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

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trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 1219 by xsun, Wed Jan 23 21:23:32 2008 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1873 by gezelter, Fri May 10 16:09:34 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	>
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 73 | Line 83 | namespace oopse {
83		return data == NULL ? false : true;
84		}
85
86	<	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
87	<	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	<
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	<	//we need to convert linear into 4 different atoms
526	<	//Vector3d c1(0.0, 0.0, -6.25);
527	<	//Vector3d c2(0.0, 0.0, -2.1);
528	<	//Vector3d c3(0.0, 0.0,  2.1);
529	<	//Vector3d c4(0.0, 0.0,  6.25);
530	<	Vector3d c1(0.0, 0.0, 0.0);
531	<	Vector3d c2(0.0, 0.0, 1.0);
532	<	RotMat3x3d rotMatrix;
533	<	RotMat3x3d rotTrans;
534	<	AtomInfo* atomInfo;
535	<	Vector3d pos;
536	<	Vector3d newVec;
537	<	Vector3d dVec;
538	<	Quat4d q;
539	<	AtomData* atomData;
540	<	GenericData* data;
541	<	bool haveAtomData;
542	<
543	<	//if atom is not GBlipid atom, just skip it
544	<	if(!isGBLipidAtom(datom->getType()))
545	<	return;
546	<
547	<	data = datom->getPropertyByName("ATOMDATA");
548	<	if(data != NULL){
549	<	atomData = dynamic_cast<AtomData*>(data);
550	<	if(atomData == NULL){
551	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
552	<	atomData = new AtomData;
553	<	haveAtomData = false;
554	<	} else {
555	<	haveAtomData = true;
556	<	}
557	<	} else {
558	<	atomData = new AtomData;
559	<	haveAtomData = false;
560	<	}
561	<
562	<
563	<	pos = datom->getPos();
564	<	q = datom->getQ();
565	<	rotMatrix = datom->getA();
566	<
567	<	// We need A^T to convert from body-fixed to space-fixed:
568	<	rotTrans = rotMatrix.transpose();
569	<
570	<	newVec = rotTrans * c1;
571	<	dVec = rotTrans * c2;
572	<	atomInfo = new AtomInfo;
573	<	atomInfo->atomTypeName = "GB";
574	<	atomInfo->pos[0] = pos[0] + newVec[0];
575	<	atomInfo->pos[1] = pos[1] + newVec[1];
576	<	atomInfo->pos[2] = pos[2] + newVec[2];
577	<	atomInfo->dipole[0] = dVec[0];
578	<	atomInfo->dipole[1] = dVec[1];
579	<	atomInfo->dipole[2] = dVec[2];
580	<	atomInfo->hasVector = true;
581	<	atomInfo->charge = 3.0;
582	<	atomInfo->hasCharge = true;
583	<	atomData->addAtomInfo(atomInfo);
584	<
585	<	//newVec = rotTrans * c2;
586	<	//atomInfo = new AtomInfo;
587	<	//atomInfo->atomTypeName = "K";
588	<	//atomInfo->pos[0] = pos[0] + newVec[0];
589	<	//atomInfo->pos[1] = pos[1] + newVec[1];
590	<	//atomInfo->pos[2] = pos[2] + newVec[2];
591	<	//atomInfo->dipole[0] = 0.0;
592	<	//atomInfo->dipole[1] = 0.0;
593	<	//atomInfo->dipole[2] = 0.0;
594	<	//atomData->addAtomInfo(atomInfo);
595	<
596	<	//newVec = rotTrans * c3;
597	<	//atomInfo = new AtomInfo;
598	<	//atomInfo->atomTypeName = "K";
599	<	//atomInfo->pos[0] = pos[0] + newVec[0];
600	<	//atomInfo->pos[1] = pos[1] + newVec[1];
601	<	//atomInfo->pos[2] = pos[2] + newVec[2];
602	<	//atomInfo->dipole[0] = 0.0;
603	<	//atomInfo->dipole[1] = 0.0;
604	<	//atomInfo->dipole[2] = 0.0;
605	<	//atomData->addAtomInfo(atomInfo);
606	<
607	<	//newVec = rotTrans * c4;
608	<	//atomInfo = new AtomInfo;
609	<	//atomInfo->atomTypeName = "K";
610	<	//atomInfo->pos[0] = pos[0] + newVec[0];
611	<	//atomInfo->pos[1] = pos[1] + newVec[1];
612	<	//atomInfo->pos[2] = pos[2] + newVec[2];
613	<	//atomInfo->dipole[0] = 0.0;
614	<	//atomInfo->dipole[1] = 0.0;
615	<	//atomInfo->dipole[2] = 0.0;
616	<	//atomData->addAtomInfo(atomInfo);
617	<
618	<	//add atom data into atom's property
619	<
620	<	if(!haveAtomData){
621	<	atomData->setID("ATOMDATA");
622	<	datom->addProperty(atomData);
623	<	}
624	<
625	<	setVisited(datom);
626	<
627	<	}
628	<
629	<	const std::string GBLipidAtomVisitor::toString(){
630	<	char buffer[65535];
631	<	std::string result;
632	<
633	<	sprintf(buffer ,"------------------------------------------------------------------\n");
634	<	result += buffer;
635	<
636	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
637	<	result += buffer;
638	<
639	<	sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
640	<	result += buffer;
641	<
642	<	sprintf(buffer ,"------------------------------------------------------------------\n");
643	<	result += buffer;
644	<
645	<	return result;
646	<	}
647	<
648	<	bool Ring5gbAtomVisitor::isRing5gbAtom(const std::string& atomType){
649	<	std::set<std::string>::iterator strIter;
650	<	strIter = Ring5gbAtomType.find(atomType);
651	<
652	<	return strIter != Ring5gbAtomType.end() ? true : false;
653	<	}
654	<
655	<	void Ring5gbAtomVisitor::visit(DirectionalAtom* datom){
656	<	std::vector<AtomInfo*> atoms;
657	<	//we need to convert linear into 4 different atoms
658	<	Vector3d c1(0.0, 0.0, -5.5);
659	<	Vector3d c2(0.0, 0.0, -1.8);
660	<	Vector3d c3(0.0, 0.0,  1.8);
661	<	Vector3d c4(0.0, 0.0,  5.5);
662	<	RotMat3x3d rotMatrix;
663	<	RotMat3x3d rotTrans;
664	<	AtomInfo* atomInfo;
665	<	Vector3d pos;
666	<	Vector3d newVec;
667	<	Vector3d dVec;
668	<	Quat4d q;
669	<	AtomData* atomData;
670	<	GenericData* data;
671	<	bool haveAtomData;
672	<
673	<	//if atom is not Ring5GB atom, just skip it
674	<	if(!isRing5gbAtom(datom->getType()))
675	<	return;
676	<
677	<	data = datom->getPropertyByName("ATOMDATA");
678	<	if(data != NULL){
679	<	atomData = dynamic_cast<AtomData*>(data);
680	<	if(atomData == NULL){
681	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
682	<	atomData = new AtomData;
683	<	haveAtomData = false;
684	<	} else {
685	<	haveAtomData = true;
686	<	}
687	<	} else {
688	<	atomData = new AtomData;
689	<	haveAtomData = false;
690	<	}
691	<
692	<
693	<	pos = datom->getPos();
694	<	q = datom->getQ();
695	<	rotMatrix = datom->getA();
696	<
697	<	// We need A^T to convert from body-fixed to space-fixed:
698	<	rotTrans = rotMatrix.transpose();
699	<
700	<	newVec = rotTrans * c1;
701	<	atomInfo = new AtomInfo;
702	<	atomInfo->atomTypeName = "K";
703	<	atomInfo->pos[0] = pos[0] + newVec[0];
704	<	atomInfo->pos[1] = pos[1] + newVec[1];
705	<	atomInfo->pos[2] = pos[2] + newVec[2];
706	<	atomInfo->dipole[0] = 0.0;
707	<	atomInfo->dipole[1] = 0.0;
708	<	atomInfo->dipole[2] = 0.0;
709	<	atomData->addAtomInfo(atomInfo);
710	<
711	<	newVec = rotTrans * c2;
712	<	atomInfo = new AtomInfo;
713	<	atomInfo->atomTypeName = "K";
714	<	atomInfo->pos[0] = pos[0] + newVec[0];
715	<	atomInfo->pos[1] = pos[1] + newVec[1];
716	<	atomInfo->pos[2] = pos[2] + newVec[2];
717	<	atomInfo->dipole[0] = 0.0;
718	<	atomInfo->dipole[1] = 0.0;
719	<	atomInfo->dipole[2] = 0.0;
720	<	atomData->addAtomInfo(atomInfo);
721	<
722	<	newVec = rotTrans * c3;
723	<	atomInfo = new AtomInfo;
724	<	atomInfo->atomTypeName = "K";
725	<	atomInfo->pos[0] = pos[0] + newVec[0];
726	<	atomInfo->pos[1] = pos[1] + newVec[1];
727	<	atomInfo->pos[2] = pos[2] + newVec[2];
728	<	atomInfo->dipole[0] = 0.0;
729	<	atomInfo->dipole[1] = 0.0;
730	<	atomInfo->dipole[2] = 0.0;
731	<	atomData->addAtomInfo(atomInfo);
732	<
733	<	newVec = rotTrans * c4;
734	<	atomInfo = new AtomInfo;
735	<	atomInfo->atomTypeName = "K";
736	<	atomInfo->pos[0] = pos[0] + newVec[0];
737	<	atomInfo->pos[1] = pos[1] + newVec[1];
738	<	atomInfo->pos[2] = pos[2] + newVec[2];
739	<	atomInfo->dipole[0] = 0.0;
740	<	atomInfo->dipole[1] = 0.0;
741	<	atomInfo->dipole[2] = 0.0;
742	<	atomData->addAtomInfo(atomInfo);
743	<
744	<	//add atom data into atom's property
745	<
746	<	if(!haveAtomData){
747	<	atomData->setID("ATOMDATA");
748	<	datom->addProperty(atomData);
749	<	}
750	<
751	<	setVisited(datom);
752	<
753	<	}
754	<
755	<	const std::string Ring5gbAtomVisitor::toString(){
756	<	char buffer[65535];
757	<	std::string result;
758	<
759	<	sprintf(buffer ,"------------------------------------------------------------------\n");
760	<	result += buffer;
761	<
762	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
763	<	result += buffer;
764	<
765	<	sprintf(buffer , "Visitor Description: Convert Ring5GB into 4 different K atoms\n");
766	<	result += buffer;
767	<
768	<	sprintf(buffer ,"------------------------------------------------------------------\n");
769	<	result += buffer;
770	<
771	<	return result;
772	<	}
773	<
774	<	bool HeadAtomVisitor::isHeadAtom(const std::string& atomType){
775	<	std::set<std::string>::iterator strIter;
776	<	strIter = HeadAtomType.find(atomType);
777	<
778	<	return strIter != HeadAtomType.end() ? true : false;
779	<	}
780	<
781	<	void HeadAtomVisitor::visit(DirectionalAtom* datom){
782	<	std::vector<AtomInfo*> atoms;
783	<	//we need to convert linear into 2 different atoms
784	<	Vector3d c1(0.0, 0.0, -1.5);
785	<	Vector3d c2(0.0, 0.0, 1.5);
786	<	RotMat3x3d rotMatrix;
787	<	RotMat3x3d rotTrans;
788	<	AtomInfo* atomInfo;
789	<	Vector3d pos;
790	<	Vector3d newVec;
791	<	Vector3d dVec;
792	<	Quat4d q;
793	<	AtomData* atomData;
794	<	GenericData* data;
795	<	bool haveAtomData;
796	<
797	<	//if atom is not Head atom, just skip it
798	<	if(!isHeadAtom(datom->getType()))
799	<	return;
800	<
801	<	data = datom->getPropertyByName("ATOMDATA");
802	<	if(data != NULL){
803	<	atomData = dynamic_cast<AtomData*>(data);
804	<	if(atomData == NULL){
805	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
806	<	atomData = new AtomData;
807	<	haveAtomData = false;
808	<	} else {
809	<	haveAtomData = true;
810	<	}
811	<	} else {
812	<	atomData = new AtomData;
813	<	haveAtomData = false;
814	<	}
815	<
816	<
817	<	pos = datom->getPos();
818	<	q = datom->getQ();
819	<	rotMatrix = datom->getA();
820	<
821	<	// We need A^T to convert from body-fixed to space-fixed:
822	<	rotTrans = rotMatrix.transpose();
823	<
824	<	newVec = rotTrans * c1;
825	<	atomInfo = new AtomInfo;
826	<	atomInfo->atomTypeName = "C";
827	<	atomInfo->pos[0] = pos[0] + newVec[0];
828	<	atomInfo->pos[1] = pos[1] + newVec[1];
829	<	atomInfo->pos[2] = pos[2] + newVec[2];
830	<	atomInfo->dipole[0] = 0.0;
831	<	atomInfo->dipole[1] = 0.0;
832	<	atomInfo->dipole[2] = 0.0;
833	<	atomData->addAtomInfo(atomInfo);
834	<
835	<	newVec = rotTrans * c2;
836	<	atomInfo = new AtomInfo;
837	<	atomInfo->atomTypeName = "O";
838	<	atomInfo->pos[0] = pos[0] + newVec[0];
839	<	atomInfo->pos[1] = pos[1] + newVec[1];
840	<	atomInfo->pos[2] = pos[2] + newVec[2];
841	<	atomInfo->dipole[0] = 0.0;
842	<	atomInfo->dipole[1] = 0.0;
843	<	atomInfo->dipole[2] = 0.0;
844	<	atomData->addAtomInfo(atomInfo);
845	<
846	<	//add atom data into atom's property
847	<
848	<	if(!haveAtomData){
849	<	atomData->setID("ATOMDATA");
850	<	datom->addProperty(atomData);
851	<	}
852	<
853	<	setVisited(datom);
854	<
855	<	}
856	<
857	<	const std::string HeadAtomVisitor::toString(){
858	<	char buffer[65535];
859	<	std::string result;
860	<
861	<	sprintf(buffer ,"------------------------------------------------------------------\n");
862	<	result += buffer;
863	<
864	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
865	<	result += buffer;
866	<
867	<	sprintf(buffer , "Visitor Description: Convert HEAD into C atom and O atom\n");
868	<	result += buffer;
869	<
870	<	sprintf(buffer ,"------------------------------------------------------------------\n");
871	<	result += buffer;
872	<
873	<	return result;
874	<	}
875	<
876	<
877	<	//----------------------------------------------------------------------------//
878	<
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;
888	–
889	–	atomData = new AtomData;
890	–	atomData->setID("ATOMDATA");
891	–
892	–	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;
912	<	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()) {
921	<	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];
932	<	atomInfo->dipole[1] = u[1];
933	<	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 944 | Line 191 | namespace oopse {
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 955 | Line 202 | namespace oopse {
202		result += buffer;
203
204		sprintf(buffer,
205	<	"------------------------------------------------------------------\n");
205	>	"--------------------------------------------------------------\n");
206		result += buffer;
207
208		return result;
209		}
210	<	} //namespace oopse
210	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1219 by xsun, Wed Jan 23 21:23:32 2008 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
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