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

Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1821 by gezelter, Mon Jan 7 20:05:43 2013 UTC

#	Line 36 | Line 36
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).
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 OpenMD {
51		void BaseAtomVisitor::visit(RigidBody *rb) {
#	Line 71 | Line 74 | namespace OpenMD {
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	–	//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 = OPENMD_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	–
77		}
78
79	<	const std::string LinearAtomVisitor::toString(){
80	<	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	<
714	<	}
715	<
716	<	const std::string Ring5gbAtomVisitor::toString(){
717	<	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	<
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	>	u = datom->getA().transpose()*V3Z;
148		}
149		atomData = new AtomData;
150		atomData->setID("ATOMDATA");
#	Line 889 | Line 154 | namespace OpenMD {
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

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 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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