146 |
|
delete ffStream; |
147 |
|
} |
148 |
|
|
149 |
– |
|
149 |
|
void DUFF::parseAtomType(const std::string& line, int lineNo, int& ident){ |
150 |
|
StringTokenizer tokenizer(line); |
151 |
|
int nTokens = tokenizer.countTokens(); |
238 |
|
StringTokenizer tokenizer(line); |
239 |
|
int nTokens = tokenizer.countTokens(); |
240 |
|
|
241 |
< |
//in irectionalAtomTypeSection, a line at least contains 6 tokens |
241 |
> |
//in DirectionalAtomTypeSection, a line at least contains 6 tokens |
242 |
|
//AtomTypeName, isDipole, isSticky, I_xx, I_yy and I_zz |
243 |
|
if (nTokens < 6) { |
244 |
< |
|
244 |
> |
std::cerr << "Not enought tokens" << std::endl; |
245 |
|
} else { |
246 |
|
|
247 |
|
|
274 |
|
|
275 |
|
Mat3x3d inertialMat; |
276 |
|
inertialMat(0, 0) = Ixx; |
277 |
< |
inertialMat(1, 1) = Ixx; |
278 |
< |
inertialMat(2, 2) = Ixx; |
277 |
> |
inertialMat(1, 1) = Iyy; |
278 |
> |
inertialMat(2, 2) = Izz; |
279 |
|
dAtomType->setI(inertialMat); |
280 |
|
|
281 |
|
//read dipole moment |
358 |
|
|
359 |
|
//switch is a maintain nightmare |
360 |
|
switch(bt) { |
361 |
< |
case "FixedBondType" : |
361 |
> |
case "Fixed" : |
362 |
|
bondType = new FixedBondType(); |
363 |
|
break; |
364 |
|
|
365 |
< |
case "HarmonicBondType" : |
365 |
> |
case "Harmonic" : |
366 |
|
if (nTokens < 1) { |
367 |
|
|
368 |
|
} else { |
373 |
|
|
374 |
|
break; |
375 |
|
|
376 |
< |
case "CubicBondType" : |
376 |
> |
case "Cubic" : |
377 |
|
if (nTokens < 4) { |
378 |
|
|
379 |
|
} else { |
387 |
|
} |
388 |
|
break; |
389 |
|
|
390 |
< |
case "QuadraticBondType" : |
390 |
> |
case "Quartic" : |
391 |
|
if (nTokens < 5) { |
392 |
|
|
393 |
|
} else { |
403 |
|
} |
404 |
|
break; |
405 |
|
|
406 |
< |
case "PolynomialBondType " : |
406 |
> |
case "Polynomial" : |
407 |
|
if (nTokens < 2 || nTokens % 2 != 0) { |
408 |
|
|
409 |
|
} else { |
456 |
|
//switch is a maintain nightmare |
457 |
|
switch(bt) { |
458 |
|
|
459 |
< |
case "HarmonicBendType" : |
459 |
> |
case "Harmonic" : |
460 |
|
|
461 |
|
if (nTokens < 1) { |
462 |
|
|
466 |
|
bendType = new HarmonicBendType(theta0, ktheta); |
467 |
|
} |
468 |
|
break; |
469 |
< |
case "GhostBendType" : |
469 |
> |
case "GhostBend" : |
470 |
|
if (nTokens < 1) { |
471 |
|
|
472 |
|
} else { |
475 |
|
} |
476 |
|
break; |
477 |
|
|
478 |
< |
case "UreyBradleyBendType" : |
478 |
> |
case "UreyBradley" : |
479 |
|
if (nTokens < 3) { |
480 |
|
|
481 |
|
} else { |
486 |
|
} |
487 |
|
break; |
488 |
|
|
489 |
< |
case "CubicBendType" : |
489 |
> |
case "Cubic" : |
490 |
|
if (nTokens < 4) { |
491 |
|
|
492 |
|
} else { |
500 |
|
} |
501 |
|
break; |
502 |
|
|
503 |
< |
case "QuadraticBendType" : |
503 |
> |
case "Quartic" : |
504 |
|
if (nTokens < 5) { |
505 |
|
|
506 |
|
} else { |
516 |
|
} |
517 |
|
break; |
518 |
|
|
519 |
< |
case "PolynomialBendType " : |
519 |
> |
case "Polynomial" : |
520 |
|
if (nTokens < 2 || nTokens % 2 != 0) { |
521 |
|
|
522 |
|
} else { |
551 |
|
std::string at3; |
552 |
|
std::string at4; |
553 |
|
std::string tt; |
554 |
< |
TorsionType* bendType = NULL; |
554 |
> |
TorsionType* torsionType = NULL; |
555 |
|
|
556 |
|
int nTokens = tokenizer.countTokens(); |
557 |
|
|
570 |
|
|
571 |
|
switch(tt) { |
572 |
|
|
573 |
< |
case "CubicTorsionType" : |
573 |
> |
case "Cubic" : |
574 |
|
if (nTokens < 4) { |
575 |
|
|
576 |
|
} else { |
584 |
|
} |
585 |
|
break; |
586 |
|
|
587 |
< |
case "QuadraticTorsionType" : |
587 |
> |
case "Quartic" : |
588 |
|
if (nTokens < 5) { |
589 |
|
|
590 |
|
} else { |
600 |
|
} |
601 |
|
break; |
602 |
|
|
603 |
< |
case "PolynomialTorsionType " : |
603 |
> |
case "Polynomial" : |
604 |
|
if (nTokens < 2 || nTokens % 2 != 0) { |
605 |
|
|
606 |
|
} else { |
617 |
|
} |
618 |
|
|
619 |
|
break; |
620 |
< |
case "CharmmTorsionType" : |
620 |
> |
case "Charmm" : |
621 |
|
|
622 |
|
if (nTokens < 3 || nTokens % 3 != 0) { |
623 |
|
|
638 |
|
|
639 |
|
} |
640 |
|
|
641 |
< |
if (bendType != NULL) { |
642 |
< |
addTorsionType(at1, at2, at3, bendType); |
641 |
> |
if (torsionType != NULL) { |
642 |
> |
addTorsionType(at1, at2, at3, at4, torsionType); |
643 |
|
} |
644 |
|
} |
645 |
|
|