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
File size:	5616 byte(s)
Log Message:	more changes to make Dump2XYZ do velocities & forces
#	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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include "visitors/RigidBodyVisitor.hpp"
43	#include "primitives/RigidBody.hpp"
44
45
46	namespace OpenMD {
47
48	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
58	if(!canVisit(rb->getType()))
59	return;
60
61	pos = rb->getPos();
62	rotMatrix = rb->getA();
63	//matVecMul3(rotMatrix, u, newVec);
64	newVec = rotMatrix * u;
65
66	data = rb->getPropertyByName("ATOMDATA");
67
68	if(data != NULL){
69	atomData = dynamic_cast<AtomData*>(data);
70
71	if(atomData == NULL){
72	std::cerr << "can not get Atom Data from " << rb->getType() << std::endl;
73
74	atomData = new AtomData;
75	haveAtomData = false;
76
77	} else
78	haveAtomData = true;
79
80	} else {
81	atomData = new AtomData;
82	haveAtomData = false;
83
84	}
85
86	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	atomInfo->vec[0] = newVec[0];
92	atomInfo->vec[1] = newVec[1];
93	atomInfo->vec[2] = newVec[2];
94
95	atomData->addAtomInfo(atomInfo);
96
97	if(!haveAtomData){
98	atomData->setID("ATOMDATA");
99	rb->addProperty(atomData);
100	}
101
102	}
103
104
105	void LipidHeadVisitor::addLipidHeadName(const std::string& name){
106	lipidHeadName.insert(name);
107
108	}
109
110	bool LipidHeadVisitor::canVisit(const std::string& name){
111	return lipidHeadName.find(name) != lipidHeadName.end() ? true : false;
112
113	}
114
115
116	const std::string LipidHeadVisitor::toString(){
117	char buffer[65535];
118	std::string result;
119	std::set<std::string>::iterator i;
120
121	sprintf(buffer ,"------------------------------------------------------------------\n");
122	result += buffer;
123
124	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
125	result += buffer;
126
127	//print the ignore type list
128	sprintf(buffer , "lipidHeadName list contains below types:\n");
129	result += buffer;
130
131	for(i = lipidHeadName.begin(); i != lipidHeadName.end(); ++i){
132	sprintf(buffer ,"%s\t", i->c_str());
133	result += buffer;
134	}
135
136	sprintf(buffer ,"\n");
137	result += buffer;
138
139	sprintf(buffer ,"------------------------------------------------------------------\n");
140	result += buffer;
141
142	return result;
143
144	}
145
146
147	void RBCOMVisitor::visit(RigidBody* rb){
148	AtomData* atomData;
149	AtomInfo* atomInfo;
150	Vector3d pos;
151
152	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	atomInfo->vec[0] = 0;
159	atomInfo->vec[1] = 0;
160	atomInfo->vec[2] = 0;
161
162	atomData = new AtomData;
163	atomData->setID("ATOMDATA");
164	atomData->addAtomInfo(atomInfo);
165
166	rb->addProperty(atomData);
167
168	}
169
170
171	const std::string RBCOMVisitor::toString(){
172	char buffer[65535];
173	std::string result;
174
175	sprintf(buffer ,"------------------------------------------------------------------\n");
176	result += buffer;
177
178	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
179	result += buffer;
180
181	//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
185	sprintf(buffer ,"------------------------------------------------------------------\n");
186	result += buffer;
187
188	return result;
189
190	}
191
192	}//namespace OpenMD
193