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

Comparing trunk/src/applications/staticProps/P2OrderParameter.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

#	Line 36 | Line 36
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]  Vardeman & Gezelter, in progress (2009).
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"
#	Line 44 | Line 45
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 std::string& filename, const std::string& sele1, const std::string& sele2)
64	<	: StaticAnalyser(info, filename),
65	<	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
66	<	seleMan1_(info), seleMan2_(info){
67	<
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	<
70	>
71		evaluator1_.loadScriptString(sele1);
72	<	evaluator2_.loadScriptString(sele2);
72	>	evaluator2_.loadScriptString(sele2);
73	>	}
74
75	<	if (!evaluator1_.isDynamic()) {
76	<	seleMan1_.setSelectionSet(evaluator1_.evaluate());
77	<	}else {
78	<	sprintf( painCave.errMsg,
79	<	"--sele1 must be static selection\n");
65	<	painCave.severity = OPENMD_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 = OPENMD_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 = OPENMD_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	<
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() {
#	Line 105 | Line 88 | namespace OpenMD {
88		RigidBody* rb;
89		SimInfo::MoleculeIterator mi;
90		Molecule::RigidBodyIterator rbIter;
91	<
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	<
105	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
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; rb = mol->nextRigidBody(rbIter)) {
107	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
108	>	rb = mol->nextRigidBody(rbIter)) {
109		rb->updateAtoms();
110	<	}
122	<
110	>	}
111		}
112
113		Mat3x3d orderTensor(0.0);
114	<	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
115	<	Vector3d vec = j->first->getPos() - j->second->getPos();
116	<	if (usePeriodicBoundaryConditions_)
117	<	currentSnapshot_->wrapVector(vec);
118	<	vec.normalize();
119	<	orderTensor +=outProduct(vec, vec);
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	<	orderTensor /= sdPairs_.size();
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;
#	Line 155 | Line 222 | namespace OpenMD {
222		}
223
224		RealType angle = 0.0;
225	<	for (std::vector<std::pair<StuntDouble*, StuntDouble*> >::iterator j = sdPairs_.begin(); j != sdPairs_.end(); ++j) {
226	<	Vector3d vec = j->first->getPos() - j->second->getPos();
227	<	if (usePeriodicBoundaryConditions_)
228	<	currentSnapshot_->wrapVector(vec);
229	<	vec.normalize();
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	<	angle += acos(dot(vec, director)) ;
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		}
166	–	angle = angle / (sdPairs_.size() * NumericConstant::PI) * 180.0;
279
280		OrderParam param;
281		param.p2 = p2;
#	Line 173 | Line 285 | namespace OpenMD {
285		orderParams_.push_back(param);
286
287		}
288	<
288	>
289		writeP2();
290	<
290	>
291		}
292
293		void P2OrderParameter::writeP2() {
294
295	<	std::ofstream os(getOutputFileName().c_str());
295	>	ofstream os(getOutputFileName().c_str());
296		os << "#radial distribution function\n";
297		os<< "#selection1: (" << selectionScript1_ << ")\t";
298	<	os << "selection2: (" << selectionScript2_ << ")\n";
298	>	if (!doVect_) {
299	>	os << "selection2: (" << selectionScript2_ << ")\n";
300	>	}
301		os << "#p2\tdirector_x\tdirector_y\tdiretor_z\tangle(degree)\n";
302
303	<	for (std::size_t i = 0; i < orderParams_.size(); ++i) {
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"

Comparing trunk/src/applications/staticProps/P2OrderParameter.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1819 by gezelter, Thu Dec 13 16:57:39 2012 UTC

#	Line 0 | Line 1
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