src/visitors/ReplacementVisitor.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/ReplacementVisitor.hpp"
#include "primitives/DirectionalAtom.hpp"
#include "primitives/RigidBody.hpp"

namespace OpenMD { 

  void ReplacementVisitor::addReplacedAtomName(const std::string& repName) {
    myTypes_.insert(repName);
  }

  ReplacementVisitor::~ReplacementVisitor(){
    delete sites_;
    myTypes_.clear();
  }
   
  bool ReplacementVisitor::isReplacedAtom(const std::string& atomType) {
    std::set<std::string>::iterator strIter;
    strIter = myTypes_.find(atomType);
    return strIter != myTypes_.end() ? true : false;
  }

  void ReplacementVisitor::addSite(const std::string& name, 
                                   const Vector3d refPos) {
    AtomInfo* atomInfo = new AtomInfo();
    atomInfo->atomTypeName = name;
    atomInfo->pos = refPos;
    sites_->addAtomInfo(atomInfo);
  }
  void ReplacementVisitor::addSite(const std::string& name, 
                                   const Vector3d refPos, 
                                   const Vector3d refVec) {
    AtomInfo* atomInfo = new AtomInfo();
    atomInfo->atomTypeName = name;
    atomInfo->pos = refPos;
    atomInfo->dipole = refVec;
    atomInfo->hasVector = true;
    sites_->addAtomInfo(atomInfo);
  }
  
  void ReplacementVisitor::visit(DirectionalAtom *datom) {
    std::vector<AtomInfo*>atoms;
    
    RotMat3x3d   rotMatrix;
    RotMat3x3d   rotTrans;
    AtomInfo *   atomInfo;
    Vector3d     pos;
    Vector3d     newVec;
    Quat4d       q;
    AtomData *   atomData;
    GenericData *data;
    bool         haveAtomData;
    
    //if atom is not one of our recognized atom types, just skip it
    if (!isReplacedAtom(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();
    
    AtomInfo* siteInfo;
    std::vector<AtomInfo*>::iterator iter;
    
    for( siteInfo = sites_->beginAtomInfo(iter); siteInfo; 
         siteInfo = sites_->nextAtomInfo(iter) ) {

      newVec = rotTrans * siteInfo->pos;    
      
      atomInfo = new AtomInfo;
      atomInfo->atomTypeName = siteInfo->atomTypeName;
      atomInfo->pos = pos + newVec;
      
      if (siteInfo->hasVector) {
        newVec = rotTrans * siteInfo->dipole;
        atomInfo->dipole = newVec;
      } else {
        atomInfo->dipole = V3Zero;
      }
      
      atomData->addAtomInfo(atomInfo);
    }
    if (!haveAtomData) {
      atomData->setID("ATOMDATA");
      datom->addProperty(atomData);
    }
    
    setVisited(datom);
  }
  
  const std::string ReplacementVisitor::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: replace atom with other sites\n");
    result += buffer;
  
    sprintf(buffer,
            "------------------------------------------------------------------\n");
    result += buffer;
    
    return result;
  }
}
Revision:	1455
Committed:	Thu Jun 24 20:44:18 2010 UTC (14 years, 10 months ago) by gezelter
Original Path:	*trunk/src/visitors/ReplacementVisitor.cpp*
File size:	5777 byte(s)
Log Message:	Updating visitor architecture to something a bit more modern
#	User	Rev	Content
1	gezelter	1455	/*
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. Redistributions of source code must retain the above copyright
10			* notice, this list of conditions and the following disclaimer.
11			*
12			* 2. Redistributions in binary form must reproduce the above copyright
13			* 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			*
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			*/
41
42			#include <cstring>
43			#include "visitors/ReplacementVisitor.hpp"
44			#include "primitives/DirectionalAtom.hpp"
45			#include "primitives/RigidBody.hpp"
46
47			namespace OpenMD {
48
49			void ReplacementVisitor::addReplacedAtomName(const std::string& repName) {
50			myTypes_.insert(repName);
51			}
52
53			ReplacementVisitor::~ReplacementVisitor(){
54			delete sites_;
55			myTypes_.clear();
56			}
57
58			bool ReplacementVisitor::isReplacedAtom(const std::string& atomType) {
59			std::set<std::string>::iterator strIter;
60			strIter = myTypes_.find(atomType);
61			return strIter != myTypes_.end() ? true : false;
62			}
63
64			void ReplacementVisitor::addSite(const std::string& name,
65			const Vector3d refPos) {
66			AtomInfo* atomInfo = new AtomInfo();
67			atomInfo->atomTypeName = name;
68			atomInfo->pos = refPos;
69			sites_->addAtomInfo(atomInfo);
70			}
71			void ReplacementVisitor::addSite(const std::string& name,
72			const Vector3d refPos,
73			const Vector3d refVec) {
74			AtomInfo* atomInfo = new AtomInfo();
75			atomInfo->atomTypeName = name;
76			atomInfo->pos = refPos;
77			atomInfo->dipole = refVec;
78			atomInfo->hasVector = true;
79			sites_->addAtomInfo(atomInfo);
80			}
81
82			void ReplacementVisitor::visit(DirectionalAtom *datom) {
83			std::vector<AtomInfo*>atoms;
84
85			RotMat3x3d rotMatrix;
86			RotMat3x3d rotTrans;
87			AtomInfo * atomInfo;
88			Vector3d pos;
89			Vector3d newVec;
90			Quat4d q;
91			AtomData * atomData;
92			GenericData *data;
93			bool haveAtomData;
94
95			//if atom is not one of our recognized atom types, just skip it
96			if (!isReplacedAtom(datom->getType()))
97			return;
98
99			data = datom->getPropertyByName("ATOMDATA");
100
101			if (data != NULL) {
102			atomData = dynamic_cast<AtomData *>(data);
103
104			if (atomData == NULL) {
105			std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
106			atomData = new AtomData;
107			haveAtomData = false;
108			} else
109			haveAtomData = true;
110			} else {
111			atomData = new AtomData;
112			haveAtomData = false;
113			}
114
115
116			pos = datom->getPos();
117			q = datom->getQ();
118			rotMatrix = datom->getA();
119
120			// We need A^T to convert from body-fixed to space-fixed:
121			rotTrans = rotMatrix.transpose();
122
123			AtomInfo* siteInfo;
124			std::vector<AtomInfo*>::iterator iter;
125
126			for( siteInfo = sites_->beginAtomInfo(iter); siteInfo;
127			siteInfo = sites_->nextAtomInfo(iter) ) {
128
129			newVec = rotTrans * siteInfo->pos;
130
131			atomInfo = new AtomInfo;
132			atomInfo->atomTypeName = siteInfo->atomTypeName;
133			atomInfo->pos = pos + newVec;
134
135			if (siteInfo->hasVector) {
136			newVec = rotTrans * siteInfo->dipole;
137			atomInfo->dipole = newVec;
138			} else {
139			atomInfo->dipole = V3Zero;
140			}
141
142			atomData->addAtomInfo(atomInfo);
143			}
144			if (!haveAtomData) {
145			atomData->setID("ATOMDATA");
146			datom->addProperty(atomData);
147			}
148
149			setVisited(datom);
150			}
151
152			const std::string ReplacementVisitor::toString() {
153			char buffer[65535];
154			std::string result;
155
156			sprintf(buffer,
157			"------------------------------------------------------------------\n");
158			result += buffer;
159
160			sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
161			result += buffer;
162
163			sprintf(buffer,
164			"Visitor Description: replace atom with other sites\n");
165			result += buffer;
166
167			sprintf(buffer,
168			"------------------------------------------------------------------\n");
169			result += buffer;
170
171			return result;
172			}
173			}