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

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trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 1291 by gezelter, Thu Sep 11 19:40:59 2008 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 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]  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 {
47	>	namespace OpenMD {
48		void BaseAtomVisitor::visit(RigidBody *rb) {
49		//vector<Atom*> myAtoms;
50		//vector<Atom*>::iterator atomIter;
#	Line 71 | Line 71 | namespace oopse {
71		GenericData *data;
72		data = atom->getPropertyByName("VISITED");
73		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 different atoms
86	–	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of
87	–	//the mass 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	–
218	–	bool TREDAtomVisitor::isTREDAtom(const std::string&atomType) {
219	–	std::set<std::string>::iterator strIter;
220	–	strIter = tredAtomType.find(atomType);
221	–	return strIter != tredAtomType.end() ? true : false;
222	–	}
223	–
224	–	void TREDAtomVisitor::visit(DirectionalAtom *datom) {
225	–	std::vector<AtomInfo*>atoms;
226	–
227	–	// we need to convert a TRED into 4 different atoms:
228	–	// one oxygen atom, two hydrogen atoms, and one atom which is the center of
229	–	// the mass of the water with a dipole moment
230	–	Vector3d h1(0.0, -0.75695, 0.5206);
231	–	Vector3d h2(0.0, 0.75695, 0.5206);
232	–	Vector3d ox(0.0, 0.0, -0.0654);
233	–	Vector3d u(0, 0, 1);
234	–	RotMat3x3d   rotMatrix;
235	–	RotMat3x3d   rotTrans;
236	–	AtomInfo *   atomInfo;
237	–	Vector3d     pos;
238	–	Vector3d     newVec;
239	–	Quat4d       q;
240	–	AtomData *   atomData;
241	–	GenericData *data;
242	–	bool         haveAtomData;
243	–
244	–	// if the atom is not a TRED atom, skip it
245	–	if (!isTREDAtom(datom->getType()))
246	–	return;
247	–
248	–	data = datom->getPropertyByName("ATOMDATA");
249	–
250	–	if (data != NULL) {
251	–	atomData = dynamic_cast<AtomData *>(data);
252	–
253	–	if (atomData == NULL) {
254	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
255	–	atomData = new AtomData;
256	–	haveAtomData = false;
257	–	} else
258	–	haveAtomData = true;
259	–	} else {
260	–	atomData = new AtomData;
261	–	haveAtomData = false;
262	–	}
263	–
264	–	pos = datom->getPos();
265	–	q = datom->getQ();
266	–	rotMatrix = datom->getA();
267	–
268	–	// We need A^T to convert from body-fixed to space-fixed:
269	–	// transposeMat3(rotMatrix, rotTrans);
270	–	rotTrans = rotMatrix.transpose();
271	–
272	–	// center of mass of the water molecule
273	–	// matVecMul3(rotTrans, u, newVec);
274	–	newVec = rotTrans * u;
275	–
276	–	atomInfo = new AtomInfo;
277	–	atomInfo->atomTypeName = "TRED";
278	–	atomInfo->pos[0] = pos[0];
279	–	atomInfo->pos[1] = pos[1];
280	–	atomInfo->pos[2] = pos[2];
281	–	atomInfo->dipole[0] = newVec[0];
282	–	atomInfo->dipole[1] = newVec[1];
283	–	atomInfo->dipole[2] = newVec[2];
284	–
285	–	atomData->addAtomInfo(atomInfo);
286	–
287	–	// oxygen
288	–	// matVecMul3(rotTrans, ox, newVec);
289	–	newVec = rotTrans * ox;
290	–
291	–	atomInfo = new AtomInfo;
292	–	atomInfo->atomTypeName = "O";
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	–	// hydrogen1
302	–	// matVecMul3(rotTrans, h1, newVec);
303	–	newVec = rotTrans * h1;
304	–	atomInfo = new AtomInfo;
305	–	atomInfo->atomTypeName = "H";
306	–	atomInfo->pos[0] = pos[0] + newVec[0];
307	–	atomInfo->pos[1] = pos[1] + newVec[1];
308	–	atomInfo->pos[2] = pos[2] + newVec[2];
309	–	atomInfo->dipole[0] = 0.0;
310	–	atomInfo->dipole[1] = 0.0;
311	–	atomInfo->dipole[2] = 0.0;
312	–	atomData->addAtomInfo(atomInfo);
313	–
314	–	// hydrogen2
315	–	// matVecMul3(rotTrans, h2, newVec);
316	–	newVec = rotTrans * h2;
317	–	atomInfo = new AtomInfo;
318	–	atomInfo->atomTypeName = "H";
319	–	atomInfo->pos[0] = pos[0] + newVec[0];
320	–	atomInfo->pos[1] = pos[1] + newVec[1];
321	–	atomInfo->pos[2] = pos[2] + newVec[2];
322	–	atomInfo->dipole[0] = 0.0;
323	–	atomInfo->dipole[1] = 0.0;
324	–	atomInfo->dipole[2] = 0.0;
325	–	atomData->addAtomInfo(atomInfo);
326	–
327	–	// add atom data into atom's property
328	–
329	–	if (!haveAtomData) {
330	–	atomData->setID("ATOMDATA");
331	–	datom->addProperty(atomData);
332	–	}
333	–
334	–	setVisited(datom);
335	–	}
336	–
337	–	const std::string TREDAtomVisitor::toString() {
338	–	char   buffer[65535];
339	–	std::string result;
340	–
341	–	sprintf(buffer,
342	–	"------------------------------------------------------------------\n");
343	–	result += buffer;
344	–
345	–	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
346	–	result += buffer;
347	–
348	–	sprintf(buffer,
349	–	"Visitor Description: Convert the TRED atom into 4 different atoms\n");
350	–	result += buffer;
351	–
352	–	sprintf(buffer,
353	–	"------------------------------------------------------------------\n");
354	–	result += buffer;
355	–
356	–	return result;
357	–	}
358	–
359	–
360	–	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
361	–	std::set<std::string>::iterator strIter;
362	–	strIter = linearAtomType.find(atomType);
363	–
364	–	return strIter != linearAtomType.end() ? true : false;
365	–	}
366	–
367	–	void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
368	–	linearAtomType.insert(atomType);
369	–	}
370	–
371	–	void LinearAtomVisitor::visit(DirectionalAtom* datom){
372	–	std::vector<AtomInfo*> atoms;
373	–	//we need to convert linear into 4 different atoms
374	–	Vector3d c1(0.0, 0.0, -1.8);
375	–	Vector3d c2(0.0, 0.0, -0.6);
376	–	Vector3d c3(0.0, 0.0,  0.6);
377	–	Vector3d c4(0.0, 0.0,  1.8);
378	–	RotMat3x3d rotMatrix;
379	–	RotMat3x3d rotTrans;
380	–	AtomInfo* atomInfo;
381	–	Vector3d pos;
382	–	Vector3d newVec;
383	–	Quat4d q;
384	–	AtomData* atomData;
385	–	GenericData* data;
386	–	bool haveAtomData;
387	–	//if atom is not linear atom, just skip it
388	–	if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
389	–	return;
390	–
391	–	//setup GayBerne type in fortran side
392	–	data = datom->getAtomType()->getPropertyByName("GayBerne");
393	–	if (data != NULL) {
394	–	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
395	–
396	–	if (gayBerneData != NULL) {
397	–	GayBerneParam gayBerneParam = gayBerneData->getData();
398	–
399	–	// double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
400	–	double halfLen = gayBerneParam.GB_l/2.0;
401	–	c1[2] = -halfLen;
402	–	c2[2] = -halfLen /2;
403	–	c3[2] = halfLen/2;
404	–	c4[2] = halfLen;
405	–
406	–	}
407	–
408	–	else {
409	–	sprintf( painCave.errMsg,
410	–	"Can not cast GenericData to GayBerneParam\n");
411	–	painCave.severity = OOPSE_ERROR;
412	–	painCave.isFatal = 1;
413	–	simError();
414	–	}
415	–	}
416	–
417	–
418	–	data = datom->getPropertyByName("ATOMDATA");
419	–	if(data != NULL){
420	–	atomData = dynamic_cast<AtomData*>(data);
421	–	if(atomData == NULL){
422	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
423	–	atomData = new AtomData;
424	–	haveAtomData = false;
425	–	} else {
426	–	haveAtomData = true;
427	–	}
428	–	} else {
429	–	atomData = new AtomData;
430	–	haveAtomData = false;
431	–	}
432	–
433	–
434	–	pos = datom->getPos();
435	–	q = datom->getQ();
436	–	rotMatrix = datom->getA();
437	–
438	–	// We need A^T to convert from body-fixed to space-fixed:
439	–	rotTrans = rotMatrix.transpose();
440	–
441	–	newVec = rotTrans * c1;
442	–	atomInfo = new AtomInfo;
443	–	atomInfo->atomTypeName = "C";
444	–	atomInfo->pos[0] = pos[0] + newVec[0];
445	–	atomInfo->pos[1] = pos[1] + newVec[1];
446	–	atomInfo->pos[2] = pos[2] + newVec[2];
447	–	atomInfo->dipole[0] = 0.0;
448	–	atomInfo->dipole[1] = 0.0;
449	–	atomInfo->dipole[2] = 0.0;
450	–	atomData->addAtomInfo(atomInfo);
451	–
452	–	newVec = rotTrans * c2;
453	–	atomInfo = new AtomInfo;
454	–	atomInfo->atomTypeName = "C";
455	–	atomInfo->pos[0] = pos[0] + newVec[0];
456	–	atomInfo->pos[1] = pos[1] + newVec[1];
457	–	atomInfo->pos[2] = pos[2] + newVec[2];
458	–	atomInfo->dipole[0] = 0.0;
459	–	atomInfo->dipole[1] = 0.0;
460	–	atomInfo->dipole[2] = 0.0;
461	–	atomData->addAtomInfo(atomInfo);
462	–
463	–	newVec = rotTrans * c3;
464	–	atomInfo = new AtomInfo;
465	–	atomInfo->atomTypeName = "C";
466	–	atomInfo->pos[0] = pos[0] + newVec[0];
467	–	atomInfo->pos[1] = pos[1] + newVec[1];
468	–	atomInfo->pos[2] = pos[2] + newVec[2];
469	–	atomInfo->dipole[0] = 0.0;
470	–	atomInfo->dipole[1] = 0.0;
471	–	atomInfo->dipole[2] = 0.0;
472	–	atomData->addAtomInfo(atomInfo);
473	–
474	–	newVec = rotTrans * c4;
475	–	atomInfo = new AtomInfo;
476	–	atomInfo->atomTypeName = "C";
477	–	atomInfo->pos[0] = pos[0] + newVec[0];
478	–	atomInfo->pos[1] = pos[1] + newVec[1];
479	–	atomInfo->pos[2] = pos[2] + newVec[2];
480	–	atomInfo->dipole[0] = 0.0;
481	–	atomInfo->dipole[1] = 0.0;
482	–	atomInfo->dipole[2] = 0.0;
483	–	atomData->addAtomInfo(atomInfo);
484	–
485	–	//add atom data into atom's property
486	–
487	–	if(!haveAtomData){
488	–	atomData->setID("ATOMDATA");
489	–	datom->addProperty(atomData);
490	–	}
491	–
492	–	setVisited(datom);
493	–
494	–	}
495	–
496	–	const std::string LinearAtomVisitor::toString(){
497	–	char buffer[65535];
498	–	std::string result;
499	–
500	–	sprintf(buffer ,"------------------------------------------------------------------\n");
501	–	result += buffer;
502	–
503	–	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
504	–	result += buffer;
505	–
506	–	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
507	–	result += buffer;
508	–
509	–	sprintf(buffer ,"------------------------------------------------------------------\n");
510	–	result += buffer;
511	–
512	–	return result;
513	–	}
514	–
515	–	bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
516	–	std::set<std::string>::iterator strIter;
517	–	strIter = GBLipidAtomType.find(atomType);
518	–
519	–	return strIter != GBLipidAtomType.end() ? true : false;
520	–	}
521	–
522	–	void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
523	–	std::vector<AtomInfo*> atoms;
524	–	Vector3d c1(0.0, 0.0, 0.0);
525	–	Vector3d c2(0.0, 0.0, 1.0);
526	–	RotMat3x3d rotMatrix;
527	–	RotMat3x3d rotTrans;
528	–	AtomInfo* atomInfo;
529	–	Vector3d pos;
530	–	Vector3d newVec;
531	–	Vector3d dVec;
532	–	Quat4d q;
533	–	AtomData* atomData;
534	–	GenericData* data;
535	–	bool haveAtomData;
536	–
537	–	//if atom is not GBlipid atom, just skip it
538	–	if(!isGBLipidAtom(datom->getType()))
539	–	return;
540	–
541	–	data = datom->getPropertyByName("ATOMDATA");
542	–	if(data != NULL){
543	–	atomData = dynamic_cast<AtomData*>(data);
544	–	if(atomData == NULL){
545	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
546	–	atomData = new AtomData;
547	–	haveAtomData = false;
548	–	} else {
549	–	haveAtomData = true;
550	–	}
551	–	} else {
552	–	atomData = new AtomData;
553	–	haveAtomData = false;
554	–	}
555	–
556	–
557	–	pos = datom->getPos();
558	–	q = datom->getQ();
559	–	rotMatrix = datom->getA();
560	–
561	–	// We need A^T to convert from body-fixed to space-fixed:
562	–	rotTrans = rotMatrix.transpose();
563	–
564	–	newVec = rotTrans * c1;
565	–	dVec = rotTrans * c2;
566	–	atomInfo = new AtomInfo;
567	–	atomInfo->atomTypeName = "GB";
568	–	atomInfo->pos[0] = pos[0] + newVec[0];
569	–	atomInfo->pos[1] = pos[1] + newVec[1];
570	–	atomInfo->pos[2] = pos[2] + newVec[2];
571	–	atomInfo->dipole[0] = dVec[0];
572	–	atomInfo->dipole[1] = dVec[1];
573	–	atomInfo->dipole[2] = dVec[2];
574	–	atomInfo->hasVector = true;
575	–	atomInfo->charge = 3.0;
576	–	atomInfo->hasCharge = true;
577	–	atomData->addAtomInfo(atomInfo);
578	–
579	–	//add atom data into atom's property
580	–
581	–	if(!haveAtomData){
582	–	atomData->setID("ATOMDATA");
583	–	datom->addProperty(atomData);
584	–	}
585	–
586	–	setVisited(datom);
587	–
588	–	}
589	–
590	–	const std::string GBLipidAtomVisitor::toString(){
591	–	char buffer[65535];
592	–	std::string result;
593	–
594	–	sprintf(buffer ,"------------------------------------------------------------------\n");
595	–	result += buffer;
596	–
597	–	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
598	–	result += buffer;
599	–
600	–	sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
601	–	result += buffer;
602	–
603	–	sprintf(buffer ,"------------------------------------------------------------------\n");
604	–	result += buffer;
605	–
606	–	return result;
607	–	}
608	–
609	–	bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
610	–	std::set<std::string>::iterator strIter;
611	–	strIter = Ring5gbAtomType.find(atomType);
612	–
613	–	return strIter != Ring5gbAtomType.end() ? true : false;
614	–	}
615	–
616	–	void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
617	–	std::vector<AtomInfo*> atoms;
618	–	//we need to convert linear into 4 different atoms
619	–	Vector3d c1(0.0, 0.0, -5.5);
620	–	Vector3d c2(0.0, 0.0, -1.8);
621	–	Vector3d c3(0.0, 0.0,  1.8);
622	–	Vector3d c4(0.0, 0.0,  5.5);
623	–	RotMat3x3d rotMatrix;
624	–	RotMat3x3d rotTrans;
625	–	AtomInfo* atomInfo;
626	–	Vector3d pos;
627	–	Vector3d newVec;
628	–	Vector3d dVec;
629	–	Quat4d q;
630	–	AtomData* atomData;
631	–	GenericData* data;
632	–	bool haveAtomData;
633	–
634	–	//if atom is not Ring5GB atom, just skip it
635	–	if(!isRing5gbAtom(datom->getType()))
636	–	return;
637	–
638	–	data = datom->getPropertyByName("ATOMDATA");
639	–	if(data != NULL){
640	–	atomData = dynamic_cast<AtomData*>(data);
641	–	if(atomData == NULL){
642	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
643	–	atomData = new AtomData;
644	–	haveAtomData = false;
645	–	} else {
646	–	haveAtomData = true;
647	–	}
648	–	} else {
649	–	atomData = new AtomData;
650	–	haveAtomData = false;
651	–	}
652	–
653	–
654	–	pos = datom->getPos();
655	–	q = datom->getQ();
656	–	rotMatrix = datom->getA();
657	–
658	–	// We need A^T to convert from body-fixed to space-fixed:
659	–	rotTrans = rotMatrix.transpose();
660	–
661	–	newVec = rotTrans * c1;
662	–	atomInfo = new AtomInfo;
663	–	atomInfo->atomTypeName = "K";
664	–	atomInfo->pos[0] = pos[0] + newVec[0];
665	–	atomInfo->pos[1] = pos[1] + newVec[1];
666	–	atomInfo->pos[2] = pos[2] + newVec[2];
667	–	atomInfo->dipole[0] = 0.0;
668	–	atomInfo->dipole[1] = 0.0;
669	–	atomInfo->dipole[2] = 0.0;
670	–	atomData->addAtomInfo(atomInfo);
671	–
672	–	newVec = rotTrans * c2;
673	–	atomInfo = new AtomInfo;
674	–	atomInfo->atomTypeName = "K";
675	–	atomInfo->pos[0] = pos[0] + newVec[0];
676	–	atomInfo->pos[1] = pos[1] + newVec[1];
677	–	atomInfo->pos[2] = pos[2] + newVec[2];
678	–	atomInfo->dipole[0] = 0.0;
679	–	atomInfo->dipole[1] = 0.0;
680	–	atomInfo->dipole[2] = 0.0;
681	–	atomData->addAtomInfo(atomInfo);
682	–
683	–	newVec = rotTrans * c3;
684	–	atomInfo = new AtomInfo;
685	–	atomInfo->atomTypeName = "K";
686	–	atomInfo->pos[0] = pos[0] + newVec[0];
687	–	atomInfo->pos[1] = pos[1] + newVec[1];
688	–	atomInfo->pos[2] = pos[2] + newVec[2];
689	–	atomInfo->dipole[0] = 0.0;
690	–	atomInfo->dipole[1] = 0.0;
691	–	atomInfo->dipole[2] = 0.0;
692	–	atomData->addAtomInfo(atomInfo);
693	–
694	–	newVec = rotTrans * c4;
695	–	atomInfo = new AtomInfo;
696	–	atomInfo->atomTypeName = "K";
697	–	atomInfo->pos[0] = pos[0] + newVec[0];
698	–	atomInfo->pos[1] = pos[1] + newVec[1];
699	–	atomInfo->pos[2] = pos[2] + newVec[2];
700	–	atomInfo->dipole[0] = 0.0;
701	–	atomInfo->dipole[1] = 0.0;
702	–	atomInfo->dipole[2] = 0.0;
703	–	atomData->addAtomInfo(atomInfo);
704	–
705	–	//add atom data into atom's property
706	–
707	–	if(!haveAtomData){
708	–	atomData->setID("ATOMDATA");
709	–	datom->addProperty(atomData);
710	–	}
711	–
712	–	setVisited(datom);
713	–
74		}
75
76	<	const std::string Ring5gbAtomVisitor::toString(){
77	<	char buffer[65535];
718	<	std::string result;
719	<
720	<	sprintf(buffer ,"------------------------------------------------------------------\n");
721	<	result += buffer;
722	<
723	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
724	<	result += buffer;
725	<
726	<	sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
727	<	result += buffer;
728	<
729	<	sprintf(buffer ,"------------------------------------------------------------------\n");
730	<	result += buffer;
731	<
732	<	return result;
733	<	}
734	<
735	<	bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
736	<	std::set<std::string>::iterator strIter;
737	<	strIter = HeadAtomType.find(atomType);
738	<
739	<	return strIter != HeadAtomType.end() ? true : false;
740	<	}
741	<
742	<	void HeadAtomVisitor::visit(DirectionalAtom* datom){
743	<	std::vector<AtomInfo*> atoms;
744	<	//we need to convert linear into 2 different atoms
745	<	Vector3d c1(0.0, 0.0, -1.5);
746	<	Vector3d c2(0.0, 0.0, 1.5);
747	<	RotMat3x3d rotMatrix;
748	<	RotMat3x3d rotTrans;
749	<	AtomInfo* atomInfo;
750	<	Vector3d pos;
751	<	Vector3d newVec;
752	<	Vector3d dVec;
753	<	Quat4d q;
754	<	AtomData* atomData;
755	<	GenericData* data;
756	<	bool haveAtomData;
757	<
758	<	//if atom is not Head atom, just skip it
759	<	if(!isHeadAtom(datom->getType()))
760	<	return;
761	<
762	<	data = datom->getPropertyByName("ATOMDATA");
763	<	if(data != NULL){
764	<	atomData = dynamic_cast<AtomData*>(data);
765	<	if(atomData == NULL){
766	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
767	<	atomData = new AtomData;
768	<	haveAtomData = false;
769	<	} else {
770	<	haveAtomData = true;
771	<	}
772	<	} else {
773	<	atomData = new AtomData;
774	<	haveAtomData = false;
775	<	}
776	<
777	<
778	<	pos = datom->getPos();
779	<	q = datom->getQ();
780	<	rotMatrix = datom->getA();
781	<
782	<	// We need A^T to convert from body-fixed to space-fixed:
783	<	rotTrans = rotMatrix.transpose();
784	<
785	<	newVec = rotTrans * c1;
786	<	atomInfo = new AtomInfo;
787	<	atomInfo->atomTypeName = "C";
788	<	atomInfo->pos[0] = pos[0] + newVec[0];
789	<	atomInfo->pos[1] = pos[1] + newVec[1];
790	<	atomInfo->pos[2] = pos[2] + newVec[2];
791	<	atomInfo->dipole[0] = 0.0;
792	<	atomInfo->dipole[1] = 0.0;
793	<	atomInfo->dipole[2] = 0.0;
794	<	atomData->addAtomInfo(atomInfo);
795	<
796	<	newVec = rotTrans * c2;
797	<	atomInfo = new AtomInfo;
798	<	atomInfo->atomTypeName = "O";
799	<	atomInfo->pos[0] = pos[0] + newVec[0];
800	<	atomInfo->pos[1] = pos[1] + newVec[1];
801	<	atomInfo->pos[2] = pos[2] + newVec[2];
802	<	atomInfo->dipole[0] = 0.0;
803	<	atomInfo->dipole[1] = 0.0;
804	<	atomInfo->dipole[2] = 0.0;
805	<	atomData->addAtomInfo(atomInfo);
806	<
807	<	//add atom data into atom's property
808	<
809	<	if(!haveAtomData){
810	<	atomData->setID("ATOMDATA");
811	<	datom->addProperty(atomData);
812	<	}
813	<
814	<	setVisited(datom);
815	<
816	<	}
817	<
818	<	const std::string HeadAtomVisitor::toString(){
819	<	char buffer[65535];
820	<	std::string result;
821	<
822	<	sprintf(buffer ,"------------------------------------------------------------------\n");
823	<	result += buffer;
824	<
825	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
826	<	result += buffer;
827	<
828	<	sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
829	<	result += buffer;
830	<
831	<	sprintf(buffer ,"------------------------------------------------------------------\n");
832	<	result += buffer;
833	<
834	<	return result;
835	<	}
836	<
837	<
838	<	//----------------------------------------------------------------------------//
839	<
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	<
89	>
90		atomInfo = new AtomInfo;
91	<
91	>
92		atomData = new AtomData;
93		atomData->setID("ATOMDATA");
94	<
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->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	<
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	<
132	>
133		pos = datom->getPos();
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()) {
#	Line 889 | Line 146 | namespace oopse {
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
#	Line 921 | Line 187 | namespace oopse {
187
188		return result;
189		}
190	<	} //namespace oopse
190	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1291 by gezelter, Thu Sep 11 19:40:59 2008 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1465 by chuckv, Fri Jul 9 23:08:25 2010 UTC

#	Line 0 | Line 1
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