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root/OpenMD/trunk/src/visitors/AtomVisitor.cpp
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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 1008 by chrisfen, Wed Jul 19 12:35:31 2006 UTC vs.
Revision 1244 by xsun, Wed May 14 21:04:13 2008 UTC

# Line 522 | Line 522 | namespace oopse {
522  
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);
525 >    Vector3d c1(0.0, 0.0, 0.0);
526 >    Vector3d c2(0.0, 0.0, 1.0);
527      RotMat3x3d rotMatrix;
528      RotMat3x3d rotTrans;
529      AtomInfo* atomInfo;
530      Vector3d pos;
531      Vector3d newVec;
532 +    Vector3d dVec;
533      Quat4d q;
534      AtomData* atomData;
535      GenericData* data;
# Line 539 | Line 537 | namespace oopse {
537  
538      //if atom is not GBlipid atom, just skip it
539      if(!isGBLipidAtom(datom->getType()))
540 +      return;
541 +
542 +    data = datom->getPropertyByName("ATOMDATA");
543 +    if(data != NULL){
544 +      atomData = dynamic_cast<AtomData*>(data);  
545 +      if(atomData == NULL){
546 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
547 +        atomData = new AtomData;
548 +        haveAtomData = false;      
549 +      } else {
550 +        haveAtomData = true;
551 +      }
552 +    } else {
553 +      atomData = new AtomData;
554 +      haveAtomData = false;
555 +    }
556 +  
557 +  
558 +    pos = datom->getPos();
559 +    q = datom->getQ();
560 +    rotMatrix = datom->getA();
561 +
562 +    // We need A^T to convert from body-fixed to space-fixed:  
563 +    rotTrans = rotMatrix.transpose();
564 +
565 +    newVec = rotTrans * c1;
566 +    dVec = rotTrans * c2;
567 +    atomInfo = new AtomInfo;
568 +    atomInfo->atomTypeName = "GB";
569 +    atomInfo->pos[0] = pos[0] + newVec[0];
570 +    atomInfo->pos[1] = pos[1] + newVec[1];
571 +    atomInfo->pos[2] = pos[2] + newVec[2];
572 +    atomInfo->dipole[0] = dVec[0];
573 +    atomInfo->dipole[1] = dVec[1];
574 +    atomInfo->dipole[2] = dVec[2];
575 +    atomInfo->hasVector = true;
576 +    atomInfo->charge = 3.0;
577 +    atomInfo->hasCharge = true;
578 +    atomData->addAtomInfo(atomInfo);
579 +
580 +    //add atom data into atom's property
581 +
582 +    if(!haveAtomData){
583 +      atomData->setID("ATOMDATA");
584 +      datom->addProperty(atomData);
585 +    }
586 +
587 +    setVisited(datom);
588 +
589 +  }
590 +
591 +  const std::string GBLipidAtomVisitor::toString(){
592 +    char buffer[65535];
593 +    std::string result;
594 +  
595 +    sprintf(buffer ,"------------------------------------------------------------------\n");
596 +    result += buffer;
597 +
598 +    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
599 +    result += buffer;
600 +
601 +    sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
602 +    result += buffer;
603 +
604 +    sprintf(buffer ,"------------------------------------------------------------------\n");
605 +    result += buffer;
606 +
607 +    return result;
608 +  }
609 +
610 +  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
611 +    std::set<std::string>::iterator strIter;
612 +    strIter = Ring5gbAtomType.find(atomType);
613 +
614 +    return strIter != Ring5gbAtomType.end() ? true : false;
615 +  }
616 +
617 +  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
618 +    std::vector<AtomInfo*> atoms;
619 +    //we need to convert linear into 4 different atoms
620 +    Vector3d c1(0.0, 0.0, -5.5);
621 +    Vector3d c2(0.0, 0.0, -1.8);
622 +    Vector3d c3(0.0, 0.0,  1.8);
623 +    Vector3d c4(0.0, 0.0,  5.5);
624 +    RotMat3x3d rotMatrix;
625 +    RotMat3x3d rotTrans;
626 +    AtomInfo* atomInfo;
627 +    Vector3d pos;
628 +    Vector3d newVec;
629 +    Vector3d dVec;
630 +    Quat4d q;
631 +    AtomData* atomData;
632 +    GenericData* data;
633 +    bool haveAtomData;
634 +
635 +    //if atom is not Ring5GB atom, just skip it
636 +    if(!isRing5gbAtom(datom->getType()))
637        return;
638  
639      data = datom->getPropertyByName("ATOMDATA");
# Line 619 | Line 714 | namespace oopse {
714  
715    }
716  
717 <  const std::string GBLipidAtomVisitor::toString(){
717 >  const std::string Ring5gbAtomVisitor::toString(){
718      char buffer[65535];
719      std::string result;
720    
# Line 629 | Line 724 | namespace oopse {
724      sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
725      result += buffer;
726  
727 <    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
727 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
728      result += buffer;
729  
730      sprintf(buffer ,"------------------------------------------------------------------\n");
# Line 638 | Line 733 | namespace oopse {
733      return result;
734    }
735  
736 +  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
737 +    std::set<std::string>::iterator strIter;
738 +    strIter = HeadAtomType.find(atomType);
739 +
740 +    return strIter != HeadAtomType.end() ? true : false;
741 +  }
742 +
743 +  void HeadAtomVisitor::visit(DirectionalAtom* datom){
744 +    std::vector<AtomInfo*> atoms;
745 +    //we need to convert linear into 2 different atoms
746 +    Vector3d c1(0.0, 0.0, -1.5);
747 +    Vector3d c2(0.0, 0.0, 1.5);
748 +    RotMat3x3d rotMatrix;
749 +    RotMat3x3d rotTrans;
750 +    AtomInfo* atomInfo;
751 +    Vector3d pos;
752 +    Vector3d newVec;
753 +    Vector3d dVec;
754 +    Quat4d q;
755 +    AtomData* atomData;
756 +    GenericData* data;
757 +    bool haveAtomData;
758 +
759 +    //if atom is not Head atom, just skip it
760 +    if(!isHeadAtom(datom->getType()))
761 +      return;
762 +
763 +    data = datom->getPropertyByName("ATOMDATA");
764 +    if(data != NULL){
765 +      atomData = dynamic_cast<AtomData*>(data);  
766 +      if(atomData == NULL){
767 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
768 +        atomData = new AtomData;
769 +        haveAtomData = false;      
770 +      } else {
771 +        haveAtomData = true;
772 +      }
773 +    } else {
774 +      atomData = new AtomData;
775 +      haveAtomData = false;
776 +    }
777 +  
778 +  
779 +    pos = datom->getPos();
780 +    q = datom->getQ();
781 +    rotMatrix = datom->getA();
782 +
783 +    // We need A^T to convert from body-fixed to space-fixed:  
784 +    rotTrans = rotMatrix.transpose();
785 +
786 +    newVec = rotTrans * c1;
787 +    atomInfo = new AtomInfo;
788 +    atomInfo->atomTypeName = "C";
789 +    atomInfo->pos[0] = pos[0] + newVec[0];
790 +    atomInfo->pos[1] = pos[1] + newVec[1];
791 +    atomInfo->pos[2] = pos[2] + newVec[2];
792 +    atomInfo->dipole[0] = 0.0;
793 +    atomInfo->dipole[1] = 0.0;
794 +    atomInfo->dipole[2] = 0.0;
795 +    atomData->addAtomInfo(atomInfo);
796 +
797 +    newVec = rotTrans * c2;
798 +    atomInfo = new AtomInfo;
799 +    atomInfo->atomTypeName = "O";
800 +    atomInfo->pos[0] = pos[0] + newVec[0];
801 +    atomInfo->pos[1] = pos[1] + newVec[1];
802 +    atomInfo->pos[2] = pos[2] + newVec[2];
803 +    atomInfo->dipole[0] = 0.0;
804 +    atomInfo->dipole[1] = 0.0;
805 +    atomInfo->dipole[2] = 0.0;
806 +    atomData->addAtomInfo(atomInfo);
807 +
808 +    //add atom data into atom's property
809 +
810 +    if(!haveAtomData){
811 +      atomData->setID("ATOMDATA");
812 +      datom->addProperty(atomData);
813 +    }
814 +
815 +    setVisited(datom);
816 +
817 +  }
818 +
819 +  const std::string HeadAtomVisitor::toString(){
820 +    char buffer[65535];
821 +    std::string result;
822 +  
823 +    sprintf(buffer ,"------------------------------------------------------------------\n");
824 +    result += buffer;
825 +
826 +    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
827 +    result += buffer;
828 +
829 +    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
830 +    result += buffer;
831 +
832 +    sprintf(buffer ,"------------------------------------------------------------------\n");
833 +    result += buffer;
834 +
835 +    return result;
836 +  }
837 +
838 +
839    //----------------------------------------------------------------------------//
840  
841    void DefaultAtomVisitor::visit(Atom *atom) {

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