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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 275 by tim, Wed Jan 26 15:15:09 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>
43		#include "visitors/AtomVisitor.hpp"
44		#include "primitives/DirectionalAtom.hpp"
45	–	#include "math/MatVec3.h"
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	<	}
76	<
77	<	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
78	<	std::set<std::string>::iterator strIter;
79	<	strIter = ssdAtomType.find(atomType);
80	<	return strIter != ssdAtomType.end() ? true : false;
81	<	}
82	<
83	<	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
84	<	std::vector<AtomInfo*>atoms;
85	<
86	<	//we need to convert SSD into 4 differnet atoms
87	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
88	<	//of the water with a dipole moment
89	<	Vector3d h1(0.0, -0.75695, 0.5206);
90	<	Vector3d h2(0.0, 0.75695, 0.5206);
91	<	Vector3d ox(0.0, 0.0, -0.0654);
92	<	Vector3d u(0, 0, 1);
93	<	RotMat3x3d   rotMatrix;
94	<	RotMat3x3d   rotTrans;
95	<	AtomInfo *   atomInfo;
96	<	Vector3d     pos;
97	<	Vector3d     newVec;
98	<	Quat4d       q;
99	<	AtomData *   atomData;
100	<	GenericData *data;
101	<	bool         haveAtomData;
102	<
103	<	//if atom is not SSD atom, just skip it
104	<	if (!isSSDAtom(datom->getType()))
105	<	return;
106	<
107	<	data = datom->getPropertyByName("ATOMDATA");
108	<
109	<	if (data != NULL) {
110	<	atomData = dynamic_cast<AtomData *>(data);
111	<
112	<	if (atomData == NULL) {
113	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
114	<	atomData = new AtomData;
115	<	haveAtomData = false;
116	<	} else
117	<	haveAtomData = true;
118	<	} else {
119	<	atomData = new AtomData;
120	<	haveAtomData = false;
121	<	}
122	<
123	<	pos = datom->getPos();
124	<	q = datom->getQ();
125	<	rotMatrix = datom->getA();
126	<
127	<	// We need A^T to convert from body-fixed to space-fixed:
128	<	//transposeMat3(rotMatrix, rotTrans);
129	<	rotTrans = rotMatrix.transpose();
130	<
131	<	//center of mass of the water molecule
132	<	//matVecMul3(rotTrans, u, newVec);
133	<	newVec = rotTrans * u;
134	<
135	<	atomInfo = new AtomInfo;
136	<	atomInfo->AtomType = "X";
137	<	atomInfo->pos[0] = pos[0];
138	<	atomInfo->pos[1] = pos[1];
139	<	atomInfo->pos[2] = pos[2];
140	<	atomInfo->dipole[0] = newVec[0];
141	<	atomInfo->dipole[1] = newVec[1];
142	<	atomInfo->dipole[2] = newVec[2];
143	<
144	<	atomData->addAtomInfo(atomInfo);
145	<
146	<	//oxygen
147	<	//matVecMul3(rotTrans, ox, newVec);
148	<	newVec = rotTrans * ox;
149	<
150	<	atomInfo = new AtomInfo;
151	<	atomInfo->AtomType = "O";
152	<	atomInfo->pos[0] = pos[0] + newVec[0];
153	<	atomInfo->pos[1] = pos[1] + newVec[1];
154	<	atomInfo->pos[2] = pos[2] + newVec[2];
155	<	atomInfo->dipole[0] = 0.0;
156	<	atomInfo->dipole[1] = 0.0;
157	<	atomInfo->dipole[2] = 0.0;
158	<	atomData->addAtomInfo(atomInfo);
159	<
160	<	//hydrogen1
161	<	//matVecMul3(rotTrans, h1, newVec);
162	<	newVec = rotTrans * h1;
163	<	atomInfo = new AtomInfo;
164	<	atomInfo->AtomType = "H";
165	<	atomInfo->pos[0] = pos[0] + newVec[0];
166	<	atomInfo->pos[1] = pos[1] + newVec[1];
167	<	atomInfo->pos[2] = pos[2] + newVec[2];
168	<	atomInfo->dipole[0] = 0.0;
169	<	atomInfo->dipole[1] = 0.0;
170	<	atomInfo->dipole[2] = 0.0;
171	<	atomData->addAtomInfo(atomInfo);
172	<
173	<	//hydrogen2
174	<	//matVecMul3(rotTrans, h2, newVec);
175	<	newVec = rotTrans * h2;
176	<	atomInfo = new AtomInfo;
177	<	atomInfo->AtomType = "H";
178	<	atomInfo->pos[0] = pos[0] + newVec[0];
179	<	atomInfo->pos[1] = pos[1] + newVec[1];
180	<	atomInfo->pos[2] = pos[2] + newVec[2];
181	<	atomInfo->dipole[0] = 0.0;
182	<	atomInfo->dipole[1] = 0.0;
183	<	atomInfo->dipole[2] = 0.0;
184	<	atomData->addAtomInfo(atomInfo);
185	<
186	<	//add atom data into atom's property
187	<
188	<	if (!haveAtomData) {
189	<	atomData->setID("ATOMDATA");
190	<	datom->addProperty(atomData);
191	<	}
192	<
193	<	setVisited(datom);
194	<	}
195	<
196	<	const std::string SSDAtomVisitor::toString() {
197	<	char   buffer[65535];
198	<	std::string result;
199	<
200	<	sprintf(buffer,
201	<	"------------------------------------------------------------------\n");
202	<	result += buffer;
203	<
204	<	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
205	<	result += buffer;
206	<
207	<	sprintf(buffer,
208	<	"Visitor Description: Convert SSD into 4 different atoms\n");
209	<	result += buffer;
210	<
211	<	sprintf(buffer,
212	<	"------------------------------------------------------------------\n");
213	<	result += buffer;
74	>	}
75
76	<	return result;
77	<	}
78	<
218	<	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
219	<	std::set<std::string>::iterator strIter;
220	<	strIter = linearAtomType.find(atomType);
221	<
222	<	return strIter != linearAtomType.end() ? true : false;
223	<	}
224	<
225	<	void LinearAtomVisitor::visit(DirectionalAtom* datom){
226	<	std::vector<AtomInfo*> atoms;
227	<	//we need to convert linear into 4 different atoms
228	<	Vector3d c1(0.0, 0.0, -1.8);
229	<	Vector3d c2(0.0, 0.0, -0.6);
230	<	Vector3d c3(0.0, 0.0,  0.6);
231	<	Vector3d c4(0.0, 0.0,  1.8);
232	<	RotMat3x3d rotMatrix;
233	<	RotMat3x3d rotTrans;
234	<	AtomInfo* atomInfo;
235	<	Vector3d pos;
236	<	Vector3d newVec;
237	<	Quat4d q;
238	<	AtomData* atomData;
239	<	GenericData* data;
240	<	bool haveAtomData;
241	<
242	<	//if atom is not SSD atom, just skip it
243	<	if(!isLinearAtom(datom->getType()))
244	<	return;
245	<
246	<	data = datom->getPropertyByName("ATOMDATA");
247	<	if(data != NULL){
248	<	atomData = dynamic_cast<AtomData*>(data);
249	<	if(atomData == NULL){
250	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
251	<	atomData = new AtomData;
252	<	haveAtomData = false;
253	<	} else {
254	<	haveAtomData = true;
255	<	}
256	<	} else {
257	<	atomData = new AtomData;
258	<	haveAtomData = false;
259	<	}
260	<
261	<
262	<	pos = datom->getPos();
263	<	q = datom->getQ();
264	<	rotMatrix = datom->getA();
265	<
266	<	// We need A^T to convert from body-fixed to space-fixed:
267	<	rotTrans = rotMatrix.transpose();
268	<
269	<	newVec = rotTrans * c1;
270	<	atomInfo = new AtomInfo;
271	<	atomInfo->AtomType = "C";
272	<	atomInfo->pos[0] = pos[0] + newVec[0];
273	<	atomInfo->pos[1] = pos[1] + newVec[1];
274	<	atomInfo->pos[2] = pos[2] + newVec[2];
275	<	atomInfo->dipole[0] = 0.0;
276	<	atomInfo->dipole[1] = 0.0;
277	<	atomInfo->dipole[2] = 0.0;
278	<	atomData->addAtomInfo(atomInfo);
279	<
280	<	newVec = rotTrans * c2;
281	<	atomInfo = new AtomInfo;
282	<	atomInfo->AtomType = "C";
283	<	atomInfo->pos[0] = pos[0] + newVec[0];
284	<	atomInfo->pos[1] = pos[1] + newVec[1];
285	<	atomInfo->pos[2] = pos[2] + newVec[2];
286	<	atomInfo->dipole[0] = 0.0;
287	<	atomInfo->dipole[1] = 0.0;
288	<	atomInfo->dipole[2] = 0.0;
289	<	atomData->addAtomInfo(atomInfo);
290	<
291	<	newVec = rotTrans * c3;
292	<	atomInfo = new AtomInfo;
293	<	atomInfo->AtomType = "C";
294	<	atomInfo->pos[0] = pos[0] + newVec[0];
295	<	atomInfo->pos[1] = pos[1] + newVec[1];
296	<	atomInfo->pos[2] = pos[2] + newVec[2];
297	<	atomInfo->dipole[0] = 0.0;
298	<	atomInfo->dipole[1] = 0.0;
299	<	atomInfo->dipole[2] = 0.0;
300	<	atomData->addAtomInfo(atomInfo);
301	<
302	<	newVec = rotTrans * c4;
303	<	atomInfo = new AtomInfo;
304	<	atomInfo->AtomType = "C";
305	<	atomInfo->pos[0] = pos[0] + newVec[0];
306	<	atomInfo->pos[1] = pos[1] + newVec[1];
307	<	atomInfo->pos[2] = pos[2] + newVec[2];
308	<	atomInfo->dipole[0] = 0.0;
309	<	atomInfo->dipole[1] = 0.0;
310	<	atomInfo->dipole[2] = 0.0;
311	<	atomData->addAtomInfo(atomInfo);
312	<
313	<	//add atom data into atom's property
314	<
315	<	if(!haveAtomData){
316	<	atomData->setID("ATOMDATA");
317	<	datom->addProperty(atomData);
318	<	}
319	<
320	<	setVisited(datom);
321	<
322	<	}
323	<
324	<	const std::string LinearAtomVisitor::toString(){
325	<	char buffer[65535];
326	<	std::string result;
327	<
328	<	sprintf(buffer ,"------------------------------------------------------------------\n");
329	<	result += buffer;
330	<
331	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
332	<	result += buffer;
333	<
334	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
335	<	result += buffer;
336	<
337	<	sprintf(buffer ,"------------------------------------------------------------------\n");
338	<	result += buffer;
339	<
340	<	return result;
341	<	}
342	<
343	<	//----------------------------------------------------------------------------//
344	<
345	<	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->AtomType = atom->getType();
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	<
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;
125
126	<	atomInfo->AtomType = datom->getType();
126	>	atomInfo->atomTypeName = datom->getType();
127		atomInfo->pos[0] = pos[0];
128		atomInfo->pos[1] = pos[1];
129		atomInfo->pos[2] = pos[2];
#	Line 400 | 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 422 | 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 275 by tim, Wed Jan 26 15:15:09 2005 UTC vs.
Revision 1455 by gezelter, Thu Jun 24 20:44:18 2010 UTC

#	Line 0 | Line 1
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