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root/OpenMD/trunk/src/applications/staticProps/P2OrderParameter.cpp

Comparing trunk/src/applications/staticProps/P2OrderParameter.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 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. 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
19	<	*    notice, this list of conditions and the following disclaimer.
20	<	*
21	<	* 3. Redistributions in binary form must reproduce the above copyright
22	<	*    notice, this list of conditions and the following disclaimer in the
23	<	*    documentation and/or other materials provided with the
24	<	*    distribution.
25	<	*
26	<	* This software is provided "AS IS," without a warranty of any
27	<	* kind. All express or implied conditions, representations and
28	<	* warranties, including any implied warranty of merchantability,
29	<	* fitness for a particular purpose or non-infringement, are hereby
30	<	* excluded.  The University of Notre Dame and its licensors shall not
31	<	* be liable for any damages suffered by licensee as a result of
32	<	* using, modifying or distributing the software or its
33	<	* derivatives. In no event will the University of Notre Dame or its
34	<	* licensors be liable for any lost revenue, profit or data, or for
35	<	* direct, indirect, special, consequential, incidental or punitive
36	<	* damages, however caused and regardless of the theory of liability,
37	<	* arising out of the use of or inability to use software, even if the
38	<	* University of Notre Dame has been advised of the possibility of
39	<	* such damages.
40	<	*/
41	<
42	<	#include "applications/staticProps/P2OrderParameter.hpp"
43	<	#include "utils/simError.h"
44	<	#include "io/DumpReader.hpp"
45	<	#include "primitives/Molecule.hpp"
46	<	#include "utils/NumericConstant.hpp"
47	<	namespace oopse {
48	<
49	<
50	<	P2OrderParameter::P2OrderParameter(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
51	<	: StaticAnalyser(info, filename),
52	<	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
53	<	seleMan1_(info), seleMan2_(info){
54	<
55	<	setOutputName(getPrefix(filename) + ".p2");
56	<
57	<	evaluator1_.loadScriptString(sele1);
58	<	evaluator2_.loadScriptString(sele2);
59	<
60	<	if (!evaluator1_.isDynamic()) {
61	<	seleMan1_.setSelectionSet(evaluator1_.evaluate());
62	<	}else {
63	<	sprintf( painCave.errMsg,
64	<	"--sele1 must be static selection\n");
65	<	painCave.severity = OOPSE_ERROR;
66	<	painCave.isFatal = 1;
67	<	simError();
68	<	}
69	<
70	<	if (!evaluator2_.isDynamic()) {
71	<	seleMan2_.setSelectionSet(evaluator2_.evaluate());
72	<	}else {
73	<	sprintf( painCave.errMsg,
74	<	"--sele2 must be static selection\n");
75	<	painCave.severity = OOPSE_ERROR;
76	<	painCave.isFatal = 1;
77	<	simError();
78	<	}
79	<
80	<	if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
81	<	sprintf( painCave.errMsg,
82	<	"The number of selected Stuntdoubles are not the same in --sele1 and sele2\n");
83	<	painCave.severity = OOPSE_ERROR;
84	<	painCave.isFatal = 1;
85	<	simError();
86	<
87	<	}
88	<
89	<	int i;
90	<	int j;
91	<	StuntDouble* sd1;
92	<	StuntDouble* sd2;
93	<	for (sd1 = seleMan1_.beginSelected(i), sd2 = seleMan2_.beginSelected(j);
94	<	sd1 != NULL && sd2 != NULL;
95	<	sd1 = seleMan1_.nextSelected(i), sd2 = seleMan2_.nextSelected(j)) {
96	<
97	<	sdPairs_.push_back(std::make_pair(sd1, sd2));
98	<	}
99	<
100	<
101	<	}
102	<
103	<	void P2OrderParameter::process() {
104	<	Molecule* mol;
105	<	RigidBody* rb;
106	<	SimInfo::MoleculeIterator mi;
107	<	Molecule::RigidBodyIterator rbIter;
108	<
109	<	DumpReader reader(info_, dumpFilename_);
110	<	int nFrames = reader.getNFrames();
111	<
112	<	for (int i = 0; i < nFrames; i += step_) {
113	<	reader.readFrame(i);
114	<	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
115	<
116	<
117	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
118	<	//change the positions of atoms which belong to the rigidbodies
119	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
120	<	rb->updateAtoms();
121	<	}
122	<
123	<	}
124	<
125	<	Mat3x3d orderTensor(0.0);
126	<	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
127	<	Vector3d vec = j->first->getPos() - j->second->getPos();
128	<	currentSnapshot_->wrapVector(vec);
129	<	vec.normalize();
130	<	orderTensor +=outProduct(vec, vec);
131	<	}
132	<
133	<	orderTensor /= sdPairs_.size();
134	<	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
135	<
136	<	Vector3d eigenvalues;
137	<	Mat3x3d eigenvectors;
138	<	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
139	<
140	<	int which;
141	<	RealType maxEval = 0.0;
142	<	for(int k = 0; k< 3; k++){
143	<	if(fabs(eigenvalues[k]) > maxEval){
144	<	which = k;
145	<	maxEval = fabs(eigenvalues[k]);
146	<	}
147	<	}
148	<	RealType p2 = 1.5 * maxEval;
149	<
150	<	//the eigen vector is already normalized in SquareMatrix3::diagonalize
151	<	Vector3d director = eigenvectors.getColumn(which);
152	<	if (director[0] < 0) {
153	<	director.negate();
154	<	}
155	<
156	<	RealType angle = 0.0;
157	<	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
158	<	Vector3d vec = j->first->getPos() - j->second->getPos();
159	<	currentSnapshot_->wrapVector(vec);
160	<	vec.normalize();
161	<
162	<	angle += acos(dot(vec, director)) ;
163	<	}
164	<	angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
165	<
166	<	OrderParam param;
167	<	param.p2 = p2;
168	<	param.director = director;
169	<	param.angle = angle;
170	<
171	<	orderParams_.push_back(param);
172	<
173	<	}
174	<
175	<	writeP2();
176	<
177	<	}
178	<
179	<	void P2OrderParameter::writeP2() {
180	<
181	<	std::ofstream os(getOutputFileName().c_str());
182	<	os << "#radial distribution function\n";
183	<	os<< "#selection1: (" << selectionScript1_ << ")\t";
184	<	os << "selection2: (" << selectionScript2_ << ")\n";
185	<	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
186	<
187	<	for (std::size_t i = 0; i < orderParams_.size(); ++i) {
188	<	os <<  orderParams_[i].p2 << "\t"
189	<	<<  orderParams_[i].director[0] << "\t"
190	<	<<  orderParams_[i].director[1] << "\t"
191	<	<<  orderParams_[i].director[2] << "\t"
192	<	<<  orderParams_[i].angle << "\n";
193	<
194	<	}
195	<
196	<	}
197	<
198	<	}
199	<
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, 24107 (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 "applications/staticProps/P2OrderParameter.hpp"
44	>	#include "utils/simError.h"
45	>	#include "io/DumpReader.hpp"
46	>	#include "primitives/Molecule.hpp"
47	>	#include "utils/NumericConstant.hpp"
48	>
49	>	using namespace std;
50	>	namespace OpenMD {
51	>
52	>	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
53	>	const string& sele1)
54	>	: StaticAnalyser(info, filename), doVect_(true), doOffset_(false),
55	>	selectionScript1_(sele1), evaluator1_(info),
56	>	evaluator2_(info), seleMan1_(info), seleMan2_(info) {
57	>
58	>	setOutputName(getPrefix(filename) + ".p2");
59	>
60	>	evaluator1_.loadScriptString(sele1);
61	>	}
62	>
63	>	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
64	>	const string& sele1, const string& sele2)
65	>	: StaticAnalyser(info, filename), doVect_(false), doOffset_(false),
66	>	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info),
67	>	evaluator2_(info), seleMan1_(info), seleMan2_(info) {
68	>
69	>	setOutputName(getPrefix(filename) + ".p2");
70	>
71	>	evaluator1_.loadScriptString(sele1);
72	>	evaluator2_.loadScriptString(sele2);
73	>	}
74	>
75	>	P2OrderParameter::P2OrderParameter(SimInfo* info, const string& filename,
76	>	const string& sele1, int seleOffset)
77	>	: StaticAnalyser(info, filename), doVect_(false), doOffset_(true),
78	>	seleOffset_(seleOffset), selectionScript1_(sele1), evaluator1_(info),
79	>	evaluator2_(info), seleMan1_(info), seleMan2_(info) {
80	>
81	>	setOutputName(getPrefix(filename) + ".p2");
82	>
83	>	evaluator1_.loadScriptString(sele1);
84	>	}
85	>
86	>	void P2OrderParameter::process() {
87	>	Molecule* mol;
88	>	RigidBody* rb;
89	>	SimInfo::MoleculeIterator mi;
90	>	Molecule::RigidBodyIterator rbIter;
91	>	StuntDouble* sd1;
92	>	StuntDouble* sd2;
93	>	int ii;
94	>	int jj;
95	>	int vecCount;
96	>
97	>	DumpReader reader(info_, dumpFilename_);
98	>	int nFrames = reader.getNFrames();
99	>
100	>	for (int i = 0; i < nFrames; i += step_) {
101	>	reader.readFrame(i);
102	>	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
103	>
104	>	for (mol = info_->beginMolecule(mi); mol != NULL;
105	>	mol = info_->nextMolecule(mi)) {
106	>	//change the positions of atoms which belong to the rigidbodies
107	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
108	>	rb = mol->nextRigidBody(rbIter)) {
109	>	rb->updateAtoms();
110	>	}
111	>	}
112	>
113	>	Mat3x3d orderTensor(0.0);
114	>	vecCount = 0;
115	>
116	>	seleMan1_.setSelectionSet(evaluator1_.evaluate());
117	>
118	>	if (doVect_) {
119	>
120	>	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
121	>	sd1 = seleMan1_.nextSelected(ii)) {
122	>	if (sd1->isDirectional()) {
123	>	Vector3d vec = sd1->getA().getColumn(2);
124	>	vec.normalize();
125	>	orderTensor += outProduct(vec, vec);
126	>	vecCount++;
127	>	}
128	>	}
129	>
130	>	orderTensor /= vecCount;
131	>
132	>	} else {
133	>
134	>	if (doOffset_) {
135	>
136	>	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
137	>	sd1 = seleMan1_.nextSelected(ii)) {
138	>
139	>	// This will require careful rewriting if StaticProps is
140	>	// ever parallelized.  For an example, see
141	>	// Thermo::getTaggedAtomPairDistance
142	>
143	>	int sd2Index = sd1->getGlobalIndex() + seleOffset_;
144	>	sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
145	>
146	>	Vector3d vec = sd1->getPos() - sd2->getPos();
147	>
148	>	if (usePeriodicBoundaryConditions_)
149	>	currentSnapshot_->wrapVector(vec);
150	>
151	>	vec.normalize();
152	>
153	>	orderTensor +=outProduct(vec, vec);
154	>	vecCount++;
155	>	}
156	>
157	>	orderTensor /= vecCount;
158	>	} else {
159	>
160	>	seleMan2_.setSelectionSet(evaluator2_.evaluate());
161	>
162	>	if (seleMan1_.getSelectionCount() != seleMan2_.getSelectionCount() ) {
163	>	sprintf( painCave.errMsg,
164	>	"In frame %d, the number of selected StuntDoubles are\n"
165	>	"\tnot the same in --sele1 and sele2\n", i);
166	>	painCave.severity = OPENMD_INFO;
167	>	painCave.isFatal = 0;
168	>	simError();
169	>	}
170	>
171	>	for (sd1 = seleMan1_.beginSelected(ii),
172	>	sd2 = seleMan2_.beginSelected(jj);
173	>	sd1 != NULL && sd2 != NULL;
174	>	sd1 = seleMan1_.nextSelected(ii),
175	>	sd2 = seleMan2_.nextSelected(jj)) {
176	>
177	>	Vector3d vec = sd1->getPos() - sd2->getPos();
178	>
179	>	if (usePeriodicBoundaryConditions_)
180	>	currentSnapshot_->wrapVector(vec);
181	>
182	>	vec.normalize();
183	>
184	>	orderTensor +=outProduct(vec, vec);
185	>	vecCount++;
186	>	}
187	>
188	>	orderTensor /= vecCount;
189	>	}
190	>	}
191	>
192	>	if (vecCount == 0) {
193	>	sprintf( painCave.errMsg,
194	>	"In frame %d, the number of selected vectors was zero.\n"
195	>	"\tThis will not give a meaningful order parameter.", i);
196	>	painCave.severity = OPENMD_ERROR;
197	>	painCave.isFatal = 1;
198	>	simError();
199	>	}
200	>
201	>	orderTensor -= (RealType)(1.0/3.0) * Mat3x3d::identity();
202	>
203	>	Vector3d eigenvalues;
204	>	Mat3x3d eigenvectors;
205	>
206	>	Mat3x3d::diagonalize(orderTensor, eigenvalues, eigenvectors);
207	>
208	>	int which;
209	>	RealType maxEval = 0.0;
210	>	for(int k = 0; k< 3; k++){
211	>	if(fabs(eigenvalues[k]) > maxEval){
212	>	which = k;
213	>	maxEval = fabs(eigenvalues[k]);
214	>	}
215	>	}
216	>	RealType p2 = 1.5 * maxEval;
217	>
218	>	//the eigen vector is already normalized in SquareMatrix3::diagonalize
219	>	Vector3d director = eigenvectors.getColumn(which);
220	>	if (director[0] < 0) {
221	>	director.negate();
222	>	}
223	>
224	>	RealType angle = 0.0;
225	>	vecCount = 0;
226	>
227	>	if (doVect_) {
228	>	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
229	>	sd1 = seleMan1_.nextSelected(ii)) {
230	>	if (sd1->isDirectional()) {
231	>	Vector3d vec = sd1->getA().getColumn(2);
232	>	vec.normalize();
233	>	angle += acos(dot(vec, director));
234	>	vecCount++;
235	>	}
236	>	}
237	>	angle = angle/(vecCount*NumericConstant::PI)*180.0;
238	>
239	>	} else {
240	>	if (doOffset_) {
241	>
242	>	for (sd1 = seleMan1_.beginSelected(ii); sd1 != NULL;
243	>	sd1 = seleMan1_.nextSelected(ii)) {
244	>
245	>	// This will require careful rewriting if StaticProps is
246	>	// ever parallelized.  For an example, see
247	>	// Thermo::getTaggedAtomPairDistance
248	>
249	>	int sd2Index = sd1->getGlobalIndex() + seleOffset_;
250	>	sd2 = info_->getIOIndexToIntegrableObject(sd2Index);
251	>
252	>	Vector3d vec = sd1->getPos() - sd2->getPos();
253	>	if (usePeriodicBoundaryConditions_)
254	>	currentSnapshot_->wrapVector(vec);
255	>	vec.normalize();
256	>	angle += acos(dot(vec, director)) ;
257	>	vecCount++;
258	>	}
259	>	angle = angle / (vecCount * NumericConstant::PI) * 180.0;
260	>
261	>	} else {
262	>
263	>	for (sd1 = seleMan1_.beginSelected(ii),
264	>	sd2 = seleMan2_.beginSelected(jj);
265	>	sd1 != NULL && sd2 != NULL;
266	>	sd1 = seleMan1_.nextSelected(ii),
267	>	sd2 = seleMan2_.nextSelected(jj)) {
268	>
269	>	Vector3d vec = sd1->getPos() - sd2->getPos();
270	>	if (usePeriodicBoundaryConditions_)
271	>	currentSnapshot_->wrapVector(vec);
272	>	vec.normalize();
273	>	angle += acos(dot(vec, director)) ;
274	>	vecCount++;
275	>	}
276	>	angle = angle / (vecCount * NumericConstant::PI) * 180.0;
277	>	}
278	>	}
279	>
280	>	OrderParam param;
281	>	param.p2 = p2;
282	>	param.director = director;
283	>	param.angle = angle;
284	>
285	>	orderParams_.push_back(param);
286	>
287	>	}
288	>
289	>	writeP2();
290	>
291	>	}
292	>
293	>	void P2OrderParameter::writeP2() {
294	>
295	>	ofstream os(getOutputFileName().c_str());
296	>	os << "#radial distribution function\n";
297	>	os<< "#selection1: (" << selectionScript1_ << ")\t";
298	>	if (!doVect_) {
299	>	os << "selection2: (" << selectionScript2_ << ")\n";
300	>	}
301	>	os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
302	>
303	>	for (size_t i = 0; i < orderParams_.size(); ++i) {
304	>	os <<  orderParams_[i].p2 << "\t"
305	>	<<  orderParams_[i].director[0] << "\t"
306	>	<<  orderParams_[i].director[1] << "\t"
307	>	<<  orderParams_[i].director[2] << "\t"
308	>	<<  orderParams_[i].angle << "\n";
309	>
310	>	}
311	>
312	>	}
313	>
314	>	}
315	>

Comparing trunk/src/applications/staticProps/P2OrderParameter.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

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