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Comparing:
trunk/src/applications/staticProps/RadialDistrFunc.cpp (file contents), Revision 306 by tim, Wed Feb 9 17:08:22 2005 UTC vs.
branches/development/src/applications/staticProps/RadialDistrFunc.cpp (file contents), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 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>
44
45		#include "RadialDistrFunc.hpp"
46	+	#include "io/DumpReader.hpp"
47	+	#include "primitives/Molecule.hpp"
48	+	namespace OpenMD {
49
50	<	namespace oopse {
51	<
52	<	RadialDistrFunc::        RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2, double len)
53	<	: info_(info), currentSnapshot_(NULL), dumpFilename_(filename), len_(len), nbins_(50), step_(1),
50	<	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info){
50	>	RadialDistrFunc::RadialDistrFunc(SimInfo* info, const std::string& filename, const std::string& sele1, const std::string& sele2)
51	>	: StaticAnalyser(info, filename),
52	>	selectionScript1_(sele1), selectionScript2_(sele2), evaluator1_(info), evaluator2_(info),
53	>	seleMan1_(info), seleMan2_(info), common_(info), sele1_minus_common_(info), sele2_minus_common_(info){
54
55	<	evaluator1_.loadScriptString(sele1);
56	<	evaluator2_.loadScriptString(sele2);
55	>	evaluator1_.loadScriptString(sele1);
56	>	evaluator2_.loadScriptString(sele2);
57
58	<	if (!evaluator1_->isDynamic()) {
59	<	seleMan1_.setSelectionSet(evaluator1_->evaluate());
60	<	}
61	<	if (!evaluator2_->isDynamic()) {
62	<	seleMan2_.setSelectionSet(evaluator2_->evaluate());
63	<	}
58	>	if (!evaluator1_.isDynamic()) {
59	>	seleMan1_.setSelectionSet(evaluator1_.evaluate());
60	>	validateSelection1(seleMan1_);
61	>	}
62	>	if (!evaluator2_.isDynamic()) {
63	>	seleMan2_.setSelectionSet(evaluator2_.evaluate());
64	>	validateSelection2(seleMan2_);
65	>	}
66
67	<	delta_ = len_ /nbins_;
68	<	}
67	>	if (!evaluator1_.isDynamic() && !evaluator2_.isDynamic()) {
68	>	//if all selections are static,  we can precompute the number of real pairs
69	>	common_ = seleMan1_ & seleMan2_;
70	>	sele1_minus_common_ = seleMan1_ - common_;
71	>	sele2_minus_common_ = seleMan2_ - common_;
72
73	<	void RadialDistrFunc::process() {
73	>	int nSelected1 = seleMan1_.getSelectionCount();
74	>	int nSelected2 = seleMan2_.getSelectionCount();
75	>	int nIntersect = common_.getSelectionCount();
76	>
77	>	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
78	>	}
79	>
80	>	}
81
82	+	void RadialDistrFunc::process() {
83	+	Molecule* mol;
84	+	RigidBody* rb;
85	+	SimInfo::MoleculeIterator mi;
86	+	Molecule::RigidBodyIterator rbIter;
87	+
88		preProcess();
89
90		DumpReader reader(info_, dumpFilename_);
91	<	int nFrames = reader->getNFrames();
91	>	int nFrames = reader.getNFrames();
92	>	nProcessed_ = nFrames / step_;
93
94		for (int i = 0; i < nFrames; i += step_) {
95	<	reader->readFrame(i);
96	<	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
95	>	reader.readFrame(i);
96	>	currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
97
98	<	if (evaluator1_->isDynamic()) {
99	<	seleMan1_.setSelectionSet(evaluator1_->evaluate());
100	<	}
101	<	if (evaluator2_->isDynamic()) {
102	<	seleMan2_.setSelectionSet(evaluator2_->evaluate());
103	<	}
98	>	if (evaluator1_.isDynamic()) {
99	>	seleMan1_.setSelectionSet(evaluator1_.evaluate());
100	>	validateSelection1(seleMan1_);
101	>	}
102	>	if (evaluator2_.isDynamic()) {
103	>	seleMan2_.setSelectionSet(evaluator2_.evaluate());
104	>	validateSelection2(seleMan2_);
105	>	}
106
107	<	initalizeHistogram();
107	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
108
109	<	StuntDouble* sd1;
110	<	int j;
111	<	for (sd1 = seleMan1_->beginSelected(j); sd1 != NULL; sd1 = seleMan1_->nextSelected(j)) {
109	>	//change the positions of atoms which belong to the rigidbodies
110	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
111	>	rb->updateAtoms();
112	>	}
113	>	}
114	>
115	>	initalizeHistogram();
116
89	–	StuntDouble* sd2;
90	–	int k;
91	–	for (sd2 = seleMan2_->beginSelected(k); sd2 != NULL; sd2 = seleMan2_->nextSelected(k)) {
92	–	collectHistogram(sd1, sd2);
93	–	}
94	–	}
117
96	–	processHistogram();
118
119	+	//selections may overlap.
120	+	//
121	+	// |s1 -c | c |
122	+	//            | c |s2 - c|
123	+	//
124	+	// s1 : number of selected stuntdoubles in selection1
125	+	// s2 : number of selected stuntdoubles in selection2
126	+	// c   : number of intersect stuntdouble between selection1 and selection2
127	+	//when loop over the pairs, we can divide the looping into 3 stages
128	+	//stage 1 :     [s1-c]      [s2]
129	+	//stage 2 :     [c]            [s2 - c]
130	+	//stage 3 :     [c]            [c]
131	+	//stage 1 and stage 2 are completly non-overlapping
132	+	//stage 3 are completely overlapping
133	+
134	+	if (evaluator1_.isDynamic() || evaluator2_.isDynamic()) {
135	+	common_ = seleMan1_ & seleMan2_;
136	+	sele1_minus_common_ = seleMan1_ - common_;
137	+	sele2_minus_common_ = seleMan2_ - common_;
138	+	int nSelected1 = seleMan1_.getSelectionCount();
139	+	int nSelected2 = seleMan2_.getSelectionCount();
140	+	int nIntersect = common_.getSelectionCount();
141	+
142	+	nPairs_ = nSelected1 * nSelected2 - (nIntersect +1) * nIntersect/2;
143	+	}
144	+	processNonOverlapping(sele1_minus_common_, seleMan2_);
145	+	processNonOverlapping(common_, sele2_minus_common_);
146	+	processOverlapping(common_);
147	+
148	+	processHistogram();
149	+
150		}
151
152		postProcess();
153
154	+	writeRdf();
155	+	}
156	+
157	+	void RadialDistrFunc::processNonOverlapping( SelectionManager& sman1, SelectionManager& sman2) {
158	+	StuntDouble* sd1;
159	+	StuntDouble* sd2;
160	+	int i;
161	+	int j;
162
163	<	}
163	>	for (sd1 = sman1.beginSelected(i); sd1 != NULL; sd1 = sman1.nextSelected(i)) {
164
165	+	for (sd2 = sman2.beginSelected(j); sd2 != NULL; sd2 = sman2.nextSelected(j)) {
166	+	collectHistogram(sd1, sd2);
167	+	}
168	+	}
169	+
170	+	}
171	+
172	+	void RadialDistrFunc::processOverlapping( SelectionManager& sman) {
173	+	StuntDouble* sd1;
174	+	StuntDouble* sd2;
175	+	int i;
176	+	int j;
177	+
178	+	//basically, it is the same as below loop
179	+	//for (int i = 0;  i < n; ++i )
180	+	//  for (int j = i + 1; j < n; ++j) {}
181	+
182	+	for (sd1 = sman.beginSelected(i); sd1 != NULL; sd1 = sman.nextSelected(i)) {
183	+	for (j  = i, sd2 = sman.nextSelected(j); sd2 != NULL; sd2 = sman.nextSelected(j)) {
184	+	collectHistogram(sd1, sd2);
185	+	}
186	+	}
187	+
188	+	}
189	+
190		}

Comparing:
trunk/src/applications/staticProps/RadialDistrFunc.cpp (property svn:keywords), Revision 306 by tim, Wed Feb 9 17:08:22 2005 UTC vs.
branches/development/src/applications/staticProps/RadialDistrFunc.cpp (property svn:keywords), Revision 1665 by gezelter, Tue Nov 22 20:38:56 2011 UTC

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