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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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:	1456
Committed:	Fri Jun 25 17:40:24 2010 UTC (14 years, 10 months ago) by gezelter
Original Path:	*trunk/src/visitors/RigidBodyVisitor.cpp*
File size:	5616 byte(s)
Log Message:	more changes to make Dump2XYZ do velocities & forces
#	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	tim	3	#include "visitors/RigidBodyVisitor.hpp"
43			#include "primitives/RigidBody.hpp"
44	gezelter	246
45	gezelter	2
46	gezelter	1390	namespace OpenMD {
47	tim	132
48	gezelter	507	void LipidHeadVisitor::visit(RigidBody* rb){
49			Vector3d pos;
50			Vector3d u(0, 0, 1);
51			Vector3d newVec;
52			GenericData* data;
53			AtomData* atomData;
54			AtomInfo* atomInfo;
55			bool haveAtomData;
56			RotMat3x3d rotMatrix;
57	gezelter	246
58	gezelter	507	if(!canVisit(rb->getType()))
59			return;
60	gezelter	2
61	gezelter	507	pos = rb->getPos();
62			rotMatrix = rb->getA();
63			//matVecMul3(rotMatrix, u, newVec);
64			newVec = rotMatrix * u;
65	gezelter	246
66	gezelter	507	data = rb->getPropertyByName("ATOMDATA");
67	gezelter	246
68	gezelter	507	if(data != NULL){
69			atomData = dynamic_cast<AtomData*>(data);
70	chrisfen	1008
71	gezelter	507	if(atomData == NULL){
72			std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
73	chrisfen	1008
74	gezelter	507	atomData = new AtomData;
75			haveAtomData = false;
76	chrisfen	1008
77			} else
78	gezelter	507	haveAtomData = true;
79	chrisfen	1008
80			} else {
81	gezelter	507	atomData = new AtomData;
82			haveAtomData = false;
83	chrisfen	1008
84	gezelter	507	}
85	gezelter	2
86	gezelter	507	atomInfo = new AtomInfo;
87			atomInfo->atomTypeName = "X";
88			atomInfo->pos[0] = pos[0];
89			atomInfo->pos[1] = pos[1];
90			atomInfo->pos[2] = pos[2];
91	gezelter	1456	atomInfo->vec[0] = newVec[0];
92			atomInfo->vec[1] = newVec[1];
93			atomInfo->vec[2] = newVec[2];
94	gezelter	2
95	gezelter	507	atomData->addAtomInfo(atomInfo);
96	gezelter	2
97	gezelter	507	if(!haveAtomData){
98			atomData->setID("ATOMDATA");
99			rb->addProperty(atomData);
100			}
101	gezelter	246
102	gezelter	507	}
103	gezelter	2
104	gezelter	246
105	gezelter	507	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
106			lipidHeadName.insert(name);
107	gezelter	2
108	gezelter	507	}
109	gezelter	2
110	gezelter	507	bool LipidHeadVisitor::canVisit(const std::string& name){
111			return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
112	gezelter	2
113	gezelter	507	}
114	gezelter	2
115	gezelter	246
116	gezelter	507	const std::string LipidHeadVisitor::toString(){
117			char buffer[65535];
118			std::string result;
119			std::set<std::string>::iterator i;
120	gezelter	246
121	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
122			result += buffer;
123	gezelter	246
124	gezelter	507	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
125			result += buffer;
126	gezelter	2
127	gezelter	507	//print the ignore type list
128			sprintf(buffer , "lipidHeadName list contains below types:\n");
129			result += buffer;
130	gezelter	2
131	gezelter	507	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
132			sprintf(buffer ,"%s\t", i->c_str());
133			result += buffer;
134			}
135	gezelter	2
136	gezelter	507	sprintf(buffer ,"\n");
137			result += buffer;
138	gezelter	2
139	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
140			result += buffer;
141	gezelter	2
142	gezelter	507	return result;
143	gezelter	2
144	gezelter	507	}
145	gezelter	2
146	gezelter	246
147	gezelter	507	void RBCOMVisitor::visit(RigidBody* rb){
148			AtomData* atomData;
149			AtomInfo* atomInfo;
150			Vector3d pos;
151	gezelter	246
152	gezelter	507	pos = rb->getPos();
153			atomInfo = new AtomInfo;
154			atomInfo->atomTypeName = "X";
155			atomInfo->pos[0] = pos[0];
156			atomInfo->pos[1] = pos[1];
157			atomInfo->pos[2] = pos[2];
158	gezelter	1456	atomInfo->vec[0] = 0;
159			atomInfo->vec[1] = 0;
160			atomInfo->vec[2] = 0;
161	gezelter	2
162	gezelter	507	atomData = new AtomData;
163			atomData->setID("ATOMDATA");
164			atomData->addAtomInfo(atomInfo);
165	gezelter	2
166	gezelter	507	rb->addProperty(atomData);
167	gezelter	246
168	gezelter	507	}
169	gezelter	2
170	gezelter	246
171	gezelter	507	const std::string RBCOMVisitor::toString(){
172			char buffer[65535];
173			std::string result;
174	gezelter	246
175	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
176			result += buffer;
177	gezelter	246
178	gezelter	507	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
179			result += buffer;
180	gezelter	2
181	gezelter	507	//print the ignore type list
182			sprintf(buffer , "Visitor Description: add a pseudo atom at the center of the mass of the rigidbody\n");
183			result += buffer;
184	gezelter	2
185	gezelter	507	sprintf(buffer ,"------------------------------------------------------------------\n");
186			result += buffer;
187	gezelter	2
188	gezelter	507	return result;
189	gezelter	2
190	gezelter	507	}
191	gezelter	2
192	gezelter	1390	}//namespace OpenMD
193	gezelter	246