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 |
|
|
494 |
|
|
495 |
|
int cutChanged = 0; |
496 |
|
|
497 |
+ |
|
498 |
+ |
|
499 |
|
if( boxIsInit ){ |
500 |
|
|
501 |
|
//we need to check cutOffs against the box |
502 |
< |
|
503 |
< |
if( maxCutoff > rCut ){ |
502 |
> |
|
503 |
> |
if(( maxCutoff > rCut )&&(usePBC)){ |
504 |
|
if( rCut < origRcut ){ |
505 |
|
rCut = origRcut; |
506 |
|
if (rCut > maxCutoff) rCut = maxCutoff; |
516 |
|
|
517 |
|
if( maxCutoff > ecr ){ |
518 |
|
if( ecr < origEcr ){ |
519 |
< |
rCut = origEcr; |
519 |
> |
ecr = origEcr; |
520 |
|
if (ecr > maxCutoff) ecr = maxCutoff; |
521 |
|
|
522 |
|
sprintf( painCave.errMsg, |
529 |
|
} |
530 |
|
|
531 |
|
|
532 |
< |
if (rCut > maxCutoff) { |
532 |
> |
if ((rCut > maxCutoff)&&(usePBC)) { |
533 |
|
sprintf( painCave.errMsg, |
534 |
|
"New Box size is setting the long range cutoff radius " |
535 |
|
"to %lf\n", |
549 |
|
ecr = maxCutoff; |
550 |
|
} |
551 |
|
|
552 |
< |
|
553 |
< |
} |
526 |
< |
|
552 |
> |
|
553 |
> |
if( (oldEcr != ecr) || ( oldRcut != rCut ) ) cutChanged = 1; |
554 |
|
|
555 |
< |
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 ){ |
555 |
> |
// rlist is the 1.0 plus max( rcut, ecr ) |
556 |
|
|
557 |
< |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
557 |
> |
( rCut > ecr )? rList = rCut + 1.0: rList = ecr + 1.0; |
558 |
> |
|
559 |
> |
if( cutChanged ){ |
560 |
> |
|
561 |
> |
notifyFortranCutOffs( &rCut, &rList, &ecr, &est ); |
562 |
> |
} |
563 |
> |
|
564 |
> |
oldEcr = ecr; |
565 |
> |
oldRcut = rCut; |
566 |
> |
|
567 |
> |
} else { |
568 |
> |
// initialize this stuff before using it, OK? |
569 |
> |
sprintf( painCave.errMsg, |
570 |
> |
"Trying to check cutoffs without a box. Be smarter.\n" ); |
571 |
> |
painCave.isFatal = 1; |
572 |
> |
simError(); |
573 |
|
} |
574 |
|
|
539 |
– |
oldEcr = ecr; |
540 |
– |
oldRcut = rCut; |
575 |
|
} |
576 |
|
|
577 |
|
void SimInfo::addProperty(GenericData* prop){ |
621 |
|
return result; |
622 |
|
} |
623 |
|
|
624 |
+ |
double SimInfo::matTrace3(double m[3][3]){ |
625 |
+ |
double trace; |
626 |
+ |
trace = m[0][0] + m[1][1] + m[2][2]; |
627 |
|
|
628 |
+ |
return trace; |
629 |
+ |
} |