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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 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
12 > * 2. Redistributions in binary form must reproduce the above copyright
13   *    notice, this list of conditions and the following disclaimer in the
14   *    documentation and/or other materials provided with the
15   *    distribution.
# Line 37 | Line 28
28   * arising out of the use of or inability to use software, even if the
29   * University of Notre Dame has been advised of the possibility of
30   * such damages.
31 + *
32 + * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33 + * research, please cite the appropriate papers when you publish your
34 + * work.  Good starting points are:
35 + *                                                                      
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).                        
40   */
41  
42   #include <cstring>
# Line 44 | Line 44
44   #include "primitives/DirectionalAtom.hpp"
45   #include "primitives/RigidBody.hpp"
46  
47 < namespace oopse {
47 > namespace OpenMD {
48    void BaseAtomVisitor::visit(RigidBody *rb) {
49      //vector<Atom*> myAtoms;
50      //vector<Atom*>::iterator atomIter;
# Line 384 | Line 384 | namespace oopse {
384      AtomData* atomData;
385      GenericData* data;
386      bool haveAtomData;
387 –    AtomType* atomType;
387      //if atom is not linear atom, just skip it
388      if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
389        return;
# Line 409 | Line 408 | namespace oopse {
408                else {
409                      sprintf( painCave.errMsg,
410                             "Can not cast GenericData to GayBerneParam\n");
411 <                    painCave.severity = OOPSE_ERROR;
411 >                    painCave.severity = OPENMD_ERROR;
412                      painCave.isFatal = 1;
413                      simError();          
414          }            
# Line 522 | Line 521 | namespace oopse {
521  
522    void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
523      std::vector<AtomInfo*> atoms;
524 <    //we need to convert linear into 4 different atoms
525 <    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);
524 >    Vector3d c1(0.0, 0.0, 0.0);
525 >    Vector3d c2(0.0, 0.0, 1.0);
526      RotMat3x3d rotMatrix;
527      RotMat3x3d rotTrans;
528      AtomInfo* atomInfo;
529      Vector3d pos;
530      Vector3d newVec;
531 +    Vector3d dVec;
532      Quat4d q;
533      AtomData* atomData;
534      GenericData* data;
# Line 565 | Line 562 | namespace oopse {
562      rotTrans = rotMatrix.transpose();
563  
564      newVec = rotTrans * c1;
565 +    dVec = rotTrans * c2;
566      atomInfo = new AtomInfo;
567 +    atomInfo->atomTypeName = "GB";
568 +    atomInfo->pos[0] = pos[0] + newVec[0];
569 +    atomInfo->pos[1] = pos[1] + newVec[1];
570 +    atomInfo->pos[2] = pos[2] + newVec[2];
571 +    atomInfo->dipole[0] = dVec[0];
572 +    atomInfo->dipole[1] = dVec[1];
573 +    atomInfo->dipole[2] = dVec[2];
574 +    atomInfo->hasVector = true;
575 +    atomInfo->charge = 3.0;
576 +    atomInfo->hasCharge = true;
577 +    atomData->addAtomInfo(atomInfo);
578 +
579 +    //add atom data into atom's property
580 +
581 +    if(!haveAtomData){
582 +      atomData->setID("ATOMDATA");
583 +      datom->addProperty(atomData);
584 +    }
585 +
586 +    setVisited(datom);
587 +
588 +  }
589 +
590 +  const std::string GBLipidAtomVisitor::toString(){
591 +    char buffer[65535];
592 +    std::string result;
593 +  
594 +    sprintf(buffer ,"------------------------------------------------------------------\n");
595 +    result += buffer;
596 +
597 +    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
598 +    result += buffer;
599 +
600 +    sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
601 +    result += buffer;
602 +
603 +    sprintf(buffer ,"------------------------------------------------------------------\n");
604 +    result += buffer;
605 +
606 +    return result;
607 +  }
608 +
609 +  bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
610 +    std::set<std::string>::iterator strIter;
611 +    strIter = Ring5gbAtomType.find(atomType);
612 +
613 +    return strIter != Ring5gbAtomType.end() ? true : false;
614 +  }
615 +
616 +  void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
617 +    std::vector<AtomInfo*> atoms;
618 +    //we need to convert linear into 4 different atoms
619 +    Vector3d c1(0.0, 0.0, -5.5);
620 +    Vector3d c2(0.0, 0.0, -1.8);
621 +    Vector3d c3(0.0, 0.0,  1.8);
622 +    Vector3d c4(0.0, 0.0,  5.5);
623 +    RotMat3x3d rotMatrix;
624 +    RotMat3x3d rotTrans;
625 +    AtomInfo* atomInfo;
626 +    Vector3d pos;
627 +    Vector3d newVec;
628 +    Vector3d dVec;
629 +    Quat4d q;
630 +    AtomData* atomData;
631 +    GenericData* data;
632 +    bool haveAtomData;
633 +
634 +    //if atom is not Ring5GB atom, just skip it
635 +    if(!isRing5gbAtom(datom->getType()))
636 +      return;
637 +
638 +    data = datom->getPropertyByName("ATOMDATA");
639 +    if(data != NULL){
640 +      atomData = dynamic_cast<AtomData*>(data);  
641 +      if(atomData == NULL){
642 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
643 +        atomData = new AtomData;
644 +        haveAtomData = false;      
645 +      } else {
646 +        haveAtomData = true;
647 +      }
648 +    } else {
649 +      atomData = new AtomData;
650 +      haveAtomData = false;
651 +    }
652 +  
653 +  
654 +    pos = datom->getPos();
655 +    q = datom->getQ();
656 +    rotMatrix = datom->getA();
657 +
658 +    // We need A^T to convert from body-fixed to space-fixed:  
659 +    rotTrans = rotMatrix.transpose();
660 +
661 +    newVec = rotTrans * c1;
662 +    atomInfo = new AtomInfo;
663      atomInfo->atomTypeName = "K";
664      atomInfo->pos[0] = pos[0] + newVec[0];
665      atomInfo->pos[1] = pos[1] + newVec[1];
# Line 619 | Line 713 | namespace oopse {
713  
714    }
715  
716 <  const std::string GBLipidAtomVisitor::toString(){
716 >  const std::string Ring5gbAtomVisitor::toString(){
717      char buffer[65535];
718      std::string result;
719    
# Line 629 | Line 723 | namespace oopse {
723      sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
724      result += buffer;
725  
726 <    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
726 >    sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
727      result += buffer;
728  
729      sprintf(buffer ,"------------------------------------------------------------------\n");
# Line 638 | Line 732 | namespace oopse {
732      return result;
733    }
734  
735 +  bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
736 +    std::set<std::string>::iterator strIter;
737 +    strIter = HeadAtomType.find(atomType);
738 +
739 +    return strIter != HeadAtomType.end() ? true : false;
740 +  }
741 +
742 +  void HeadAtomVisitor::visit(DirectionalAtom* datom){
743 +    std::vector<AtomInfo*> atoms;
744 +    //we need to convert linear into 2 different atoms
745 +    Vector3d c1(0.0, 0.0, -1.5);
746 +    Vector3d c2(0.0, 0.0, 1.5);
747 +    RotMat3x3d rotMatrix;
748 +    RotMat3x3d rotTrans;
749 +    AtomInfo* atomInfo;
750 +    Vector3d pos;
751 +    Vector3d newVec;
752 +    Vector3d dVec;
753 +    Quat4d q;
754 +    AtomData* atomData;
755 +    GenericData* data;
756 +    bool haveAtomData;
757 +
758 +    //if atom is not Head atom, just skip it
759 +    if(!isHeadAtom(datom->getType()))
760 +      return;
761 +
762 +    data = datom->getPropertyByName("ATOMDATA");
763 +    if(data != NULL){
764 +      atomData = dynamic_cast<AtomData*>(data);  
765 +      if(atomData == NULL){
766 +        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
767 +        atomData = new AtomData;
768 +        haveAtomData = false;      
769 +      } else {
770 +        haveAtomData = true;
771 +      }
772 +    } else {
773 +      atomData = new AtomData;
774 +      haveAtomData = false;
775 +    }
776 +  
777 +  
778 +    pos = datom->getPos();
779 +    q = datom->getQ();
780 +    rotMatrix = datom->getA();
781 +
782 +    // We need A^T to convert from body-fixed to space-fixed:  
783 +    rotTrans = rotMatrix.transpose();
784 +
785 +    newVec = rotTrans * c1;
786 +    atomInfo = new AtomInfo;
787 +    atomInfo->atomTypeName = "C";
788 +    atomInfo->pos[0] = pos[0] + newVec[0];
789 +    atomInfo->pos[1] = pos[1] + newVec[1];
790 +    atomInfo->pos[2] = pos[2] + newVec[2];
791 +    atomInfo->dipole[0] = 0.0;
792 +    atomInfo->dipole[1] = 0.0;
793 +    atomInfo->dipole[2] = 0.0;
794 +    atomData->addAtomInfo(atomInfo);
795 +
796 +    newVec = rotTrans * c2;
797 +    atomInfo = new AtomInfo;
798 +    atomInfo->atomTypeName = "O";
799 +    atomInfo->pos[0] = pos[0] + newVec[0];
800 +    atomInfo->pos[1] = pos[1] + newVec[1];
801 +    atomInfo->pos[2] = pos[2] + newVec[2];
802 +    atomInfo->dipole[0] = 0.0;
803 +    atomInfo->dipole[1] = 0.0;
804 +    atomInfo->dipole[2] = 0.0;
805 +    atomData->addAtomInfo(atomInfo);
806 +
807 +    //add atom data into atom's property
808 +
809 +    if(!haveAtomData){
810 +      atomData->setID("ATOMDATA");
811 +      datom->addProperty(atomData);
812 +    }
813 +
814 +    setVisited(datom);
815 +
816 +  }
817 +
818 +  const std::string HeadAtomVisitor::toString(){
819 +    char buffer[65535];
820 +    std::string result;
821 +  
822 +    sprintf(buffer ,"------------------------------------------------------------------\n");
823 +    result += buffer;
824 +
825 +    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
826 +    result += buffer;
827 +
828 +    sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
829 +    result += buffer;
830 +
831 +    sprintf(buffer ,"------------------------------------------------------------------\n");
832 +    result += buffer;
833 +
834 +    return result;
835 +  }
836 +
837 +
838    //----------------------------------------------------------------------------//
839  
840    void DefaultAtomVisitor::visit(Atom *atom) {
# Line 724 | Line 921 | namespace oopse {
921  
922      return result;
923    }
924 < } //namespace oopse
924 > } //namespace OpenMD

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