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 "math/MatVec3.h"
#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::vector<std::string>::iterator strIter;

    for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end();
        ++strIter )
  if (*strIter == atomType)
      return true;

    return 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->AtomType = "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->AtomType = "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->AtomType = "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->AtomType = "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 string& atomType){
  vector<string>::iterator strIter;
  
  for(strIter = linearAtomType.begin(); strIter != linearAtomType.end(); 
      ++strIter)
    if(*strIter == atomType)
      return true;
  
  return false;  
}

void LinearAtomVisitor::visit(DirectionalAtom* datom){

  vector<AtomInfo*> atoms;

  //we need to convert linear into 4 different atoms
  double c1[3] = {0.0, 0.0, -1.8};
  double c2[3] = {0.0, 0.0, -0.6};
  double c3[3] = {0.0, 0.0,  0.6};
  double c4[3] = {0.0, 0.0,  1.8};
  double rotMatrix[3][3];
  double rotTrans[3][3];
  AtomInfo* atomInfo;
  double pos[3];
  double newVec[3];
  double q[4];
  AtomData* atomData;
  GenericData* data;
  bool haveAtomData;
  
  //if atom is not SSD atom, just skip it
  if(!isLinearAtom(datom->getType()))
    return;
  
  data = datom->getProperty("ATOMDATA");
  if(data != NULL){

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

  // We need A^T to convert from body-fixed to space-fixed:
  transposeMat3(rotMatrix, rotTrans);
  
  matVecMul3(rotTrans, c1, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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);

  matVecMul3(rotTrans, c2, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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);

  matVecMul3(rotTrans, c3, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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);

  matVecMul3(rotTrans, c4, newVec);
  atomInfo = new AtomInfo;
  atomInfo->AtomType = "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 string LinearAtomVisitor::toString(){
  char buffer[65535];
  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;
}

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

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->AtomType = 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();
    u = datom->getElectroFrame().getColumn(3);

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

    atomInfo->AtomType = 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:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 6 months ago) by gezelter
File size:	12422 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
2			* 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 "math/MatVec3.h"
46			#include "primitives/RigidBody.hpp"
47	gezelter	1490
48	tim	1625	namespace oopse {
49	gezelter	1930	void BaseAtomVisitor::visit(RigidBody *rb) {
50			//vector<Atom*> myAtoms;
51			//vector<Atom*>::iterator atomIter;
52	tim	1625
53	gezelter	1930	//myAtoms = rb->getAtoms();
54	gezelter	1490
55	gezelter	1930	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56			// (*atomIter)->accept(this);
57			}
58	gezelter	1490
59	gezelter	1930	void BaseAtomVisitor::setVisited(Atom *atom) {
60			GenericData *data;
61			data = atom->getPropertyByName("VISITED");
62	gezelter	1490
63	gezelter	1930	//if visited property is not existed, add it as new property
64			if (data == NULL) {
65			data = new GenericData();
66			data->setID("VISITED");
67			atom->addProperty(data);
68			}
69	gezelter	1490	}
70
71	gezelter	1930	bool BaseAtomVisitor::isVisited(Atom *atom) {
72			GenericData *data;
73			data = atom->getPropertyByName("VISITED");
74			return data == NULL ? false : true;
75	gezelter	1490	}
76
77	gezelter	1930	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
78			std::vector<std::string>::iterator strIter;
79
80			for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end();
81			++strIter )
82			if (*strIter == atomType)
83			return true;
84
85			return false;
86	gezelter	1490	}
87
88	gezelter	1930	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
89			std::vector<AtomInfo *>atoms;
90	gezelter	1490
91	gezelter	1930	//we need to convert SSD into 4 differnet atoms
92			//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
93			//of the water with a dipole moment
94			Vector3d h1(0.0, -0.75695, 0.5206);
95			Vector3d h2(0.0, 0.75695, 0.5206);
96			Vector3d ox(0.0, 0.0, -0.0654);
97			Vector3d u(0, 0, 1);
98			RotMat3x3d rotMatrix;
99			RotMat3x3d rotTrans;
100			AtomInfo * atomInfo;
101			Vector3d pos;
102			Vector3d newVec;
103			Quat4d q;
104			AtomData * atomData;
105			GenericData *data;
106			bool haveAtomData;
107	gezelter	1490
108	gezelter	1930	//if atom is not SSD atom, just skip it
109			if (!isSSDAtom(datom->getType()))
110			return;
111	gezelter	1490
112	gezelter	1930	data = datom->getPropertyByName("ATOMDATA");
113	gezelter	1490
114	gezelter	1930	if (data != NULL) {
115			atomData = dynamic_cast<AtomData *>(data);
116
117			if (atomData == NULL) {
118			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
119			atomData = new AtomData;
120			haveAtomData = false;
121			} else
122			haveAtomData = true;
123			} else {
124			atomData = new AtomData;
125			haveAtomData = false;
126	gezelter	1490	}
127
128	gezelter	1930	pos = datom->getPos();
129			q = datom->getQ();
130			rotMatrix = datom->getA();
131	gezelter	1490
132	gezelter	1930	// We need A^T to convert from body-fixed to space-fixed:
133			//transposeMat3(rotMatrix, rotTrans);
134			rotTrans = rotMatrix.transpose();
135	gezelter	1490
136	gezelter	1930	//center of mass of the water molecule
137			//matVecMul3(rotTrans, u, newVec);
138			newVec = rotTrans * u;
139	gezelter	1490
140	gezelter	1930	atomInfo = new AtomInfo;
141			atomInfo->AtomType = "X";
142			atomInfo->pos[0] = pos[0];
143			atomInfo->pos[1] = pos[1];
144			atomInfo->pos[2] = pos[2];
145			atomInfo->dipole[0] = newVec[0];
146			atomInfo->dipole[1] = newVec[1];
147			atomInfo->dipole[2] = newVec[2];
148	gezelter	1490
149	gezelter	1930	atomData->addAtomInfo(atomInfo);
150	gezelter	1490
151	gezelter	1930	//oxygen
152			//matVecMul3(rotTrans, ox, newVec);
153			newVec = rotTrans * ox;
154	gezelter	1490
155	gezelter	1930	atomInfo = new AtomInfo;
156			atomInfo->AtomType = "O";
157			atomInfo->pos[0] = pos[0] + newVec[0];
158			atomInfo->pos[1] = pos[1] + newVec[1];
159			atomInfo->pos[2] = pos[2] + newVec[2];
160			atomInfo->dipole[0] = 0.0;
161			atomInfo->dipole[1] = 0.0;
162			atomInfo->dipole[2] = 0.0;
163			atomData->addAtomInfo(atomInfo);
164	gezelter	1490
165	gezelter	1930	//hydrogen1
166			//matVecMul3(rotTrans, h1, newVec);
167			newVec = rotTrans * h1;
168			atomInfo = new AtomInfo;
169			atomInfo->AtomType = "H";
170			atomInfo->pos[0] = pos[0] + newVec[0];
171			atomInfo->pos[1] = pos[1] + newVec[1];
172			atomInfo->pos[2] = pos[2] + newVec[2];
173			atomInfo->dipole[0] = 0.0;
174			atomInfo->dipole[1] = 0.0;
175			atomInfo->dipole[2] = 0.0;
176			atomData->addAtomInfo(atomInfo);
177	gezelter	1490
178	gezelter	1930	//hydrogen2
179			//matVecMul3(rotTrans, h2, newVec);
180			newVec = rotTrans * h2;
181			atomInfo = new AtomInfo;
182			atomInfo->AtomType = "H";
183			atomInfo->pos[0] = pos[0] + newVec[0];
184			atomInfo->pos[1] = pos[1] + newVec[1];
185			atomInfo->pos[2] = pos[2] + newVec[2];
186			atomInfo->dipole[0] = 0.0;
187			atomInfo->dipole[1] = 0.0;
188			atomInfo->dipole[2] = 0.0;
189			atomData->addAtomInfo(atomInfo);
190	gezelter	1490
191	gezelter	1930	//add atom data into atom's property
192
193			if (!haveAtomData) {
194			atomData->setID("ATOMDATA");
195			datom->addProperty(atomData);
196			}
197
198			setVisited(datom);
199	gezelter	1490	}
200
201	gezelter	1930	const std::string SSDAtomVisitor::toString() {
202			char buffer[65535];
203			std::string result;
204	gezelter	1490
205	gezelter	1930	sprintf(buffer,
206			"------------------------------------------------------------------\n");
207			result += buffer;
208	gezelter	1490
209	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
210			result += buffer;
211	gezelter	1490
212	gezelter	1930	sprintf(buffer,
213			"Visitor Description: Convert SSD into 4 different atoms\n");
214			result += buffer;
215	gezelter	1490
216	gezelter	1930	sprintf(buffer,
217			"------------------------------------------------------------------\n");
218			result += buffer;
219
220			return result;
221	gezelter	1490	}
222
223	chrisfen	1718	bool LinearAtomVisitor::isLinearAtom(const string& atomType){
224			vector<string>::iterator strIter;
225
226			for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
227			++strIter)
228			if(*strIter == atomType)
229			return true;
230
231			return false;
232			}
233
234			void LinearAtomVisitor::visit(DirectionalAtom* datom){
235
236			vector<AtomInfo*> atoms;
237
238			//we need to convert linear into 4 different atoms
239			double c1[3] = {0.0, 0.0, -1.8};
240			double c2[3] = {0.0, 0.0, -0.6};
241			double c3[3] = {0.0, 0.0, 0.6};
242			double c4[3] = {0.0, 0.0, 1.8};
243			double rotMatrix[3][3];
244			double rotTrans[3][3];
245			AtomInfo* atomInfo;
246			double pos[3];
247			double newVec[3];
248			double q[4];
249			AtomData* atomData;
250			GenericData* data;
251			bool haveAtomData;
252
253			//if atom is not SSD atom, just skip it
254			if(!isLinearAtom(datom->getType()))
255			return;
256
257			data = datom->getProperty("ATOMDATA");
258			if(data != NULL){
259
260			atomData = dynamic_cast<AtomData*>(data);
261			if(atomData == NULL){
262			cerr << "can not get Atom Data from " << datom->getType() << endl;
263			atomData = new AtomData;
264			haveAtomData = false;
265			}
266			else
267			haveAtomData = true;
268			}
269			else{
270			atomData = new AtomData;
271			haveAtomData = false;
272			}
273
274
275			datom->getPos(pos);
276			datom->getQ(q);
277			datom->getA(rotMatrix);
278
279			// We need A^T to convert from body-fixed to space-fixed:
280			transposeMat3(rotMatrix, rotTrans);
281
282			matVecMul3(rotTrans, c1, newVec);
283			atomInfo = new AtomInfo;
284			atomInfo->AtomType = "C";
285			atomInfo->pos[0] = pos[0] + newVec[0];
286			atomInfo->pos[1] = pos[1] + newVec[1];
287			atomInfo->pos[2] = pos[2] + newVec[2];
288			atomInfo->dipole[0] = 0.0;
289			atomInfo->dipole[1] = 0.0;
290			atomInfo->dipole[2] = 0.0;
291			atomData->addAtomInfo(atomInfo);
292
293			matVecMul3(rotTrans, c2, newVec);
294			atomInfo = new AtomInfo;
295			atomInfo->AtomType = "C";
296			atomInfo->pos[0] = pos[0] + newVec[0];
297			atomInfo->pos[1] = pos[1] + newVec[1];
298			atomInfo->pos[2] = pos[2] + newVec[2];
299			atomInfo->dipole[0] = 0.0;
300			atomInfo->dipole[1] = 0.0;
301			atomInfo->dipole[2] = 0.0;
302			atomData->addAtomInfo(atomInfo);
303
304			matVecMul3(rotTrans, c3, newVec);
305			atomInfo = new AtomInfo;
306			atomInfo->AtomType = "C";
307			atomInfo->pos[0] = pos[0] + newVec[0];
308			atomInfo->pos[1] = pos[1] + newVec[1];
309			atomInfo->pos[2] = pos[2] + newVec[2];
310			atomInfo->dipole[0] = 0.0;
311			atomInfo->dipole[1] = 0.0;
312			atomInfo->dipole[2] = 0.0;
313			atomData->addAtomInfo(atomInfo);
314
315			matVecMul3(rotTrans, c4, newVec);
316			atomInfo = new AtomInfo;
317			atomInfo->AtomType = "C";
318			atomInfo->pos[0] = pos[0] + newVec[0];
319			atomInfo->pos[1] = pos[1] + newVec[1];
320			atomInfo->pos[2] = pos[2] + newVec[2];
321			atomInfo->dipole[0] = 0.0;
322			atomInfo->dipole[1] = 0.0;
323			atomInfo->dipole[2] = 0.0;
324			atomData->addAtomInfo(atomInfo);
325
326			//add atom data into atom's property
327
328			if(!haveAtomData){
329			atomData->setID("ATOMDATA");
330			datom->addProperty(atomData);
331			}
332
333			setVisited(datom);
334
335			}
336
337			const string LinearAtomVisitor::toString(){
338			char buffer[65535];
339			string result;
340
341			sprintf(buffer ,"------------------------------------------------------------------\n");
342			result += buffer;
343
344			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
345			result += buffer;
346
347			sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
348			result += buffer;
349
350			sprintf(buffer ,"------------------------------------------------------------------\n");
351			result += buffer;
352
353			return result;
354			}
355
356	gezelter	1490	//----------------------------------------------------------------------------//
357
358	gezelter	1930	void DefaultAtomVisitor::visit(Atom *atom) {
359			AtomData *atomData;
360			AtomInfo *atomInfo;
361			Vector3d pos;
362	gezelter	1490
363	gezelter	1930	if (isVisited(atom))
364			return;
365	gezelter	1490
366	gezelter	1930	atomInfo = new AtomInfo;
367	gezelter	1490
368	gezelter	1930	atomData = new AtomData;
369			atomData->setID("ATOMDATA");
370	gezelter	1490
371	gezelter	1930	pos = atom->getPos();
372			atomInfo->AtomType = atom->getType();
373			atomInfo->pos[0] = pos[0];
374			atomInfo->pos[1] = pos[1];
375			atomInfo->pos[2] = pos[2];
376			atomInfo->dipole[0] = 0.0;
377			atomInfo->dipole[1] = 0.0;
378			atomInfo->dipole[2] = 0.0;
379	gezelter	1490
380	gezelter	1930	atomData->addAtomInfo(atomInfo);
381	gezelter	1490
382	gezelter	1930	atom->addProperty(atomData);
383
384			setVisited(atom);
385	gezelter	1490	}
386
387	gezelter	1930	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
388			AtomData *atomData;
389			AtomInfo *atomInfo;
390			Vector3d pos;
391			Vector3d u;
392	gezelter	1490
393	gezelter	1930	if (isVisited(datom))
394			return;
395	gezelter	1490
396	gezelter	1930	pos = datom->getPos();
397			u = datom->getElectroFrame().getColumn(3);
398	gezelter	1490
399	gezelter	1930	atomData = new AtomData;
400			atomData->setID("ATOMDATA");
401			atomInfo = new AtomInfo;
402	gezelter	1490
403	gezelter	1930	atomInfo->AtomType = datom->getType();
404			atomInfo->pos[0] = pos[0];
405			atomInfo->pos[1] = pos[1];
406			atomInfo->pos[2] = pos[2];
407			atomInfo->dipole[0] = u[0];
408			atomInfo->dipole[1] = u[1];
409			atomInfo->dipole[2] = u[2];
410
411			atomData->addAtomInfo(atomInfo);
412
413			datom->addProperty(atomData);
414
415			setVisited(datom);
416	gezelter	1490	}
417
418	gezelter	1930	const std::string DefaultAtomVisitor::toString() {
419			char buffer[65535];
420			std::string result;
421	gezelter	1490
422	gezelter	1930	sprintf(buffer,
423			"------------------------------------------------------------------\n");
424			result += buffer;
425	gezelter	1490
426	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
427			result += buffer;
428	gezelter	1490
429	gezelter	1930	sprintf(buffer,
430			"Visitor Description: copy atom infomation into atom data\n");
431			result += buffer;
432	gezelter	1490
433	gezelter	1930	sprintf(buffer,
434			"------------------------------------------------------------------\n");
435			result += buffer;
436	gezelter	1490
437	gezelter	1930	return result;
438			}
439			} //namespace oopse