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

Comparing trunk/src/applications/staticProps/pAngle.cpp (file contents):
Revision 1413 by gezelter, Mon Mar 22 19:21:22 2010 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 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).
40	<	*
39	>	* [4] Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	>	* [4] , Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). *
41		*/
42
43		/* Calculates Rho(theta) */
44
45		#include <algorithm>
46	<	#include <fstream>
46	>	#include <fstream>
47		#include "applications/staticProps/pAngle.hpp"
48		#include "utils/simError.h"
49		#include "io/DumpReader.hpp"
50		#include "primitives/Molecule.hpp"
51	+	#include "brains/Thermo.hpp"
52	+
53		namespace OpenMD {
54
55		pAngle::pAngle(SimInfo* info, const std::string& filename,
#	Line 74 | Line 76 | namespace OpenMD {
76		Molecule::RigidBodyIterator rbIter;
77		int i;
78
79	+	Thermo thermo(info_);
80		DumpReader reader(info_, dumpFilename_);
81		int nFrames = reader.getNFrames();
82		nProcessed_ = nFrames/step_;
#	Line 94 | Line 97 | namespace OpenMD {
97		}
98		}
99
100	<	Vector3d CenterOfMass = info_->getCom();
100	>	Vector3d CenterOfMass = thermo.getCom();
101
102		if  (evaluator_.isDynamic()) {
103		seleMan_.setSelectionSet(evaluator_.evaluate());
#	Line 130 | Line 133 | namespace OpenMD {
133		void pAngle::processHistogram() {
134
135		int atot = 0;
136	<	for(int i = 0; i < count_.size(); ++i)
136	>	for(unsigned int i = 0; i < count_.size(); ++i)
137		atot += count_[i];
138
139	<	for(int i = 0; i < count_.size(); ++i) {
140	<	histogram_[i] = double(count_[i] / atot);
139	>	for(unsigned int i = 0; i < count_.size(); ++i) {
140	>	histogram_[i] = double(count_[i] / double(atot));
141		}
142		}
143
#	Line 147 | Line 150 | namespace OpenMD {
150		rdfStream << "#nFrames:\t" << nProcessed_ << "\n";
151		rdfStream << "#selection: (" << selectionScript_ << ")\n";
152		rdfStream << "#cos(theta)\tp(cos(theta))\n";
153	<	for (int i = 0; i < histogram_.size(); ++i) {
154	<	RealType ct = -1.0 + i / histogram_.size();
155	<	rdfStream << ct << "\t" << histogram_[i] << "\n";
153	>	RealType dct = 2.0 / histogram_.size();
154	>	for (unsigned int i = 0; i < histogram_.size(); ++i) {
155	>	RealType ct = -1.0 + (2.0 * i + 1) / (histogram_.size());
156	>	rdfStream << ct << "\t" << histogram_[i]/dct << "\n";
157		}
158
159		} else {

Comparing trunk/src/applications/staticProps/pAngle.cpp (property svn:keywords):
Revision 1413 by gezelter, Mon Mar 22 19:21:22 2010 UTC vs.
Revision 1796 by gezelter, Mon Sep 10 18:38:44 2012 UTC

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

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