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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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;
    
    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();
    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->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 OpenMD
Revision:	1455
Committed:	Thu Jun 24 20:44:18 2010 UTC (14 years, 10 months ago) by gezelter
Original Path:	*trunk/src/visitors/AtomVisitor.cpp*
File size:	5190 byte(s)
Log Message:	Updating visitor architecture to something a bit more modern
#	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			* [4] Vardeman & Gezelter, in progress (2009).
40	gezelter	246	*/
41
42	gezelter	2	#include <cstring>
43	tim	3	#include "visitors/AtomVisitor.hpp"
44			#include "primitives/DirectionalAtom.hpp"
45			#include "primitives/RigidBody.hpp"
46	gezelter	2
47	gezelter	1390	namespace OpenMD {
48	gezelter	507	void BaseAtomVisitor::visit(RigidBody *rb) {
49			//vector<Atom*> myAtoms;
50			//vector<Atom*>::iterator atomIter;
51	tim	132
52	gezelter	507	//myAtoms = rb->getAtoms();
53	gezelter	2
54	gezelter	507	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55			// (*atomIter)->accept(this);
56			}
57	gezelter	2
58	gezelter	507	void BaseAtomVisitor::setVisited(Atom *atom) {
59	gezelter	246	GenericData *data;
60			data = atom->getPropertyByName("VISITED");
61	gezelter	2
62	gezelter	246	//if visited property is not existed, add it as new property
63			if (data == NULL) {
64	gezelter	507	data = new GenericData();
65			data->setID("VISITED");
66			atom->addProperty(data);
67	gezelter	246	}
68	gezelter	507	}
69	gezelter	2
70	gezelter	507	bool BaseAtomVisitor::isVisited(Atom *atom) {
71	gezelter	246	GenericData *data;
72			data = atom->getPropertyByName("VISITED");
73			return data == NULL ? false : true;
74	gezelter	507	}
75	gezelter	2
76	gezelter	1455	//------------------------------------------------------------------------//
77
78	gezelter	507	void DefaultAtomVisitor::visit(Atom *atom) {
79	gezelter	246	AtomData *atomData;
80			AtomInfo *atomInfo;
81			Vector3d pos;
82	gezelter	1455
83	gezelter	246	if (isVisited(atom))
84	gezelter	507	return;
85	gezelter	1455
86	gezelter	246	atomInfo = new AtomInfo;
87	gezelter	1455
88	gezelter	246	atomData = new AtomData;
89			atomData->setID("ATOMDATA");
90	gezelter	1455
91	gezelter	246	pos = atom->getPos();
92	gezelter	407	atomInfo->atomTypeName = atom->getType();
93	gezelter	246	atomInfo->pos[0] = pos[0];
94			atomInfo->pos[1] = pos[1];
95			atomInfo->pos[2] = pos[2];
96			atomInfo->dipole[0] = 0.0;
97			atomInfo->dipole[1] = 0.0;
98			atomInfo->dipole[2] = 0.0;
99	gezelter	1455
100	gezelter	246	atomData->addAtomInfo(atomInfo);
101	gezelter	1455
102	gezelter	246	atom->addProperty(atomData);
103	gezelter	1455
104	gezelter	246	setVisited(atom);
105	gezelter	507	}
106	gezelter	1455
107	gezelter	507	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
108	gezelter	246	AtomData *atomData;
109			AtomInfo *atomInfo;
110			Vector3d pos;
111			Vector3d u;
112	gezelter	2
113	gezelter	246	if (isVisited(datom))
114	gezelter	507	return;
115	gezelter	2
116	gezelter	246	pos = datom->getPos();
117	tim	989	if (datom->getAtomType()->isGayBerne()) {
118			u = datom->getA().transpose()*V3Z;
119			} else if (datom->getAtomType()->isMultipole()) {
120			u = datom->getElectroFrame().getColumn(2);
121			}
122	gezelter	246	atomData = new AtomData;
123			atomData->setID("ATOMDATA");
124			atomInfo = new AtomInfo;
125	gezelter	2
126	gezelter	407	atomInfo->atomTypeName = datom->getType();
127	gezelter	246	atomInfo->pos[0] = pos[0];
128			atomInfo->pos[1] = pos[1];
129			atomInfo->pos[2] = pos[2];
130			atomInfo->dipole[0] = u[0];
131			atomInfo->dipole[1] = u[1];
132			atomInfo->dipole[2] = u[2];
133
134			atomData->addAtomInfo(atomInfo);
135
136			datom->addProperty(atomData);
137
138			setVisited(datom);
139	gezelter	507	}
140	gezelter	2
141	gezelter	507	const std::string DefaultAtomVisitor::toString() {
142	gezelter	246	char buffer[65535];
143			std::string result;
144	gezelter	2
145	gezelter	246	sprintf(buffer,
146			"------------------------------------------------------------------\n");
147			result += buffer;
148	gezelter	2
149	gezelter	246	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
150			result += buffer;
151	gezelter	2
152	gezelter	246	sprintf(buffer,
153			"Visitor Description: copy atom infomation into atom data\n");
154			result += buffer;
155	gezelter	2
156	gezelter	246	sprintf(buffer,
157			"------------------------------------------------------------------\n");
158			result += buffer;
159	gezelter	2
160	gezelter	246	return result;
161	gezelter	507	}
162	gezelter	1390	} //namespace OpenMD