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

Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 211 by chrisfen, Fri Nov 5 21:45:14 2004 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	+	/*
2	+	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3	+	*
4	+	* The University of Notre Dame grants you ("Licensee") a
5	+	* non-exclusive, royalty free, license to use, modify and
6	+	* redistribute this software in source and binary code form, provided
7	+	* that the following conditions are met:
8	+	*
9	+	* 1. Redistributions of source code must retain the above copyright
10	+	*    notice, this list of conditions and the following disclaimer.
11	+	*
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.
16	+	*
17	+	* This software is provided "AS IS," without a warranty of any
18	+	* kind. All express or implied conditions, representations and
19	+	* warranties, including any implied warranty of merchantability,
20	+	* fitness for a particular purpose or non-infringement, are hereby
21	+	* excluded.  The University of Notre Dame and its licensors shall not
22	+	* be liable for any damages suffered by licensee as a result of
23	+	* using, modifying or distributing the software or its
24	+	* derivatives. In no event will the University of Notre Dame or its
25	+	* licensors be liable for any lost revenue, profit or data, or for
26	+	* direct, indirect, special, consequential, incidental or punitive
27	+	* damages, however caused and regardless of the theory of liability,
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"
4	–	#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 {
52	>	namespace OpenMD {
53
54	<	void BaseAtomVisitor::visit(RigidBody* rb){
55	<	//vector<Atom*> myAtoms;
56	<	//vector<Atom*>::iterator atomIter;
12	<
13	<	//myAtoms = rb->getAtoms();
54	>	BaseAtomVisitor::BaseAtomVisitor(SimInfo* info) : BaseVisitor() {
55	>	storageLayout_ = info->getStorageLayout();
56	>	}
57
58	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
59	<	//  (*atomIter)->accept(this);
60	<	}
58	>	void BaseAtomVisitor::visit(RigidBody *rb) {
59	>	//vector<Atom*> myAtoms;
60	>	//vector<Atom*>::iterator atomIter;
61
62	<	void BaseAtomVisitor::setVisited(Atom* atom){
20	<	GenericData* data;
21	<	data = atom->getProperty("VISITED");
62	>	//myAtoms = rb->getAtoms();
63
64	<	//if visited property is not existed, add it as new property
65	<	if(data == NULL){
25	<	data = new GenericData();
26	<	data->setID("VISITED");
27	<	atom->addProperty(data);
64	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
65	>	//  (*atomIter)->accept(this);
66		}
29	–	}
67
68	<	bool BaseAtomVisitor::isVisited(Atom* atom){
69	<	GenericData* data;
70	<	data = atom->getProperty("VISITED");
34	<	return data == NULL ?  false : true;
35	<	}
68	>	void BaseAtomVisitor::setVisited(Atom *atom) {
69	>	GenericData *data;
70	>	data = atom->getPropertyByName("VISITED");
71
72	<	bool SSDAtomVisitor::isSSDAtom(const string& atomType){
73	<	vector<string>::iterator strIter;
74	<
75	<	for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
76	<	if(*strIter == atomType)
77	<	return true;
78	<
44	<	return false;
45	<	}
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);
77	>	}
78	>	}
79
80	<	void SSDAtomVisitor::visit(DirectionalAtom* datom){
80	>	bool BaseAtomVisitor::isVisited(Atom *atom) {
81	>	GenericData *data;
82	>	data = atom->getPropertyByName("VISITED");
83	>	return data == NULL ? false : true;
84	>	}
85
86	<	vector<AtomInfo*> atoms;
87	<
88	<	//we need to convert SSD into 4 differnet atoms
89	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
90	<	//of the water with a dipole moment
91	<	double h1[3] = {0.0, -0.75695, 0.5206};
92	<	double h2[3] = {0.0, 0.75695, 0.5206};
93	<	double ox[3] = {0.0, 0.0, -0.0654};
94	<	double u[3] = {0, 0, 1};
95	<	double rotMatrix[3][3];
96	<	double rotTrans[3][3];
97	<	AtomInfo* atomInfo;
98	<	double pos[3];
99	<	double newVec[3];
100	<	double q[4];
101	<	AtomData* atomData;
102	<	GenericData* data;
103	<	bool haveAtomData;
104	<
105	<	//if atom is not SSD atom, just skip it
106	<	if(!isSSDAtom(datom->getType()))
107	<	return;
108	<
72	<	data = datom->getProperty("ATOMDATA");
73	<	if(data != NULL){
74	<
75	<	atomData = dynamic_cast<AtomData*>(data);
76	<	if(atomData == NULL){
77	<	cerr << "can not get Atom Data from " << datom->getType() << endl;
78	<	atomData = new AtomData;
79	<	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	<	else
111	<	haveAtomData = true;
112	<	}
113	<	else{
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	<	haveAtomData = false;
124	>	atomData->setID("ATOMDATA");
125	>	atomData->addAtomInfo(atomInfo);
126	>
127	>	atom->addProperty(atomData);
128	>
129	>	setVisited(atom);
130		}
88	–
131
132	<	datom->getPos(pos);
133	<	datom->getQ(q);
134	<	datom->getA(rotMatrix);
132	>	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
133	>	AtomData *atomData;
134	>	AtomInfo *atomInfo;
135	>	AtomType* atype = datom->getAtomType();
136
137	<	// We need A^T to convert from body-fixed to space-fixed:
138	<	transposeMat3(rotMatrix, rotTrans);
139	<
140	<	//center of mass of the water molecule
141	<	matVecMul3(rotTrans, u, newVec);
142	<	atomInfo = new AtomInfo;
143	<	atomInfo->AtomType = "X";
144	<	atomInfo->pos[0] = pos[0];
145	<	atomInfo->pos[1] = pos[1];
146	<	atomInfo->pos[2] = pos[2];
104	<	atomInfo->dipole[0] = newVec[0];
105	<	atomInfo->dipole[1] = newVec[1];
106	<	atomInfo->dipole[2] = newVec[2];
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	<	atomData->addAtomInfo(atomInfo);
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	<	//oxygen
161	<	matVecMul3(rotTrans, ox, newVec);
162	<	atomInfo = new AtomInfo;
163	<	atomInfo->AtomType = "O";
164	<	atomInfo->pos[0] = pos[0] + newVec[0];
115	<	atomInfo->pos[1] = pos[1] + newVec[1];
116	<	atomInfo->pos[2] = pos[2] + newVec[2];
117	<	atomInfo->dipole[0] = 0.0;
118	<	atomInfo->dipole[1] = 0.0;
119	<	atomInfo->dipole[2] = 0.0;
120	<	atomData->addAtomInfo(atomInfo);
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	<	//hydrogen1
181	<	matVecMul3(rotTrans, h1, newVec);
182	<	atomInfo = new AtomInfo;
126	<	atomInfo->AtomType = "H";
127	<	atomInfo->pos[0] = pos[0] + newVec[0];
128	<	atomInfo->pos[1] = pos[1] + newVec[1];
129	<	atomInfo->pos[2] = pos[2] + newVec[2];
130	<	atomInfo->dipole[0] = 0.0;
131	<	atomInfo->dipole[1] = 0.0;
132	<	atomInfo->dipole[2] = 0.0;
133	<	atomData->addAtomInfo(atomInfo);
134	<
135	<	//hydrogen2
136	<	matVecMul3(rotTrans, h2, newVec);
137	<	atomInfo = new AtomInfo;
138	<	atomInfo->AtomType = "H";
139	<	atomInfo->pos[0] = pos[0] + newVec[0];
140	<	atomInfo->pos[1] = pos[1] + newVec[1];
141	<	atomInfo->pos[2] = pos[2] + newVec[2];
142	<	atomInfo->dipole[0] = 0.0;
143	<	atomInfo->dipole[1] = 0.0;
144	<	atomInfo->dipole[2] = 0.0;
145	<	atomData->addAtomInfo(atomInfo);
180	>	atomData = new AtomData;
181	>	atomData->setID("ATOMDATA");
182	>	atomData->addAtomInfo(atomInfo);
183
147	–	//add atom data into atom's property
148	–
149	–	if(!haveAtomData){
150	–	atomData->setID("ATOMDATA");
184		datom->addProperty(atomData);
152	–	}
185
186	<	setVisited(datom);
155	<
156	<	}
157	<
158	<	const string SSDAtomVisitor::toString(){
159	<	char buffer[65535];
160	<	string result;
161	<
162	<	sprintf(buffer ,"------------------------------------------------------------------\n");
163	<	result += buffer;
164	<
165	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
166	<	result += buffer;
167	<
168	<	sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
169	<	result += buffer;
170	<
171	<	sprintf(buffer ,"------------------------------------------------------------------\n");
172	<	result += buffer;
173	<
174	<	return result;
175	<	}
176	<
177	<	bool LinearAtomVisitor::isLinearAtom(const string& atomType){
178	<	vector<string>::iterator strIter;
179	<
180	<	for(strIter = linearAtomType.begin(); strIter != linearAtomType.end();
181	<	++strIter)
182	<	if(*strIter == atomType)
183	<	return true;
184	<
185	<	return false;
186	<	}
187	<
188	<	void LinearAtomVisitor::visit(DirectionalAtom* datom){
189	<
190	<	vector<AtomInfo*> atoms;
191	<
192	<	//we need to convert linear into 4 different atoms
193	<	double c1[3] = {0.0, 0.0, -1.8};
194	<	double c2[3] = {0.0, 0.0, -0.6};
195	<	double c3[3] = {0.0, 0.0,  0.6};
196	<	double c4[3] = {0.0, 0.0,  1.8};
197	<	double rotMatrix[3][3];
198	<	double rotTrans[3][3];
199	<	AtomInfo* atomInfo;
200	<	double pos[3];
201	<	double newVec[3];
202	<	double q[4];
203	<	AtomData* atomData;
204	<	GenericData* data;
205	<	bool haveAtomData;
206	<
207	<	//if atom is not SSD atom, just skip it
208	<	if(!isLinearAtom(datom->getType()))
209	<	return;
210	<
211	<	data = datom->getProperty("ATOMDATA");
212	<	if(data != NULL){
213	<
214	<	atomData = dynamic_cast<AtomData*>(data);
215	<	if(atomData == NULL){
216	<	cerr << "can not get Atom Data from " << datom->getType() << endl;
217	<	atomData = new AtomData;
218	<	haveAtomData = false;
219	<	}
220	<	else
221	<	haveAtomData = true;
186	>	setVisited(datom);
187		}
223	–	else{
224	–	atomData = new AtomData;
225	–	haveAtomData = false;
226	–	}
227	–
228	–
229	–	datom->getPos(pos);
230	–	datom->getQ(q);
231	–	datom->getA(rotMatrix);
188
189	<	// We need A^T to convert from body-fixed to space-fixed:
190	<	transposeMat3(rotMatrix, rotTrans);
191	<
236	<	matVecMul3(rotTrans, c1, newVec);
237	<	atomInfo = new AtomInfo;
238	<	atomInfo->AtomType = "C";
239	<	atomInfo->pos[0] = pos[0] + newVec[0];
240	<	atomInfo->pos[1] = pos[1] + newVec[1];
241	<	atomInfo->pos[2] = pos[2] + newVec[2];
242	<	atomInfo->dipole[0] = 0.0;
243	<	atomInfo->dipole[1] = 0.0;
244	<	atomInfo->dipole[2] = 0.0;
245	<	atomData->addAtomInfo(atomInfo);
189	>	const std::string DefaultAtomVisitor::toString() {
190	>	char   buffer[65535];
191	>	std::string result;
192
193	<	matVecMul3(rotTrans, c2, newVec);
194	<	atomInfo = new AtomInfo;
195	<	atomInfo->AtomType = "C";
250	<	atomInfo->pos[0] = pos[0] + newVec[0];
251	<	atomInfo->pos[1] = pos[1] + newVec[1];
252	<	atomInfo->pos[2] = pos[2] + newVec[2];
253	<	atomInfo->dipole[0] = 0.0;
254	<	atomInfo->dipole[1] = 0.0;
255	<	atomInfo->dipole[2] = 0.0;
256	<	atomData->addAtomInfo(atomInfo);
193	>	sprintf(buffer,
194	>	"--------------------------------------------------------------\n");
195	>	result += buffer;
196
197	<	matVecMul3(rotTrans, c3, newVec);
198	<	atomInfo = new AtomInfo;
260	<	atomInfo->AtomType = "C";
261	<	atomInfo->pos[0] = pos[0] + newVec[0];
262	<	atomInfo->pos[1] = pos[1] + newVec[1];
263	<	atomInfo->pos[2] = pos[2] + newVec[2];
264	<	atomInfo->dipole[0] = 0.0;
265	<	atomInfo->dipole[1] = 0.0;
266	<	atomInfo->dipole[2] = 0.0;
267	<	atomData->addAtomInfo(atomInfo);
197	>	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
198	>	result += buffer;
199
200	<	matVecMul3(rotTrans, c4, newVec);
201	<	atomInfo = new AtomInfo;
202	<	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);
200	>	sprintf(buffer,
201	>	"Visitor Description: copy atom infomation into atom data\n");
202	>	result += buffer;
203
204	<	//add atom data into atom's property
204	>	sprintf(buffer,
205	>	"--------------------------------------------------------------\n");
206	>	result += buffer;
207
208	<	if(!haveAtomData){
283	<	atomData->setID("ATOMDATA");
284	<	datom->addProperty(atomData);
208	>	return result;
209		}
210	<
287	<	setVisited(datom);
288	<
289	<	}
290	<
291	<	const string LinearAtomVisitor::toString(){
292	<	char buffer[65535];
293	<	string result;
294	<
295	<	sprintf(buffer ,"------------------------------------------------------------------\n");
296	<	result += buffer;
297	<
298	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
299	<	result += buffer;
300	<
301	<	sprintf(buffer , "Visitor Description: Convert linear into 4 different atoms\n");
302	<	result += buffer;
303	<
304	<	sprintf(buffer ,"------------------------------------------------------------------\n");
305	<	result += buffer;
306	<
307	<	return result;
308	<	}
309	<
310	<	//----------------------------------------------------------------------------//
311	<
312	<	void DefaultAtomVisitor::visit(Atom* atom){
313	<	AtomData* atomData;
314	<	AtomInfo* atomInfo;
315	<	double pos[3];
316	<
317	<	if(isVisited(atom))
318	<	return;
319	<
320	<	atomInfo =new AtomInfo;
321	<
322	<	atomData = new AtomData;
323	<	atomData->setID("ATOMDATA");
324	<
325	<	atom->getPos(pos);
326	<	atomInfo->AtomType = atom->getType();
327	<	atomInfo->pos[0] = pos[0];
328	<	atomInfo->pos[1] = pos[1];
329	<	atomInfo->pos[2] = pos[2];
330	<	atomInfo->dipole[0] = 0.0;
331	<	atomInfo->dipole[1] = 0.0;
332	<	atomInfo->dipole[2] = 0.0;
333	<
334	<
335	<	atomData->addAtomInfo(atomInfo);
336	<
337	<	atom->addProperty(atomData);
338	<
339	<	setVisited(atom);
340	<	}
341	<	void DefaultAtomVisitor::visit(DirectionalAtom* datom){
342	<	AtomData* atomData;
343	<	AtomInfo* atomInfo;
344	<	double pos[3];
345	<	double u[3];
346	<
347	<	if(isVisited(datom))
348	<	return;
349	<
350	<	datom->getPos(pos);
351	<	datom->getU(u);
352	<
353	<	atomData = new AtomData;
354	<	atomData->setID("ATOMDATA");
355	<	atomInfo =new AtomInfo;
356	<
357	<	atomInfo->AtomType = datom->getType();
358	<	atomInfo->pos[0] = pos[0];
359	<	atomInfo->pos[1] = pos[1];
360	<	atomInfo->pos[2] = pos[2];
361	<	atomInfo->dipole[0] = u[0];
362	<	atomInfo->dipole[1] = u[1];
363	<	atomInfo->dipole[2] = u[2];
364	<
365	<	atomData->addAtomInfo(atomInfo);
366	<
367	<	datom->addProperty(atomData);
368	<
369	<	setVisited(datom);
370	<	}
371	<
372	<
373	<	const string DefaultAtomVisitor::toString(){
374	<	char buffer[65535];
375	<	string result;
376	<
377	<	sprintf(buffer ,"------------------------------------------------------------------\n");
378	<	result += buffer;
379	<
380	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
381	<	result += buffer;
382	<
383	<	sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
384	<	result += buffer;
385	<
386	<	sprintf(buffer ,"------------------------------------------------------------------\n");
387	<	result += buffer;
388	<
389	<	return result;
390	<	}
391	<
392	<	}//namespace oopse
210	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 211 by chrisfen, Fri Nov 5 21:45:14 2004 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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