src/visitors/RigidBodyVisitor.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 "visitors/RigidBodyVisitor.hpp"
#include "primitives/RigidBody.hpp"


namespace OpenMD {

  void LipidHeadVisitor::visit(RigidBody* rb){
    Vector3d pos;
    Vector3d u(0, 0, 1);
    Vector3d newVec;
    GenericData* data;
    AtomData* atomData;
    AtomInfo* atomInfo;
    bool haveAtomData;
    RotMat3x3d rotMatrix;

    if(!canVisit(rb->getType()))
      return;

    pos = rb->getPos();
    rotMatrix = rb->getA();
    //matVecMul3(rotMatrix, u, newVec);
    newVec = rotMatrix * u;

    data = rb->getPropertyByName("ATOMDATA");

    if(data != NULL){
      atomData = dynamic_cast<AtomData*>(data);  
      
      if(atomData == NULL){
        std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
        
        atomData = new AtomData; 
        haveAtomData = false;      
        
      } else
        haveAtomData = true;
      
    } else {
      atomData = new AtomData;
      haveAtomData = false;
      
    }

    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "X";
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->vec[0] = newVec[0];
    atomInfo->vec[1] = newVec[1];
    atomInfo->vec[2] = newVec[2];

    atomData->addAtomInfo(atomInfo);

    if(!haveAtomData){
      atomData->setID("ATOMDATA");
      rb->addProperty(atomData);
    }

  }


  void LipidHeadVisitor::addLipidHeadName(const std::string& name){
    lipidHeadName.insert(name);

  }

  bool LipidHeadVisitor::canVisit(const std::string& name){
    return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;

  }


  const  std::string LipidHeadVisitor::toString(){
    char buffer[65535];
    std::string result;
    std::set<std::string>::iterator i;

    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    //print the ignore type list
    sprintf(buffer , "lipidHeadName list contains below types:\n");
    result += buffer;

    for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
      sprintf(buffer ,"%s\t", i->c_str());
      result += buffer;
    }

    sprintf(buffer ,"\n");
    result += buffer;

    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    return result;

  }


  void RBCOMVisitor::visit(RigidBody* rb){
    AtomData* atomData;
    AtomInfo* atomInfo;
    Vector3d pos;

    pos = rb->getPos();
    atomInfo = new AtomInfo;
    atomInfo->atomTypeName = "X";
    atomInfo->pos[0] = pos[0];
    atomInfo->pos[1] = pos[1];
    atomInfo->pos[2] = pos[2];
    atomInfo->vec[0] = 0;
    atomInfo->vec[1] = 0;
    atomInfo->vec[2] = 0;

    atomData = new AtomData; 
    atomData->setID("ATOMDATA");
    atomData->addAtomInfo(atomInfo);

    rb->addProperty(atomData);

  }


  const  std::string RBCOMVisitor::toString(){
    char buffer[65535];
    std::string result;

    sprintf(buffer ,"------------------------------------------------------------------\n");
    result += buffer;

    sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
    result += buffer;

    //print the ignore type list
    sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\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, 11 months ago) by gezelter
File size:	5682 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	tim	3	#include "visitors/RigidBodyVisitor.hpp"
44			#include "primitives/RigidBody.hpp"
45	gezelter	246
46	gezelter	2
47	gezelter	1390	namespace OpenMD {
48	tim	132
49	gezelter	507	void LipidHeadVisitor::visit(RigidBody* rb){
50			Vector3d pos;
51			Vector3d u(0, 0, 1);
52			Vector3d newVec;
53			GenericData* data;
54			AtomData* atomData;
55			AtomInfo* atomInfo;
56			bool haveAtomData;
57			RotMat3x3d rotMatrix;
58	gezelter	246
59	gezelter	507	if(!canVisit(rb->getType()))
60			return;
61	gezelter	2
62	gezelter	507	pos = rb->getPos();
63			rotMatrix = rb->getA();
64			//matVecMul3(rotMatrix, u, newVec);
65			newVec = rotMatrix * u;
66	gezelter	246
67	gezelter	507	data = rb->getPropertyByName("ATOMDATA");
68	gezelter	246
69	gezelter	507	if(data != NULL){
70			atomData = dynamic_cast<AtomData*>(data);
71	chrisfen	1008
72	gezelter	507	if(atomData == NULL){
73			std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
74	chrisfen	1008
75	gezelter	507	atomData = new AtomData;
76			haveAtomData = false;
77	chrisfen	1008
78			} else
79	gezelter	507	haveAtomData = true;
80	chrisfen	1008
81			} else {
82	gezelter	507	atomData = new AtomData;
83			haveAtomData = false;
84	chrisfen	1008
85	gezelter	507	}
86	gezelter	2
87	gezelter	507	atomInfo = new AtomInfo;
88			atomInfo->atomTypeName = "X";
89			atomInfo->pos[0] = pos[0];
90			atomInfo->pos[1] = pos[1];
91			atomInfo->pos[2] = pos[2];
92	gezelter	1456	atomInfo->vec[0] = newVec[0];
93			atomInfo->vec[1] = newVec[1];
94			atomInfo->vec[2] = newVec[2];
95	gezelter	2
96	gezelter	507	atomData->addAtomInfo(atomInfo);
97	gezelter	2
98	gezelter	507	if(!haveAtomData){
99			atomData->setID("ATOMDATA");
100			rb->addProperty(atomData);
101			}
102	gezelter	246
103	gezelter	507	}
104	gezelter	2
105	gezelter	246
106	gezelter	507	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
107			lipidHeadName.insert(name);
108	gezelter	2
109	gezelter	507	}
110	gezelter	2
111	gezelter	507	bool LipidHeadVisitor::canVisit(const std::string& name){
112			return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
113	gezelter	2
114	gezelter	507	}
115	gezelter	2
116	gezelter	246
117	gezelter	507	const std::string LipidHeadVisitor::toString(){
118			char buffer[65535];
119			std::string result;
120			std::set<std::string>::iterator i;
121	gezelter	246
122	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
123			result += buffer;
124	gezelter	246
125	gezelter	507	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
126			result += buffer;
127	gezelter	2
128	gezelter	507	//print the ignore type list
129			sprintf(buffer , "lipidHeadName list contains below types:\n");
130			result += buffer;
131	gezelter	2
132	gezelter	507	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
133			sprintf(buffer ,"%s\t", i->c_str());
134			result += buffer;
135			}
136	gezelter	2
137	gezelter	507	sprintf(buffer ,"\n");
138			result += buffer;
139	gezelter	2
140	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
141			result += buffer;
142	gezelter	2
143	gezelter	507	return result;
144	gezelter	2
145	gezelter	507	}
146	gezelter	2
147	gezelter	246
148	gezelter	507	void RBCOMVisitor::visit(RigidBody* rb){
149			AtomData* atomData;
150			AtomInfo* atomInfo;
151			Vector3d pos;
152	gezelter	246
153	gezelter	507	pos = rb->getPos();
154			atomInfo = new AtomInfo;
155			atomInfo->atomTypeName = "X";
156			atomInfo->pos[0] = pos[0];
157			atomInfo->pos[1] = pos[1];
158			atomInfo->pos[2] = pos[2];
159	gezelter	1456	atomInfo->vec[0] = 0;
160			atomInfo->vec[1] = 0;
161			atomInfo->vec[2] = 0;
162	gezelter	2
163	gezelter	507	atomData = new AtomData;
164			atomData->setID("ATOMDATA");
165			atomData->addAtomInfo(atomInfo);
166	gezelter	2
167	gezelter	507	rb->addProperty(atomData);
168	gezelter	246
169	gezelter	507	}
170	gezelter	2
171	gezelter	246
172	gezelter	507	const std::string RBCOMVisitor::toString(){
173			char buffer[65535];
174			std::string result;
175	gezelter	246
176	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
177			result += buffer;
178	gezelter	246
179	gezelter	507	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
180			result += buffer;
181	gezelter	2
182	gezelter	507	//print the ignore type list
183			sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
184			result += buffer;
185	gezelter	2
186	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
187			result += buffer;
188	gezelter	2
189	gezelter	507	return result;
190	gezelter	2
191	gezelter	507	}
192	gezelter	2
193	gezelter	1390	}//namespace OpenMD
194	gezelter	246