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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include <cstring>
#include "visitors/AtomVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"

namespace OpenMD {
  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;
  }

  //------------------------------------------------------------------------//
        
  void DefaultAtomVisitor::visit(Atom *atom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;
    Vector3d  vel;
    Vector3d  frc;
    Vector3d  u;
    RealType  c;

    if (isVisited(atom))
      return;
    
    atomInfo = new AtomInfo;
    
    atomData = new AtomData;
    atomData->setID("ATOMDATA");
    
    pos = atom->getPos();
    vel = atom->getVel();
    frc = atom->getFrc();
    atomInfo->atomTypeName = atom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->vel[0] = vel[0];
    atomInfo->vel[1] = vel[1];
    atomInfo->vel[2] = vel[2];
    atomInfo->hasVelocity = true;
    atomInfo->frc[0] = frc[0];
    atomInfo->frc[1] = frc[1];
    atomInfo->frc[2] = frc[2];
    atomInfo->hasForce = true;
    atomInfo->vec[0] = 0.0;
    atomInfo->vec[1] = 0.0;
    atomInfo->vec[2] = 0.0;
    
    atomData->addAtomInfo(atomInfo);
    
    atom->addProperty(atomData);
    
    setVisited(atom);
  }
  
  void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
    AtomData *atomData;
    AtomInfo *atomInfo;
    Vector3d  pos;
    Vector3d  vel;
    Vector3d  frc;
    Vector3d  u;
    RealType  c;

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

    atomInfo->atomTypeName = datom->getType();
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->vel[0] = vel[0];
    atomInfo->vel[1] = vel[1];
    atomInfo->vel[2] = vel[2];
    atomInfo->hasVelocity = true;
    atomInfo->frc[0] = frc[0];
    atomInfo->frc[1] = frc[1];
    atomInfo->frc[2] = frc[2];
    atomInfo->hasForce = true;
    atomInfo->vec[0] = u[0];
    atomInfo->vec[1] = u[1];
    atomInfo->vec[2] = u[2];
    atomInfo->hasVector = true;

    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 OpenMD
Revision:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	6005 byte(s)
Log Message:	updated copyright notices
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* 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	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	2	#include <cstring>
44	tim	3	#include "visitors/AtomVisitor.hpp"
45			#include "primitives/DirectionalAtom.hpp"
46			#include "primitives/RigidBody.hpp"
47	gezelter	2
48	gezelter	1390	namespace OpenMD {
49	gezelter	507	void BaseAtomVisitor::visit(RigidBody *rb) {
50			//vector<Atom*> myAtoms;
51			//vector<Atom*>::iterator atomIter;
52	tim	132
53	gezelter	507	//myAtoms = rb->getAtoms();
54	gezelter	2
55	gezelter	507	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56			// (*atomIter)->accept(this);
57			}
58	gezelter	2
59	gezelter	507	void BaseAtomVisitor::setVisited(Atom *atom) {
60	gezelter	246	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	gezelter	507	data = new GenericData();
66			data->setID("VISITED");
67			atom->addProperty(data);
68	gezelter	246	}
69	gezelter	507	}
70	gezelter	2
71	gezelter	507	bool BaseAtomVisitor::isVisited(Atom *atom) {
72	gezelter	246	GenericData *data;
73			data = atom->getPropertyByName("VISITED");
74			return data == NULL ? false : true;
75	gezelter	507	}
76	gezelter	2
77	gezelter	1455	//------------------------------------------------------------------------//
78
79	gezelter	507	void DefaultAtomVisitor::visit(Atom *atom) {
80	gezelter	246	AtomData *atomData;
81			AtomInfo *atomInfo;
82			Vector3d pos;
83	gezelter	1456	Vector3d vel;
84			Vector3d frc;
85			Vector3d u;
86			RealType c;
87
88	gezelter	246	if (isVisited(atom))
89	gezelter	507	return;
90	gezelter	1455
91	gezelter	246	atomInfo = new AtomInfo;
92	gezelter	1455
93	gezelter	246	atomData = new AtomData;
94			atomData->setID("ATOMDATA");
95	gezelter	1455
96	gezelter	246	pos = atom->getPos();
97	gezelter	1456	vel = atom->getVel();
98			frc = atom->getFrc();
99	gezelter	407	atomInfo->atomTypeName = atom->getType();
100	gezelter	246	atomInfo->pos[0] = pos[0];
101			atomInfo->pos[1] = pos[1];
102			atomInfo->pos[2] = pos[2];
103	gezelter	1456	atomInfo->vel[0] = vel[0];
104			atomInfo->vel[1] = vel[1];
105			atomInfo->vel[2] = vel[2];
106			atomInfo->hasVelocity = true;
107			atomInfo->frc[0] = frc[0];
108			atomInfo->frc[1] = frc[1];
109			atomInfo->frc[2] = frc[2];
110			atomInfo->hasForce = true;
111			atomInfo->vec[0] = 0.0;
112			atomInfo->vec[1] = 0.0;
113			atomInfo->vec[2] = 0.0;
114	gezelter	1455
115	gezelter	246	atomData->addAtomInfo(atomInfo);
116	gezelter	1455
117	gezelter	246	atom->addProperty(atomData);
118	gezelter	1455
119	gezelter	246	setVisited(atom);
120	gezelter	507	}
121	gezelter	1455
122	gezelter	507	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
123	gezelter	246	AtomData *atomData;
124			AtomInfo *atomInfo;
125			Vector3d pos;
126	gezelter	1456	Vector3d vel;
127			Vector3d frc;
128	gezelter	246	Vector3d u;
129	gezelter	1456	RealType c;
130	gezelter	2
131	gezelter	246	if (isVisited(datom))
132	gezelter	507	return;
133	gezelter	1456
134	gezelter	246	pos = datom->getPos();
135	gezelter	1456	vel = datom->getVel();
136			frc = datom->getFrc();
137	tim	989	if (datom->getAtomType()->isGayBerne()) {
138			u = datom->getA().transpose()*V3Z;
139			} else if (datom->getAtomType()->isMultipole()) {
140			u = datom->getElectroFrame().getColumn(2);
141			}
142	gezelter	246	atomData = new AtomData;
143			atomData->setID("ATOMDATA");
144			atomInfo = new AtomInfo;
145	gezelter	2
146	gezelter	407	atomInfo->atomTypeName = datom->getType();
147	gezelter	246	atomInfo->pos[0] = pos[0];
148			atomInfo->pos[1] = pos[1];
149			atomInfo->pos[2] = pos[2];
150	gezelter	1456	atomInfo->vel[0] = vel[0];
151			atomInfo->vel[1] = vel[1];
152			atomInfo->vel[2] = vel[2];
153			atomInfo->hasVelocity = true;
154			atomInfo->frc[0] = frc[0];
155			atomInfo->frc[1] = frc[1];
156			atomInfo->frc[2] = frc[2];
157			atomInfo->hasForce = true;
158			atomInfo->vec[0] = u[0];
159			atomInfo->vec[1] = u[1];
160			atomInfo->vec[2] = u[2];
161			atomInfo->hasVector = true;
162	gezelter	246
163			atomData->addAtomInfo(atomInfo);
164
165			datom->addProperty(atomData);
166
167			setVisited(datom);
168	gezelter	507	}
169	gezelter	2
170	gezelter	507	const std::string DefaultAtomVisitor::toString() {
171	gezelter	246	char buffer[65535];
172			std::string result;
173	gezelter	2
174	gezelter	246	sprintf(buffer,
175			"------------------------------------------------------------------\n");
176			result += buffer;
177	gezelter	2
178	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
179			result += buffer;
180	gezelter	2
181	gezelter	246	sprintf(buffer,
182			"Visitor Description: copy atom infomation into atom data\n");
183			result += buffer;
184	gezelter	2
185	gezelter	246	sprintf(buffer,
186			"------------------------------------------------------------------\n");
187			result += buffer;
188	gezelter	2
189	gezelter	246	return result;
190	gezelter	507	}
191	gezelter	1390	} //namespace OpenMD