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;
}

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

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:	1927
Committed:	Wed Jan 12 17:14:35 2005 UTC (21 years, 1 month ago) by tim
File size:	9007 byte(s)
Log Message:	change license
#	User	Rev	Content
1	tim	1927	/*
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	tim	1725	#include <cstring>
43			#include "visitors/AtomVisitor.hpp"
44			#include "primitives/DirectionalAtom.hpp"
45			#include "math/MatVec3.h"
46			#include "primitives/RigidBody.hpp"
47
48			namespace oopse {
49			void BaseAtomVisitor::visit(RigidBody *rb) {
50			//vector<Atom*> myAtoms;
51			//vector<Atom*>::iterator atomIter;
52
53			//myAtoms = rb->getAtoms();
54
55			//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56			// (*atomIter)->accept(this);
57			}
58
59			void BaseAtomVisitor::setVisited(Atom *atom) {
60			GenericData *data;
61			data = atom->getPropertyByName("VISITED");
62
63			//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			}
70
71			bool BaseAtomVisitor::isVisited(Atom *atom) {
72			GenericData *data;
73			data = atom->getPropertyByName("VISITED");
74			return data == NULL ? false : true;
75			}
76
77	tim	1832	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
78			std::vector<std::string>::iterator strIter;
79	tim	1725
80			for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end();
81			++strIter )
82			if (*strIter == atomType)
83			return true;
84
85			return false;
86			}
87
88			void SSDAtomVisitor::visit(DirectionalAtom *datom) {
89	tim	1816	std::vector<AtomInfo *>atoms;
90	tim	1725
91			//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
108			//if atom is not SSD atom, just skip it
109			if (!isSSDAtom(datom->getType()))
110			return;
111
112			data = datom->getPropertyByName("ATOMDATA");
113
114			if (data != NULL) {
115			atomData = dynamic_cast<AtomData *>(data);
116
117			if (atomData == NULL) {
118	tim	1830	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
119	tim	1725	atomData = new AtomData;
120			haveAtomData = false;
121			} else
122			haveAtomData = true;
123			} else {
124			atomData = new AtomData;
125			haveAtomData = false;
126			}
127
128			pos = datom->getPos();
129			q = datom->getQ();
130			rotMatrix = datom->getA();
131
132			// We need A^T to convert from body-fixed to space-fixed:
133			//transposeMat3(rotMatrix, rotTrans);
134			rotTrans = rotMatrix.transpose();
135
136			//center of mass of the water molecule
137			//matVecMul3(rotTrans, u, newVec);
138			newVec = rotTrans * u;
139
140			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
149			atomData->addAtomInfo(atomInfo);
150
151			//oxygen
152			//matVecMul3(rotTrans, ox, newVec);
153			newVec = rotTrans * ox;
154
155			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
165			//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
178			//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
191			//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			}
200
201	tim	1816	const std::string SSDAtomVisitor::toString() {
202	tim	1725	char buffer[65535];
203	tim	1816	std::string result;
204	tim	1725
205			sprintf(buffer,
206			"------------------------------------------------------------------\n");
207			result += buffer;
208
209			sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
210			result += buffer;
211
212			sprintf(buffer,
213			"Visitor Description: Convert SSD into 4 different atoms\n");
214			result += buffer;
215
216			sprintf(buffer,
217			"------------------------------------------------------------------\n");
218			result += buffer;
219
220			return result;
221			}
222
223			//----------------------------------------------------------------------------//
224
225			void DefaultAtomVisitor::visit(Atom *atom) {
226			AtomData *atomData;
227			AtomInfo *atomInfo;
228			Vector3d pos;
229
230			if (isVisited(atom))
231			return;
232
233			atomInfo = new AtomInfo;
234
235			atomData = new AtomData;
236			atomData->setID("ATOMDATA");
237
238			pos = atom->getPos();
239			atomInfo->AtomType = atom->getType();
240			atomInfo->pos[0] = pos[0];
241			atomInfo->pos[1] = pos[1];
242			atomInfo->pos[2] = pos[2];
243			atomInfo->dipole[0] = 0.0;
244			atomInfo->dipole[1] = 0.0;
245			atomInfo->dipole[2] = 0.0;
246
247			atomData->addAtomInfo(atomInfo);
248
249			atom->addProperty(atomData);
250
251			setVisited(atom);
252			}
253
254			void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
255			AtomData *atomData;
256			AtomInfo *atomInfo;
257			Vector3d pos;
258			Vector3d u;
259
260			if (isVisited(datom))
261			return;
262
263			pos = datom->getPos();
264	tim	1816	u = datom->getElectroFrame().getColumn(3);
265	tim	1725
266			atomData = new AtomData;
267			atomData->setID("ATOMDATA");
268			atomInfo = new AtomInfo;
269
270			atomInfo->AtomType = datom->getType();
271			atomInfo->pos[0] = pos[0];
272			atomInfo->pos[1] = pos[1];
273			atomInfo->pos[2] = pos[2];
274			atomInfo->dipole[0] = u[0];
275			atomInfo->dipole[1] = u[1];
276			atomInfo->dipole[2] = u[2];
277
278			atomData->addAtomInfo(atomInfo);
279
280			datom->addProperty(atomData);
281
282			setVisited(datom);
283			}
284
285	tim	1816	const std::string DefaultAtomVisitor::toString() {
286	tim	1725	char buffer[65535];
287	tim	1816	std::string result;
288	tim	1725
289			sprintf(buffer,
290			"------------------------------------------------------------------\n");
291			result += buffer;
292
293			sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
294			result += buffer;
295
296			sprintf(buffer,
297			"Visitor Description: copy atom infomation into atom data\n");
298			result += buffer;
299
300			sprintf(buffer,
301			"------------------------------------------------------------------\n");
302			result += buffer;
303
304			return result;
305			}
306			} //namespace oopse