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::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->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 std::string& atomType){
    std::set<std::string>::iterator strIter;
    strIter = linearAtomType.find(atomType);

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

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;

    //if atom is not SSD atom, just skip it
    if(!isLinearAtom(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->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);

    newVec = rotTrans * c2;
    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);

    newVec = rotTrans * c3;
    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);

    newVec = rotTrans * c4;
    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 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;
}

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

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(2);

    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:	275
Committed:	Wed Jan 26 15:15:09 2005 UTC (20 years, 9 months ago) by tim
File size:	12484 byte(s)
Log Message:	(1)Cast wrong atom to DirectionalAtom in GhostTorsion (2)get the wrong column of electroframe
#	User	Rev	Content
1	gezelter	246	/*
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	2	#include <cstring>
43	tim	3	#include "visitors/AtomVisitor.hpp"
44			#include "primitives/DirectionalAtom.hpp"
45			#include "math/MatVec3.h"
46			#include "primitives/RigidBody.hpp"
47	gezelter	2
48	tim	132	namespace oopse {
49	gezelter	246	void BaseAtomVisitor::visit(RigidBody *rb) {
50			//vector<Atom*> myAtoms;
51			//vector<Atom*>::iterator atomIter;
52	tim	132
53	gezelter	246	//myAtoms = rb->getAtoms();
54	gezelter	2
55	gezelter	246	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56			// (*atomIter)->accept(this);
57			}
58	gezelter	2
59	gezelter	246	void BaseAtomVisitor::setVisited(Atom *atom) {
60			GenericData *data;
61			data = atom->getPropertyByName("VISITED");
62	gezelter	2
63	gezelter	246	//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	2	}
70
71	gezelter	246	bool BaseAtomVisitor::isVisited(Atom *atom) {
72			GenericData *data;
73			data = atom->getPropertyByName("VISITED");
74			return data == NULL ? false : true;
75	gezelter	2	}
76
77	gezelter	246	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
78	tim	247	std::set<std::string>::iterator strIter;
79			strIter = ssdAtomType.find(atomType);
80			return strIter != ssdAtomType.end() ? true : false;
81	gezelter	2	}
82
83	gezelter	246	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
84	tim	247	std::vector<AtomInfo*>atoms;
85	gezelter	2
86	gezelter	246	//we need to convert SSD into 4 differnet atoms
87			//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
88			//of the water with a dipole moment
89			Vector3d h1(0.0, -0.75695, 0.5206);
90			Vector3d h2(0.0, 0.75695, 0.5206);
91			Vector3d ox(0.0, 0.0, -0.0654);
92			Vector3d u(0, 0, 1);
93			RotMat3x3d rotMatrix;
94			RotMat3x3d rotTrans;
95			AtomInfo * atomInfo;
96			Vector3d pos;
97			Vector3d newVec;
98			Quat4d q;
99			AtomData * atomData;
100			GenericData *data;
101			bool haveAtomData;
102	gezelter	2
103	gezelter	246	//if atom is not SSD atom, just skip it
104			if (!isSSDAtom(datom->getType()))
105			return;
106	gezelter	2
107	gezelter	246	data = datom->getPropertyByName("ATOMDATA");
108	gezelter	2
109	gezelter	246	if (data != NULL) {
110			atomData = dynamic_cast<AtomData *>(data);
111
112			if (atomData == NULL) {
113			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
114			atomData = new AtomData;
115			haveAtomData = false;
116			} else
117			haveAtomData = true;
118			} else {
119			atomData = new AtomData;
120			haveAtomData = false;
121	gezelter	2	}
122
123	gezelter	246	pos = datom->getPos();
124			q = datom->getQ();
125			rotMatrix = datom->getA();
126	gezelter	2
127	gezelter	246	// We need A^T to convert from body-fixed to space-fixed:
128			//transposeMat3(rotMatrix, rotTrans);
129			rotTrans = rotMatrix.transpose();
130	gezelter	2
131	gezelter	246	//center of mass of the water molecule
132			//matVecMul3(rotTrans, u, newVec);
133			newVec = rotTrans * u;
134	gezelter	2
135	gezelter	246	atomInfo = new AtomInfo;
136			atomInfo->AtomType = "X";
137			atomInfo->pos[0] = pos[0];
138			atomInfo->pos[1] = pos[1];
139			atomInfo->pos[2] = pos[2];
140			atomInfo->dipole[0] = newVec[0];
141			atomInfo->dipole[1] = newVec[1];
142			atomInfo->dipole[2] = newVec[2];
143	gezelter	2
144	gezelter	246	atomData->addAtomInfo(atomInfo);
145	gezelter	2
146	gezelter	246	//oxygen
147			//matVecMul3(rotTrans, ox, newVec);
148			newVec = rotTrans * ox;
149	gezelter	2
150	gezelter	246	atomInfo = new AtomInfo;
151			atomInfo->AtomType = "O";
152			atomInfo->pos[0] = pos[0] + newVec[0];
153			atomInfo->pos[1] = pos[1] + newVec[1];
154			atomInfo->pos[2] = pos[2] + newVec[2];
155			atomInfo->dipole[0] = 0.0;
156			atomInfo->dipole[1] = 0.0;
157			atomInfo->dipole[2] = 0.0;
158			atomData->addAtomInfo(atomInfo);
159	gezelter	2
160	gezelter	246	//hydrogen1
161			//matVecMul3(rotTrans, h1, newVec);
162			newVec = rotTrans * h1;
163			atomInfo = new AtomInfo;
164			atomInfo->AtomType = "H";
165			atomInfo->pos[0] = pos[0] + newVec[0];
166			atomInfo->pos[1] = pos[1] + newVec[1];
167			atomInfo->pos[2] = pos[2] + newVec[2];
168			atomInfo->dipole[0] = 0.0;
169			atomInfo->dipole[1] = 0.0;
170			atomInfo->dipole[2] = 0.0;
171			atomData->addAtomInfo(atomInfo);
172	gezelter	2
173	gezelter	246	//hydrogen2
174			//matVecMul3(rotTrans, h2, newVec);
175			newVec = rotTrans * h2;
176			atomInfo = new AtomInfo;
177			atomInfo->AtomType = "H";
178			atomInfo->pos[0] = pos[0] + newVec[0];
179			atomInfo->pos[1] = pos[1] + newVec[1];
180			atomInfo->pos[2] = pos[2] + newVec[2];
181			atomInfo->dipole[0] = 0.0;
182			atomInfo->dipole[1] = 0.0;
183			atomInfo->dipole[2] = 0.0;
184			atomData->addAtomInfo(atomInfo);
185	gezelter	2
186	gezelter	246	//add atom data into atom's property
187
188			if (!haveAtomData) {
189			atomData->setID("ATOMDATA");
190			datom->addProperty(atomData);
191			}
192
193			setVisited(datom);
194	gezelter	2	}
195
196	gezelter	246	const std::string SSDAtomVisitor::toString() {
197			char buffer[65535];
198			std::string result;
199	gezelter	2
200	gezelter	246	sprintf(buffer,
201			"------------------------------------------------------------------\n");
202			result += buffer;
203	gezelter	2
204	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
205			result += buffer;
206	gezelter	2
207	gezelter	246	sprintf(buffer,
208			"Visitor Description: Convert SSD into 4 different atoms\n");
209			result += buffer;
210	gezelter	2
211	gezelter	246	sprintf(buffer,
212			"------------------------------------------------------------------\n");
213			result += buffer;
214
215			return result;
216	gezelter	2	}
217
218	tim	247	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
219			std::set<std::string>::iterator strIter;
220			strIter = linearAtomType.find(atomType);
221
222			return strIter != linearAtomType.end() ? true : false;
223	chrisfen	211	}
224
225			void LinearAtomVisitor::visit(DirectionalAtom* datom){
226	tim	247	std::vector<AtomInfo*> atoms;
227			//we need to convert linear into 4 different atoms
228			Vector3d c1(0.0, 0.0, -1.8);
229			Vector3d c2(0.0, 0.0, -0.6);
230			Vector3d c3(0.0, 0.0, 0.6);
231			Vector3d c4(0.0, 0.0, 1.8);
232			RotMat3x3d rotMatrix;
233			RotMat3x3d rotTrans;
234			AtomInfo* atomInfo;
235			Vector3d pos;
236			Vector3d newVec;
237			Quat4d q;
238			AtomData* atomData;
239			GenericData* data;
240			bool haveAtomData;
241	chrisfen	211
242	tim	247	//if atom is not SSD atom, just skip it
243			if(!isLinearAtom(datom->getType()))
244			return;
245	chrisfen	211
246	tim	247	data = datom->getPropertyByName("ATOMDATA");
247			if(data != NULL){
248			atomData = dynamic_cast<AtomData*>(data);
249			if(atomData == NULL){
250			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
251			atomData = new AtomData;
252			haveAtomData = false;
253			} else {
254			haveAtomData = true;
255			}
256			} else {
257			atomData = new AtomData;
258			haveAtomData = false;
259	chrisfen	211	}
260
261
262	tim	247	pos = datom->getPos();
263			q = datom->getQ();
264			rotMatrix = datom->getA();
265	chrisfen	211
266	tim	247	// We need A^T to convert from body-fixed to space-fixed:
267			rotTrans = rotMatrix.transpose();
268	chrisfen	211
269	tim	247	newVec = rotTrans * c1;
270			atomInfo = new AtomInfo;
271			atomInfo->AtomType = "C";
272			atomInfo->pos[0] = pos[0] + newVec[0];
273			atomInfo->pos[1] = pos[1] + newVec[1];
274			atomInfo->pos[2] = pos[2] + newVec[2];
275			atomInfo->dipole[0] = 0.0;
276			atomInfo->dipole[1] = 0.0;
277			atomInfo->dipole[2] = 0.0;
278			atomData->addAtomInfo(atomInfo);
279	chrisfen	211
280	tim	247	newVec = rotTrans * c2;
281			atomInfo = new AtomInfo;
282			atomInfo->AtomType = "C";
283			atomInfo->pos[0] = pos[0] + newVec[0];
284			atomInfo->pos[1] = pos[1] + newVec[1];
285			atomInfo->pos[2] = pos[2] + newVec[2];
286			atomInfo->dipole[0] = 0.0;
287			atomInfo->dipole[1] = 0.0;
288			atomInfo->dipole[2] = 0.0;
289			atomData->addAtomInfo(atomInfo);
290	chrisfen	211
291	tim	247	newVec = rotTrans * c3;
292			atomInfo = new AtomInfo;
293			atomInfo->AtomType = "C";
294			atomInfo->pos[0] = pos[0] + newVec[0];
295			atomInfo->pos[1] = pos[1] + newVec[1];
296			atomInfo->pos[2] = pos[2] + newVec[2];
297			atomInfo->dipole[0] = 0.0;
298			atomInfo->dipole[1] = 0.0;
299			atomInfo->dipole[2] = 0.0;
300			atomData->addAtomInfo(atomInfo);
301	chrisfen	211
302	tim	247	newVec = rotTrans * c4;
303			atomInfo = new AtomInfo;
304			atomInfo->AtomType = "C";
305			atomInfo->pos[0] = pos[0] + newVec[0];
306			atomInfo->pos[1] = pos[1] + newVec[1];
307			atomInfo->pos[2] = pos[2] + newVec[2];
308			atomInfo->dipole[0] = 0.0;
309			atomInfo->dipole[1] = 0.0;
310			atomInfo->dipole[2] = 0.0;
311			atomData->addAtomInfo(atomInfo);
312	chrisfen	211
313	tim	247	//add atom data into atom's property
314	chrisfen	211
315	tim	247	if(!haveAtomData){
316			atomData->setID("ATOMDATA");
317			datom->addProperty(atomData);
318			}
319	chrisfen	211
320	tim	247	setVisited(datom);
321
322	chrisfen	211	}
323
324	tim	247	const std::string LinearAtomVisitor::toString(){
325	chrisfen	211	char buffer[65535];
326	tim	247	std::string result;
327	chrisfen	211
328			sprintf(buffer ,"------------------------------------------------------------------\n");
329			result += buffer;
330
331			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
332			result += buffer;
333
334			sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
335			result += buffer;
336
337			sprintf(buffer ,"------------------------------------------------------------------\n");
338			result += buffer;
339
340			return result;
341			}
342
343	gezelter	2	//----------------------------------------------------------------------------//
344
345	gezelter	246	void DefaultAtomVisitor::visit(Atom *atom) {
346			AtomData *atomData;
347			AtomInfo *atomInfo;
348			Vector3d pos;
349	gezelter	2
350	gezelter	246	if (isVisited(atom))
351			return;
352	gezelter	2
353	gezelter	246	atomInfo = new AtomInfo;
354	gezelter	2
355	gezelter	246	atomData = new AtomData;
356			atomData->setID("ATOMDATA");
357	gezelter	2
358	gezelter	246	pos = atom->getPos();
359			atomInfo->AtomType = atom->getType();
360			atomInfo->pos[0] = pos[0];
361			atomInfo->pos[1] = pos[1];
362			atomInfo->pos[2] = pos[2];
363			atomInfo->dipole[0] = 0.0;
364			atomInfo->dipole[1] = 0.0;
365			atomInfo->dipole[2] = 0.0;
366	gezelter	2
367	gezelter	246	atomData->addAtomInfo(atomInfo);
368	gezelter	2
369	gezelter	246	atom->addProperty(atomData);
370
371			setVisited(atom);
372	gezelter	2	}
373
374	gezelter	246	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
375			AtomData *atomData;
376			AtomInfo *atomInfo;
377			Vector3d pos;
378			Vector3d u;
379	gezelter	2
380	gezelter	246	if (isVisited(datom))
381			return;
382	gezelter	2
383	gezelter	246	pos = datom->getPos();
384	tim	275	u = datom->getElectroFrame().getColumn(2);
385	gezelter	2
386	gezelter	246	atomData = new AtomData;
387			atomData->setID("ATOMDATA");
388			atomInfo = new AtomInfo;
389	gezelter	2
390	gezelter	246	atomInfo->AtomType = datom->getType();
391			atomInfo->pos[0] = pos[0];
392			atomInfo->pos[1] = pos[1];
393			atomInfo->pos[2] = pos[2];
394			atomInfo->dipole[0] = u[0];
395			atomInfo->dipole[1] = u[1];
396			atomInfo->dipole[2] = u[2];
397
398			atomData->addAtomInfo(atomInfo);
399
400			datom->addProperty(atomData);
401
402			setVisited(datom);
403	gezelter	2	}
404
405	gezelter	246	const std::string DefaultAtomVisitor::toString() {
406			char buffer[65535];
407			std::string result;
408	gezelter	2
409	gezelter	246	sprintf(buffer,
410			"------------------------------------------------------------------\n");
411			result += buffer;
412	gezelter	2
413	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
414			result += buffer;
415	gezelter	2
416	gezelter	246	sprintf(buffer,
417			"Visitor Description: copy atom infomation into atom data\n");
418			result += buffer;
419	gezelter	2
420	gezelter	246	sprintf(buffer,
421			"------------------------------------------------------------------\n");
422			result += buffer;
423	gezelter	2
424	gezelter	246	return result;
425			}
426			} //namespace oopse