# | Line 36 | Line 36 | |
---|---|---|
36 | * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). | |
37 | * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). | |
38 | * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). | |
39 | < | * [4] Vardeman & Gezelter, in progress (2009). |
39 | > | * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
40 | > | * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
41 | */ | |
42 | ||
43 | #define _LARGEFILE_SOURCE64 | |
# | Line 57 | Line 58 | |
58 | #include "utils/simError.h" | |
59 | #include "utils/MemoryUtils.hpp" | |
60 | #include "utils/StringTokenizer.hpp" | |
61 | + | #include "brains/Thermo.hpp" |
62 | ||
63 | #ifdef IS_MPI | |
62 | – | |
64 | #include <mpi.h> | |
65 | < | #define TAKE_THIS_TAG_CHAR 0 |
65 | < | #define TAKE_THIS_TAG_INT 1 |
65 | > | #endif |
66 | ||
67 | – | #endif // is_mpi |
67 | ||
69 | – | |
68 | namespace OpenMD { | |
69 | ||
70 | DumpReader::DumpReader(SimInfo* info, const std::string& filename) | |
# | Line 142 | Line 140 | namespace OpenMD { | |
140 | prevPos = currPos; | |
141 | bool foundOpenSnapshotTag = false; | |
142 | bool foundClosedSnapshotTag = false; | |
143 | + | bool foundOpenSiteDataTag = false; |
144 | while(inFile_->getline(buffer, bufferSize)) { | |
145 | ++lineNo; | |
146 | ||
# | Line 243 | Line 242 | namespace OpenMD { | |
242 | ||
243 | if (needCOMprops_) { | |
244 | Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); | |
245 | + | Thermo thermo(info_); |
246 | Vector3d com; | |
247 | < | Vector3d comvel; |
248 | < | Vector3d comw; |
249 | < | if (needPos_ && needVel_){ |
250 | < | info_->getComAll(com, comvel); |
251 | < | comw = info_->getAngularMomentum(); |
252 | < | }else{ |
253 | < | com = info_->getCom(); |
254 | < | comvel = 0.0; |
255 | < | comw = 0.0; |
256 | < | } |
257 | < | s->setCOMprops(com, comvel, comw); |
258 | < | } |
259 | < | |
247 | > | |
248 | > | if (needPos_ && needVel_) { |
249 | > | Vector3d comvel; |
250 | > | Vector3d comw; |
251 | > | thermo.getComAll(com, comvel); |
252 | > | comw = thermo.getAngularMomentum(); |
253 | > | } else { |
254 | > | com = thermo.getCom(); |
255 | > | } |
256 | > | } |
257 | } | |
258 | ||
259 | void DumpReader::readSet(int whichFrame) { | |
# | Line 324 | Line 321 | namespace OpenMD { | |
321 | ||
322 | inputStream.getline(buffer, bufferSize); | |
323 | line = buffer; | |
324 | < | if (line.find("</Snapshot>") == std::string::npos) { |
325 | < | sprintf(painCave.errMsg, |
326 | < | "DumpReader Error: can not find </Snapshot>\n"); |
327 | < | painCave.isFatal = 1; |
328 | < | simError(); |
329 | < | } |
330 | < | |
324 | > | |
325 | > | if (line.find("<SiteData>") != std::string::npos) { |
326 | > | //read SiteData |
327 | > | readSiteData(inputStream); |
328 | > | } else { |
329 | > | if (line.find("</Snapshot>") == std::string::npos) { |
330 | > | sprintf(painCave.errMsg, |
331 | > | "DumpReader Error: can not find </Snapshot>\n"); |
332 | > | painCave.isFatal = 1; |
333 | > | simError(); |
334 | > | } |
335 | > | } |
336 | } | |
337 | ||
338 | void DumpReader::parseDumpLine(const std::string& line) { | |
# | Line 350 | Line 352 | namespace OpenMD { | |
352 | ||
353 | int index = tokenizer.nextTokenAsInt(); | |
354 | ||
355 | < | StuntDouble* integrableObject = info_->getIOIndexToIntegrableObject(index); |
355 | > | StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); |
356 | ||
357 | < | if (integrableObject == NULL) { |
357 | > | if (sd == NULL) { |
358 | return; | |
359 | } | |
360 | std::string type = tokenizer.nextToken(); | |
# | Line 372 | Line 374 | namespace OpenMD { | |
374 | } | |
375 | } | |
376 | ||
377 | < | if (integrableObject->isDirectional()) { |
377 | > | if (sd->isDirectional()) { |
378 | if (needQuaternion_) { | |
379 | found = type.find("q"); | |
380 | if (found == std::string::npos) { | |
# | Line 395 | Line 397 | namespace OpenMD { | |
397 | pos[1] = tokenizer.nextTokenAsDouble(); | |
398 | pos[2] = tokenizer.nextTokenAsDouble(); | |
399 | if (needPos_) { | |
400 | < | integrableObject->setPos(pos); |
400 | > | sd->setPos(pos); |
401 | } | |
402 | break; | |
403 | } | |
# | Line 405 | Line 407 | namespace OpenMD { | |
407 | vel[1] = tokenizer.nextTokenAsDouble(); | |
408 | vel[2] = tokenizer.nextTokenAsDouble(); | |
409 | if (needVel_) { | |
410 | < | integrableObject->setVel(vel); |
410 | > | sd->setVel(vel); |
411 | } | |
412 | break; | |
413 | } | |
414 | ||
415 | case 'q' : { | |
416 | Quat4d q; | |
417 | < | if (integrableObject->isDirectional()) { |
417 | > | if (sd->isDirectional()) { |
418 | ||
419 | q[0] = tokenizer.nextTokenAsDouble(); | |
420 | q[1] = tokenizer.nextTokenAsDouble(); | |
# | Line 431 | Line 433 | namespace OpenMD { | |
433 | ||
434 | q.normalize(); | |
435 | if (needQuaternion_) { | |
436 | < | integrableObject->setQ(q); |
436 | > | sd->setQ(q); |
437 | } | |
438 | } | |
439 | break; | |
440 | } | |
441 | case 'j' : { | |
442 | Vector3d ji; | |
443 | < | if (integrableObject->isDirectional()) { |
443 | > | if (sd->isDirectional()) { |
444 | ji[0] = tokenizer.nextTokenAsDouble(); | |
445 | ji[1] = tokenizer.nextTokenAsDouble(); | |
446 | ji[2] = tokenizer.nextTokenAsDouble(); | |
447 | if (needAngMom_) { | |
448 | < | integrableObject->setJ(ji); |
448 | > | sd->setJ(ji); |
449 | } | |
450 | } | |
451 | break; | |
# | Line 454 | Line 456 | namespace OpenMD { | |
456 | force[0] = tokenizer.nextTokenAsDouble(); | |
457 | force[1] = tokenizer.nextTokenAsDouble(); | |
458 | force[2] = tokenizer.nextTokenAsDouble(); | |
459 | < | integrableObject->setFrc(force); |
459 | > | sd->setFrc(force); |
460 | break; | |
461 | } | |
462 | case 't' : { | |
# | Line 463 | Line 465 | namespace OpenMD { | |
465 | torque[0] = tokenizer.nextTokenAsDouble(); | |
466 | torque[1] = tokenizer.nextTokenAsDouble(); | |
467 | torque[2] = tokenizer.nextTokenAsDouble(); | |
468 | < | integrableObject->setTrq(torque); |
468 | > | sd->setTrq(torque); |
469 | break; | |
470 | } | |
471 | + | case 'u' : { |
472 | + | |
473 | + | RealType particlePot; |
474 | + | particlePot = tokenizer.nextTokenAsDouble(); |
475 | + | sd->setParticlePot(particlePot); |
476 | + | break; |
477 | + | } |
478 | + | case 'c' : { |
479 | + | |
480 | + | RealType flucQPos; |
481 | + | flucQPos = tokenizer.nextTokenAsDouble(); |
482 | + | sd->setFlucQPos(flucQPos); |
483 | + | break; |
484 | + | } |
485 | + | case 'w' : { |
486 | + | |
487 | + | RealType flucQVel; |
488 | + | flucQVel = tokenizer.nextTokenAsDouble(); |
489 | + | sd->setFlucQVel(flucQVel); |
490 | + | break; |
491 | + | } |
492 | + | case 'g' : { |
493 | + | |
494 | + | RealType flucQFrc; |
495 | + | flucQFrc = tokenizer.nextTokenAsDouble(); |
496 | + | sd->setFlucQFrc(flucQFrc); |
497 | + | break; |
498 | + | } |
499 | + | case 'e' : { |
500 | + | |
501 | + | Vector3d eField; |
502 | + | eField[0] = tokenizer.nextTokenAsDouble(); |
503 | + | eField[1] = tokenizer.nextTokenAsDouble(); |
504 | + | eField[2] = tokenizer.nextTokenAsDouble(); |
505 | + | sd->setElectricField(eField); |
506 | + | break; |
507 | + | } |
508 | default: { | |
509 | sprintf(painCave.errMsg, | |
510 | "DumpReader Error: %s is an unrecognized type\n", type.c_str()); | |
# | Line 480 | Line 519 | namespace OpenMD { | |
519 | } | |
520 | ||
521 | ||
522 | < | void DumpReader::readStuntDoubles(std::istream& inputStream) { |
522 | > | void DumpReader::parseSiteLine(const std::string& line) { |
523 | ||
524 | + | StringTokenizer tokenizer(line); |
525 | + | int nTokens; |
526 | + | |
527 | + | nTokens = tokenizer.countTokens(); |
528 | + | |
529 | + | if (nTokens < 2) { |
530 | + | sprintf(painCave.errMsg, |
531 | + | "DumpReader Error: Not enough Tokens.\n%s\n", line.c_str()); |
532 | + | painCave.isFatal = 1; |
533 | + | simError(); |
534 | + | } |
535 | + | |
536 | + | /** |
537 | + | * The first token is the global integrable object index. |
538 | + | */ |
539 | + | |
540 | + | int index = tokenizer.nextTokenAsInt(); |
541 | + | StuntDouble* sd = info_->getIOIndexToIntegrableObject(index); |
542 | + | if (sd == NULL) { |
543 | + | return; |
544 | + | } |
545 | + | |
546 | + | /** |
547 | + | * Test to see if the next token is an integer or not. If not, |
548 | + | * we've got data on the integrable object itself. If there is an |
549 | + | * integer, we're parsing data for a site on a rigid body. |
550 | + | */ |
551 | + | |
552 | + | std::string indexTest = tokenizer.peekNextToken(); |
553 | + | std::istringstream i(indexTest); |
554 | + | int siteIndex; |
555 | + | if (i >> siteIndex) { |
556 | + | // chew up this token and parse as an int: |
557 | + | siteIndex = tokenizer.nextTokenAsInt(); |
558 | + | RigidBody* rb = static_cast<RigidBody*>(sd); |
559 | + | sd = rb->getAtoms()[siteIndex]; |
560 | + | } |
561 | + | |
562 | + | /** |
563 | + | * The next token contains information on what follows. |
564 | + | */ |
565 | + | std::string type = tokenizer.nextToken(); |
566 | + | int size = type.size(); |
567 | + | |
568 | + | for(int i = 0; i < size; ++i) { |
569 | + | switch(type[i]) { |
570 | + | |
571 | + | case 'u' : { |
572 | + | |
573 | + | RealType particlePot; |
574 | + | particlePot = tokenizer.nextTokenAsDouble(); |
575 | + | sd->setParticlePot(particlePot); |
576 | + | break; |
577 | + | } |
578 | + | case 'c' : { |
579 | + | |
580 | + | RealType flucQPos; |
581 | + | flucQPos = tokenizer.nextTokenAsDouble(); |
582 | + | sd->setFlucQPos(flucQPos); |
583 | + | break; |
584 | + | } |
585 | + | case 'w' : { |
586 | + | |
587 | + | RealType flucQVel; |
588 | + | flucQVel = tokenizer.nextTokenAsDouble(); |
589 | + | sd->setFlucQVel(flucQVel); |
590 | + | break; |
591 | + | } |
592 | + | case 'g' : { |
593 | + | |
594 | + | RealType flucQFrc; |
595 | + | flucQFrc = tokenizer.nextTokenAsDouble(); |
596 | + | sd->setFlucQFrc(flucQFrc); |
597 | + | break; |
598 | + | } |
599 | + | case 'e' : { |
600 | + | |
601 | + | Vector3d eField; |
602 | + | eField[0] = tokenizer.nextTokenAsDouble(); |
603 | + | eField[1] = tokenizer.nextTokenAsDouble(); |
604 | + | eField[2] = tokenizer.nextTokenAsDouble(); |
605 | + | sd->setElectricField(eField); |
606 | + | break; |
607 | + | } |
608 | + | default: { |
609 | + | sprintf(painCave.errMsg, |
610 | + | "DumpReader Error: %s is an unrecognized type\n", type.c_str()); |
611 | + | painCave.isFatal = 1; |
612 | + | simError(); |
613 | + | break; |
614 | + | } |
615 | + | } |
616 | + | } |
617 | + | } |
618 | + | |
619 | + | |
620 | + | void DumpReader::readStuntDoubles(std::istream& inputStream) { |
621 | + | |
622 | inputStream.getline(buffer, bufferSize); | |
623 | std::string line(buffer); | |
624 | ||
# | Line 504 | Line 641 | namespace OpenMD { | |
641 | ||
642 | } | |
643 | ||
644 | + | void DumpReader::readSiteData(std::istream& inputStream) { |
645 | + | |
646 | + | inputStream.getline(buffer, bufferSize); |
647 | + | std::string line(buffer); |
648 | + | |
649 | + | if (line.find("<SiteData>") == std::string::npos) { |
650 | + | // site data isn't required for a simulation, so skip |
651 | + | return; |
652 | + | } |
653 | + | |
654 | + | while(inputStream.getline(buffer, bufferSize)) { |
655 | + | line = buffer; |
656 | + | |
657 | + | if(line.find("</SiteData>") != std::string::npos) { |
658 | + | break; |
659 | + | } |
660 | + | |
661 | + | parseSiteLine(line); |
662 | + | } |
663 | + | |
664 | + | } |
665 | + | |
666 | void DumpReader::readFrameProperties(std::istream& inputStream) { | |
667 | ||
668 | Snapshot* s = info_->getSnapshotManager()->getCurrentSnapshot(); | |
# | Line 549 | Line 708 | namespace OpenMD { | |
708 | hmat(2, 2) = tokenizer.nextTokenAsDouble(); | |
709 | s->setHmat(hmat); | |
710 | } else if (propertyName == "Thermostat") { | |
711 | < | RealType chi = tokenizer.nextTokenAsDouble(); |
712 | < | RealType integralOfChiDt = tokenizer.nextTokenAsDouble(); |
713 | < | s->setChi(chi); |
714 | < | s->setIntegralOfChiDt(integralOfChiDt); |
711 | > | pair<RealType, RealType> thermostat; |
712 | > | thermostat.first = tokenizer.nextTokenAsDouble(); |
713 | > | thermostat.second = tokenizer.nextTokenAsDouble(); |
714 | > | s->setThermostat(thermostat); |
715 | } else if (propertyName == "Barostat") { | |
716 | Mat3x3d eta; | |
717 | eta(0, 0) = tokenizer.nextTokenAsDouble(); | |
# | Line 564 | Line 723 | namespace OpenMD { | |
723 | eta(2, 0) = tokenizer.nextTokenAsDouble(); | |
724 | eta(2, 1) = tokenizer.nextTokenAsDouble(); | |
725 | eta(2, 2) = tokenizer.nextTokenAsDouble(); | |
726 | < | s->setEta(eta); |
726 | > | s->setBarostat(eta); |
727 | } else { | |
728 | sprintf(painCave.errMsg, | |
729 | "DumpReader Error: %s is an invalid property in <FrameData>\n", propertyName.c_str()); |
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