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

Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1872 by gezelter, Fri May 10 15:10:41 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 "AtomVisitor.hpp"
45	<	#include "DirectionalAtom.hpp"
46	<	#include "MatVec3.h"
47	<	#include "RigidBody.hpp"
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	<	void BaseAtomVisitor::visit(RigidBody* rb){
53	<	//vector<Atom*> myAtoms;
54	<	//vector<Atom*>::iterator atomIter;
52	>	namespace OpenMD {
53	>	void BaseAtomVisitor::visit(RigidBody *rb) {
54	>	//vector<Atom*> myAtoms;
55	>	//vector<Atom*>::iterator atomIter;
56
57	<	//myAtoms = rb->getAtoms();
12	<
13	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
14	<	//  (*atomIter)->accept(this);
15	<	}
57	>	//myAtoms = rb->getAtoms();
58
59	<	void BaseAtomVisitor::setVisited(Atom* atom){
60	<	GenericData* data;
19	<	data = atom->getProperty("VISITED");
20	<
21	<	//if visited property is not existed, add it as new property
22	<	if(data == NULL){
23	<	data = new GenericData();
24	<	data->setID("VISITED");
25	<	atom->addProperty(data);
59	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
60	>	//  (*atomIter)->accept(this);
61		}
27	–	}
62
63	<	bool BaseAtomVisitor::isVisited(Atom* atom){
64	<	GenericData* data;
65	<	data = atom->getProperty("VISITED");
32	<	return data == NULL ?  false : true;
33	<	}
63	>	void BaseAtomVisitor::setVisited(Atom *atom) {
64	>	GenericData *data;
65	>	data = atom->getPropertyByName("VISITED");
66
67	<	bool SSDAtomVisitor::isSSDAtom(const string& atomType){
68	<	vector<string>::iterator strIter;
69	<
70	<	for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
71	<	if(*strIter == atomType)
72	<	return true;
73	<
42	<	return false;
43	<	}
67	>	//if visited property is not existed, add it as new property
68	>	if (data == NULL) {
69	>	data = new GenericData();
70	>	data->setID("VISITED");
71	>	atom->addProperty(data);
72	>	}
73	>	}
74
75	<	void SSDAtomVisitor::visit(DirectionalAtom* datom){
75	>	bool BaseAtomVisitor::isVisited(Atom *atom) {
76	>	GenericData *data;
77	>	data = atom->getPropertyByName("VISITED");
78	>	return data == NULL ? false : true;
79	>	}
80
81	<	vector<AtomInfo*> atoms;
81	>	//------------------------------------------------------------------------//
82	>
83	>	void DefaultAtomVisitor::visit(Atom *atom) {
84	>	AtomData *atomData;
85	>	AtomInfo *atomInfo;
86	>	AtomType* atype = atom->getAtomType();
87	>
88	>	if (isVisited(atom))
89	>	return;
90	>
91	>	atomInfo = new AtomInfo;
92	>	atomInfo->atomTypeName = atom->getType();
93	>	atomInfo->pos = atom->getPos();
94	>	atomInfo->vel = atom->getVel();
95	>	atomInfo->frc = atom->getFrc();
96	>	atomInfo->vec = V3Zero;
97	>	atomInfo->hasVelocity = true;
98	>	atomInfo->hasForce = true;
99	>
100	>	FixedChargeAdapter fca = FixedChargeAdapter(atype);
101	>	if ( fca.isFixedCharge() ) {
102	>	atomInfo->hasCharge = true;
103	>	atomInfo->charge = fca.getCharge();
104	>	}
105	>
106	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
107	>	if ( fqa.isFluctuatingCharge() ) {
108	>	atomInfo->hasCharge = true;
109	>	atomInfo->charge += atom->getFlucQPos();
110	>	}
111
112	<	//we need to convert SSD into 4 differnet atoms
113	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
114	<	//of the water with a dipole moment
52	<	double h1[3] = {0.0, -0.75695, 0.5206};
53	<	double h2[3] = {0.0, 0.75695, 0.5206};
54	<	double ox[3] = {0.0, 0.0, -0.0654};
55	<	double u[3] = {0, 0, 1};
56	<	double rotMatrix[3][3];
57	<	double rotTrans[3][3];
58	<	AtomInfo* atomInfo;
59	<	double pos[3];
60	<	double newVec[3];
61	<	double q[4];
62	<	AtomData* atomData;
63	<	GenericData* data;
64	<	bool haveAtomData;
65	<
66	<	//if atom is not SSD atom, just skip it
67	<	if(!isSSDAtom(datom->getType()))
68	<	return;
69	<
70	<	data = datom->getProperty("ATOMDATA");
71	<	if(data != NULL){
72	<
73	<	atomData = dynamic_cast<AtomData*>(data);
74	<	if(atomData == NULL){
75	<	cerr << "can not get Atom Data from " << datom->getType() << endl;
76	<	atomData = new AtomData;
77	<	haveAtomData = false;
112	>	if (atype->isElectrostatic()) {
113	>	atomInfo->hasElectricField = true;
114	>	atomInfo->eField = atom->getElectricField();
115		}
116	<	else
80	<	haveAtomData = true;
81	<	}
82	<	else{
116	>
117		atomData = new AtomData;
118	<	haveAtomData = false;
118	>	atomData->setID("ATOMDATA");
119	>	atomData->addAtomInfo(atomInfo);
120	>
121	>	atom->addProperty(atomData);
122	>
123	>	setVisited(atom);
124		}
86	–
125
126	<	datom->getPos(pos);
127	<	datom->getQ(q);
128	<	datom->getA(rotMatrix);
126	>	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
127	>	AtomData *atomData;
128	>	AtomInfo *atomInfo;
129	>	AtomType* atype = datom->getAtomType();
130
131	<	// We need A^T to convert from body-fixed to space-fixed:
132	<	transposeMat3(rotMatrix, rotTrans);
133	<
134	<	//center of mass of the water molecule
135	<	matVecMul3(rotTrans, u, newVec);
136	<	atomInfo = new AtomInfo;
137	<	atomInfo->AtomType = "X";
138	<	atomInfo->pos[0] = pos[0];
139	<	atomInfo->pos[1] = pos[1];
140	<	atomInfo->pos[2] = pos[2];
102	<	atomInfo->dipole[0] = newVec[0];
103	<	atomInfo->dipole[1] = newVec[1];
104	<	atomInfo->dipole[2] = newVec[2];
131	>	if (isVisited(datom))
132	>	return;
133	>
134	>	atomInfo = new AtomInfo;
135	>	atomInfo->atomTypeName = datom->getType();
136	>	atomInfo->pos = datom->getPos();
137	>	atomInfo->vel = datom->getVel();
138	>	atomInfo->frc = datom->getFrc();
139	>	atomInfo->hasVelocity = true;
140	>	atomInfo->hasForce = true;
141
142	<	atomData->addAtomInfo(atomInfo);
142	>	FixedChargeAdapter fca = FixedChargeAdapter(atype);
143	>	if ( fca.isFixedCharge() ) {
144	>	atomInfo->hasCharge = true;
145	>	atomInfo->charge = fca.getCharge();
146	>	}
147	>
148	>	FluctuatingChargeAdapter fqa = FluctuatingChargeAdapter(atype);
149	>	if ( fqa.isFluctuatingCharge() ) {
150	>	atomInfo->hasCharge = true;
151	>	atomInfo->charge += datom->getFlucQPos();
152	>	}
153
154	<	//oxygen
155	<	matVecMul3(rotTrans, ox, newVec);
156	<	atomInfo = new AtomInfo;
157	<	atomInfo->AtomType = "O";
112	<	atomInfo->pos[0] = pos[0] + newVec[0];
113	<	atomInfo->pos[1] = pos[1] + newVec[1];
114	<	atomInfo->pos[2] = pos[2] + newVec[2];
115	<	atomInfo->dipole[0] = 0.0;
116	<	atomInfo->dipole[1] = 0.0;
117	<	atomInfo->dipole[2] = 0.0;
118	<	atomData->addAtomInfo(atomInfo);
154	>	if (atype->isElectrostatic()) {
155	>	atomInfo->hasElectricField = true;
156	>	atomInfo->eField = datom->getElectricField();
157	>	}
158
159	+	GayBerneAdapter gba = GayBerneAdapter(atype);
160	+	MultipoleAdapter ma = MultipoleAdapter(atype);
161	+
162	+	if (gba.isGayBerne()) {
163	+	atomInfo->hasVector = true;
164	+	atomInfo->vec = datom->getA().transpose()*V3Z;
165	+	} else if (ma.isDipole()) {
166	+	atomInfo->hasVector = true;
167	+	atomInfo->vec = datom->getDipole();
168	+	} else if (ma.isQuadrupole()) {
169	+	atomInfo->hasVector = true;
170	+	atomInfo->vec = datom->getA().transpose()*V3Z;
171	+	}
172
173	<	//hydrogen1
174	<	matVecMul3(rotTrans, h1, newVec);
175	<	atomInfo = new AtomInfo;
124	<	atomInfo->AtomType = "H";
125	<	atomInfo->pos[0] = pos[0] + newVec[0];
126	<	atomInfo->pos[1] = pos[1] + newVec[1];
127	<	atomInfo->pos[2] = pos[2] + newVec[2];
128	<	atomInfo->dipole[0] = 0.0;
129	<	atomInfo->dipole[1] = 0.0;
130	<	atomInfo->dipole[2] = 0.0;
131	<	atomData->addAtomInfo(atomInfo);
173	>	atomData = new AtomData;
174	>	atomData->setID("ATOMDATA");
175	>	atomData->addAtomInfo(atomInfo);
176
133	–	//hydrogen2
134	–	matVecMul3(rotTrans, h2, newVec);
135	–	atomInfo = new AtomInfo;
136	–	atomInfo->AtomType = "H";
137	–	atomInfo->pos[0] = pos[0] + newVec[0];
138	–	atomInfo->pos[1] = pos[1] + newVec[1];
139	–	atomInfo->pos[2] = pos[2] + newVec[2];
140	–	atomInfo->dipole[0] = 0.0;
141	–	atomInfo->dipole[1] = 0.0;
142	–	atomInfo->dipole[2] = 0.0;
143	–	atomData->addAtomInfo(atomInfo);
144	–
145	–	//add atom data into atom's property
146	–
147	–	if(!haveAtomData){
148	–	atomData->setID("ATOMDATA");
177		datom->addProperty(atomData);
178	+
179	+	setVisited(datom);
180		}
181
182	<	setVisited(datom);
182	>	const std::string DefaultAtomVisitor::toString() {
183	>	char   buffer[65535];
184	>	std::string result;
185
186	<	}
186	>	sprintf(buffer,
187	>	"--------------------------------------------------------------\n");
188	>	result += buffer;
189
190	<	const string SSDAtomVisitor::toString(){
191	<	char buffer[65535];
158	<	string result;
159	<
160	<	sprintf(buffer ,"------------------------------------------------------------------\n");
161	<	result += buffer;
190	>	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
191	>	result += buffer;
192
193	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
194	<	result += buffer;
193	>	sprintf(buffer,
194	>	"Visitor Description: copy atom infomation into atom data\n");
195	>	result += buffer;
196
197	<	sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
198	<	result += buffer;
197	>	sprintf(buffer,
198	>	"--------------------------------------------------------------\n");
199	>	result += buffer;
200
201	<	sprintf(buffer ,"------------------------------------------------------------------\n");
202	<	result += buffer;
203	<
172	<	return result;
173	<	}
174	<
175	<	//----------------------------------------------------------------------------//
176	<
177	<	void DefaultAtomVisitor::visit(Atom* atom){
178	<	AtomData* atomData;
179	<	AtomInfo* atomInfo;
180	<	double pos[3];
181	<
182	<	if(isVisited(atom))
183	<	return;
184	<
185	<	atomInfo =new AtomInfo;
186	<
187	<	atomData = new AtomData;
188	<	atomData->setID("ATOMDATA");
189	<
190	<	atom->getPos(pos);
191	<	atomInfo->AtomType = atom->getType();
192	<	atomInfo->pos[0] = pos[0];
193	<	atomInfo->pos[1] = pos[1];
194	<	atomInfo->pos[2] = pos[2];
195	<	atomInfo->dipole[0] = 0.0;
196	<	atomInfo->dipole[1] = 0.0;
197	<	atomInfo->dipole[2] = 0.0;
198	<
199	<
200	<	atomData->addAtomInfo(atomInfo);
201	<
202	<	atom->addProperty(atomData);
203	<
204	<	setVisited(atom);
205	<	}
206	<	void DefaultAtomVisitor::visit(DirectionalAtom* datom){
207	<	AtomData* atomData;
208	<	AtomInfo* atomInfo;
209	<	double pos[3];
210	<	double u[3];
211	<
212	<	if(isVisited(datom))
213	<	return;
214	<
215	<	datom->getPos(pos);
216	<	datom->getU(u);
217	<
218	<	atomData = new AtomData;
219	<	atomData->setID("ATOMDATA");
220	<	atomInfo =new AtomInfo;
221	<
222	<	atomInfo->AtomType = datom->getType();
223	<	atomInfo->pos[0] = pos[0];
224	<	atomInfo->pos[1] = pos[1];
225	<	atomInfo->pos[2] = pos[2];
226	<	atomInfo->dipole[0] = u[0];
227	<	atomInfo->dipole[1] = u[1];
228	<	atomInfo->dipole[2] = u[2];
229	<
230	<	atomData->addAtomInfo(atomInfo);
231	<
232	<	datom->addProperty(atomData);
233	<
234	<	setVisited(datom);
235	<	}
236	<
237	<
238	<	const string DefaultAtomVisitor::toString(){
239	<	char buffer[65535];
240	<	string result;
241	<
242	<	sprintf(buffer ,"------------------------------------------------------------------\n");
243	<	result += buffer;
244	<
245	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
246	<	result += buffer;
247	<
248	<	sprintf(buffer , "Visitor Description: copy atom infomation into atom data\n");
249	<	result += buffer;
250	<
251	<	sprintf(buffer ,"------------------------------------------------------------------\n");
252	<	result += buffer;
253	<
254	<	return result;
255	<	}
201	>	return result;
202	>	}
203	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 2 by gezelter, Fri Sep 24 04:16:43 2004 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1872 by gezelter, Fri May 10 15:10:41 2013 UTC

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