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

Comparing trunk/src/applications/staticProps/GofXyz.cpp (file contents):
Revision 310 by tim, Thu Feb 10 18:14:03 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/GofXyz.hpp"
46		#include "utils/simError.h"
47	+	#include "primitives/Molecule.hpp"
48	+	#include "types/MultipoleAdapter.hpp"
49
50	<	namespace oopse {
50	>	namespace OpenMD {
51
52	<	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
53	<	: RadialDistrFunc(info, filename, sele1, sele2){
52	>	GofXyz::GofXyz(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, const std::string& sele3, RealType len, int nrbins)
53	>	: RadialDistrFunc(info, filename, sele1, sele2), evaluator3_(info), seleMan3_(info), len_(len), halfLen_(len/2), nRBins_(nrbins) {
54	>	setOutputName(getPrefix(filename) + ".gxyz");
55
56	<	}
56	>	evaluator3_.loadScriptString(sele3);
57	>	if (!evaluator3_.isDynamic()) {
58	>	seleMan3_.setSelectionSet(evaluator3_.evaluate());
59	>	}
60
61	+	deltaR_ =  len_ / nRBins_;
62	+
63	+	histogram_.resize(nRBins_);
64	+	for (int i = 0 ; i < nRBins_; ++i) {
65	+	histogram_[i].resize(nRBins_);
66	+	for(int j = 0; j < nRBins_; ++j) {
67	+	histogram_[i][j].resize(nRBins_);
68	+	}
69	+	}
70	+
71	+	}
72
55	–	void GofXyz::preProcess() {
73
74	<	for (int i = 0; i < avgGofr_.size(); ++i) {
75	<	std::fill(avgGofr_[i].begin(), avgGofr_[i].end(), 0);
76	<	}
77	<	}
74	>	void GofXyz::preProcess() {
75	>	for (int i = 0 ; i < nRBins_; ++i) {
76	>	histogram_[i].resize(nRBins_);
77	>	for(int j = 0; j < nRBins_; ++j) {
78	>	std::fill(histogram_[i][j].begin(), histogram_[i][j].end(), 0);
79	>	}
80	>	}
81	>	}
82
62	–	void GofXyz::initalizeHistogram() {
63	–	npairs_ = 0;
64	–	for (int i = 0; i < histogram_.size(); ++i)
65	–	std::fill(histogram_[i].begin(), histogram_[i].end(), 0);
66	–	}
83
84	+	void GofXyz::initializeHistogram() {
85	+	//calculate the center of mass of the molecule of selected stuntdouble in selection1
86
87	<	void GofXyz::processHistogram() {
87	>	if (!evaluator3_.isDynamic()) {
88	>	seleMan3_.setSelectionSet(evaluator3_.evaluate());
89	>	}
90
91	<	double volume = info_->getSnapshotManager()->getCurrentSnapshot()->getVolume();
92	<	double pairDensity = npairs_ /volume;
93	<	double pairConstant = ( 4.0 * PI * pairDensity ) / 3.0;
91	>	assert(seleMan1_.getSelectionCount() == seleMan3_.getSelectionCount());
92	>
93	>	//dipole direction of selection3 and position of selection3 will be used to determine the y-z plane
94	>	//v1 = s3 -s1,
95	>	//z = origin.dipole
96	>	//x = v1 X z
97	>	//y = z X x
98	>	rotMats_.clear();
99
100	<	for(int i = 0 ; i < histogram_.size(); ++i){
100	>	int i;
101	>	int j;
102	>	StuntDouble* sd1;
103	>	StuntDouble* sd3;
104	>
105	>	for (sd1 = seleMan1_.beginSelected(i), sd3 = seleMan3_.beginSelected(j);
106	>	sd1 != NULL || sd3 != NULL;
107	>	sd1 = seleMan1_.nextSelected(i), sd3 = seleMan3_.nextSelected(j)) {
108
109	<	double rLower = i * deltaR_;
110	<	double rUpper = rLower + deltaR_;
111	<	double volSlice = ( rUpper * rUpper * rUpper ) - ( rLower * rLower * rLower );
112	<	double nIdeal = volSlice * pairConstant;
109	>	Vector3d r3 = sd3->getPos();
110	>	Vector3d r1 = sd1->getPos();
111	>	Vector3d v1 =  r3 - r1;
112	>	if (usePeriodicBoundaryConditions_)
113	>	info_->getSnapshotManager()->getCurrentSnapshot()->wrapVector(v1);
114
115	<	for (int j = 0; j < histogram_[i].size(); ++j){
116	<	avgGofr_[i][j] += histogram_[i][j] / nIdeal;
84	<	}
85	<	}
115	>	AtomType* atype1 = static_cast<Atom*>(sd1)->getAtomType();
116	>	MultipoleAdapter ma1 = MultipoleAdapter(atype1);
117
118	<	}
118	>	Vector3d zaxis;
119	>	if (ma1.isDipole())
120	>	zaxis = sd1->getDipole();
121	>	else
122	>	zaxis = sd1->getA().transpose() * V3Z;
123
124	<	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
124	>	Vector3d xaxis = cross(v1, zaxis);
125	>	Vector3d yaxis = cross(zaxis, xaxis);
126
127	<	if (sd1 == sd2) {
128	<	return;
127	>	xaxis.normalize();
128	>	yaxis.normalize();
129	>	zaxis.normalize();
130	>
131	>	RotMat3x3d rotMat;
132	>	rotMat.setRow(0, xaxis);
133	>	rotMat.setRow(1, yaxis);
134	>	rotMat.setRow(2, zaxis);
135	>
136	>	rotMats_.insert(std::map<int, RotMat3x3d>::value_type(sd1->getGlobalIndex(), rotMat));
137		}
138	<
138	>
139	>	}
140	>
141	>	void GofXyz::collectHistogram(StuntDouble* sd1, StuntDouble* sd2) {
142	>
143		Vector3d pos1 = sd1->getPos();
144		Vector3d pos2 = sd2->getPos();
145	<	Vector3d r12 = pos1 - pos2;
146	<	currentSnapshot_->wrapVector(r12);
145	>	Vector3d r12 = pos2 - pos1;
146	>	if (usePeriodicBoundaryConditions_)
147	>	currentSnapshot_->wrapVector(r12);
148
149	<	double distance = r12.length();
150	<	int whichRBin = distance / deltaR_;
149	>	std::map<int, RotMat3x3d>::iterator i = rotMats_.find(sd1->getGlobalIndex());
150	>	assert(i != rotMats_.end());
151	>
152	>	Vector3d newR12 = i->second * r12;
153	>	// x, y and z's possible values range -halfLen_ to halfLen_
154	>	int xbin = int( (newR12.x() + halfLen_) / deltaR_);
155	>	int ybin = int( (newR12.y() + halfLen_) / deltaR_);
156	>	int zbin = int( (newR12.z() + halfLen_) / deltaR_);
157
158	+	if (xbin < nRBins_ && xbin >=0 &&
159	+	ybin < nRBins_ && ybin >= 0 &&
160	+	zbin < nRBins_ && zbin >=0 ) {
161	+	++histogram_[xbin][ybin][zbin];
162	+	}
163
164	<	double cosAngle = evaluateAngle(sd1, sd2);
105	<	double halfBin = (nAngleBins_ - 1) * 0.5;
106	<	int whichThetaBin = halfBin * (cosAngle + 1.0)
107	<	++histogram_[whichRBin][whichThetaBin];
108	<
109	<	++npairs_;
110	<	}
164	>	}
165
166	<	void GofXyz::writeRdf() {
167	<	std::ofstream rdfStream(outputFilename_.c_str());
166	>	void GofXyz::writeRdf() {
167	>	std::ofstream rdfStream(outputFilename_.c_str(), std::ios::binary);
168		if (rdfStream.is_open()) {
169	<	rdfStream << "#radial distribution function\n";
170	<	rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
171	<	rdfStream << "selection2: (" << selectionScript2_ << ")\n";
172	<	rdfStream << "#r\tcorrValue\n";
173	<	for (int i = 0; i < histogram_.size(); ++i) {
174	<	double x = deltaR_ * (i + 0.5);
175	<
176	<	for(int j = 0; j < histogram_[i].size(); ++j) {
177	<	double y = deltaR_ * (j+ 0.5);
178	<
179	<	for(int k = 0;k < histogram_[i].size(); ++k) {
180	<	double z = deltaR_ * (k + 0.5);
127	<	rdfStream << x << "\t" << y << "\t" <<  z << "\t" << histogram_[i][j][k]/nProcessed_ << "\n";
128	<	}
129	<	}
169	>	//rdfStream << "#g(x, y, z)\n";
170	>	//rdfStream << "#selection1: (" << selectionScript1_ << ")\t";
171	>	//rdfStream << "selection2: (" << selectionScript2_ << ")\n";
172	>	//rdfStream << "#nRBins = " << nRBins_ << "\t maxLen = " << len_ << "deltaR = " << deltaR_ <<"\n";
173	>	for (unsigned int i = 0; i < histogram_.size(); ++i) {
174	>	for(unsigned int j = 0; j < histogram_[i].size(); ++j) {
175	>	for(unsigned int k = 0;k < histogram_[i][j].size(); ++k) {
176	>	rdfStream.write(reinterpret_cast<char *>(&histogram_[i][j][k] ),
177	>	sizeof(histogram_[i][j][k] ));
178	>	}
179	>	}
180	>	}
181
182		} else {
183
184	<
184	>	sprintf(painCave.errMsg, "GofXyz: unable to open %s\n", outputFilename_.c_str());
185	>	painCave.isFatal = 1;
186	>	simError();
187		}
188
189		rdfStream.close();
190	<	}
190	>	}
191
192		}
140	–
141	–
142	–

Comparing trunk/src/applications/staticProps/GofXyz.cpp (property svn:keywords):
Revision 310 by tim, Thu Feb 10 18:14:03 2005 UTC vs.
Revision 1879 by gezelter, Sun Jun 16 15:15:42 2013 UTC

#	Line 0 | Line 1
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