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

Comparing trunk/src/applications/staticProps/RhoR.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 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		/* Calculates Rho(R) for nanoparticle with radius R*/
#	Line 47 | Line 48
48		#include "utils/NumericConstant.hpp"
49		#include "io/DumpReader.hpp"
50		#include "primitives/Molecule.hpp"
51	+	#include "brains/Thermo.hpp"
52		#include <math.h>
53
54		namespace OpenMD {
#	Line 72 | Line 74 | namespace OpenMD {
74
75
76		void RhoR::process() {
77	<
78	<
77	<
77	>
78	>	Thermo thermo(info_);
79		DumpReader reader(info_, dumpFilename_);
80		int nFrames = reader.getNFrames();
81		nProcessed_ = nFrames/step_;
#	Line 88 | Line 89 | namespace OpenMD {
89		StuntDouble* sd;
90		reader.readFrame(istep);
91		currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
92	<	Vector3d CenterOfMass = info_->getCom();
92	>	Vector3d CenterOfMass = thermo.getCom();
93
93	–
94	–
95	–
94		if (evaluator_.isDynamic()) {
95		seleMan_.setSelectionSet(evaluator_.evaluate());
96		}
#	Line 105 | Line 103 | namespace OpenMD {
103		RealType distance = r12.length();
104
105		if (distance < len_) {
106	<	int whichBin = distance / deltaR_;
106	>	int whichBin = int(distance / deltaR_);
107		histogram_[whichBin] += 1;
108		}
109
#	Line 124 | Line 122 | namespace OpenMD {
122		RealType particleDensity =  3.0 * info_->getNGlobalMolecules() / (4.0 * NumericConstant::PI * pow(particleR_,3));
123		RealType pairConstant = ( 4.0 * NumericConstant::PI * particleDensity ) / 3.0;
124
125	<	for(int i = 0 ; i < histogram_.size(); ++i){
125	>	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
126
127		RealType rLower = i * deltaR_;
128		RealType rUpper = rLower + deltaR_;
#	Line 143 | Line 141 | namespace OpenMD {
141		if (rdfStream.is_open()) {
142		rdfStream << "#radial density function rho(r)\n";
143		rdfStream << "#r\tcorrValue\n";
144	<	for (int i = 0; i < avgRhoR_.size(); ++i) {
144	>	for (unsigned int i = 0; i < avgRhoR_.size(); ++i) {
145		RealType r = deltaR_ * (i + 0.5);
146		rdfStream << r << "\t" << avgRhoR_[i]/nProcessed_ << "\n";
147		}

Comparing trunk/src/applications/staticProps/RhoR.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1790 by gezelter, Thu Aug 30 17:18:22 2012 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

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