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

Comparing trunk/src/applications/staticProps/GofRZ.cpp (file contents):
Revision 1441 by gezelter, Thu Apr 29 14:48:10 2010 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC

#	Line 46 | Line 46 | namespace OpenMD {
46
47		namespace OpenMD {
48
49	<	GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1,
50	<	const std::string& sele2, RealType len, int nrbins, int nZBins)
51	<	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nZBins_(nZBins){
49	>	GofRZ::GofRZ(SimInfo* info, const std::string& filename, const std::string& sele1,
50	>	const std::string& sele2, RealType len, RealType zlen, int nrbins, int nZBins)
51	>	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), zLen_(zlen), nRBins_(nrbins), nZBins_(nZBins){
52
53	<	setOutputName(getPrefix(filename) + ".gofrz");
53	>	setOutputName(getPrefix(filename) + ".gofrz");
54
55	<	deltaR_ = len_ / (double) nRBins_;
56	<	deltaZ_ = len_ / (double)nZBins_;
57	<	histogram_.resize(nRBins_);
58	<	avgGofr_.resize(nRBins_);
59	<	for (int i = 0 ; i < nRBins_; ++i) {
60	<	histogram_[i].resize(nZBins_);
61	<	avgGofr_[i].resize(nZBins_);
62	<	}
55	>	deltaR_ = len_ / (double) nRBins_;
56	>	deltaZ_ = zLen_ / (double)nZBins_;    // for solvated_NVT.md4
57	>
58	>	histogram_.resize(nRBins_);
59	>	avgGofr_.resize(nRBins_);
60	>	for (int i = 0 ; i < nRBins_; ++i) {
61	>	histogram_[i].resize(nZBins_);
62	>	avgGofr_[i].resize(nZBins_);
63	>	}
64		}
65
66	<
67	<	void GofRZ::preProcess() {
68	<	for (int i = 0; i < avgGofr_.size(); ++i) {
69	<	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
66	>	void GofRZ::preProcess() {
67	>	for (int i = 0; i < avgGofr_.size(); ++i) {
68	>	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
69	>	}
70		}
70	–	}
71
72	<	void GofRZ::initalizeHistogram() {
73	<	npairs_ = 0;
74	<	for (int i = 0; i < histogram_.size(); ++i){
75	<	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
72	>	void GofRZ::initalizeHistogram() {
73	>	npairs_ = 0;
74	>	for (int i = 0; i < histogram_.size(); ++i){
75	>	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
76	>	}
77		}
77	–	}
78
79	<	void GofRZ::processHistogram() {
80	<	int nPairs = getNPairs();
81	<	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
82	<	RealType pairDensity = nPairs / volume;
79	>	void GofRZ::processHistogram() {
80	>	int nPairs = getNPairs();
81	>	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
82	>	RealType pairDensity = nPairs / volume * 2.0;
83
84	<	for(int i = 0 ; i < histogram_.size(); ++i){
84	>	for(int i = 0 ; i < histogram_.size(); ++i){
85
86	<	RealType rLower = i * deltaR_;
87	<	RealType rUpper = rLower + deltaR_;
88	<	RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
89	<	RealType nIdeal = volSlice * pairDensity;
86	>	RealType rLower = i * deltaR_;
87	>	RealType rUpper = rLower + deltaR_;
88	>	RealType volSlice = NumericConstant::PI * deltaZ_ * (( rUpper * rUpper ) - ( rLower * rLower ));
89	>	RealType nIdeal = volSlice * pairDensity;
90
91	<	for (int j = 0; j < histogram_[i].size(); ++j){
92	<	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
93	<	}
91	>	for (int j = 0; j < histogram_[i].size(); ++j){
92	>	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
93	>	}
94	>	}
95	>
96		}
97
98	<	}
98	>	void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
99
100	<	void GofRZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
100	>	if (sd1 == sd2) {
101	>	return;
102	>	}
103	>	Vector3d pos1 = sd1->getPos();
104	>	Vector3d pos2 = sd2->getPos();
105	>	Vector3d r12 = pos2 - pos1;
106	>	if (usePeriodicBoundaryConditions_)
107	>	currentSnapshot_->wrapVector(r12);
108
109	<	if (sd1 == sd2) {
101	<	return;
102	<	}
103	<	Vector3d pos1 = sd1->getPos();
104	<	Vector3d pos2 = sd2->getPos();
105	<	Vector3d r12 = pos2 - pos1;
106	<	if (usePeriodicBoundaryConditions_)
107	<	currentSnapshot_->wrapVector(r12);
109	>	RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
110
111	<	RealType distance = sqrt(pow(r12.x(), 2) + pow(r12.y(), 2));
111	>	int whichRBin = distance / deltaR_;
112
113	<	int whichRBin = distance / deltaR_;
112	<
113	<	if (distance <= len_) {
113	>	if (distance <= len_) {
114
115	<	RealType Z = abs(r12.z());
115	>	RealType Z = fabs(r12.z());
116
117	<	if (Z <= len_) {
118	<	int whichZBin = Z / deltaZ_;
119	<	++histogram_[whichRBin][whichZBin];
120	<	++npairs_;
121	<	}
117	>	if (Z <= zLen_) {
118	>	int whichZBin = Z / deltaZ_;
119	>
120	>	++histogram_[whichRBin][whichZBin];
121	>	++npairs_;
122	>	}
123	>	}
124		}
123	–	}
125
126	<	void GofRZ::writeRdf() {
127	<	std::ofstream rdfStream(outputFilename_.c_str());
128	<	if (rdfStream.is_open()) {
129	<	rdfStream << "#radial distribution function\n";
130	<	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
131	<	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
132	<	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
133	<	rdfStream << "#nZBins =" << nZBins_ << "deltaZ = " << deltaZ_ << "\n";
134	<	for (int i = 0; i < avgGofr_.size(); ++i) {
135	<	RealType r = deltaR_ * (i + 0.5);
126	>	void GofRZ::writeRdf() {
127	>	std::ofstream rdfStream(outputFilename_.c_str());
128	>	if (rdfStream.is_open()) {
129	>	rdfStream << "#radial distribution function\n";
130	>	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
131	>	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
132	>	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
133	>	rdfStream << "#nZBins =" << nZBins_ << "\t deltaZ = " << deltaZ_ << "\n";
134	>	for (int i = 0; i < avgGofr_.size(); ++i) {
135	>	RealType r = deltaR_ * (i + 0.5);
136
137	<	for(int j = 0; j < avgGofr_[i].size(); ++j) {
138	<	RealType z = deltaZ_ * (j + 0.5);
139	<	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
140	<	}
137	>	for(int j = 0; j < avgGofr_[i].size(); ++j) {
138	>	RealType z = deltaZ_ * (j + 0.5);
139	>	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
140	>	}
141
142	<	rdfStream << "\n";
143	<	}
142	>	rdfStream << "\n";
143	>	}
144
145	<	} else {
146	<	sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
147	<	painCave.isFatal = 1;
148	<	simError();
145	>	} else {
146	>	sprintf(painCave.errMsg, "GofRZ: unable to open %s\n", outputFilename_.c_str());
147	>	painCave.isFatal = 1;
148	>	simError();
149	>	}
150	>
151	>	rdfStream.close();
152		}
153
150	–	rdfStream.close();
151	–	}
152	–
154		}
155
156

Comparing trunk/src/applications/staticProps/GofRZ.cpp (property svn:keywords):
Revision 1441 by gezelter, Thu Apr 29 14:48:10 2010 UTC vs.
Revision 1445 by chuckv, Tue Jun 8 20:26:50 2010 UTC

#	Line 0 | Line 1
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