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

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trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 954 by tim, Wed May 10 01:44:48 2006 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1821 by gezelter, Mon Jan 7 20:05:43 2013 UTC

#	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]  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"
46		#include "primitives/RigidBody.hpp"
47	+	#include "types/MultipoleAdapter.hpp"
48	+	#include "types/GayBerneAdapter.hpp"
49
50	<	namespace oopse {
50	>	namespace OpenMD {
51		void BaseAtomVisitor::visit(RigidBody *rb) {
52		//vector<Atom*> myAtoms;
53		//vector<Atom*>::iterator atomIter;
#	Line 71 | Line 74 | namespace oopse {
74		GenericData *data;
75		data = atom->getPropertyByName("VISITED");
76		return data == NULL ? false : true;
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::addGayBerneAtomType(const std::string& atomType){
225	–	linearAtomType.insert(atomType);
226	–	}
227	–
228	–	void LinearAtomVisitor::visit(DirectionalAtom* datom){
229	–	std::vector<AtomInfo*> atoms;
230	–	//we need to convert linear into 4 different atoms
231	–	Vector3d c1(0.0, 0.0, -1.8);
232	–	Vector3d c2(0.0, 0.0, -0.6);
233	–	Vector3d c3(0.0, 0.0,  0.6);
234	–	Vector3d c4(0.0, 0.0,  1.8);
235	–	RotMat3x3d rotMatrix;
236	–	RotMat3x3d rotTrans;
237	–	AtomInfo* atomInfo;
238	–	Vector3d pos;
239	–	Vector3d newVec;
240	–	Quat4d q;
241	–	AtomData* atomData;
242	–	GenericData* data;
243	–	bool haveAtomData;
244	–
245	–	//if atom is not SSD atom, just skip it
246	–	if(!isLinearAtom(datom->getType()))
247	–	return;
248	–
249	–	data = datom->getPropertyByName("ATOMDATA");
250	–	if(data != NULL){
251	–	atomData = dynamic_cast<AtomData*>(data);
252	–	if(atomData == NULL){
253	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
254	–	atomData = new AtomData;
255	–	haveAtomData = false;
256	–	} else {
257	–	haveAtomData = true;
258	–	}
259	–	} else {
260	–	atomData = new AtomData;
261	–	haveAtomData = false;
262	–	}
263	–
264	–
265	–	pos = datom->getPos();
266	–	q = datom->getQ();
267	–	rotMatrix = datom->getA();
268	–
269	–	// We need A^T to convert from body-fixed to space-fixed:
270	–	rotTrans = rotMatrix.transpose();
271	–
272	–	newVec = rotTrans * c1;
273	–	atomInfo = new AtomInfo;
274	–	atomInfo->atomTypeName = "C";
275	–	atomInfo->pos[0] = pos[0] + newVec[0];
276	–	atomInfo->pos[1] = pos[1] + newVec[1];
277	–	atomInfo->pos[2] = pos[2] + newVec[2];
278	–	atomInfo->dipole[0] = 0.0;
279	–	atomInfo->dipole[1] = 0.0;
280	–	atomInfo->dipole[2] = 0.0;
281	–	atomData->addAtomInfo(atomInfo);
282	–
283	–	newVec = rotTrans * c2;
284	–	atomInfo = new AtomInfo;
285	–	atomInfo->atomTypeName = "C";
286	–	atomInfo->pos[0] = pos[0] + newVec[0];
287	–	atomInfo->pos[1] = pos[1] + newVec[1];
288	–	atomInfo->pos[2] = pos[2] + newVec[2];
289	–	atomInfo->dipole[0] = 0.0;
290	–	atomInfo->dipole[1] = 0.0;
291	–	atomInfo->dipole[2] = 0.0;
292	–	atomData->addAtomInfo(atomInfo);
293	–
294	–	newVec = rotTrans * c3;
295	–	atomInfo = new AtomInfo;
296	–	atomInfo->atomTypeName = "C";
297	–	atomInfo->pos[0] = pos[0] + newVec[0];
298	–	atomInfo->pos[1] = pos[1] + newVec[1];
299	–	atomInfo->pos[2] = pos[2] + newVec[2];
300	–	atomInfo->dipole[0] = 0.0;
301	–	atomInfo->dipole[1] = 0.0;
302	–	atomInfo->dipole[2] = 0.0;
303	–	atomData->addAtomInfo(atomInfo);
304	–
305	–	newVec = rotTrans * c4;
306	–	atomInfo = new AtomInfo;
307	–	atomInfo->atomTypeName = "C";
308	–	atomInfo->pos[0] = pos[0] + newVec[0];
309	–	atomInfo->pos[1] = pos[1] + newVec[1];
310	–	atomInfo->pos[2] = pos[2] + newVec[2];
311	–	atomInfo->dipole[0] = 0.0;
312	–	atomInfo->dipole[1] = 0.0;
313	–	atomInfo->dipole[2] = 0.0;
314	–	atomData->addAtomInfo(atomInfo);
315	–
316	–	//add atom data into atom's property
317	–
318	–	if(!haveAtomData){
319	–	atomData->setID("ATOMDATA");
320	–	datom->addProperty(atomData);
321	–	}
322	–
323	–	setVisited(datom);
324	–
77		}
78
79	<	const std::string LinearAtomVisitor::toString(){
80	<	char buffer[65535];
329	<	std::string result;
330	<
331	<	sprintf(buffer ,"------------------------------------------------------------------\n");
332	<	result += buffer;
333	<
334	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
335	<	result += buffer;
336	<
337	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
338	<	result += buffer;
339	<
340	<	sprintf(buffer ,"------------------------------------------------------------------\n");
341	<	result += buffer;
342	<
343	<	return result;
344	<	}
345	<
346	<	bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
347	<	std::set<std::string>::iterator strIter;
348	<	strIter = GBLipidAtomType.find(atomType);
349	<
350	<	return strIter != GBLipidAtomType.end() ? true : false;
351	<	}
352	<
353	<	void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
354	<	std::vector<AtomInfo*> atoms;
355	<	//we need to convert linear into 4 different atoms
356	<	Vector3d c1(0.0, 0.0, -6.25);
357	<	Vector3d c2(0.0, 0.0, -2.1);
358	<	Vector3d c3(0.0, 0.0,  2.1);
359	<	Vector3d c4(0.0, 0.0,  6.25);
360	<	RotMat3x3d rotMatrix;
361	<	RotMat3x3d rotTrans;
362	<	AtomInfo* atomInfo;
363	<	Vector3d pos;
364	<	Vector3d newVec;
365	<	Quat4d q;
366	<	AtomData* atomData;
367	<	GenericData* data;
368	<	bool haveAtomData;
369	<
370	<	//if atom is not GBlipid atom, just skip it
371	<	if(!isGBLipidAtom(datom->getType()))
372	<	return;
373	<
374	<	data = datom->getPropertyByName("ATOMDATA");
375	<	if(data != NULL){
376	<	atomData = dynamic_cast<AtomData*>(data);
377	<	if(atomData == NULL){
378	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
379	<	atomData = new AtomData;
380	<	haveAtomData = false;
381	<	} else {
382	<	haveAtomData = true;
383	<	}
384	<	} else {
385	<	atomData = new AtomData;
386	<	haveAtomData = false;
387	<	}
388	<
389	<
390	<	pos = datom->getPos();
391	<	q = datom->getQ();
392	<	rotMatrix = datom->getA();
393	<
394	<	// We need A^T to convert from body-fixed to space-fixed:
395	<	rotTrans = rotMatrix.transpose();
396	<
397	<	newVec = rotTrans * c1;
398	<	atomInfo = new AtomInfo;
399	<	atomInfo->atomTypeName = "K";
400	<	atomInfo->pos[0] = pos[0] + newVec[0];
401	<	atomInfo->pos[1] = pos[1] + newVec[1];
402	<	atomInfo->pos[2] = pos[2] + newVec[2];
403	<	atomInfo->dipole[0] = 0.0;
404	<	atomInfo->dipole[1] = 0.0;
405	<	atomInfo->dipole[2] = 0.0;
406	<	atomData->addAtomInfo(atomInfo);
407	<
408	<	newVec = rotTrans * c2;
409	<	atomInfo = new AtomInfo;
410	<	atomInfo->atomTypeName = "K";
411	<	atomInfo->pos[0] = pos[0] + newVec[0];
412	<	atomInfo->pos[1] = pos[1] + newVec[1];
413	<	atomInfo->pos[2] = pos[2] + newVec[2];
414	<	atomInfo->dipole[0] = 0.0;
415	<	atomInfo->dipole[1] = 0.0;
416	<	atomInfo->dipole[2] = 0.0;
417	<	atomData->addAtomInfo(atomInfo);
418	<
419	<	newVec = rotTrans * c3;
420	<	atomInfo = new AtomInfo;
421	<	atomInfo->atomTypeName = "K";
422	<	atomInfo->pos[0] = pos[0] + newVec[0];
423	<	atomInfo->pos[1] = pos[1] + newVec[1];
424	<	atomInfo->pos[2] = pos[2] + newVec[2];
425	<	atomInfo->dipole[0] = 0.0;
426	<	atomInfo->dipole[1] = 0.0;
427	<	atomInfo->dipole[2] = 0.0;
428	<	atomData->addAtomInfo(atomInfo);
429	<
430	<	newVec = rotTrans * c4;
431	<	atomInfo = new AtomInfo;
432	<	atomInfo->atomTypeName = "K";
433	<	atomInfo->pos[0] = pos[0] + newVec[0];
434	<	atomInfo->pos[1] = pos[1] + newVec[1];
435	<	atomInfo->pos[2] = pos[2] + newVec[2];
436	<	atomInfo->dipole[0] = 0.0;
437	<	atomInfo->dipole[1] = 0.0;
438	<	atomInfo->dipole[2] = 0.0;
439	<	atomData->addAtomInfo(atomInfo);
440	<
441	<	//add atom data into atom's property
442	<
443	<	if(!haveAtomData){
444	<	atomData->setID("ATOMDATA");
445	<	datom->addProperty(atomData);
446	<	}
447	<
448	<	setVisited(datom);
449	<
450	<	}
451	<
452	<	const std::string GBLipidAtomVisitor::toString(){
453	<	char buffer[65535];
454	<	std::string result;
455	<
456	<	sprintf(buffer ,"------------------------------------------------------------------\n");
457	<	result += buffer;
458	<
459	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
460	<	result += buffer;
461	<
462	<	sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
463	<	result += buffer;
464	<
465	<	sprintf(buffer ,"------------------------------------------------------------------\n");
466	<	result += buffer;
467	<
468	<	return result;
469	<	}
470	<
471	<	//----------------------------------------------------------------------------//
472	<
79	>	//------------------------------------------------------------------------//
80	>
81		void DefaultAtomVisitor::visit(Atom *atom) {
82		AtomData *atomData;
83		AtomInfo *atomInfo;
84		Vector3d  pos;
85	+	Vector3d  vel;
86	+	Vector3d  frc;
87	+	Vector3d  u;
88
89		if (isVisited(atom))
90		return;
91	<
91	>
92		atomInfo = new AtomInfo;
93	<
93	>
94		atomData = new AtomData;
95		atomData->setID("ATOMDATA");
96	<
96	>
97		pos = atom->getPos();
98	+	vel = atom->getVel();
99	+	frc = atom->getFrc();
100		atomInfo->atomTypeName = atom->getType();
101		atomInfo->pos[0] = pos[0];
102		atomInfo->pos[1] = pos[1];
103		atomInfo->pos[2] = pos[2];
104	<	atomInfo->dipole[0] = 0.0;
105	<	atomInfo->dipole[1] = 0.0;
106	<	atomInfo->dipole[2] = 0.0;
107	<
104	>	atomInfo->vel[0] = vel[0];
105	>	atomInfo->vel[1] = vel[1];
106	>	atomInfo->vel[2] = vel[2];
107	>	atomInfo->hasVelocity = true;
108	>	atomInfo->frc[0] = frc[0];
109	>	atomInfo->frc[1] = frc[1];
110	>	atomInfo->frc[2] = frc[2];
111	>	atomInfo->hasForce = true;
112	>	atomInfo->vec[0] = 0.0;
113	>	atomInfo->vec[1] = 0.0;
114	>	atomInfo->vec[2] = 0.0;
115	>
116		atomData->addAtomInfo(atomInfo);
117	<
117	>
118		atom->addProperty(atomData);
119	<
119	>
120		setVisited(atom);
121		}
122	<
122	>
123		void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
124		AtomData *atomData;
125		AtomInfo *atomInfo;
126		Vector3d  pos;
127	+	Vector3d  vel;
128	+	Vector3d  frc;
129		Vector3d  u;
130
131		if (isVisited(datom))
132		return;
133	<
133	>
134		pos = datom->getPos();
135	<	u = datom->getElectroFrame().getColumn(2);
135	>	vel = datom->getVel();
136	>	frc = datom->getFrc();
137
138	+	GayBerneAdapter gba = GayBerneAdapter(datom->getAtomType());
139	+	MultipoleAdapter ma = MultipoleAdapter(datom->getAtomType());
140	+
141	+	if (gba.isGayBerne()) {
142	+	u = datom->getA().transpose()*V3Z;
143	+	} else if (ma.isDipole()) {
144	+	u = datom->getDipole();
145	+	} else if (ma.isQuadrupole()) {
146	+	//u = datom->getQuadrupole().getColumn(2);
147	+	u = datom->getA().transpose()*V3Z;
148	+	}
149		atomData = new AtomData;
150		atomData->setID("ATOMDATA");
151		atomInfo = new AtomInfo;
#	Line 519 | Line 154 | namespace oopse {
154		atomInfo->pos[0] = pos[0];
155		atomInfo->pos[1] = pos[1];
156		atomInfo->pos[2] = pos[2];
157	<	atomInfo->dipole[0] = u[0];
158	<	atomInfo->dipole[1] = u[1];
159	<	atomInfo->dipole[2] = u[2];
157	>	atomInfo->vel[0] = vel[0];
158	>	atomInfo->vel[1] = vel[1];
159	>	atomInfo->vel[2] = vel[2];
160	>	atomInfo->hasVelocity = true;
161	>	atomInfo->frc[0] = frc[0];
162	>	atomInfo->frc[1] = frc[1];
163	>	atomInfo->frc[2] = frc[2];
164	>	atomInfo->hasForce = true;
165	>	atomInfo->vec[0] = u[0];
166	>	atomInfo->vec[1] = u[1];
167	>	atomInfo->vec[2] = u[2];
168	>	atomInfo->hasVector = true;
169
170		atomData->addAtomInfo(atomInfo);
171
#	Line 551 | Line 195 | namespace oopse {
195
196		return result;
197		}
198	<	} //namespace oopse
198	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 954 by tim, Wed May 10 01:44:48 2006 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1821 by gezelter, Mon Jan 7 20:05:43 2013 UTC

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