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

Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 275 by tim, Wed Jan 26 15:15:09 2005 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1873 by gezelter, Fri May 10 16:09:34 2013 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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"
45	–	#include "math/MatVec3.h"
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 {
49	<	void BaseAtomVisitor::visit(RigidBody *rb) {
50	<	//vector<Atom*> myAtoms;
51	<	//vector<Atom*>::iterator atomIter;
52	>	namespace OpenMD {
53
54	<	//myAtoms = rb->getAtoms();
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;
61
62	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
56	<	//  (*atomIter)->accept(this);
57	<	}
62	>	//myAtoms = rb->getAtoms();
63
64	<	void BaseAtomVisitor::setVisited(Atom *atom) {
64	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
65	>	//  (*atomIter)->accept(this);
66	>	}
67	>
68	>	void BaseAtomVisitor::setVisited(Atom *atom) {
69		GenericData *data;
70		data = atom->getPropertyByName("VISITED");
71
72		//if visited property is not existed, add it as new property
73		if (data == NULL) {
74	<	data = new GenericData();
75	<	data->setID("VISITED");
76	<	atom->addProperty(data);
74	>	data = new GenericData();
75	>	data->setID("VISITED");
76	>	atom->addProperty(data);
77		}
78	<	}
78	>	}
79
80	<	bool BaseAtomVisitor::isVisited(Atom *atom) {
80	>	bool BaseAtomVisitor::isVisited(Atom *atom) {
81		GenericData *data;
82		data = atom->getPropertyByName("VISITED");
83		return data == NULL ? false : true;
84	<	}
84	>	}
85
86	<	bool SSDAtomVisitor::isSSDAtom(const std::string&atomType) {
87	<	std::set<std::string>::iterator strIter;
88	<	strIter = ssdAtomType.find(atomType);
89	<	return strIter != ssdAtomType.end() ? true : false;
90	<	}
91	<
92	<	void SSDAtomVisitor::visit(DirectionalAtom *datom) {
93	<	std::vector<AtomInfo*>atoms;
94	<
95	<	//we need to convert SSD into 4 differnet atoms
96	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
97	<	//of the water with a dipole moment
98	<	Vector3d h1(0.0, -0.75695, 0.5206);
99	<	Vector3d h2(0.0, 0.75695, 0.5206);
100	<	Vector3d ox(0.0, 0.0, -0.0654);
101	<	Vector3d u(0, 0, 1);
102	<	RotMat3x3d   rotMatrix;
103	<	RotMat3x3d   rotTrans;
104	<	AtomInfo *   atomInfo;
105	<	Vector3d     pos;
106	<	Vector3d     newVec;
107	<	Quat4d       q;
108	<	AtomData *   atomData;
100	<	GenericData *data;
101	<	bool         haveAtomData;
102	<
103	<	//if atom is not SSD atom, just skip it
104	<	if (!isSSDAtom(datom->getType()))
105	<	return;
106	<
107	<	data = datom->getPropertyByName("ATOMDATA");
108	<
109	<	if (data != NULL) {
110	<	atomData = dynamic_cast<AtomData *>(data);
111	<
112	<	if (atomData == NULL) {
113	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
114	<	atomData = new AtomData;
115	<	haveAtomData = false;
116	<	} else
117	<	haveAtomData = true;
118	<	} else {
119	<	atomData = new AtomData;
120	<	haveAtomData = false;
86	>	//------------------------------------------------------------------------//
87	>
88	>	void DefaultAtomVisitor::visit(Atom *atom) {
89	>	AtomData *atomData;
90	>	AtomInfo *atomInfo;
91	>	AtomType* atype = atom->getAtomType();
92	>
93	>	if (isVisited(atom))
94	>	return;
95	>
96	>	atomInfo = new AtomInfo;
97	>	atomInfo->atomTypeName = atom->getType();
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	<	pos = datom->getPos();
124	<	q = datom->getQ();
125	<	rotMatrix = datom->getA();
126	<
127	<	// We need A^T to convert from body-fixed to space-fixed:
128	<	//transposeMat3(rotMatrix, rotTrans);
129	<	rotTrans = rotMatrix.transpose();
130	<
131	<	//center of mass of the water molecule
132	<	//matVecMul3(rotTrans, u, newVec);
133	<	newVec = rotTrans * u;
134	<
135	<	atomInfo = new AtomInfo;
136	<	atomInfo->AtomType = "X";
137	<	atomInfo->pos[0] = pos[0];
138	<	atomInfo->pos[1] = pos[1];
139	<	atomInfo->pos[2] = pos[2];
140	<	atomInfo->dipole[0] = newVec[0];
141	<	atomInfo->dipole[1] = newVec[1];
142	<	atomInfo->dipole[2] = newVec[2];
143	<
123	>	atomData = new AtomData;
124	>	atomData->setID("ATOMDATA");
125		atomData->addAtomInfo(atomInfo);
126	+
127	+	atom->addProperty(atomData);
128	+
129	+	setVisited(atom);
130	+	}
131	+
132	+	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
133	+	AtomData *atomData;
134	+	AtomInfo *atomInfo;
135	+	AtomType* atype = datom->getAtomType();
136
137	<	//oxygen
138	<	//matVecMul3(rotTrans, ox, newVec);
139	<	newVec = rotTrans * ox;
149	<
137	>	if (isVisited(datom))
138	>	return;
139	>
140		atomInfo = new AtomInfo;
141	<	atomInfo->AtomType = "O";
142	<	atomInfo->pos[0] = pos[0] + newVec[0];
143	<	atomInfo->pos[1] = pos[1] + newVec[1];
144	<	atomInfo->pos[2] = pos[2] + newVec[2];
145	<	atomInfo->dipole[0] = 0.0;
146	<	atomInfo->dipole[1] = 0.0;
157	<	atomInfo->dipole[2] = 0.0;
158	<	atomData->addAtomInfo(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	<	//hydrogen1
149	<	//matVecMul3(rotTrans, h1, newVec);
150	<	newVec = rotTrans * h1;
151	<	atomInfo = new AtomInfo;
152	<	atomInfo->AtomType = "H";
153	<	atomInfo->pos[0] = pos[0] + newVec[0];
154	<	atomInfo->pos[1] = pos[1] + newVec[1];
155	<	atomInfo->pos[2] = pos[2] + newVec[2];
156	<	atomInfo->dipole[0] = 0.0;
157	<	atomInfo->dipole[1] = 0.0;
158	<	atomInfo->dipole[2] = 0.0;
171	<	atomData->addAtomInfo(atomInfo);
172	<
173	<	//hydrogen2
174	<	//matVecMul3(rotTrans, h2, newVec);
175	<	newVec = rotTrans * h2;
176	<	atomInfo = new AtomInfo;
177	<	atomInfo->AtomType = "H";
178	<	atomInfo->pos[0] = pos[0] + newVec[0];
179	<	atomInfo->pos[1] = pos[1] + newVec[1];
180	<	atomInfo->pos[2] = pos[2] + newVec[2];
181	<	atomInfo->dipole[0] = 0.0;
182	<	atomInfo->dipole[1] = 0.0;
183	<	atomInfo->dipole[2] = 0.0;
184	<	atomData->addAtomInfo(atomInfo);
185	<
186	<	//add atom data into atom's property
148	>	FixedChargeAdapter fca = FixedChargeAdapter(atype);
149	>	if ( fca.isFixedCharge() ) {
150	>	atomInfo->hasCharge = true;
151	>	atomInfo->charge = fca.getCharge();
152	>	}
153	>
154	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
155	>	if ( fqa.isFluctuatingCharge() ) {
156	>	atomInfo->hasCharge = true;
157	>	atomInfo->charge += datom->getFlucQPos();
158	>	}
159
160	<	if (!haveAtomData) {
161	<	atomData->setID("ATOMDATA");
162	<	datom->addProperty(atomData);
160	>	if ((storageLayout_ & DataStorage::dslElectricField) &&
161	>	(atype->isElectrostatic())) {
162	>	atomInfo->hasElectricField = true;
163	>	atomInfo->eField = datom->getElectricField();
164		}
165
166	<	setVisited(datom);
167	<	}
168	<
169	<	const std::string SSDAtomVisitor::toString() {
170	<	char   buffer[65535];
171	<	std::string result;
172	<
173	<	sprintf(buffer,
174	<	"------------------------------------------------------------------\n");
175	<	result += buffer;
176	<
177	<	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
205	<	result += buffer;
206	<
207	<	sprintf(buffer,
208	<	"Visitor Description: Convert SSD into 4 different atoms\n");
209	<	result += buffer;
210	<
211	<	sprintf(buffer,
212	<	"------------------------------------------------------------------\n");
213	<	result += buffer;
214	<
215	<	return result;
216	<	}
217	<
218	<	bool LinearAtomVisitor::isLinearAtom(const std::string& atomType){
219	<	std::set<std::string>::iterator strIter;
220	<	strIter = linearAtomType.find(atomType);
221	<
222	<	return strIter != linearAtomType.end() ? true : false;
223	<	}
224	<
225	<	void LinearAtomVisitor::visit(DirectionalAtom* datom){
226	<	std::vector<AtomInfo*> atoms;
227	<	//we need to convert linear into 4 different atoms
228	<	Vector3d c1(0.0, 0.0, -1.8);
229	<	Vector3d c2(0.0, 0.0, -0.6);
230	<	Vector3d c3(0.0, 0.0,  0.6);
231	<	Vector3d c4(0.0, 0.0,  1.8);
232	<	RotMat3x3d rotMatrix;
233	<	RotMat3x3d rotTrans;
234	<	AtomInfo* atomInfo;
235	<	Vector3d pos;
236	<	Vector3d newVec;
237	<	Quat4d q;
238	<	AtomData* atomData;
239	<	GenericData* data;
240	<	bool haveAtomData;
241	<
242	<	//if atom is not SSD atom, just skip it
243	<	if(!isLinearAtom(datom->getType()))
244	<	return;
245	<
246	<	data = datom->getPropertyByName("ATOMDATA");
247	<	if(data != NULL){
248	<	atomData = dynamic_cast<AtomData*>(data);
249	<	if(atomData == NULL){
250	<	std::cerr << "can not get Atom Data from " << datom->getType() << std::endl;
251	<	atomData = new AtomData;
252	<	haveAtomData = false;
253	<	} else {
254	<	haveAtomData = true;
255	<	}
256	<	} else {
257	<	atomData = new AtomData;
258	<	haveAtomData = false;
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		}
260	–
261	–
262	–	pos = datom->getPos();
263	–	q = datom->getQ();
264	–	rotMatrix = datom->getA();
179
266	–	// We need A^T to convert from body-fixed to space-fixed:
267	–	rotTrans = rotMatrix.transpose();
268	–
269	–	newVec = rotTrans * c1;
270	–	atomInfo = new AtomInfo;
271	–	atomInfo->AtomType = "C";
272	–	atomInfo->pos[0] = pos[0] + newVec[0];
273	–	atomInfo->pos[1] = pos[1] + newVec[1];
274	–	atomInfo->pos[2] = pos[2] + newVec[2];
275	–	atomInfo->dipole[0] = 0.0;
276	–	atomInfo->dipole[1] = 0.0;
277	–	atomInfo->dipole[2] = 0.0;
278	–	atomData->addAtomInfo(atomInfo);
279	–
280	–	newVec = rotTrans * c2;
281	–	atomInfo = new AtomInfo;
282	–	atomInfo->AtomType = "C";
283	–	atomInfo->pos[0] = pos[0] + newVec[0];
284	–	atomInfo->pos[1] = pos[1] + newVec[1];
285	–	atomInfo->pos[2] = pos[2] + newVec[2];
286	–	atomInfo->dipole[0] = 0.0;
287	–	atomInfo->dipole[1] = 0.0;
288	–	atomInfo->dipole[2] = 0.0;
289	–	atomData->addAtomInfo(atomInfo);
290	–
291	–	newVec = rotTrans * c3;
292	–	atomInfo = new AtomInfo;
293	–	atomInfo->AtomType = "C";
294	–	atomInfo->pos[0] = pos[0] + newVec[0];
295	–	atomInfo->pos[1] = pos[1] + newVec[1];
296	–	atomInfo->pos[2] = pos[2] + newVec[2];
297	–	atomInfo->dipole[0] = 0.0;
298	–	atomInfo->dipole[1] = 0.0;
299	–	atomInfo->dipole[2] = 0.0;
300	–	atomData->addAtomInfo(atomInfo);
301	–
302	–	newVec = rotTrans * c4;
303	–	atomInfo = new AtomInfo;
304	–	atomInfo->AtomType = "C";
305	–	atomInfo->pos[0] = pos[0] + newVec[0];
306	–	atomInfo->pos[1] = pos[1] + newVec[1];
307	–	atomInfo->pos[2] = pos[2] + newVec[2];
308	–	atomInfo->dipole[0] = 0.0;
309	–	atomInfo->dipole[1] = 0.0;
310	–	atomInfo->dipole[2] = 0.0;
311	–	atomData->addAtomInfo(atomInfo);
312	–
313	–	//add atom data into atom's property
314	–
315	–	if(!haveAtomData){
316	–	atomData->setID("ATOMDATA");
317	–	datom->addProperty(atomData);
318	–	}
319	–
320	–	setVisited(datom);
321	–
322	–	}
323	–
324	–	const std::string LinearAtomVisitor::toString(){
325	–	char buffer[65535];
326	–	std::string result;
327	–
328	–	sprintf(buffer ,"------------------------------------------------------------------\n");
329	–	result += buffer;
330	–
331	–	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
332	–	result += buffer;
333	–
334	–	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
335	–	result += buffer;
336	–
337	–	sprintf(buffer ,"------------------------------------------------------------------\n");
338	–	result += buffer;
339	–
340	–	return result;
341	–	}
342	–
343	–	//----------------------------------------------------------------------------//
344	–
345	–	void DefaultAtomVisitor::visit(Atom *atom) {
346	–	AtomData *atomData;
347	–	AtomInfo *atomInfo;
348	–	Vector3d  pos;
349	–
350	–	if (isVisited(atom))
351	–	return;
352	–
353	–	atomInfo = new AtomInfo;
354	–
180		atomData = new AtomData;
181	<	atomData->setID("ATOMDATA");
357	<
358	<	pos = atom->getPos();
359	<	atomInfo->AtomType = atom->getType();
360	<	atomInfo->pos[0] = pos[0];
361	<	atomInfo->pos[1] = pos[1];
362	<	atomInfo->pos[2] = pos[2];
363	<	atomInfo->dipole[0] = 0.0;
364	<	atomInfo->dipole[1] = 0.0;
365	<	atomInfo->dipole[2] = 0.0;
366	<
181	>	atomData->setID("ATOMDATA");
182		atomData->addAtomInfo(atomInfo);
183
369	–	atom->addProperty(atomData);
370	–
371	–	setVisited(atom);
372	–	}
373	–
374	–	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
375	–	AtomData *atomData;
376	–	AtomInfo *atomInfo;
377	–	Vector3d  pos;
378	–	Vector3d  u;
379	–
380	–	if (isVisited(datom))
381	–	return;
382	–
383	–	pos = datom->getPos();
384	–	u = datom->getElectroFrame().getColumn(2);
385	–
386	–	atomData = new AtomData;
387	–	atomData->setID("ATOMDATA");
388	–	atomInfo = new AtomInfo;
389	–
390	–	atomInfo->AtomType = datom->getType();
391	–	atomInfo->pos[0] = pos[0];
392	–	atomInfo->pos[1] = pos[1];
393	–	atomInfo->pos[2] = pos[2];
394	–	atomInfo->dipole[0] = u[0];
395	–	atomInfo->dipole[1] = u[1];
396	–	atomInfo->dipole[2] = u[2];
397	–
398	–	atomData->addAtomInfo(atomInfo);
399	–
184		datom->addProperty(atomData);
185
186		setVisited(datom);
187	<	}
187	>	}
188
189	<	const std::string DefaultAtomVisitor::toString() {
189	>	const std::string DefaultAtomVisitor::toString() {
190		char   buffer[65535];
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 418 | Line 202 | const std::string DefaultAtomVisitor::toString() {
202		result += buffer;
203
204		sprintf(buffer,
205	<	"------------------------------------------------------------------\n");
205	>	"--------------------------------------------------------------\n");
206		result += buffer;
207
208		return result;
209	<	}
210	<	} //namespace oopse
209	>	}
210	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 275 by tim, Wed Jan 26 15:15:09 2005 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1873 by gezelter, Fri May 10 16:09:34 2013 UTC

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