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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 1 | Line 1
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 <cstring>
43		#include "visitors/AtomVisitor.hpp"
44		#include "primitives/DirectionalAtom.hpp"
4	–	#include "math/MatVec3.h"
45		#include "primitives/RigidBody.hpp"
46
47	<	namespace oopse {
47	>	namespace OpenMD {
48	>	void BaseAtomVisitor::visit(RigidBody *rb) {
49	>	//vector<Atom*> myAtoms;
50	>	//vector<Atom*>::iterator atomIter;
51
52	<	void BaseAtomVisitor::visit(RigidBody* rb){
10	<	//vector<Atom*> myAtoms;
11	<	//vector<Atom*>::iterator atomIter;
52	>	//myAtoms = rb->getAtoms();
53
54	<	//myAtoms = rb->getAtoms();
55	<
15	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
16	<	//  (*atomIter)->accept(this);
17	<	}
18	<
19	<	void BaseAtomVisitor::setVisited(Atom* atom){
20	<	GenericData* data;
21	<	data = atom->getProperty("VISITED");
22	<
23	<	//if visited property is not existed, add it as new property
24	<	if(data == NULL){
25	<	data = new GenericData();
26	<	data->setID("VISITED");
27	<	atom->addProperty(data);
54	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55	>	//  (*atomIter)->accept(this);
56		}
29	–	}
57
58	<	bool BaseAtomVisitor::isVisited(Atom* atom){
59	<	GenericData* data;
60	<	data = atom->getProperty("VISITED");
34	<	return data == NULL ?  false : true;
35	<	}
58	>	void BaseAtomVisitor::setVisited(Atom *atom) {
59	>	GenericData *data;
60	>	data = atom->getPropertyByName("VISITED");
61
62	<	bool SSDAtomVisitor::isSSDAtom(const string& atomType){
63	<	vector<string>::iterator strIter;
64	<
65	<	for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
66	<	if(*strIter == atomType)
42	<	return true;
43	<
44	<	return false;
45	<	}
46	<
47	<	void SSDAtomVisitor::visit(DirectionalAtom* datom){
48	<
49	<	vector<AtomInfo*> atoms;
50	<
51	<	//we need to convert SSD into 4 differnet atoms
52	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
53	<	//of the water with a dipole moment
54	<	double h1[3] = {0.0, -0.75695, 0.5206};
55	<	double h2[3] = {0.0, 0.75695, 0.5206};
56	<	double ox[3] = {0.0, 0.0, -0.0654};
57	<	double u[3] = {0, 0, 1};
58	<	double rotMatrix[3][3];
59	<	double rotTrans[3][3];
60	<	AtomInfo* atomInfo;
61	<	double pos[3];
62	<	double newVec[3];
63	<	double q[4];
64	<	AtomData* atomData;
65	<	GenericData* data;
66	<	bool haveAtomData;
67	<
68	<	//if atom is not SSD atom, just skip it
69	<	if(!isSSDAtom(datom->getType()))
70	<	return;
71	<
72	<	data = datom->getProperty("ATOMDATA");
73	<	if(data != NULL){
74	<
75	<	atomData = dynamic_cast<AtomData*>(data);
76	<	if(atomData == NULL){
77	<	cerr << "can not get Atom Data from " << datom->getType() << endl;
78	<	atomData = new AtomData;
79	<	haveAtomData = false;
62	>	//if visited property is not existed, add it as new property
63	>	if (data == NULL) {
64	>	data = new GenericData();
65	>	data->setID("VISITED");
66	>	atom->addProperty(data);
67		}
81	–	else
82	–	haveAtomData = true;
68		}
69	<	else{
70	<	atomData = new AtomData;
71	<	haveAtomData = false;
69	>
70	>	bool BaseAtomVisitor::isVisited(Atom *atom) {
71	>	GenericData *data;
72	>	data = atom->getPropertyByName("VISITED");
73	>	return data == NULL ? false : true;
74		}
88	–
89	–
90	–	datom->getPos(pos);
91	–	datom->getQ(q);
92	–	datom->getA(rotMatrix);
75
76	<	// We need A^T to convert from body-fixed to space-fixed:
77	<	transposeMat3(rotMatrix, rotTrans);
78	<
79	<	//center of mass of the water molecule
80	<	matVecMul3(rotTrans, u, newVec);
81	<	atomInfo = new AtomInfo;
82	<	atomInfo->AtomType = "X";
83	<	atomInfo->pos[0] = pos[0];
84	<	atomInfo->pos[1] = pos[1];
85	<	atomInfo->pos[2] = pos[2];
86	<	atomInfo->dipole[0] = newVec[0];
87	<	atomInfo->dipole[1] = newVec[1];
88	<	atomInfo->dipole[2] = newVec[2];
107	<
108	<	atomData->addAtomInfo(atomInfo);
109	<
110	<	//oxygen
111	<	matVecMul3(rotTrans, ox, newVec);
112	<	atomInfo = new AtomInfo;
113	<	atomInfo->AtomType = "O";
114	<	atomInfo->pos[0] = pos[0] + newVec[0];
115	<	atomInfo->pos[1] = pos[1] + newVec[1];
116	<	atomInfo->pos[2] = pos[2] + newVec[2];
117	<	atomInfo->dipole[0] = 0.0;
118	<	atomInfo->dipole[1] = 0.0;
119	<	atomInfo->dipole[2] = 0.0;
120	<	atomData->addAtomInfo(atomInfo);
121	<
122	<
123	<	//hydrogen1
124	<	matVecMul3(rotTrans, h1, newVec);
125	<	atomInfo = new AtomInfo;
126	<	atomInfo->AtomType = "H";
127	<	atomInfo->pos[0] = pos[0] + newVec[0];
128	<	atomInfo->pos[1] = pos[1] + newVec[1];
129	<	atomInfo->pos[2] = pos[2] + newVec[2];
130	<	atomInfo->dipole[0] = 0.0;
131	<	atomInfo->dipole[1] = 0.0;
132	<	atomInfo->dipole[2] = 0.0;
133	<	atomData->addAtomInfo(atomInfo);
134	<
135	<	//hydrogen2
136	<	matVecMul3(rotTrans, h2, newVec);
137	<	atomInfo = new AtomInfo;
138	<	atomInfo->AtomType = "H";
139	<	atomInfo->pos[0] = pos[0] + newVec[0];
140	<	atomInfo->pos[1] = pos[1] + newVec[1];
141	<	atomInfo->pos[2] = pos[2] + newVec[2];
142	<	atomInfo->dipole[0] = 0.0;
143	<	atomInfo->dipole[1] = 0.0;
144	<	atomInfo->dipole[2] = 0.0;
145	<	atomData->addAtomInfo(atomInfo);
146	<
147	<	//add atom data into atom's property
148	<
149	<	if(!haveAtomData){
76	>	//------------------------------------------------------------------------//
77	>
78	>	void DefaultAtomVisitor::visit(Atom *atom) {
79	>	AtomData *atomData;
80	>	AtomInfo *atomInfo;
81	>	Vector3d  pos;
82	>
83	>	if (isVisited(atom))
84	>	return;
85	>
86	>	atomInfo = new AtomInfo;
87	>
88	>	atomData = new AtomData;
89		atomData->setID("ATOMDATA");
90	<	datom->addProperty(atomData);
90	>
91	>	pos = atom->getPos();
92	>	atomInfo->atomTypeName = atom->getType();
93	>	atomInfo->pos[0] = pos[0];
94	>	atomInfo->pos[1] = pos[1];
95	>	atomInfo->pos[2] = pos[2];
96	>	atomInfo->dipole[0] = 0.0;
97	>	atomInfo->dipole[1] = 0.0;
98	>	atomInfo->dipole[2] = 0.0;
99	>
100	>	atomData->addAtomInfo(atomInfo);
101	>
102	>	atom->addProperty(atomData);
103	>
104	>	setVisited(atom);
105		}
153	–
154	–	setVisited(datom);
155	–
156	–	}
157	–
158	–	const string SSDAtomVisitor::toString(){
159	–	char buffer[65535];
160	–	string result;
106
107	<	sprintf(buffer ,"------------------------------------------------------------------\n");
108	<	result += buffer;
107	>	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
108	>	AtomData *atomData;
109	>	AtomInfo *atomInfo;
110	>	Vector3d  pos;
111	>	Vector3d  u;
112
113	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
114	<	result += buffer;
113	>	if (isVisited(datom))
114	>	return;
115
116	<	sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
117	<	result += buffer;
116	>	pos = datom->getPos();
117	>	if (datom->getAtomType()->isGayBerne()) {
118	>	u = datom->getA().transpose()*V3Z;
119	>	} else if (datom->getAtomType()->isMultipole()) {
120	>	u = datom->getElectroFrame().getColumn(2);
121	>	}
122	>	atomData = new AtomData;
123	>	atomData->setID("ATOMDATA");
124	>	atomInfo = new AtomInfo;
125
126	<	sprintf(buffer ,"------------------------------------------------------------------\n");
127	<	result += buffer;
126	>	atomInfo->atomTypeName = datom->getType();
127	>	atomInfo->pos[0] = pos[0];
128	>	atomInfo->pos[1] = pos[1];
129	>	atomInfo->pos[2] = pos[2];
130	>	atomInfo->dipole[0] = u[0];
131	>	atomInfo->dipole[1] = u[1];
132	>	atomInfo->dipole[2] = u[2];
133
134	<	return result;
175	<	}
134	>	atomData->addAtomInfo(atomInfo);
135
136	<	//----------------------------------------------------------------------------//
136	>	datom->addProperty(atomData);
137
138	<	void DefaultAtomVisitor::visit(Atom* atom){
139	<	AtomData* atomData;
181	<	AtomInfo* atomInfo;
182	<	double pos[3];
138	>	setVisited(datom);
139	>	}
140
141	<	if(isVisited(atom))
142	<	return;
141	>	const std::string DefaultAtomVisitor::toString() {
142	>	char   buffer[65535];
143	>	std::string result;
144
145	<	atomInfo =new AtomInfo;
145	>	sprintf(buffer,
146	>	"------------------------------------------------------------------\n");
147	>	result += buffer;
148
149	<	atomData = new AtomData;
150	<	atomData->setID("ATOMDATA");
191	<
192	<	atom->getPos(pos);
193	<	atomInfo->AtomType = atom->getType();
194	<	atomInfo->pos[0] = pos[0];
195	<	atomInfo->pos[1] = pos[1];
196	<	atomInfo->pos[2] = pos[2];
197	<	atomInfo->dipole[0] = 0.0;
198	<	atomInfo->dipole[1] = 0.0;
199	<	atomInfo->dipole[2] = 0.0;
149	>	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
150	>	result += buffer;
151
152	+	sprintf(buffer,
153	+	"Visitor Description: copy atom infomation into atom data\n");
154	+	result += buffer;
155
156	<	atomData->addAtomInfo(atomInfo);
157	<
158	<	atom->addProperty(atomData);
156	>	sprintf(buffer,
157	>	"------------------------------------------------------------------\n");
158	>	result += buffer;
159
160	<	setVisited(atom);
161	<	}
162	<	void DefaultAtomVisitor::visit(DirectionalAtom* datom){
209	<	AtomData* atomData;
210	<	AtomInfo* atomInfo;
211	<	double pos[3];
212	<	double u[3];
213	<
214	<	if(isVisited(datom))
215	<	return;
216	<
217	<	datom->getPos(pos);
218	<	datom->getU(u);
219	<
220	<	atomData = new AtomData;
221	<	atomData->setID("ATOMDATA");
222	<	atomInfo =new AtomInfo;
223	<
224	<	atomInfo->AtomType = datom->getType();
225	<	atomInfo->pos[0] = pos[0];
226	<	atomInfo->pos[1] = pos[1];
227	<	atomInfo->pos[2] = pos[2];
228	<	atomInfo->dipole[0] = u[0];
229	<	atomInfo->dipole[1] = u[1];
230	<	atomInfo->dipole[2] = u[2];
231	<
232	<	atomData->addAtomInfo(atomInfo);
233	<
234	<	datom->addProperty(atomData);
235	<
236	<	setVisited(datom);
237	<	}
238	<
239	<
240	<	const string DefaultAtomVisitor::toString(){
241	<	char buffer[65535];
242	<	string result;
243	<
244	<	sprintf(buffer ,"------------------------------------------------------------------\n");
245	<	result += buffer;
246	<
247	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
248	<	result += buffer;
249	<
250	<	sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
251	<	result += buffer;
252	<
253	<	sprintf(buffer ,"------------------------------------------------------------------\n");
254	<	result += buffer;
255	<
256	<	return result;
257	<	}
258	<
259	<	}//namespace oopse
160	>	return result;
161	>	}
162	>	} //namespace OpenMD

Comparing trunk/src/visitors/AtomVisitor.cpp (property svn:keywords):
Revision 132 by tim, Thu Oct 21 16:22:01 2004 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

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