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Comparing trunk/src/visitors/AtomVisitor.cpp (file contents):
Revision 992 by chrisfen, Wed Jun 21 18:28:27 2006 UTC vs.
Revision 1456 by gezelter, Fri Jun 25 17:40:24 2010 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		#include <cstring>
#	Line 44 | Line 44
44		#include "primitives/DirectionalAtom.hpp"
45		#include "primitives/RigidBody.hpp"
46
47	<	namespace oopse {
47	>	namespace OpenMD {
48		void BaseAtomVisitor::visit(RigidBody *rb) {
49		//vector<Atom*> myAtoms;
50		//vector<Atom*>::iterator atomIter;
#	Line 71 | Line 71 | namespace oopse {
71		GenericData *data;
72		data = atom->getPropertyByName("VISITED");
73		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 differnet atoms
86	–	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
87	–	//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	–	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
218	–	std::set<std::string>::iterator strIter;
219	–	strIter = linearAtomType.find(atomType);
220	–
221	–	return strIter != linearAtomType.end() ? true : false;
222	–	}
223	–
224	–	void LinearAtomVisitor::addGayBerneAtomType(const std::string& atomType){
225	–	linearAtomType.insert(atomType);
226	–	}
227	–
228	–	void LinearAtomVisitor::visit(DirectionalAtom* datom){
229	–	std::vector<AtomInfo*> atoms;
230	–	//we need to convert linear into 4 different atoms
231	–	Vector3d c1(0.0, 0.0, -1.8);
232	–	Vector3d c2(0.0, 0.0, -0.6);
233	–	Vector3d c3(0.0, 0.0,  0.6);
234	–	Vector3d c4(0.0, 0.0,  1.8);
235	–	RotMat3x3d rotMatrix;
236	–	RotMat3x3d rotTrans;
237	–	AtomInfo* atomInfo;
238	–	Vector3d pos;
239	–	Vector3d newVec;
240	–	Quat4d q;
241	–	AtomData* atomData;
242	–	GenericData* data;
243	–	bool haveAtomData;
244	–	AtomType* atomType;
245	–	//if atom is not SSD atom, just skip it
246	–	if(!isLinearAtom(datom->getType()) || !datom->getAtomType()->isGayBerne())
247	–	return;
248	–
249	–	//setup GayBerne type in fortran side
250	–	data = datom->getAtomType()->getPropertyByName("GayBerne");
251	–	if (data != NULL) {
252	–	GayBerneParamGenericData* gayBerneData = dynamic_cast<GayBerneParamGenericData*>(data);
253	–
254	–	if (gayBerneData != NULL) {
255	–	GayBerneParam gayBerneParam = gayBerneData->getData();
256	–
257	–	// double halfLen = gayBerneParam.GB_sigma * gayBerneParam.GB_l2b_ratio/2.0;
258	–	double halfLen = gayBerneParam.GB_l/2.0;
259	–	c1[2] = -halfLen;
260	–	c2[2] = -halfLen /2;
261	–	c3[2] = halfLen/2;
262	–	c4[2] = halfLen;
263	–
264	–	}
265	–
266	–	else {
267	–	sprintf( painCave.errMsg,
268	–	"Can not cast GenericData to GayBerneParam\n");
269	–	painCave.severity = OOPSE_ERROR;
270	–	painCave.isFatal = 1;
271	–	simError();
272	–	}
273	–	}
274	–
275	–
276	–	data = datom->getPropertyByName("ATOMDATA");
277	–	if(data != NULL){
278	–	atomData = dynamic_cast<AtomData*>(data);
279	–	if(atomData == NULL){
280	–	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
281	–	atomData = new AtomData;
282	–	haveAtomData = false;
283	–	} else {
284	–	haveAtomData = true;
285	–	}
286	–	} else {
287	–	atomData = new AtomData;
288	–	haveAtomData = false;
289	–	}
290	–
291	–
292	–	pos = datom->getPos();
293	–	q = datom->getQ();
294	–	rotMatrix = datom->getA();
295	–
296	–	// We need A^T to convert from body-fixed to space-fixed:
297	–	rotTrans = rotMatrix.transpose();
298	–
299	–	newVec = rotTrans * c1;
300	–	atomInfo = new AtomInfo;
301	–	atomInfo->atomTypeName = "C";
302	–	atomInfo->pos[0] = pos[0] + newVec[0];
303	–	atomInfo->pos[1] = pos[1] + newVec[1];
304	–	atomInfo->pos[2] = pos[2] + newVec[2];
305	–	atomInfo->dipole[0] = 0.0;
306	–	atomInfo->dipole[1] = 0.0;
307	–	atomInfo->dipole[2] = 0.0;
308	–	atomData->addAtomInfo(atomInfo);
309	–
310	–	newVec = rotTrans * c2;
311	–	atomInfo = new AtomInfo;
312	–	atomInfo->atomTypeName = "C";
313	–	atomInfo->pos[0] = pos[0] + newVec[0];
314	–	atomInfo->pos[1] = pos[1] + newVec[1];
315	–	atomInfo->pos[2] = pos[2] + newVec[2];
316	–	atomInfo->dipole[0] = 0.0;
317	–	atomInfo->dipole[1] = 0.0;
318	–	atomInfo->dipole[2] = 0.0;
319	–	atomData->addAtomInfo(atomInfo);
320	–
321	–	newVec = rotTrans * c3;
322	–	atomInfo = new AtomInfo;
323	–	atomInfo->atomTypeName = "C";
324	–	atomInfo->pos[0] = pos[0] + newVec[0];
325	–	atomInfo->pos[1] = pos[1] + newVec[1];
326	–	atomInfo->pos[2] = pos[2] + newVec[2];
327	–	atomInfo->dipole[0] = 0.0;
328	–	atomInfo->dipole[1] = 0.0;
329	–	atomInfo->dipole[2] = 0.0;
330	–	atomData->addAtomInfo(atomInfo);
331	–
332	–	newVec = rotTrans * c4;
333	–	atomInfo = new AtomInfo;
334	–	atomInfo->atomTypeName = "C";
335	–	atomInfo->pos[0] = pos[0] + newVec[0];
336	–	atomInfo->pos[1] = pos[1] + newVec[1];
337	–	atomInfo->pos[2] = pos[2] + newVec[2];
338	–	atomInfo->dipole[0] = 0.0;
339	–	atomInfo->dipole[1] = 0.0;
340	–	atomInfo->dipole[2] = 0.0;
341	–	atomData->addAtomInfo(atomInfo);
342	–
343	–	//add atom data into atom's property
344	–
345	–	if(!haveAtomData){
346	–	atomData->setID("ATOMDATA");
347	–	datom->addProperty(atomData);
348	–	}
349	–
350	–	setVisited(datom);
351	–
74		}
75
76	<	const std::string LinearAtomVisitor::toString(){
77	<	char buffer[65535];
356	<	std::string result;
357	<
358	<	sprintf(buffer ,"------------------------------------------------------------------\n");
359	<	result += buffer;
360	<
361	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
362	<	result += buffer;
363	<
364	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
365	<	result += buffer;
366	<
367	<	sprintf(buffer ,"------------------------------------------------------------------\n");
368	<	result += buffer;
369	<
370	<	return result;
371	<	}
372	<
373	<	bool GBLipidAtomVisitor::isGBLipidAtom(const std::string& atomType){
374	<	std::set<std::string>::iterator strIter;
375	<	strIter = GBLipidAtomType.find(atomType);
376	<
377	<	return strIter != GBLipidAtomType.end() ? true : false;
378	<	}
379	<
380	<	void GBLipidAtomVisitor::visit(DirectionalAtom* datom){
381	<	std::vector<AtomInfo*> atoms;
382	<	//we need to convert linear into 4 different atoms
383	<	Vector3d c1(0.0, 0.0, -6.25);
384	<	Vector3d c2(0.0, 0.0, -2.1);
385	<	Vector3d c3(0.0, 0.0,  2.1);
386	<	Vector3d c4(0.0, 0.0,  6.25);
387	<	RotMat3x3d rotMatrix;
388	<	RotMat3x3d rotTrans;
389	<	AtomInfo* atomInfo;
390	<	Vector3d pos;
391	<	Vector3d newVec;
392	<	Quat4d q;
393	<	AtomData* atomData;
394	<	GenericData* data;
395	<	bool haveAtomData;
396	<
397	<	//if atom is not GBlipid atom, just skip it
398	<	if(!isGBLipidAtom(datom->getType()))
399	<	return;
400	<
401	<	data = datom->getPropertyByName("ATOMDATA");
402	<	if(data != NULL){
403	<	atomData = dynamic_cast<AtomData*>(data);
404	<	if(atomData == NULL){
405	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
406	<	atomData = new AtomData;
407	<	haveAtomData = false;
408	<	} else {
409	<	haveAtomData = true;
410	<	}
411	<	} else {
412	<	atomData = new AtomData;
413	<	haveAtomData = false;
414	<	}
415	<
416	<
417	<	pos = datom->getPos();
418	<	q = datom->getQ();
419	<	rotMatrix = datom->getA();
420	<
421	<	// We need A^T to convert from body-fixed to space-fixed:
422	<	rotTrans = rotMatrix.transpose();
423	<
424	<	newVec = rotTrans * c1;
425	<	atomInfo = new AtomInfo;
426	<	atomInfo->atomTypeName = "K";
427	<	atomInfo->pos[0] = pos[0] + newVec[0];
428	<	atomInfo->pos[1] = pos[1] + newVec[1];
429	<	atomInfo->pos[2] = pos[2] + newVec[2];
430	<	atomInfo->dipole[0] = 0.0;
431	<	atomInfo->dipole[1] = 0.0;
432	<	atomInfo->dipole[2] = 0.0;
433	<	atomData->addAtomInfo(atomInfo);
434	<
435	<	newVec = rotTrans * c2;
436	<	atomInfo = new AtomInfo;
437	<	atomInfo->atomTypeName = "K";
438	<	atomInfo->pos[0] = pos[0] + newVec[0];
439	<	atomInfo->pos[1] = pos[1] + newVec[1];
440	<	atomInfo->pos[2] = pos[2] + newVec[2];
441	<	atomInfo->dipole[0] = 0.0;
442	<	atomInfo->dipole[1] = 0.0;
443	<	atomInfo->dipole[2] = 0.0;
444	<	atomData->addAtomInfo(atomInfo);
445	<
446	<	newVec = rotTrans * c3;
447	<	atomInfo = new AtomInfo;
448	<	atomInfo->atomTypeName = "K";
449	<	atomInfo->pos[0] = pos[0] + newVec[0];
450	<	atomInfo->pos[1] = pos[1] + newVec[1];
451	<	atomInfo->pos[2] = pos[2] + newVec[2];
452	<	atomInfo->dipole[0] = 0.0;
453	<	atomInfo->dipole[1] = 0.0;
454	<	atomInfo->dipole[2] = 0.0;
455	<	atomData->addAtomInfo(atomInfo);
456	<
457	<	newVec = rotTrans * c4;
458	<	atomInfo = new AtomInfo;
459	<	atomInfo->atomTypeName = "K";
460	<	atomInfo->pos[0] = pos[0] + newVec[0];
461	<	atomInfo->pos[1] = pos[1] + newVec[1];
462	<	atomInfo->pos[2] = pos[2] + newVec[2];
463	<	atomInfo->dipole[0] = 0.0;
464	<	atomInfo->dipole[1] = 0.0;
465	<	atomInfo->dipole[2] = 0.0;
466	<	atomData->addAtomInfo(atomInfo);
467	<
468	<	//add atom data into atom's property
469	<
470	<	if(!haveAtomData){
471	<	atomData->setID("ATOMDATA");
472	<	datom->addProperty(atomData);
473	<	}
474	<
475	<	setVisited(datom);
476	<
477	<	}
478	<
479	<	const std::string GBLipidAtomVisitor::toString(){
480	<	char buffer[65535];
481	<	std::string result;
482	<
483	<	sprintf(buffer ,"------------------------------------------------------------------\n");
484	<	result += buffer;
485	<
486	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
487	<	result += buffer;
488	<
489	<	sprintf(buffer , "Visitor Description: Convert GBlipid into 4 different K atoms\n");
490	<	result += buffer;
491	<
492	<	sprintf(buffer ,"------------------------------------------------------------------\n");
493	<	result += buffer;
494	<
495	<	return result;
496	<	}
497	<
498	<	//----------------------------------------------------------------------------//
499	<
76	>	//------------------------------------------------------------------------//
77	>
78		void DefaultAtomVisitor::visit(Atom *atom) {
79		AtomData *atomData;
80		AtomInfo *atomInfo;
81		Vector3d  pos;
82	+	Vector3d  vel;
83	+	Vector3d  frc;
84	+	Vector3d  u;
85	+	RealType  c;
86
87		if (isVisited(atom))
88		return;
89	<
89	>
90		atomInfo = new AtomInfo;
91	<
91	>
92		atomData = new AtomData;
93		atomData->setID("ATOMDATA");
94	<
94	>
95		pos = atom->getPos();
96	+	vel = atom->getVel();
97	+	frc = atom->getFrc();
98		atomInfo->atomTypeName = atom->getType();
99		atomInfo->pos[0] = pos[0];
100		atomInfo->pos[1] = pos[1];
101		atomInfo->pos[2] = pos[2];
102	<	atomInfo->dipole[0] = 0.0;
103	<	atomInfo->dipole[1] = 0.0;
104	<	atomInfo->dipole[2] = 0.0;
105	<
102	>	atomInfo->vel[0] = vel[0];
103	>	atomInfo->vel[1] = vel[1];
104	>	atomInfo->vel[2] = vel[2];
105	>	atomInfo->hasVelocity = true;
106	>	atomInfo->frc[0] = frc[0];
107	>	atomInfo->frc[1] = frc[1];
108	>	atomInfo->frc[2] = frc[2];
109	>	atomInfo->hasForce = true;
110	>	atomInfo->vec[0] = 0.0;
111	>	atomInfo->vec[1] = 0.0;
112	>	atomInfo->vec[2] = 0.0;
113	>
114		atomData->addAtomInfo(atomInfo);
115	<
115	>
116		atom->addProperty(atomData);
117	<
117	>
118		setVisited(atom);
119		}
120	<
120	>
121		void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
122		AtomData *atomData;
123		AtomInfo *atomInfo;
124		Vector3d  pos;
125	+	Vector3d  vel;
126	+	Vector3d  frc;
127		Vector3d  u;
128	+	RealType  c;
129
130		if (isVisited(datom))
131		return;
132	<
132	>
133		pos = datom->getPos();
134	+	vel = datom->getVel();
135	+	frc = datom->getFrc();
136		if (datom->getAtomType()->isGayBerne()) {
137		u = datom->getA().transpose()*V3Z;
138		} else if (datom->getAtomType()->isMultipole()) {
#	Line 549 | Line 146 | namespace oopse {
146		atomInfo->pos[0] = pos[0];
147		atomInfo->pos[1] = pos[1];
148		atomInfo->pos[2] = pos[2];
149	<	atomInfo->dipole[0] = u[0];
150	<	atomInfo->dipole[1] = u[1];
151	<	atomInfo->dipole[2] = u[2];
149	>	atomInfo->vel[0] = vel[0];
150	>	atomInfo->vel[1] = vel[1];
151	>	atomInfo->vel[2] = vel[2];
152	>	atomInfo->hasVelocity = true;
153	>	atomInfo->frc[0] = frc[0];
154	>	atomInfo->frc[1] = frc[1];
155	>	atomInfo->frc[2] = frc[2];
156	>	atomInfo->hasForce = true;
157	>	atomInfo->vec[0] = u[0];
158	>	atomInfo->vec[1] = u[1];
159	>	atomInfo->vec[2] = u[2];
160	>	atomInfo->hasVector = true;
161
162		atomData->addAtomInfo(atomInfo);
163
#	Line 581 | Line 187 | namespace oopse {
187
188		return result;
189		}
190	<	} //namespace oopse
190	>	} //namespace OpenMD

Comparing trunk/src/visitors/AtomVisitor.cpp (property svn:keywords):
Revision 992 by chrisfen, Wed Jun 21 18:28:27 2006 UTC vs.
Revision 1456 by gezelter, Fri Jun 25 17:40:24 2010 UTC

#	Line 0 | Line 1
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