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root/OpenMD/branches/development/src/visitors/AtomVisitor.cpp

Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 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;
75	–	}
76	–
77	–	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
78	–	std::vector<std::string>::iterator strIter;
79	–
80	–	for( strIter = ssdAtomType.begin(); strIter != ssdAtomType.end();
81	–	++strIter )
82	–	if (*strIter == atomType)
83	–	return true;
84	–
85	–	return false;
86	–	}
87	–
88	–	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
89	–	std::vector<AtomInfo *>atoms;
90	–
91	–	//we need to convert SSD into 4 differnet atoms
92	–	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
93	–	//of the water with a dipole moment
94	–	Vector3d h1(0.0, -0.75695, 0.5206);
95	–	Vector3d h2(0.0, 0.75695, 0.5206);
96	–	Vector3d ox(0.0, 0.0, -0.0654);
97	–	Vector3d u(0, 0, 1);
98	–	RotMat3x3d   rotMatrix;
99	–	RotMat3x3d   rotTrans;
100	–	AtomInfo *   atomInfo;
101	–	Vector3d     pos;
102	–	Vector3d     newVec;
103	–	Quat4d       q;
104	–	AtomData *   atomData;
105	–	GenericData *data;
106	–	bool         haveAtomData;
107	–
108	–	//if atom is not SSD atom, just skip it
109	–	if (!isSSDAtom(datom->getType()))
110	–	return;
111	–
112	–	data = datom->getPropertyByName("ATOMDATA");
113	–
114	–	if (data != NULL) {
115	–	atomData = dynamic_cast<AtomData *>(data);
116	–
117	–	if (atomData == NULL) {
118	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
119	–	atomData = new AtomData;
120	–	haveAtomData = false;
121	–	} else
122	–	haveAtomData = true;
123	–	} else {
124	–	atomData = new AtomData;
125	–	haveAtomData = false;
126	–	}
127	–
128	–	pos = datom->getPos();
129	–	q = datom->getQ();
130	–	rotMatrix = datom->getA();
131	–
132	–	// We need A^T to convert from body-fixed to space-fixed:
133	–	//transposeMat3(rotMatrix, rotTrans);
134	–	rotTrans = rotMatrix.transpose();
135	–
136	–	//center of mass of the water molecule
137	–	//matVecMul3(rotTrans, u, newVec);
138	–	newVec = rotTrans * u;
139	–
140	–	atomInfo = new AtomInfo;
141	–	atomInfo->AtomType = "X";
142	–	atomInfo->pos[0] = pos[0];
143	–	atomInfo->pos[1] = pos[1];
144	–	atomInfo->pos[2] = pos[2];
145	–	atomInfo->dipole[0] = newVec[0];
146	–	atomInfo->dipole[1] = newVec[1];
147	–	atomInfo->dipole[2] = newVec[2];
148	–
149	–	atomData->addAtomInfo(atomInfo);
150	–
151	–	//oxygen
152	–	//matVecMul3(rotTrans, ox, newVec);
153	–	newVec = rotTrans * ox;
154	–
155	–	atomInfo = new AtomInfo;
156	–	atomInfo->AtomType = "O";
157	–	atomInfo->pos[0] = pos[0] + newVec[0];
158	–	atomInfo->pos[1] = pos[1] + newVec[1];
159	–	atomInfo->pos[2] = pos[2] + newVec[2];
160	–	atomInfo->dipole[0] = 0.0;
161	–	atomInfo->dipole[1] = 0.0;
162	–	atomInfo->dipole[2] = 0.0;
163	–	atomData->addAtomInfo(atomInfo);
164	–
165	–	//hydrogen1
166	–	//matVecMul3(rotTrans, h1, newVec);
167	–	newVec = rotTrans * h1;
168	–	atomInfo = new AtomInfo;
169	–	atomInfo->AtomType = "H";
170	–	atomInfo->pos[0] = pos[0] + newVec[0];
171	–	atomInfo->pos[1] = pos[1] + newVec[1];
172	–	atomInfo->pos[2] = pos[2] + newVec[2];
173	–	atomInfo->dipole[0] = 0.0;
174	–	atomInfo->dipole[1] = 0.0;
175	–	atomInfo->dipole[2] = 0.0;
176	–	atomData->addAtomInfo(atomInfo);
177	–
178	–	//hydrogen2
179	–	//matVecMul3(rotTrans, h2, newVec);
180	–	newVec = rotTrans * h2;
181	–	atomInfo = new AtomInfo;
182	–	atomInfo->AtomType = "H";
183	–	atomInfo->pos[0] = pos[0] + newVec[0];
184	–	atomInfo->pos[1] = pos[1] + newVec[1];
185	–	atomInfo->pos[2] = pos[2] + newVec[2];
186	–	atomInfo->dipole[0] = 0.0;
187	–	atomInfo->dipole[1] = 0.0;
188	–	atomInfo->dipole[2] = 0.0;
189	–	atomData->addAtomInfo(atomInfo);
190	–
191	–	//add atom data into atom's property
192	–
193	–	if (!haveAtomData) {
194	–	atomData->setID("ATOMDATA");
195	–	datom->addProperty(atomData);
196	–	}
197	–
198	–	setVisited(datom);
199	–	}
200	–
201	–	const std::string SSDAtomVisitor::toString() {
202	–	char   buffer[65535];
203	–	std::string result;
204	–
205	–	sprintf(buffer,
206	–	"------------------------------------------------------------------\n");
207	–	result += buffer;
208	–
209	–	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
210	–	result += buffer;
211	–
212	–	sprintf(buffer,
213	–	"Visitor Description: Convert SSD into 4 different atoms\n");
214	–	result += buffer;
215	–
216	–	sprintf(buffer,
217	–	"------------------------------------------------------------------\n");
218	–	result += buffer;
219	–
220	–	return result;
221	–	}
222	–
223	–	bool LinearAtomVisitor::isLinearAtom(const string& atomType){
224	–	vector<string>::iterator strIter;
225	–
226	–	for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
227	–	++strIter)
228	–	if(*strIter == atomType)
229	–	return true;
230	–
231	–	return false;
232	–	}
233	–
234	–	void LinearAtomVisitor::visit(DirectionalAtom* datom){
235	–
236	–	vector<AtomInfo*> atoms;
237	–
238	–	//we need to convert linear into 4 different atoms
239	–	double c1[3] = {0.0, 0.0, -1.8};
240	–	double c2[3] = {0.0, 0.0, -0.6};
241	–	double c3[3] = {0.0, 0.0,  0.6};
242	–	double c4[3] = {0.0, 0.0,  1.8};
243	–	double rotMatrix[3][3];
244	–	double rotTrans[3][3];
245	–	AtomInfo* atomInfo;
246	–	double pos[3];
247	–	double newVec[3];
248	–	double q[4];
249	–	AtomData* atomData;
250	–	GenericData* data;
251	–	bool haveAtomData;
252	–
253	–	//if atom is not SSD atom, just skip it
254	–	if(!isLinearAtom(datom->getType()))
255	–	return;
256	–
257	–	data = datom->getProperty("ATOMDATA");
258	–	if(data != NULL){
259	–
260	–	atomData = dynamic_cast<AtomData*>(data);
261	–	if(atomData == NULL){
262	–	cerr << "can not get Atom Data from " << datom->getType() << endl;
263	–	atomData = new AtomData;
264	–	haveAtomData = false;
265	–	}
266	–	else
267	–	haveAtomData = true;
74		}
269	–	else{
270	–	atomData = new AtomData;
271	–	haveAtomData = false;
272	–	}
273	–
274	–
275	–	datom->getPos(pos);
276	–	datom->getQ(q);
277	–	datom->getA(rotMatrix);
75
76	<	// We need A^T to convert from body-fixed to space-fixed:
77	<	transposeMat3(rotMatrix, rotTrans);
78	<
282	<	matVecMul3(rotTrans, c1, newVec);
283	<	atomInfo = new AtomInfo;
284	<	atomInfo->AtomType = "C";
285	<	atomInfo->pos[0] = pos[0] + newVec[0];
286	<	atomInfo->pos[1] = pos[1] + newVec[1];
287	<	atomInfo->pos[2] = pos[2] + newVec[2];
288	<	atomInfo->dipole[0] = 0.0;
289	<	atomInfo->dipole[1] = 0.0;
290	<	atomInfo->dipole[2] = 0.0;
291	<	atomData->addAtomInfo(atomInfo);
292	<
293	<	matVecMul3(rotTrans, c2, newVec);
294	<	atomInfo = new AtomInfo;
295	<	atomInfo->AtomType = "C";
296	<	atomInfo->pos[0] = pos[0] + newVec[0];
297	<	atomInfo->pos[1] = pos[1] + newVec[1];
298	<	atomInfo->pos[2] = pos[2] + newVec[2];
299	<	atomInfo->dipole[0] = 0.0;
300	<	atomInfo->dipole[1] = 0.0;
301	<	atomInfo->dipole[2] = 0.0;
302	<	atomData->addAtomInfo(atomInfo);
303	<
304	<	matVecMul3(rotTrans, c3, newVec);
305	<	atomInfo = new AtomInfo;
306	<	atomInfo->AtomType = "C";
307	<	atomInfo->pos[0] = pos[0] + newVec[0];
308	<	atomInfo->pos[1] = pos[1] + newVec[1];
309	<	atomInfo->pos[2] = pos[2] + newVec[2];
310	<	atomInfo->dipole[0] = 0.0;
311	<	atomInfo->dipole[1] = 0.0;
312	<	atomInfo->dipole[2] = 0.0;
313	<	atomData->addAtomInfo(atomInfo);
314	<
315	<	matVecMul3(rotTrans, c4, newVec);
316	<	atomInfo = new AtomInfo;
317	<	atomInfo->AtomType = "C";
318	<	atomInfo->pos[0] = pos[0] + newVec[0];
319	<	atomInfo->pos[1] = pos[1] + newVec[1];
320	<	atomInfo->pos[2] = pos[2] + newVec[2];
321	<	atomInfo->dipole[0] = 0.0;
322	<	atomInfo->dipole[1] = 0.0;
323	<	atomInfo->dipole[2] = 0.0;
324	<	atomData->addAtomInfo(atomInfo);
325	<
326	<	//add atom data into atom's property
327	<
328	<	if(!haveAtomData){
329	<	atomData->setID("ATOMDATA");
330	<	datom->addProperty(atomData);
331	<	}
332	<
333	<	setVisited(datom);
334	<
335	<	}
336	<
337	<	const string LinearAtomVisitor::toString(){
338	<	char buffer[65535];
339	<	string result;
340	<
341	<	sprintf(buffer ,"------------------------------------------------------------------\n");
342	<	result += buffer;
343	<
344	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
345	<	result += buffer;
346	<
347	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
348	<	result += buffer;
349	<
350	<	sprintf(buffer ,"------------------------------------------------------------------\n");
351	<	result += buffer;
352	<
353	<	return result;
354	<	}
355	<
356	<	//----------------------------------------------------------------------------//
357	<
358	<	void DefaultAtomVisitor::visit(Atom *atom) {
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		if (isVisited(atom))
88	<	return;
89	<
88	>	return;
89	>
90		atomInfo = new AtomInfo;
91	<
91	>
92		atomData = new AtomData;
93		atomData->setID("ATOMDATA");
94	<
94	>
95		pos = atom->getPos();
96	<	atomInfo->AtomType = atom->getType();
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->dipole[0] = 0.0;
103	<	atomInfo->dipole[1] = 0.0;
104	<	atomInfo->dipole[2] = 0.0;
105	<
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	<
115	>
116		atom->addProperty(atomData);
117	<
117	>
118		setVisited(atom);
119	<	}
120	<
121	<	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
119	>	}
120	>
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		if (isVisited(datom))
131	<	return;
132	<
131	>	return;
132	>
133		pos = datom->getPos();
134	<	u = datom->getElectroFrame().getColumn(3);
135	<
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	<	atomInfo->AtomType = datom->getType();
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->dipole[0] = u[0];
150	<	atomInfo->dipole[1] = u[1];
151	<	atomInfo->dipole[2] = u[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		atomData->addAtomInfo(atomInfo);
163
164		datom->addProperty(atomData);
165
166		setVisited(datom);
167	<	}
167	>	}
168
169	<	const std::string DefaultAtomVisitor::toString() {
169	>	const std::string DefaultAtomVisitor::toString() {
170		char   buffer[65535];
171		std::string result;
172
#	Line 435 | Line 186 | const std::string DefaultAtomVisitor::toString() {
186		result += buffer;
187
188		return result;
189	<	}
190	<	} //namespace oopse
189	>	}
190	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

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