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::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->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;
}

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

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();
    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:	2097
Committed:	Wed Mar 9 17:30:29 2005 UTC (19 years, 4 months ago) by tim
File size:	12498 byte(s)
Log Message:	adding IndexFinder which is used to select the molecules; Seperate ElectrostaticAtomTypesSectionParser into ChargeAtomTypesSectionParser and MultipoleAtomTypesSectionParser;remove print dipole option from Dump2XYZ;
#	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 "primitives/RigidBody.hpp"
46	gezelter	1490
47	tim	1625	namespace oopse {
48	gezelter	1930	void BaseAtomVisitor::visit(RigidBody *rb) {
49			//vector<Atom*> myAtoms;
50			//vector<Atom*>::iterator atomIter;
51	tim	1625
52	gezelter	1930	//myAtoms = rb->getAtoms();
53	gezelter	1490
54	gezelter	1930	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55			// (*atomIter)->accept(this);
56			}
57	gezelter	1490
58	gezelter	1930	void BaseAtomVisitor::setVisited(Atom *atom) {
59			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			data = new GenericData();
65			data->setID("VISITED");
66			atom->addProperty(data);
67			}
68	gezelter	1490	}
69
70	gezelter	1930	bool BaseAtomVisitor::isVisited(Atom *atom) {
71			GenericData *data;
72			data = atom->getPropertyByName("VISITED");
73			return data == NULL ? false : true;
74	gezelter	1490	}
75
76	gezelter	1930	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	1490	}
81
82	gezelter	1930	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			return;
105	gezelter	1490
106	gezelter	1930	data = datom->getPropertyByName("ATOMDATA");
107	gezelter	1490
108	gezelter	1930	if (data != NULL) {
109			atomData = dynamic_cast<AtomData *>(data);
110
111			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			} else {
118			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			atomData->setID("ATOMDATA");
189			datom->addProperty(atomData);
190			}
191
192			setVisited(datom);
193	gezelter	1490	}
194
195	gezelter	1930	const std::string SSDAtomVisitor::toString() {
196			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	1490	}
216
217	tim	1931	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218			std::set<std::string>::iterator strIter;
219			strIter = linearAtomType.find(atomType);
220
221			return strIter != linearAtomType.end() ? true : false;
222	chrisfen	1718	}
223
224			void LinearAtomVisitor::visit(DirectionalAtom* datom){
225	tim	1931	std::vector<AtomInfo*> atoms;
226			//we need to convert linear into 4 different atoms
227			Vector3d c1(0.0, 0.0, -1.8);
228			Vector3d c2(0.0, 0.0, -0.6);
229			Vector3d c3(0.0, 0.0, 0.6);
230			Vector3d c4(0.0, 0.0, 1.8);
231			RotMat3x3d rotMatrix;
232			RotMat3x3d rotTrans;
233			AtomInfo* atomInfo;
234			Vector3d pos;
235			Vector3d newVec;
236			Quat4d q;
237			AtomData* atomData;
238			GenericData* data;
239			bool haveAtomData;
240	chrisfen	1718
241	tim	1931	//if atom is not SSD atom, just skip it
242			if(!isLinearAtom(datom->getType()))
243			return;
244	chrisfen	1718
245	tim	1931	data = datom->getPropertyByName("ATOMDATA");
246			if(data != NULL){
247			atomData = dynamic_cast<AtomData*>(data);
248			if(atomData == NULL){
249			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
250			atomData = new AtomData;
251			haveAtomData = false;
252			} else {
253			haveAtomData = true;
254			}
255			} else {
256			atomData = new AtomData;
257			haveAtomData = false;
258	chrisfen	1718	}
259
260
261	tim	1931	pos = datom->getPos();
262			q = datom->getQ();
263			rotMatrix = datom->getA();
264	chrisfen	1718
265	tim	1931	// We need A^T to convert from body-fixed to space-fixed:
266			rotTrans = rotMatrix.transpose();
267	chrisfen	1718
268	tim	1931	newVec = rotTrans * c1;
269			atomInfo = new AtomInfo;
270	gezelter	2091	atomInfo->atomTypeName = "C";
271	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
272			atomInfo->pos[1] = pos[1] + newVec[1];
273			atomInfo->pos[2] = pos[2] + newVec[2];
274			atomInfo->dipole[0] = 0.0;
275			atomInfo->dipole[1] = 0.0;
276			atomInfo->dipole[2] = 0.0;
277			atomData->addAtomInfo(atomInfo);
278	chrisfen	1718
279	tim	1931	newVec = rotTrans * c2;
280			atomInfo = new AtomInfo;
281	gezelter	2091	atomInfo->atomTypeName = "C";
282	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
283			atomInfo->pos[1] = pos[1] + newVec[1];
284			atomInfo->pos[2] = pos[2] + newVec[2];
285			atomInfo->dipole[0] = 0.0;
286			atomInfo->dipole[1] = 0.0;
287			atomInfo->dipole[2] = 0.0;
288			atomData->addAtomInfo(atomInfo);
289	chrisfen	1718
290	tim	1931	newVec = rotTrans * c3;
291			atomInfo = new AtomInfo;
292	gezelter	2091	atomInfo->atomTypeName = "C";
293	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
294			atomInfo->pos[1] = pos[1] + newVec[1];
295			atomInfo->pos[2] = pos[2] + newVec[2];
296			atomInfo->dipole[0] = 0.0;
297			atomInfo->dipole[1] = 0.0;
298			atomInfo->dipole[2] = 0.0;
299			atomData->addAtomInfo(atomInfo);
300	chrisfen	1718
301	tim	1931	newVec = rotTrans * c4;
302			atomInfo = new AtomInfo;
303	gezelter	2091	atomInfo->atomTypeName = "C";
304	tim	1931	atomInfo->pos[0] = pos[0] + newVec[0];
305			atomInfo->pos[1] = pos[1] + newVec[1];
306			atomInfo->pos[2] = pos[2] + newVec[2];
307			atomInfo->dipole[0] = 0.0;
308			atomInfo->dipole[1] = 0.0;
309			atomInfo->dipole[2] = 0.0;
310			atomData->addAtomInfo(atomInfo);
311	chrisfen	1718
312	tim	1931	//add atom data into atom's property
313	chrisfen	1718
314	tim	1931	if(!haveAtomData){
315			atomData->setID("ATOMDATA");
316			datom->addProperty(atomData);
317			}
318	chrisfen	1718
319	tim	1931	setVisited(datom);
320
321	chrisfen	1718	}
322
323	tim	1931	const std::string LinearAtomVisitor::toString(){
324	chrisfen	1718	char buffer[65535];
325	tim	1931	std::string result;
326	chrisfen	1718
327			sprintf(buffer ,"------------------------------------------------------------------\n");
328			result += buffer;
329
330			sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
331			result += buffer;
332
333			sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
334			result += buffer;
335
336			sprintf(buffer ,"------------------------------------------------------------------\n");
337			result += buffer;
338
339			return result;
340			}
341
342	gezelter	1490	//----------------------------------------------------------------------------//
343
344	gezelter	1930	void DefaultAtomVisitor::visit(Atom *atom) {
345			AtomData *atomData;
346			AtomInfo *atomInfo;
347			Vector3d pos;
348	gezelter	1490
349	gezelter	1930	if (isVisited(atom))
350			return;
351	gezelter	1490
352	gezelter	1930	atomInfo = new AtomInfo;
353	gezelter	1490
354	gezelter	1930	atomData = new AtomData;
355			atomData->setID("ATOMDATA");
356	gezelter	1490
357	gezelter	1930	pos = atom->getPos();
358	gezelter	2091	atomInfo->atomTypeName = atom->getType();
359	gezelter	1930	atomInfo->pos[0] = pos[0];
360			atomInfo->pos[1] = pos[1];
361			atomInfo->pos[2] = pos[2];
362			atomInfo->dipole[0] = 0.0;
363			atomInfo->dipole[1] = 0.0;
364			atomInfo->dipole[2] = 0.0;
365	gezelter	1490
366	gezelter	1930	atomData->addAtomInfo(atomInfo);
367	gezelter	1490
368	gezelter	1930	atom->addProperty(atomData);
369
370			setVisited(atom);
371	gezelter	1490	}
372
373	gezelter	1930	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
374			AtomData *atomData;
375			AtomInfo *atomInfo;
376			Vector3d pos;
377			Vector3d u;
378	gezelter	1490
379	gezelter	1930	if (isVisited(datom))
380			return;
381	gezelter	1490
382	gezelter	1930	pos = datom->getPos();
383	tim	1959	u = datom->getElectroFrame().getColumn(2);
384	gezelter	1490
385	gezelter	1930	atomData = new AtomData;
386			atomData->setID("ATOMDATA");
387			atomInfo = new AtomInfo;
388	gezelter	1490
389	gezelter	2091	atomInfo->atomTypeName = datom->getType();
390	gezelter	1930	atomInfo->pos[0] = pos[0];
391			atomInfo->pos[1] = pos[1];
392			atomInfo->pos[2] = pos[2];
393			atomInfo->dipole[0] = u[0];
394			atomInfo->dipole[1] = u[1];
395			atomInfo->dipole[2] = u[2];
396
397			atomData->addAtomInfo(atomInfo);
398
399			datom->addProperty(atomData);
400
401			setVisited(datom);
402	gezelter	1490	}
403
404	gezelter	1930	const std::string DefaultAtomVisitor::toString() {
405			char buffer[65535];
406			std::string result;
407	gezelter	1490
408	gezelter	1930	sprintf(buffer,
409			"------------------------------------------------------------------\n");
410			result += buffer;
411	gezelter	1490
412	gezelter	1930	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
413			result += buffer;
414	gezelter	1490
415	gezelter	1930	sprintf(buffer,
416			"Visitor Description: copy atom infomation into atom data\n");
417			result += buffer;
418	gezelter	1490
419	gezelter	1930	sprintf(buffer,
420			"------------------------------------------------------------------\n");
421			result += buffer;
422	gezelter	1490
423	gezelter	1930	return result;
424			}
425			} //namespace oopse