat[2][1] << ", " << Hmat[2][2] << " ]\n"; |
87 |
– |
|
112 |
|
calcBoxL(); |
113 |
|
calcHmatInv(); |
114 |
|
|
121 |
|
|
122 |
|
setFortranBoxSize(FortranHmat, FortranHmatInv, &orthoRhombic); |
123 |
|
|
100 |
– |
smallestBoxL = boxLx; |
101 |
– |
if (boxLy < smallestBoxL) smallestBoxL = boxLy; |
102 |
– |
if (boxLz < smallestBoxL) smallestBoxL = boxLz; |
103 |
– |
|
104 |
– |
maxCutoff = smallestBoxL / 2.0; |
105 |
– |
|
106 |
– |
if (rList > maxCutoff) { |
107 |
– |
sprintf( painCave.errMsg, |
108 |
– |
"New Box size is forcing neighborlist radius down to %lf\n", |
109 |
– |
maxCutoff ); |
110 |
– |
painCave.isFatal = 0; |
111 |
– |
simError(); |
112 |
– |
|
113 |
– |
rList = maxCutoff; |
114 |
– |
|
115 |
– |
sprintf( painCave.errMsg, |
116 |
– |
"New Box size is forcing cutoff radius down to %lf\n", |
117 |
– |
maxCutoff - 1.0 ); |
118 |
– |
painCave.isFatal = 0; |
119 |
– |
simError(); |
120 |
– |
|
121 |
– |
rCut = rList - 1.0; |
122 |
– |
|
123 |
– |
// list radius changed so we have to refresh the simulation structure. |
124 |
– |
refreshSim(); |
125 |
– |
} |
126 |
– |
|
127 |
– |
if( ecr > maxCutoff ){ |
128 |
– |
|
129 |
– |
sprintf( painCave.errMsg, |
130 |
– |
"New Box size is forcing electrostatic cutoff radius " |
131 |
– |
"down to %lf\n", |
132 |
– |
maxCutoff ); |
133 |
– |
painCave.isFatal = 0; |
134 |
– |
simError(); |
135 |
– |
|
136 |
– |
ecr = maxCutoff; |
137 |
– |
est = 0.05 * ecr; |
138 |
– |
|
139 |
– |
refreshSim(); |
140 |
– |
} |
141 |
– |
|
124 |
|
} |
125 |
|
|
126 |
|
|
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; |
312 |
|
|
313 |
|
dx = Hmat[0][0]; dy = Hmat[1][0]; dz = Hmat[2][0]; |
314 |
|
dsq = dx*dx + dy*dy + dz*dz; |
315 |
< |
boxLx = sqrt( dsq ); |
315 |
> |
boxL[0] = sqrt( dsq ); |
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 |
< |
boxLy = sqrt( dsq ); |
322 |
> |
boxL[1] = sqrt( dsq ); |
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 |
< |
boxLz = sqrt( dsq ); |
330 |
> |
boxL[2] = sqrt( dsq ); |
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; |
420 |
|
ndf = ndf_local; |
421 |
|
#endif |
422 |
|
|
423 |
< |
ndf = ndf - 3; |
423 |
> |
ndf = ndf - 3 - nZconstraints; |
424 |
|
|
425 |
|
return ndf; |
426 |
|
} |
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; |
462 |
|
int isError; |
463 |
|
int n_global; |
464 |
|
int* excl; |
465 |
< |
|
410 |
< |
fInfo.rrf = 0.0; |
411 |
< |
fInfo.rt = 0.0; |
465 |
> |
|
466 |
|
fInfo.dielect = 0.0; |
467 |
|
|
414 |
– |
fInfo.rlist = rList; |
415 |
– |
fInfo.rcut = rCut; |
416 |
– |
|
468 |
|
if( useDipole ){ |
418 |
– |
fInfo.rrf = ecr; |
419 |
– |
fInfo.rt = ecr - est; |
469 |
|
if( useReactionField )fInfo.dielect = dielectric; |
470 |
|
} |
471 |
|
|
511 |
|
|
512 |
|
this->ndf = this->getNDF(); |
513 |
|
this->ndfRaw = this->getNDFraw(); |
514 |
+ |
this->ndfTrans = this->getNDFtranslational(); |
515 |
+ |
} |
516 |
|
|
517 |
+ |
|
518 |
+ |
void SimInfo::setRcut( double theRcut ){ |
519 |
+ |
|
520 |
+ |
if( !haveOrigRcut ){ |
521 |
+ |
haveOrigRcut = 1; |
522 |
+ |
origRcut = theRcut; |
523 |
+ |
} |
524 |
+ |
|
525 |
+ |
rCut = theRcut; |
526 |
+ |
checkCutOffs(); |
527 |
|
} |
528 |
|
|
529 |
+ |
void SimInfo::setEcr( double theEcr ){ |
530 |
+ |
|
531 |
+ |
if( !haveOrigEcr ){ |
532 |
+ |
haveOrigEcr = 1; |
533 |
+ |
origEcr = theEcr; |
534 |
+ |
} |
535 |
+ |
|
536 |
+ |
ecr = theEcr; |
537 |
+ |
checkCutOffs(); |
538 |
+ |
} |
539 |
+ |
|
540 |
+ |
void SimInfo::setEcr( double theEcr, double theEst ){ |
541 |
+ |
|
542 |
+ |
est = theEst; |
543 |
+ |
setEcr( theEcr ); |
544 |
+ |
} |
545 |
+ |
|
546 |
+ |
|
547 |
+ |
void SimInfo::checkCutOffs( void ){ |
548 |
+ |
|
549 |
+ |
int cutChanged = 0; |
550 |
+ |
|
551 |
+ |
if( boxIsInit ){ |
552 |
+ |
|
553 |
+ |
//we need to check cutOffs against the box |
554 |
+ |
|
555 |
+ |
//detect the change of rCut |
556 |
+ |
if(( maxCutoff > rCut )&&(usePBC)){ |
557 |
+ |
if( rCut < origRcut ){ |
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 |
+ |
else if ((rCut > maxCutoff)&&(usePBC)) { |
572 |
+ |
sprintf( painCave.errMsg, |
573 |
+ |
"New Box size is setting the long range cutoff radius " |
574 |
+ |
"to %lf at time %lf\n", |
575 |
+ |
maxCutoff, currentTime ); |
576 |
+ |
painCave.isFatal = 0; |
577 |
+ |
simError(); |
578 |
+ |
rCut = maxCutoff; |
579 |
+ |
} |
580 |
+ |
|
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 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 |
+ |
// rlist is the 1.0 plus max( rcut, ecr ) |
609 |
+ |
|
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 |
+ |
|
628 |
+ |
} |
629 |
+ |
|
630 |
+ |
void SimInfo::addProperty(GenericData* prop){ |
631 |
+ |
|
632 |
+ |
map<string, GenericData*>::iterator result; |
633 |
+ |
result = properties.find(prop->getID()); |
634 |
+ |
|
635 |
+ |
//we can't simply use properties[prop->getID()] = prop, |
636 |
+ |
//it will cause memory leak if we already contain a propery which has the same name of prop |
637 |
+ |
|
638 |
+ |
if(result != properties.end()){ |
639 |
+ |
|
640 |
+ |
delete (*result).second; |
641 |
+ |
(*result).second = prop; |
642 |
+ |
|
643 |
+ |
} |
644 |
+ |
else{ |
645 |
+ |
|
646 |
+ |
properties[prop->getID()] = prop; |
647 |
+ |
|
648 |
+ |
} |
649 |
+ |
|
650 |
+ |
} |
651 |
+ |
|
652 |
+ |
GenericData* SimInfo::getProperty(const string& propName){ |
653 |
+ |
|
654 |
+ |
map<string, GenericData*>::iterator result; |
655 |
+ |
|
656 |
+ |
//string lowerCaseName = (); |
657 |
+ |
|
658 |
+ |
result = properties.find(propName); |
659 |
+ |
|
660 |
+ |
if(result != properties.end()) |
661 |
+ |
return (*result).second; |
662 |
+ |
else |
663 |
+ |
return NULL; |
664 |
+ |
} |
665 |
+ |
|
666 |
+ |
vector<GenericData*> SimInfo::getProperties(){ |
667 |
+ |
|
668 |
+ |
vector<GenericData*> result; |
669 |
+ |
map<string, GenericData*>::iterator i; |
670 |
+ |
|
671 |
+ |
for(i = properties.begin(); i != properties.end(); i++) |
672 |
+ |
result.push_back((*i).second); |
673 |
+ |
|
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 |
+ |
} |