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

Comparing trunk/src/applications/staticProps/GofZ.cpp (file contents):
Revision 1221 by xsun, Wed Jan 23 21:48:44 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 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, 234107 (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/GofZ.hpp"
46		#include "utils/simError.h"
47
48	<	namespace oopse {
48	>	namespace OpenMD {
49
50		GofZ::GofZ(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, RealType len, int nrbins)
51		: RadialDistrFunc(info, filename, sele1, sele2), len_(len), nRBins_(nrbins){
#	Line 63 | Line 64 | namespace oopse {
64		std::fill(avgGofz_.begin(), avgGofz_.end(), 0.0);
65		}
66
67	<	void GofZ::initalizeHistogram() {
67	>	void GofZ::initializeHistogram() {
68		std::fill(histogram_.begin(), histogram_.end(), 0);
69		}
70
#	Line 75 | Line 76 | namespace oopse {
76		RealType pairDensity = nPairs /volume * 2.0;
77		RealType pairConstant = ( 2.0 * NumericConstant::PI * pairDensity );
78
79	<	for(int i = 0 ; i < histogram_.size(); ++i){
79	>	for(unsigned int i = 0 ; i < histogram_.size(); ++i){
80
81		RealType zLower = i * deltaZ_;
82		RealType zUpper = zLower + deltaZ_;
#	Line 89 | Line 90 | namespace oopse {
90
91		void GofZ::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
92
92	–	RealType thisZ;
93	–
93		if (sd1 == sd2) {
94		return;
95		}
#	Line 106 | Line 105 | namespace oopse {
105		RealType xydist = sqrt(distance*distance - z2);
106
107		if (xydist < rC_) {
108	<	thisZ = abs(r12.z());
109	<	int whichBin = thisZ / deltaZ_;
108	>	RealType thisZ = abs(r12.z());
109	>	int whichBin = int(thisZ / deltaZ_);
110		histogram_[whichBin] += 2;
111		}
112		}
#	Line 120 | Line 119 | namespace oopse {
119		rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
120		rdfStream << "selection2: (" << selectionScript2_ << ")\n";
121		rdfStream << "#r\tcorrValue\n";
122	<	for (int i = 0; i < avgGofz_.size(); ++i) {
122	>	for (unsigned int i = 0; i < avgGofz_.size(); ++i) {
123		RealType z = deltaZ_ * (i + 0.5);
124		rdfStream << z << "\t" << avgGofz_[i]/nProcessed_ << "\n";
125		}

Comparing trunk/src/applications/staticProps/GofZ.cpp (property svn:keywords):
Revision 1221 by xsun, Wed Jan 23 21:48:44 2008 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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