ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/OpenMD/branches/development/src/visitors/AtomVisitor.cpp
(Generate patch)

Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 1008 by chrisfen, Wed Jul 19 12:35:31 2006 UTC vs.
Revision 1219 by xsun, Wed Jan 23 21:23:32 2008 UTC

# Line 523 | Line 523 | namespace oopse {
523    void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
524      std::vector<AtomInfo*> atoms;
525      //we need to convert linear into 4 different atoms
526 <    Vector3d c1(0.0, 0.0, -6.25);
527 <    Vector3d c2(0.0, 0.0, -2.1);
528 <    Vector3d c3(0.0, 0.0,  2.1);
529 <    Vector3d c4(0.0, 0.0,  6.25);
526 >    //Vector3d c1(0.0, 0.0, -6.25);
527 >    //Vector3d c2(0.0, 0.0, -2.1);
528 >    //Vector3d c3(0.0, 0.0,  2.1);
529 >    //Vector3d c4(0.0, 0.0,  6.25);
530 >    Vector3d c1(0.0, 0.0, 0.0);
531 >    Vector3d c2(0.0, 0.0, 1.0);
532      RotMat3x3d rotMatrix;
533      RotMat3x3d rotTrans;
534      AtomInfo* atomInfo;
535      Vector3d pos;
536      Vector3d newVec;
537 +    Vector3d dVec;
538      Quat4d q;
539      AtomData* atomData;
540      GenericData* data;
# Line 539 | Line 542 | namespace oopse {
542  
543      //if atom is not GBlipid atom, just skip it
544      if(!isGBLipidAtom(datom->getType()))
545 +      return;
546 +
547 +    data = datom->getPropertyByName("ATOMDATA");
548 +    if(data != NULL){
549 +      atomData = dynamic_cast<AtomData*>(data);  
550 +      if(atomData == NULL){
551 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
552 +        atomData = new AtomData;
553 +        haveAtomData = false;      
554 +      } else {
555 +        haveAtomData = true;
556 +      }
557 +    } else {
558 +      atomData = new AtomData;
559 +      haveAtomData = false;
560 +    }
561 +  
562 +  
563 +    pos = datom->getPos();
564 +    q = datom->getQ();
565 +    rotMatrix = datom->getA();
566 +
567 +    // We need A^T to convert from body-fixed to space-fixed:  
568 +    rotTrans = rotMatrix.transpose();
569 +
570 +    newVec = rotTrans * c1;
571 +    dVec = rotTrans * c2;
572 +    atomInfo = new AtomInfo;
573 +    atomInfo->atomTypeName = "GB";
574 +    atomInfo->pos[0] = pos[0] + newVec[0];
575 +    atomInfo->pos[1] = pos[1] + newVec[1];
576 +    atomInfo->pos[2] = pos[2] + newVec[2];
577 +    atomInfo->dipole[0] = dVec[0];
578 +    atomInfo->dipole[1] = dVec[1];
579 +    atomInfo->dipole[2] = dVec[2];
580 +    atomInfo->hasVector = true;
581 +    atomInfo->charge = 3.0;
582 +    atomInfo->hasCharge = true;
583 +    atomData->addAtomInfo(atomInfo);
584 +
585 +    //newVec = rotTrans * c2;
586 +    //atomInfo = new AtomInfo;
587 +    //atomInfo->atomTypeName = "K";
588 +    //atomInfo->pos[0] = pos[0] + newVec[0];
589 +    //atomInfo->pos[1] = pos[1] + newVec[1];
590 +    //atomInfo->pos[2] = pos[2] + newVec[2];
591 +    //atomInfo->dipole[0] = 0.0;
592 +    //atomInfo->dipole[1] = 0.0;
593 +    //atomInfo->dipole[2] = 0.0;
594 +    //atomData->addAtomInfo(atomInfo);
595 +
596 +    //newVec = rotTrans * c3;
597 +    //atomInfo = new AtomInfo;
598 +    //atomInfo->atomTypeName = "K";
599 +    //atomInfo->pos[0] = pos[0] + newVec[0];
600 +    //atomInfo->pos[1] = pos[1] + newVec[1];
601 +    //atomInfo->pos[2] = pos[2] + newVec[2];
602 +    //atomInfo->dipole[0] = 0.0;
603 +    //atomInfo->dipole[1] = 0.0;
604 +    //atomInfo->dipole[2] = 0.0;
605 +    //atomData->addAtomInfo(atomInfo);
606 +
607 +    //newVec = rotTrans * c4;
608 +    //atomInfo = new AtomInfo;
609 +    //atomInfo->atomTypeName = "K";
610 +    //atomInfo->pos[0] = pos[0] + newVec[0];
611 +    //atomInfo->pos[1] = pos[1] + newVec[1];
612 +    //atomInfo->pos[2] = pos[2] + newVec[2];
613 +    //atomInfo->dipole[0] = 0.0;
614 +    //atomInfo->dipole[1] = 0.0;
615 +    //atomInfo->dipole[2] = 0.0;
616 +    //atomData->addAtomInfo(atomInfo);
617 +
618 +    //add atom data into atom's property
619 +
620 +    if(!haveAtomData){
621 +      atomData->setID("ATOMDATA");
622 +      datom->addProperty(atomData);
623 +    }
624 +
625 +    setVisited(datom);
626 +
627 +  }
628 +
629 +  const std::string GBLipidAtomVisitor::toString(){
630 +    char buffer[65535];
631 +    std::string result;
632 +  
633 +    sprintf(buffer ,"------------------------------------------------------------------\n");
634 +    result += buffer;
635 +
636 +    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
637 +    result += buffer;
638 +
639 +    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
640 +    result += buffer;
641 +
642 +    sprintf(buffer ,"------------------------------------------------------------------\n");
643 +    result += buffer;
644 +
645 +    return result;
646 +  }
647 +
648 +  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
649 +    std::set<std::string>::iterator strIter;
650 +    strIter = Ring5gbAtomType.find(atomType);
651 +
652 +    return strIter != Ring5gbAtomType.end() ? true : false;
653 +  }
654 +
655 +  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
656 +    std::vector<AtomInfo*> atoms;
657 +    //we need to convert linear into 4 different atoms
658 +    Vector3d c1(0.0, 0.0, -5.5);
659 +    Vector3d c2(0.0, 0.0, -1.8);
660 +    Vector3d c3(0.0, 0.0,  1.8);
661 +    Vector3d c4(0.0, 0.0,  5.5);
662 +    RotMat3x3d rotMatrix;
663 +    RotMat3x3d rotTrans;
664 +    AtomInfo* atomInfo;
665 +    Vector3d pos;
666 +    Vector3d newVec;
667 +    Vector3d dVec;
668 +    Quat4d q;
669 +    AtomData* atomData;
670 +    GenericData* data;
671 +    bool haveAtomData;
672 +
673 +    //if atom is not Ring5GB atom, just skip it
674 +    if(!isRing5gbAtom(datom->getType()))
675        return;
676  
677      data = datom->getPropertyByName("ATOMDATA");
# Line 619 | Line 752 | namespace oopse {
752  
753    }
754  
755 <  const std::string GBLipidAtomVisitor::toString(){
755 >  const std::string Ring5gbAtomVisitor::toString(){
756      char buffer[65535];
757      std::string result;
758    
# Line 629 | Line 762 | namespace oopse {
762      sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
763      result += buffer;
764  
765 <    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
765 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
766      result += buffer;
767  
768      sprintf(buffer ,"------------------------------------------------------------------\n");
# Line 638 | Line 771 | namespace oopse {
771      return result;
772    }
773  
774 +  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
775 +    std::set<std::string>::iterator strIter;
776 +    strIter = HeadAtomType.find(atomType);
777 +
778 +    return strIter != HeadAtomType.end() ? true : false;
779 +  }
780 +
781 +  void HeadAtomVisitor::visit(DirectionalAtom* datom){
782 +    std::vector<AtomInfo*> atoms;
783 +    //we need to convert linear into 2 different atoms
784 +    Vector3d c1(0.0, 0.0, -1.5);
785 +    Vector3d c2(0.0, 0.0, 1.5);
786 +    RotMat3x3d rotMatrix;
787 +    RotMat3x3d rotTrans;
788 +    AtomInfo* atomInfo;
789 +    Vector3d pos;
790 +    Vector3d newVec;
791 +    Vector3d dVec;
792 +    Quat4d q;
793 +    AtomData* atomData;
794 +    GenericData* data;
795 +    bool haveAtomData;
796 +
797 +    //if atom is not Head atom, just skip it
798 +    if(!isHeadAtom(datom->getType()))
799 +      return;
800 +
801 +    data = datom->getPropertyByName("ATOMDATA");
802 +    if(data != NULL){
803 +      atomData = dynamic_cast<AtomData*>(data);  
804 +      if(atomData == NULL){
805 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
806 +        atomData = new AtomData;
807 +        haveAtomData = false;      
808 +      } else {
809 +        haveAtomData = true;
810 +      }
811 +    } else {
812 +      atomData = new AtomData;
813 +      haveAtomData = false;
814 +    }
815 +  
816 +  
817 +    pos = datom->getPos();
818 +    q = datom->getQ();
819 +    rotMatrix = datom->getA();
820 +
821 +    // We need A^T to convert from body-fixed to space-fixed:  
822 +    rotTrans = rotMatrix.transpose();
823 +
824 +    newVec = rotTrans * c1;
825 +    atomInfo = new AtomInfo;
826 +    atomInfo->atomTypeName = "C";
827 +    atomInfo->pos[0] = pos[0] + newVec[0];
828 +    atomInfo->pos[1] = pos[1] + newVec[1];
829 +    atomInfo->pos[2] = pos[2] + newVec[2];
830 +    atomInfo->dipole[0] = 0.0;
831 +    atomInfo->dipole[1] = 0.0;
832 +    atomInfo->dipole[2] = 0.0;
833 +    atomData->addAtomInfo(atomInfo);
834 +
835 +    newVec = rotTrans * c2;
836 +    atomInfo = new AtomInfo;
837 +    atomInfo->atomTypeName = "O";
838 +    atomInfo->pos[0] = pos[0] + newVec[0];
839 +    atomInfo->pos[1] = pos[1] + newVec[1];
840 +    atomInfo->pos[2] = pos[2] + newVec[2];
841 +    atomInfo->dipole[0] = 0.0;
842 +    atomInfo->dipole[1] = 0.0;
843 +    atomInfo->dipole[2] = 0.0;
844 +    atomData->addAtomInfo(atomInfo);
845 +
846 +    //add atom data into atom's property
847 +
848 +    if(!haveAtomData){
849 +      atomData->setID("ATOMDATA");
850 +      datom->addProperty(atomData);
851 +    }
852 +
853 +    setVisited(datom);
854 +
855 +  }
856 +
857 +  const std::string HeadAtomVisitor::toString(){
858 +    char buffer[65535];
859 +    std::string result;
860 +  
861 +    sprintf(buffer ,"------------------------------------------------------------------\n");
862 +    result += buffer;
863 +
864 +    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
865 +    result += buffer;
866 +
867 +    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
868 +    result += buffer;
869 +
870 +    sprintf(buffer ,"------------------------------------------------------------------\n");
871 +    result += buffer;
872 +
873 +    return result;
874 +  }
875 +
876 +
877    //----------------------------------------------------------------------------//
878  
879    void DefaultAtomVisitor::visit(Atom *atom) {

Diff Legend

– Removed lines
+ Added lines
< Changed lines
> Changed lines