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

Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 211 by chrisfen, Fri Nov 5 21:45:14 2004 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	+	*/
42	+
43		#include <cstring>
44		#include "visitors/AtomVisitor.hpp"
45		#include "primitives/DirectionalAtom.hpp"
4	–	#include "math/MatVec3.h"
46		#include "primitives/RigidBody.hpp"
47
48	<	namespace oopse {
48	>	namespace OpenMD {
49	>	void BaseAtomVisitor::visit(RigidBody *rb) {
50	>	//vector<Atom*> myAtoms;
51	>	//vector<Atom*>::iterator atomIter;
52
53	<	void BaseAtomVisitor::visit(RigidBody* rb){
10	<	//vector<Atom*> myAtoms;
11	<	//vector<Atom*>::iterator atomIter;
53	>	//myAtoms = rb->getAtoms();
54
55	<	//myAtoms = rb->getAtoms();
56	<
57	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
16	<	//  (*atomIter)->accept(this);
17	<	}
55	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56	>	//  (*atomIter)->accept(this);
57	>	}
58
59	<	void BaseAtomVisitor::setVisited(Atom* atom){
60	<	GenericData* data;
61	<	data = atom->getProperty("VISITED");
59	>	void BaseAtomVisitor::setVisited(Atom *atom) {
60	>	GenericData *data;
61	>	data = atom->getPropertyByName("VISITED");
62
63	<	//if visited property is not existed, add it as new property
64	<	if(data == NULL){
65	<	data = new GenericData();
66	<	data->setID("VISITED");
67	<	atom->addProperty(data);
63	>	//if visited property is not existed, add it as new property
64	>	if (data == NULL) {
65	>	data = new GenericData();
66	>	data->setID("VISITED");
67	>	atom->addProperty(data);
68	>	}
69		}
29	–	}
70
71	<	bool BaseAtomVisitor::isVisited(Atom* atom){
72	<	GenericData* data;
73	<	data = atom->getProperty("VISITED");
74	<	return data == NULL ?  false : true;
75	<	}
71	>	bool BaseAtomVisitor::isVisited(Atom *atom) {
72	>	GenericData *data;
73	>	data = atom->getPropertyByName("VISITED");
74	>	return data == NULL ? false : true;
75	>	}
76
77	<	bool SSDAtomVisitor::isSSDAtom(const string& atomType){
78	<	vector<string>::iterator strIter;
77	>	//------------------------------------------------------------------------//
78	>
79	>	void DefaultAtomVisitor::visit(Atom *atom) {
80	>	AtomData *atomData;
81	>	AtomInfo *atomInfo;
82	>	Vector3d  pos;
83	>	Vector3d  vel;
84	>	Vector3d  frc;
85	>	Vector3d  u;
86	>
87	>	if (isVisited(atom))
88	>	return;
89	>
90	>	atomInfo = new AtomInfo;
91	>
92	>	atomData = new AtomData;
93	>	atomData->setID("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	>	}
120
121	<	for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
122	<	if(*strIter == atomType)
123	<	return true;
124	<
125	<	return false;
126	<	}
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
129	<	void SSDAtomVisitor::visit(DirectionalAtom* datom){
129	>	if (isVisited(datom))
130	>	return;
131	>
132	>	pos = datom->getPos();
133	>	vel = datom->getVel();
134	>	frc = datom->getFrc();
135	>	if (datom->getAtomType()->isGayBerne()) {
136	>	u = datom->getA().transpose()*V3Z;
137	>	} else if (datom->getAtomType()->isMultipole()) {
138	>	u = datom->getElectroFrame().getColumn(2);
139	>	}
140	>	atomData = new AtomData;
141	>	atomData->setID("ATOMDATA");
142	>	atomInfo = new AtomInfo;
143
144	<	vector<AtomInfo*> atoms;
144	>	atomInfo->atomTypeName = datom->getType();
145	>	atomInfo->pos[0] = pos[0];
146	>	atomInfo->pos[1] = pos[1];
147	>	atomInfo->pos[2] = pos[2];
148	>	atomInfo->vel[0] = vel[0];
149	>	atomInfo->vel[1] = vel[1];
150	>	atomInfo->vel[2] = vel[2];
151	>	atomInfo->hasVelocity = true;
152	>	atomInfo->frc[0] = frc[0];
153	>	atomInfo->frc[1] = frc[1];
154	>	atomInfo->frc[2] = frc[2];
155	>	atomInfo->hasForce = true;
156	>	atomInfo->vec[0] = u[0];
157	>	atomInfo->vec[1] = u[1];
158	>	atomInfo->vec[2] = u[2];
159	>	atomInfo->hasVector = true;
160
161	<	//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;
161	>	atomData->addAtomInfo(atomInfo);
162
163	<	data = datom->getProperty("ATOMDATA");
73	<	if(data != NULL){
163	>	datom->addProperty(atomData);
164
165	<	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;
80	<	}
81	<	else
82	<	haveAtomData = true;
165	>	setVisited(datom);
166		}
84	–	else{
85	–	atomData = new AtomData;
86	–	haveAtomData = false;
87	–	}
88	–
89	–
90	–	datom->getPos(pos);
91	–	datom->getQ(q);
92	–	datom->getA(rotMatrix);
167
168	<	// We need A^T to convert from body-fixed to space-fixed:
169	<	transposeMat3(rotMatrix, rotTrans);
170	<
97	<	//center of mass of the water molecule
98	<	matVecMul3(rotTrans, u, newVec);
99	<	atomInfo = new AtomInfo;
100	<	atomInfo->AtomType = "X";
101	<	atomInfo->pos[0] = pos[0];
102	<	atomInfo->pos[1] = pos[1];
103	<	atomInfo->pos[2] = pos[2];
104	<	atomInfo->dipole[0] = newVec[0];
105	<	atomInfo->dipole[1] = newVec[1];
106	<	atomInfo->dipole[2] = newVec[2];
168	>	const std::string DefaultAtomVisitor::toString() {
169	>	char   buffer[65535];
170	>	std::string result;
171
172	<	atomData->addAtomInfo(atomInfo);
172	>	sprintf(buffer,
173	>	"------------------------------------------------------------------\n");
174	>	result += buffer;
175
176	<	//oxygen
177	<	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);
176	>	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
177	>	result += buffer;
178
179	+	sprintf(buffer,
180	+	"Visitor Description: copy atom infomation into atom data\n");
181	+	result += buffer;
182
183	<	//hydrogen1
184	<	matVecMul3(rotTrans, h1, newVec);
185	<	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);
183	>	sprintf(buffer,
184	>	"------------------------------------------------------------------\n");
185	>	result += buffer;
186
187	<	//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){
150	<	atomData->setID("ATOMDATA");
151	<	datom->addProperty(atomData);
187	>	return result;
188		}
189	<
154	<	setVisited(datom);
155	<
156	<	}
157	<
158	<	const string SSDAtomVisitor::toString(){
159	<	char buffer[65535];
160	<	string result;
161	<
162	<	sprintf(buffer ,"------------------------------------------------------------------\n");
163	<	result += buffer;
164	<
165	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
166	<	result += buffer;
167	<
168	<	sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
169	<	result += buffer;
170	<
171	<	sprintf(buffer ,"------------------------------------------------------------------\n");
172	<	result += buffer;
173	<
174	<	return result;
175	<	}
176	<
177	<	bool LinearAtomVisitor::isLinearAtom(const string& atomType){
178	<	vector<string>::iterator strIter;
179	<
180	<	for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
181	<	++strIter)
182	<	if(*strIter == atomType)
183	<	return true;
184	<
185	<	return false;
186	<	}
187	<
188	<	void LinearAtomVisitor::visit(DirectionalAtom* datom){
189	<
190	<	vector<AtomInfo*> atoms;
191	<
192	<	//we need to convert linear into 4 different atoms
193	<	double c1[3] = {0.0, 0.0, -1.8};
194	<	double c2[3] = {0.0, 0.0, -0.6};
195	<	double c3[3] = {0.0, 0.0,  0.6};
196	<	double c4[3] = {0.0, 0.0,  1.8};
197	<	double rotMatrix[3][3];
198	<	double rotTrans[3][3];
199	<	AtomInfo* atomInfo;
200	<	double pos[3];
201	<	double newVec[3];
202	<	double q[4];
203	<	AtomData* atomData;
204	<	GenericData* data;
205	<	bool haveAtomData;
206	<
207	<	//if atom is not SSD atom, just skip it
208	<	if(!isLinearAtom(datom->getType()))
209	<	return;
210	<
211	<	data = datom->getProperty("ATOMDATA");
212	<	if(data != NULL){
213	<
214	<	atomData = dynamic_cast<AtomData*>(data);
215	<	if(atomData == NULL){
216	<	cerr << "can not get Atom Data from " << datom->getType() << endl;
217	<	atomData = new AtomData;
218	<	haveAtomData = false;
219	<	}
220	<	else
221	<	haveAtomData = true;
222	<	}
223	<	else{
224	<	atomData = new AtomData;
225	<	haveAtomData = false;
226	<	}
227	<
228	<
229	<	datom->getPos(pos);
230	<	datom->getQ(q);
231	<	datom->getA(rotMatrix);
232	<
233	<	// We need A^T to convert from body-fixed to space-fixed:
234	<	transposeMat3(rotMatrix, rotTrans);
235	<
236	<	matVecMul3(rotTrans, c1, newVec);
237	<	atomInfo = new AtomInfo;
238	<	atomInfo->AtomType = "C";
239	<	atomInfo->pos[0] = pos[0] + newVec[0];
240	<	atomInfo->pos[1] = pos[1] + newVec[1];
241	<	atomInfo->pos[2] = pos[2] + newVec[2];
242	<	atomInfo->dipole[0] = 0.0;
243	<	atomInfo->dipole[1] = 0.0;
244	<	atomInfo->dipole[2] = 0.0;
245	<	atomData->addAtomInfo(atomInfo);
246	<
247	<	matVecMul3(rotTrans, c2, newVec);
248	<	atomInfo = new AtomInfo;
249	<	atomInfo->AtomType = "C";
250	<	atomInfo->pos[0] = pos[0] + newVec[0];
251	<	atomInfo->pos[1] = pos[1] + newVec[1];
252	<	atomInfo->pos[2] = pos[2] + newVec[2];
253	<	atomInfo->dipole[0] = 0.0;
254	<	atomInfo->dipole[1] = 0.0;
255	<	atomInfo->dipole[2] = 0.0;
256	<	atomData->addAtomInfo(atomInfo);
257	<
258	<	matVecMul3(rotTrans, c3, newVec);
259	<	atomInfo = new AtomInfo;
260	<	atomInfo->AtomType = "C";
261	<	atomInfo->pos[0] = pos[0] + newVec[0];
262	<	atomInfo->pos[1] = pos[1] + newVec[1];
263	<	atomInfo->pos[2] = pos[2] + newVec[2];
264	<	atomInfo->dipole[0] = 0.0;
265	<	atomInfo->dipole[1] = 0.0;
266	<	atomInfo->dipole[2] = 0.0;
267	<	atomData->addAtomInfo(atomInfo);
268	<
269	<	matVecMul3(rotTrans, c4, newVec);
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	<	//add atom data into atom's property
281	<
282	<	if(!haveAtomData){
283	<	atomData->setID("ATOMDATA");
284	<	datom->addProperty(atomData);
285	<	}
286	<
287	<	setVisited(datom);
288	<
289	<	}
290	<
291	<	const string LinearAtomVisitor::toString(){
292	<	char buffer[65535];
293	<	string result;
294	<
295	<	sprintf(buffer ,"------------------------------------------------------------------\n");
296	<	result += buffer;
297	<
298	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
299	<	result += buffer;
300	<
301	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
302	<	result += buffer;
303	<
304	<	sprintf(buffer ,"------------------------------------------------------------------\n");
305	<	result += buffer;
306	<
307	<	return result;
308	<	}
309	<
310	<	//----------------------------------------------------------------------------//
311	<
312	<	void DefaultAtomVisitor::visit(Atom* atom){
313	<	AtomData* atomData;
314	<	AtomInfo* atomInfo;
315	<	double pos[3];
316	<
317	<	if(isVisited(atom))
318	<	return;
319	<
320	<	atomInfo =new AtomInfo;
321	<
322	<	atomData = new AtomData;
323	<	atomData->setID("ATOMDATA");
324	<
325	<	atom->getPos(pos);
326	<	atomInfo->AtomType = atom->getType();
327	<	atomInfo->pos[0] = pos[0];
328	<	atomInfo->pos[1] = pos[1];
329	<	atomInfo->pos[2] = pos[2];
330	<	atomInfo->dipole[0] = 0.0;
331	<	atomInfo->dipole[1] = 0.0;
332	<	atomInfo->dipole[2] = 0.0;
333	<
334	<
335	<	atomData->addAtomInfo(atomInfo);
336	<
337	<	atom->addProperty(atomData);
338	<
339	<	setVisited(atom);
340	<	}
341	<	void DefaultAtomVisitor::visit(DirectionalAtom* datom){
342	<	AtomData* atomData;
343	<	AtomInfo* atomInfo;
344	<	double pos[3];
345	<	double u[3];
346	<
347	<	if(isVisited(datom))
348	<	return;
349	<
350	<	datom->getPos(pos);
351	<	datom->getU(u);
352	<
353	<	atomData = new AtomData;
354	<	atomData->setID("ATOMDATA");
355	<	atomInfo =new AtomInfo;
356	<
357	<	atomInfo->AtomType = datom->getType();
358	<	atomInfo->pos[0] = pos[0];
359	<	atomInfo->pos[1] = pos[1];
360	<	atomInfo->pos[2] = pos[2];
361	<	atomInfo->dipole[0] = u[0];
362	<	atomInfo->dipole[1] = u[1];
363	<	atomInfo->dipole[2] = u[2];
364	<
365	<	atomData->addAtomInfo(atomInfo);
366	<
367	<	datom->addProperty(atomData);
368	<
369	<	setVisited(datom);
370	<	}
371	<
372	<
373	<	const string DefaultAtomVisitor::toString(){
374	<	char buffer[65535];
375	<	string result;
376	<
377	<	sprintf(buffer ,"------------------------------------------------------------------\n");
378	<	result += buffer;
379	<
380	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
381	<	result += buffer;
382	<
383	<	sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
384	<	result += buffer;
385	<
386	<	sprintf(buffer ,"------------------------------------------------------------------\n");
387	<	result += buffer;
388	<
389	<	return result;
390	<	}
391	<
392	<	}//namespace oopse
189	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 211 by chrisfen, Fri Nov 5 21:45:14 2004 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1767 by gezelter, Fri Jul 6 22:01:58 2012 UTC

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