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

Comparing:
trunk/src/visitors/AtomVisitor.cpp (file contents), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (file contents), Revision 1850 by gezelter, Wed Feb 20 15:39:39 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/MultipoleAdapter.hpp"
48	+	#include "types/GayBerneAdapter.hpp"
49
50	<	void BaseAtomVisitor::visit(RigidBody* rb){
51	<	//vector<Atom*> myAtoms;
52	<	//vector<Atom*>::iterator atomIter;
50	>	namespace OpenMD {
51	>	void BaseAtomVisitor::visit(RigidBody *rb) {
52	>	//vector<Atom*> myAtoms;
53	>	//vector<Atom*>::iterator atomIter;
54
55	<	//myAtoms = rb->getAtoms();
12	<
13	<	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
14	<	//  (*atomIter)->accept(this);
15	<	}
55	>	//myAtoms = rb->getAtoms();
56
57	<	void BaseAtomVisitor::setVisited(Atom* atom){
58	<	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);
57	>	//for(atomIter = myAtoms.begin(); atomIter != myAtoms.end(); ++atomIter)
58	>	//  (*atomIter)->accept(this);
59		}
27	–	}
60
61	<	bool BaseAtomVisitor::isVisited(Atom* atom){
62	<	GenericData* data;
63	<	data = atom->getProperty("VISITED");
32	<	return data == NULL ?  false : true;
33	<	}
61	>	void BaseAtomVisitor::setVisited(Atom *atom) {
62	>	GenericData *data;
63	>	data = atom->getPropertyByName("VISITED");
64
65	<	bool SSDAtomVisitor::isSSDAtom(const string& atomType){
66	<	vector<string>::iterator strIter;
67	<
68	<	for(strIter = ssdAtomType.begin(); strIter != ssdAtomType.end(); ++strIter)
69	<	if(*strIter == atomType)
40	<	return true;
41	<
42	<	return false;
43	<	}
44	<
45	<	void SSDAtomVisitor::visit(DirectionalAtom* datom){
46	<
47	<	vector<AtomInfo*> atoms;
48	<
49	<	//we need to convert SSD into 4 differnet atoms
50	<	//one oxygen atom, two hydrogen atoms and one pseudo atom which is the center of the mass
51	<	//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;
65	>	//if visited property is not existed, add it as new property
66	>	if (data == NULL) {
67	>	data = new GenericData();
68	>	data->setID("VISITED");
69	>	atom->addProperty(data);
70		}
79	–	else
80	–	haveAtomData = true;
71		}
72	<	else{
73	<	atomData = new AtomData;
74	<	haveAtomData = false;
72	>
73	>	bool BaseAtomVisitor::isVisited(Atom *atom) {
74	>	GenericData *data;
75	>	data = atom->getPropertyByName("VISITED");
76	>	return data == NULL ? false : true;
77		}
86	–
87	–
88	–	datom->getPos(pos);
89	–	datom->getQ(q);
90	–	datom->getA(rotMatrix);
78
79	<	// We need A^T to convert from body-fixed to space-fixed:
80	<	transposeMat3(rotMatrix, rotTrans);
81	<
82	<	//center of mass of the water molecule
83	<	matVecMul3(rotTrans, u, newVec);
84	<	atomInfo = new AtomInfo;
85	<	atomInfo->AtomType = "X";
86	<	atomInfo->pos[0] = pos[0];
87	<	atomInfo->pos[1] = pos[1];
101	<	atomInfo->pos[2] = pos[2];
102	<	atomInfo->dipole[0] = newVec[0];
103	<	atomInfo->dipole[1] = newVec[1];
104	<	atomInfo->dipole[2] = newVec[2];
79	>	//------------------------------------------------------------------------//
80	>
81	>	void DefaultAtomVisitor::visit(Atom *atom) {
82	>	AtomData *atomData;
83	>	AtomInfo *atomInfo;
84	>	Vector3d  pos;
85	>	Vector3d  vel;
86	>	Vector3d  frc;
87	>	Vector3d  u;
88
89	<	atomData->addAtomInfo(atomInfo);
90	<
91	<	//oxygen
92	<	matVecMul3(rotTrans, ox, newVec);
93	<	atomInfo = new AtomInfo;
94	<	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);
119	<
120	<
121	<	//hydrogen1
122	<	matVecMul3(rotTrans, h1, newVec);
123	<	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);
132	<
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){
89	>	if (isVisited(atom))
90	>	return;
91	>
92	>	atomInfo = new AtomInfo;
93	>
94	>	atomData = new AtomData;
95		atomData->setID("ATOMDATA");
96	<	datom->addProperty(atomData);
96	>
97	>	pos = atom->getPos();
98	>	vel = atom->getVel();
99	>	frc = atom->getFrc();
100	>	atomInfo->atomTypeName = atom->getType();
101	>	atomInfo->pos[0] = pos[0];
102	>	atomInfo->pos[1] = pos[1];
103	>	atomInfo->pos[2] = pos[2];
104	>	atomInfo->vel[0] = vel[0];
105	>	atomInfo->vel[1] = vel[1];
106	>	atomInfo->vel[2] = vel[2];
107	>	atomInfo->hasVelocity = true;
108	>	atomInfo->frc[0] = frc[0];
109	>	atomInfo->frc[1] = frc[1];
110	>	atomInfo->frc[2] = frc[2];
111	>	atomInfo->hasForce = true;
112	>	atomInfo->vec[0] = 0.0;
113	>	atomInfo->vec[1] = 0.0;
114	>	atomInfo->vec[2] = 0.0;
115	>
116	>	atomData->addAtomInfo(atomInfo);
117	>
118	>	atom->addProperty(atomData);
119	>
120	>	setVisited(atom);
121		}
151	–
152	–	setVisited(datom);
153	–
154	–	}
155	–
156	–	const string SSDAtomVisitor::toString(){
157	–	char buffer[65535];
158	–	string result;
122
123	<	sprintf(buffer ,"------------------------------------------------------------------\n");
124	<	result += buffer;
123	>	void DefaultAtomVisitor::visit(DirectionalAtom *datom) {
124	>	AtomData *atomData;
125	>	AtomInfo *atomInfo;
126	>	Vector3d  pos;
127	>	Vector3d  vel;
128	>	Vector3d  frc;
129	>	Vector3d  u;
130
131	<	sprintf(buffer ,"Visitor name: %s\n", visitorName.c_str());
132	<	result += buffer;
131	>	if (isVisited(datom))
132	>	return;
133	>
134	>	pos = datom->getPos();
135	>	vel = datom->getVel();
136	>	frc = datom->getFrc();
137
138	<	sprintf(buffer , "Visitor Description: Convert SSD into 4 different atoms\n");
139	<	result += buffer;
138	>	GayBerneAdapter gba = GayBerneAdapter(datom->getAtomType());
139	>	MultipoleAdapter ma = MultipoleAdapter(datom->getAtomType());
140	>
141	>	if (gba.isGayBerne()) {
142	>	u = datom->getA().transpose()*V3Z;
143	>	} else if (ma.isDipole()) {
144	>	u = datom->getDipole();
145	>	} else if (ma.isQuadrupole()) {
146	>	//u = datom->getQuadrupole().getColumn(2);
147	>	u = datom->getA().transpose()*V3Z;
148	>	}
149	>	atomData = new AtomData;
150	>	atomData->setID("ATOMDATA");
151	>	atomInfo = new AtomInfo;
152
153	<	sprintf(buffer ,"------------------------------------------------------------------\n");
154	<	result += buffer;
153	>	atomInfo->atomTypeName = datom->getType();
154	>	atomInfo->pos[0] = pos[0];
155	>	atomInfo->pos[1] = pos[1];
156	>	atomInfo->pos[2] = pos[2];
157	>	atomInfo->vel[0] = vel[0];
158	>	atomInfo->vel[1] = vel[1];
159	>	atomInfo->vel[2] = vel[2];
160	>	atomInfo->hasVelocity = true;
161	>	atomInfo->frc[0] = frc[0];
162	>	atomInfo->frc[1] = frc[1];
163	>	atomInfo->frc[2] = frc[2];
164	>	atomInfo->hasForce = true;
165	>	atomInfo->vec[0] = u[0];
166	>	atomInfo->vec[1] = u[1];
167	>	atomInfo->vec[2] = u[2];
168	>	atomInfo->hasVector = true;
169
170	<	return result;
173	<	}
170	>	atomData->addAtomInfo(atomInfo);
171
172	<	//----------------------------------------------------------------------------//
172	>	datom->addProperty(atomData);
173
174	<	void DefaultAtomVisitor::visit(Atom* atom){
175	<	AtomData* atomData;
179	<	AtomInfo* atomInfo;
180	<	double pos[3];
174	>	setVisited(datom);
175	>	}
176
177	<	if(isVisited(atom))
178	<	return;
177	>	const std::string DefaultAtomVisitor::toString() {
178	>	char   buffer[65535];
179	>	std::string result;
180
181	<	atomInfo =new AtomInfo;
181	>	sprintf(buffer,
182	>	"------------------------------------------------------------------\n");
183	>	result += buffer;
184
185	<	atomData = new AtomData;
186	<	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;
185	>	sprintf(buffer, "Visitor name: %s\n", visitorName.c_str());
186	>	result += buffer;
187
188	+	sprintf(buffer,
189	+	"Visitor Description: copy atom infomation into atom data\n");
190	+	result += buffer;
191
192	<	atomData->addAtomInfo(atomInfo);
193	<
194	<	atom->addProperty(atomData);
192	>	sprintf(buffer,
193	>	"------------------------------------------------------------------\n");
194	>	result += buffer;
195
196	<	setVisited(atom);
197	<	}
198	<	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	<	}
196	>	return result;
197	>	}
198	>	} //namespace OpenMD

Comparing:
trunk/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 3 by tim, Fri Sep 24 16:27:58 2004 UTC vs.
branches/development/src/visitors/AtomVisitor.cpp (property svn:keywords), Revision 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC

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