# | Line 26 | Line 26 | SimInfo::SimInfo(){ | |
---|---|---|
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; | |
# | Line 54 | Line 58 | SimInfo::SimInfo(){ | |
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]) { | |
# | Line 302 | Line 310 | void SimInfo::calcBoxL( void ){ | |
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 | ||
# | Line 356 | Line 366 | int SimInfo::getNDF(){ | |
366 | ndf = ndf_local; | |
367 | #endif | |
368 | ||
369 | < | ndf = ndf - 3; |
369 | > | ndf = ndf - 3 - nZconstraints; |
370 | ||
371 | return ndf; | |
372 | } | |
# | Line 375 | Line 385 | int SimInfo::getNDFraw() { | |
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; | |
# | Line 431 | Line 457 | void SimInfo::refreshSim(){ | |
457 | ||
458 | this->ndf = this->getNDF(); | |
459 | this->ndfRaw = this->getNDFraw(); | |
460 | < | |
460 | > | this->ndfTrans = this->getNDFtranslational(); |
461 | } | |
462 | ||
463 | ||
# | Line 467 | Line 493 | void SimInfo::checkCutOffs( void ){ | |
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){ | |
# | Line 587 | Line 618 | vector<GenericData*> SimInfo::getProperties(){ | |
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 | + | } |
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