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

Comparing trunk/src/applications/staticProps/GofRAngle.cpp (file contents):
Revision 348 by tim, Tue Feb 15 17:24:12 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 6 | Line 6
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
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
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.
#	Line 37 | Line 28
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 <algorithm>
#	Line 44 | Line 45
45		#include "applications/staticProps/GofRAngle.hpp"
46		#include "utils/simError.h"
47
48	<	namespace oopse {
48	>	namespace OpenMD {
49
50	<	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
51	<	: RadialDistrFunc(info, filename, sele1, sele2){
50	>	GofRAngle::GofRAngle(SimInfo* info, const std::string& filename, const std::string& sele1,
51	>	const std::string& sele2, RealType len, int nrbins, int nangleBins)
52	>	: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins), nAngleBins_(nangleBins){
53
54	<	}
54	>	deltaR_ = len_ /(double) nRBins_;
55	>	deltaCosAngle_ = 2.0 / (double)nAngleBins_;
56	>	histogram_.resize(nRBins_);
57	>	avgGofr_.resize(nRBins_);
58	>	for (int i = 0 ; i < nRBins_; ++i) {
59	>	histogram_[i].resize(nAngleBins_);
60	>	avgGofr_[i].resize(nAngleBins_);
61	>	}
62	>	}
63
64
65	<	void GofRAngle::preProcess() {
66	<
67	<	for (int i = 0; i < avgGofr_.size(); ++i) {
58	<	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
65	>	void GofRAngle::preProcess() {
66	>	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
67	>	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
68		}
69	<	}
69	>	}
70
71	<	void GofRAngle::initalizeHistogram() {
71	>	void GofRAngle::initalizeHistogram() {
72		npairs_ = 0;
73	<	for (int i = 0; i < histogram_.size(); ++i)
74	<	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
75	<	}
73	>	for (unsigned int i = 0; i < histogram_.size(); ++i){
74	>	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
75	>	}
76	>	}
77
78	+	void GofRAngle::processHistogram() {
79	+	int nPairs = getNPairs();
80	+	RealType volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
81	+	RealType pairDensity = nPairs /volume;
82	+	RealType pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
83
84	<	void GofRAngle::processHistogram() {
70	<	int nRealPairs = getNRealPairs();
71	<	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
72	<	double pairDensity = nRealPairs /volume;
73	<	double pairConstant = ( 4.0 * NumericConstant::PI * pairDensity ) / 3.0;
84	>	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
85
86	<	for(int i = 0 ; i < histogram_.size(); ++i){
86	>	RealType rLower = i * deltaR_;
87	>	RealType rUpper = rLower + deltaR_;
88	>	RealType volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
89	>	RealType nIdeal = volSlice * pairConstant;
90
91	<	double rLower = i * deltaR_;
92	<	double rUpper = rLower + deltaR_;
93	<	double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
80	<	double nIdeal = volSlice * pairConstant;
81	<
82	<	for (int j = 0; j < histogram_[i].size(); ++j){
83	<	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
84	<	}
91	>	for (unsigned int j = 0; j < histogram_[i].size(); ++j){
92	>	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
93	>	}
94		}
95
96	<	}
96	>	}
97
98	<	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
98	>	void GofRAngle::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
99
100		if (sd1 == sd2) {
101	<	return;
101	>	return;
102		}
94	–
103		Vector3d pos1 = sd1->getPos();
104		Vector3d pos2 = sd2->getPos();
105	<	Vector3d r12 = pos1 - pos2;
106	<	currentSnapshot_->wrapVector(r12);
105	>	Vector3d r12 = pos2 - pos1;
106	>	if (usePeriodicBoundaryConditions_)
107	>	currentSnapshot_->wrapVector(r12);
108
109	<	double distance = r12.length();
109	>	RealType distance = r12.length();
110		int whichRBin = distance / deltaR_;
111
112		if (distance <= len_) {
113	<	double cosAngle = evaluateAngle(sd1, sd2);
114	<	double halfBin = (nAngleBins_ - 1) * 0.5;
115	<	int whichThetaBin = halfBin * (cosAngle + 1.0);
116	<	++histogram_[whichRBin][whichThetaBin];
113	>
114	>	RealType cosAngle = evaluateAngle(sd1, sd2);
115	>	RealType halfBin = (nAngleBins_ - 1) * 0.5;
116	>	int whichThetaBin = halfBin * (cosAngle + 1.0);
117	>	++histogram_[whichRBin][whichThetaBin];
118
119	<	++npairs_;
119	>	++npairs_;
120		}
121	<	}
121	>	}
122
123	<	void GofRAngle::writeRdf() {
123	>	void GofRAngle::writeRdf() {
124		std::ofstream rdfStream(outputFilename_.c_str());
125		if (rdfStream.is_open()) {
126	<	rdfStream << "#radial distribution function\n";
127	<	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
128	<	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
129	<	rdfStream << "#r\tcorrValue\n";
130	<	for (int i = 0; i < avgGofr_.size(); ++i) {
131	<	double r = deltaR_ * (i + 0.5);
126	>	rdfStream << "#radial distribution function\n";
127	>	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
128	>	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
129	>	rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
130	>	rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
131	>	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
132	>	RealType r = deltaR_ * (i + 0.5);
133
134	<	for(int j = 0; j < avgGofr_[i].size(); ++j) {
135	<	double cosAngle = -1.0 + (i + 0.5)*deltaCosAngle_;
136	<	rdfStream << r << "\t" << cosAngle << "\t" << avgGofr_[i][j]/nProcessed_ << "\n";
137	<	}
138	<	}
134	>	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
135	>	RealType cosAngle = -1.0 + (j + 0.5)*deltaCosAngle_;
136	>	rdfStream << avgGofr_[i][j]/nProcessed_ << "\t";
137	>	}
138	>
139	>	rdfStream << "\n";
140	>	}
141
142		} else {
143	<
144	<
143	>	sprintf(painCave.errMsg, "GofRAngle: unable to open %s\n", outputFilename_.c_str());
144	>	painCave.isFatal = 1;
145	>	simError();
146		}
147
148		rdfStream.close();
149	<	}
149	>	}
150
151	<	double GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
151	>	RealType GofRTheta::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
152		Vector3d pos1 = sd1->getPos();
153		Vector3d pos2 = sd2->getPos();
154	<	Vector3d r12 = pos1 - pos2;
155	<	currentSnapshot_->wrapVector(r12);
154	>	Vector3d r12 = pos2 - pos1;
155	>
156	>	if (usePeriodicBoundaryConditions_)
157	>	currentSnapshot_->wrapVector(r12);
158	>
159		r12.normalize();
160		Vector3d dipole = sd1->getElectroFrame().getColumn(2);
161		dipole.normalize();
162		return dot(r12, dipole);
163	<	}
163	>	}
164
165	<	double GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
165	>	RealType GofROmega::evaluateAngle(StuntDouble* sd1, StuntDouble* sd2) {
166		Vector3d v1 = sd1->getElectroFrame().getColumn(2);
167	<	Vector3d v2 = sd1->getElectroFrame().getColumn(2);
167	>	Vector3d v2 = sd2->getElectroFrame().getColumn(2);
168		v1.normalize();
169		v2.normalize();
170		return dot(v1, v2);
171	<	}
171	>	}
172
173
174		}

Comparing trunk/src/applications/staticProps/GofRAngle.cpp (property svn:keywords):
Revision 348 by tim, Tue Feb 15 17:24:12 2005 UTC vs.
Revision 1782 by gezelter, Wed Aug 22 02:28:28 2012 UTC

#	Line 0 | Line 1
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