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, 9 months ago) by gezelter
File size:	5682 byte(s)
Log Message:	updated copyright notices
#	Content
1	/*
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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "visitors/RigidBodyVisitor.hpp"
44	#include "primitives/RigidBody.hpp"
45
46
47	namespace OpenMD {
48
49	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
59	if(!canVisit(rb->getType()))
60	return;
61
62	pos = rb->getPos();
63	rotMatrix = rb->getA();
64	//matVecMul3(rotMatrix, u, newVec);
65	newVec = rotMatrix * u;
66
67	data = rb->getPropertyByName("ATOMDATA");
68
69	if(data != NULL){
70	atomData = dynamic_cast<AtomData*>(data);
71
72	if(atomData == NULL){
73	std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
74
75	atomData = new AtomData;
76	haveAtomData = false;
77
78	} else
79	haveAtomData = true;
80
81	} else {
82	atomData = new AtomData;
83	haveAtomData = false;
84
85	}
86
87	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	atomInfo->vec[0] = newVec[0];
93	atomInfo->vec[1] = newVec[1];
94	atomInfo->vec[2] = newVec[2];
95
96	atomData->addAtomInfo(atomInfo);
97
98	if(!haveAtomData){
99	atomData->setID("ATOMDATA");
100	rb->addProperty(atomData);
101	}
102
103	}
104
105
106	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
107	lipidHeadName.insert(name);
108
109	}
110
111	bool LipidHeadVisitor::canVisit(const std::string& name){
112	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
113
114	}
115
116
117	const std::string LipidHeadVisitor::toString(){
118	char buffer[65535];
119	std::string result;
120	std::set<std::string>::iterator i;
121
122	sprintf(buffer ,"------------------------------------------------------------------\n");
123	result += buffer;
124
125	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
126	result += buffer;
127
128	//print the ignore type list
129	sprintf(buffer , "lipidHeadName list contains below types:\n");
130	result += buffer;
131
132	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
133	sprintf(buffer ,"%s\t", i->c_str());
134	result += buffer;
135	}
136
137	sprintf(buffer ,"\n");
138	result += buffer;
139
140	sprintf(buffer ,"------------------------------------------------------------------\n");
141	result += buffer;
142
143	return result;
144
145	}
146
147
148	void RBCOMVisitor::visit(RigidBody* rb){
149	AtomData* atomData;
150	AtomInfo* atomInfo;
151	Vector3d pos;
152
153	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	atomInfo->vec[0] = 0;
160	atomInfo->vec[1] = 0;
161	atomInfo->vec[2] = 0;
162
163	atomData = new AtomData;
164	atomData->setID("ATOMDATA");
165	atomData->addAtomInfo(atomInfo);
166
167	rb->addProperty(atomData);
168
169	}
170
171
172	const std::string RBCOMVisitor::toString(){
173	char buffer[65535];
174	std::string result;
175
176	sprintf(buffer ,"------------------------------------------------------------------\n");
177	result += buffer;
178
179	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
180	result += buffer;
181
182	//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
186	sprintf(buffer ,"------------------------------------------------------------------\n");
187	result += buffer;
188
189	return result;
190
191	}
192
193	}//namespace OpenMD
194