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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 1 | Line 1
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
#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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>
#	Line 44 | Line 44
44		#include "primitives/DirectionalAtom.hpp"
45		#include "primitives/RigidBody.hpp"
46
47	<	namespace oopse {
48	<	void BaseAtomVisitor::visit(RigidBody *rb) {
49	<	//vector<Atom*> myAtoms;
50	<	//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();
52	>	//myAtoms = rb->getAtoms();
53
54	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55	<	//  (*atomIter)->accept(this);
56	<	}
54	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
55	>	//  (*atomIter)->accept(this);
56	>	}
57
58	<	void BaseAtomVisitor::setVisited(Atom *atom) {
58	>	void BaseAtomVisitor::setVisited(Atom *atom) {
59		GenericData *data;
60		data = atom->getPropertyByName("VISITED");
61
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);
64	>	data = new GenericData();
65	>	data->setID("VISITED");
66	>	atom->addProperty(data);
67		}
68	<	}
68	>	}
69
70	<	bool BaseAtomVisitor::isVisited(Atom *atom) {
70	>	bool BaseAtomVisitor::isVisited(Atom *atom) {
71		GenericData *data;
72		data = atom->getPropertyByName("VISITED");
73		return data == NULL ? false : true;
74	<	}
74	>	}
75
76	<	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
77	<	std::set<std::string>::iterator strIter;
78	<	strIter = ssdAtomType.find(atomType);
79	<	return strIter != ssdAtomType.end() ? true : false;
80	<	}
81	<
82	<	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
83	<	std::vector<AtomInfo*>atoms;
84	<
85	<	//we need to convert SSD into 4 differnet atoms
86	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87	<	//of the water with a dipole moment
88	<	Vector3d h1(0.0, -0.75695, 0.5206);
89	<	Vector3d h2(0.0, 0.75695, 0.5206);
90	<	Vector3d ox(0.0, 0.0, -0.0654);
91	<	Vector3d u(0, 0, 1);
92	<	RotMat3x3d   rotMatrix;
93	<	RotMat3x3d   rotTrans;
94	<	AtomInfo *   atomInfo;
95	<	Vector3d     pos;
96	<	Vector3d     newVec;
97	<	Quat4d       q;
98	<	AtomData *   atomData;
99	<	GenericData *data;
100	<	bool         haveAtomData;
101	<
102	<	//if atom is not SSD atom, just skip it
103	<	if (!isSSDAtom(datom->getType()))
104	<	return;
105	<
106	<	data = datom->getPropertyByName("ATOMDATA");
107	<
108	<	if (data != NULL) {
109	<	atomData = dynamic_cast<AtomData *>(data);
110	<
111	<	if (atomData == NULL) {
112	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
113	<	atomData = new AtomData;
114	<	haveAtomData = false;
115	<	} else
116	<	haveAtomData = true;
117	<	} else {
118	<	atomData = new AtomData;
119	<	haveAtomData = false;
120	<	}
121	<
122	<	pos = datom->getPos();
123	<	q = datom->getQ();
124	<	rotMatrix = datom->getA();
125	<
126	<	// We need A^T to convert from body-fixed to space-fixed:
127	<	//transposeMat3(rotMatrix, rotTrans);
128	<	rotTrans = rotMatrix.transpose();
129	<
130	<	//center of mass of the water molecule
131	<	//matVecMul3(rotTrans, u, newVec);
132	<	newVec = rotTrans * u;
133	<
134	<	atomInfo = new AtomInfo;
135	<	atomInfo->atomTypeName = "X";
136	<	atomInfo->pos[0] = pos[0];
137	<	atomInfo->pos[1] = pos[1];
138	<	atomInfo->pos[2] = pos[2];
139	<	atomInfo->dipole[0] = newVec[0];
140	<	atomInfo->dipole[1] = newVec[1];
141	<	atomInfo->dipole[2] = newVec[2];
142	<
143	<	atomData->addAtomInfo(atomInfo);
144	<
145	<	//oxygen
146	<	//matVecMul3(rotTrans, ox, newVec);
147	<	newVec = rotTrans * ox;
148	<
149	<	atomInfo = new AtomInfo;
150	<	atomInfo->atomTypeName = "O";
151	<	atomInfo->pos[0] = pos[0] + newVec[0];
152	<	atomInfo->pos[1] = pos[1] + newVec[1];
153	<	atomInfo->pos[2] = pos[2] + newVec[2];
154	<	atomInfo->dipole[0] = 0.0;
155	<	atomInfo->dipole[1] = 0.0;
156	<	atomInfo->dipole[2] = 0.0;
157	<	atomData->addAtomInfo(atomInfo);
158	<
159	<	//hydrogen1
160	<	//matVecMul3(rotTrans, h1, newVec);
161	<	newVec = rotTrans * h1;
162	<	atomInfo = new AtomInfo;
163	<	atomInfo->atomTypeName = "H";
164	<	atomInfo->pos[0] = pos[0] + newVec[0];
165	<	atomInfo->pos[1] = pos[1] + newVec[1];
166	<	atomInfo->pos[2] = pos[2] + newVec[2];
167	<	atomInfo->dipole[0] = 0.0;
168	<	atomInfo->dipole[1] = 0.0;
169	<	atomInfo->dipole[2] = 0.0;
170	<	atomData->addAtomInfo(atomInfo);
171	<
172	<	//hydrogen2
173	<	//matVecMul3(rotTrans, h2, newVec);
174	<	newVec = rotTrans * h2;
175	<	atomInfo = new AtomInfo;
176	<	atomInfo->atomTypeName = "H";
177	<	atomInfo->pos[0] = pos[0] + newVec[0];
178	<	atomInfo->pos[1] = pos[1] + newVec[1];
179	<	atomInfo->pos[2] = pos[2] + newVec[2];
180	<	atomInfo->dipole[0] = 0.0;
181	<	atomInfo->dipole[1] = 0.0;
182	<	atomInfo->dipole[2] = 0.0;
183	<	atomData->addAtomInfo(atomInfo);
184	<
185	<	//add atom data into atom's property
186	<
187	<	if (!haveAtomData) {
188	<	atomData->setID("ATOMDATA");
189	<	datom->addProperty(atomData);
190	<	}
191	<
192	<	setVisited(datom);
193	<	}
194	<
195	<	const std::string SSDAtomVisitor::toString() {
196	<	char   buffer[65535];
197	<	std::string result;
198	<
199	<	sprintf(buffer,
200	<	"------------------------------------------------------------------\n");
201	<	result += buffer;
202	<
203	<	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
204	<	result += buffer;
205	<
206	<	sprintf(buffer,
207	<	"Visitor Description: Convert SSD into 4 different atoms\n");
208	<	result += buffer;
209	<
210	<	sprintf(buffer,
211	<	"------------------------------------------------------------------\n");
212	<	result += buffer;
213	<
214	<	return result;
215	<	}
216	<
217	<	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218	<	std::set<std::string>::iterator strIter;
219	<	strIter = linearAtomType.find(atomType);
220	<
221	<	return strIter != linearAtomType.end() ? true : false;
222	<	}
223	<
224	<	void LinearAtomVisitor::visit(DirectionalAtom* datom){
225	<	std::vector<AtomInfo*> atoms;
226	<	//we need to convert linear into 4 different atoms
227	<	Vector3d c1(0.0, 0.0, -1.8);
228	<	Vector3d c2(0.0, 0.0, -0.6);
229	<	Vector3d c3(0.0, 0.0,  0.6);
230	<	Vector3d c4(0.0, 0.0,  1.8);
231	<	RotMat3x3d rotMatrix;
232	<	RotMat3x3d rotTrans;
233	<	AtomInfo* atomInfo;
234	<	Vector3d pos;
235	<	Vector3d newVec;
236	<	Quat4d q;
237	<	AtomData* atomData;
238	<	GenericData* data;
239	<	bool haveAtomData;
240	<
241	<	//if atom is not SSD atom, just skip it
242	<	if(!isLinearAtom(datom->getType()))
243	<	return;
244	<
245	<	data = datom->getPropertyByName("ATOMDATA");
246	<	if(data != NULL){
247	<	atomData = dynamic_cast<AtomData*>(data);
248	<	if(atomData == NULL){
249	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
250	<	atomData = new AtomData;
251	<	haveAtomData = false;
252	<	} else {
253	<	haveAtomData = true;
254	<	}
255	<	} else {
256	<	atomData = new AtomData;
257	<	haveAtomData = false;
258	<	}
259	<
260	<
261	<	pos = datom->getPos();
262	<	q = datom->getQ();
263	<	rotMatrix = datom->getA();
264	<
265	<	// We need A^T to convert from body-fixed to space-fixed:
266	<	rotTrans = rotMatrix.transpose();
267	<
268	<	newVec = rotTrans * c1;
269	<	atomInfo = new AtomInfo;
270	<	atomInfo->atomTypeName = "C";
271	<	atomInfo->pos[0] = pos[0] + newVec[0];
272	<	atomInfo->pos[1] = pos[1] + newVec[1];
273	<	atomInfo->pos[2] = pos[2] + newVec[2];
274	<	atomInfo->dipole[0] = 0.0;
275	<	atomInfo->dipole[1] = 0.0;
276	<	atomInfo->dipole[2] = 0.0;
277	<	atomData->addAtomInfo(atomInfo);
278	<
279	<	newVec = rotTrans * c2;
280	<	atomInfo = new AtomInfo;
281	<	atomInfo->atomTypeName = "C";
282	<	atomInfo->pos[0] = pos[0] + newVec[0];
283	<	atomInfo->pos[1] = pos[1] + newVec[1];
284	<	atomInfo->pos[2] = pos[2] + newVec[2];
285	<	atomInfo->dipole[0] = 0.0;
286	<	atomInfo->dipole[1] = 0.0;
287	<	atomInfo->dipole[2] = 0.0;
288	<	atomData->addAtomInfo(atomInfo);
289	<
290	<	newVec = rotTrans * c3;
291	<	atomInfo = new AtomInfo;
292	<	atomInfo->atomTypeName = "C";
293	<	atomInfo->pos[0] = pos[0] + newVec[0];
294	<	atomInfo->pos[1] = pos[1] + newVec[1];
295	<	atomInfo->pos[2] = pos[2] + newVec[2];
296	<	atomInfo->dipole[0] = 0.0;
297	<	atomInfo->dipole[1] = 0.0;
298	<	atomInfo->dipole[2] = 0.0;
299	<	atomData->addAtomInfo(atomInfo);
300	<
301	<	newVec = rotTrans * c4;
302	<	atomInfo = new AtomInfo;
303	<	atomInfo->atomTypeName = "C";
304	<	atomInfo->pos[0] = pos[0] + newVec[0];
305	<	atomInfo->pos[1] = pos[1] + newVec[1];
306	<	atomInfo->pos[2] = pos[2] + newVec[2];
307	<	atomInfo->dipole[0] = 0.0;
308	<	atomInfo->dipole[1] = 0.0;
309	<	atomInfo->dipole[2] = 0.0;
310	<	atomData->addAtomInfo(atomInfo);
311	<
312	<	//add atom data into atom's property
313	<
314	<	if(!haveAtomData){
315	<	atomData->setID("ATOMDATA");
316	<	datom->addProperty(atomData);
317	<	}
318	<
319	<	setVisited(datom);
320	<
321	<	}
322	<
323	<	const std::string LinearAtomVisitor::toString(){
324	<	char buffer[65535];
325	<	std::string result;
326	<
327	<	sprintf(buffer ,"------------------------------------------------------------------\n");
328	<	result += buffer;
329	<
330	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
331	<	result += buffer;
332	<
333	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
334	<	result += buffer;
335	<
336	<	sprintf(buffer ,"------------------------------------------------------------------\n");
337	<	result += buffer;
338	<
339	<	return result;
340	<	}
341	<
342	<	//----------------------------------------------------------------------------//
343	<
344	<	void DefaultAtomVisitor::visit(Atom *atom) {
76	>	//------------------------------------------------------------------------//
77	>
78	>	void DefaultAtomVisitor::visit(Atom *atom) {
79		AtomData *atomData;
80		AtomInfo *atomInfo;
81		Vector3d  pos;
82	<
82	>
83		if (isVisited(atom))
84	<	return;
85	<
84	>	return;
85	>
86		atomInfo = new AtomInfo;
87	<
87	>
88		atomData = new AtomData;
89		atomData->setID("ATOMDATA");
90	<
90	>
91		pos = atom->getPos();
92		atomInfo->atomTypeName = atom->getType();
93		atomInfo->pos[0] = pos[0];
#	Line 362 | Line 96 | void DefaultAtomVisitor::visit(Atom *atom) {
96		atomInfo->dipole[0] = 0.0;
97		atomInfo->dipole[1] = 0.0;
98		atomInfo->dipole[2] = 0.0;
99	<
99	>
100		atomData->addAtomInfo(atomInfo);
101	<
101	>
102		atom->addProperty(atomData);
103	<
103	>
104		setVisited(atom);
105	<	}
106	<
107	<	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
105	>	}
106	>
107	>	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
108		AtomData *atomData;
109		AtomInfo *atomInfo;
110		Vector3d  pos;
111		Vector3d  u;
112
113		if (isVisited(datom))
114	<	return;
114	>	return;
115
116		pos = datom->getPos();
117	<	u = datom->getElectroFrame().getColumn(2);
118	<
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;
#	Line 399 | Line 136 | void DefaultAtomVisitor::visit(DirectionalAtom *datom)
136		datom->addProperty(atomData);
137
138		setVisited(datom);
139	<	}
139	>	}
140
141	<	const std::string DefaultAtomVisitor::toString() {
141	>	const std::string DefaultAtomVisitor::toString() {
142		char   buffer[65535];
143		std::string result;
144
#	Line 421 | Line 158 | const std::string DefaultAtomVisitor::toString() {
158		result += buffer;
159
160		return result;
161	<	}
162	<	} //namespace oopse
161	>	}
162	>	} //namespace OpenMD

Comparing trunk/src/visitors/AtomVisitor.cpp (property svn:keywords):
Revision 413 by tim, Wed Mar 9 17:30:29 2005 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 0 | Line 1
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