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root/OpenMD/trunk/src/visitors/AtomVisitor.cpp

Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1456 by gezelter, Fri Jun 25 17:40:24 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	<	void BaseAtomVisitor::visit(RigidBody* rb){
48	<	//vector<Atom*> myAtoms;
49	<	//vector<Atom*>::iterator atomIter;
47	>	namespace OpenMD {
48	>	void BaseAtomVisitor::visit(RigidBody *rb) {
49	>	//vector<Atom*> myAtoms;
50	>	//vector<Atom*>::iterator atomIter;
51
52	<	//myAtoms = rb->getAtoms();
12	<
13	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
14	<	//  (*atomIter)->accept(this);
15	<	}
52	>	//myAtoms = rb->getAtoms();
53
54	<	void BaseAtomVisitor::setVisited(Atom* atom){
55	<	GenericData* data;
19	<	data = atom->getProperty("VISITED");
20	<
21	<	//if visited property is not existed, add it as new property
22	<	if(data == NULL){
23	<	data = new GenericData();
24	<	data->setID("VISITED");
25	<	atom->addProperty(data);
54	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55	>	//  (*atomIter)->accept(this);
56		}
27	–	}
57
58	<	bool BaseAtomVisitor::isVisited(Atom* atom){
59	<	GenericData* data;
60	<	data = atom->getProperty("VISITED");
32	<	return data == NULL ?  false : true;
33	<	}
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)
40	<	return true;
41	<
42	<	return false;
43	<	}
44	<
45	<	void SSDAtomVisitor::visit(DirectionalAtom* datom){
46	<
47	<	vector<AtomInfo*> atoms;
48	<
49	<	//we need to convert SSD into 4 differnet atoms
50	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
51	<	//of the water with a dipole moment
52	<	double h1[3] = {0.0, -0.75695, 0.5206};
53	<	double h2[3] = {0.0, 0.75695, 0.5206};
54	<	double ox[3] = {0.0, 0.0, -0.0654};
55	<	double u[3] = {0, 0, 1};
56	<	double rotMatrix[3][3];
57	<	double rotTrans[3][3];
58	<	AtomInfo* atomInfo;
59	<	double pos[3];
60	<	double newVec[3];
61	<	double q[4];
62	<	AtomData* atomData;
63	<	GenericData* data;
64	<	bool haveAtomData;
65	<
66	<	//if atom is not SSD atom, just skip it
67	<	if(!isSSDAtom(datom->getType()))
68	<	return;
69	<
70	<	data = datom->getProperty("ATOMDATA");
71	<	if(data != NULL){
72	<
73	<	atomData = dynamic_cast<AtomData*>(data);
74	<	if(atomData == NULL){
75	<	cerr << "can not get Atom Data from " << datom->getType() << endl;
76	<	atomData = new AtomData;
77	<	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		}
79	–	else
80	–	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		}
86	–
87	–
88	–	datom->getPos(pos);
89	–	datom->getQ(q);
90	–	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];
102	<	atomInfo->dipole[0] = newVec[0];
103	<	atomInfo->dipole[1] = newVec[1];
104	<	atomInfo->dipole[2] = newVec[2];
76	>	//------------------------------------------------------------------------//
77	>
78	>	void DefaultAtomVisitor::visit(Atom *atom) {
79	>	AtomData *atomData;
80	>	AtomInfo *atomInfo;
81	>	Vector3d  pos;
82	>	Vector3d  vel;
83	>	Vector3d  frc;
84	>	Vector3d  u;
85	>	RealType  c;
86
87	<	atomData->addAtomInfo(atomInfo);
88	<
89	<	//oxygen
90	<	matVecMul3(rotTrans, ox, newVec);
91	<	atomInfo = new AtomInfo;
92	<	atomInfo->AtomType = "O";
112	<	atomInfo->pos[0] = pos[0] + newVec[0];
113	<	atomInfo->pos[1] = pos[1] + newVec[1];
114	<	atomInfo->pos[2] = pos[2] + newVec[2];
115	<	atomInfo->dipole[0] = 0.0;
116	<	atomInfo->dipole[1] = 0.0;
117	<	atomInfo->dipole[2] = 0.0;
118	<	atomData->addAtomInfo(atomInfo);
119	<
120	<
121	<	//hydrogen1
122	<	matVecMul3(rotTrans, h1, newVec);
123	<	atomInfo = new AtomInfo;
124	<	atomInfo->AtomType = "H";
125	<	atomInfo->pos[0] = pos[0] + newVec[0];
126	<	atomInfo->pos[1] = pos[1] + newVec[1];
127	<	atomInfo->pos[2] = pos[2] + newVec[2];
128	<	atomInfo->dipole[0] = 0.0;
129	<	atomInfo->dipole[1] = 0.0;
130	<	atomInfo->dipole[2] = 0.0;
131	<	atomData->addAtomInfo(atomInfo);
132	<
133	<	//hydrogen2
134	<	matVecMul3(rotTrans, h2, newVec);
135	<	atomInfo = new AtomInfo;
136	<	atomInfo->AtomType = "H";
137	<	atomInfo->pos[0] = pos[0] + newVec[0];
138	<	atomInfo->pos[1] = pos[1] + newVec[1];
139	<	atomInfo->pos[2] = pos[2] + newVec[2];
140	<	atomInfo->dipole[0] = 0.0;
141	<	atomInfo->dipole[1] = 0.0;
142	<	atomInfo->dipole[2] = 0.0;
143	<	atomData->addAtomInfo(atomInfo);
144	<
145	<	//add atom data into atom's property
146	<
147	<	if(!haveAtomData){
87	>	if (isVisited(atom))
88	>	return;
89	>
90	>	atomInfo = new AtomInfo;
91	>
92	>	atomData = new AtomData;
93		atomData->setID("ATOMDATA");
94	<	datom->addProperty(atomData);
94	>
95	>	pos = atom->getPos();
96	>	vel = atom->getVel();
97	>	frc = atom->getFrc();
98	>	atomInfo->atomTypeName = atom->getType();
99	>	atomInfo->pos[0] = pos[0];
100	>	atomInfo->pos[1] = pos[1];
101	>	atomInfo->pos[2] = pos[2];
102	>	atomInfo->vel[0] = vel[0];
103	>	atomInfo->vel[1] = vel[1];
104	>	atomInfo->vel[2] = vel[2];
105	>	atomInfo->hasVelocity = true;
106	>	atomInfo->frc[0] = frc[0];
107	>	atomInfo->frc[1] = frc[1];
108	>	atomInfo->frc[2] = frc[2];
109	>	atomInfo->hasForce = true;
110	>	atomInfo->vec[0] = 0.0;
111	>	atomInfo->vec[1] = 0.0;
112	>	atomInfo->vec[2] = 0.0;
113	>
114	>	atomData->addAtomInfo(atomInfo);
115	>
116	>	atom->addProperty(atomData);
117	>
118	>	setVisited(atom);
119		}
151	–
152	–	setVisited(datom);
153	–
154	–	}
155	–
156	–	const string SSDAtomVisitor::toString(){
157	–	char buffer[65535];
158	–	string result;
120
121	<	sprintf(buffer ,"------------------------------------------------------------------\n");
122	<	result += buffer;
121	>	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
122	>	AtomData *atomData;
123	>	AtomInfo *atomInfo;
124	>	Vector3d  pos;
125	>	Vector3d  vel;
126	>	Vector3d  frc;
127	>	Vector3d  u;
128	>	RealType  c;
129
130	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
131	<	result += buffer;
130	>	if (isVisited(datom))
131	>	return;
132	>
133	>	pos = datom->getPos();
134	>	vel = datom->getVel();
135	>	frc = datom->getFrc();
136	>	if (datom->getAtomType()->isGayBerne()) {
137	>	u = datom->getA().transpose()*V3Z;
138	>	} else if (datom->getAtomType()->isMultipole()) {
139	>	u = datom->getElectroFrame().getColumn(2);
140	>	}
141	>	atomData = new AtomData;
142	>	atomData->setID("ATOMDATA");
143	>	atomInfo = new AtomInfo;
144
145	<	sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
146	<	result += buffer;
145	>	atomInfo->atomTypeName = datom->getType();
146	>	atomInfo->pos[0] = pos[0];
147	>	atomInfo->pos[1] = pos[1];
148	>	atomInfo->pos[2] = pos[2];
149	>	atomInfo->vel[0] = vel[0];
150	>	atomInfo->vel[1] = vel[1];
151	>	atomInfo->vel[2] = vel[2];
152	>	atomInfo->hasVelocity = true;
153	>	atomInfo->frc[0] = frc[0];
154	>	atomInfo->frc[1] = frc[1];
155	>	atomInfo->frc[2] = frc[2];
156	>	atomInfo->hasForce = true;
157	>	atomInfo->vec[0] = u[0];
158	>	atomInfo->vec[1] = u[1];
159	>	atomInfo->vec[2] = u[2];
160	>	atomInfo->hasVector = true;
161
162	<	sprintf(buffer ,"------------------------------------------------------------------\n");
170	<	result += buffer;
162	>	atomData->addAtomInfo(atomInfo);
163
164	<	return result;
173	<	}
164	>	datom->addProperty(atomData);
165
166	<	//----------------------------------------------------------------------------//
166	>	setVisited(datom);
167	>	}
168
169	<	void DefaultAtomVisitor::visit(Atom* atom){
170	<	AtomData* atomData;
171	<	AtomInfo* atomInfo;
180	<	double pos[3];
169	>	const std::string DefaultAtomVisitor::toString() {
170	>	char   buffer[65535];
171	>	std::string result;
172
173	<	if(isVisited(atom))
174	<	return;
173	>	sprintf(buffer,
174	>	"------------------------------------------------------------------\n");
175	>	result += buffer;
176
177	<	atomInfo =new AtomInfo;
177	>	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
178	>	result += buffer;
179
180	<	atomData = new AtomData;
181	<	atomData->setID("ATOMDATA");
182	<
190	<	atom->getPos(pos);
191	<	atomInfo->AtomType = atom->getType();
192	<	atomInfo->pos[0] = pos[0];
193	<	atomInfo->pos[1] = pos[1];
194	<	atomInfo->pos[2] = pos[2];
195	<	atomInfo->dipole[0] = 0.0;
196	<	atomInfo->dipole[1] = 0.0;
197	<	atomInfo->dipole[2] = 0.0;
180	>	sprintf(buffer,
181	>	"Visitor Description: copy atom infomation into atom data\n");
182	>	result += buffer;
183
184	+	sprintf(buffer,
185	+	"------------------------------------------------------------------\n");
186	+	result += buffer;
187
188	<	atomData->addAtomInfo(atomInfo);
189	<
190	<	atom->addProperty(atomData);
203	<
204	<	setVisited(atom);
205	<	}
206	<	void DefaultAtomVisitor::visit(DirectionalAtom* datom){
207	<	AtomData* atomData;
208	<	AtomInfo* atomInfo;
209	<	double pos[3];
210	<	double u[3];
211	<
212	<	if(isVisited(datom))
213	<	return;
214	<
215	<	datom->getPos(pos);
216	<	datom->getU(u);
217	<
218	<	atomData = new AtomData;
219	<	atomData->setID("ATOMDATA");
220	<	atomInfo =new AtomInfo;
221	<
222	<	atomInfo->AtomType = datom->getType();
223	<	atomInfo->pos[0] = pos[0];
224	<	atomInfo->pos[1] = pos[1];
225	<	atomInfo->pos[2] = pos[2];
226	<	atomInfo->dipole[0] = u[0];
227	<	atomInfo->dipole[1] = u[1];
228	<	atomInfo->dipole[2] = u[2];
229	<
230	<	atomData->addAtomInfo(atomInfo);
231	<
232	<	datom->addProperty(atomData);
233	<
234	<	setVisited(datom);
235	<	}
236	<
237	<
238	<	const string DefaultAtomVisitor::toString(){
239	<	char buffer[65535];
240	<	string result;
241	<
242	<	sprintf(buffer ,"------------------------------------------------------------------\n");
243	<	result += buffer;
244	<
245	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
246	<	result += buffer;
247	<
248	<	sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
249	<	result += buffer;
250	<
251	<	sprintf(buffer ,"------------------------------------------------------------------\n");
252	<	result += buffer;
253	<
254	<	return result;
255	<	}
188	>	return result;
189	>	}
190	>	} //namespace OpenMD

Comparing trunk/src/visitors/AtomVisitor.cpp (property svn:keywords):
Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
Revision 1456 by gezelter, Fri Jun 25 17:40:24 2010 UTC

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