src/visitors/AtomVisitor.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include <cstring>
#include "visitors/AtomVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"

namespace oopse {
  void BaseAtomVisitor::visit(RigidBody *rb) {
    //vector<Atom*> myAtoms;
    //vector<Atom*>::iterator atomIter;

    //myAtoms = rb->getAtoms();

    //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
    //  (*atomIter)->accept(this);
  }

  void BaseAtomVisitor::setVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");

    //if visited property is not existed, add it as new property
    if (data == NULL) {
      data = new GenericData();
      data->setID("VISITED");
      atom->addProperty(data);
    }
  }

  bool BaseAtomVisitor::isVisited(Atom *atom) {
    GenericData *data;
    data = atom->getPropertyByName("VISITED");
    return data == NULL ? false : true;
  }

  bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
    std::set<std::string>::iterator strIter;
    strIter = ssdAtomType.find(atomType);
    return strIter != ssdAtomType.end() ? true : false;
  }

  void SSDAtomVisitor::visit(DirectionalAtom *datom) {
    std::vector<AtomInfo*>atoms;

    //we need to convert SSD into 4 differnet atoms
    //one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
    //of the water with a dipole moment
    Vector3d h1(0.0, -0.75695, 0.5206);
    Vector3d h2(0.0, 0.75695, 0.5206);
    Vector3d ox(0.0, 0.0, -0.0654);
    Vector3d u(0, 0, 1);
    RotMat3x3d   rotMatrix;
    RotMat3x3d   rotTrans;
    AtomInfo *   atomInfo;
    Vector3d     pos;
    Vector3d     newVec;
    Quat4d       q;
    AtomData *   atomData;
    GenericData *data;
    bool         haveAtomData;

    //if atom is not SSD atom, just skip it
    if (!isSSDAtom(datom->getType()))
      return;

    data = datom->getPropertyByName("ATOMDATA");

    if (data != NULL) {
      atomData = dynamic_cast<AtomData *>(data);

      if (atomData == NULL) {
        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
        atomData = new AtomData;
        haveAtomData = false;
      } else
        haveAtomData = true;
    } else {
      atomData = new AtomData;
      haveAtomData = false;
    }

    pos = datom->getPos();
    q = datom->getQ();
    rotMatrix = datom->getA();

    // We need A^T to convert from body-fixed to space-fixed:
    //transposeMat3(rotMatrix, rotTrans);
    rotTrans = rotMatrix.transpose();

    //center of mass of the water molecule
    //matVecMul3(rotTrans, u, newVec);
    newVec = rotTrans * u;

    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "X";
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->dipole[0] = newVec[0];
    atomInfo->dipole[1] = newVec[1];
    atomInfo->dipole[2] = newVec[2];

    atomData->addAtomInfo(atomInfo);

    //oxygen
    //matVecMul3(rotTrans, ox, newVec);
    newVec = rotTrans * ox;

    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "O";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //hydrogen1
    //matVecMul3(rotTrans, h1, newVec);
    newVec = rotTrans * h1;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "H";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //hydrogen2
    //matVecMul3(rotTrans, h2, newVec);
    newVec = rotTrans * h2;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "H";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //add atom data into atom's property

    if (!haveAtomData) {
      atomData->setID("ATOMDATA");
      datom->addProperty(atomData);
    }

    setVisited(datom);
  }

  const std::string SSDAtomVisitor::toString() {
    char   buffer[65535];
    std::string result;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer,
            "Visitor Description: Convert SSD into 4 different atoms\n");
    result += buffer;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    return result;
  }

  bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
    std::set<std::string>::iterator strIter;
    strIter = linearAtomType.find(atomType);

    return strIter != linearAtomType.end() ? true : false;
  }

  void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
   linearAtomType.insert(atomType); 
  }

  void LinearAtomVisitor::visit(DirectionalAtom* datom){
    std::vector<AtomInfo*> atoms;
    //we need to convert linear into 4 different atoms
    Vector3d c1(0.0, 0.0, -1.8);
    Vector3d c2(0.0, 0.0, -0.6);
    Vector3d c3(0.0, 0.0,  0.6);
    Vector3d c4(0.0, 0.0,  1.8);
    RotMat3x3d rotMatrix;
    RotMat3x3d rotTrans;
    AtomInfo* atomInfo;
    Vector3d pos;
    Vector3d newVec;
    Quat4d q;
    AtomData* atomData;
    GenericData* data;
    bool haveAtomData;
    AtomType* atomType;
    //if atom is not SSD atom, just skip it
    if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
      return;

    //setup GayBerne type in fortran side
    data = datom->getAtomType()->getPropertyByName("GayBerne");
    if (data != NULL) {
       GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);

       if (gayBerneData != NULL) {
           GayBerneParam gayBerneParam = gayBerneData->getData();

                                          double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
                                                        c1[2] = -halfLen;
              c2[2] = -halfLen /2;
              c3[2] = halfLen/2;
              c4[2] = halfLen;
                
            } 
            
              else {
                    sprintf( painCave.errMsg,
                           "Can not cast GenericData to GayBerneParam\n");
                    painCave.severity = OOPSE_ERROR;
                    painCave.isFatal = 1;
                    simError();          
        }            
    } 


    data = datom->getPropertyByName("ATOMDATA");
    if(data != NULL){
      atomData = dynamic_cast<AtomData*>(data);  
      if(atomData == NULL){
        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
        atomData = new AtomData; 
        haveAtomData = false;      
      } else {
        haveAtomData = true;
      }
    } else {
      atomData = new AtomData;
      haveAtomData = false;
    }
   
  
    pos = datom->getPos();
    q = datom->getQ();
    rotMatrix = datom->getA();

    // We need A^T to convert from body-fixed to space-fixed:  
    rotTrans = rotMatrix.transpose();

    newVec = rotTrans * c1;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c2;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c3;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c4;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "C";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //add atom data into atom's property

    if(!haveAtomData){
      atomData->setID("ATOMDATA");
      datom->addProperty(atomData);
    }

    setVisited(datom);

  }

  const std::string LinearAtomVisitor::toString(){
    char buffer[65535];
    std::string result;
  
    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
    result += buffer;

    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    return result;
  }

  bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
    std::set<std::string>::iterator strIter;
    strIter = GBLipidAtomType.find(atomType);

    return strIter != GBLipidAtomType.end() ? true : false;
  }

  void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
    std::vector<AtomInfo*> atoms;
    //we need to convert linear into 4 different atoms
    Vector3d c1(0.0, 0.0, -6.25);
    Vector3d c2(0.0, 0.0, -2.1);
    Vector3d c3(0.0, 0.0,  2.1);
    Vector3d c4(0.0, 0.0,  6.25);
    RotMat3x3d rotMatrix;
    RotMat3x3d rotTrans;
    AtomInfo* atomInfo;
    Vector3d pos;
    Vector3d newVec;
    Quat4d q;
    AtomData* atomData;
    GenericData* data;
    bool haveAtomData;

    //if atom is not GBlipid atom, just skip it
    if(!isGBLipidAtom(datom->getType()))
      return;

    data = datom->getPropertyByName("ATOMDATA");
    if(data != NULL){
      atomData = dynamic_cast<AtomData*>(data);  
      if(atomData == NULL){
        std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
        atomData = new AtomData; 
        haveAtomData = false;      
      } else {
        haveAtomData = true;
      }
    } else {
      atomData = new AtomData;
      haveAtomData = false;
    }
   
  
    pos = datom->getPos();
    q = datom->getQ();
    rotMatrix = datom->getA();

    // We need A^T to convert from body-fixed to space-fixed:  
    rotTrans = rotMatrix.transpose();

    newVec = rotTrans * c1;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c2;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c3;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    newVec = rotTrans * c4;
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "K";
    atomInfo->pos[0] = pos[0] + newVec[0];
    atomInfo->pos[1] = pos[1] + newVec[1];
    atomInfo->pos[2] = pos[2] + newVec[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;
    atomData->addAtomInfo(atomInfo);

    //add atom data into atom's property

    if(!haveAtomData){
      atomData->setID("ATOMDATA");
      datom->addProperty(atomData);
    }

    setVisited(datom);

  }

  const std::string GBLipidAtomVisitor::toString(){
    char buffer[65535];
    std::string result;
  
    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
    result += buffer;

    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    return result;
  }

  //----------------------------------------------------------------------------//

  void DefaultAtomVisitor::visit(Atom *atom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;

    if (isVisited(atom))
      return;

    atomInfo = new AtomInfo;

    atomData = new AtomData;
    atomData->setID("ATOMDATA");

    pos = atom->getPos();
    atomInfo->atomTypeName = atom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->dipole[0] = 0.0;
    atomInfo->dipole[1] = 0.0;
    atomInfo->dipole[2] = 0.0;

    atomData->addAtomInfo(atomInfo);

    atom->addProperty(atomData);

    setVisited(atom);
  }

  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;
    Vector3d  u;

    if (isVisited(datom))
      return;

    pos = datom->getPos();
    if (datom->getAtomType()->isGayBerne()) {
        u = datom->getA().transpose()*V3Z;         
    } else if (datom->getAtomType()->isMultipole()) {
        u = datom->getElectroFrame().getColumn(2);
    }
    atomData = new AtomData;
    atomData->setID("ATOMDATA");
    atomInfo = new AtomInfo;

    atomInfo->atomTypeName = datom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->dipole[0] = u[0];
    atomInfo->dipole[1] = u[1];
    atomInfo->dipole[2] = u[2];

    atomData->addAtomInfo(atomInfo);

    datom->addProperty(atomData);

    setVisited(datom);
  }

  const std::string DefaultAtomVisitor::toString() {
    char   buffer[65535];
    std::string result;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    sprintf(buffer,
            "Visitor Description: copy atom infomation into atom data\n");
    result += buffer;

    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;

    return result;
  }
} //namespace oopse
Revision:	2866
Committed:	Sat Jun 17 17:02:33 2006 UTC (18 years, 3 months ago) by tim
File size:	17212 byte(s)
Log Message:	output the principle axis of GB
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
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
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42	gezelter	1490	#include <cstring>
43	tim	1492	#include "visitors/AtomVisitor.hpp"
44			#include "primitives/DirectionalAtom.hpp"
45			#include "primitives/RigidBody.hpp"
46	gezelter	1490
47	tim	1625	namespace oopse {
48	gezelter	2204	void BaseAtomVisitor::visit(RigidBody *rb) {
49			//vector<Atom*> myAtoms;
50			//vector<Atom*>::iterator atomIter;
51	tim	1625
52	gezelter	2204	//myAtoms = rb->getAtoms();
53	gezelter	1490
54	gezelter	2204	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55			// (*atomIter)->accept(this);
56			}
57	gezelter	1490
58	gezelter	2204	void BaseAtomVisitor::setVisited(Atom *atom) {
59	gezelter	1930	GenericData *data;
60			data = atom->getPropertyByName("VISITED");
61	gezelter	1490
62	gezelter	1930	//if visited property is not existed, add it as new property
63			if (data == NULL) {
64	gezelter	2204	data = new GenericData();
65			data->setID("VISITED");
66			atom->addProperty(data);
67	gezelter	1930	}
68	gezelter	2204	}
69	gezelter	1490
70	gezelter	2204	bool BaseAtomVisitor::isVisited(Atom *atom) {
71	gezelter	1930	GenericData *data;
72			data = atom->getPropertyByName("VISITED");
73			return data == NULL ? false : true;
74	gezelter	2204	}
75	gezelter	1490
76	gezelter	2204	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
77	tim	1931	std::set<std::string>::iterator strIter;
78			strIter = ssdAtomType.find(atomType);
79			return strIter != ssdAtomType.end() ? true : false;
80	gezelter	2204	}
81	gezelter	1490
82	gezelter	2204	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83	tim	1931	std::vector<AtomInfo*>atoms;
84	gezelter	1490
85	gezelter	1930	//we need to convert SSD into 4 differnet atoms
86			//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87			//of the water with a dipole moment
88			Vector3d h1(0.0, -0.75695, 0.5206);
89			Vector3d h2(0.0, 0.75695, 0.5206);
90			Vector3d ox(0.0, 0.0, -0.0654);
91			Vector3d u(0, 0, 1);
92			RotMat3x3d rotMatrix;
93			RotMat3x3d rotTrans;
94			AtomInfo * atomInfo;
95			Vector3d pos;
96			Vector3d newVec;
97			Quat4d q;
98			AtomData * atomData;
99			GenericData *data;
100			bool haveAtomData;
101	gezelter	1490
102	gezelter	1930	//if atom is not SSD atom, just skip it
103			if (!isSSDAtom(datom->getType()))
104	gezelter	2204	return;
105	gezelter	1490
106	gezelter	1930	data = datom->getPropertyByName("ATOMDATA");
107	gezelter	1490
108	gezelter	1930	if (data != NULL) {
109	gezelter	2204	atomData = dynamic_cast<AtomData *>(data);
110	gezelter	1930
111	gezelter	2204	if (atomData == NULL) {
112			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113			atomData = new AtomData;
114			haveAtomData = false;
115			} else
116			haveAtomData = true;
117	gezelter	1930	} else {
118	gezelter	2204	atomData = new AtomData;
119			haveAtomData = false;
120	gezelter	1490	}
121
122	gezelter	1930	pos = datom->getPos();
123			q = datom->getQ();
124			rotMatrix = datom->getA();
125	gezelter	1490
126	gezelter	1930	// We need A^T to convert from body-fixed to space-fixed:
127			//transposeMat3(rotMatrix, rotTrans);
128			rotTrans = rotMatrix.transpose();
129	gezelter	1490
130	gezelter	1930	//center of mass of the water molecule
131			//matVecMul3(rotTrans, u, newVec);
132			newVec = rotTrans * u;
133	gezelter	1490
134	gezelter	1930	atomInfo = new AtomInfo;
135	gezelter	2091	atomInfo->atomTypeName = "X";
136	gezelter	1930	atomInfo->pos[0] = pos[0];
137			atomInfo->pos[1] = pos[1];
138			atomInfo->pos[2] = pos[2];
139			atomInfo->dipole[0] = newVec[0];
140			atomInfo->dipole[1] = newVec[1];
141			atomInfo->dipole[2] = newVec[2];
142	gezelter	1490
143	gezelter	1930	atomData->addAtomInfo(atomInfo);
144	gezelter	1490
145	gezelter	1930	//oxygen
146			//matVecMul3(rotTrans, ox, newVec);
147			newVec = rotTrans * ox;
148	gezelter	1490
149	gezelter	1930	atomInfo = new AtomInfo;
150	gezelter	2091	atomInfo->atomTypeName = "O";
151	gezelter	1930	atomInfo->pos[0] = pos[0] + newVec[0];
152			atomInfo->pos[1] = pos[1] + newVec[1];
153			atomInfo->pos[2] = pos[2] + newVec[2];
154			atomInfo->dipole[0] = 0.0;
155			atomInfo->dipole[1] = 0.0;
156			atomInfo->dipole[2] = 0.0;
157			atomData->addAtomInfo(atomInfo);
158	gezelter	1490
159	gezelter	1930	//hydrogen1
160			//matVecMul3(rotTrans, h1, newVec);
161			newVec = rotTrans * h1;
162			atomInfo = new AtomInfo;
163	gezelter	2091	atomInfo->atomTypeName = "H";
164	gezelter	1930	atomInfo->pos[0] = pos[0] + newVec[0];
165			atomInfo->pos[1] = pos[1] + newVec[1];
166			atomInfo->pos[2] = pos[2] + newVec[2];
167			atomInfo->dipole[0] = 0.0;
168			atomInfo->dipole[1] = 0.0;
169			atomInfo->dipole[2] = 0.0;
170			atomData->addAtomInfo(atomInfo);
171	gezelter	1490
172	gezelter	1930	//hydrogen2
173			//matVecMul3(rotTrans, h2, newVec);
174			newVec = rotTrans * h2;
175			atomInfo = new AtomInfo;
176	gezelter	2091	atomInfo->atomTypeName = "H";
177	gezelter	1930	atomInfo->pos[0] = pos[0] + newVec[0];
178			atomInfo->pos[1] = pos[1] + newVec[1];
179			atomInfo->pos[2] = pos[2] + newVec[2];
180			atomInfo->dipole[0] = 0.0;
181			atomInfo->dipole[1] = 0.0;
182			atomInfo->dipole[2] = 0.0;
183			atomData->addAtomInfo(atomInfo);
184	gezelter	1490
185	gezelter	1930	//add atom data into atom's property
186
187			if (!haveAtomData) {
188	gezelter	2204	atomData->setID("ATOMDATA");
189			datom->addProperty(atomData);
190	gezelter	1930	}
191
192			setVisited(datom);
193	gezelter	2204	}
194	gezelter	1490
195	gezelter	2204	const std::string SSDAtomVisitor::toString() {
196	gezelter	1930	char buffer[65535];
197			std::string result;
198	gezelter	1490
199	gezelter	1930	sprintf(buffer,
200			"------------------------------------------------------------------\n");
201			result += buffer;
202	gezelter	1490
203	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204			result += buffer;
205	gezelter	1490
206	gezelter	1930	sprintf(buffer,
207			"Visitor Description: Convert SSD into 4 different atoms\n");
208			result += buffer;
209	gezelter	1490
210	gezelter	1930	sprintf(buffer,
211			"------------------------------------------------------------------\n");
212			result += buffer;
213
214			return result;
215	gezelter	2204	}
216	gezelter	1490
217	gezelter	2204	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218	tim	1931	std::set<std::string>::iterator strIter;
219			strIter = linearAtomType.find(atomType);
220
221			return strIter != linearAtomType.end() ? true : false;
222	gezelter	2204	}
223	chrisfen	1718
224	tim	2749	void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
225			linearAtomType.insert(atomType);
226			}
227
228	gezelter	2204	void LinearAtomVisitor::visit(DirectionalAtom* datom){
229	tim	1931	std::vector<AtomInfo*> atoms;
230			//we need to convert linear into 4 different atoms
231			Vector3d c1(0.0, 0.0, -1.8);
232			Vector3d c2(0.0, 0.0, -0.6);
233			Vector3d c3(0.0, 0.0, 0.6);
234			Vector3d c4(0.0, 0.0, 1.8);
235			RotMat3x3d rotMatrix;
236			RotMat3x3d rotTrans;
237			AtomInfo* atomInfo;
238			Vector3d pos;
239			Vector3d newVec;
240			Quat4d q;
241			AtomData* atomData;
242			GenericData* data;
243			bool haveAtomData;
244	tim	2866	AtomType* atomType;
245	tim	1931	//if atom is not SSD atom, just skip it
246	tim	2866	if(!isLinearAtom(datom->getType()) \|\| !datom->getAtomType()->isGayBerne())
247	gezelter	2204	return;
248	chrisfen	1718
249	tim	2866	//setup GayBerne type in fortran side
250			data = datom->getAtomType()->getPropertyByName("GayBerne");
251			if (data != NULL) {
252			GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
253
254			if (gayBerneData != NULL) {
255			GayBerneParam gayBerneParam = gayBerneData->getData();
256
257			double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
258			c1[2] = -halfLen;
259			c2[2] = -halfLen /2;
260			c3[2] = halfLen/2;
261			c4[2] = halfLen;
262
263			}
264
265			else {
266			sprintf( painCave.errMsg,
267			"Can not cast GenericData to GayBerneParam\n");
268			painCave.severity = OOPSE_ERROR;
269			painCave.isFatal = 1;
270			simError();
271			}
272			}
273
274
275	tim	1931	data = datom->getPropertyByName("ATOMDATA");
276			if(data != NULL){
277	gezelter	2204	atomData = dynamic_cast<AtomData*>(data);
278			if(atomData == NULL){
279			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
280			atomData = new AtomData;
281			haveAtomData = false;
282			} else {
283			haveAtomData = true;
284			}
285	tim	1931	} else {
286	gezelter	2204	atomData = new AtomData;
287			haveAtomData = false;
288	chrisfen	1718	}
289
290
291	tim	1931	pos = datom->getPos();
292			q = datom->getQ();
293			rotMatrix = datom->getA();
294	chrisfen	1718
295	tim	1931	// We need A^T to convert from body-fixed to space-fixed:
296			rotTrans = rotMatrix.transpose();
297	chrisfen	1718
298	tim	1931	newVec = rotTrans * c1;
299			atomInfo = new AtomInfo;
300	gezelter	2091	atomInfo->atomTypeName = "C";
301	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
302			atomInfo->pos[1] = pos[1] + newVec[1];
303			atomInfo->pos[2] = pos[2] + newVec[2];
304			atomInfo->dipole[0] = 0.0;
305			atomInfo->dipole[1] = 0.0;
306			atomInfo->dipole[2] = 0.0;
307			atomData->addAtomInfo(atomInfo);
308	chrisfen	1718
309	tim	1931	newVec = rotTrans * c2;
310			atomInfo = new AtomInfo;
311	gezelter	2091	atomInfo->atomTypeName = "C";
312	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
313			atomInfo->pos[1] = pos[1] + newVec[1];
314			atomInfo->pos[2] = pos[2] + newVec[2];
315			atomInfo->dipole[0] = 0.0;
316			atomInfo->dipole[1] = 0.0;
317			atomInfo->dipole[2] = 0.0;
318			atomData->addAtomInfo(atomInfo);
319	chrisfen	1718
320	tim	1931	newVec = rotTrans * c3;
321			atomInfo = new AtomInfo;
322	gezelter	2091	atomInfo->atomTypeName = "C";
323	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
324			atomInfo->pos[1] = pos[1] + newVec[1];
325			atomInfo->pos[2] = pos[2] + newVec[2];
326			atomInfo->dipole[0] = 0.0;
327			atomInfo->dipole[1] = 0.0;
328			atomInfo->dipole[2] = 0.0;
329			atomData->addAtomInfo(atomInfo);
330	chrisfen	1718
331	tim	1931	newVec = rotTrans * c4;
332			atomInfo = new AtomInfo;
333	gezelter	2091	atomInfo->atomTypeName = "C";
334	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
335			atomInfo->pos[1] = pos[1] + newVec[1];
336			atomInfo->pos[2] = pos[2] + newVec[2];
337			atomInfo->dipole[0] = 0.0;
338			atomInfo->dipole[1] = 0.0;
339			atomInfo->dipole[2] = 0.0;
340			atomData->addAtomInfo(atomInfo);
341	chrisfen	1718
342	tim	1931	//add atom data into atom's property
343	chrisfen	1718
344	tim	1931	if(!haveAtomData){
345	gezelter	2204	atomData->setID("ATOMDATA");
346			datom->addProperty(atomData);
347	tim	1931	}
348	chrisfen	1718
349	tim	1931	setVisited(datom);
350
351	gezelter	2204	}
352	chrisfen	1718
353	gezelter	2204	const std::string LinearAtomVisitor::toString(){
354			char buffer[65535];
355			std::string result;
356	chrisfen	1718
357	gezelter	2204	sprintf(buffer ,"------------------------------------------------------------------\n");
358			result += buffer;
359	chrisfen	1718
360	gezelter	2204	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
361			result += buffer;
362	chrisfen	1718
363	gezelter	2204	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
364			result += buffer;
365	chrisfen	1718
366	gezelter	2204	sprintf(buffer ,"------------------------------------------------------------------\n");
367			result += buffer;
368	chrisfen	1718
369	gezelter	2204	return result;
370			}
371	chrisfen	1718
372	xsun	2581	bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
373			std::set<std::string>::iterator strIter;
374			strIter = GBLipidAtomType.find(atomType);
375
376			return strIter != GBLipidAtomType.end() ? true : false;
377			}
378
379			void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
380			std::vector<AtomInfo*> atoms;
381			//we need to convert linear into 4 different atoms
382			Vector3d c1(0.0, 0.0, -6.25);
383			Vector3d c2(0.0, 0.0, -2.1);
384			Vector3d c3(0.0, 0.0, 2.1);
385			Vector3d c4(0.0, 0.0, 6.25);
386			RotMat3x3d rotMatrix;
387			RotMat3x3d rotTrans;
388			AtomInfo* atomInfo;
389			Vector3d pos;
390			Vector3d newVec;
391			Quat4d q;
392			AtomData* atomData;
393			GenericData* data;
394			bool haveAtomData;
395
396			//if atom is not GBlipid atom, just skip it
397			if(!isGBLipidAtom(datom->getType()))
398			return;
399
400			data = datom->getPropertyByName("ATOMDATA");
401			if(data != NULL){
402			atomData = dynamic_cast<AtomData*>(data);
403			if(atomData == NULL){
404			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
405			atomData = new AtomData;
406			haveAtomData = false;
407			} else {
408			haveAtomData = true;
409			}
410			} else {
411			atomData = new AtomData;
412			haveAtomData = false;
413			}
414
415
416			pos = datom->getPos();
417			q = datom->getQ();
418			rotMatrix = datom->getA();
419
420			// We need A^T to convert from body-fixed to space-fixed:
421			rotTrans = rotMatrix.transpose();
422
423			newVec = rotTrans * c1;
424			atomInfo = new AtomInfo;
425			atomInfo->atomTypeName = "K";
426			atomInfo->pos[0] = pos[0] + newVec[0];
427			atomInfo->pos[1] = pos[1] + newVec[1];
428			atomInfo->pos[2] = pos[2] + newVec[2];
429			atomInfo->dipole[0] = 0.0;
430			atomInfo->dipole[1] = 0.0;
431			atomInfo->dipole[2] = 0.0;
432			atomData->addAtomInfo(atomInfo);
433
434			newVec = rotTrans * c2;
435			atomInfo = new AtomInfo;
436			atomInfo->atomTypeName = "K";
437			atomInfo->pos[0] = pos[0] + newVec[0];
438			atomInfo->pos[1] = pos[1] + newVec[1];
439			atomInfo->pos[2] = pos[2] + newVec[2];
440			atomInfo->dipole[0] = 0.0;
441			atomInfo->dipole[1] = 0.0;
442			atomInfo->dipole[2] = 0.0;
443			atomData->addAtomInfo(atomInfo);
444
445			newVec = rotTrans * c3;
446			atomInfo = new AtomInfo;
447			atomInfo->atomTypeName = "K";
448			atomInfo->pos[0] = pos[0] + newVec[0];
449			atomInfo->pos[1] = pos[1] + newVec[1];
450			atomInfo->pos[2] = pos[2] + newVec[2];
451			atomInfo->dipole[0] = 0.0;
452			atomInfo->dipole[1] = 0.0;
453			atomInfo->dipole[2] = 0.0;
454			atomData->addAtomInfo(atomInfo);
455
456			newVec = rotTrans * c4;
457			atomInfo = new AtomInfo;
458			atomInfo->atomTypeName = "K";
459			atomInfo->pos[0] = pos[0] + newVec[0];
460			atomInfo->pos[1] = pos[1] + newVec[1];
461			atomInfo->pos[2] = pos[2] + newVec[2];
462			atomInfo->dipole[0] = 0.0;
463			atomInfo->dipole[1] = 0.0;
464			atomInfo->dipole[2] = 0.0;
465			atomData->addAtomInfo(atomInfo);
466
467			//add atom data into atom's property
468
469			if(!haveAtomData){
470			atomData->setID("ATOMDATA");
471			datom->addProperty(atomData);
472			}
473
474			setVisited(datom);
475
476			}
477
478			const std::string GBLipidAtomVisitor::toString(){
479			char buffer[65535];
480			std::string result;
481
482			sprintf(buffer ,"------------------------------------------------------------------\n");
483			result += buffer;
484
485			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
486			result += buffer;
487
488			sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
489			result += buffer;
490
491			sprintf(buffer ,"------------------------------------------------------------------\n");
492			result += buffer;
493
494			return result;
495			}
496
497	gezelter	2204	//----------------------------------------------------------------------------//
498	gezelter	1490
499	gezelter	2204	void DefaultAtomVisitor::visit(Atom *atom) {
500	gezelter	1930	AtomData *atomData;
501			AtomInfo *atomInfo;
502			Vector3d pos;
503	gezelter	1490
504	gezelter	1930	if (isVisited(atom))
505	gezelter	2204	return;
506	gezelter	1490
507	gezelter	1930	atomInfo = new AtomInfo;
508	gezelter	1490
509	gezelter	1930	atomData = new AtomData;
510			atomData->setID("ATOMDATA");
511	gezelter	1490
512	gezelter	1930	pos = atom->getPos();
513	gezelter	2091	atomInfo->atomTypeName = atom->getType();
514	gezelter	1930	atomInfo->pos[0] = pos[0];
515			atomInfo->pos[1] = pos[1];
516			atomInfo->pos[2] = pos[2];
517			atomInfo->dipole[0] = 0.0;
518			atomInfo->dipole[1] = 0.0;
519			atomInfo->dipole[2] = 0.0;
520	gezelter	1490
521	gezelter	1930	atomData->addAtomInfo(atomInfo);
522	gezelter	1490
523	gezelter	1930	atom->addProperty(atomData);
524
525			setVisited(atom);
526	gezelter	2204	}
527	gezelter	1490
528	gezelter	2204	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
529	gezelter	1930	AtomData *atomData;
530			AtomInfo *atomInfo;
531			Vector3d pos;
532			Vector3d u;
533	gezelter	1490
534	gezelter	1930	if (isVisited(datom))
535	gezelter	2204	return;
536	gezelter	1490
537	gezelter	1930	pos = datom->getPos();
538	tim	2866	if (datom->getAtomType()->isGayBerne()) {
539			u = datom->getA().transpose()*V3Z;
540			} else if (datom->getAtomType()->isMultipole()) {
541			u = datom->getElectroFrame().getColumn(2);
542			}
543	gezelter	1930	atomData = new AtomData;
544			atomData->setID("ATOMDATA");
545			atomInfo = new AtomInfo;
546	gezelter	1490
547	gezelter	2091	atomInfo->atomTypeName = datom->getType();
548	gezelter	1930	atomInfo->pos[0] = pos[0];
549			atomInfo->pos[1] = pos[1];
550			atomInfo->pos[2] = pos[2];
551			atomInfo->dipole[0] = u[0];
552			atomInfo->dipole[1] = u[1];
553			atomInfo->dipole[2] = u[2];
554
555			atomData->addAtomInfo(atomInfo);
556
557			datom->addProperty(atomData);
558
559			setVisited(datom);
560	gezelter	2204	}
561	gezelter	1490
562	gezelter	2204	const std::string DefaultAtomVisitor::toString() {
563	gezelter	1930	char buffer[65535];
564			std::string result;
565	gezelter	1490
566	gezelter	1930	sprintf(buffer,
567			"------------------------------------------------------------------\n");
568			result += buffer;
569	gezelter	1490
570	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
571			result += buffer;
572	gezelter	1490
573	gezelter	1930	sprintf(buffer,
574			"Visitor Description: copy atom infomation into atom data\n");
575			result += buffer;
576	gezelter	1490
577	gezelter	1930	sprintf(buffer,
578			"------------------------------------------------------------------\n");
579			result += buffer;
580	gezelter	1490
581	gezelter	1930	return result;
582	gezelter	2204	}
583	gezelter	1930	} //namespace oopse