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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 1871 by gezelter, Fri May 10 14:59:13 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, 234107 (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/FixedChargeAdapter.hpp"
48	+	#include "types/FluctuatingChargeAdapter.hpp"
49	+	#include "types/MultipoleAdapter.hpp"
50	+	#include "types/GayBerneAdapter.hpp"
51
52	<	namespace oopse {
52	>	namespace OpenMD {
53		void BaseAtomVisitor::visit(RigidBody *rb) {
54		//vector<Atom*> myAtoms;
55		//vector<Atom*>::iterator atomIter;
#	Line 71 | Line 76 | namespace oopse {
76		GenericData *data;
77		data = atom->getPropertyByName("VISITED");
78		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);
79		}
80
81	<	const std::string TREDAtomVisitor::toString() {
82	<	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	<
495	<	}
496	<
497	<	const std::string LinearAtomVisitor::toString(){
498	<	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	<
81	>	//------------------------------------------------------------------------//
82	>
83		void DefaultAtomVisitor::visit(Atom *atom) {
84		AtomData *atomData;
85		AtomInfo *atomInfo;
86	<	Vector3d  pos;
87	<
86	>	AtomType* atype = atom->getAtomType();
87	>
88		if (isVisited(atom))
89		return;
90	<
90	>
91		atomInfo = new AtomInfo;
850	–
851	–	atomData = new AtomData;
852	–	atomData->setID("ATOMDATA");
853	–
854	–	pos = atom->getPos();
92		atomInfo->atomTypeName = atom->getType();
93	<	atomInfo->pos[0] = pos[0];
94	<	atomInfo->pos[1] = pos[1];
95	<	atomInfo->pos[2] = pos[2];
96	<	atomInfo->dipole[0] = 0.0;
97	<	atomInfo->dipole[1] = 0.0;
98	<	atomInfo->dipole[2] = 0.0;
93	>	atomInfo->pos = atom->getPos();
94	>	atomInfo->vel = atom->getVel();
95	>	atomInfo->frc = atom->getFrc();
96	>	atomInfo->vec = V3Zero;
97	>	atomInfo->hasVelocity = true;
98	>	atomInfo->hasForce = true;
99	>
100	>	FixedChargeAdapter fca = FixedChargeAdapter(atype);
101	>	if ( fca.isFixedCharge() ) {
102	>	atomInfo->hasCharge = true;
103	>	atomInfo->charge = fca.getCharge();
104	>	}
105	>
106	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
107	>	if ( fqa.isFluctuatingCharge() ) {
108	>	atomInfo->hasCharge = true;
109	>	atomInfo->charge += atom->getFlucQPos();
110	>	}
111
112	<	atomData->addAtomInfo(atomInfo);
112	>	if (atype->isElectrostatic()) {
113	>	atomInfo->hasElectricField = true;
114	>	atomInfo->eField = atom->getElectricField();
115	>	}
116
117	+	atomData = new AtomData;
118	+	atomData->setID("ATOMDATA");
119	+	atomData->addAtomInfo(atomInfo);
120	+
121		atom->addProperty(atomData);
122	<
122	>
123		setVisited(atom);
124		}
125	<
125	>
126		void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
127		AtomData *atomData;
128		AtomInfo *atomInfo;
129	<	Vector3d  pos;
874	<	Vector3d  u;
129	>	AtomType* atype = datom->getAtomType();
130
131		if (isVisited(datom))
132		return;
133	+
134	+	atomInfo = new AtomInfo;
135	+	atomInfo->atomTypeName = datom->getType();
136	+	atomInfo->pos = datom->getPos();
137	+	atomInfo->vel = datom->getVel();
138	+	atomInfo->frc = datom->getFrc();
139	+	atomInfo->hasVelocity = true;
140	+	atomInfo->hasForce = true;
141
142	<	pos = datom->getPos();
143	<	if (datom->getAtomType()->isGayBerne()) {
144	<	u = datom->getA().transpose()*V3Z;
145	<	} else if (datom->getAtomType()->isMultipole()) {
883	<	u = datom->getElectroFrame().getColumn(2);
142	>	FixedChargeAdapter fca = FixedChargeAdapter(atype);
143	>	if ( fca.isFixedCharge() ) {
144	>	atomInfo->hasCharge = true;
145	>	atomInfo->charge = fca.getCharge();
146		}
147	<	atomData = new AtomData;
148	<	atomData->setID("ATOMDATA");
149	<	atomInfo = new AtomInfo;
147	>
148	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
149	>	if ( fqa.isFluctuatingCharge() ) {
150	>	atomInfo->hasCharge = true;
151	>	atomInfo->charge += datom->getFlucQPos();
152	>	}
153
154	<	atomInfo->atomTypeName = datom->getType();
155	<	atomInfo->pos[0] = pos[0];
156	<	atomInfo->pos[1] = pos[1];
157	<	atomInfo->pos[2] = pos[2];
893	<	atomInfo->dipole[0] = u[0];
894	<	atomInfo->dipole[1] = u[1];
895	<	atomInfo->dipole[2] = u[2];
154	>	if (atype->isElectrostatic()) {
155	>	atomInfo->hasElectricField = true;
156	>	atomInfo->eField = datom->getElectricField();
157	>	}
158
159	<	atomData->addAtomInfo(atomInfo);
159	>	GayBerneAdapter gba = GayBerneAdapter(atype);
160	>	MultipoleAdapter ma = MultipoleAdapter(atype);
161	>
162	>	if (gba.isGayBerne()) {
163	>	atomInfo->hasVector = true;
164	>	atomInfo->vec = datom->getA().transpose()*V3Z;
165	>	} else if (ma.isDipole()) {
166	>	atomInfo->hasVector = true;
167	>	atomInfo->vec = datom->getDipole();
168	>	} else if (ma.isQuadrupole()) {
169	>	atomInfo->hasVector = true;
170	>	atomInfo->vec = datom->getA().transpose()*V3Z;
171	>	}
172
173	+	atomData->addAtomInfo(atomInfo);
174		datom->addProperty(atomData);
175
176		setVisited(datom);
#	Line 906 | Line 181 | namespace oopse {
181		std::string result;
182
183		sprintf(buffer,
184	<	"------------------------------------------------------------------\n");
184	>	"--------------------------------------------------------------\n");
185		result += buffer;
186
187		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
#	Line 917 | Line 192 | namespace oopse {
192		result += buffer;
193
194		sprintf(buffer,
195	<	"------------------------------------------------------------------\n");
195	>	"--------------------------------------------------------------\n");
196		result += buffer;
197
198		return result;
199		}
200	<	} //namespace oopse
200	>	} //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 1871 by gezelter, Fri May 10 14:59:13 2013 UTC

#	Line 0 | Line 1
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