ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

root/OpenMD/trunk/src/applications/staticProps/GofAngle2.cpp

Comparing trunk/src/applications/staticProps/GofAngle2.cpp (file contents):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 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/GofAngle2.hpp"
46		#include "utils/simError.h"
47
48	<	namespace oopse {
48	>	namespace OpenMD {
49
50		GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
51		const std::string& sele2, int nangleBins)
#	Line 66 | Line 67 | namespace oopse {
67
68		void GofAngle2::preProcess() {
69
70	<	for (int i = 0; i < avgGofr_.size(); ++i) {
70	>	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
71		std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
72		}
73		}
74
75	<	void GofAngle2::initalizeHistogram() {
75	>	void GofAngle2::initializeHistogram() {
76		npairs_ = 0;
77	<	for (int i = 0; i < histogram_.size(); ++i)
77	>	for (unsigned int i = 0; i < histogram_.size(); ++i)
78		std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
79		}
80
#	Line 93 | Line 94 | namespace oopse {
94		Vector3d pos1 = sd1->getPos();
95		Vector3d pos2 = sd2->getPos();
96		Vector3d r12 = pos1 - pos2;
97	<	currentSnapshot_->wrapVector(r12);
97	>	if (usePeriodicBoundaryConditions_)
98	>	currentSnapshot_->wrapVector(r12);
99		Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
100		Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
101
#	Line 107 | Line 109 | namespace oopse {
109
110		RealType halfBin = (nAngleBins_ - 1) * 0.5;
111		int angleBin1 = halfBin * (cosAngle1 + 1.0);
112	<	int angleBin2 = halfBin * (cosAngle1 + 1.0);
112	>	int angleBin2 = halfBin * (cosAngle2 + 1.0);
113
114	<	++histogram_[angleBin1][angleBin1];
114	>	++histogram_[angleBin1][angleBin2];
115		++npairs_;
116		}
117
#	Line 120 | Line 122 | namespace oopse {
122		rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
123		rdfStream << "selection2: (" << selectionScript2_ << ")\n";
124		rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
125	<	for (int i = 0; i < avgGofr_.size(); ++i) {
125	>	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
126		RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
127
128	<	for(int j = 0; j < avgGofr_[i].size(); ++j) {
128	>	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
129		RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
130		rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
131		}

Comparing trunk/src/applications/staticProps/GofAngle2.cpp (property svn:keywords):
Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
Revision 1785 by jmichalk, Wed Aug 22 18:43:27 2012 UTC

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

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines