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root/OpenMD/branches/development/src/visitors/AtomVisitor.cpp
Revision: 1872
Committed: Fri May 10 15:10:41 2013 UTC (11 years, 11 months ago) by gezelter
File size: 6680 byte(s)
Log Message:
Fixed a minor visitor bug

File Contents

# 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 gezelter 1850 * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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 1871 #include "types/FixedChargeAdapter.hpp"
48     #include "types/FluctuatingChargeAdapter.hpp"
49 gezelter 1787 #include "types/MultipoleAdapter.hpp"
50     #include "types/GayBerneAdapter.hpp"
51 gezelter 2
52 gezelter 1390 namespace OpenMD {
53 gezelter 507 void BaseAtomVisitor::visit(RigidBody *rb) {
54     //vector<Atom*> myAtoms;
55     //vector<Atom*>::iterator atomIter;
56 tim 132
57 gezelter 507 //myAtoms = rb->getAtoms();
58 gezelter 2
59 gezelter 507 //for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
60     // (*atomIter)->accept(this);
61     }
62 gezelter 2
63 gezelter 507 void BaseAtomVisitor::setVisited(Atom *atom) {
64 gezelter 246 GenericData *data;
65     data = atom->getPropertyByName("VISITED");
66 gezelter 2
67 gezelter 246 //if visited property is not existed, add it as new property
68     if (data == NULL) {
69 gezelter 507 data = new GenericData();
70     data->setID("VISITED");
71     atom->addProperty(data);
72 gezelter 246 }
73 gezelter 507 }
74 gezelter 2
75 gezelter 507 bool BaseAtomVisitor::isVisited(Atom *atom) {
76 gezelter 246 GenericData *data;
77     data = atom->getPropertyByName("VISITED");
78     return data == NULL ? false : true;
79 gezelter 507 }
80 gezelter 2
81 gezelter 1455 //------------------------------------------------------------------------//
82    
83 gezelter 507 void DefaultAtomVisitor::visit(Atom *atom) {
84 gezelter 246 AtomData *atomData;
85     AtomInfo *atomInfo;
86 gezelter 1871 AtomType* atype = atom->getAtomType();
87    
88 gezelter 246 if (isVisited(atom))
89 gezelter 507 return;
90 gezelter 1455
91 gezelter 246 atomInfo = new AtomInfo;
92 gezelter 407 atomInfo->atomTypeName = atom->getType();
93 gezelter 1871 atomInfo->pos = atom->getPos();
94     atomInfo->vel = atom->getVel();
95     atomInfo->frc = atom->getFrc();
96     atomInfo->vec = V3Zero;
97 gezelter 1456 atomInfo->hasVelocity = true;
98     atomInfo->hasForce = true;
99 gezelter 1871
100     FixedChargeAdapter fca = FixedChargeAdapter(atype);
101     if ( fca.isFixedCharge() ) {
102     atomInfo->hasCharge = true;
103     atomInfo->charge = fca.getCharge();
104     }
105    
106     FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
107     if ( fqa.isFluctuatingCharge() ) {
108     atomInfo->hasCharge = true;
109     atomInfo->charge += atom->getFlucQPos();
110     }
111    
112     if (atype->isElectrostatic()) {
113     atomInfo->hasElectricField = true;
114     atomInfo->eField = atom->getElectricField();
115     }
116    
117     atomData = new AtomData;
118     atomData->setID("ATOMDATA");
119 gezelter 246 atomData->addAtomInfo(atomInfo);
120 gezelter 1455
121 gezelter 246 atom->addProperty(atomData);
122 gezelter 1455
123 gezelter 246 setVisited(atom);
124 gezelter 507 }
125 gezelter 1455
126 gezelter 507 void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
127 gezelter 246 AtomData *atomData;
128     AtomInfo *atomInfo;
129 gezelter 1871 AtomType* atype = datom->getAtomType();
130 gezelter 2
131 gezelter 246 if (isVisited(datom))
132 gezelter 507 return;
133 gezelter 1456
134 gezelter 1871 atomInfo = new AtomInfo;
135     atomInfo->atomTypeName = datom->getType();
136     atomInfo->pos = datom->getPos();
137     atomInfo->vel = datom->getVel();
138     atomInfo->frc = datom->getFrc();
139     atomInfo->hasVelocity = true;
140     atomInfo->hasForce = true;
141 gezelter 1787
142 gezelter 1871 FixedChargeAdapter fca = FixedChargeAdapter(atype);
143     if ( fca.isFixedCharge() ) {
144     atomInfo->hasCharge = true;
145     atomInfo->charge = fca.getCharge();
146     }
147    
148     FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
149     if ( fqa.isFluctuatingCharge() ) {
150     atomInfo->hasCharge = true;
151     atomInfo->charge += datom->getFlucQPos();
152     }
153    
154     if (atype->isElectrostatic()) {
155     atomInfo->hasElectricField = true;
156     atomInfo->eField = datom->getElectricField();
157     }
158    
159     GayBerneAdapter gba = GayBerneAdapter(atype);
160     MultipoleAdapter ma = MultipoleAdapter(atype);
161 gezelter 1787
162     if (gba.isGayBerne()) {
163 gezelter 1871 atomInfo->hasVector = true;
164     atomInfo->vec = datom->getA().transpose()*V3Z;
165 gezelter 1787 } else if (ma.isDipole()) {
166 gezelter 1871 atomInfo->hasVector = true;
167     atomInfo->vec = datom->getDipole();
168 gezelter 1814 } else if (ma.isQuadrupole()) {
169 gezelter 1871 atomInfo->hasVector = true;
170     atomInfo->vec = datom->getA().transpose()*V3Z;
171 tim 989 }
172 gezelter 2
173 gezelter 1872 atomData = new AtomData;
174     atomData->setID("ATOMDATA");
175 gezelter 246 atomData->addAtomInfo(atomInfo);
176 gezelter 1872
177 gezelter 246 datom->addProperty(atomData);
178    
179     setVisited(datom);
180 gezelter 507 }
181 gezelter 2
182 gezelter 507 const std::string DefaultAtomVisitor::toString() {
183 gezelter 246 char buffer[65535];
184     std::string result;
185 gezelter 2
186 gezelter 246 sprintf(buffer,
187 gezelter 1871 "--------------------------------------------------------------\n");
188 gezelter 246 result += buffer;
189 gezelter 2
190 gezelter 246 sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
191     result += buffer;
192 gezelter 2
193 gezelter 246 sprintf(buffer,
194     "Visitor Description: copy atom infomation into atom data\n");
195     result += buffer;
196 gezelter 2
197 gezelter 246 sprintf(buffer,
198 gezelter 1871 "--------------------------------------------------------------\n");
199 gezelter 246 result += buffer;
200 gezelter 2
201 gezelter 246 return result;
202 gezelter 507 }
203 gezelter 1390 } //namespace OpenMD

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