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

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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 1873 by gezelter, Fri May 10 16:09:34 2013 UTC

#	Line 35 | Line 35
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).
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 OpenMD {
53	+
54	+	BaseAtomVisitor::BaseAtomVisitor(SimInfo* info) : BaseVisitor() {
55	+	storageLayout_ = info->getStorageLayout();
56	+	}
57	+
58		void BaseAtomVisitor::visit(RigidBody *rb) {
59		//vector<Atom*> myAtoms;
60		//vector<Atom*>::iterator atomIter;
#	Line 71 | Line 81 | namespace OpenMD {
81		GenericData *data;
82		data = atom->getPropertyByName("VISITED");
83		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	–
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	–
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;
84		}
85
86	<	void HeadAtomVisitor::visit(DirectionalAtom* datom){
87	<	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	<
86	>	//------------------------------------------------------------------------//
87	>
88		void DefaultAtomVisitor::visit(Atom *atom) {
89		AtomData *atomData;
90		AtomInfo *atomInfo;
91	<	Vector3d  pos;
92	<
91	>	AtomType* atype = atom->getAtomType();
92	>
93		if (isVisited(atom))
94		return;
95	<
95	>
96		atomInfo = new AtomInfo;
849	–
850	–	atomData = new AtomData;
851	–	atomData->setID("ATOMDATA");
852	–
853	–	pos = atom->getPos();
97		atomInfo->atomTypeName = atom->getType();
98	<	atomInfo->pos[0] = pos[0];
99	<	atomInfo->pos[1] = pos[1];
100	<	atomInfo->pos[2] = pos[2];
101	<	atomInfo->dipole[0] = 0.0;
102	<	atomInfo->dipole[1] = 0.0;
103	<	atomInfo->dipole[2] = 0.0;
98	>	atomInfo->pos = atom->getPos();
99	>	atomInfo->vel = atom->getVel();
100	>	atomInfo->frc = atom->getFrc();
101	>	atomInfo->vec = V3Zero;
102	>	atomInfo->hasVelocity = true;
103	>	atomInfo->hasForce = true;
104	>
105	>	FixedChargeAdapter fca = FixedChargeAdapter(atype);
106	>	if ( fca.isFixedCharge() ) {
107	>	atomInfo->hasCharge = true;
108	>	atomInfo->charge = fca.getCharge();
109	>	}
110	>
111	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
112	>	if ( fqa.isFluctuatingCharge() ) {
113	>	atomInfo->hasCharge = true;
114	>	atomInfo->charge += atom->getFlucQPos();
115	>	}
116	>
117	>	if ((storageLayout_ & DataStorage::dslElectricField) &&
118	>	(atype->isElectrostatic())) {
119	>	atomInfo->hasElectricField = true;
120	>	atomInfo->eField = atom->getElectricField();
121	>	}
122
123	+	atomData = new AtomData;
124	+	atomData->setID("ATOMDATA");
125		atomData->addAtomInfo(atomInfo);
126	<
126	>
127		atom->addProperty(atomData);
128	<
128	>
129		setVisited(atom);
130		}
131	<
131	>
132		void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
133		AtomData *atomData;
134		AtomInfo *atomInfo;
135	<	Vector3d  pos;
873	<	Vector3d  u;
135	>	AtomType* atype = datom->getAtomType();
136
137		if (isVisited(datom))
138		return;
139	+
140	+	atomInfo = new AtomInfo;
141	+	atomInfo->atomTypeName = datom->getType();
142	+	atomInfo->pos = datom->getPos();
143	+	atomInfo->vel = datom->getVel();
144	+	atomInfo->frc = datom->getFrc();
145	+	atomInfo->hasVelocity = true;
146	+	atomInfo->hasForce = true;
147
148	<	pos = datom->getPos();
149	<	if (datom->getAtomType()->isGayBerne()) {
150	<	u = datom->getA().transpose()*V3Z;
151	<	} else if (datom->getAtomType()->isMultipole()) {
882	<	u = datom->getElectroFrame().getColumn(2);
148	>	FixedChargeAdapter fca = FixedChargeAdapter(atype);
149	>	if ( fca.isFixedCharge() ) {
150	>	atomInfo->hasCharge = true;
151	>	atomInfo->charge = fca.getCharge();
152		}
153	<	atomData = new AtomData;
154	<	atomData->setID("ATOMDATA");
155	<	atomInfo = new AtomInfo;
153	>
154	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
155	>	if ( fqa.isFluctuatingCharge() ) {
156	>	atomInfo->hasCharge = true;
157	>	atomInfo->charge += datom->getFlucQPos();
158	>	}
159
160	<	atomInfo->atomTypeName = datom->getType();
161	<	atomInfo->pos[0] = pos[0];
162	<	atomInfo->pos[1] = pos[1];
163	<	atomInfo->pos[2] = pos[2];
164	<	atomInfo->dipole[0] = u[0];
893	<	atomInfo->dipole[1] = u[1];
894	<	atomInfo->dipole[2] = u[2];
160	>	if ((storageLayout_ & DataStorage::dslElectricField) &&
161	>	(atype->isElectrostatic())) {
162	>	atomInfo->hasElectricField = true;
163	>	atomInfo->eField = datom->getElectricField();
164	>	}
165
166	+	GayBerneAdapter gba = GayBerneAdapter(atype);
167	+	MultipoleAdapter ma = MultipoleAdapter(atype);
168	+
169	+	if (gba.isGayBerne()) {
170	+	atomInfo->hasVector = true;
171	+	atomInfo->vec = datom->getA().transpose()*V3Z;
172	+	} else if (ma.isDipole()) {
173	+	atomInfo->hasVector = true;
174	+	atomInfo->vec = datom->getDipole();
175	+	} else if (ma.isQuadrupole()) {
176	+	atomInfo->hasVector = true;
177	+	atomInfo->vec = datom->getA().transpose()*V3Z;
178	+	}
179	+
180	+	atomData = new AtomData;
181	+	atomData->setID("ATOMDATA");
182		atomData->addAtomInfo(atomInfo);
183
184		datom->addProperty(atomData);
#	Line 905 | Line 191 | namespace OpenMD {
191		std::string result;
192
193		sprintf(buffer,
194	<	"------------------------------------------------------------------\n");
194	>	"--------------------------------------------------------------\n");
195		result += buffer;
196
197		sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
#	Line 916 | Line 202 | namespace OpenMD {
202		result += buffer;
203
204		sprintf(buffer,
205	<	"------------------------------------------------------------------\n");
205	>	"--------------------------------------------------------------\n");
206		result += buffer;
207
208		return result;

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 1873 by gezelter, Fri May 10 16:09:34 2013 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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