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

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trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 1244 by xsun, Wed May 14 21:04:13 2008 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1814 by gezelter, Tue Nov 27 21:13:48 2012 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 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	–	AtomType* atomType;
388	–	//if atom is not linear atom, just skip it
389	–	if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
390	–	return;
391	–
392	–	//setup GayBerne type in fortran side
393	–	data = datom->getAtomType()->getPropertyByName("GayBerne");
394	–	if (data != NULL) {
395	–	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
396	–
397	–	if (gayBerneData != NULL) {
398	–	GayBerneParam gayBerneParam = gayBerneData->getData();
399	–
400	–	// double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
401	–	double halfLen = gayBerneParam.GB_l/2.0;
402	–	c1[2] = -halfLen;
403	–	c2[2] = -halfLen /2;
404	–	c3[2] = halfLen/2;
405	–	c4[2] = halfLen;
406	–
407	–	}
408	–
409	–	else {
410	–	sprintf( painCave.errMsg,
411	–	"Can not cast GenericData to GayBerneParam\n");
412	–	painCave.severity = OOPSE_ERROR;
413	–	painCave.isFatal = 1;
414	–	simError();
415	–	}
416	–	}
417	–
418	–
419	–	data = datom->getPropertyByName("ATOMDATA");
420	–	if(data != NULL){
421	–	atomData = dynamic_cast<AtomData*>(data);
422	–	if(atomData == NULL){
423	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
424	–	atomData = new AtomData;
425	–	haveAtomData = false;
426	–	} else {
427	–	haveAtomData = true;
428	–	}
429	–	} else {
430	–	atomData = new AtomData;
431	–	haveAtomData = false;
432	–	}
433	–
434	–
435	–	pos = datom->getPos();
436	–	q = datom->getQ();
437	–	rotMatrix = datom->getA();
438	–
439	–	// We need A^T to convert from body-fixed to space-fixed:
440	–	rotTrans = rotMatrix.transpose();
441	–
442	–	newVec = rotTrans * c1;
443	–	atomInfo = new AtomInfo;
444	–	atomInfo->atomTypeName = "C";
445	–	atomInfo->pos[0] = pos[0] + newVec[0];
446	–	atomInfo->pos[1] = pos[1] + newVec[1];
447	–	atomInfo->pos[2] = pos[2] + newVec[2];
448	–	atomInfo->dipole[0] = 0.0;
449	–	atomInfo->dipole[1] = 0.0;
450	–	atomInfo->dipole[2] = 0.0;
451	–	atomData->addAtomInfo(atomInfo);
452	–
453	–	newVec = rotTrans * c2;
454	–	atomInfo = new AtomInfo;
455	–	atomInfo->atomTypeName = "C";
456	–	atomInfo->pos[0] = pos[0] + newVec[0];
457	–	atomInfo->pos[1] = pos[1] + newVec[1];
458	–	atomInfo->pos[2] = pos[2] + newVec[2];
459	–	atomInfo->dipole[0] = 0.0;
460	–	atomInfo->dipole[1] = 0.0;
461	–	atomInfo->dipole[2] = 0.0;
462	–	atomData->addAtomInfo(atomInfo);
463	–
464	–	newVec = rotTrans * c3;
465	–	atomInfo = new AtomInfo;
466	–	atomInfo->atomTypeName = "C";
467	–	atomInfo->pos[0] = pos[0] + newVec[0];
468	–	atomInfo->pos[1] = pos[1] + newVec[1];
469	–	atomInfo->pos[2] = pos[2] + newVec[2];
470	–	atomInfo->dipole[0] = 0.0;
471	–	atomInfo->dipole[1] = 0.0;
472	–	atomInfo->dipole[2] = 0.0;
473	–	atomData->addAtomInfo(atomInfo);
474	–
475	–	newVec = rotTrans * c4;
476	–	atomInfo = new AtomInfo;
477	–	atomInfo->atomTypeName = "C";
478	–	atomInfo->pos[0] = pos[0] + newVec[0];
479	–	atomInfo->pos[1] = pos[1] + newVec[1];
480	–	atomInfo->pos[2] = pos[2] + newVec[2];
481	–	atomInfo->dipole[0] = 0.0;
482	–	atomInfo->dipole[1] = 0.0;
483	–	atomInfo->dipole[2] = 0.0;
484	–	atomData->addAtomInfo(atomInfo);
485	–
486	–	//add atom data into atom's property
487	–
488	–	if(!haveAtomData){
489	–	atomData->setID("ATOMDATA");
490	–	datom->addProperty(atomData);
491	–	}
492	–
493	–	setVisited(datom);
494	–
77		}
78
79	<	const std::string LinearAtomVisitor::toString(){
80	<	char buffer[65535];
499	<	std::string result;
500	<
501	<	sprintf(buffer ,"------------------------------------------------------------------\n");
502	<	result += buffer;
503	<
504	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
505	<	result += buffer;
506	<
507	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
508	<	result += buffer;
509	<
510	<	sprintf(buffer ,"------------------------------------------------------------------\n");
511	<	result += buffer;
512	<
513	<	return result;
514	<	}
515	<
516	<	bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
517	<	std::set<std::string>::iterator strIter;
518	<	strIter = GBLipidAtomType.find(atomType);
519	<
520	<	return strIter != GBLipidAtomType.end() ? true : false;
521	<	}
522	<
523	<	void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
524	<	std::vector<AtomInfo*> atoms;
525	<	Vector3d c1(0.0, 0.0, 0.0);
526	<	Vector3d c2(0.0, 0.0, 1.0);
527	<	RotMat3x3d rotMatrix;
528	<	RotMat3x3d rotTrans;
529	<	AtomInfo* atomInfo;
530	<	Vector3d pos;
531	<	Vector3d newVec;
532	<	Vector3d dVec;
533	<	Quat4d q;
534	<	AtomData* atomData;
535	<	GenericData* data;
536	<	bool haveAtomData;
537	<
538	<	//if atom is not GBlipid atom, just skip it
539	<	if(!isGBLipidAtom(datom->getType()))
540	<	return;
541	<
542	<	data = datom->getPropertyByName("ATOMDATA");
543	<	if(data != NULL){
544	<	atomData = dynamic_cast<AtomData*>(data);
545	<	if(atomData == NULL){
546	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
547	<	atomData = new AtomData;
548	<	haveAtomData = false;
549	<	} else {
550	<	haveAtomData = true;
551	<	}
552	<	} else {
553	<	atomData = new AtomData;
554	<	haveAtomData = false;
555	<	}
556	<
557	<
558	<	pos = datom->getPos();
559	<	q = datom->getQ();
560	<	rotMatrix = datom->getA();
561	<
562	<	// We need A^T to convert from body-fixed to space-fixed:
563	<	rotTrans = rotMatrix.transpose();
564	<
565	<	newVec = rotTrans * c1;
566	<	dVec = rotTrans * c2;
567	<	atomInfo = new AtomInfo;
568	<	atomInfo->atomTypeName = "GB";
569	<	atomInfo->pos[0] = pos[0] + newVec[0];
570	<	atomInfo->pos[1] = pos[1] + newVec[1];
571	<	atomInfo->pos[2] = pos[2] + newVec[2];
572	<	atomInfo->dipole[0] = dVec[0];
573	<	atomInfo->dipole[1] = dVec[1];
574	<	atomInfo->dipole[2] = dVec[2];
575	<	atomInfo->hasVector = true;
576	<	atomInfo->charge = 3.0;
577	<	atomInfo->hasCharge = true;
578	<	atomData->addAtomInfo(atomInfo);
579	<
580	<	//add atom data into atom's property
581	<
582	<	if(!haveAtomData){
583	<	atomData->setID("ATOMDATA");
584	<	datom->addProperty(atomData);
585	<	}
586	<
587	<	setVisited(datom);
588	<
589	<	}
590	<
591	<	const std::string GBLipidAtomVisitor::toString(){
592	<	char buffer[65535];
593	<	std::string result;
594	<
595	<	sprintf(buffer ,"------------------------------------------------------------------\n");
596	<	result += buffer;
597	<
598	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
599	<	result += buffer;
600	<
601	<	sprintf(buffer , "Visitor Description: Convert GBlipid into xyz-formatted atom for use with xyz2pov\n");
602	<	result += buffer;
603	<
604	<	sprintf(buffer ,"------------------------------------------------------------------\n");
605	<	result += buffer;
606	<
607	<	return result;
608	<	}
609	<
610	<	bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
611	<	std::set<std::string>::iterator strIter;
612	<	strIter = Ring5gbAtomType.find(atomType);
613	<
614	<	return strIter != Ring5gbAtomType.end() ? true : false;
615	<	}
616	<
617	<	void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
618	<	std::vector<AtomInfo*> atoms;
619	<	//we need to convert linear into 4 different atoms
620	<	Vector3d c1(0.0, 0.0, -5.5);
621	<	Vector3d c2(0.0, 0.0, -1.8);
622	<	Vector3d c3(0.0, 0.0,  1.8);
623	<	Vector3d c4(0.0, 0.0,  5.5);
624	<	RotMat3x3d rotMatrix;
625	<	RotMat3x3d rotTrans;
626	<	AtomInfo* atomInfo;
627	<	Vector3d pos;
628	<	Vector3d newVec;
629	<	Vector3d dVec;
630	<	Quat4d q;
631	<	AtomData* atomData;
632	<	GenericData* data;
633	<	bool haveAtomData;
634	<
635	<	//if atom is not Ring5GB atom, just skip it
636	<	if(!isRing5gbAtom(datom->getType()))
637	<	return;
638	<
639	<	data = datom->getPropertyByName("ATOMDATA");
640	<	if(data != NULL){
641	<	atomData = dynamic_cast<AtomData*>(data);
642	<	if(atomData == NULL){
643	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
644	<	atomData = new AtomData;
645	<	haveAtomData = false;
646	<	} else {
647	<	haveAtomData = true;
648	<	}
649	<	} else {
650	<	atomData = new AtomData;
651	<	haveAtomData = false;
652	<	}
653	<
654	<
655	<	pos = datom->getPos();
656	<	q = datom->getQ();
657	<	rotMatrix = datom->getA();
658	<
659	<	// We need A^T to convert from body-fixed to space-fixed:
660	<	rotTrans = rotMatrix.transpose();
661	<
662	<	newVec = rotTrans * c1;
663	<	atomInfo = new AtomInfo;
664	<	atomInfo->atomTypeName = "K";
665	<	atomInfo->pos[0] = pos[0] + newVec[0];
666	<	atomInfo->pos[1] = pos[1] + newVec[1];
667	<	atomInfo->pos[2] = pos[2] + newVec[2];
668	<	atomInfo->dipole[0] = 0.0;
669	<	atomInfo->dipole[1] = 0.0;
670	<	atomInfo->dipole[2] = 0.0;
671	<	atomData->addAtomInfo(atomInfo);
672	<
673	<	newVec = rotTrans * c2;
674	<	atomInfo = new AtomInfo;
675	<	atomInfo->atomTypeName = "K";
676	<	atomInfo->pos[0] = pos[0] + newVec[0];
677	<	atomInfo->pos[1] = pos[1] + newVec[1];
678	<	atomInfo->pos[2] = pos[2] + newVec[2];
679	<	atomInfo->dipole[0] = 0.0;
680	<	atomInfo->dipole[1] = 0.0;
681	<	atomInfo->dipole[2] = 0.0;
682	<	atomData->addAtomInfo(atomInfo);
683	<
684	<	newVec = rotTrans * c3;
685	<	atomInfo = new AtomInfo;
686	<	atomInfo->atomTypeName = "K";
687	<	atomInfo->pos[0] = pos[0] + newVec[0];
688	<	atomInfo->pos[1] = pos[1] + newVec[1];
689	<	atomInfo->pos[2] = pos[2] + newVec[2];
690	<	atomInfo->dipole[0] = 0.0;
691	<	atomInfo->dipole[1] = 0.0;
692	<	atomInfo->dipole[2] = 0.0;
693	<	atomData->addAtomInfo(atomInfo);
694	<
695	<	newVec = rotTrans * c4;
696	<	atomInfo = new AtomInfo;
697	<	atomInfo->atomTypeName = "K";
698	<	atomInfo->pos[0] = pos[0] + newVec[0];
699	<	atomInfo->pos[1] = pos[1] + newVec[1];
700	<	atomInfo->pos[2] = pos[2] + newVec[2];
701	<	atomInfo->dipole[0] = 0.0;
702	<	atomInfo->dipole[1] = 0.0;
703	<	atomInfo->dipole[2] = 0.0;
704	<	atomData->addAtomInfo(atomInfo);
705	<
706	<	//add atom data into atom's property
707	<
708	<	if(!haveAtomData){
709	<	atomData->setID("ATOMDATA");
710	<	datom->addProperty(atomData);
711	<	}
712	<
713	<	setVisited(datom);
714	<
715	<	}
716	<
717	<	const std::string Ring5gbAtomVisitor::toString(){
718	<	char buffer[65535];
719	<	std::string result;
720	<
721	<	sprintf(buffer ,"------------------------------------------------------------------\n");
722	<	result += buffer;
723	<
724	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
725	<	result += buffer;
726	<
727	<	sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
728	<	result += buffer;
729	<
730	<	sprintf(buffer ,"------------------------------------------------------------------\n");
731	<	result += buffer;
732	<
733	<	return result;
734	<	}
735	<
736	<	bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
737	<	std::set<std::string>::iterator strIter;
738	<	strIter = HeadAtomType.find(atomType);
739	<
740	<	return strIter != HeadAtomType.end() ? true : false;
741	<	}
742	<
743	<	void HeadAtomVisitor::visit(DirectionalAtom* datom){
744	<	std::vector<AtomInfo*> atoms;
745	<	//we need to convert linear into 2 different atoms
746	<	Vector3d c1(0.0, 0.0, -1.5);
747	<	Vector3d c2(0.0, 0.0, 1.5);
748	<	RotMat3x3d rotMatrix;
749	<	RotMat3x3d rotTrans;
750	<	AtomInfo* atomInfo;
751	<	Vector3d pos;
752	<	Vector3d newVec;
753	<	Vector3d dVec;
754	<	Quat4d q;
755	<	AtomData* atomData;
756	<	GenericData* data;
757	<	bool haveAtomData;
758	<
759	<	//if atom is not Head atom, just skip it
760	<	if(!isHeadAtom(datom->getType()))
761	<	return;
762	<
763	<	data = datom->getPropertyByName("ATOMDATA");
764	<	if(data != NULL){
765	<	atomData = dynamic_cast<AtomData*>(data);
766	<	if(atomData == NULL){
767	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
768	<	atomData = new AtomData;
769	<	haveAtomData = false;
770	<	} else {
771	<	haveAtomData = true;
772	<	}
773	<	} else {
774	<	atomData = new AtomData;
775	<	haveAtomData = false;
776	<	}
777	<
778	<
779	<	pos = datom->getPos();
780	<	q = datom->getQ();
781	<	rotMatrix = datom->getA();
782	<
783	<	// We need A^T to convert from body-fixed to space-fixed:
784	<	rotTrans = rotMatrix.transpose();
785	<
786	<	newVec = rotTrans * c1;
787	<	atomInfo = new AtomInfo;
788	<	atomInfo->atomTypeName = "C";
789	<	atomInfo->pos[0] = pos[0] + newVec[0];
790	<	atomInfo->pos[1] = pos[1] + newVec[1];
791	<	atomInfo->pos[2] = pos[2] + newVec[2];
792	<	atomInfo->dipole[0] = 0.0;
793	<	atomInfo->dipole[1] = 0.0;
794	<	atomInfo->dipole[2] = 0.0;
795	<	atomData->addAtomInfo(atomInfo);
796	<
797	<	newVec = rotTrans * c2;
798	<	atomInfo = new AtomInfo;
799	<	atomInfo->atomTypeName = "O";
800	<	atomInfo->pos[0] = pos[0] + newVec[0];
801	<	atomInfo->pos[1] = pos[1] + newVec[1];
802	<	atomInfo->pos[2] = pos[2] + newVec[2];
803	<	atomInfo->dipole[0] = 0.0;
804	<	atomInfo->dipole[1] = 0.0;
805	<	atomInfo->dipole[2] = 0.0;
806	<	atomData->addAtomInfo(atomInfo);
807	<
808	<	//add atom data into atom's property
809	<
810	<	if(!haveAtomData){
811	<	atomData->setID("ATOMDATA");
812	<	datom->addProperty(atomData);
813	<	}
814	<
815	<	setVisited(datom);
816	<
817	<	}
818	<
819	<	const std::string HeadAtomVisitor::toString(){
820	<	char buffer[65535];
821	<	std::string result;
822	<
823	<	sprintf(buffer ,"------------------------------------------------------------------\n");
824	<	result += buffer;
825	<
826	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
827	<	result += buffer;
828	<
829	<	sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
830	<	result += buffer;
831	<
832	<	sprintf(buffer ,"------------------------------------------------------------------\n");
833	<	result += buffer;
834	<
835	<	return result;
836	<	}
837	<
838	<
839	<	//----------------------------------------------------------------------------//
840	<
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	<	if (datom->getAtomType()->isGayBerne()) {
136	<	u = datom->getA().transpose()*V3Z;
137	<	} else if (datom->getAtomType()->isMultipole()) {
138	<	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		}
148		atomData = new AtomData;
149		atomData->setID("ATOMDATA");
#	Line 890 | Line 153 | namespace oopse {
153		atomInfo->pos[0] = pos[0];
154		atomInfo->pos[1] = pos[1];
155		atomInfo->pos[2] = pos[2];
156	<	atomInfo->dipole[0] = u[0];
157	<	atomInfo->dipole[1] = u[1];
158	<	atomInfo->dipole[2] = u[2];
156	>	atomInfo->vel[0] = vel[0];
157	>	atomInfo->vel[1] = vel[1];
158	>	atomInfo->vel[2] = vel[2];
159	>	atomInfo->hasVelocity = true;
160	>	atomInfo->frc[0] = frc[0];
161	>	atomInfo->frc[1] = frc[1];
162	>	atomInfo->frc[2] = frc[2];
163	>	atomInfo->hasForce = true;
164	>	atomInfo->vec[0] = u[0];
165	>	atomInfo->vec[1] = u[1];
166	>	atomInfo->vec[2] = u[2];
167	>	atomInfo->hasVector = true;
168
169		atomData->addAtomInfo(atomInfo);
170
#	Line 922 | Line 194 | namespace oopse {
194
195		return result;
196		}
197	<	} //namespace oopse
197	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1244 by xsun, Wed May 14 21:04:13 2008 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1814 by gezelter, Tue Nov 27 21:13:48 2012 UTC

#	Line 0 | Line 1
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