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

Comparing trunk/src/applications/staticProps/GofAngle2.cpp (file contents):
Revision 353 by tim, Wed Feb 16 19:36:30 2005 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>
44		#include <fstream>
45		#include "applications/staticProps/GofAngle2.hpp"
46	+	#include "primitives/Atom.hpp"
47	+	#include "types/MultipoleAdapter.hpp"
48		#include "utils/simError.h"
49
50	<	namespace oopse {
50	>	namespace OpenMD {
51
52	<	GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
53	<	: RadialDistrFunc(info, filename, sele1, sele2){
54	<	setOutputName(getPrefix(filename) + ".gfotw");
52	>	GofAngle2::GofAngle2(SimInfo* info, const std::string& filename, const std::string& sele1,
53	>	const std::string& sele2, int nangleBins)
54	>	: RadialDistrFunc(info, filename, sele1, sele2), nAngleBins_(nangleBins) {
55
56	<	}
56	>	setOutputName(getPrefix(filename) + ".gto");
57
58	+	deltaCosAngle_ = 2.0 / nAngleBins_;
59
60	<	void GofAngle2::preProcess() {
60	>	histogram_.resize(nAngleBins_);
61	>	avgGofr_.resize(nAngleBins_);
62	>	for (int i = 0 ; i < nAngleBins_; ++i) {
63	>	histogram_[i].resize(nAngleBins_);
64	>	avgGofr_[i].resize(nAngleBins_);
65	>	}
66
58	–	for (int i = 0; i < avgGofr_.size(); ++i) {
59	–	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
67		}
61	–	}
68
69	<	void GofAngle2::initalizeHistogram() {
69	>
70	>	void GofAngle2::preProcess() {
71	>
72	>	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
73	>	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
74	>	}
75	>	}
76	>
77	>	void GofAngle2::initializeHistogram() {
78		npairs_ = 0;
79	<	for (int i = 0; i < histogram_.size(); ++i)
80	<	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
81	<	}
79	>	for (unsigned int i = 0; i < histogram_.size(); ++i)
80	>	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
81	>	}
82
83
84	<	void GofAngle2::processHistogram() {
84	>	void GofAngle2::processHistogram() {
85
86		//std::for_each(avgGofr_.begin(), avgGofr_.end(), std::plus<std::vector<int>>)
87
88	<	}
88	>	}
89
90	<	void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
90	>	void GofAngle2::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
91
92		if (sd1 == sd2) {
93	<	return;
93	>	return;
94		}
95
96		Vector3d pos1 = sd1->getPos();
97		Vector3d pos2 = sd2->getPos();
98		Vector3d r12 = pos1 - pos2;
99	<	currentSnapshot_->wrapVector(r12);
100	<	Vector3d dipole1 = sd1->getElectroFrame().getColumn(2);
101	<	Vector3d dipole2 = sd2->getElectroFrame().getColumn(2);
99	>	if (usePeriodicBoundaryConditions_)
100	>	currentSnapshot_->wrapVector(r12);
101	>
102	>	AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
103	>	AtomType* atype2 = static_cast<Atom*>(sd2)->getAtomType();
104	>	MultipoleAdapter ma1 = MultipoleAdapter(atype1);
105	>	MultipoleAdapter ma2 = MultipoleAdapter(atype2);
106	>
107	>	Vector3d dipole1, dipole2;
108	>	if (ma1.isDipole())
109	>	dipole1 = sd1->getDipole();
110	>	else
111	>	dipole1 = sd1->getA().transpose() * V3Z;
112	>
113	>	if (ma2.isDipole())
114	>	dipole2 = sd2->getDipole();
115	>	else
116	>	dipole2 = sd2->getA().transpose() * V3Z;
117
118		r12.normalize();
119		dipole1.normalize();
120		dipole2.normalize();
121
122
123	<	double cosAngle1 = dot(r12, dipole1);
124	<	double cosAngle2 = dot(dipole1, dipole2);
123	>	RealType cosAngle1 = dot(r12, dipole1);
124	>	RealType cosAngle2 = dot(dipole1, dipole2);
125
126	<	double halfBin = (nAngleBins_ - 1) * 0.5;
127	<	int angleBin1 = halfBin * (cosAngle1 + 1.0);
128	<	int angleBin2 = halfBin * (cosAngle1 + 1.0);
126	>	RealType halfBin = (nAngleBins_ - 1) * 0.5;
127	>	int angleBin1 = int(halfBin * (cosAngle1 + 1.0));
128	>	int angleBin2 = int(halfBin * (cosAngle2 + 1.0));
129
130	<	++histogram_[angleBin1][angleBin1];
130	>	++histogram_[angleBin1][angleBin2];
131		++npairs_;
132	<	}
132	>	}
133
134	<	void GofAngle2::writeRdf() {
134	>	void GofAngle2::writeRdf() {
135		std::ofstream rdfStream(outputFilename_.c_str());
136		if (rdfStream.is_open()) {
137	<	rdfStream << "#radial distribution function\n";
138	<	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
139	<	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
140	<	rdfStream << "#r\tcorrValue\n";
141	<	for (int i = 0; i < avgGofr_.size(); ++i) {
142	<	double cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
137	>	rdfStream << "#radial distribution function\n";
138	>	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
139	>	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
140	>	rdfStream << "#nAngleBins =" << nAngleBins_ << "deltaCosAngle = " << deltaCosAngle_ << "\n";
141	>	for (unsigned int i = 0; i < avgGofr_.size(); ++i) {
142	>	// RealType cosAngle1 = -1.0 + (i + 0.5)*deltaCosAngle_;
143	>
144	>	for(unsigned int j = 0; j < avgGofr_[i].size(); ++j) {
145	>	// RealType cosAngle2 = -1.0 + (j + 0.5)*deltaCosAngle_;
146	>	rdfStream <<avgGofr_[i][j]/nProcessed_ << "\t";
147	>	}
148
149	<	for(int j = 0; j < avgGofr_[i].size(); ++j) {
150	<	double cosAngle2 = -1.0 + (i + 0.5)*deltaCosAngle_;
117	<	rdfStream << cosAngle1 << "\t" << cosAngle2 << "\t" << avgGofr_[i][j]/nProcessed_ << "\n";
118	<	}
119	<	}
149	>	rdfStream << "\n";
150	>	}
151
152		} else {
153
154	<
154	>	sprintf(painCave.errMsg, "GofAngle2: unable to open %s\n", outputFilename_.c_str());
155	>	painCave.isFatal = 1;
156	>	simError();
157		}
158
159		rdfStream.close();
160	<	}
160	>	}
161
162		}

Comparing trunk/src/applications/staticProps/GofAngle2.cpp (property svn:keywords):
Revision 353 by tim, Wed Feb 16 19:36:30 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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